From 889a29547f4220002137ea69946ee0e498ec5cd2 Mon Sep 17 00:00:00 2001
From: shajoezhu <shajoezhu@users.noreply.github.com>
Date: Tue, 3 Dec 2024 22:09:13 +0000
Subject: [PATCH] [actions skip] Built site for
 tern@d0b25f59ffc6f465f0c2045ecd950466dfb3648c

---
 main/404.html                                 |   36 +-
 main/CODE_OF_CONDUCT.html                     |  136 +-
 main/CONTRIBUTING.html                        |  164 ++-
 main/LICENSE-text.html                        |   91 +-
 main/SECURITY.html                            |  103 +-
 main/articles/index.html                      |  110 +-
 main/articles/missing_values.html             |   36 +-
 main/articles/tables.html                     |   36 +-
 main/articles/tern.html                       |   36 +-
 main/articles/tern_formats.html               |   36 +-
 main/articles/tern_functions_guide.html       |   36 +-
 main/authors.html                             |   97 +-
 main/index.html                               |   36 +-
 main/news/index.html                          | 1119 +++++++++++------
 main/reference/abnormal.html                  |  200 ++-
 main/reference/abnormal_by_baseline.html      |  222 +++-
 main/reference/abnormal_by_marked.html        |  191 ++-
 main/reference/abnormal_by_worst_grade.html   |  188 ++-
 .../abnormal_by_worst_grade_worsen.html       |  196 ++-
 main/reference/add_riskdiff.html              |  128 +-
 main/reference/add_rowcounts.html             |  122 +-
 main/reference/aesi_label.html                |  115 +-
 main/reference/afun_riskdiff.html             |  164 ++-
 main/reference/afun_selected_stats.html       |  112 +-
 main/reference/analyze_colvars_functions.html |  113 +-
 main/reference/analyze_functions.html         |  113 +-
 main/reference/analyze_variables.html         |  289 +++--
 main/reference/analyze_vars_in_cols.html      |  173 ++-
 main/reference/append_varlabels.html          |  128 +-
 main/reference/apply_auto_formatting.html     |  119 +-
 main/reference/argument_convention.html       |  247 +++-
 main/reference/arrange_grobs.html             |  140 ++-
 main/reference/as.rtable.html                 |  134 +-
 main/reference/as_factor_keep_attributes.html |  122 +-
 main/reference/assertions.html                |  157 ++-
 main/reference/bins_percent_labels.html       |  116 +-
 main/reference/c_label_n.html                 |  125 +-
 main/reference/c_label_n_alt.html             |  119 +-
 main/reference/cfun_by_flag.html              |  115 +-
 main/reference/check_diff_prop_ci.html        |  122 +-
 main/reference/check_same_n.html              |  112 +-
 main/reference/combination_function.html      |  134 +-
 main/reference/combine_counts.html            |  118 +-
 main/reference/combine_groups.html            |  122 +-
 main/reference/combine_levels.html            |  122 +-
 main/reference/combine_vectors.html           |  115 +-
 main/reference/compare_variables.html         |  210 +++-
 main/reference/control_analyze_vars.html      |  122 +-
 main/reference/control_annot.html             |  143 ++-
 main/reference/control_coxph.html             |  119 +-
 main/reference/control_coxreg.html            |  128 +-
 main/reference/control_incidence_rate.html    |  128 +-
 main/reference/control_lineplot_vars.html     |  137 +-
 main/reference/control_logistic.html          |  119 +-
 main/reference/control_riskdiff.html          |  131 +-
 main/reference/control_step.html              |  128 +-
 main/reference/control_surv_time.html         |  119 +-
 main/reference/control_surv_timepoint.html    |  116 +-
 main/reference/count_cumulative.html          |  210 +++-
 main/reference/count_missed_doses.html        |  214 +++-
 main/reference/count_occurrences.html         |  229 +++-
 .../reference/count_occurrences_by_grade.html |  226 +++-
 .../count_patients_events_in_cols.html        |  180 ++-
 main/reference/count_patients_with_event.html |  210 +++-
 main/reference/count_patients_with_flags.html |  222 +++-
 main/reference/count_values.html              |  207 ++-
 main/reference/cox_regression.html            |  219 +++-
 main/reference/cox_regression_inter.html      |  199 ++-
 main/reference/cut_quantile_bins.html         |  131 +-
 .../d_count_abnormal_by_baseline.html         |  119 +-
 main/reference/d_count_cumulative.html        |  119 +-
 main/reference/d_count_missed_doses.html      |  115 +-
 main/reference/d_onco_rsp_label.html          |  119 +-
 main/reference/d_pkparam.html                 |  102 +-
 main/reference/d_proportion.html              |  119 +-
 main/reference/d_proportion_diff.html         |  122 +-
 main/reference/d_rsp_subgroups_colvars.html   |  119 +-
 .../d_survival_subgroups_colvars.html         |  133 +-
 main/reference/d_test_proportion_diff.html    |  113 +-
 main/reference/day2month.html                 |  112 +-
 main/reference/decorate_grob.html             |  161 ++-
 main/reference/decorate_grob_factory.html     |  112 +-
 main/reference/decorate_grob_set.html         |  119 +-
 main/reference/default_na_str.html            |  135 +-
 .../default_stats_formats_labels.html         |  206 ++-
 main/reference/desctools_binom.html           |  146 ++-
 main/reference/df2gg.html                     |  134 +-
 main/reference/df_explicit_na.html            |  134 +-
 main/reference/dot-is_equal_float.html        |  112 +-
 main/reference/draw_grob.html                 |  125 +-
 main/reference/empty_vector_if_na.html        |  112 +-
 main/reference/estimate_coef.html             |  151 ++-
 main/reference/estimate_multinomial_rsp.html  |  184 ++-
 main/reference/estimate_proportion.html       |  202 ++-
 main/reference/ex_data.html                   |  108 +-
 main/reference/explicit_na.html               |  119 +-
 main/reference/extract_by_name.html           |  125 +-
 main/reference/extract_rsp_biomarkers.html    |  134 +-
 main/reference/extract_rsp_subgroups.html     |  138 +-
 .../extract_survival_biomarkers.html          |  128 +-
 .../reference/extract_survival_subgroups.html |  145 ++-
 main/reference/extreme_format.html            |  144 ++-
 main/reference/f_conf_level.html              |  109 +-
 main/reference/f_pval.html                    |  109 +-
 main/reference/fct_collapse_only.html         |  128 +-
 main/reference/fct_discard.html               |  119 +-
 main/reference/fct_explicit_na_if.html        |  125 +-
 main/reference/fit_coxreg.html                |  166 ++-
 main/reference/fit_logistic.html              |  132 +-
 main/reference/fit_rsp_step.html              |  128 +-
 main/reference/fit_survival_step.html         |  128 +-
 main/reference/forest_viewport.html           |  130 +-
 main/reference/format_auto.html               |  125 +-
 main/reference/format_count_fraction.html     |  122 +-
 .../format_count_fraction_fixed_dp.html       |  122 +-
 .../reference/format_count_fraction_lt10.html |  122 +-
 main/reference/format_extreme_values.html     |  119 +-
 main/reference/format_extreme_values_ci.html  |  119 +-
 main/reference/format_fraction.html           |  122 +-
 main/reference/format_fraction_fixed_dp.html  |  122 +-
 main/reference/format_fraction_threshold.html |  119 +-
 main/reference/format_sigfig.html             |  121 +-
 main/reference/format_xx.html                 |  119 +-
 main/reference/formatting_functions.html      |   99 +-
 main/reference/g_bland_altman.html            |  122 +-
 main/reference/g_forest.html                  |  178 ++-
 main/reference/g_ipp.html                     |  170 ++-
 main/reference/g_km.html                      |  267 ++--
 main/reference/g_lineplot.html                |  229 +++-
 main/reference/g_step.html                    |  131 +-
 main/reference/g_waterfall.html               |  137 +-
 main/reference/get_covariates.html            |  109 +-
 main/reference/get_smooths.html               |  125 +-
 main/reference/groups_list_to_df.html         |  112 +-
 .../h_adlb_abnormal_by_worst_grade.html       |  149 ++-
 main/reference/h_adlb_worsen.html             |  138 +-
 .../h_adsl_adlb_merge_using_worst_flag.html   |  138 +-
 main/reference/h_ancova.html                  |  129 +-
 main/reference/h_append_grade_groups.html     |  128 +-
 main/reference/h_col_indices.html             |  116 +-
 main/reference/h_count_cumulative.html        |  144 ++-
 main/reference/h_cox_regression.html          |  169 ++-
 main/reference/h_data_plot.html               |  129 +-
 main/reference/h_decompose_gg.html            |  126 +-
 main/reference/h_format_row.html              |  118 +-
 main/reference/h_g_ipp.html                   |  155 ++-
 main/reference/h_ggkm.html                    |  164 ++-
 main/reference/h_glm_count.html               |  167 ++-
 main/reference/h_grob_coxph.html              |  128 +-
 main/reference/h_grob_median_surv.html        |  131 +-
 main/reference/h_grob_tbl_at_risk.html        |  125 +-
 main/reference/h_grob_y_annot.html            |  119 +-
 main/reference/h_incidence_rate.html          |  143 ++-
 main/reference/h_km_layout.html               |  141 ++-
 main/reference/h_logistic_regression.html     |  170 ++-
 main/reference/h_map_for_count_abnormal.html  |  134 +-
 main/reference/h_odds_ratio.html              |  134 +-
 main/reference/h_pkparam_sort.html            |  115 +-
 main/reference/h_ppmeans.html                 |  131 +-
 main/reference/h_prop_diff.html               |  142 ++-
 main/reference/h_prop_diff_test.html          |  130 +-
 main/reference/h_proportions.html             |  146 ++-
 .../h_response_biomarkers_subgroups.html      |  170 ++-
 main/reference/h_response_subgroups.html      |  172 ++-
 main/reference/h_split_by_subgroups.html      |  125 +-
 main/reference/h_split_param.html             |  122 +-
 main/reference/h_stack_by_baskets.html        |  131 +-
 main/reference/h_step.html                    |  166 ++-
 .../h_survival_biomarkers_subgroups.html      |  174 ++-
 .../h_survival_duration_subgroups.html        |  182 ++-
 main/reference/h_tab_one_biomarker.html       |  128 +-
 main/reference/h_tbl_coxph_pairwise.html      |  146 ++-
 main/reference/h_tbl_median_surv.html         |  119 +-
 main/reference/h_worsen_counter.html          |  144 ++-
 main/reference/h_xticks.html                  |  122 +-
 main/reference/imputation_rule.html           |  130 +-
 main/reference/incidence_rate.html            |  224 +++-
 main/reference/index.html                     | 1065 ++++++++++++----
 main/reference/labels_or_names.html           |  113 +-
 main/reference/labels_use_control.html        |  122 +-
 main/reference/logistic_regression_cols.html  |  116 +-
 main/reference/logistic_summary_by_flag.html  |  119 +-
 main/reference/make_names.html                |  109 +-
 main/reference/month2day.html                 |  116 +-
 main/reference/muffled_car_anova.html         |  119 +-
 main/reference/n_available.html               |  109 +-
 main/reference/odds_ratio.html                |  214 +++-
 main/reference/prop_diff.html                 |  208 ++-
 main/reference/prop_diff_test.html            |  199 ++-
 main/reference/prune_occurrences.html         |  171 ++-
 main/reference/range_noinf.html               |  119 +-
 main/reference/reapply_varlabels.html         |  115 +-
 .../response_biomarkers_subgroups.html        |  142 ++-
 main/reference/response_subgroups.html        |  166 ++-
 main/reference/rtable2gg.html                 |  125 +-
 main/reference/rtables_access.html            |  172 ++-
 main/reference/s_bland_altman.html            |  129 +-
 main/reference/s_cox_multivariate.html        |  134 +-
 main/reference/sas_na.html                    |  125 +-
 main/reference/score_occurrences.html         |  155 ++-
 main/reference/split_cols_by_groups.html      |  127 +-
 main/reference/split_text_grob.html           |  142 ++-
 main/reference/stack_grobs.html               |  131 +-
 main/reference/stat_mean_ci.html              |  131 +-
 main/reference/stat_mean_pval.html            |  125 +-
 main/reference/stat_median_ci.html            |  128 +-
 main/reference/stat_propdiff_ci.html          |  137 +-
 main/reference/strata_normal_quantile.html    |  125 +-
 main/reference/study_arm.html                 |  109 +-
 main/reference/summarize_ancova.html          |  219 +++-
 main/reference/summarize_change.html          |  190 ++-
 main/reference/summarize_colvars.html         |  137 +-
 main/reference/summarize_functions.html       |  115 +-
 main/reference/summarize_glm_count.html       |  226 +++-
 main/reference/summarize_logistic.html        |  128 +-
 main/reference/summarize_num_patients.html    |  215 +++-
 .../summarize_patients_exposure_in_cols.html  |  203 ++-
 .../survival_biomarkers_subgroups.html        |  163 ++-
 main/reference/survival_coxph_pairwise.html   |  218 +++-
 .../survival_duration_subgroups.html          |  169 ++-
 main/reference/survival_time.html             |  215 +++-
 main/reference/survival_timepoint.html        |  232 +++-
 main/reference/tern-package.html              |  119 +-
 main/reference/tidy.glm.html                  |  128 +-
 main/reference/tidy.step.html                 |  122 +-
 main/reference/tidy_coxreg.html               |  152 ++-
 main/reference/to_n.html                      |  119 +-
 main/reference/to_string_matrix.html          |  131 +-
 main/reference/try_car_anova.html             |  119 +-
 main/reference/ungroup_stats.html             |  121 +-
 main/reference/univariate.html                |  123 +-
 main/reference/unlist_and_blank_na.html       |  109 +-
 .../update_weights_strat_wilson.html          |  140 ++-
 .../util_handling_additional_fun_params.html  |  137 +-
 main/reference/utils_split_funs.html          |  141 ++-
 main/search.json                              |    2 +-
 236 files changed, 27227 insertions(+), 7560 deletions(-)

diff --git a/main/404.html b/main/404.html
index 6173dfe45b..67c2e89ec7 100644
--- a/main/404.html
+++ b/main/404.html
@@ -1,5 +1,4 @@
-<!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en">
+<html lang="en">
 <head>
 <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
 <meta charset="utf-8">
@@ -58,7 +57,38 @@
     <li><a class="dropdown-item" href="https://insightsengineering.github.io/tern/unit-test-report-non-cran/">Non-CRAN unit test report</a></li>
   </ul>
 </li>
-      </ul>
+      <div><li class="nav-item dropdown">
+    <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-versions">Versions</a>
+    <div class="dropdown-menu" aria-labelledby="dropdown-versions">
+    <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/main">main</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.5">v0.9.5</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.4">v0.9.4</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.3">v0.9.3</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1-rc3">v0.9.1-rc3</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a>
+</div>
+</li></div>
+</ul>
 <ul class="navbar-nav">
 <li class="nav-item"><form class="form-inline" role="search">
  <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="search.json">
diff --git a/main/CODE_OF_CONDUCT.html b/main/CODE_OF_CONDUCT.html
index a9ed7e5826..321aeb8cb1 100644
--- a/main/CODE_OF_CONDUCT.html
+++ b/main/CODE_OF_CONDUCT.html
@@ -1,5 +1,26 @@
-<!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Contributor Covenant Code of Conduct • tern</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="apple-touch-icon-60x60.png"><script src="deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="deps/headroom-0.11.0/headroom.min.js"></script><script src="deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="deps/search-1.0.0/fuse.min.js"></script><script src="deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="pkgdown.js"></script><meta property="og:title" content="Contributor Covenant Code of Conduct"><meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png"><link rel="stylesheet" href="consent.css"><script src="consent.js" type="text/javascript" charset="utf-8"></script></head><body>
+<html lang="en">
+<head>
+<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+<meta charset="utf-8">
+<meta http-equiv="X-UA-Compatible" content="IE=edge">
+<meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<title>Contributor Covenant Code of Conduct • tern</title>
+<!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="favicon-16x16.png">
+<link rel="icon" type="image/png" sizes="32x32" href="favicon-32x32.png">
+<link rel="apple-touch-icon" type="image/png" sizes="180x180" href="apple-touch-icon.png">
+<link rel="apple-touch-icon" type="image/png" sizes="120x120" href="apple-touch-icon-120x120.png">
+<link rel="apple-touch-icon" type="image/png" sizes="76x76" href="apple-touch-icon-76x76.png">
+<link rel="apple-touch-icon" type="image/png" sizes="60x60" href="apple-touch-icon-60x60.png">
+<script src="deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<link href="deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet">
+<script src="deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet">
+<link href="deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet">
+<script src="deps/headroom-0.11.0/headroom.min.js"></script><script src="deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="deps/search-1.0.0/fuse.min.js"></script><script src="deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="pkgdown.js"></script><meta property="og:title" content="Contributor Covenant Code of Conduct">
+<meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png">
+<link rel="stylesheet" href="consent.css">
+<script src="consent.js" type="text/javascript" charset="utf-8"></script>
+</head>
+<body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
 
 
@@ -15,26 +36,66 @@
     </button>
 
     <div id="navbar" class="collapse navbar-collapse ms-3">
-      <ul class="navbar-nav me-auto"><li class="nav-item"><a class="nav-link" href="articles/tern.html">Get started</a></li>
+      <ul class="navbar-nav me-auto">
+<li class="nav-item"><a class="nav-link" href="articles/tern.html">Get started</a></li>
 <li class="nav-item"><a class="nav-link" href="reference/index.html">Reference</a></li>
 <li class="nav-item dropdown">
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-articles" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Articles</button>
-  <ul class="dropdown-menu" aria-labelledby="dropdown-articles"><li><a class="dropdown-item" href="articles/missing_values.html">Missing Values in Tern</a></li>
+  <ul class="dropdown-menu" aria-labelledby="dropdown-articles">
+<li><a class="dropdown-item" href="articles/missing_values.html">Missing Values in Tern</a></li>
     <li><a class="dropdown-item" href="articles/tables.html">Tabulation</a></li>
     <li><a class="dropdown-item" href="articles/tern_formats.html">Formatting Functions</a></li>
     <li><a class="dropdown-item" href="articles/tern_functions_guide.html">Understanding `tern` functions</a></li>
-  </ul></li>
+  </ul>
+</li>
 <li class="nav-item"><a class="nav-link" href="news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
-  <ul class="dropdown-menu" aria-labelledby="dropdown-reports"><li><a class="dropdown-item" href="coverage-report/">Coverage report</a></li>
+  <ul class="dropdown-menu" aria-labelledby="dropdown-reports">
+<li><a class="dropdown-item" href="coverage-report/">Coverage report</a></li>
     <li><a class="dropdown-item" href="unit-test-report/">Unit test report</a></li>
     <li><a class="dropdown-item" href="unit-test-report-non-cran/">Non-CRAN unit test report</a></li>
-  </ul></li>
-      </ul><ul class="navbar-nav"><li class="nav-item"><form class="form-inline" role="search">
- <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="search.json"></form></li>
+  </ul>
+</li>
+      <div><li class="nav-item dropdown">
+    <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-versions">Versions</a>
+    <div class="dropdown-menu" aria-labelledby="dropdown-versions">
+    <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/main">main</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.5">v0.9.5</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.4">v0.9.4</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.3">v0.9.3</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1-rc3">v0.9.1-rc3</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a>
+</div>
+</li></div>
+</ul>
+<ul class="navbar-nav">
+<li class="nav-item"><form class="form-inline" role="search">
+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="search.json">
+</form></li>
 <li class="nav-item"><a class="external-link nav-link" href="https://github.com/insightsengineering/tern" aria-label="GitHub"><span class="fa fa-github"></span></a></li>
-      </ul></div>
+      </ul>
+</div>
 
 
   </div>
@@ -48,65 +109,80 @@
 <div id="contributor-covenant-code-of-conduct" class="section level1">
 
 <div class="section level2">
-<h2 id="our-pledge">Our Pledge<a class="anchor" aria-label="anchor" href="#our-pledge"></a></h2>
+<h2 id="our-pledge">Our Pledge<a class="anchor" aria-label="anchor" href="#our-pledge"></a>
+</h2>
 <p>We as members, contributors, and leaders pledge to make participation in our community a harassment-free experience for everyone, regardless of age, body size, visible or invisible disability, ethnicity, sex characteristics, gender identity and expression, level of experience, education, socio-economic status, nationality, personal appearance, race, caste, color, religion, or sexual identity and orientation.</p>
 <p>We pledge to act and interact in ways that contribute to an open, welcoming, diverse, inclusive, and healthy community.</p>
 </div>
 <div class="section level2">
-<h2 id="our-standards">Our Standards<a class="anchor" aria-label="anchor" href="#our-standards"></a></h2>
+<h2 id="our-standards">Our Standards<a class="anchor" aria-label="anchor" href="#our-standards"></a>
+</h2>
 <p>Examples of behavior that contributes to a positive environment for our community include:</p>
-<ul><li>Demonstrating empathy and kindness toward other people</li>
+<ul>
+<li>Demonstrating empathy and kindness toward other people</li>
 <li>Being respectful of differing opinions, viewpoints, and experiences</li>
 <li>Giving and gracefully accepting constructive feedback</li>
 <li>Accepting responsibility and apologizing to those affected by our mistakes, and learning from the experience</li>
 <li>Focusing on what is best not just for us as individuals, but for the overall community</li>
-</ul><p>Examples of unacceptable behavior include:</p>
-<ul><li>The use of sexualized language or imagery, and sexual attention or advances of any kind</li>
+</ul>
+<p>Examples of unacceptable behavior include:</p>
+<ul>
+<li>The use of sexualized language or imagery, and sexual attention or advances of any kind</li>
 <li>Trolling, insulting or derogatory comments, and personal or political attacks</li>
 <li>Public or private harassment</li>
 <li>Publishing others’ private information, such as a physical or email address, without their explicit permission</li>
 <li>Other conduct which could reasonably be considered inappropriate in a professional setting</li>
-</ul></div>
+</ul>
+</div>
 <div class="section level2">
-<h2 id="enforcement-responsibilities">Enforcement Responsibilities<a class="anchor" aria-label="anchor" href="#enforcement-responsibilities"></a></h2>
+<h2 id="enforcement-responsibilities">Enforcement Responsibilities<a class="anchor" aria-label="anchor" href="#enforcement-responsibilities"></a>
+</h2>
 <p>Community leaders are responsible for clarifying and enforcing our standards of acceptable behavior and will take appropriate and fair corrective action in response to any behavior that they deem inappropriate, threatening, offensive, or harmful.</p>
 <p>Community leaders have the right and responsibility to remove, edit, or reject comments, commits, code, wiki edits, issues, and other contributions that are not aligned to this Code of Conduct, and will communicate reasons for moderation decisions when appropriate.</p>
 </div>
 <div class="section level2">
-<h2 id="scope">Scope<a class="anchor" aria-label="anchor" href="#scope"></a></h2>
+<h2 id="scope">Scope<a class="anchor" aria-label="anchor" href="#scope"></a>
+</h2>
 <p>This Code of Conduct applies within all community spaces, and also applies when an individual is officially representing the community in public spaces. Examples of representing our community include using an official e-mail address, posting via an official social media account, or acting as an appointed representative at an online or offline event.</p>
 </div>
 <div class="section level2">
-<h2 id="enforcement">Enforcement<a class="anchor" aria-label="anchor" href="#enforcement"></a></h2>
+<h2 id="enforcement">Enforcement<a class="anchor" aria-label="anchor" href="#enforcement"></a>
+</h2>
 <p>Instances of abusive, harassing, or otherwise unacceptable behavior may be reported to the community leaders responsible for enforcement at [INSERT CONTACT METHOD]. All complaints will be reviewed and investigated promptly and fairly.</p>
 <p>All community leaders are obligated to respect the privacy and security of the reporter of any incident.</p>
 </div>
 <div class="section level2">
-<h2 id="enforcement-guidelines">Enforcement Guidelines<a class="anchor" aria-label="anchor" href="#enforcement-guidelines"></a></h2>
+<h2 id="enforcement-guidelines">Enforcement Guidelines<a class="anchor" aria-label="anchor" href="#enforcement-guidelines"></a>
+</h2>
 <p>Community leaders will follow these Community Impact Guidelines in determining the consequences for any action they deem in violation of this Code of Conduct:</p>
 <div class="section level3">
-<h3 id="id_1-correction">1. Correction<a class="anchor" aria-label="anchor" href="#id_1-correction"></a></h3>
+<h3 id="id_1-correction">1. Correction<a class="anchor" aria-label="anchor" href="#id_1-correction"></a>
+</h3>
 <p><strong>Community Impact</strong>: Use of inappropriate language or other behavior deemed unprofessional or unwelcome in the community.</p>
 <p><strong>Consequence</strong>: A private, written warning from community leaders, providing clarity around the nature of the violation and an explanation of why the behavior was inappropriate. A public apology may be requested.</p>
 </div>
 <div class="section level3">
-<h3 id="id_2-warning">2. Warning<a class="anchor" aria-label="anchor" href="#id_2-warning"></a></h3>
+<h3 id="id_2-warning">2. Warning<a class="anchor" aria-label="anchor" href="#id_2-warning"></a>
+</h3>
 <p><strong>Community Impact</strong>: A violation through a single incident or series of actions.</p>
 <p><strong>Consequence</strong>: A warning with consequences for continued behavior. No interaction with the people involved, including unsolicited interaction with those enforcing the Code of Conduct, for a specified period of time. This includes avoiding interactions in community spaces as well as external channels like social media. Violating these terms may lead to a temporary or permanent ban.</p>
 </div>
 <div class="section level3">
-<h3 id="id_3-temporary-ban">3. Temporary Ban<a class="anchor" aria-label="anchor" href="#id_3-temporary-ban"></a></h3>
+<h3 id="id_3-temporary-ban">3. Temporary Ban<a class="anchor" aria-label="anchor" href="#id_3-temporary-ban"></a>
+</h3>
 <p><strong>Community Impact</strong>: A serious violation of community standards, including sustained inappropriate behavior.</p>
 <p><strong>Consequence</strong>: A temporary ban from any sort of interaction or public communication with the community for a specified period of time. No public or private interaction with the people involved, including unsolicited interaction with those enforcing the Code of Conduct, is allowed during this period. Violating these terms may lead to a permanent ban.</p>
 </div>
 <div class="section level3">
-<h3 id="id_4-permanent-ban">4. Permanent Ban<a class="anchor" aria-label="anchor" href="#id_4-permanent-ban"></a></h3>
+<h3 id="id_4-permanent-ban">4. Permanent Ban<a class="anchor" aria-label="anchor" href="#id_4-permanent-ban"></a>
+</h3>
 <p><strong>Community Impact</strong>: Demonstrating a pattern of violation of community standards, including sustained inappropriate behavior, harassment of an individual, or aggression toward or disparagement of classes of individuals.</p>
 <p><strong>Consequence</strong>: A permanent ban from any sort of public interaction within the community.</p>
 </div>
 </div>
 <div class="section level2">
-<h2 id="attribution">Attribution<a class="anchor" aria-label="anchor" href="#attribution"></a></h2>
+<h2 id="attribution">Attribution<a class="anchor" aria-label="anchor" href="#attribution"></a>
+</h2>
 <p>This Code of Conduct is adapted from the <a href="https://www.contributor-covenant.org" class="external-link">Contributor Covenant</a>, version 2.1, available at <a href="https://www.contributor-covenant.org/version/2/1/code_of_conduct.html" class="external-link">https://www.contributor-covenant.org/version/2/1/code_of_conduct.html</a>.</p>
 <p>Community Impact Guidelines were inspired by <a href="https://github.com/mozilla/diversity" class="external-link">Mozilla’s code of conduct enforcement ladder</a>.</p>
 <p>For answers to common questions about this code of conduct, see the FAQ at <a href="https://www.contributor-covenant.org/faq" class="external-link">https://www.contributor-covenant.org/faq</a>. Translations are available at <a href="https://www.contributor-covenant.org/translations" class="external-link">https://www.contributor-covenant.org/translations</a>.</p>
@@ -114,17 +190,19 @@ <h2 id="attribution">Attribution<a class="anchor" aria-label="anchor" href="#att
 </div>
 
   </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
-    </nav></aside></div>
+    </nav></aside>
+</div>
 
 
     <footer><div class="nest">
   <p>tern is a part of the <strong>NEST</strong> and <a href="https://pharmaverse.org/" class="external-link"><strong>pharmaverse</strong></a>.</p>
 </div>
-<script type="text/javascript" src="analytics.js"></script></footer></div>
-
+<script type="text/javascript" src="analytics.js"></script></footer>
+</div>
 
 
 
 
-  </body></html>
 
+  </body>
+</html>
diff --git a/main/CONTRIBUTING.html b/main/CONTRIBUTING.html
index b4b8b0afa8..2aef5eab1f 100644
--- a/main/CONTRIBUTING.html
+++ b/main/CONTRIBUTING.html
@@ -1,5 +1,26 @@
-<!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Contribution Guidelines • tern</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="apple-touch-icon-60x60.png"><script src="deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="deps/headroom-0.11.0/headroom.min.js"></script><script src="deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="deps/search-1.0.0/fuse.min.js"></script><script src="deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="pkgdown.js"></script><meta property="og:title" content="Contribution Guidelines"><meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png"><link rel="stylesheet" href="consent.css"><script src="consent.js" type="text/javascript" charset="utf-8"></script></head><body>
+<html lang="en">
+<head>
+<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+<meta charset="utf-8">
+<meta http-equiv="X-UA-Compatible" content="IE=edge">
+<meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<title>Contribution Guidelines • tern</title>
+<!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="favicon-16x16.png">
+<link rel="icon" type="image/png" sizes="32x32" href="favicon-32x32.png">
+<link rel="apple-touch-icon" type="image/png" sizes="180x180" href="apple-touch-icon.png">
+<link rel="apple-touch-icon" type="image/png" sizes="120x120" href="apple-touch-icon-120x120.png">
+<link rel="apple-touch-icon" type="image/png" sizes="76x76" href="apple-touch-icon-76x76.png">
+<link rel="apple-touch-icon" type="image/png" sizes="60x60" href="apple-touch-icon-60x60.png">
+<script src="deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<link href="deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet">
+<script src="deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet">
+<link href="deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet">
+<script src="deps/headroom-0.11.0/headroom.min.js"></script><script src="deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="deps/search-1.0.0/fuse.min.js"></script><script src="deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="pkgdown.js"></script><meta property="og:title" content="Contribution Guidelines">
+<meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png">
+<link rel="stylesheet" href="consent.css">
+<script src="consent.js" type="text/javascript" charset="utf-8"></script>
+</head>
+<body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
 
 
@@ -15,26 +36,66 @@
     </button>
 
     <div id="navbar" class="collapse navbar-collapse ms-3">
-      <ul class="navbar-nav me-auto"><li class="nav-item"><a class="nav-link" href="articles/tern.html">Get started</a></li>
+      <ul class="navbar-nav me-auto">
+<li class="nav-item"><a class="nav-link" href="articles/tern.html">Get started</a></li>
 <li class="nav-item"><a class="nav-link" href="reference/index.html">Reference</a></li>
 <li class="nav-item dropdown">
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-articles" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Articles</button>
-  <ul class="dropdown-menu" aria-labelledby="dropdown-articles"><li><a class="dropdown-item" href="articles/missing_values.html">Missing Values in Tern</a></li>
+  <ul class="dropdown-menu" aria-labelledby="dropdown-articles">
+<li><a class="dropdown-item" href="articles/missing_values.html">Missing Values in Tern</a></li>
     <li><a class="dropdown-item" href="articles/tables.html">Tabulation</a></li>
     <li><a class="dropdown-item" href="articles/tern_formats.html">Formatting Functions</a></li>
     <li><a class="dropdown-item" href="articles/tern_functions_guide.html">Understanding `tern` functions</a></li>
-  </ul></li>
+  </ul>
+</li>
 <li class="nav-item"><a class="nav-link" href="news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
-  <ul class="dropdown-menu" aria-labelledby="dropdown-reports"><li><a class="dropdown-item" href="coverage-report/">Coverage report</a></li>
+  <ul class="dropdown-menu" aria-labelledby="dropdown-reports">
+<li><a class="dropdown-item" href="coverage-report/">Coverage report</a></li>
     <li><a class="dropdown-item" href="unit-test-report/">Unit test report</a></li>
     <li><a class="dropdown-item" href="unit-test-report-non-cran/">Non-CRAN unit test report</a></li>
-  </ul></li>
-      </ul><ul class="navbar-nav"><li class="nav-item"><form class="form-inline" role="search">
- <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="search.json"></form></li>
+  </ul>
+</li>
+      <div><li class="nav-item dropdown">
+    <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-versions">Versions</a>
+    <div class="dropdown-menu" aria-labelledby="dropdown-versions">
+    <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/main">main</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.5">v0.9.5</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.4">v0.9.4</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.3">v0.9.3</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1-rc3">v0.9.1-rc3</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a>
+</div>
+</li></div>
+</ul>
+<ul class="navbar-nav">
+<li class="nav-item"><form class="form-inline" role="search">
+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="search.json">
+</form></li>
 <li class="nav-item"><a class="external-link nav-link" href="https://github.com/insightsengineering/tern" aria-label="GitHub"><span class="fa fa-github"></span></a></li>
-      </ul></div>
+      </ul>
+</div>
 
 
   </div>
@@ -50,7 +111,8 @@
 <p>🙏 Thank you for taking the time to contribute!</p>
 <p>Your input is deeply valued, whether an issue, a pull request, or even feedback, regardless of size, content or scope.</p>
 <div class="section level2">
-<h2 id="table-of-contents">Table of contents<a class="anchor" aria-label="anchor" href="#table-of-contents"></a></h2>
+<h2 id="table-of-contents">Table of contents<a class="anchor" aria-label="anchor" href="#table-of-contents"></a>
+</h2>
 <p><a href="#getting-started">👶 Getting started</a></p>
 <p><a href="#code-of-conduct">📔 Code of Conduct</a></p>
 <p><a href="#license">🗃 License</a></p>
@@ -61,38 +123,47 @@ <h2 id="table-of-contents">Table of contents<a class="anchor" aria-label="anchor
 <p><a href="#questions">❓ Questions</a></p>
 </div>
 <div class="section level2">
-<h2 id="getting-started">Getting started<a class="anchor" aria-label="anchor" href="#getting-started"></a></h2>
+<h2 id="getting-started">Getting started<a class="anchor" aria-label="anchor" href="#getting-started"></a>
+</h2>
 <p>Please refer the project <a href="https://insightsengineering.github.io/tern/index.html">documentation</a> for a brief introduction. Please also see other <a href="https://insightsengineering.github.io/tern/main/articles/index.html">articles</a> within the project documentation for additional information.</p>
 </div>
 <div class="section level2">
-<h2 id="code-of-conduct">Code of Conduct<a class="anchor" aria-label="anchor" href="#code-of-conduct"></a></h2>
+<h2 id="code-of-conduct">Code of Conduct<a class="anchor" aria-label="anchor" href="#code-of-conduct"></a>
+</h2>
 <p>A <a href="CODE_OF_CONDUCT.html">Code of Conduct</a> governs this project. Participants and contributors are expected to follow the rules outlined therein.</p>
 </div>
 <div class="section level2">
-<h2 id="license">License<a class="anchor" aria-label="anchor" href="#license"></a></h2>
+<h2 id="license">License<a class="anchor" aria-label="anchor" href="#license"></a>
+</h2>
 <p>All your contributions will be covered by this project’s <a href="https://insightsengineering.github.io/tern/main/LICENSE-text.html">license</a>.</p>
 </div>
 <div class="section level2">
-<h2 id="issues">Issues<a class="anchor" aria-label="anchor" href="#issues"></a></h2>
+<h2 id="issues">Issues<a class="anchor" aria-label="anchor" href="#issues"></a>
+</h2>
 <p>We use GitHub to track issues, feature requests, and bugs. Before submitting a new issue, please check if the issue has already been reported. If the issue already exists, please upvote the existing issue 👍.</p>
 <p>For new feature requests, please elaborate on the context and the benefit the feature will have for users, developers, or other relevant personas.</p>
 </div>
 <div class="section level2">
-<h2 id="pull-requests">Pull requests<a class="anchor" aria-label="anchor" href="#pull-requests"></a></h2>
+<h2 id="pull-requests">Pull requests<a class="anchor" aria-label="anchor" href="#pull-requests"></a>
+</h2>
 <div class="section level3">
-<h3 id="github-flow">GitHub Flow<a class="anchor" aria-label="anchor" href="#github-flow"></a></h3>
+<h3 id="github-flow">GitHub Flow<a class="anchor" aria-label="anchor" href="#github-flow"></a>
+</h3>
 <p>This repository uses the <a href="https://docs.github.com/en/get-started/quickstart/github-flow" class="external-link">GitHub Flow</a> model for collaboration. To submit a pull request:</p>
-<ol style="list-style-type: decimal"><li>
+<ol style="list-style-type: decimal">
+<li>
 <p>Create a branch</p>
 <p>Please see the <a href="#branch-naming-convention">branch naming convention</a> below. If you don’t have write access to this repository, please fork it.</p>
 </li>
 <li>
 <p>Make changes</p>
 <p>Make sure your code</p>
-<ul><li>passes all checks imposed by GitHub Actions</li>
+<ul>
+<li>passes all checks imposed by GitHub Actions</li>
 <li>is well documented</li>
 <li>is well tested with unit tests sufficiently covering the changes introduced</li>
-</ul></li>
+</ul>
+</li>
 <li>
 <p>Create a pull request (PR)</p>
 <p>In the pull request description, please link the relevant issue (if any), provide a detailed description of the change, and include any assumptions.</p>
@@ -106,76 +177,93 @@ <h3 id="github-flow">GitHub Flow<a class="anchor" aria-label="anchor" href="#git
 <p>Pat yourself on the back</p>
 <p>Congratulations! 🎉 You are now an official contributor to this project! We are grateful for your contribution.</p>
 </li>
-</ol></div>
+</ol>
+</div>
 <div class="section level3">
-<h3 id="branch-naming-convention">Branch naming convention<a class="anchor" aria-label="anchor" href="#branch-naming-convention"></a></h3>
+<h3 id="branch-naming-convention">Branch naming convention<a class="anchor" aria-label="anchor" href="#branch-naming-convention"></a>
+</h3>
 <p>Suppose your changes are related to a current issue in the current project; please name your branch as follows: <code>&lt;issue_id&gt;_&lt;short_description&gt;</code>. Please use underscore (<code>_</code>) as a delimiter for word separation. For example, <code>420_fix_ui_bug</code> would be a suitable branch name if your change is resolving and UI-related bug reported in issue number <code>420</code> in the current project.</p>
 <p>If your change affects multiple repositories, please name your branches as follows: <code>&lt;issue_id&gt;_&lt;issue_repo&gt;_&lt;short description&gt;</code>. For example, <code>69_awesomeproject_fix_spelling_error</code> would reference issue <code>69</code> reported in project <code>awesomeproject</code> and aims to resolve one or more spelling errors in multiple (likely related) repositories.</p>
 </div>
 <div class="section level3">
 <h3 id="monorepo-and-stageddependencies">
 <code>monorepo</code> and <code>staged.dependencies</code>
-<a class="anchor" aria-label="anchor" href="#monorepo-and-stageddependencies"></a></h3>
+<a class="anchor" aria-label="anchor" href="#monorepo-and-stageddependencies"></a>
+</h3>
 <p>Sometimes you might need to change upstream dependent package(s) to be able to submit a meaningful change. We are using <a href="https://github.com/openpharma/staged.dependencies" class="external-link"><code>staged.dependencies</code></a> functionality to simulate a <code>monorepo</code> behavior. The dependency configuration is already specified in this project’s <code>staged_dependencies.yaml</code> file. You need to name the feature branches appropriately. <em>This is the only exception from the branch naming convention described above</em>.</p>
 <p>Please refer to the <a href="https://openpharma.github.io/staged.dependencies/" class="external-link">staged.dependencies package documentation</a> for more details.</p>
 </div>
 </div>
 <div class="section level2">
-<h2 id="coding-guidelines">Coding guidelines<a class="anchor" aria-label="anchor" href="#coding-guidelines"></a></h2>
+<h2 id="coding-guidelines">Coding guidelines<a class="anchor" aria-label="anchor" href="#coding-guidelines"></a>
+</h2>
 <p>This repository follows some unified processes and standards adopted by its maintainers to ensure software development is carried out consistently within teams and cohesively across other repositories.</p>
 <div class="section level3">
-<h3 id="style-guide">Style guide<a class="anchor" aria-label="anchor" href="#style-guide"></a></h3>
+<h3 id="style-guide">Style guide<a class="anchor" aria-label="anchor" href="#style-guide"></a>
+</h3>
 <p>This repository follows the standard <a href="https://style.tidyverse.org/" class="external-link"><code>tidyverse</code> style guide</a> and uses <a href="https://github.com/r-lib/lintr" class="external-link"><code>lintr</code></a> for lint checks. Customized lint configurations are available in this repository’s <code>.lintr</code> file.</p>
 </div>
 <div class="section level3">
-<h3 id="dependency-management">Dependency management<a class="anchor" aria-label="anchor" href="#dependency-management"></a></h3>
+<h3 id="dependency-management">Dependency management<a class="anchor" aria-label="anchor" href="#dependency-management"></a>
+</h3>
 <p>Lightweight is the right weight. This repository follows <a href="https://www.tinyverse.org/" class="external-link">tinyverse</a> recommedations of limiting dependencies to minimum.</p>
 </div>
 <div class="section level3">
-<h3 id="dependency-version-management">Dependency version management<a class="anchor" aria-label="anchor" href="#dependency-version-management"></a></h3>
+<h3 id="dependency-version-management">Dependency version management<a class="anchor" aria-label="anchor" href="#dependency-version-management"></a>
+</h3>
 <p>If the code is not compatible with all (!) historical versions of a given dependenct package, it is required to specify minimal version in the <code>DESCRIPTION</code> file. In particular: if the development version requires (imports) the development version of another package - it is required to put <code>abc (&gt;= 1.2.3.9000)</code>.</p>
 </div>
 <div class="section level3">
-<h3 id="recommended-development-environment--tools">Recommended development environment &amp; tools<a class="anchor" aria-label="anchor" href="#recommended-development-environment--tools"></a></h3>
+<h3 id="recommended-development-environment--tools">Recommended development environment &amp; tools<a class="anchor" aria-label="anchor" href="#recommended-development-environment--tools"></a>
+</h3>
 <div class="section level4">
-<h4 id="r--package-versions">R &amp; package versions<a class="anchor" aria-label="anchor" href="#r--package-versions"></a></h4>
+<h4 id="r--package-versions">R &amp; package versions<a class="anchor" aria-label="anchor" href="#r--package-versions"></a>
+</h4>
 <p>We continuously test our packages against the newest R version along with the most recent dependencies from CRAN and BioConductor. We recommend that your working environment is also set up in the same way. You can find the details about the R version and packages used in the <code>R CMD check</code> GitHub Action execution log - there is a step that prints out the R <code><a href="https://rdrr.io/r/utils/sessionInfo.html" class="external-link">sessionInfo()</a></code>.</p>
 <p>If you discover bugs on older R versions or with an older set of dependencies, please create the relevant bug reports.</p>
 </div>
 <div class="section level4">
-<h4 id="pre-commit"><code>pre-commit</code><a class="anchor" aria-label="anchor" href="#pre-commit"></a></h4>
+<h4 id="pre-commit">
+<code>pre-commit</code><a class="anchor" aria-label="anchor" href="#pre-commit"></a>
+</h4>
 <p>We highly recommend that you use the <a href="https://pre-commit.com/" class="external-link"><code>pre-commit</code></a> tool combined with <a href="https://github.com/lorenzwalthert/precommit" class="external-link"><code>R hooks for pre-commit</code></a> to execute some of the checks before committing and pushing your changes.</p>
 <p>Pre-commit hooks are already available in this repository’s <code>.pre-commit-config.yaml</code> file.</p>
 </div>
 </div>
 </div>
 <div class="section level2">
-<h2 id="recognition-model">Recognition model<a class="anchor" aria-label="anchor" href="#recognition-model"></a></h2>
+<h2 id="recognition-model">Recognition model<a class="anchor" aria-label="anchor" href="#recognition-model"></a>
+</h2>
 <p>As mentioned previously, all contributions are deeply valued and appreciated. While all contribution data is available as part of the <a href="https://github.com/insightsengineering/tern/pulse" class="external-link">repository insights</a>, to recognize a <em>significant</em> contribution and hence add the contributor to the package authors list, the following rules are enforced:</p>
-<ul><li>Minimum 5% of lines of code authored* (determined by <code>git blame</code> query) OR</li>
+<ul>
+<li>Minimum 5% of lines of code authored* (determined by <code>git blame</code> query) OR</li>
 <li>Being at the top 5 contributors in terms of number of commits OR lines added OR lines removed*</li>
-</ul><p>*Excluding auto-generated code, including but not limited to <code>roxygen</code> comments or <code>renv.lock</code> files.</p>
+</ul>
+<p>*Excluding auto-generated code, including but not limited to <code>roxygen</code> comments or <code>renv.lock</code> files.</p>
 <p>The package maintainer also reserves the right to adjust the criteria to recognize contributions.</p>
 </div>
 <div class="section level2">
-<h2 id="questions">Questions<a class="anchor" aria-label="anchor" href="#questions"></a></h2>
+<h2 id="questions">Questions<a class="anchor" aria-label="anchor" href="#questions"></a>
+</h2>
 <p>If you have further questions regarding the contribution guidelines, please contact the package/repository maintainer.</p>
 <!-- urls -->
 </div>
 </div>
 
   </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
-    </nav></aside></div>
+    </nav></aside>
+</div>
 
 
     <footer><div class="nest">
   <p>tern is a part of the <strong>NEST</strong> and <a href="https://pharmaverse.org/" class="external-link"><strong>pharmaverse</strong></a>.</p>
 </div>
-<script type="text/javascript" src="analytics.js"></script></footer></div>
-
+<script type="text/javascript" src="analytics.js"></script></footer>
+</div>
 
 
 
 
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+  </body>
+</html>
diff --git a/main/LICENSE-text.html b/main/LICENSE-text.html
index 3a9b2f46ae..0bb17d5a88 100644
--- a/main/LICENSE-text.html
+++ b/main/LICENSE-text.html
@@ -1,5 +1,26 @@
-<!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>License • tern</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="apple-touch-icon-60x60.png"><script src="deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="deps/headroom-0.11.0/headroom.min.js"></script><script src="deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="deps/search-1.0.0/fuse.min.js"></script><script src="deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="pkgdown.js"></script><meta property="og:title" content="License"><meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png"><link rel="stylesheet" href="consent.css"><script src="consent.js" type="text/javascript" charset="utf-8"></script></head><body>
+<html lang="en">
+<head>
+<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+<meta charset="utf-8">
+<meta http-equiv="X-UA-Compatible" content="IE=edge">
+<meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<title>License • tern</title>
+<!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="favicon-16x16.png">
+<link rel="icon" type="image/png" sizes="32x32" href="favicon-32x32.png">
+<link rel="apple-touch-icon" type="image/png" sizes="180x180" href="apple-touch-icon.png">
+<link rel="apple-touch-icon" type="image/png" sizes="120x120" href="apple-touch-icon-120x120.png">
+<link rel="apple-touch-icon" type="image/png" sizes="76x76" href="apple-touch-icon-76x76.png">
+<link rel="apple-touch-icon" type="image/png" sizes="60x60" href="apple-touch-icon-60x60.png">
+<script src="deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<link href="deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet">
+<script src="deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet">
+<link href="deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet">
+<script src="deps/headroom-0.11.0/headroom.min.js"></script><script src="deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="deps/search-1.0.0/fuse.min.js"></script><script src="deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="pkgdown.js"></script><meta property="og:title" content="License">
+<meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png">
+<link rel="stylesheet" href="consent.css">
+<script src="consent.js" type="text/javascript" charset="utf-8"></script>
+</head>
+<body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
 
 
@@ -15,26 +36,66 @@
     </button>
 
     <div id="navbar" class="collapse navbar-collapse ms-3">
-      <ul class="navbar-nav me-auto"><li class="nav-item"><a class="nav-link" href="articles/tern.html">Get started</a></li>
+      <ul class="navbar-nav me-auto">
+<li class="nav-item"><a class="nav-link" href="articles/tern.html">Get started</a></li>
 <li class="nav-item"><a class="nav-link" href="reference/index.html">Reference</a></li>
 <li class="nav-item dropdown">
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-articles" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Articles</button>
-  <ul class="dropdown-menu" aria-labelledby="dropdown-articles"><li><a class="dropdown-item" href="articles/missing_values.html">Missing Values in Tern</a></li>
+  <ul class="dropdown-menu" aria-labelledby="dropdown-articles">
+<li><a class="dropdown-item" href="articles/missing_values.html">Missing Values in Tern</a></li>
     <li><a class="dropdown-item" href="articles/tables.html">Tabulation</a></li>
     <li><a class="dropdown-item" href="articles/tern_formats.html">Formatting Functions</a></li>
     <li><a class="dropdown-item" href="articles/tern_functions_guide.html">Understanding `tern` functions</a></li>
-  </ul></li>
+  </ul>
+</li>
 <li class="nav-item"><a class="nav-link" href="news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
-  <ul class="dropdown-menu" aria-labelledby="dropdown-reports"><li><a class="dropdown-item" href="coverage-report/">Coverage report</a></li>
+  <ul class="dropdown-menu" aria-labelledby="dropdown-reports">
+<li><a class="dropdown-item" href="coverage-report/">Coverage report</a></li>
     <li><a class="dropdown-item" href="unit-test-report/">Unit test report</a></li>
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- <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="search.json"></form></li>
+  </ul>
+</li>
+      <div><li class="nav-item dropdown">
+    <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-versions">Versions</a>
+    <div class="dropdown-menu" aria-labelledby="dropdown-versions">
+    <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
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+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.5">v0.9.5</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.4">v0.9.4</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.3">v0.9.3</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1-rc3">v0.9.1-rc3</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a>
+</div>
+</li></div>
+</ul>
+<ul class="navbar-nav">
+<li class="nav-item"><form class="form-inline" role="search">
+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="search.json">
+</form></li>
 <li class="nav-item"><a class="external-link nav-link" href="https://github.com/insightsengineering/tern" aria-label="GitHub"><span class="fa fa-github"></span></a></li>
-      </ul></div>
+      </ul>
+</div>
 
 
   </div>
@@ -60,17 +121,19 @@
 limitations under the License.
 </pre>
 
-  </main></div>
+  </main>
+</div>
 
 
     <footer><div class="nest">
   <p>tern is a part of the <strong>NEST</strong> and <a href="https://pharmaverse.org/" class="external-link"><strong>pharmaverse</strong></a>.</p>
 </div>
-<script type="text/javascript" src="analytics.js"></script></footer></div>
-
+<script type="text/javascript" src="analytics.js"></script></footer>
+</div>
 
 
 
 
-  </body></html>
 
+  </body>
+</html>
diff --git a/main/SECURITY.html b/main/SECURITY.html
index 139d0fae7a..855f39c68d 100644
--- a/main/SECURITY.html
+++ b/main/SECURITY.html
@@ -1,5 +1,26 @@
-<!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Security Policy • tern</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="apple-touch-icon-60x60.png"><script src="deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="deps/headroom-0.11.0/headroom.min.js"></script><script src="deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="deps/search-1.0.0/fuse.min.js"></script><script src="deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="pkgdown.js"></script><meta property="og:title" content="Security Policy"><meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png"><link rel="stylesheet" href="consent.css"><script src="consent.js" type="text/javascript" charset="utf-8"></script></head><body>
+<html lang="en">
+<head>
+<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+<meta charset="utf-8">
+<meta http-equiv="X-UA-Compatible" content="IE=edge">
+<meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<title>Security Policy • tern</title>
+<!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="favicon-16x16.png">
+<link rel="icon" type="image/png" sizes="32x32" href="favicon-32x32.png">
+<link rel="apple-touch-icon" type="image/png" sizes="180x180" href="apple-touch-icon.png">
+<link rel="apple-touch-icon" type="image/png" sizes="120x120" href="apple-touch-icon-120x120.png">
+<link rel="apple-touch-icon" type="image/png" sizes="76x76" href="apple-touch-icon-76x76.png">
+<link rel="apple-touch-icon" type="image/png" sizes="60x60" href="apple-touch-icon-60x60.png">
+<script src="deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<link href="deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet">
+<script src="deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet">
+<link href="deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet">
+<script src="deps/headroom-0.11.0/headroom.min.js"></script><script src="deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="deps/search-1.0.0/fuse.min.js"></script><script src="deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="pkgdown.js"></script><meta property="og:title" content="Security Policy">
+<meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png">
+<link rel="stylesheet" href="consent.css">
+<script src="consent.js" type="text/javascript" charset="utf-8"></script>
+</head>
+<body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
 
 
@@ -15,26 +36,66 @@
     </button>
 
     <div id="navbar" class="collapse navbar-collapse ms-3">
-      <ul class="navbar-nav me-auto"><li class="nav-item"><a class="nav-link" href="articles/tern.html">Get started</a></li>
+      <ul class="navbar-nav me-auto">
+<li class="nav-item"><a class="nav-link" href="articles/tern.html">Get started</a></li>
 <li class="nav-item"><a class="nav-link" href="reference/index.html">Reference</a></li>
 <li class="nav-item dropdown">
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-articles" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Articles</button>
-  <ul class="dropdown-menu" aria-labelledby="dropdown-articles"><li><a class="dropdown-item" href="articles/missing_values.html">Missing Values in Tern</a></li>
+  <ul class="dropdown-menu" aria-labelledby="dropdown-articles">
+<li><a class="dropdown-item" href="articles/missing_values.html">Missing Values in Tern</a></li>
     <li><a class="dropdown-item" href="articles/tables.html">Tabulation</a></li>
     <li><a class="dropdown-item" href="articles/tern_formats.html">Formatting Functions</a></li>
     <li><a class="dropdown-item" href="articles/tern_functions_guide.html">Understanding `tern` functions</a></li>
-  </ul></li>
+  </ul>
+</li>
 <li class="nav-item"><a class="nav-link" href="news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
-  <ul class="dropdown-menu" aria-labelledby="dropdown-reports"><li><a class="dropdown-item" href="coverage-report/">Coverage report</a></li>
+  <ul class="dropdown-menu" aria-labelledby="dropdown-reports">
+<li><a class="dropdown-item" href="coverage-report/">Coverage report</a></li>
     <li><a class="dropdown-item" href="unit-test-report/">Unit test report</a></li>
     <li><a class="dropdown-item" href="unit-test-report-non-cran/">Non-CRAN unit test report</a></li>
-  </ul></li>
-      </ul><ul class="navbar-nav"><li class="nav-item"><form class="form-inline" role="search">
- <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="search.json"></form></li>
+  </ul>
+</li>
+      <div><li class="nav-item dropdown">
+    <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-versions">Versions</a>
+    <div class="dropdown-menu" aria-labelledby="dropdown-versions">
+    <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/main">main</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.5">v0.9.5</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.4">v0.9.4</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.3">v0.9.3</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1-rc3">v0.9.1-rc3</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a>
+</div>
+</li></div>
+</ul>
+<ul class="navbar-nav">
+<li class="nav-item"><form class="form-inline" role="search">
+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="search.json">
+</form></li>
 <li class="nav-item"><a class="external-link nav-link" href="https://github.com/insightsengineering/tern" aria-label="GitHub"><span class="fa fa-github"></span></a></li>
-      </ul></div>
+      </ul>
+</div>
 
 
   </div>
@@ -48,38 +109,44 @@
 <div id="security-policy" class="section level1">
 
 <div class="section level2">
-<h2 id="reporting-security-issues">Reporting Security Issues<a class="anchor" aria-label="anchor" href="#reporting-security-issues"></a></h2>
+<h2 id="reporting-security-issues">Reporting Security Issues<a class="anchor" aria-label="anchor" href="#reporting-security-issues"></a>
+</h2>
 <p>If you believe you have found a security vulnerability in any of the repositories in this organization, please report it to us through coordinated disclosure.</p>
 <p><strong>Please do not report security vulnerabilities through public GitHub issues, discussions, or pull requests.</strong></p>
 <p>Instead, please send an email to vulnerability.management[@]roche.com.</p>
 <p>Please include as much of the information listed below as you can to help us better understand and resolve the issue:</p>
-<ul><li>The type of issue (e.g., buffer overflow, SQL injection, or cross-site scripting)</li>
+<ul>
+<li>The type of issue (e.g., buffer overflow, SQL injection, or cross-site scripting)</li>
 <li>Full paths of source file(s) related to the manifestation of the issue</li>
 <li>The location of the affected source code (tag/branch/commit or direct URL)</li>
 <li>Any special configuration required to reproduce the issue</li>
 <li>Step-by-step instructions to reproduce the issue</li>
 <li>Proof-of-concept or exploit code (if possible)</li>
 <li>Impact of the issue, including how an attacker might exploit the issue</li>
-</ul><p>This information will help us triage your report more quickly.</p>
+</ul>
+<p>This information will help us triage your report more quickly.</p>
 </div>
 <div class="section level2">
-<h2 id="data-security-standards-dss">Data Security Standards (DSS)<a class="anchor" aria-label="anchor" href="#data-security-standards-dss"></a></h2>
+<h2 id="data-security-standards-dss">Data Security Standards (DSS)<a class="anchor" aria-label="anchor" href="#data-security-standards-dss"></a>
+</h2>
 <p>Please make sure that while reporting issues in the form a bug, feature, or pull request, <em>all</em> sensitive information such as <a href="https://www.dhs.gov/privacy-training/what-personally-identifiable-information" class="external-link">PII</a>, <a href="https://www.hhs.gov/hipaa/for-professionals/security/laws-regulations/index.html" class="external-link">PHI</a>, and <a href="https://www.pcisecuritystandards.org/pci_security/standards_overview" class="external-link">PCI</a> is completely removed from any text and attachments, including pictures and videos.</p>
 </div>
 </div>
 
   </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
-    </nav></aside></div>
+    </nav></aside>
+</div>
 
 
     <footer><div class="nest">
   <p>tern is a part of the <strong>NEST</strong> and <a href="https://pharmaverse.org/" class="external-link"><strong>pharmaverse</strong></a>.</p>
 </div>
-<script type="text/javascript" src="analytics.js"></script></footer></div>
-
+<script type="text/javascript" src="analytics.js"></script></footer>
+</div>
 
 
 
 
-  </body></html>
 
+  </body>
+</html>
diff --git a/main/articles/index.html b/main/articles/index.html
index d7ff44a8f1..ca88bcc8ff 100644
--- a/main/articles/index.html
+++ b/main/articles/index.html
@@ -1,5 +1,26 @@
-<!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Articles • tern</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Articles"><meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png"><link rel="stylesheet" href="../consent.css"><script src="../consent.js" type="text/javascript" charset="utf-8"></script></head><body>
+<html lang="en">
+<head>
+<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+<meta charset="utf-8">
+<meta http-equiv="X-UA-Compatible" content="IE=edge">
+<meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<title>Articles • tern</title>
+<!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png">
+<link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png">
+<link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png">
+<link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png">
+<link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png">
+<link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png">
+<script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet">
+<script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet">
+<link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet">
+<script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Articles">
+<meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png">
+<link rel="stylesheet" href="../consent.css">
+<script src="../consent.js" type="text/javascript" charset="utf-8"></script>
+</head>
+<body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
 
 
@@ -15,26 +36,66 @@
     </button>
 
     <div id="navbar" class="collapse navbar-collapse ms-3">
-      <ul class="navbar-nav me-auto"><li class="nav-item"><a class="nav-link" href="../articles/tern.html">Get started</a></li>
+      <ul class="navbar-nav me-auto">
+<li class="nav-item"><a class="nav-link" href="../articles/tern.html">Get started</a></li>
 <li class="nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
 <li class="nav-item dropdown">
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-articles" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Articles</button>
-  <ul class="dropdown-menu" aria-labelledby="dropdown-articles"><li><a class="dropdown-item" href="../articles/missing_values.html">Missing Values in Tern</a></li>
+  <ul class="dropdown-menu" aria-labelledby="dropdown-articles">
+<li><a class="dropdown-item" href="../articles/missing_values.html">Missing Values in Tern</a></li>
     <li><a class="dropdown-item" href="../articles/tables.html">Tabulation</a></li>
     <li><a class="dropdown-item" href="../articles/tern_formats.html">Formatting Functions</a></li>
     <li><a class="dropdown-item" href="../articles/tern_functions_guide.html">Understanding `tern` functions</a></li>
-  </ul></li>
+  </ul>
+</li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
-  <ul class="dropdown-menu" aria-labelledby="dropdown-reports"><li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
+  <ul class="dropdown-menu" aria-labelledby="dropdown-reports">
+<li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
     <li><a class="dropdown-item" href="../unit-test-report/">Unit test report</a></li>
     <li><a class="dropdown-item" href="../unit-test-report-non-cran/">Non-CRAN unit test report</a></li>
-  </ul></li>
-      </ul><ul class="navbar-nav"><li class="nav-item"><form class="form-inline" role="search">
- <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json"></form></li>
+  </ul>
+</li>
+      <div><li class="nav-item dropdown">
+    <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-versions">Versions</a>
+    <div class="dropdown-menu" aria-labelledby="dropdown-versions">
+    <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/main">main</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.5">v0.9.5</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.4">v0.9.4</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.3">v0.9.3</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1-rc3">v0.9.1-rc3</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a>
+</div>
+</li></div>
+</ul>
+<ul class="navbar-nav">
+<li class="nav-item"><form class="form-inline" role="search">
+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json">
+</form></li>
 <li class="nav-item"><a class="external-link nav-link" href="https://github.com/insightsengineering/tern" aria-label="GitHub"><span class="fa fa-github"></span></a></li>
-      </ul></div>
+      </ul>
+</div>
 
 
   </div>
@@ -48,28 +109,37 @@
       <h3>All vignettes</h3>
       <div class="section-desc"></div>
 
-      <dl><dt><a href="missing_values.html">Missing Values in Tern</a></dt>
+      <dl>
+<dt><a href="missing_values.html">Missing Values in Tern</a></dt>
         <dd>
-        </dd><dt><a href="tables.html">Tabulation</a></dt>
+        </dd>
+<dt><a href="tables.html">Tabulation</a></dt>
         <dd>
-        </dd><dt><a href="tern_formats.html">Formatting Functions</a></dt>
+        </dd>
+<dt><a href="tern_formats.html">Formatting Functions</a></dt>
         <dd>
-        </dd><dt><a href="tern_functions_guide.html">Understanding `tern` functions</a></dt>
+        </dd>
+<dt><a href="tern_functions_guide.html">Understanding `tern` functions</a></dt>
         <dd>
-        </dd><dt><a href="tern.html">Introduction to tern</a></dt>
+        </dd>
+<dt><a href="tern.html">Introduction to tern</a></dt>
         <dd>
-      </dd></dl></div>
-  </main></div>
+      </dd>
+</dl>
+</div>
+  </main>
+</div>
 
 
     <footer><div class="nest">
   <p>tern is a part of the <strong>NEST</strong> and <a href="https://pharmaverse.org/" class="external-link"><strong>pharmaverse</strong></a>.</p>
 </div>
-<script type="text/javascript" src="../analytics.js"></script></footer></div>
-
+<script type="text/javascript" src="../analytics.js"></script></footer>
+</div>
 
 
 
 
-  </body></html>
 
+  </body>
+</html>
diff --git a/main/articles/missing_values.html b/main/articles/missing_values.html
index 3019f11397..139a89fe75 100644
--- a/main/articles/missing_values.html
+++ b/main/articles/missing_values.html
@@ -1,5 +1,4 @@
-<!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en">
+<html lang="en">
 <head>
 <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
 <meta charset="utf-8">
@@ -57,7 +56,38 @@
     <li><a class="dropdown-item" href="../unit-test-report-non-cran/">Non-CRAN unit test report</a></li>
   </ul>
 </li>
-      </ul>
+      <div><li class="nav-item dropdown">
+    <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-versions">Versions</a>
+    <div class="dropdown-menu" aria-labelledby="dropdown-versions">
+    <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/main">main</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.5">v0.9.5</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.4">v0.9.4</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.3">v0.9.3</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1-rc3">v0.9.1-rc3</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a>
+</div>
+</li></div>
+</ul>
 <ul class="navbar-nav">
 <li class="nav-item"><form class="form-inline" role="search">
  <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json">
diff --git a/main/articles/tables.html b/main/articles/tables.html
index f89b70dd78..867898c205 100644
--- a/main/articles/tables.html
+++ b/main/articles/tables.html
@@ -1,5 +1,4 @@
-<!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en">
+<html lang="en">
 <head>
 <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
 <meta charset="utf-8">
@@ -57,7 +56,38 @@
     <li><a class="dropdown-item" href="../unit-test-report-non-cran/">Non-CRAN unit test report</a></li>
   </ul>
 </li>
-      </ul>
+      <div><li class="nav-item dropdown">
+    <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-versions">Versions</a>
+    <div class="dropdown-menu" aria-labelledby="dropdown-versions">
+    <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/main">main</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.5">v0.9.5</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.4">v0.9.4</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.3">v0.9.3</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1-rc3">v0.9.1-rc3</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a>
+</div>
+</li></div>
+</ul>
 <ul class="navbar-nav">
 <li class="nav-item"><form class="form-inline" role="search">
  <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json">
diff --git a/main/articles/tern.html b/main/articles/tern.html
index e2f24da856..b7f84f077f 100644
--- a/main/articles/tern.html
+++ b/main/articles/tern.html
@@ -1,5 +1,4 @@
-<!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en">
+<html lang="en">
 <head>
 <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
 <meta charset="utf-8">
@@ -57,7 +56,38 @@
     <li><a class="dropdown-item" href="../unit-test-report-non-cran/">Non-CRAN unit test report</a></li>
   </ul>
 </li>
-      </ul>
+      <div><li class="nav-item dropdown">
+    <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-versions">Versions</a>
+    <div class="dropdown-menu" aria-labelledby="dropdown-versions">
+    <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/main">main</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.5">v0.9.5</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.4">v0.9.4</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.3">v0.9.3</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1-rc3">v0.9.1-rc3</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a>
+</div>
+</li></div>
+</ul>
 <ul class="navbar-nav">
 <li class="nav-item"><form class="form-inline" role="search">
  <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json">
diff --git a/main/articles/tern_formats.html b/main/articles/tern_formats.html
index 49d0b74e69..3694015f2b 100644
--- a/main/articles/tern_formats.html
+++ b/main/articles/tern_formats.html
@@ -1,5 +1,4 @@
-<!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en">
+<html lang="en">
 <head>
 <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
 <meta charset="utf-8">
@@ -57,7 +56,38 @@
     <li><a class="dropdown-item" href="../unit-test-report-non-cran/">Non-CRAN unit test report</a></li>
   </ul>
 </li>
-      </ul>
+      <div><li class="nav-item dropdown">
+    <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-versions">Versions</a>
+    <div class="dropdown-menu" aria-labelledby="dropdown-versions">
+    <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/main">main</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.5">v0.9.5</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.4">v0.9.4</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.3">v0.9.3</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1-rc3">v0.9.1-rc3</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a>
+</div>
+</li></div>
+</ul>
 <ul class="navbar-nav">
 <li class="nav-item"><form class="form-inline" role="search">
  <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json">
diff --git a/main/articles/tern_functions_guide.html b/main/articles/tern_functions_guide.html
index f60de22458..dc2087ab31 100644
--- a/main/articles/tern_functions_guide.html
+++ b/main/articles/tern_functions_guide.html
@@ -1,5 +1,4 @@
-<!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en">
+<html lang="en">
 <head>
 <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
 <meta charset="utf-8">
@@ -57,7 +56,38 @@
     <li><a class="dropdown-item" href="../unit-test-report-non-cran/">Non-CRAN unit test report</a></li>
   </ul>
 </li>
-      </ul>
+      <div><li class="nav-item dropdown">
+    <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-versions">Versions</a>
+    <div class="dropdown-menu" aria-labelledby="dropdown-versions">
+    <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/main">main</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.5">v0.9.5</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.4">v0.9.4</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.3">v0.9.3</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1-rc3">v0.9.1-rc3</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a>
+</div>
+</li></div>
+</ul>
 <ul class="navbar-nav">
 <li class="nav-item"><form class="form-inline" role="search">
  <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json">
diff --git a/main/authors.html b/main/authors.html
index 763d0985ca..ac8459dd2a 100644
--- a/main/authors.html
+++ b/main/authors.html
@@ -1,5 +1,26 @@
-<!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Authors and Citation • tern</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="apple-touch-icon-60x60.png"><script src="deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="deps/headroom-0.11.0/headroom.min.js"></script><script src="deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="deps/search-1.0.0/fuse.min.js"></script><script src="deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="pkgdown.js"></script><meta property="og:title" content="Authors and Citation"><meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png"><link rel="stylesheet" href="consent.css"><script src="consent.js" type="text/javascript" charset="utf-8"></script></head><body>
+<html lang="en">
+<head>
+<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+<meta charset="utf-8">
+<meta http-equiv="X-UA-Compatible" content="IE=edge">
+<meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<title>Authors and Citation • tern</title>
+<!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="favicon-16x16.png">
+<link rel="icon" type="image/png" sizes="32x32" href="favicon-32x32.png">
+<link rel="apple-touch-icon" type="image/png" sizes="180x180" href="apple-touch-icon.png">
+<link rel="apple-touch-icon" type="image/png" sizes="120x120" href="apple-touch-icon-120x120.png">
+<link rel="apple-touch-icon" type="image/png" sizes="76x76" href="apple-touch-icon-76x76.png">
+<link rel="apple-touch-icon" type="image/png" sizes="60x60" href="apple-touch-icon-60x60.png">
+<script src="deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<link href="deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet">
+<script src="deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet">
+<link href="deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet">
+<script src="deps/headroom-0.11.0/headroom.min.js"></script><script src="deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="deps/search-1.0.0/fuse.min.js"></script><script src="deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="pkgdown.js"></script><meta property="og:title" content="Authors and Citation">
+<meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png">
+<link rel="stylesheet" href="consent.css">
+<script src="consent.js" type="text/javascript" charset="utf-8"></script>
+</head>
+<body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
 
 
@@ -15,26 +36,66 @@
     </button>
 
     <div id="navbar" class="collapse navbar-collapse ms-3">
-      <ul class="navbar-nav me-auto"><li class="nav-item"><a class="nav-link" href="articles/tern.html">Get started</a></li>
+      <ul class="navbar-nav me-auto">
+<li class="nav-item"><a class="nav-link" href="articles/tern.html">Get started</a></li>
 <li class="nav-item"><a class="nav-link" href="reference/index.html">Reference</a></li>
 <li class="nav-item dropdown">
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-articles" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Articles</button>
-  <ul class="dropdown-menu" aria-labelledby="dropdown-articles"><li><a class="dropdown-item" href="articles/missing_values.html">Missing Values in Tern</a></li>
+  <ul class="dropdown-menu" aria-labelledby="dropdown-articles">
+<li><a class="dropdown-item" href="articles/missing_values.html">Missing Values in Tern</a></li>
     <li><a class="dropdown-item" href="articles/tables.html">Tabulation</a></li>
     <li><a class="dropdown-item" href="articles/tern_formats.html">Formatting Functions</a></li>
     <li><a class="dropdown-item" href="articles/tern_functions_guide.html">Understanding `tern` functions</a></li>
-  </ul></li>
+  </ul>
+</li>
 <li class="nav-item"><a class="nav-link" href="news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
-  <ul class="dropdown-menu" aria-labelledby="dropdown-reports"><li><a class="dropdown-item" href="coverage-report/">Coverage report</a></li>
+  <ul class="dropdown-menu" aria-labelledby="dropdown-reports">
+<li><a class="dropdown-item" href="coverage-report/">Coverage report</a></li>
     <li><a class="dropdown-item" href="unit-test-report/">Unit test report</a></li>
     <li><a class="dropdown-item" href="unit-test-report-non-cran/">Non-CRAN unit test report</a></li>
-  </ul></li>
-      </ul><ul class="navbar-nav"><li class="nav-item"><form class="form-inline" role="search">
- <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="search.json"></form></li>
+  </ul>
+</li>
+      <div><li class="nav-item dropdown">
+    <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-versions">Versions</a>
+    <div class="dropdown-menu" aria-labelledby="dropdown-versions">
+    <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/main">main</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.5">v0.9.5</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.4">v0.9.4</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.3">v0.9.3</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1-rc3">v0.9.1-rc3</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a>
+</div>
+</li></div>
+</ul>
+<ul class="navbar-nav">
+<li class="nav-item"><form class="form-inline" role="search">
+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="search.json">
+</form></li>
 <li class="nav-item"><a class="external-link nav-link" href="https://github.com/insightsengineering/tern" aria-label="GitHub"><span class="fa fa-github"></span></a></li>
-      </ul></div>
+      </ul>
+</div>
 
 
   </div>
@@ -47,7 +108,8 @@
     <div class="section level2">
       <h2>Authors</h2>
 
-      <ul class="list-unstyled"><li>
+      <ul class="list-unstyled">
+<li>
           <p><strong>Joe Zhu</strong>. Author, maintainer.
           </p>
         </li>
@@ -99,7 +161,8 @@ <h2>Authors</h2>
           <p><strong>F. Hoffmann-La Roche AG</strong>. Copyright holder, funder.
           </p>
         </li>
-      </ul></div>
+      </ul>
+</div>
 
     <div class="section level2">
       <h2 id="citation">Citation</h2>
@@ -121,17 +184,19 @@ <h2 id="citation">Citation</h2>
     </div>
 
   </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
-    </nav></aside></div>
+    </nav></aside>
+</div>
 
 
     <footer><div class="nest">
   <p>tern is a part of the <strong>NEST</strong> and <a href="https://pharmaverse.org/" class="external-link"><strong>pharmaverse</strong></a>.</p>
 </div>
-<script type="text/javascript" src="analytics.js"></script></footer></div>
-
+<script type="text/javascript" src="analytics.js"></script></footer>
+</div>
 
 
 
 
-  </body></html>
 
+  </body>
+</html>
diff --git a/main/index.html b/main/index.html
index 350b513496..4f2b5628c8 100644
--- a/main/index.html
+++ b/main/index.html
@@ -1,5 +1,4 @@
-<!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en">
+<html lang="en">
 <head>
 <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
 <meta charset="utf-8">
@@ -60,7 +59,38 @@
     <li><a class="dropdown-item" href="unit-test-report-non-cran/">Non-CRAN unit test report</a></li>
   </ul>
 </li>
-      </ul>
+      <div><li class="nav-item dropdown">
+    <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-versions">Versions</a>
+    <div class="dropdown-menu" aria-labelledby="dropdown-versions">
+    <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/main">main</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.5">v0.9.5</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.4">v0.9.4</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.3">v0.9.3</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1-rc3">v0.9.1-rc3</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a>
+</div>
+</li></div>
+</ul>
 <ul class="navbar-nav">
 <li class="nav-item"><form class="form-inline" role="search">
  <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="search.json">
diff --git a/main/news/index.html b/main/news/index.html
index 7b0e5397b6..dbb2efd2c5 100644
--- a/main/news/index.html
+++ b/main/news/index.html
@@ -1,5 +1,26 @@
-<!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Changelog • tern</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Changelog"><meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png"><link rel="stylesheet" href="../consent.css"><script src="../consent.js" type="text/javascript" charset="utf-8"></script></head><body>
+<html lang="en">
+<head>
+<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+<meta charset="utf-8">
+<meta http-equiv="X-UA-Compatible" content="IE=edge">
+<meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<title>Changelog • tern</title>
+<!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png">
+<link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png">
+<link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png">
+<link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png">
+<link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png">
+<link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png">
+<script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet">
+<script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet">
+<link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet">
+<script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Changelog">
+<meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png">
+<link rel="stylesheet" href="../consent.css">
+<script src="../consent.js" type="text/javascript" charset="utf-8"></script>
+</head>
+<body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
 
 
@@ -15,26 +36,66 @@
     </button>
 
     <div id="navbar" class="collapse navbar-collapse ms-3">
-      <ul class="navbar-nav me-auto"><li class="nav-item"><a class="nav-link" href="../articles/tern.html">Get started</a></li>
+      <ul class="navbar-nav me-auto">
+<li class="nav-item"><a class="nav-link" href="../articles/tern.html">Get started</a></li>
 <li class="nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
 <li class="nav-item dropdown">
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-articles" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Articles</button>
-  <ul class="dropdown-menu" aria-labelledby="dropdown-articles"><li><a class="dropdown-item" href="../articles/missing_values.html">Missing Values in Tern</a></li>
+  <ul class="dropdown-menu" aria-labelledby="dropdown-articles">
+<li><a class="dropdown-item" href="../articles/missing_values.html">Missing Values in Tern</a></li>
     <li><a class="dropdown-item" href="../articles/tables.html">Tabulation</a></li>
     <li><a class="dropdown-item" href="../articles/tern_formats.html">Formatting Functions</a></li>
     <li><a class="dropdown-item" href="../articles/tern_functions_guide.html">Understanding `tern` functions</a></li>
-  </ul></li>
+  </ul>
+</li>
 <li class="active nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
-  <ul class="dropdown-menu" aria-labelledby="dropdown-reports"><li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
+  <ul class="dropdown-menu" aria-labelledby="dropdown-reports">
+<li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
     <li><a class="dropdown-item" href="../unit-test-report/">Unit test report</a></li>
     <li><a class="dropdown-item" href="../unit-test-report-non-cran/">Non-CRAN unit test report</a></li>
-  </ul></li>
-      </ul><ul class="navbar-nav"><li class="nav-item"><form class="form-inline" role="search">
- <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json"></form></li>
+  </ul>
+</li>
+      <div><li class="nav-item dropdown">
+    <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-versions">Versions</a>
+    <div class="dropdown-menu" aria-labelledby="dropdown-versions">
+    <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/main">main</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.5">v0.9.5</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.4">v0.9.4</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.3">v0.9.3</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1-rc3">v0.9.1-rc3</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a>
+</div>
+</li></div>
+</ul>
+<ul class="navbar-nav">
+<li class="nav-item"><form class="form-inline" role="search">
+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json">
+</form></li>
 <li class="nav-item"><a class="external-link nav-link" href="https://github.com/insightsengineering/tern" aria-label="GitHub"><span class="fa fa-github"></span></a></li>
-      </ul></div>
+      </ul>
+</div>
 
 
   </div>
@@ -46,10 +107,13 @@
     </div>
 
     <div class="section level2">
-<h2 class="pkg-version" data-toc-text="0.9.6.9016" id="tern-0969016">tern 0.9.6.9016<a class="anchor" aria-label="anchor" href="#tern-0969016"></a></h2>
+<h2 class="pkg-version" data-toc-text="0.9.6.9016" id="tern-0969016">tern 0.9.6.9016<a class="anchor" aria-label="anchor" href="#tern-0969016"></a>
+</h2>
 <div class="section level4">
-<h4 id="enhancements-0-9-6-9016">Enhancements<a class="anchor" aria-label="anchor" href="#enhancements-0-9-6-9016"></a></h4>
-<ul><li>Added the <code>denom</code> parameter to <code><a href="../reference/count_cumulative.html">s_count_cumulative()</a></code>, <code><a href="../reference/count_missed_doses.html">s_count_missed_doses()</a></code>, and <code><a href="../reference/count_occurrences_by_grade.html">s_count_occurrences_by_grade()</a></code>.</li>
+<h4 id="enhancements-0-9-6-9016">Enhancements<a class="anchor" aria-label="anchor" href="#enhancements-0-9-6-9016"></a>
+</h4>
+<ul>
+<li>Added the <code>denom</code> parameter to <code><a href="../reference/count_cumulative.html">s_count_cumulative()</a></code>, <code><a href="../reference/count_missed_doses.html">s_count_missed_doses()</a></code>, and <code><a href="../reference/count_occurrences_by_grade.html">s_count_occurrences_by_grade()</a></code>.</li>
 <li>Added <code>"N_row"</code> as an optional input to <code>denom</code> in <code><a href="../reference/count_occurrences.html">s_count_occurrences()</a></code>.</li>
 <li>Refactored <code><a href="../reference/count_occurrences_by_grade.html">a_count_occurrences_by_grade()</a></code>, <code><a href="../reference/count_patients_with_event.html">a_count_patients_with_event()</a></code>, and <code><a href="../reference/count_patients_with_flags.html">a_count_patients_with_flags()</a></code> to no longer use <code><a href="https://insightsengineering.github.io/rtables/latest-tag/reference/make_afun.html" class="external-link">make_afun()</a></code>.</li>
 <li>Added <code>rel_height_plot</code> parameter to <code><a href="../reference/g_lineplot.html">g_lineplot()</a></code> to control the line plot height relative to annotation table height.</li>
@@ -57,22 +121,33 @@ <h4 id="enhancements-0-9-6-9016">Enhancements<a class="anchor" aria-label="ancho
 <li>Added <code>as_list</code> parameter to <code><a href="../reference/g_lineplot.html">g_lineplot()</a></code> to allow users to return the line plot and annotation table elements as a list instead of stacked for more complex customization.</li>
 <li>Refactored <code><a href="../reference/summarize_change.html">summarize_change()</a></code> to work without <code><a href="https://insightsengineering.github.io/rtables/latest-tag/reference/make_afun.html" class="external-link">make_afun()</a></code> and access all additional function parameter.</li>
 <li>Added vignette “Understanding <code>tern</code> functions” for future reference.</li>
-</ul></div>
+</ul>
+</div>
 <div class="section level4">
-<h4 id="bug-fixes-0-9-6-9016">Bug Fixes<a class="anchor" aria-label="anchor" href="#bug-fixes-0-9-6-9016"></a></h4>
-<ul><li>Fixed bug in <code><a href="../reference/analyze_variables.html">a_summary()</a></code> causing non-unique <code>row_name</code> values to occur when multiple statistics are selected for count variables.</li>
-</ul></div>
+<h4 id="bug-fixes-0-9-6-9016">Bug Fixes<a class="anchor" aria-label="anchor" href="#bug-fixes-0-9-6-9016"></a>
+</h4>
+<ul>
+<li>Fixed bug in <code><a href="../reference/analyze_variables.html">a_summary()</a></code> causing non-unique <code>row_name</code> values to occur when multiple statistics are selected for count variables.</li>
+</ul>
+</div>
 <div class="section level4">
-<h4 id="miscellaneous-0-9-6-9016">Miscellaneous<a class="anchor" aria-label="anchor" href="#miscellaneous-0-9-6-9016"></a></h4>
-<ul><li>Reverted deprecation of quick get functions <code><a href="../reference/default_stats_formats_labels.html">summary_formats()</a></code> and <code><a href="../reference/default_stats_formats_labels.html">summary_labels()</a></code>. Added disclaimer about underlying use of <code>get_stats</code>.</li>
+<h4 id="miscellaneous-0-9-6-9016">Miscellaneous<a class="anchor" aria-label="anchor" href="#miscellaneous-0-9-6-9016"></a>
+</h4>
+<ul>
+<li>Reverted deprecation of quick get functions <code><a href="../reference/default_stats_formats_labels.html">summary_formats()</a></code> and <code><a href="../reference/default_stats_formats_labels.html">summary_labels()</a></code>. Added disclaimer about underlying use of <code>get_stats</code>.</li>
 <li>Corrected handling of extra arguments and <code>NA</code> for <code><a href="../reference/summarize_change.html">summarize_change()</a></code>.</li>
-</ul></div>
+</ul>
+</div>
 </div>
     <div class="section level2">
-<h2 class="pkg-version" data-toc-text="0.9.6" id="tern-096">tern 0.9.6<a class="anchor" aria-label="anchor" href="#tern-096"></a></h2><p class="text-muted">CRAN release: 2024-09-24</p>
-<div class="section level4">
-<h4 id="enhancements-0-9-6">Enhancements<a class="anchor" aria-label="anchor" href="#enhancements-0-9-6"></a></h4>
-<ul><li>Added <code>median_ci_3d</code> to <code>s_summary</code> which includes estimate and confidence interval in one statistic.</li>
+<h2 class="pkg-version" data-toc-text="0.9.6" id="tern-096">tern 0.9.6<a class="anchor" aria-label="anchor" href="#tern-096"></a>
+</h2>
+<p class="text-muted">CRAN release: 2024-09-24</p>
+<div class="section level4">
+<h4 id="enhancements-0-9-6">Enhancements<a class="anchor" aria-label="anchor" href="#enhancements-0-9-6"></a>
+</h4>
+<ul>
+<li>Added <code>median_ci_3d</code> to <code>s_summary</code> which includes estimate and confidence interval in one statistic.</li>
 <li>Added <code>median_ci_3d</code>, <code>quantiles_lower</code> and <code>quantiles_upper</code> to <code>s_surv_time</code> which includes estimate and confidence interval in one statistic.</li>
 <li>Added <code>hr_ci_3d</code> to <code>s_coxph_pairwise</code> which includes estimate and confidence interval in one statistic.</li>
 <li>Added <code>event_free_rate_3d</code> to <code>s_surv_timepoint</code> which includes estimate and confidence interval in one statistic.</li>
@@ -87,10 +162,13 @@ <h4 id="enhancements-0-9-6">Enhancements<a class="anchor" aria-label="anchor" hr
 <li>Added <code>fraction</code> statistic to the <code>analyze_var_count</code> method group.</li>
 <li>Improved <code><a href="../reference/summarize_glm_count.html">summarize_glm_count()</a></code> documentation and all its associated functions to better describe the results and the functions’ purpose.</li>
 <li>Added <code>method</code> argument to <code><a href="../reference/odds_ratio.html">s_odds_ratio()</a></code> and <code><a href="../reference/odds_ratio.html">estimate_odds_ratio()</a></code> to control whether exact or approximate conditional likelihood calculations are used.</li>
-</ul></div>
+</ul>
+</div>
 <div class="section level4">
-<h4 id="bug-fixes-0-9-6">Bug Fixes<a class="anchor" aria-label="anchor" href="#bug-fixes-0-9-6"></a></h4>
-<ul><li>Added defaults for <code>d_count_cumulative</code> parameters as described in the documentation.</li>
+<h4 id="bug-fixes-0-9-6">Bug Fixes<a class="anchor" aria-label="anchor" href="#bug-fixes-0-9-6"></a>
+</h4>
+<ul>
+<li>Added defaults for <code>d_count_cumulative</code> parameters as described in the documentation.</li>
 <li>Fixed a bug of empty levels on <code>g_lineplot</code> x-axis were not shown in either plots.</li>
 <li>Fixed a bug in <code>a_surv_time</code> that threw an error when split only has <code>"is_event"</code>.</li>
 <li>Fixed disappearing line in <code>g_lineplot</code> when using only one group or strata level.</li>
@@ -99,60 +177,88 @@ <h4 id="bug-fixes-0-9-6">Bug Fixes<a class="anchor" aria-label="anchor" href="#b
 <li>Fixed bug in <code>decorate_grob</code> that did not handle well empty strings or <code>NULL</code> values for title and footers.</li>
 <li>Fixed bug in <code>g_km</code> that caused an error when multiple records in the data had estimates at max time.</li>
 <li>Fixed issue with wrong wrapping due to different <code>\n</code> and vector behavior that did not cope well with <code>split_string()</code>.</li>
-</ul></div>
+</ul>
+</div>
 <div class="section level4">
-<h4 id="miscellaneous-0-9-6">Miscellaneous<a class="anchor" aria-label="anchor" href="#miscellaneous-0-9-6"></a></h4>
-<ul><li>Began deprecation of the confusing functions <code>summary_formats</code> and <code>summary_labels</code>.</li>
+<h4 id="miscellaneous-0-9-6">Miscellaneous<a class="anchor" aria-label="anchor" href="#miscellaneous-0-9-6"></a>
+</h4>
+<ul>
+<li>Began deprecation of the confusing functions <code>summary_formats</code> and <code>summary_labels</code>.</li>
 <li>Enhanced general descriptions of analyze and summarize functions throughout package documentation.</li>
 <li>Finalized deprecation of the <code>strata</code> and <code>cohort_id</code> arguments to <code>g_lineplot</code>.</li>
 <li>Moved incidence rate helper functions into a separate <code>h_incidence_rate.R</code> file.</li>
-</ul></div>
+</ul>
+</div>
 </div>
     <div class="section level2">
-<h2 class="pkg-version" data-toc-text="0.9.5" id="tern-095">tern 0.9.5<a class="anchor" aria-label="anchor" href="#tern-095"></a></h2><p class="text-muted">CRAN release: 2024-06-21</p>
-<div class="section level4">
-<h4 id="enhancements-0-9-5">Enhancements<a class="anchor" aria-label="anchor" href="#enhancements-0-9-5"></a></h4>
-<ul><li>Added <code>facet_var</code> to <code>g_lineplot</code> to allow plot faceting by a factor variable.</li>
+<h2 class="pkg-version" data-toc-text="0.9.5" id="tern-095">tern 0.9.5<a class="anchor" aria-label="anchor" href="#tern-095"></a>
+</h2>
+<p class="text-muted">CRAN release: 2024-06-21</p>
+<div class="section level4">
+<h4 id="enhancements-0-9-5">Enhancements<a class="anchor" aria-label="anchor" href="#enhancements-0-9-5"></a>
+</h4>
+<ul>
+<li>Added <code>facet_var</code> to <code>g_lineplot</code> to allow plot faceting by a factor variable.</li>
 <li>Added examples and tests for <code>label_all</code> parameter to <code>extract_survival_biomarkers</code> and <code>extract_survival_subgroups</code>.</li>
 <li>Added the <code>xticks</code>, <code>xlim</code>, and <code>ylim</code> arguments to <code>g_lineplot</code> to allow for customization of the x and y axes.</li>
 <li>Updated <code>g_lineplot</code> legend to follow factor levels set by users.</li>
-</ul></div>
+</ul>
+</div>
 <div class="section level4">
-<h4 id="bug-fixes-0-9-5">Bug Fixes<a class="anchor" aria-label="anchor" href="#bug-fixes-0-9-5"></a></h4>
-<ul><li>Fixed a bug in <code>s_ancova</code> that prevented statistics from being printed when arm levels include special characters.</li>
+<h4 id="bug-fixes-0-9-5">Bug Fixes<a class="anchor" aria-label="anchor" href="#bug-fixes-0-9-5"></a>
+</h4>
+<ul>
+<li>Fixed a bug in <code>s_ancova</code> that prevented statistics from being printed when arm levels include special characters.</li>
 <li>Fixed a bug in <code>decorate_grob</code> that prevented the right margins to be respected when adding title and footers decorations.</li>
-</ul></div>
+</ul>
+</div>
 <div class="section level4">
-<h4 id="miscellaneous-0-9-5">Miscellaneous<a class="anchor" aria-label="anchor" href="#miscellaneous-0-9-5"></a></h4>
-<ul><li>Began deprecation of the unused <code>label_all</code> parameter to <code>tabulate_survival_biomarkers</code> and <code>tabulate_survival_subgroups</code>, with redirection to the same parameter in their associated <code>extract_*</code> functions.</li>
-</ul></div>
+<h4 id="miscellaneous-0-9-5">Miscellaneous<a class="anchor" aria-label="anchor" href="#miscellaneous-0-9-5"></a>
+</h4>
+<ul>
+<li>Began deprecation of the unused <code>label_all</code> parameter to <code>tabulate_survival_biomarkers</code> and <code>tabulate_survival_subgroups</code>, with redirection to the same parameter in their associated <code>extract_*</code> functions.</li>
+</ul>
+</div>
 </div>
     <div class="section level2">
-<h2 class="pkg-version" data-toc-text="0.9.4" id="tern-094">tern 0.9.4<a class="anchor" aria-label="anchor" href="#tern-094"></a></h2><p class="text-muted">CRAN release: 2024-04-17</p>
-<div class="section level4">
-<h4 id="new-features-0-9-4">New Features<a class="anchor" aria-label="anchor" href="#new-features-0-9-4"></a></h4>
-<ul><li>Added <code>h_glm_negbin</code> to <code>h_glm_count</code> to enable count data analysis using a negative binomial model.</li>
+<h2 class="pkg-version" data-toc-text="0.9.4" id="tern-094">tern 0.9.4<a class="anchor" aria-label="anchor" href="#tern-094"></a>
+</h2>
+<p class="text-muted">CRAN release: 2024-04-17</p>
+<div class="section level4">
+<h4 id="new-features-0-9-4">New Features<a class="anchor" aria-label="anchor" href="#new-features-0-9-4"></a>
+</h4>
+<ul>
+<li>Added <code>h_glm_negbin</code> to <code>h_glm_count</code> to enable count data analysis using a negative binomial model.</li>
 <li>Added argument <code>grade_groups_only</code> to <code>count_occurrences_by_grade</code> to allow users to only display rows for specified grade groups.</li>
 <li>Added internal function <code>df2gg</code> that converts <code>data.frame</code> objects to <code>ggplot</code> objects.</li>
 <li>Added functions <code>control_surv_med_annot</code> and <code>control_coxph_annot</code> to configure <code>g_km</code> annotation table sizes/positions.</li>
 <li>Refactored <code>g_km</code> to output a <code>ggplot</code> object instead of a <code>grob</code> object.</li>
 <li>Refactored <code>g_forest</code> to output a <code>ggplot</code> object instead of a <code>grob</code> object.</li>
-</ul></div>
+</ul>
+</div>
 <div class="section level4">
-<h4 id="enhancements-0-9-4">Enhancements<a class="anchor" aria-label="anchor" href="#enhancements-0-9-4"></a></h4>
-<ul><li>Default format for mean p-values (<code>mean_pval</code>) updated from <code>"xx.xx"</code> to <code>"x.xxxx | (&lt;0.0001)"</code>.</li>
-</ul></div>
+<h4 id="enhancements-0-9-4">Enhancements<a class="anchor" aria-label="anchor" href="#enhancements-0-9-4"></a>
+</h4>
+<ul>
+<li>Default format for mean p-values (<code>mean_pval</code>) updated from <code>"xx.xx"</code> to <code>"x.xxxx | (&lt;0.0001)"</code>.</li>
+</ul>
+</div>
 <div class="section level4">
-<h4 id="bug-fixes-0-9-4">Bug Fixes<a class="anchor" aria-label="anchor" href="#bug-fixes-0-9-4"></a></h4>
-<ul><li>Fixed nested column split label overlay issue in <code>rtable2gg</code> to clean up appearance of text labels.</li>
+<h4 id="bug-fixes-0-9-4">Bug Fixes<a class="anchor" aria-label="anchor" href="#bug-fixes-0-9-4"></a>
+</h4>
+<ul>
+<li>Fixed nested column split label overlay issue in <code>rtable2gg</code> to clean up appearance of text labels.</li>
 <li>Fixed bug in <code>s_ancova</code> causing incorrect difference calculations for arm variables with irregular levels.</li>
 <li>Fixed bug in <code>format_count_fraction_fixed_dp</code> that did not have the same print when the fraction was 1 (100%).</li>
 <li>Fixed bug in <code>g_lineplot</code> causing default labels not to update according to specified <code>control</code> settings.</li>
 <li>Fixed bug causing an error when automatic value formatting was applied to <code>NA</code> values.</li>
-</ul></div>
+</ul>
+</div>
 <div class="section level4">
-<h4 id="miscellaneous-0-9-4">Miscellaneous<a class="anchor" aria-label="anchor" href="#miscellaneous-0-9-4"></a></h4>
-<ul><li>Added function <code>expect_snapshot_ggplot</code> to test setup file to process plot snapshot tests and allow plot dimensions to be set.</li>
+<h4 id="miscellaneous-0-9-4">Miscellaneous<a class="anchor" aria-label="anchor" href="#miscellaneous-0-9-4"></a>
+</h4>
+<ul>
+<li>Added function <code>expect_snapshot_ggplot</code> to test setup file to process plot snapshot tests and allow plot dimensions to be set.</li>
 <li>Adapted to argument renames introduced in <code>ggplot2</code> 3.5.0.</li>
 <li>Renamed <code>individual_patient_plot.R</code> to <code>g_ipp.R</code>.</li>
 <li>Removed all instances of deprecated parameters <code>time_unit_input</code>, <code>time_unit_output</code>, <code>na_level</code> and <code>indent_mod</code>.</li>
@@ -163,13 +269,18 @@ <h4 id="miscellaneous-0-9-4">Miscellaneous<a class="anchor" aria-label="anchor"
 <li>Began deprecation of the <code>forest_grob</code>, <code>forest_dot_line</code>, <code>forest_viewport</code>, <code>vp_forest_table_part</code>, and <code>grid.forest</code> functions.</li>
 <li>Began deprecation of no longer used Kaplan-Meier helper functions <code>h_ggkm</code>, <code>h_decompose_gg</code>, <code>h_km_layout</code>, <code>h_grob_tbl_at_risk</code>, <code>h_grob_median_surv</code>, <code>h_grob_y_annot</code>, and <code>h_grob_coxph</code>.</li>
 <li>Began deprecation of <code>grob</code>/<code>grid</code> related functions <code>stack_grobs</code>, <code>arrange_grobs</code>, and <code>draw_grob</code> which are no longer used in <code>tern</code>.</li>
-</ul></div>
+</ul>
+</div>
 </div>
     <div class="section level2">
-<h2 class="pkg-version" data-toc-text="0.9.3" id="tern-093">tern 0.9.3<a class="anchor" aria-label="anchor" href="#tern-093"></a></h2><p class="text-muted">CRAN release: 2023-12-08</p>
-<div class="section level4">
-<h4 id="new-features-0-9-3">New Features<a class="anchor" aria-label="anchor" href="#new-features-0-9-3"></a></h4>
-<ul><li>Added <code>ref_group_position</code> function to place the reference group facet last, first or at a certain position.</li>
+<h2 class="pkg-version" data-toc-text="0.9.3" id="tern-093">tern 0.9.3<a class="anchor" aria-label="anchor" href="#tern-093"></a>
+</h2>
+<p class="text-muted">CRAN release: 2023-12-08</p>
+<div class="section level4">
+<h4 id="new-features-0-9-3">New Features<a class="anchor" aria-label="anchor" href="#new-features-0-9-3"></a>
+</h4>
+<ul>
+<li>Added <code>ref_group_position</code> function to place the reference group facet last, first or at a certain position.</li>
 <li>Added <code>keep_level_order</code> split function to retain original order of levels in a split.</li>
 <li>Added <code>level_order</code> split function to reorder manually the levels.</li>
 <li>Added function <code>get_indents_from_stats</code> to format and return indent modifiers for a given set of statistics.</li>
@@ -182,171 +293,253 @@ <h4 id="new-features-0-9-3">New Features<a class="anchor" aria-label="anchor" hr
 <li>Added <code>s_bland_altman</code> function to assess agreement between two numerical vectors.</li>
 <li>Added function <code>rtable2gg</code> that converts <code>rtable</code> objects to <code>ggplot</code> objects.</li>
 <li>Added helper function to set default <code>na_str</code> globally with <code><a href="../reference/default_na_str.html">set_default_na_str()</a></code> and added <code><a href="../reference/default_na_str.html">default_na_str()</a></code> for all interested functions.</li>
-</ul></div>
+</ul>
+</div>
 <div class="section level4">
-<h4 id="enhancements-0-9-3">Enhancements<a class="anchor" aria-label="anchor" href="#enhancements-0-9-3"></a></h4>
-<ul><li>Added <code>ref_group_coxph</code> parameter to <code>g_km</code> to specify the reference group used for pairwise Cox-PH calculations when <code>annot_coxph = TRUE</code>.</li>
+<h4 id="enhancements-0-9-3">Enhancements<a class="anchor" aria-label="anchor" href="#enhancements-0-9-3"></a>
+</h4>
+<ul>
+<li>Added <code>ref_group_coxph</code> parameter to <code>g_km</code> to specify the reference group used for pairwise Cox-PH calculations when <code>annot_coxph = TRUE</code>.</li>
 <li>Added <code>annot_coxph_ref_lbls</code> parameter to <code>g_km</code> to enable printing the reference group in table labels when <code>annot_coxph = TRUE</code>.</li>
 <li>Added <code>x_lab</code> parameter to <code>g_lineplot</code> to customize x-axis label.</li>
 <li>Remove 25% padding of y-axis in <code>g_lineplot</code>.</li>
 <li>Added support for creating multiple risk difference columns, each comparing to a single comparison group. Multiple comparison groups can be specified as a vector via the <code>arm_y</code> argument.</li>
 <li>Allowed numeric vector as <code>count_by</code> input in <code>analyze_num_patients</code> and <code>summarize_num_patients</code>.</li>
 <li>Aligned plot and table vertically in <code>g_lineplot</code>.</li>
-</ul></div>
+</ul>
+</div>
 <div class="section level4">
-<h4 id="bug-fixes-0-9-3">Bug Fixes<a class="anchor" aria-label="anchor" href="#bug-fixes-0-9-3"></a></h4>
-<ul><li>Fixed bug in <code>decorate_grob</code> preventing text wrapping from accounting for font size.</li>
+<h4 id="bug-fixes-0-9-3">Bug Fixes<a class="anchor" aria-label="anchor" href="#bug-fixes-0-9-3"></a>
+</h4>
+<ul>
+<li>Fixed bug in <code>decorate_grob</code> preventing text wrapping from accounting for font size.</li>
 <li>Fixed implementation of <code>na_str</code> argument in all column-wise analysis and tabulation functions.</li>
-</ul></div>
+</ul>
+</div>
 <div class="section level4">
-<h4 id="miscellaneous-0-9-3">Miscellaneous<a class="anchor" aria-label="anchor" href="#miscellaneous-0-9-3"></a></h4>
-<ul><li>Specified minimal version of package dependencies.</li>
+<h4 id="miscellaneous-0-9-3">Miscellaneous<a class="anchor" aria-label="anchor" href="#miscellaneous-0-9-3"></a>
+</h4>
+<ul>
+<li>Specified minimal version of package dependencies.</li>
 <li>Upgraded <code>to_string_matrix</code> to take into account <code>widths</code> and other printing parameters.</li>
-</ul></div>
+</ul>
+</div>
 </div>
     <div class="section level2">
-<h2 class="pkg-version" data-toc-text="0.9.2" id="tern-092">tern 0.9.2<a class="anchor" aria-label="anchor" href="#tern-092"></a></h2>
-<div class="section level4">
-<h4 id="new-features-0-9-2">New Features<a class="anchor" aria-label="anchor" href="#new-features-0-9-2"></a></h4>
-<ul><li>Added the <code>na_str</code> argument to <code>analyze</code> &amp; <code>summarize_row_groups</code> wrapper functions <code>count_abnormal</code>, <code>count_abnormal_by_baseline</code>, <code>count_abnormal_by_marked</code>, <code>count_abnormal_by_worst_grade</code>, <code>count_abnormal_lab_worsen_by_baseline</code>, <code>count_cumulative</code>, <code>count_missed_doses</code>, <code>count_occurrences</code>, <code>count_occurrences_by_grade</code>, <code>summarize_occurrences_by_grade</code>, <code>summarize_patients_events_in_cols</code>, <code>count_patients_with_event</code>, <code>count_patients_with_flags</code>, <code>count_values</code>, <code>estimate_multinomial_response</code>, <code>estimate_proportion</code>, <code>h_tab_one_biomarker</code>, <code>estimate_incidence_rate</code>, <code>logistic_summary_by_flag</code>, <code>estimate_odds_ratio</code>, <code>estimate_proportion_diff</code>, <code>test_proportion_diff</code>, <code>summarize_ancova</code>, <code>summarize_change</code>, <code>summarize_glm_count</code>, <code>summarize_num_patients</code>, <code>analyze_num_patients</code>, <code>summarize_patients_exposure_in_cols</code>, <code>coxph_pairwise</code>, <code>tabulate_survival_subgroups</code>, <code>surv_time</code>, and <code>surv_timepoint</code>.</li>
-</ul></div>
+<h2 class="pkg-version" data-toc-text="0.9.2" id="tern-092">tern 0.9.2<a class="anchor" aria-label="anchor" href="#tern-092"></a>
+</h2>
+<div class="section level4">
+<h4 id="new-features-0-9-2">New Features<a class="anchor" aria-label="anchor" href="#new-features-0-9-2"></a>
+</h4>
+<ul>
+<li>Added the <code>na_str</code> argument to <code>analyze</code> &amp; <code>summarize_row_groups</code> wrapper functions <code>count_abnormal</code>, <code>count_abnormal_by_baseline</code>, <code>count_abnormal_by_marked</code>, <code>count_abnormal_by_worst_grade</code>, <code>count_abnormal_lab_worsen_by_baseline</code>, <code>count_cumulative</code>, <code>count_missed_doses</code>, <code>count_occurrences</code>, <code>count_occurrences_by_grade</code>, <code>summarize_occurrences_by_grade</code>, <code>summarize_patients_events_in_cols</code>, <code>count_patients_with_event</code>, <code>count_patients_with_flags</code>, <code>count_values</code>, <code>estimate_multinomial_response</code>, <code>estimate_proportion</code>, <code>h_tab_one_biomarker</code>, <code>estimate_incidence_rate</code>, <code>logistic_summary_by_flag</code>, <code>estimate_odds_ratio</code>, <code>estimate_proportion_diff</code>, <code>test_proportion_diff</code>, <code>summarize_ancova</code>, <code>summarize_change</code>, <code>summarize_glm_count</code>, <code>summarize_num_patients</code>, <code>analyze_num_patients</code>, <code>summarize_patients_exposure_in_cols</code>, <code>coxph_pairwise</code>, <code>tabulate_survival_subgroups</code>, <code>surv_time</code>, and <code>surv_timepoint</code>.</li>
+</ul>
+</div>
 <div class="section level4">
-<h4 id="enhancements-0-9-2">Enhancements<a class="anchor" aria-label="anchor" href="#enhancements-0-9-2"></a></h4>
-<ul><li>Added formatting function <code>format_count_fraction_lt10</code> for formatting <code>count_fraction</code> with special consideration when count is less than 10.</li>
+<h4 id="enhancements-0-9-2">Enhancements<a class="anchor" aria-label="anchor" href="#enhancements-0-9-2"></a>
+</h4>
+<ul>
+<li>Added formatting function <code>format_count_fraction_lt10</code> for formatting <code>count_fraction</code> with special consideration when count is less than 10.</li>
 <li>Updated <code>s_summary.logical</code> output for <code>count_fraction</code> when denominator is zero to display as <code>NA</code> instead of <code>0</code> in tables.</li>
 <li>Updated <code>analyze_vars_in_cols</code> to allow character input to indicate whether nominal time point is post-dose or pre-dose when applying the 1/3 imputation rule.</li>
-</ul></div>
+</ul>
+</div>
 <div class="section level4">
-<h4 id="bug-fixes-0-9-2">Bug Fixes<a class="anchor" aria-label="anchor" href="#bug-fixes-0-9-2"></a></h4>
-<ul><li>Fixed bug in <code>g_km</code> causing an error when converting certain annotation width units.</li>
-</ul></div>
+<h4 id="bug-fixes-0-9-2">Bug Fixes<a class="anchor" aria-label="anchor" href="#bug-fixes-0-9-2"></a>
+</h4>
+<ul>
+<li>Fixed bug in <code>g_km</code> causing an error when converting certain annotation width units.</li>
+</ul>
+</div>
 <div class="section level4">
-<h4 id="miscellaneous-0-9-2">Miscellaneous<a class="anchor" aria-label="anchor" href="#miscellaneous-0-9-2"></a></h4>
-<ul><li>Began deprecation of <code>na_level</code> argument in <code>s_count_abnormal_by_baseline</code>, <code>a_summary</code>, <code>analyze_vars</code>, <code>analyze_vars_in_cols</code>, <code>compare_vars</code>, <code>h_map_for_count_abnormal</code>, <code>h_stack_by_baskets</code>, <code>summarize_colvars</code>, <code>a_coxreg</code>, and <code>summarize_coxreg</code> and replaced it with the <code>na_str</code> argument.</li>
+<h4 id="miscellaneous-0-9-2">Miscellaneous<a class="anchor" aria-label="anchor" href="#miscellaneous-0-9-2"></a>
+</h4>
+<ul>
+<li>Began deprecation of <code>na_level</code> argument in <code>s_count_abnormal_by_baseline</code>, <code>a_summary</code>, <code>analyze_vars</code>, <code>analyze_vars_in_cols</code>, <code>compare_vars</code>, <code>h_map_for_count_abnormal</code>, <code>h_stack_by_baskets</code>, <code>summarize_colvars</code>, <code>a_coxreg</code>, and <code>summarize_coxreg</code> and replaced it with the <code>na_str</code> argument.</li>
 <li>
 <code>strata</code> and <code>cohort_id</code> parameters renamed to <code>group_var</code> and <code>subject_var</code> respectively in <code>g_lineplot</code> and <code>control_lineplot_vars</code> .</li>
-</ul></div>
+</ul>
+</div>
 </div>
     <div class="section level2">
-<h2 class="pkg-version" data-toc-text="0.9.1" id="tern-091">tern 0.9.1<a class="anchor" aria-label="anchor" href="#tern-091"></a></h2>
+<h2 class="pkg-version" data-toc-text="0.9.1" id="tern-091">tern 0.9.1<a class="anchor" aria-label="anchor" href="#tern-091"></a>
+</h2>
 <div class="section level4">
-<h4 id="new-features-0-9-1">New Features<a class="anchor" aria-label="anchor" href="#new-features-0-9-1"></a></h4>
-<ul><li>Added <code>imputation_rule</code> function to apply imputation rule to data.</li>
+<h4 id="new-features-0-9-1">New Features<a class="anchor" aria-label="anchor" href="#new-features-0-9-1"></a>
+</h4>
+<ul>
+<li>Added <code>imputation_rule</code> function to apply imputation rule to data.</li>
 <li>Added new format function <code>format_sigfig</code> to allow for numeric value formatting by a specified number of significant figures.</li>
 <li>Added vectors containing default statistic formats and labels as <code>tern_default_formats</code> and <code>tern_default_labels</code>, respectively.</li>
 <li>Added function <code>get_stats</code> to return methods from given statistical method groups.</li>
 <li>Added function <code>get_formats_from_stats</code> to return formats and <code>get_labels_from_stats</code> to return labels for a given set of statistics.</li>
 <li>Added <code>"auto"</code> option for <code>.formats</code>. It uses <code>format_auto</code> to determine automatically the number of digits.</li>
 <li>Added <code>title</code> argument to <code>h_grob_tbl_at_risk</code> and <code>annot_at_risk_title</code> argument to <code>g_km</code> and <code>h_km_layout</code> which allows user to add “Patients at Risk” title to Kaplan-Meier at risk annotation table.</li>
-</ul></div>
+</ul>
+</div>
 <div class="section level4">
-<h4 id="enhancements-0-9-1">Enhancements<a class="anchor" aria-label="anchor" href="#enhancements-0-9-1"></a></h4>
-<ul><li>Refactored <code>tabulate_rsp_subgroups</code> to pass sanitation checks by preventing creation of degenerate subtables.</li>
+<h4 id="enhancements-0-9-1">Enhancements<a class="anchor" aria-label="anchor" href="#enhancements-0-9-1"></a>
+</h4>
+<ul>
+<li>Refactored <code>tabulate_rsp_subgroups</code> to pass sanitation checks by preventing creation of degenerate subtables.</li>
 <li>Updated <code>analyze_vars_in_cols</code> to use caching, allow implementation of imputation rule via the <code>imp_rule</code> argument, and allow user to specify cell alignment via the <code>.aligns</code> argument.</li>
 <li>Updated <code>add_rowcounts</code> to allow addition of row counts from <code>alt_counts_df</code> using the <code>alt_counts</code> argument.</li>
 <li>Added <code>gp</code> argument to <code>g_forest</code> to control graphical parameters such as font size.</li>
-</ul></div>
+</ul>
+</div>
 <div class="section level4">
-<h4 id="miscellaneous-0-9-1">Miscellaneous<a class="anchor" aria-label="anchor" href="#miscellaneous-0-9-1"></a></h4>
-<ul><li>Grouped functions relating to valid method names and their default formats and labels into new source file <code>utils_defaults_handling.R</code>.</li>
+<h4 id="miscellaneous-0-9-1">Miscellaneous<a class="anchor" aria-label="anchor" href="#miscellaneous-0-9-1"></a>
+</h4>
+<ul>
+<li>Grouped functions relating to valid method names and their default formats and labels into new source file <code>utils_defaults_handling.R</code>.</li>
 <li>Started deprecation of <code>summary_custom()</code> and <code><a href="../reference/analyze_variables.html">a_summary()</a></code> as a <code>S3</code> method.</li>
 <li>Renamed statistical method for <code>p-value</code> in the discrete case to <code>pval_counts</code>.</li>
 <li>Removed <code>a_summary_internal()</code> in favor of only one main <code><a href="../reference/analyze_variables.html">a_summary()</a></code>.</li>
-</ul></div>
+</ul>
+</div>
 </div>
     <div class="section level2">
-<h2 class="pkg-version" data-toc-text="0.9.0" id="tern-090">tern 0.9.0<a class="anchor" aria-label="anchor" href="#tern-090"></a></h2><p class="text-muted">CRAN release: 2023-09-01</p>
-<div class="section level4">
-<h4 id="new-features-0-9-0">New Features<a class="anchor" aria-label="anchor" href="#new-features-0-9-0"></a></h4>
-<ul><li>Added <code>stat_propdiff_ci</code> function to calculate proportion/risk difference and CI.</li>
+<h2 class="pkg-version" data-toc-text="0.9.0" id="tern-090">tern 0.9.0<a class="anchor" aria-label="anchor" href="#tern-090"></a>
+</h2>
+<p class="text-muted">CRAN release: 2023-09-01</p>
+<div class="section level4">
+<h4 id="new-features-0-9-0">New Features<a class="anchor" aria-label="anchor" href="#new-features-0-9-0"></a>
+</h4>
+<ul>
+<li>Added <code>stat_propdiff_ci</code> function to calculate proportion/risk difference and CI.</li>
 <li>Added risk difference column functionality via the <code>riskdiff</code> argument to functions <code>count_occurrences</code>, <code>count_occurrences_by_grade</code>, <code>count_patients_with_event</code>, <code>count_patients_with_flags</code>, <code>analyze_num_patients</code>, and <code>summarize_num_patients</code>.</li>
-</ul></div>
+</ul>
+</div>
 <div class="section level4">
-<h4 id="enhancements-0-9-0">Enhancements<a class="anchor" aria-label="anchor" href="#enhancements-0-9-0"></a></h4>
-<ul><li>Refactored the function <code>a_summary</code> to no longer use the helper function <code>create_afun_summary</code>.</li>
+<h4 id="enhancements-0-9-0">Enhancements<a class="anchor" aria-label="anchor" href="#enhancements-0-9-0"></a>
+</h4>
+<ul>
+<li>Refactored the function <code>a_summary</code> to no longer use the helper function <code>create_afun_summary</code>.</li>
 <li>Refactored functions <code>summarize_vars</code> and <code>compare_vars</code> to use the refactored <code>a_summary</code> function.</li>
 <li>Created new internal helper functions <code>ungroup_stats</code> to ungroup statistics calculated for factor variables, and <code>a_summary_internal</code> to perform calculations for <code>a_summary</code>.</li>
-</ul></div>
+</ul>
+</div>
 <div class="section level4">
-<h4 id="bug-fixes-0-9-0">Bug Fixes<a class="anchor" aria-label="anchor" href="#bug-fixes-0-9-0"></a></h4>
-<ul><li>Fixed bug in <code>s_count_occurrences_by_grade</code> so that “missing” grade always appears as the final level.</li>
+<h4 id="bug-fixes-0-9-0">Bug Fixes<a class="anchor" aria-label="anchor" href="#bug-fixes-0-9-0"></a>
+</h4>
+<ul>
+<li>Fixed bug in <code>s_count_occurrences_by_grade</code> so that “missing” grade always appears as the final level.</li>
 <li>Fixed bug in <code>analyze_vars_in_cols</code> when categorical data was used.</li>
 <li>Fixed bug in <code>s_count_occurrences_by_grade</code> so that levels are not relabeled when reordering to account for “missing” grades.</li>
-</ul></div>
+</ul>
+</div>
 <div class="section level4">
-<h4 id="miscellaneous-0-9-0">Miscellaneous<a class="anchor" aria-label="anchor" href="#miscellaneous-0-9-0"></a></h4>
-<ul><li>Fixed swapped descriptions for the <code>.N_row</code> and <code>.N_col</code> parameters.</li>
+<h4 id="miscellaneous-0-9-0">Miscellaneous<a class="anchor" aria-label="anchor" href="#miscellaneous-0-9-0"></a>
+</h4>
+<ul>
+<li>Fixed swapped descriptions for the <code>.N_row</code> and <code>.N_col</code> parameters.</li>
 <li>Removed internal calls to <code>df_explicit_na</code>. Changes in <code>NA</code> values should happen externally to <code>tern</code> functions, depending on users’ needs.</li>
 <li>Reinstated correct soft deprecation for <code>create_afun_summary</code> and <code>create_afun_compare</code>.</li>
-</ul></div>
+</ul>
+</div>
 </div>
     <div class="section level2">
-<h2 class="pkg-version" data-toc-text="0.8.5" id="tern-085">tern 0.8.5<a class="anchor" aria-label="anchor" href="#tern-085"></a></h2>
+<h2 class="pkg-version" data-toc-text="0.8.5" id="tern-085">tern 0.8.5<a class="anchor" aria-label="anchor" href="#tern-085"></a>
+</h2>
 <div class="section level4">
-<h4 id="enhancements-0-8-5">Enhancements<a class="anchor" aria-label="anchor" href="#enhancements-0-8-5"></a></h4>
-<ul><li>Added <code>ylim</code> argument to <code>g_km</code> to allow the user to set custom limits for the y-axis.</li>
+<h4 id="enhancements-0-8-5">Enhancements<a class="anchor" aria-label="anchor" href="#enhancements-0-8-5"></a>
+</h4>
+<ul>
+<li>Added <code>ylim</code> argument to <code>g_km</code> to allow the user to set custom limits for the y-axis.</li>
 <li>Added assertion to <code>g_km</code> which checks whether there is one arm present in the data when <code>annot_coxph</code> is true.</li>
 <li>Added <code>flag_labels</code> argument to <code>s_count_patients_with_flags</code> to enable more label handling options in <code>count_patients_by_flags</code>.</li>
 <li>Added the <code>nested</code> argument to <code>analyze</code> wrapper functions <code>count_abnormal</code>, <code>count_abnormal_by_baseline</code>, <code>count_abnormal_by_marked</code>, <code>count_abnormal_by_worst_grade</code>, <code>count_abnormal_lab_worsen_by_baseline</code>, <code>count_cumulative</code>, <code>count_missed_doses</code>, <code>count_occurrences</code>, <code>count_occurrences_by_grade</code>, <code>count_patients_with_event</code>, <code>count_patients_with_flags</code>, <code>count_values</code>, <code>estimate_multinomial_response</code>, <code>estimate_proportion</code>, <code>estimate_incidence_rate</code>, <code>estimate_odds_ratio</code>, <code>estimate_proportion_diff</code>, <code>test_proportion_diff</code>, <code>summarize_ancova</code>, <code>summarize_change</code>, <code>summarize_glm_count</code>, <code>analyze_num_patients</code>, <code>coxph_pairwise</code>, <code>surv_time</code>, and <code>surv_timepoint</code>.</li>
-</ul></div>
+</ul>
+</div>
 <div class="section level3">
-<h3 id="miscellaneous-0-8-5">Miscellaneous<a class="anchor" aria-label="anchor" href="#miscellaneous-0-8-5"></a></h3>
-<ul><li>Started deprecation cycle for <code>summarize_vars</code> and <code>control_summarize_vars</code>. Renamed into <code>analyze_vars</code> and <code>control_analyze_vars</code> to reflect underlying <code>rtables</code> machinery while keeping backward compatibility with aliases.</li>
-</ul></div>
+<h3 id="miscellaneous-0-8-5">Miscellaneous<a class="anchor" aria-label="anchor" href="#miscellaneous-0-8-5"></a>
+</h3>
+<ul>
+<li>Started deprecation cycle for <code>summarize_vars</code> and <code>control_summarize_vars</code>. Renamed into <code>analyze_vars</code> and <code>control_analyze_vars</code> to reflect underlying <code>rtables</code> machinery while keeping backward compatibility with aliases.</li>
+</ul>
+</div>
 </div>
     <div class="section level2">
-<h2 class="pkg-version" data-toc-text="0.8.4" id="tern-084">tern 0.8.4<a class="anchor" aria-label="anchor" href="#tern-084"></a></h2><p class="text-muted">CRAN release: 2023-06-27</p>
-<div class="section level4">
-<h4 id="enhancements-0-8-4">Enhancements<a class="anchor" aria-label="anchor" href="#enhancements-0-8-4"></a></h4>
-<ul><li>Added method for <code>character</code> class to <code>h_coxreg_inter_effect</code> enabling <code>character</code> covariates in <code>summarize_coxreg</code>.</li>
-</ul></div>
+<h2 class="pkg-version" data-toc-text="0.8.4" id="tern-084">tern 0.8.4<a class="anchor" aria-label="anchor" href="#tern-084"></a>
+</h2>
+<p class="text-muted">CRAN release: 2023-06-27</p>
+<div class="section level4">
+<h4 id="enhancements-0-8-4">Enhancements<a class="anchor" aria-label="anchor" href="#enhancements-0-8-4"></a>
+</h4>
+<ul>
+<li>Added method for <code>character</code> class to <code>h_coxreg_inter_effect</code> enabling <code>character</code> covariates in <code>summarize_coxreg</code>.</li>
+</ul>
+</div>
 <div class="section level4">
-<h4 id="miscellaneous-0-8-4">Miscellaneous<a class="anchor" aria-label="anchor" href="#miscellaneous-0-8-4"></a></h4>
-<ul><li>Began deprecation of <code>time_unit_input</code> and <code>time_unit_output</code> arguments and replaced them with the <code>input_time_unit</code> and <code>num_pt_year</code>, respectively, in <code>control_incidence_rate</code>.</li>
+<h4 id="miscellaneous-0-8-4">Miscellaneous<a class="anchor" aria-label="anchor" href="#miscellaneous-0-8-4"></a>
+</h4>
+<ul>
+<li>Began deprecation of <code>time_unit_input</code> and <code>time_unit_output</code> arguments and replaced them with the <code>input_time_unit</code> and <code>num_pt_year</code>, respectively, in <code>control_incidence_rate</code>.</li>
 <li>Removed deprecated <code>pairwise</code> function.</li>
 <li>Deprecated <code>a_compare</code> and replaced it with <code>a_summary</code> with argument <code>compare = TRUE</code>.</li>
 <li>Deprecated helper functions <code>create_afun_summary</code> and <code>create_afun_compare</code> which are no longer used by <code>a_summary</code> and <code>a_compare</code> respectively.</li>
-</ul></div>
+</ul>
+</div>
 <div class="section level4">
-<h4 id="bug-fixes-0-8-4">Bug Fixes<a class="anchor" aria-label="anchor" href="#bug-fixes-0-8-4"></a></h4>
-<ul><li>Fixed long double assertion check in <code>sum(weights)</code> for <code>M1mac</code> installation.</li>
-</ul></div>
+<h4 id="bug-fixes-0-8-4">Bug Fixes<a class="anchor" aria-label="anchor" href="#bug-fixes-0-8-4"></a>
+</h4>
+<ul>
+<li>Fixed long double assertion check in <code>sum(weights)</code> for <code>M1mac</code> installation.</li>
+</ul>
+</div>
 </div>
     <div class="section level2">
-<h2 class="pkg-version" data-toc-text="0.8.3" id="tern-083">tern 0.8.3<a class="anchor" aria-label="anchor" href="#tern-083"></a></h2><p class="text-muted">CRAN release: 2023-06-19</p>
-<div class="section level4">
-<h4 id="enhancements-0-8-3">Enhancements<a class="anchor" aria-label="anchor" href="#enhancements-0-8-3"></a></h4>
-<ul><li>Added explicit zero counts to <code>g_km</code> plot “at risk” annotation tables.</li>
+<h2 class="pkg-version" data-toc-text="0.8.3" id="tern-083">tern 0.8.3<a class="anchor" aria-label="anchor" href="#tern-083"></a>
+</h2>
+<p class="text-muted">CRAN release: 2023-06-19</p>
+<div class="section level4">
+<h4 id="enhancements-0-8-3">Enhancements<a class="anchor" aria-label="anchor" href="#enhancements-0-8-3"></a>
+</h4>
+<ul>
+<li>Added explicit zero counts to <code>g_km</code> plot “at risk” annotation tables.</li>
 <li>Added a flag for total level split in <code>analyze_patients_exposure_in_cols</code>.</li>
 <li>Implemented <code>.indent_mods</code> argument in functions <code>h_tab_one_biomarker</code>, <code>h_tab_rsp_one_biomarker</code>, <code>h_tab_surv_one_biomarker</code>, <code>summarize_logistic</code>, <code>logistic_summary_by_flag</code>, <code>tabulate_rsp_biomarkers</code>, <code>a_coxreg</code>, <code>summarize_coxreg</code>, <code>tabulate_survival_biomarkers</code>, <code>surv_time</code>, <code>surv_timepoint</code>, and <code>cfun_by_flag</code>.</li>
 <li>Updated <code>summarize_coxreg</code> to print covariates in data rows for univariate Cox regression with no interactions and content rows otherwise.</li>
 <li>Removed “baseline status” text from <code>d_count_abnormal_by_baseline</code> labels.</li>
 <li>Improved default sizing of annotation tables in <code>g_km</code> and added dynamic scaling of the <code>surv_med</code> and <code>coxph</code> annotation tables, with customization via the <code>width_annots</code> argument.</li>
-</ul></div>
+</ul>
+</div>
 <div class="section level4">
-<h4 id="bug-fixes-0-8-3">Bug Fixes<a class="anchor" aria-label="anchor" href="#bug-fixes-0-8-3"></a></h4>
-<ul><li>Fixed bug in <code>split_text_grob</code> preventing titles and footnotes from being properly formatted and printed by <code>decorate_grob</code>.</li>
+<h4 id="bug-fixes-0-8-3">Bug Fixes<a class="anchor" aria-label="anchor" href="#bug-fixes-0-8-3"></a>
+</h4>
+<ul>
+<li>Fixed bug in <code>split_text_grob</code> preventing titles and footnotes from being properly formatted and printed by <code>decorate_grob</code>.</li>
 <li>Fixed bug in <code>g_lineplot</code> preventing the addition of lines to the plot when midpoint statistic calculations result in <code>NA</code> value(s).</li>
 <li>Fixed <code>tern:::tidy.glm</code> formals to respect <code>broom:::tidy.default</code> formals.</li>
-</ul></div>
+</ul>
+</div>
 <div class="section level4">
-<h4 id="miscellaneous-0-8-3">Miscellaneous<a class="anchor" aria-label="anchor" href="#miscellaneous-0-8-3"></a></h4>
-<ul><li>Updated <code>README</code> to include installation instructions for CRAN.</li>
+<h4 id="miscellaneous-0-8-3">Miscellaneous<a class="anchor" aria-label="anchor" href="#miscellaneous-0-8-3"></a>
+</h4>
+<ul>
+<li>Updated <code>README</code> to include installation instructions for CRAN.</li>
 <li>Remove examples for unexported functions.</li>
 <li>Export functions <code>has_count_in_cols</code>, <code>has_counts_difference</code>, <code>combine_counts</code>, <code>h_tab_rsp_one_biomarker</code>, <code>arrange_grobs</code>, <code>a_count_patients_sum_exposure</code>, <code>a_coxreg</code>, <code>groups_list_to_df</code>, <code>forest_viewport</code>.</li>
 <li>Updated <code>README</code> to include installation instructions for CRAN.</li>
 <li>Began deprecation of <code>indent_mod</code> argument and replaced it with the <code>.indent_mods</code> argument in <code>summarize_num_patients</code> and <code>analyze_num_patients</code>.</li>
-</ul></div>
+</ul>
+</div>
 </div>
     <div class="section level2">
-<h2 class="pkg-version" data-toc-text="0.8.2" id="tern-082">tern 0.8.2<a class="anchor" aria-label="anchor" href="#tern-082"></a></h2>
-<div class="section level4">
-<h4 id="breaking-changes-0-8-2">Breaking Changes<a class="anchor" aria-label="anchor" href="#breaking-changes-0-8-2"></a></h4>
-<ul><li>Refactored <code>s_coxreg</code> and <code>summarize_coxreg</code>to work with new analysis function <code>a_coxreg</code>.</li>
-</ul></div>
+<h2 class="pkg-version" data-toc-text="0.8.2" id="tern-082">tern 0.8.2<a class="anchor" aria-label="anchor" href="#tern-082"></a>
+</h2>
+<div class="section level4">
+<h4 id="breaking-changes-0-8-2">Breaking Changes<a class="anchor" aria-label="anchor" href="#breaking-changes-0-8-2"></a>
+</h4>
+<ul>
+<li>Refactored <code>s_coxreg</code> and <code>summarize_coxreg</code>to work with new analysis function <code>a_coxreg</code>.</li>
+</ul>
+</div>
 <div class="section level4">
-<h4 id="enhancements-0-8-2">Enhancements<a class="anchor" aria-label="anchor" href="#enhancements-0-8-2"></a></h4>
-<ul><li>Added <code>section_div</code> and <code>na_level</code> arguments to <code>summarize_vars</code>.</li>
+<h4 id="enhancements-0-8-2">Enhancements<a class="anchor" aria-label="anchor" href="#enhancements-0-8-2"></a>
+</h4>
+<ul>
+<li>Added <code>section_div</code> and <code>na_level</code> arguments to <code>summarize_vars</code>.</li>
 <li>Added <code>median_range</code> as a numeric variable statistic option for <code>summarize_vars</code>.</li>
 <li>Corrected ordering of factor levels by <code>d_onco_rsp_label</code>.</li>
 <li>Added new “Analyze Functions”, “Summarize Functions”, and “Analyze Functions on Columns” overview pages.</li>
@@ -355,26 +548,36 @@ <h4 id="enhancements-0-8-2">Enhancements<a class="anchor" aria-label="anchor" hr
 <li>Added more informative error when the user selects an invalid method for unstratified analyses in <code>s_proportion_diff</code>.</li>
 <li>Updated <code>s_summary</code> and <code>s_compare</code> to allow <code>NA</code> values in input variables. For factor variables with <code>NA</code>s, if <code>na.rm = FALSE</code> an explicit <code>NA</code> level will be automatically added. <code>na.rm = TRUE</code> will also consider <code>"&lt;Missing&gt;"</code> values and exclude them.</li>
 <li>Updated purpose of <code>na_level</code> parameter in <code>s_summary</code> and <code>s_compare</code> to align with other <code>tern</code> functions. Instead of being a string to consider as <code>NA</code> when setting <code>na.rm = TRUE</code>, it now defines a string to print in place of <code>NA</code> values in the output table.</li>
-</ul></div>
+</ul>
+</div>
 <div class="section level4">
-<h4 id="bug-fixes-0-8-2">Bug Fixes<a class="anchor" aria-label="anchor" href="#bug-fixes-0-8-2"></a></h4>
-<ul><li>Fixed missing label for <code>TRTEDTM</code> in <code>tern</code> datasets.</li>
+<h4 id="bug-fixes-0-8-2">Bug Fixes<a class="anchor" aria-label="anchor" href="#bug-fixes-0-8-2"></a>
+</h4>
+<ul>
+<li>Fixed missing label for <code>TRTEDTM</code> in <code>tern</code> datasets.</li>
 <li>Fixed improper implementation of <code>na_level</code> argument in <code>summarize_vars</code> preventing it from having an effect.</li>
-</ul></div>
+</ul>
+</div>
 <div class="section level4">
-<h4 id="miscellaneous-0-8-2">Miscellaneous<a class="anchor" aria-label="anchor" href="#miscellaneous-0-8-2"></a></h4>
-<ul><li>Implemented the <code>lubridate</code> package for date variables in <code>tern</code> datasets.</li>
+<h4 id="miscellaneous-0-8-2">Miscellaneous<a class="anchor" aria-label="anchor" href="#miscellaneous-0-8-2"></a>
+</h4>
+<ul>
+<li>Implemented the <code>lubridate</code> package for date variables in <code>tern</code> datasets.</li>
 <li>Organized <code>.gitignore</code> and <code>.Rbuildignore</code> files.</li>
 <li>Removed deprecated <code>footnotes</code> functions and all related files.</li>
 <li>Started deprecation cycle for <code>pairwise</code> function.</li>
 <li>Moved <code>count_patients_with_flags</code> functions from <code>count_patients_with_event.R</code> to <code>count_patients_with_flags.R</code>.</li>
-</ul></div>
+</ul>
+</div>
 </div>
     <div class="section level2">
-<h2 class="pkg-version" data-toc-text="0.8.0" id="tern-080">tern 0.8.0<a class="anchor" aria-label="anchor" href="#tern-080"></a></h2>
+<h2 class="pkg-version" data-toc-text="0.8.0" id="tern-080">tern 0.8.0<a class="anchor" aria-label="anchor" href="#tern-080"></a>
+</h2>
 <div class="section level4">
-<h4 id="enhancements-0-8-0">Enhancements<a class="anchor" aria-label="anchor" href="#enhancements-0-8-0"></a></h4>
-<ul><li>Added <code>summarize_glm_count</code> function to analyze count data using a linear model.</li>
+<h4 id="enhancements-0-8-0">Enhancements<a class="anchor" aria-label="anchor" href="#enhancements-0-8-0"></a>
+</h4>
+<ul>
+<li>Added <code>summarize_glm_count</code> function to analyze count data using a linear model.</li>
 <li>Added legend to <code>g_step</code>.</li>
 <li>Added formatting functions <code>format_fraction_fixed_dp</code> and <code>format_count_fraction_fixed_dp</code> with fixed single decimal place in percentages.</li>
 <li>Added <code>na_level</code> and <code>labelstr</code> arguments to <code>summarize_vars_in_cols</code>.</li>
@@ -382,10 +585,13 @@ <h4 id="enhancements-0-8-0">Enhancements<a class="anchor" aria-label="anchor" hr
 <li>Added <code>h_row_first_values</code> function as a more general helper function to retrieve first values from specific rows.</li>
 <li>Added option to remove <code>"(n)"</code> suffix from <code>unique_count</code> labels for <code>s_num_patients</code>.</li>
 <li>Added options to <code>g_km</code> to annotate with statistics (<code>annot_stats</code>) and add corresponding vertical lines (<code>annot_stats_lines</code>).</li>
-</ul></div>
+</ul>
+</div>
 <div class="section level4">
-<h4 id="bug-fixes-0-8-0">Bug Fixes<a class="anchor" aria-label="anchor" href="#bug-fixes-0-8-0"></a></h4>
-<ul><li>Fixed bug causing incorrect ordering of numeric grade levels when missing grades are present in <code>s_count_occurrences_by_grade</code>.</li>
+<h4 id="bug-fixes-0-8-0">Bug Fixes<a class="anchor" aria-label="anchor" href="#bug-fixes-0-8-0"></a>
+</h4>
+<ul>
+<li>Fixed bug causing incorrect ordering of numeric grade levels when missing grades are present in <code>s_count_occurrences_by_grade</code>.</li>
 <li>Refactored <code>summarize_vars_in_cols</code> to work with pagination machinery.</li>
 <li>Fixed bug to allow passing of <code>conf_level</code> argument to <code><a href="https://rvlenth.github.io/emmeans/reference/contrast.html" class="external-link">emmeans::contrast()</a></code> in <code>s_ancova</code>.</li>
 <li>Fixed bugs in <code>rtables_access.R</code> caused by not checking for specific combinations (also the standard values that were never used) of column indices and names.</li>
@@ -393,10 +599,13 @@ <h4 id="bug-fixes-0-8-0">Bug Fixes<a class="anchor" aria-label="anchor" href="#b
 <li>Fixed bug in <code>add_rowcounts</code> that caused all row count row values to count as zero.</li>
 <li>Fixed bug in <code>h_col_indices</code> causing an error when pruning with combination columns.</li>
 <li>Fixed bug in <code>test_proportion_diff</code> missing argument for <code>var_labels</code>.</li>
-</ul></div>
+</ul>
+</div>
 <div class="section level4">
-<h4 id="documentation-and-tests-0-8-0">Documentation and Tests<a class="anchor" aria-label="anchor" href="#documentation-and-tests-0-8-0"></a></h4>
-<ul><li>Added more tests to increase code coverage.</li>
+<h4 id="documentation-and-tests-0-8-0">Documentation and Tests<a class="anchor" aria-label="anchor" href="#documentation-and-tests-0-8-0"></a>
+</h4>
+<ul>
+<li>Added more tests to increase code coverage.</li>
 <li>Created separate documentation files for functions in different sections of <code>pkgdown</code> reference.</li>
 <li>Created separate <code>.R</code> files for logistic regression and cox regression helper functions.</li>
 <li>Fixed table tests using <code>analyze_num_patients</code> to generate an initial summary so there is no repetition when paginating.</li>
@@ -405,51 +614,68 @@ <h4 id="documentation-and-tests-0-8-0">Documentation and Tests<a class="anchor"
 <li>Created vignette which saves cached synthetic CDISC dataset files to the <code>data/</code> folder and generated cached synthetic datasets.</li>
 <li>Updated all examples/tests to use datasets from the <code>data/</code> folder instead of <code>scda</code> datasets.</li>
 <li>Removed all template tests from <code>tern</code>. These tests are in internal repo <code>scda.test</code>.</li>
-</ul></div>
+</ul>
+</div>
 <div class="section level4">
-<h4 id="miscellaneous-0-8-0">Miscellaneous<a class="anchor" aria-label="anchor" href="#miscellaneous-0-8-0"></a></h4>
-<ul><li>Renamed <code>summarize_vars_in_cols</code> to <code>analyze_vars_in_cols</code> to reflect the appropriate <code>analyze</code> logic.</li>
+<h4 id="miscellaneous-0-8-0">Miscellaneous<a class="anchor" aria-label="anchor" href="#miscellaneous-0-8-0"></a>
+</h4>
+<ul>
+<li>Renamed <code>summarize_vars_in_cols</code> to <code>analyze_vars_in_cols</code> to reflect the appropriate <code>analyze</code> logic.</li>
 <li>Removed redundant <code>summary_in_cols</code> helper functions.</li>
 <li>Exported function <code>format_xx</code>.</li>
 <li>Replaced deprecated <code>ggplot2</code> functions/arguments to fix warnings.</li>
 <li>Replaced deprecated function <code><a href="https://forcats.tidyverse.org/reference/fct_explicit_na.html" class="external-link">forcats::fct_explicit_na</a></code> with <code><a href="https://forcats.tidyverse.org/reference/fct_na_value_to_level.html" class="external-link">forcats::fct_na_value_to_level</a></code>.</li>
 <li>Removed deprecated <code>wrap_text</code> function and related files.</li>
 <li>Started deprecation cycle for <code>footnotes</code> functions.</li>
-</ul></div>
+</ul>
+</div>
 </div>
     <div class="section level2">
-<h2 class="pkg-version" data-toc-text="0.7.10" id="tern-0710">tern 0.7.10<a class="anchor" aria-label="anchor" href="#tern-0710"></a></h2>
+<h2 class="pkg-version" data-toc-text="0.7.10" id="tern-0710">tern 0.7.10<a class="anchor" aria-label="anchor" href="#tern-0710"></a>
+</h2>
 <div class="section level4">
-<h4 id="new-features-0-7-10">New Features<a class="anchor" aria-label="anchor" href="#new-features-0-7-10"></a></h4>
-<ul><li>Added stratified Newcombe and stratified Wilson statistics to <code>estimate_proportion</code> and <code>estimate_proportion_diff</code> with relative tests.</li>
+<h4 id="new-features-0-7-10">New Features<a class="anchor" aria-label="anchor" href="#new-features-0-7-10"></a>
+</h4>
+<ul>
+<li>Added stratified Newcombe and stratified Wilson statistics to <code>estimate_proportion</code> and <code>estimate_proportion_diff</code> with relative tests.</li>
 <li>Added <code>stat_mean_pval</code>, a new summary statistic to calculate the p-value of the mean.</li>
 <li>Added statistic <code>mean_se</code> (mean with standard error) for <code>summarize_variables</code> and related functions.</li>
 <li>Introduced again <code>Rdpack</code> for references.</li>
-</ul></div>
+</ul>
+</div>
 <div class="section level4">
-<h4 id="enhancements-0-7-10">Enhancements<a class="anchor" aria-label="anchor" href="#enhancements-0-7-10"></a></h4>
-<ul><li>Redesign of data handling in tests by removing repetitive data loads and library calls.</li>
+<h4 id="enhancements-0-7-10">Enhancements<a class="anchor" aria-label="anchor" href="#enhancements-0-7-10"></a>
+</h4>
+<ul>
+<li>Redesign of data handling in tests by removing repetitive data loads and library calls.</li>
 <li>Added <code><a href="https://andrisignorell.github.io/DescTools/reference/BinomDiffCI.html" class="external-link">DescTools::BinomDiffCI</a></code> function within <code>tern</code>.</li>
 <li>Added new parameter to <code>summarize_logistic</code> to specify which pivoted value to use during analysis.</li>
 <li>Updated <code>s_coxph_pairwise</code> to generate log-rank p-value using original log-rank test instead of Cox Proportional-Hazards Model.</li>
 <li>Implemented <code>nestcolor</code> in all examples by adapting <code>g_km</code>, <code>g_ipp</code>, <code>g_waterfall</code>, <code>g_step</code>, <code>g_lineplot</code>, and <code>g_forest</code>.</li>
 <li>Added parameters <code>interaction_y</code> and <code>interaction_item</code> in ANCOVA to make the interaction calculations available.</li>
 <li>Added new parameter <code>footnotes</code> to add footnotes to <code>g_km</code>.</li>
-</ul></div>
+</ul>
+</div>
 <div class="section level4">
 <h4 id="migration-from-assertthat-to-checkmate-0-7-10">Migration from <code>assertthat</code> to <code>checkmate</code>
-<a class="anchor" aria-label="anchor" href="#migration-from-assertthat-to-checkmate-0-7-10"></a></h4>
-<ul><li>Implemented <code><a href="https://mllg.github.io/checkmate/reference/checkVector.html" class="external-link">checkmate::assert_vector</a></code>, <code><a href="https://mllg.github.io/checkmate/reference/checkSetEqual.html" class="external-link">checkmate::assert_set_equal</a></code>, and <code><a href="https://mllg.github.io/checkmate/reference/checkInt.html" class="external-link">checkmate::assert_int</a></code> to check vector type, length, and values.</li>
+<a class="anchor" aria-label="anchor" href="#migration-from-assertthat-to-checkmate-0-7-10"></a>
+</h4>
+<ul>
+<li>Implemented <code><a href="https://mllg.github.io/checkmate/reference/checkVector.html" class="external-link">checkmate::assert_vector</a></code>, <code><a href="https://mllg.github.io/checkmate/reference/checkSetEqual.html" class="external-link">checkmate::assert_set_equal</a></code>, and <code><a href="https://mllg.github.io/checkmate/reference/checkInt.html" class="external-link">checkmate::assert_int</a></code> to check vector type, length, and values.</li>
 <li>Replaced with standard assertions from <code>checkmate</code> the following functions: <code>all_elements_in_ref</code>, <code>is_df_with_nlevels_factor</code>, <code>is_df_with_no_na_level</code>, <code>is_proportion_vector</code>, <code>is_quantiles_vector</code>, <code>is_character_or_factor</code>, <code>is_nonnegative_count</code>, <code>is_valid_character</code>, <code>assert_character_or_factor</code>, <code>assert_equal_length</code> and <code>has_tabletree_colnames</code>.</li>
 <li>Modified <code>is_proportion</code>, <code>is_equal_length</code>, <code>is_df_with_no_na_level</code>, <code>is_df_with_nlevels_factor</code>, <code>is_variables</code>, <code>is_df_with_variables</code>, <code>is_df_with_factors</code>, <code>is_valid_factor</code> to use assertion logic.</li>
 <li>Added more verbose warnings from <code>as_factor_keep_attributes</code>.</li>
 <li>Made <code>assert_df_with_factors</code> and <code>assert_proportion_value</code> internal functions.</li>
 <li>Renamed <code>assertthat.R</code> and <code>test-assertthat.R</code> to <code>utils_checkmate.R</code> and <code>test-utils_checkmate.R</code>.</li>
-</ul></div>
+</ul>
+</div>
 <div class="section level4">
-<h4 id="documentation-and-namespace-polishing-0-7-10">Documentation and NAMESPACE Polishing<a class="anchor" aria-label="anchor" href="#documentation-and-namespace-polishing-0-7-10"></a></h4>
-<ul><li>Added stable badges for:
-<ul><li>
+<h4 id="documentation-and-namespace-polishing-0-7-10">Documentation and NAMESPACE Polishing<a class="anchor" aria-label="anchor" href="#documentation-and-namespace-polishing-0-7-10"></a>
+</h4>
+<ul>
+<li>Added stable badges for:
+<ul>
+<li>
 <code>count_abnormal_by_marked</code> (reference to <code>abnormal_by_marked</code>), <code>count_abnormal_lab_worsen_by_baseline</code> and <code>h_adlb_worsen</code> (reference to <code>abnormal_by_worst_grade_worsen_from_baseline</code>), <code>count_abnormal_by_worst_grade</code> (reference to <code>abnormal_by_worst_grade</code>), <code>to_string_matrix</code>, <code>tidy.summary.coxph</code>, <code>tidy.step</code>, <code>surv_timepoint</code>, (reference to <code>survival_timepoint</code>), <code>surv_time</code> (reference to <code>survival_time</code>), <code>coxph_pairwise</code> (reference to <code>survival_coxph_pairwise</code>), <code>extract_survival_subgroups</code> and <code>tabulate_survival_subgroups</code> (reference to <code>survival_duration_subgroups</code>), <code>extract_survival_biomarkers</code> and <code>tabulate_survival_biomarkers</code> (reference to <code>survival_biomarkers_subgroups</code>), <code>control_summarize_vars</code>, <code>s_summary</code> and <code>a_summary</code> (reference to <code>summarize_variables</code>) and kept the S3 method tree.</li>
 <li>
 <code>summarize_patients_exposure_in_cols</code>, <code>summarize_num_patients</code> with <code>s_num_patients</code>, <code>s_num_patients_content</code>, <code>summarize_num_patients</code>.</li>
@@ -458,9 +684,11 @@ <h4 id="documentation-and-namespace-polishing-0-7-10">Documentation and NAMESPAC
 <li>(statistical function controls) <code>control_coxreg</code>, <code>control_coxph</code>, <code>control_incidence_rate</code>, <code>control_lineplot_vars</code>, <code>control_surv_time</code>, <code>control_surv_timepoint</code>, <code>control_logisitic</code>, <code>control_step</code>.</li>
 <li>
 <code>stat_mean_ci</code>, <code>stat_median_ci</code>, <code>split_cols_by_groups</code>, <code>explicit_na</code>, <code>sas_na</code>, <code>extract_rsp_subgroups</code>, <code>tabulate_rsp_subgroups</code>, <code>extract_rsp_biomarkers</code>, <code>tabulate_rsp_biomarkers</code>, <code>keep_rows</code>, <code>keep_content_rows</code>, <code>has_count_in_any_col</code>, <code>has_fraction_in_cols</code>, <code>has_fraction_in_any_col</code>, <code>has_fractions_difference</code>, <code>test_proportion_diff</code>, <code>pairwise</code>, <code>logistic_regression</code>, <code>estimate_incidence_rate</code>, <code>control_incidence_rate</code> (reference to <code>incidence_rate</code>), <code>cut_quantile_bins</code>, <code>estimate_multinomial_rsp</code>, <code>decorate_grob_set</code>, <code>extreme_format</code>, <code>fit_rsp_step</code>, <code>fit_survival_step</code>, <code>footnotes</code>, <code>footnotes-set</code>, <code>format_count_fraction</code>, <code>format_fraction_threshold</code>, <code>formatting_functions</code>, <code>format_fraction</code>, <code>combination_function</code> (S4 method), <code>compare_variables</code> (S3 method), <code>kaplan_meier</code>.</li>
-</ul></li>
+</ul>
+</li>
 <li>Internal keywords added, export removed, <code>_pkgdown.yml</code> updated, and <code>tern:::</code> added for tests/examples/vignettes where present for the following functions:
-<ul><li>(chain functions, reference to <code>abnormal_by_marked</code>) <code>s_count_abnormal_by_marked</code>, <code>a_count_abnormal_by_marked</code>.</li>
+<ul>
+<li>(chain functions, reference to <code>abnormal_by_marked</code>) <code>s_count_abnormal_by_marked</code>, <code>a_count_abnormal_by_marked</code>.</li>
 <li>(chain functions, reference to <code>abnormal_by_worst_grade_worsen_from_baseline</code>) <code>a_count_abnormal_lab_worsen_by_baseline</code>, <code>s_count_abnormal_lab_worsen_by_baseline</code>.</li>
 <li>(chain functions, reference to <code>abnormal_by_worst_grade</code>) <code>s_count_abnormal_by_worst_grade</code>, <code>a_count_abnormal_by_worst_grade</code>.</li>
 <li>(chain functions, reference to <code>survival_timepoint</code>) <code>s_surv_timepoint</code>, <code>s_surv_timepoint_diff</code>, <code>a_surv_timepoint</code>, <code>a_surv_timepoint_diff</code>.</li>
@@ -474,11 +702,15 @@ <h4 id="documentation-and-namespace-polishing-0-7-10">Documentation and NAMESPAC
 <li>(cox regression helper) <code>cox_regression_inter</code>, <code>decorate_grob_factory</code>, <code>draw_grob</code>, <code>estimate_coef</code>.</li>
 <li>
 <code>summary_labels</code>, <code>summary_formats</code>, <code>s_count_patients_sum_exposure</code>, <code>a_change_from_baseline</code> <code>s_change_from_baseline</code>, <code>a_ancova</code>, <code>s_ancova</code>, <code>arrange_grobs</code>, <code>as_factor_keep_attributes</code>, <code>combine_levels</code>, <code>split_text_grob</code>, <code>groups_list_to_df</code>, <code>s_cox_multivariate</code>, <code>is_leaf_table</code>, <code>a_response_subgroups</code>, <code>range_noinf</code>, <code>has_count_in_cols</code>, <code>has_counts_difference</code>, <code>prop_chisq</code>, <code>prop_cmh</code>, <code>prop_schouten</code>, <code>prop_fisher</code>, <code>s_test_proportion_diff</code>, <code>a_test_proportion_diff</code>, <code>fct_discard</code>, <code>fct_explicit_na_if</code>.</li>
-</ul></li>
-</ul></div>
+</ul>
+</li>
+</ul>
+</div>
 <div class="section level4">
-<h4 id="bug-fixes-0-7-10">Bug Fixes<a class="anchor" aria-label="anchor" href="#bug-fixes-0-7-10"></a></h4>
-<ul><li>Fixed retrieval method of <code>stats::ancova</code> output due to version inconsistency.</li>
+<h4 id="bug-fixes-0-7-10">Bug Fixes<a class="anchor" aria-label="anchor" href="#bug-fixes-0-7-10"></a>
+</h4>
+<ul>
+<li>Fixed retrieval method of <code>stats::ancova</code> output due to version inconsistency.</li>
 <li>Fixed tests to respect the new standard print for <code>NA</code> coming from <code>rtables</code>.</li>
 <li>Fixed error in tests coming from changes in <code><a href="https://insightsengineering.github.io/formatters/latest-tag/reference/var_labels.html" class="external-link">formatters::var_labels</a></code>.</li>
 <li>Fixed <code>prop_diff</code> functions to respect success responses (<code>TRUE</code> values).</li>
@@ -489,10 +721,13 @@ <h4 id="bug-fixes-0-7-10">Bug Fixes<a class="anchor" aria-label="anchor" href="#
 <li>Fixed bug in <code>s_abnormal_by_worst_grade</code> when there is one <code>PARAM</code> level.</li>
 <li>Fixed bug in <code>prop_diff_wald</code> when selecting all responders, updated tests accordingly.</li>
 <li>Fixed bug in <code>h_ancova</code> that caused an error when deselecting all covariates.</li>
-</ul></div>
+</ul>
+</div>
 <div class="section level4">
-<h4 id="miscellaneous-0-7-10">Miscellaneous<a class="anchor" aria-label="anchor" href="#miscellaneous-0-7-10"></a></h4>
-<ul><li>Added deprecated badge to <code>g_mmrm</code>.</li>
+<h4 id="miscellaneous-0-7-10">Miscellaneous<a class="anchor" aria-label="anchor" href="#miscellaneous-0-7-10"></a>
+</h4>
+<ul>
+<li>Added deprecated badge to <code>g_mmrm</code>.</li>
 <li>Removed internal function calls in examples (<code>tern:::</code>) and added <code>dontrun</code> to internal function examples.</li>
 <li>Removed warnings and messages to console occurring in examples and tests.</li>
 <li>Deprecated functions <code>color_palette</code> and <code>h_set_nest_theme</code> in favor of <code><a href="https://rdrr.io/pkg/nestcolor/man/color_palette.html" class="external-link">nestcolor::color_palette</a></code> and <code><a href="https://rdrr.io/pkg/nestcolor/man/theme_nest.html" class="external-link">nestcolor::theme_nest</a></code>, respectively.</li>
@@ -506,34 +741,46 @@ <h4 id="miscellaneous-0-7-10">Miscellaneous<a class="anchor" aria-label="anchor"
 <li>Added <code>@md</code> and removed <code>@order</code> from <code>incidence_rate.R</code>. Modified examples accordingly.</li>
 <li>Removed hyperlink from <code>prop_schouten</code> function documentation.</li>
 <li>Exported <code>draw_grob</code> function.</li>
-</ul></div>
+</ul>
+</div>
 </div>
     <div class="section level2">
-<h2 class="pkg-version" data-toc-text="0.7.8" id="tern-078">tern 0.7.8<a class="anchor" aria-label="anchor" href="#tern-078"></a></h2>
+<h2 class="pkg-version" data-toc-text="0.7.8" id="tern-078">tern 0.7.8<a class="anchor" aria-label="anchor" href="#tern-078"></a>
+</h2>
 <div class="section level4">
-<h4 id="fix-0-7-8">Fix<a class="anchor" aria-label="anchor" href="#fix-0-7-8"></a></h4>
-<ul><li>
+<h4 id="fix-0-7-8">Fix<a class="anchor" aria-label="anchor" href="#fix-0-7-8"></a>
+</h4>
+<ul>
+<li>
 <code>h_split_by_subgroups</code> documentation warning fix for wrong placing of example block</li>
-</ul></div>
+</ul>
+</div>
 <div class="section level4">
-<h4 id="documentation-and-namespace-polishing-0-7-8">Documentation and NAMESPACE polishing<a class="anchor" aria-label="anchor" href="#documentation-and-namespace-polishing-0-7-8"></a></h4>
-<ul><li>Adopting the standard of badges for <code>@description</code> instead of every <code>@descriptionIn</code> function. Corrected accordingly <code>summarize_variables_in_cols</code>
+<h4 id="documentation-and-namespace-polishing-0-7-8">Documentation and NAMESPACE polishing<a class="anchor" aria-label="anchor" href="#documentation-and-namespace-polishing-0-7-8"></a>
+</h4>
+<ul>
+<li>Adopting the standard of badges for <code>@description</code> instead of every <code>@descriptionIn</code> function. Corrected accordingly <code>summarize_variables_in_cols</code>
 </li>
 <li>Added stable badge for <code>g_lineplot</code>, <code>g_step</code>, <code>g_waterfall</code>, <code>cox_regression</code>, <code>score_occurrences</code>, <code>add_rowcounts</code>, <code>odds_ratio</code>, <code>count_occurrences</code>, <code>count_occurrences_by_grade</code>, <code>explicit_na</code>, <code>df_explicit_na</code>, <code>count_patients_with_event</code>, <code>decorate_grob</code>, <code>combine_groups</code>, <code>append_varlabels</code>, <code>univariate</code>, <code>stack_grobs</code>, <code>count_abnormal</code> (reference to <code>abnormal</code>), <code>count_abnormal_by_baseline</code> (reference to <code>abnormal_by_baseline</code>).</li>
 <li>Internal keywords added, export removed, <code>_pkgdown.yml</code> polished and <code>tern:::</code> for tests, examples, and vignettes when present for the following functions:
-<ul><li>(helper functions) <code>h_format_row</code>, <code>h_map_for_count_abnormal</code>
+<ul>
+<li>(helper functions) <code>h_format_row</code>, <code>h_map_for_count_abnormal</code>
 </li>
 <li>(utils functions) <code>make_names</code>, <code>month2day</code>, <code>day2month</code> <code>empty_vector_if_na</code>, <code>aesi_label</code>, <code>n_available</code>, <code>format_xx</code>, <code>arm</code>.</li>
 <li>
 <code>count_values_funs</code>, <code>prop_difference</code>, <code>combine_counts</code>.</li>
 <li>(chain functions) <code>s_count_abnormal</code>, <code>a_count_abnormal</code>.</li>
 <li>(chain functions) <code>s_count_abnormal_by_baseline</code>, <code>a_count_abnormal_by_baseline</code>, <code>d_count_abnormal_by_baseline</code>.</li>
-</ul></li>
+</ul>
+</li>
 <li>Deprecated <code>s_cox_univariate</code> function has now deprecated badge.</li>
-</ul></div>
+</ul>
+</div>
 <div class="section level4">
-<h4 id="enhancements-0-7-8">Enhancements<a class="anchor" aria-label="anchor" href="#enhancements-0-7-8"></a></h4>
-<ul><li>Enhanced <code>g_lineplot</code> with table to automatically scale the table height and return a <code>ggplot</code> object.</li>
+<h4 id="enhancements-0-7-8">Enhancements<a class="anchor" aria-label="anchor" href="#enhancements-0-7-8"></a>
+</h4>
+<ul>
+<li>Enhanced <code>g_lineplot</code> with table to automatically scale the table height and return a <code>ggplot</code> object.</li>
 <li>Enhanced <code>g_ipp</code> with caption argument and adjust the position.</li>
 <li>Enhanced <code>prop_diff</code>, <code>tern</code> function and related functions to be able to apply a continuity correction in the Newcombe method.</li>
 <li>Enhanced <code>summarize_numeric_in_columns</code> and <code>summarize_variables</code> to allow factor/character summary and to be able to summarize the number of <code>BLQs</code> in <code>AVALC</code> from <code>ADPC</code> dataset.</li>
@@ -541,10 +788,13 @@ <h4 id="enhancements-0-7-8">Enhancements<a class="anchor" aria-label="anchor" hr
 <li>Added a <code>sum</code> option to <code>summarize_variables</code>.</li>
 <li>Use consistent color palette for plotting (<code>stream</code> by default).</li>
 <li>Enhanced <code>h_pkparam_sort</code> function with argument <code>key_var</code> to allow data with different column names.</li>
-</ul></div>
+</ul>
+</div>
 <div class="section level4">
-<h4 id="miscellaneous-0-7-8">Miscellaneous<a class="anchor" aria-label="anchor" href="#miscellaneous-0-7-8"></a></h4>
-<ul><li>Updated <code>test-table_aet02.R</code> variant 12.</li>
+<h4 id="miscellaneous-0-7-8">Miscellaneous<a class="anchor" aria-label="anchor" href="#miscellaneous-0-7-8"></a>
+</h4>
+<ul>
+<li>Updated <code>test-table_aet02.R</code> variant 12.</li>
 <li>Changed the <code>scda</code> data version to ‘2022-02-28’.</li>
 <li>Added a template to the <code>pkgdown</code> site.</li>
 <li>Removed package dependencies of <code>grDevices</code>, <code>stringr</code>, and <code>viridisLite</code>.</li>
@@ -552,132 +802,193 @@ <h4 id="miscellaneous-0-7-8">Miscellaneous<a class="anchor" aria-label="anchor"
 <li>Renaming <code>summarize_vars_numeric_in_cols</code> to <code>summarize_vars_in_cols</code>.</li>
 <li>Fixed a bug where points on the <code>g_lineplot</code> plot were not connected when missing values.</li>
 <li>Updated the package authors.</li>
-</ul></div>
+</ul>
+</div>
 </div>
     <div class="section level2">
-<h2 class="pkg-version" data-toc-text="0.7.7" id="tern-077">tern 0.7.7<a class="anchor" aria-label="anchor" href="#tern-077"></a></h2>
-<div class="section level4">
-<h4 id="breaking-changes-0-7-7">Breaking changes<a class="anchor" aria-label="anchor" href="#breaking-changes-0-7-7"></a></h4>
-<ul><li>Move MMRM into a separate package <code>tern.mmrm</code>.</li>
-</ul></div>
+<h2 class="pkg-version" data-toc-text="0.7.7" id="tern-077">tern 0.7.7<a class="anchor" aria-label="anchor" href="#tern-077"></a>
+</h2>
+<div class="section level4">
+<h4 id="breaking-changes-0-7-7">Breaking changes<a class="anchor" aria-label="anchor" href="#breaking-changes-0-7-7"></a>
+</h4>
+<ul>
+<li>Move MMRM into a separate package <code>tern.mmrm</code>.</li>
+</ul>
+</div>
 <div class="section level4">
-<h4 id="new-features-0-7-7">New features<a class="anchor" aria-label="anchor" href="#new-features-0-7-7"></a></h4>
-<ul><li>Added <code>h_pkparam_sort</code> to order <code>PK PARAM</code> value based on the order of the dataset generated by <code><a href="../reference/d_pkparam.html">d_pkparam()</a></code>.</li>
+<h4 id="new-features-0-7-7">New features<a class="anchor" aria-label="anchor" href="#new-features-0-7-7"></a>
+</h4>
+<ul>
+<li>Added <code>h_pkparam_sort</code> to order <code>PK PARAM</code> value based on the order of the dataset generated by <code><a href="../reference/d_pkparam.html">d_pkparam()</a></code>.</li>
 <li>Added <code>d_pkparam</code> to generate PK parameter map for sorting.</li>
-</ul></div>
+</ul>
+</div>
 <div class="section level4">
-<h4 id="enhancements-0-7-7">Enhancements<a class="anchor" aria-label="anchor" href="#enhancements-0-7-7"></a></h4>
-<ul><li>Changed the <code>nudge_y</code> argument of <code>h_g_ipp</code> to be dependent on the data, fixing an issue whereby the baseline labels were offset incorrectly.</li>
+<h4 id="enhancements-0-7-7">Enhancements<a class="anchor" aria-label="anchor" href="#enhancements-0-7-7"></a>
+</h4>
+<ul>
+<li>Changed the <code>nudge_y</code> argument of <code>h_g_ipp</code> to be dependent on the data, fixing an issue whereby the baseline labels were offset incorrectly.</li>
 <li>Enhanced <code>stat_mean_ci</code> and <code>s_summary.numeric</code> to calculate the geometric mean with its confidence intervals.</li>
-</ul></div>
+</ul>
+</div>
 <div class="section level4">
-<h4 id="miscellaneous-0-7-7">Miscellaneous<a class="anchor" aria-label="anchor" href="#miscellaneous-0-7-7"></a></h4>
-<ul><li>Updated dependencies and internal adjustments after the <code>rtables</code> package refactor.</li>
+<h4 id="miscellaneous-0-7-7">Miscellaneous<a class="anchor" aria-label="anchor" href="#miscellaneous-0-7-7"></a>
+</h4>
+<ul>
+<li>Updated dependencies and internal adjustments after the <code>rtables</code> package refactor.</li>
 <li>Removed <code>with_label</code>, <code>var_labels</code>, and <code>var_labels&lt;-</code> to resolve conflict with the <code>formatters</code> package, a new dependency.</li>
 <li>Added new “Introduction to <code>tern</code>” and “<code>tern</code> tabulation” vignettes.</li>
-</ul></div>
+</ul>
+</div>
 </div>
     <div class="section level2">
-<h2 class="pkg-version" data-toc-text="0.7.6" id="tern-076">tern 0.7.6<a class="anchor" aria-label="anchor" href="#tern-076"></a></h2>
+<h2 class="pkg-version" data-toc-text="0.7.6" id="tern-076">tern 0.7.6<a class="anchor" aria-label="anchor" href="#tern-076"></a>
+</h2>
 <div class="section level4">
-<h4 id="new-features-0-7-6">New features<a class="anchor" aria-label="anchor" href="#new-features-0-7-6"></a></h4>
-<ul><li>Added <code>h_map_for_count_abnormal</code> to create the map used in <code>trim_levels_to_map</code> split function by calling this helper function. It supports two methods: one with all observed mapping, one with at least low limit above zero and at least one non missing high limit.</li>
+<h4 id="new-features-0-7-6">New features<a class="anchor" aria-label="anchor" href="#new-features-0-7-6"></a>
+</h4>
+<ul>
+<li>Added <code>h_map_for_count_abnormal</code> to create the map used in <code>trim_levels_to_map</code> split function by calling this helper function. It supports two methods: one with all observed mapping, one with at least low limit above zero and at least one non missing high limit.</li>
 <li>Added <code>s_summary_numeric_in_cols</code> and <code>summarize_vars_numeric_in_cols</code> functions to generate summary statistics in columns, mainly used for PK datasets.</li>
 <li>Added five statistics to <code>s_summary.numeric</code> to use in <code>s_summary_numeric_in_cols</code>.</li>
-</ul></div>
+</ul>
+</div>
 <div class="section level4">
-<h4 id="enhancements-0-7-6">Enhancements<a class="anchor" aria-label="anchor" href="#enhancements-0-7-6"></a></h4>
-<ul><li>Enhanced functions <code>tabulate_survival_subgroups</code> and <code>tabulate_rsp_subgroups</code> (Survival Duration and Best Response analyses) to calculate <code>N</code>-s based on the records considered to create the model.</li>
+<h4 id="enhancements-0-7-6">Enhancements<a class="anchor" aria-label="anchor" href="#enhancements-0-7-6"></a>
+</h4>
+<ul>
+<li>Enhanced functions <code>tabulate_survival_subgroups</code> and <code>tabulate_rsp_subgroups</code> (Survival Duration and Best Response analyses) to calculate <code>N</code>-s based on the records considered to create the model.</li>
 <li>Enhanced the function <code>estimate_proportion</code> and related functions to be able to apply a continuity correction in the Wilson method.</li>
 <li>Refactored <code>count_abnormal_by_marked</code> and related statistics and formatting functions to use a more efficient layout with <code>.spl_context</code> argument used for determining denominators and with <code>trim_levels_to_map</code> split function under <code>split_rows_by</code> to show the desired levels in the table. This is a breaking change.</li>
 <li>Refactored <code>count_abnormal_by_worst_grade</code> and related statistics and formatting functions to use a more efficient layout with <code>.spl_context</code> argument used for determining denominators and with <code>trim_levels_to_map</code> split function under <code>split_rows_by</code> to show the desired levels in the table. This is a breaking change.</li>
 <li>Refactored <code>count_abnormal</code> function and related statistics and formatting functions to use a more efficient layout with <code>trim_levels_to_map</code> split function under <code>split_rows_by</code> to show the desired levels in the table. Also updated <code>abnormal</code> argument to be able to consider more than one level for each direction. This is a breaking change.</li>
 <li>Enhanced the function <code>estimate_incidence_rate</code> and related functions to consider the week as time unit for data input.</li>
-</ul></div>
+</ul>
+</div>
 <div class="section level4">
-<h4 id="bug-fixes-0-7-6">Bug fixes<a class="anchor" aria-label="anchor" href="#bug-fixes-0-7-6"></a></h4>
-<ul><li>Fixed bug in <code>assertthat</code> functions that output wrong data frame names and limited length of failure message outputs.</li>
-</ul></div>
+<h4 id="bug-fixes-0-7-6">Bug fixes<a class="anchor" aria-label="anchor" href="#bug-fixes-0-7-6"></a>
+</h4>
+<ul>
+<li>Fixed bug in <code>assertthat</code> functions that output wrong data frame names and limited length of failure message outputs.</li>
+</ul>
+</div>
 <div class="section level4">
-<h4 id="miscellaneous-0-7-6">Miscellaneous<a class="anchor" aria-label="anchor" href="#miscellaneous-0-7-6"></a></h4>
-<ul><li>Removed dependency on <code>utils.nest</code> by using the <code>checkmate</code> and <code>purrr</code> packages for validation and moved <code>get_free_cores</code> and <code>skip_if_too_deep</code> functions from <code>utils.nest</code> into <code>tern</code>.</li>
-</ul></div>
+<h4 id="miscellaneous-0-7-6">Miscellaneous<a class="anchor" aria-label="anchor" href="#miscellaneous-0-7-6"></a>
+</h4>
+<ul>
+<li>Removed dependency on <code>utils.nest</code> by using the <code>checkmate</code> and <code>purrr</code> packages for validation and moved <code>get_free_cores</code> and <code>skip_if_too_deep</code> functions from <code>utils.nest</code> into <code>tern</code>.</li>
+</ul>
+</div>
 </div>
     <div class="section level2">
-<h2 class="pkg-version" data-toc-text="0.7.5" id="tern-075">tern 0.7.5<a class="anchor" aria-label="anchor" href="#tern-075"></a></h2>
+<h2 class="pkg-version" data-toc-text="0.7.5" id="tern-075">tern 0.7.5<a class="anchor" aria-label="anchor" href="#tern-075"></a>
+</h2>
 <div class="section level4">
-<h4 id="new-features-0-7-5">New features<a class="anchor" aria-label="anchor" href="#new-features-0-7-5"></a></h4>
-<ul><li>Added functions to estimate continuous biomarker effects across subgroups for survival and binary response endpoints, used to produce corresponding forest plots, see <code>survival_biomarkers_subgroups</code> and <code>response_biomarkers_subgroups</code>.</li>
+<h4 id="new-features-0-7-5">New features<a class="anchor" aria-label="anchor" href="#new-features-0-7-5"></a>
+</h4>
+<ul>
+<li>Added functions to estimate continuous biomarker effects across subgroups for survival and binary response endpoints, used to produce corresponding forest plots, see <code>survival_biomarkers_subgroups</code> and <code>response_biomarkers_subgroups</code>.</li>
 <li>Added <code>g_lineplot</code> plot function, including new <code>h_format_row</code> helper function and <code>control_lineplot_vars</code> function. Removed <code>g_summary_by</code>.</li>
 <li>Added new safety helper function <code>h_stack_by_baskets</code> to stack events in SMQ and/or CQ basket flag in ADAE data set.</li>
-</ul></div>
+</ul>
+</div>
 <div class="section level4">
-<h4 id="enhancements-0-7-5">Enhancements<a class="anchor" aria-label="anchor" href="#enhancements-0-7-5"></a></h4>
-<ul><li>Added a couple of new statistics to <code>s_summary.numeric</code>. Added <code>names</code> attribute to each element of the final list returned by the <code>s_summary.numeric</code> function. Added <code>summary_formats</code> and <code>summary_labels</code> helper functions.</li>
+<h4 id="enhancements-0-7-5">Enhancements<a class="anchor" aria-label="anchor" href="#enhancements-0-7-5"></a>
+</h4>
+<ul>
+<li>Added a couple of new statistics to <code>s_summary.numeric</code>. Added <code>names</code> attribute to each element of the final list returned by the <code>s_summary.numeric</code> function. Added <code>summary_formats</code> and <code>summary_labels</code> helper functions.</li>
 <li>Added option to also convert logical variables to factor variables in <code>df_explicit_na</code>.</li>
 <li>Refactored <code>h_append_grade_groups</code> to improve its flexibility, robustness and clearness, and to make sure the result is ordering according to the order of <code>grade_groups</code>. Also, added <code>remove_single</code> argument which controls whether the elements of one-element grade groups are in the output or removed.</li>
 <li>Added <code>var_labels</code> and <code>show_labels</code> arguments to <code>count_occurrences</code> and <code>count_patients_with_flags</code> to allow for creation of a title row.</li>
 <li>Added <code>na_level</code> argument to <code>count_abnormal_by_baseline</code>.</li>
 <li>Updated <code>h_append_grade_groups</code> to no longer fill-in empty grade groups with zeros.</li>
-</ul></div>
+</ul>
+</div>
 <div class="section level4">
-<h4 id="bug-fixes-0-7-5">Bug Fixes<a class="anchor" aria-label="anchor" href="#bug-fixes-0-7-5"></a></h4>
-<ul><li>Fixed <code>prop_diff_cmh</code> to handle edge case of no FALSE (or TRUE) responses.</li>
+<h4 id="bug-fixes-0-7-5">Bug Fixes<a class="anchor" aria-label="anchor" href="#bug-fixes-0-7-5"></a>
+</h4>
+<ul>
+<li>Fixed <code>prop_diff_cmh</code> to handle edge case of no FALSE (or TRUE) responses.</li>
 <li>Enhanced <code>g_mmrm_diagnostic</code> to improve error handling when data is not amenable to the Locally Weighted Scatterplot Smoothing.</li>
 <li>Fixes in <code>g_km</code>:
-<ul><li>Plot can now display any combination of the annotation tables for number of patients at risk, median survival time, and Cox-PH summary.</li>
+<ul>
+<li>Plot can now display any combination of the annotation tables for number of patients at risk, median survival time, and Cox-PH summary.</li>
 <li>Function will return a warning instead of an error if the <code>arm</code> variable includes a single level and <code>annot_coxph = TRUE</code>.</li>
 <li>Lines in the plot now start at time 0 and probability 1.</li>
 <li>Category labels can include the equals sign.</li>
-</ul></li>
-</ul></div>
+</ul>
+</li>
+</ul>
+</div>
 <div class="section level4">
-<h4 id="miscellaneous-0-7-5">Miscellaneous<a class="anchor" aria-label="anchor" href="#miscellaneous-0-7-5"></a></h4>
-<ul><li>Fixed <code>day2month</code> and <code>month2day</code> to work with NA data.</li>
+<h4 id="miscellaneous-0-7-5">Miscellaneous<a class="anchor" aria-label="anchor" href="#miscellaneous-0-7-5"></a>
+</h4>
+<ul>
+<li>Fixed <code>day2month</code> and <code>month2day</code> to work with NA data.</li>
 <li>Added parameters for <code>stat_mean_ci</code> and <code>stat_median_ci</code> so that they may return different outputs.</li>
 <li>Added functionality in <code>h_row_counts</code> to handle analysis rows with <code>NULL</code> cells.</li>
 <li>Updated <code>LICENCE</code> and <code>README</code> with new package references.</li>
 <li>Added <code>error_on_lint: TRUE</code> to <code>.lintr</code>.</li>
-</ul></div>
+</ul>
+</div>
 </div>
     <div class="section level2">
-<h2 class="pkg-version" data-toc-text="0.7.4" id="tern-074">tern 0.7.4<a class="anchor" aria-label="anchor" href="#tern-074"></a></h2>
-<div class="section level4">
-<h4 id="new-features-0-7-4">New features<a class="anchor" aria-label="anchor" href="#new-features-0-7-4"></a></h4>
-<ul><li>Added new safety layout functions:
-<ul><li>
+<h2 class="pkg-version" data-toc-text="0.7.4" id="tern-074">tern 0.7.4<a class="anchor" aria-label="anchor" href="#tern-074"></a>
+</h2>
+<div class="section level4">
+<h4 id="new-features-0-7-4">New features<a class="anchor" aria-label="anchor" href="#new-features-0-7-4"></a>
+</h4>
+<ul>
+<li>Added new safety layout functions:
+<ul>
+<li>
 <code>count_abnormal_by_marked</code> tabulates marked laboratory abnormalities.</li>
 <li>
 <code>summarize_patients_exposure_in_cols</code> tabulates patient counts and sum of exposure across all patients.</li>
-</ul></li>
-</ul></div>
+</ul>
+</li>
+</ul>
+</div>
 <div class="section level4">
-<h4 id="enhancements-0-7-4">Enhancements<a class="anchor" aria-label="anchor" href="#enhancements-0-7-4"></a></h4>
-<ul><li>Enhanced MMRM-related functions for fitting models without <code>arm</code> variable.</li>
+<h4 id="enhancements-0-7-4">Enhancements<a class="anchor" aria-label="anchor" href="#enhancements-0-7-4"></a>
+</h4>
+<ul>
+<li>Enhanced MMRM-related functions for fitting models without <code>arm</code> variable.</li>
 <li>Updated <code>cox_regression</code> to work without covariates. Also in case of interaction model summary, p-values for main effect coefficients are no longer displayed.</li>
 <li>Descriptive statistics returned by <code>summarize_vars</code> now include quantiles. <code>summarize_vars</code> now accepts the control function <code>control_summarize_vars</code> to specify details about confidence level for mean and median and quantile details. The <code>control</code> argument replaces <code>conf_level</code>.</li>
 <li>Added <code>var_labels</code> and <code>show_labels</code> arguments to <code>count_occurrences_by_grade</code>.</li>
 <li>Changed <code>indent</code> argument in <code>append_varlabels</code> to accept non-negative integer to represent the indent space defined by user. Previous calls with Boolean <code>indent</code> will do an integer conversion and produce a warning.</li>
-</ul></div>
+</ul>
+</div>
 <div class="section level4">
-<h4 id="bug-fixes-0-7-4">Bug Fixes<a class="anchor" aria-label="anchor" href="#bug-fixes-0-7-4"></a></h4>
-<ul><li>Corrected <code>tabulate_survival_subgroups</code> and related survival forest plot functions to use total number of events, instead of observations, as default for scaling the symbol sizes in the plot. (The user might still use total number of observations manually if they wish to do so.)</li>
+<h4 id="bug-fixes-0-7-4">Bug Fixes<a class="anchor" aria-label="anchor" href="#bug-fixes-0-7-4"></a>
+</h4>
+<ul>
+<li>Corrected <code>tabulate_survival_subgroups</code> and related survival forest plot functions to use total number of events, instead of observations, as default for scaling the symbol sizes in the plot. (The user might still use total number of observations manually if they wish to do so.)</li>
 <li>Helper function <code>h_adsl_adlb_merge_using_worst_flag</code> will now impute <code>BTOXGR</code> for missing visits.</li>
-</ul></div>
+</ul>
+</div>
 <div class="section level4">
-<h4 id="miscellaneous-0-7-4">Miscellaneous<a class="anchor" aria-label="anchor" href="#miscellaneous-0-7-4"></a></h4>
-<ul><li>Deleted <code>count_abnormal_by_worst_grade_by_baseline</code> and its related statistic and analysis functions as a simpler design will create lab abnormality tables.</li>
+<h4 id="miscellaneous-0-7-4">Miscellaneous<a class="anchor" aria-label="anchor" href="#miscellaneous-0-7-4"></a>
+</h4>
+<ul>
+<li>Deleted <code>count_abnormal_by_worst_grade_by_baseline</code> and its related statistic and analysis functions as a simpler design will create lab abnormality tables.</li>
 <li>Switched data in examples to use <code>scda</code> instead of <code>random.cdisc.data</code> package.</li>
-</ul></div>
+</ul>
+</div>
 </div>
     <div class="section level2">
-<h2 class="pkg-version" data-toc-text="0.7.3" id="tern-073">tern 0.7.3<a class="anchor" aria-label="anchor" href="#tern-073"></a></h2>
+<h2 class="pkg-version" data-toc-text="0.7.3" id="tern-073">tern 0.7.3<a class="anchor" aria-label="anchor" href="#tern-073"></a>
+</h2>
 <div class="section level4">
-<h4 id="new-features-0-7-3">New Features<a class="anchor" aria-label="anchor" href="#new-features-0-7-3"></a></h4>
-<ul><li>Added Subgroup Treatment Effect Pattern (STEP) model fitting functions <code>fit_rsp_step</code> and <code>fit_survival_step</code>, the corresponding tidy method <code>tidy.step</code> as well as the graph function <code>g_step</code>.</li>
+<h4 id="new-features-0-7-3">New Features<a class="anchor" aria-label="anchor" href="#new-features-0-7-3"></a>
+</h4>
+<ul>
+<li>Added Subgroup Treatment Effect Pattern (STEP) model fitting functions <code>fit_rsp_step</code> and <code>fit_survival_step</code>, the corresponding tidy method <code>tidy.step</code> as well as the graph function <code>g_step</code>.</li>
 <li>Added new layout function <code>compare_vars</code> which compares variables of different types between columns and produces a p-value for the comparison to the reference column. Function built on top of the <code>summarize_vars</code> functionality.</li>
 <li>Added utility functions:
-<ul><li>
+<ul>
+<li>
 <code>cut_quantile_bins</code> cuts a numeric vector into quantile bins.</li>
 <li>
 <code>fct_collapse_only</code> collapses levels of a factor and keeps those in the order provided.</li>
@@ -685,45 +996,63 @@ <h4 id="new-features-0-7-3">New Features<a class="anchor" aria-label="anchor" hr
 <code>fct_explicit_na_if</code> inserts explicit missings in a factor based on a condition.</li>
 <li>
 <code>range_noinf</code> is a kind of a wrapper function of <code><a href="https://rdrr.io/r/base/range.html" class="external-link">base::range</a></code>. It returns <code>c(NA, NA)</code> instead of <code>c(-Inf, Inf)</code> for zero-length data.</li>
-</ul></li>
-</ul></div>
+</ul>
+</li>
+</ul>
+</div>
 <div class="section level4">
-<h4 id="enhancements-0-7-3">Enhancements<a class="anchor" aria-label="anchor" href="#enhancements-0-7-3"></a></h4>
-<ul><li>Cox regression via <code>fit_coxreg_univar</code> and <code>fit_coxreg_multivar</code> is now also possible without treatment arm. In the univariate case this means that it fits separate univariate models for the provided covariates and tabulation of corresponding effect estimates can later occur.</li>
+<h4 id="enhancements-0-7-3">Enhancements<a class="anchor" aria-label="anchor" href="#enhancements-0-7-3"></a>
+</h4>
+<ul>
+<li>Cox regression via <code>fit_coxreg_univar</code> and <code>fit_coxreg_multivar</code> is now also possible without treatment arm. In the univariate case this means that it fits separate univariate models for the provided covariates and tabulation of corresponding effect estimates can later occur.</li>
 <li>Added <code>fraction</code> in result returned by <code>s_count_occurrences</code>. It contains a list of numerators and denominators with one element per occurrence.</li>
 <li>Updated <code>sum_num_patients</code> and <code>count_occurrences</code> for the result <code>unique</code> and <code>count_fraction</code> to return (0, 0) when input is empty.</li>
 <li>Added a new argument <code>groups_lists</code> to <code>extract_survival_subgroups</code>, <code>extract_rsp_subgroups</code> and associated helper functions which allows to group factor levels of subgroup variables into manually defined groups, enhancing the flexibility of the resulting forest graphs.</li>
 <li>Forest graph function <code>g_forest</code> now extracts default arguments from attributes of the input table produced by <code>tabulate_rsp_subgroups</code> and <code>tabulate_survival_subgroups</code> so that the user does not have to do this manually anymore.</li>
 <li>In <code>g_km</code>:
-<ul><li>Remove arm variable name from arm labels in plot legend and annotation tables.</li>
+<ul>
+<li>Remove arm variable name from arm labels in plot legend and annotation tables.</li>
 <li>Show symbol used to mark censored cases and match order of arm variable factor levels in the legend.</li>
 <li>Display hazard ratio and its confidence interval to two decimal places.</li>
 <li>Updated default position of hazard ratio table to stay on the left bottom corner but above x-axis.</li>
 <li>Use arm value as strata name in when treatment arm variable has a single level.</li>
-</ul></li>
+</ul>
+</li>
 <li>Updated <code>s_surv_time</code> function to use a newly created function <code>range_noinf</code> instead of <code><a href="https://rdrr.io/r/base/range.html" class="external-link">base::range</a></code>.</li>
 <li>New argument <code>no_fillin_visits</code> added to <code>h_adsl_adlb_merge_using_worst_flag</code> to specify excluded visits from the post-baseline worst toxicity grade output. Improved <code>h_adsl_adlb_merge_using_worst_flag</code> to include variables shared between <code>adsl</code> and <code>adlb</code>, along with <code>PARAM</code>, <code>PARAMCD</code>, <code>ATOXGR</code>, <code>BTOXGR</code> and optionally <code>AVISIT</code>, <code>AVISITN</code> when <code>by_visit = TRUE</code>. Prior output contained <code>USUBJID</code>, <code>ARMCD</code>, <code>PARAMCD</code>, <code>ATOXGR</code>, and <code>BTOXGR</code>.</li>
-</ul></div>
+</ul>
+</div>
 <div class="section level4">
-<h4 id="bug-fixes-0-7-3">Bug Fixes<a class="anchor" aria-label="anchor" href="#bug-fixes-0-7-3"></a></h4>
-<ul><li>Fix bug in <code>s_surv_timepoint</code> for cases when there are zero patients at risk.</li>
+<h4 id="bug-fixes-0-7-3">Bug Fixes<a class="anchor" aria-label="anchor" href="#bug-fixes-0-7-3"></a>
+</h4>
+<ul>
+<li>Fix bug in <code>s_surv_timepoint</code> for cases when there are zero patients at risk.</li>
 <li>Modified <code>stat_median_ci</code> function so that when passing empty var with empty name, no <code>row names contain missing values</code> error would show.</li>
-</ul></div>
+</ul>
+</div>
 <div class="section level4">
-<h4 id="miscellaneous-0-7-3">Miscellaneous<a class="anchor" aria-label="anchor" href="#miscellaneous-0-7-3"></a></h4>
-<ul><li>Deprecated <code>s_cox_univariate</code> function, use <code>fit_coxreg_univar</code> function instead.</li>
+<h4 id="miscellaneous-0-7-3">Miscellaneous<a class="anchor" aria-label="anchor" href="#miscellaneous-0-7-3"></a>
+</h4>
+<ul>
+<li>Deprecated <code>s_cox_univariate</code> function, use <code>fit_coxreg_univar</code> function instead.</li>
 <li>Updated default formats of <code>hr</code> and <code>hr_ci</code> in <code>a_coxph_pairwise</code> and median in <code>s_surv_time</code> to align with STREAM.</li>
 <li>Updated the pre-processing code in the files <code>test-table_ttet01.R</code> and <code>test-table_dort01.R</code> to make sure the analysis variable <code>EVNT1</code> has both levels of the factor defined.</li>
 <li>Improved error message when number of levels in a factor variable in a data frame is not as expected.</li>
-</ul></div>
+</ul>
+</div>
 </div>
     <div class="section level2">
-<h2 class="pkg-version" data-toc-text="0.7.2" id="tern-072">tern 0.7.2<a class="anchor" aria-label="anchor" href="#tern-072"></a></h2>
-<ul><li>Fixed column label internal test errors.</li>
-</ul></div>
+<h2 class="pkg-version" data-toc-text="0.7.2" id="tern-072">tern 0.7.2<a class="anchor" aria-label="anchor" href="#tern-072"></a>
+</h2>
+<ul>
+<li>Fixed column label internal test errors.</li>
+</ul>
+</div>
     <div class="section level2">
-<h2 class="pkg-version" data-toc-text="0.7.1" id="tern-071">tern 0.7.1<a class="anchor" aria-label="anchor" href="#tern-071"></a></h2>
-<ul><li>New argument <code>position_surv_med</code> added to <code>g_km</code> to move position of the annotation table with median survival times.</li>
+<h2 class="pkg-version" data-toc-text="0.7.1" id="tern-071">tern 0.7.1<a class="anchor" aria-label="anchor" href="#tern-071"></a>
+</h2>
+<ul>
+<li>New argument <code>position_surv_med</code> added to <code>g_km</code> to move position of the annotation table with median survival times.</li>
 <li>Fixed bug in <code>g_km</code> related to the ignored arguments <code>pch</code> and <code>size</code> which were not passed on to helper function <code>h_ggkm</code>.</li>
 <li>Updated <code>xticks</code> and <code>max_time</code> arguments in <code>g_km</code> for greater functionality. <code>max_time</code> added as an argument in <code>h_xticks</code> to allow this.</li>
 <li>Fixed bug in <code>prop_diff_cmh</code> that led to <code>NaN</code> weighted proportion difference estimates and missing confidence intervals. Before this change, when including no patients from one treatment arm for at least one stratum the estimation did not lead to numeric results.</li>
@@ -736,18 +1065,25 @@ <h2 class="pkg-version" data-toc-text="0.7.1" id="tern-071">tern 0.7.1<a class="
 <li>Fixed bug in <code>get_mmrm_lsmeans</code> which did not allow MMRM analysis of more than 3000 observations.</li>
 <li>Updated <code>stat_mean_ci</code> and <code>stat_median_ci</code> to handle edge cases with number of elements in input series equal to 1. For such cases, <code>NA_real_</code> is now returned, instead of <code>NA</code> or <code>+/-Inf</code> for confidence interval (CI) estimates.</li>
 <li>Rename <code>n_lim</code> argument of <code>stat_mean_ci</code> to <code>n_min</code> to better reflect its desired meaning.</li>
-</ul></div>
+</ul>
+</div>
     <div class="section level2">
-<h2 class="pkg-version" data-toc-text="0.7.0" id="tern-070">tern 0.7.0<a class="anchor" aria-label="anchor" href="#tern-070"></a></h2>
+<h2 class="pkg-version" data-toc-text="0.7.0" id="tern-070">tern 0.7.0<a class="anchor" aria-label="anchor" href="#tern-070"></a>
+</h2>
 <p>This version of <code>tern</code> introduces a major rewriting of <code>tern</code> due to the change to layout based tabulation in <code>rtables</code>. <code>tern</code> now does not build tables directly anymore, instead it provides analysis functions to build tables, see the examples. * Counting patients with abnormal values post-baseline with <code>count_abnormal</code>. * Counting patients with graded abnormal values with <code>count_abnormal_by_worst_grade</code>. * Counting patients with abnormal values by baseline status with <code>count_abnormal_by_baseline</code>. * Counting patients with missed doses with <code>s_count_missed_doses</code> and <code>count_missed_doses</code>. * Counting patients with event flags with <code>count_patients_with_event</code> and <code>count_patients_with_flags</code>. * Summarizing variables with <code>summarize_vars</code> (supports numeric, factor, character and logical variables). Note that factors need to have <code>NA</code>s converted to <code>na_level</code> before use. * Summarizing change from baseline with <code>summarize_change</code>. * Summarizing variables in columns with <code>summarize_colvars</code>. * Estimating difference for responder proportions with <code>estimate_proportion_diff</code>. * Estimating difference for Odds Ratio with <code>estimate_odds_ratio</code>. * Testing the difference in responder proportions with <code>test_proportion_diff</code>. * Estimating the responder proportion for the level of a factor with <code>estimate_multinomial_response</code>. * Fitting and tabulating the results of Cox regressions with <code>fit_coxreg_univar</code>, <code>fit_coxreg_multivar</code> and <code>summarize_coxreg</code>, respectively. * Pruning occurrence tables (or tables with counts and fractions) with flexible rules, see <code><a href="../reference/prune_occurrences.html">?prune_occurrences</a></code> for details. * Sorting occurrence tables using different options, see <code><a href="../reference/score_occurrences.html">?score_occurrences</a></code> for details. * Fitting and tabulating MMRM models with <code>fit_mmrm</code> and <code>as.rtable</code> and <code>summarize_lsmeans</code>, see <code>?tabulate_mmrm</code> for details. * Counting the number of unique and non-unique patients with <code>summarize_num_patients</code>. * Counting occurrences with <code>count_occurrences</code>. * Counting occurrences by grade with <code>summarize_occurrences_by_grade</code> and <code>count_occurrences_by_grade</code>. * Counting patients and events in columns with <code>summarize_patients_events_in_cols</code>. * Tabulating the binary outcome response by subgroup with <code>extract_rsp_subgroups</code> and <code>tabulate_rsp_subgroups</code>. * Tabulating the survival duration by subgroup with <code>extract_survival_subgroups</code> and <code>tabulate_survival_subgroups</code>.</p>
 </div>
     <div class="section level2">
-<h2 class="pkg-version" data-toc-text="0.6.9" id="tern-069">tern 0.6.9<a class="anchor" aria-label="anchor" href="#tern-069"></a></h2>
-<ul><li>Removing not used imports.</li>
-</ul></div>
+<h2 class="pkg-version" data-toc-text="0.6.9" id="tern-069">tern 0.6.9<a class="anchor" aria-label="anchor" href="#tern-069"></a>
+</h2>
+<ul>
+<li>Removing not used imports.</li>
+</ul>
+</div>
     <div class="section level2">
-<h2 class="pkg-version" data-toc-text="0.6.8" id="tern-068">tern 0.6.8<a class="anchor" aria-label="anchor" href="#tern-068"></a></h2>
-<ul><li>Improved handling of missing data in aggregation functions: <code>a_mean_sd</code>, <code>a_median</code>, <code>a_n_true_and_freq</code>, <code>a_count</code>, <code>a_q1q3</code>, <code>a_iqr</code>, <code>a_range</code>.</li>
+<h2 class="pkg-version" data-toc-text="0.6.8" id="tern-068">tern 0.6.8<a class="anchor" aria-label="anchor" href="#tern-068"></a>
+</h2>
+<ul>
+<li>Improved handling of missing data in aggregation functions: <code>a_mean_sd</code>, <code>a_median</code>, <code>a_n_true_and_freq</code>, <code>a_count</code>, <code>a_q1q3</code>, <code>a_iqr</code>, <code>a_range</code>.</li>
 <li>New default p-value method in <code>s_test_proportion_diff</code>: Chi-Squared Test with Schouten Correction.</li>
 <li>Add new function <code>t_contingency</code> for contingency tables.</li>
 <li>Renamed the class <code>splitText</code> to <code>dynamicSplitText</code> to resolve the name conflict with the package <code>ggpubr</code>.</li>
@@ -763,10 +1099,13 @@ <h2 class="pkg-version" data-toc-text="0.6.8" id="tern-068">tern 0.6.8<a class="
 <li>Add new MMRM analysis function <code>s_mmrm</code>, as well as corresponding table functions <code>t_mmrm_lsmeans</code>, <code>t_mmrm_cov</code>, <code>t_mmrm_diagnostic</code>, <code>t_mmrm_fixed</code>, and plot functions <code>g_mmrm_lsmeans</code>, <code>g_mmrm_diagnostic</code>. The results of these match SAS results (up to numeric precision).</li>
 <li>Deprecated old MMRM functions <code>a_mmrm</code> and <code>t_mmrm</code> (they give a deprecation warning but still work) to remove in the next release. The reason is that the results of these functions don’t match SAS results.</li>
 <li>Fix bug in <code>g_km</code> related to numbers in patients at risk table to correct numbers for integer time-to-event variable inputs.</li>
-</ul></div>
+</ul>
+</div>
     <div class="section level2">
-<h2 class="pkg-version" data-toc-text="0.6.7" id="tern-067">tern 0.6.7<a class="anchor" aria-label="anchor" href="#tern-067"></a></h2>
-<ul><li>For functions with <code>row_by</code> argument, inputs no longer require use of <code>nested_by</code>.</li>
+<h2 class="pkg-version" data-toc-text="0.6.7" id="tern-067">tern 0.6.7<a class="anchor" aria-label="anchor" href="#tern-067"></a>
+</h2>
+<ul>
+<li>For functions with <code>row_by</code> argument, inputs no longer require use of <code>nested_by</code>.</li>
 <li>Add <code>stat_mean_ci</code> and <code>stat_median_ci</code> for error bars in <code>ggplot2</code>.</li>
 <li>Add new tern function <code>t_coxreg</code> as single interface for diverse cox regression types.</li>
 <li>Add compound table for binary endpoint: <code>t_binary_endpoint</code> and elementary functions: <code>t_el_proportion</code>, <code>t_el_proportion_diff</code> and <code>t_el_test_proportion_diff</code>. The supporting summary functions added are: <code>s_proportion</code>, <code>s_adj_proportion_diff</code>, <code>s_proportion_diff</code> and <code>s_test_proportion_diff</code>.</li>
@@ -778,14 +1117,20 @@ <h2 class="pkg-version" data-toc-text="0.6.7" id="tern-067">tern 0.6.7<a class="
 <li>Rename <code>t_coxph</code> to <code>t_coxph_pairwise</code> to reflect the model process, add details in documentation.</li>
 <li>Remove <code>test.nest</code> dependency.</li>
 <li>Keep column labels when splitting data into tree.</li>
-</ul></div>
+</ul>
+</div>
     <div class="section level2">
-<h2 class="pkg-version" data-toc-text="0.6.6" id="tern-066">tern 0.6.6<a class="anchor" aria-label="anchor" href="#tern-066"></a></h2>
-<ul><li>Remove <code>test.nest</code> dependency.</li>
-</ul></div>
+<h2 class="pkg-version" data-toc-text="0.6.6" id="tern-066">tern 0.6.6<a class="anchor" aria-label="anchor" href="#tern-066"></a>
+</h2>
+<ul>
+<li>Remove <code>test.nest</code> dependency.</li>
+</ul>
+</div>
     <div class="section level2">
-<h2 class="pkg-version" data-toc-text="0.6.5" id="tern-065">tern 0.6.5<a class="anchor" aria-label="anchor" href="#tern-065"></a></h2>
-<ul><li>Change default option for denominator to be <code>N</code> in <code>t_summary</code>.</li>
+<h2 class="pkg-version" data-toc-text="0.6.5" id="tern-065">tern 0.6.5<a class="anchor" aria-label="anchor" href="#tern-065"></a>
+</h2>
+<ul>
+<li>Change default option for denominator to be <code>N</code> in <code>t_summary</code>.</li>
 <li>Fix IQR bug: IQR as Q3 minus Q1.</li>
 <li>Add new function <code>t_logistic</code> for multi-variable logistic regression table.</li>
 <li>Add new function <code>df_explicit_na</code> to replace <code>NA</code> by explicit values.</li>
@@ -800,26 +1145,37 @@ <h2 class="pkg-version" data-toc-text="0.6.5" id="tern-065">tern 0.6.5<a class="
 <li>Updated <code>t_count_unique</code> to create analysis subsets, added <code>t_el_count_unique</code> for vectors.</li>
 <li>Fixed bug in <code>t_events_term_id</code> so that table sort order is by decreasing frequency instead of alphabetical.</li>
 <li>Added function <code>color_palette</code> and a new nest color palette.</li>
-</ul></div>
+</ul>
+</div>
     <div class="section level2">
-<h2 class="pkg-version" data-toc-text="0.6.4" id="tern-064">tern 0.6.4<a class="anchor" aria-label="anchor" href="#tern-064"></a></h2>
-<ul><li>Refactored after renaming functions in <code>utils.nest</code>.</li>
+<h2 class="pkg-version" data-toc-text="0.6.4" id="tern-064">tern 0.6.4<a class="anchor" aria-label="anchor" href="#tern-064"></a>
+</h2>
+<ul>
+<li>Refactored after renaming functions in <code>utils.nest</code>.</li>
 <li>Added <code>event_type</code> argument to <code>t_events_per_term_grade_id</code>.</li>
 <li>Added one/two-arm t-test functions.</li>
 <li>Improvements in <code>t_summary_by</code>.</li>
 <li>Internal code refactoring.</li>
-</ul></div>
+</ul>
+</div>
     <div class="section level2">
-<h2 class="pkg-version" data-toc-text="0.6.3" id="tern-063">tern 0.6.3<a class="anchor" aria-label="anchor" href="#tern-063"></a></h2>
-<ul><li>Added <code>node</code> S4 class to create trees:
-<ul><li>For all related tree functions see the reference under trees.</li>
-</ul></li>
+<h2 class="pkg-version" data-toc-text="0.6.3" id="tern-063">tern 0.6.3<a class="anchor" aria-label="anchor" href="#tern-063"></a>
+</h2>
+<ul>
+<li>Added <code>node</code> S4 class to create trees:
+<ul>
+<li>For all related tree functions see the reference under trees.</li>
+</ul>
+</li>
 <li>Removed functions:
-<ul><li>Moved all the label functions to <code>rtables</code>.</li>
+<ul>
+<li>Moved all the label functions to <code>rtables</code>.</li>
 <li>Deleted <code>keys</code> and <code>keys&lt;-</code> functions.</li>
-</ul></li>
+</ul>
+</li>
 <li>New helper functions:
-<ul><li>Exported <code>tabulate_pairwise</code>.</li>
+<ul>
+<li>Exported <code>tabulate_pairwise</code>.</li>
 <li>
 <code>get_N</code>, <code>col_N_add_total</code>, <code>check_id</code>.</li>
 <li>
@@ -828,51 +1184,75 @@ <h2 class="pkg-version" data-toc-text="0.6.3" id="tern-063">tern 0.6.3<a class="
 <code>as_factor_keep_attributes</code>.</li>
 <li>
 <code>r_by</code>.</li>
-</ul></li>
+</ul>
+</li>
 <li>New TLGs:
-<ul><li>Disposition elementary table <code>t_el_disposition</code>.</li>
+<ul>
+<li>Disposition elementary table <code>t_el_disposition</code>.</li>
 <li>
 <code>t_el_forest_tte</code>, <code>t_el_forest_rsp</code>.</li>
-</ul></li>
+</ul>
+</li>
 <li>Changed Arguments:
-<ul><li>All compound tables:
-<ul><li>Added <code>table_tree</code> argument which returns a <code>node</code> object.</li>
-</ul></li>
+<ul>
+<li>All compound tables:
+<ul>
+<li>Added <code>table_tree</code> argument which returns a <code>node</code> object.</li>
+</ul>
+</li>
 <li>
 <code>t_summary.numeric</code>:
-<ul><li>Added <code>f_numeric</code> to choose which statistics to calculate.</li>
-</ul></li>
+<ul>
+<li>Added <code>f_numeric</code> to choose which statistics to calculate.</li>
+</ul>
+</li>
 <li>
 <code>t_summary.factor</code>:
-<ul><li>
+<ul>
+<li>
 <code>denominator</code> now also allows for <code>omit</code> if wanting to omit percentages.</li>
-</ul></li>
+</ul>
+</li>
 <li>
 <code>t_summary_by</code>:
-<ul><li>Renamed <code>by</code> to <code>row_by</code>.</li>
-</ul></li>
+<ul>
+<li>Renamed <code>by</code> to <code>row_by</code>.</li>
+</ul>
+</li>
 <li>
 <code>t_forest_rsp</code>, <code>t_forest_tte</code>:
-<ul><li>Changed functionality of <code>group_data</code> using <code>row_by_list</code>.</li>
+<ul>
+<li>Changed functionality of <code>group_data</code> using <code>row_by_list</code>.</li>
 <li>Removed <code>na_omit_group</code>.</li>
-</ul></li>
+</ul>
+</li>
 <li>
 <code>t_count_unique</code>:
-<ul><li>Removed <code>indent</code> argument, use the <code>indent</code> function in <code>rtables</code>. instead</li>
-</ul></li>
-</ul></li>
-</ul></div>
+<ul>
+<li>Removed <code>indent</code> argument, use the <code>indent</code> function in <code>rtables</code>. instead</li>
+</ul>
+</li>
+</ul>
+</li>
+</ul>
+</div>
     <div class="section level2">
-<h2 class="pkg-version" data-toc-text="0.6.2" id="tern-062">tern 0.6.2<a class="anchor" aria-label="anchor" href="#tern-062"></a></h2>
-<ul><li>Use cached data from <code>random.cdisc.data</code> to speed up testing.</li>
+<h2 class="pkg-version" data-toc-text="0.6.2" id="tern-062">tern 0.6.2<a class="anchor" aria-label="anchor" href="#tern-062"></a>
+</h2>
+<ul>
+<li>Use cached data from <code>random.cdisc.data</code> to speed up testing.</li>
 <li>Added <code>t_summary.Date</code> method.</li>
 <li>Added <code>save_join</code>.</li>
-</ul></div>
+</ul>
+</div>
     <div class="section level2">
-<h2 class="pkg-version" data-toc-text="0.6.1" id="tern-061">tern 0.6.1<a class="anchor" aria-label="anchor" href="#tern-061"></a></h2>
-<ul><li>Fixed colors in Kaplan-Meier Plot</li>
+<h2 class="pkg-version" data-toc-text="0.6.1" id="tern-061">tern 0.6.1<a class="anchor" aria-label="anchor" href="#tern-061"></a>
+</h2>
+<ul>
+<li>Fixed colors in Kaplan-Meier Plot</li>
 <li>Refactor of all functions to pass <code>test.nest</code> tests:
-<ul><li>Changed <code>width_row.names</code> argument of <code>g_forest</code> function into <code>width_row_names</code>.</li>
+<ul>
+<li>Changed <code>width_row.names</code> argument of <code>g_forest</code> function into <code>width_row_names</code>.</li>
 <li>Changed <code>censor.show</code> argument of <code>g_km</code> function into <code>censor_show</code>.</li>
 <li>Changed <code>col.legend.title</code> argument of <code>g_waterfall</code> function into <code>col_legend_title</code>.</li>
 <li>Changed <code>na.rm</code> argument of <code>t_count_unique</code> function into <code>na_rm</code>.</li>
@@ -883,21 +1263,29 @@ <h2 class="pkg-version" data-toc-text="0.6.1" id="tern-061">tern 0.6.1<a class="
 <li>Rename <code>splotTextGrob</code> into <code>split_text_grob</code>.</li>
 <li>Fix examples.</li>
 <li>Refactor of internal functions code.</li>
-</ul></li>
-</ul></div>
+</ul>
+</li>
+</ul>
+</div>
     <div class="section level2">
-<h2 class="pkg-version" data-toc-text="0.6.0" id="tern-060">tern 0.6.0<a class="anchor" aria-label="anchor" href="#tern-060"></a></h2>
-<ul><li>Removed functions <code>addTable</code>, <code>t_summarize_by_visit</code>, <code>t_summarize_variables</code>.</li>
+<h2 class="pkg-version" data-toc-text="0.6.0" id="tern-060">tern 0.6.0<a class="anchor" aria-label="anchor" href="#tern-060"></a>
+</h2>
+<ul>
+<li>Removed functions <code>addTable</code>, <code>t_summarize_by_visit</code>, <code>t_summarize_variables</code>.</li>
 <li>Added <code>t_summary_by</code> function.</li>
 <li>Refactor of <code>g_km</code> function, renamed <code>kmGrob</code> into <code>kmCurveGrob</code>.</li>
 <li>Refactor <code>t_events_*</code> family of functions.</li>
 <li>Updated examples.</li>
-</ul></div>
+</ul>
+</div>
     <div class="section level2">
-<h2 class="pkg-version" data-toc-text="0.5.0.3" id="tern-0503">tern 0.5.0.3<a class="anchor" aria-label="anchor" href="#tern-0503"></a></h2>
+<h2 class="pkg-version" data-toc-text="0.5.0.3" id="tern-0503">tern 0.5.0.3<a class="anchor" aria-label="anchor" href="#tern-0503"></a>
+</h2>
 <div class="section level5">
-<h5 id="new-tlgs-0-5-0-3">New TLGs<a class="anchor" aria-label="anchor" href="#new-tlgs-0-5-0-3"></a></h5>
-<ul><li>
+<h5 id="new-tlgs-0-5-0-3">New TLGs<a class="anchor" aria-label="anchor" href="#new-tlgs-0-5-0-3"></a>
+</h5>
+<ul>
+<li>
 <code>t_summary</code> and methods for <code>data.frame</code>, <code>numeric</code>, <code>logical</code>, <code>character</code>, <code>factor</code>, and <code>Date</code> objects.</li>
 <li>
 <code>t_events_per_term_id</code>, <code>t_events_per_term_grade_id</code>: Adverse Events &amp; Concomitant Treatment Tables.</li>
@@ -905,17 +1293,23 @@ <h5 id="new-tlgs-0-5-0-3">New TLGs<a class="anchor" aria-label="anchor" href="#n
 <code>t_max_grade_per_id</code>, <code>t_count_unique</code>, <code>t_events_summary</code> elementary tables used for the Adverse Events &amp; Concomitant Treatment Tables.</li>
 <li>
 <code>g_waterfall</code>: Horizontal Waterfall Plot.</li>
-</ul></div>
+</ul>
+</div>
 <div class="section level5">
-<h5 id="new-helper-functions-0-5-0-3">New Helper Functions<a class="anchor" aria-label="anchor" href="#new-helper-functions-0-5-0-3"></a></h5>
-<ul><li>
+<h5 id="new-helper-functions-0-5-0-3">New Helper Functions<a class="anchor" aria-label="anchor" href="#new-helper-functions-0-5-0-3"></a>
+</h5>
+<ul>
+<li>
 <code>decorate_grob</code>, <code>decorate_grob_set</code>, <code>decorate_grob_factory</code>, <code>splitTextGrob</code>.</li>
 <li>
 <code>stack_grobs</code>, <code>arrange_grobs</code>, <code>draw_grob</code>.</li>
-</ul></div>
+</ul>
+</div>
 <div class="section level5">
-<h5 id="tlg-changes-0-5-0-3">TLG changes<a class="anchor" aria-label="anchor" href="#tlg-changes-0-5-0-3"></a></h5>
-<ul><li>
+<h5 id="tlg-changes-0-5-0-3">TLG changes<a class="anchor" aria-label="anchor" href="#tlg-changes-0-5-0-3"></a>
+</h5>
+<ul>
+<li>
 <code>t_tte</code> now shows two rows with ranges for event and censored times, respectively.</li>
 <li>
 <code>g_km</code> works with one arm <code>survfit</code> objects.</li>
@@ -924,29 +1318,38 @@ <h5 id="tlg-changes-0-5-0-3">TLG changes<a class="anchor" aria-label="anchor" hr
 <code>t_summarise_variables</code> uses now <code>n</code> instead of <code>N</code> as a denominator for calculating percentages for factors by default.</li>
 <li>
 <code>t_rsp</code> now works when all response values are <code>TRUE</code> or <code>FALSE</code>.</li>
-</ul></div>
+</ul>
+</div>
 <div class="section level5">
-<h5 id="deprecated-functions-0-5-0-3">Deprecated Functions<a class="anchor" aria-label="anchor" href="#deprecated-functions-0-5-0-3"></a></h5>
-<ul><li>Deprecated <code>t_summarize_variables</code> as <code>t_summary</code> is more powerful.</li>
+<h5 id="deprecated-functions-0-5-0-3">Deprecated Functions<a class="anchor" aria-label="anchor" href="#deprecated-functions-0-5-0-3"></a>
+</h5>
+<ul>
+<li>Deprecated <code>t_summarize_variables</code> as <code>t_summary</code> is more powerful.</li>
 <li>Replacing <code>t_summarize_by_visit</code> with <code>t_summary_by</code> will occur in an upcoming release.</li>
-</ul></div>
+</ul>
+</div>
 </div>
     <div class="section level2">
-<h2 class="pkg-version" data-toc-text="0.5.0" id="tern-050">tern 0.5.0<a class="anchor" aria-label="anchor" href="#tern-050"></a></h2>
-<ul><li>First version with harmonized analysis functions names and arguments.</li>
-</ul></div>
+<h2 class="pkg-version" data-toc-text="0.5.0" id="tern-050">tern 0.5.0<a class="anchor" aria-label="anchor" href="#tern-050"></a>
+</h2>
+<ul>
+<li>First version with harmonized analysis functions names and arguments.</li>
+</ul>
+</div>
   </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
-    </nav></aside></div>
+    </nav></aside>
+</div>
 
 
     <footer><div class="nest">
   <p>tern is a part of the <strong>NEST</strong> and <a href="https://pharmaverse.org/" class="external-link"><strong>pharmaverse</strong></a>.</p>
 </div>
-<script type="text/javascript" src="../analytics.js"></script></footer></div>
-
+<script type="text/javascript" src="../analytics.js"></script></footer>
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diff --git a/main/reference/abnormal.html b/main/reference/abnormal.html
index feaaaa3268..75adf2ee7a 100644
--- a/main/reference/abnormal.html
+++ b/main/reference/abnormal.html
@@ -1,5 +1,22 @@
-<!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Count patients with abnormal range values — abnormal • tern</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Count patients with abnormal range values — abnormal"><meta name="description" content="
+<html lang="en">
+<head>
+<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+<meta charset="utf-8">
+<meta http-equiv="X-UA-Compatible" content="IE=edge">
+<meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<title>Count patients with abnormal range values — abnormal • tern</title>
+<!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png">
+<link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png">
+<link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png">
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+<link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png">
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+<script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet">
+<script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet">
+<link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet">
+<script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Count patients with abnormal range values — abnormal">
+<meta name="description" content="
 The analyze function count_abnormal() creates a layout element to count patients with abnormal analysis range
 values in each direction.
 This function analyzes primary analysis variable var which indicates abnormal range results.
@@ -12,7 +29,8 @@
 denom: The total number of patients with at least one post-baseline assessment.
 
 
-This function assumes that df has been filtered to only include post-baseline records."><meta property="og:description" content="
+This function assumes that df has been filtered to only include post-baseline records.">
+<meta property="og:description" content="
 The analyze function count_abnormal() creates a layout element to count patients with abnormal analysis range
 values in each direction.
 This function analyzes primary analysis variable var which indicates abnormal range results.
@@ -25,7 +43,12 @@
 denom: The total number of patients with at least one post-baseline assessment.
 
 
-This function assumes that df has been filtered to only include post-baseline records."><meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png"><link rel="stylesheet" href="../consent.css"><script src="../consent.js" type="text/javascript" charset="utf-8"></script></head><body>
+This function assumes that df has been filtered to only include post-baseline records.">
+<meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png">
+<link rel="stylesheet" href="../consent.css">
+<script src="../consent.js" type="text/javascript" charset="utf-8"></script>
+</head>
+<body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
 
 
@@ -41,26 +64,66 @@
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-      <ul class="navbar-nav me-auto"><li class="nav-item"><a class="nav-link" href="../articles/tern.html">Get started</a></li>
+      <ul class="navbar-nav me-auto">
+<li class="nav-item"><a class="nav-link" href="../articles/tern.html">Get started</a></li>
 <li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
 <li class="nav-item dropdown">
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-articles" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Articles</button>
-  <ul class="dropdown-menu" aria-labelledby="dropdown-articles"><li><a class="dropdown-item" href="../articles/missing_values.html">Missing Values in Tern</a></li>
+  <ul class="dropdown-menu" aria-labelledby="dropdown-articles">
+<li><a class="dropdown-item" href="../articles/missing_values.html">Missing Values in Tern</a></li>
     <li><a class="dropdown-item" href="../articles/tables.html">Tabulation</a></li>
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     <li><a class="dropdown-item" href="../articles/tern_functions_guide.html">Understanding `tern` functions</a></li>
-  </ul></li>
+  </ul>
+</li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
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+  <ul class="dropdown-menu" aria-labelledby="dropdown-reports">
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- <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json"></form></li>
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+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
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+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a>
+</div>
+</li></div>
+</ul>
+<ul class="navbar-nav">
+<li class="nav-item"><form class="form-inline" role="search">
+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json">
+</form></li>
 <li class="nav-item"><a class="external-link nav-link" href="https://github.com/insightsengineering/tern" aria-label="GitHub"><span class="fa fa-github"></span></a></li>
-      </ul></div>
+      </ul>
+</div>
 
 
   </div>
@@ -81,13 +144,17 @@
 <code>id</code> (defaults to <code>USUBJID</code>), a variable to indicate unique subject identifiers, and <code>baseline</code>
 (defaults to <code>BNRIND</code>), a variable to indicate baseline reference ranges.</p>
 <p>For each direction specified via the <code>abnormal</code> parameter (e.g. High or Low), a fraction of
-patient counts is returned, with numerator and denominator calculated as follows:</p><ul><li><p><code>num</code>: The number of patients with this abnormality recorded while on treatment.</p></li>
+patient counts is returned, with numerator and denominator calculated as follows:</p>
+<ul>
+<li><p><code>num</code>: The number of patients with this abnormality recorded while on treatment.</p></li>
 <li><p><code>denom</code>: The total number of patients with at least one post-baseline assessment.</p></li>
-</ul><p>This function assumes that <code>df</code> has been filtered to only include post-baseline records.</p>
+</ul>
+<p>This function assumes that <code>df</code> has been filtered to only include post-baseline records.</p>
     </div>
 
     <div class="section level2">
-    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
+    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">count_abnormal</span><span class="op">(</span></span>
 <span>  <span class="va">lyt</span>,</span>
 <span>  <span class="va">var</span>,</span>
@@ -122,106 +189,139 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
     </div>
 
     <div class="section level2">
-    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
+    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a>
+</h2>
 
 
-<dl><dt id="arg-lyt">lyt<a class="anchor" aria-label="anchor" href="#arg-lyt"></a></dt>
+<dl>
+<dt id="arg-lyt">lyt<a class="anchor" aria-label="anchor" href="#arg-lyt"></a>
+</dt>
 <dd><p>(<code>PreDataTableLayouts</code>)<br> layout that analyses will be added to.</p></dd>
 
 
-<dt id="arg-abnormal">abnormal<a class="anchor" aria-label="anchor" href="#arg-abnormal"></a></dt>
+<dt id="arg-abnormal">abnormal<a class="anchor" aria-label="anchor" href="#arg-abnormal"></a>
+</dt>
 <dd><p>(named <code>list</code>)<br> list identifying the abnormal range level(s) in <code>var</code>. Defaults to
 <code>list(Low = "LOW", High = "HIGH")</code> but you can also group different levels into the named list,
 for example, <code>abnormal = list(Low = c("LOW", "LOW LOW"), High = c("HIGH", "HIGH HIGH"))</code>.</p></dd>
 
 
-<dt id="arg-variables">variables<a class="anchor" aria-label="anchor" href="#arg-variables"></a></dt>
+<dt id="arg-variables">variables<a class="anchor" aria-label="anchor" href="#arg-variables"></a>
+</dt>
 <dd><p>(named <code>list</code> of <code>string</code>)<br> list of additional analysis variables.</p></dd>
 
 
-<dt id="arg-exclude-base-abn">exclude_base_abn<a class="anchor" aria-label="anchor" href="#arg-exclude-base-abn"></a></dt>
+<dt id="arg-exclude-base-abn">exclude_base_abn<a class="anchor" aria-label="anchor" href="#arg-exclude-base-abn"></a>
+</dt>
 <dd><p>(<code>flag</code>)<br> whether to exclude subjects with baseline abnormality
 from numerator and denominator.</p></dd>
 
 
-<dt id="arg-na-str">na_str<a class="anchor" aria-label="anchor" href="#arg-na-str"></a></dt>
+<dt id="arg-na-str">na_str<a class="anchor" aria-label="anchor" href="#arg-na-str"></a>
+</dt>
 <dd><p>(<code>string</code>)<br> string used to replace all <code>NA</code> or empty values in the output.</p></dd>
 
 
-<dt id="arg-nested">nested<a class="anchor" aria-label="anchor" href="#arg-nested"></a></dt>
+<dt id="arg-nested">nested<a class="anchor" aria-label="anchor" href="#arg-nested"></a>
+</dt>
 <dd><p>(<code>flag</code>)<br> whether this layout instruction should be applied within the existing layout structure _if
 possible (<code>TRUE</code>, the default) or as a new top-level element (<code>FALSE</code>). Ignored if it would nest a split.
 underneath analyses, which is not allowed.</p></dd>
 
 
-<dt id="arg--">...<a class="anchor" aria-label="anchor" href="#arg--"></a></dt>
+<dt id="arg--">...<a class="anchor" aria-label="anchor" href="#arg--"></a>
+</dt>
 <dd><p>additional arguments for the lower level functions.</p></dd>
 
 
-<dt id="arg-table-names">table_names<a class="anchor" aria-label="anchor" href="#arg-table-names"></a></dt>
+<dt id="arg-table-names">table_names<a class="anchor" aria-label="anchor" href="#arg-table-names"></a>
+</dt>
 <dd><p>(<code>character</code>)<br> this can be customized in the case that the same <code>vars</code> are analyzed multiple
 times, to avoid warnings from <code>rtables</code>.</p></dd>
 
 
-<dt id="arg--stats">.stats<a class="anchor" aria-label="anchor" href="#arg--stats"></a></dt>
-<dd><p>(<code>character</code>)<br> statistics to select for the table.</p>
-<p>Options are: <code>'fraction'</code></p></dd>
+<dt id="arg--stats">.stats<a class="anchor" aria-label="anchor" href="#arg--stats"></a>
+</dt>
+<dd>
+<p>(<code>character</code>)<br> statistics to select for the table.</p>
+<p>Options are: <code>'fraction'</code></p>
+</dd>
 
 
-<dt id="arg--formats">.formats<a class="anchor" aria-label="anchor" href="#arg--formats"></a></dt>
+<dt id="arg--formats">.formats<a class="anchor" aria-label="anchor" href="#arg--formats"></a>
+</dt>
 <dd><p>(named <code>character</code> or <code>list</code>)<br> formats for the statistics. See Details in <code>analyze_vars</code> for more
 information on the <code>"auto"</code> setting.</p></dd>
 
 
-<dt id="arg--labels">.labels<a class="anchor" aria-label="anchor" href="#arg--labels"></a></dt>
+<dt id="arg--labels">.labels<a class="anchor" aria-label="anchor" href="#arg--labels"></a>
+</dt>
 <dd><p>(named <code>character</code>)<br> labels for the statistics (without indent).</p></dd>
 
 
-<dt id="arg--indent-mods">.indent_mods<a class="anchor" aria-label="anchor" href="#arg--indent-mods"></a></dt>
+<dt id="arg--indent-mods">.indent_mods<a class="anchor" aria-label="anchor" href="#arg--indent-mods"></a>
+</dt>
 <dd><p>(named <code>integer</code>)<br> indent modifiers for the labels. Defaults to 0, which corresponds to the
 unmodified default behavior. Can be negative.</p></dd>
 
 
-<dt id="arg-df">df<a class="anchor" aria-label="anchor" href="#arg-df"></a></dt>
+<dt id="arg-df">df<a class="anchor" aria-label="anchor" href="#arg-df"></a>
+</dt>
 <dd><p>(<code>data.frame</code>)<br> data set containing all analysis variables.</p></dd>
 
 
-<dt id="arg--var-var">.var, var<a class="anchor" aria-label="anchor" href="#arg--var-var"></a></dt>
+<dt id="arg--var-var">.var, var<a class="anchor" aria-label="anchor" href="#arg--var-var"></a>
+</dt>
 <dd><p>(<code>string</code>)<br> single variable name that is passed by <code>rtables</code> when requested
 by a statistics function.</p></dd>
 
-</dl></div>
+</dl>
+</div>
     <div class="section level2">
-    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
+    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a>
+</h2>
 
-<ul><li><p><code>count_abnormal()</code> returns a layout object suitable for passing to further layouting functions,
+<ul>
+<li><p><code>count_abnormal()</code> returns a layout object suitable for passing to further layouting functions,
 or to <code><a href="https://insightsengineering.github.io/rtables/latest-tag/reference/build_table.html" class="external-link">rtables::build_table()</a></code>. Adding this function to an <code>rtable</code> layout will add formatted rows containing
 the statistics from <code>s_count_abnormal()</code> to the table layout.</p></li>
-</ul><ul><li><p><code>s_count_abnormal()</code> returns the statistic <code>fraction</code> which is a vector with <code>num</code> and <code>denom</code> counts of patients.</p></li>
-</ul><ul><li><p><code>a_count_abnormal()</code> returns the corresponding list with formatted <code><a href="https://insightsengineering.github.io/rtables/latest-tag/reference/CellValue.html" class="external-link">rtables::CellValue()</a></code>.</p></li>
-</ul></div>
+</ul>
+<ul>
+<li><p><code>s_count_abnormal()</code> returns the statistic <code>fraction</code> which is a vector with <code>num</code> and <code>denom</code> counts of patients.</p></li>
+</ul>
+<ul>
+<li><p><code>a_count_abnormal()</code> returns the corresponding list with formatted <code><a href="https://insightsengineering.github.io/rtables/latest-tag/reference/CellValue.html" class="external-link">rtables::CellValue()</a></code>.</p></li>
+</ul>
+</div>
     <div class="section level2">
-    <h2 id="functions">Functions<a class="anchor" aria-label="anchor" href="#functions"></a></h2>
+    <h2 id="functions">Functions<a class="anchor" aria-label="anchor" href="#functions"></a>
+</h2>
 
-<ul><li><p><code>count_abnormal()</code>: Layout-creating function which can take statistics function arguments
+<ul>
+<li><p><code>count_abnormal()</code>: Layout-creating function which can take statistics function arguments
 and additional format arguments. This function is a wrapper for <code><a href="https://insightsengineering.github.io/rtables/latest-tag/reference/analyze.html" class="external-link">rtables::analyze()</a></code>.</p></li>
 <li><p><code>s_count_abnormal()</code>: Statistics function which counts patients with abnormal range values
 for a single <code>abnormal</code> level.</p></li>
 <li><p><code>a_count_abnormal()</code>: Formatted analysis function which is used as <code>afun</code> in <code>count_abnormal()</code>.</p></li>
-</ul></div>
+</ul>
+</div>
     <div class="section level2">
-    <h2 id="note">Note<a class="anchor" aria-label="anchor" href="#note"></a></h2>
+    <h2 id="note">Note<a class="anchor" aria-label="anchor" href="#note"></a>
+</h2>
 
-<ul><li><p><code>count_abnormal()</code> only considers a single variable that contains multiple abnormal levels.</p></li>
+<ul>
+<li><p><code>count_abnormal()</code> only considers a single variable that contains multiple abnormal levels.</p></li>
 <li><p><code>df</code> should be filtered to only include post-baseline records.</p></li>
 <li><p>The denominator includes patients that may have other abnormal levels at baseline,
 and patients missing baseline records. Patients with these abnormalities at
 baseline can be optionally excluded from numerator and denominator via the
 <code>exclude_base_abn</code> parameter.</p></li>
-</ul></div>
+</ul>
+</div>
 
     <div class="section level2">
-    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
+    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://dplyr.tidyverse.org" class="external-link">dplyr</a></span><span class="op">)</span></span></span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> </span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> Attaching package: ‘dplyr’</span>
@@ -284,17 +384,19 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 </code></pre></div>
     </div>
   </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
-    </nav></aside></div>
+    </nav></aside>
+</div>
 
 
     <footer><div class="nest">
   <p>tern is a part of the <strong>NEST</strong> and <a href="https://pharmaverse.org/" class="external-link"><strong>pharmaverse</strong></a>.</p>
 </div>
-<script type="text/javascript" src="../analytics.js"></script></footer></div>
-
+<script type="text/javascript" src="../analytics.js"></script></footer>
+</div>
 
 
 
 
-  </body></html>
 
+  </body>
+</html>
diff --git a/main/reference/abnormal_by_baseline.html b/main/reference/abnormal_by_baseline.html
index cb38f9361c..628442bd5a 100644
--- a/main/reference/abnormal_by_baseline.html
+++ b/main/reference/abnormal_by_baseline.html
@@ -1,5 +1,22 @@
-<!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Count patients with abnormal analysis range values by baseline status — abnormal_by_baseline • tern</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Count patients with abnormal analysis range values by baseline status — abnormal_by_baseline"><meta name="description" content="
+<html lang="en">
+<head>
+<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+<meta charset="utf-8">
+<meta http-equiv="X-UA-Compatible" content="IE=edge">
+<meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<title>Count patients with abnormal analysis range values by baseline status — abnormal_by_baseline • tern</title>
+<!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png">
+<link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png">
+<link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png">
+<link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png">
+<link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png">
+<link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png">
+<script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet">
+<script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet">
+<link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet">
+<script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Count patients with abnormal analysis range values by baseline status — abnormal_by_baseline">
+<meta name="description" content="
 The analyze function count_abnormal_by_baseline() creates a layout element to count patients with abnormal
 analysis range values, categorized by baseline status.
 This function analyzes primary analysis variable var which indicates abnormal range results. Additional
@@ -25,7 +42,8 @@
 
 
 
-This function assumes that df has been filtered to only include post-baseline records."><meta property="og:description" content="
+This function assumes that df has been filtered to only include post-baseline records.">
+<meta property="og:description" content="
 The analyze function count_abnormal_by_baseline() creates a layout element to count patients with abnormal
 analysis range values, categorized by baseline status.
 This function analyzes primary analysis variable var which indicates abnormal range results. Additional
@@ -51,7 +69,12 @@
 
 
 
-This function assumes that df has been filtered to only include post-baseline records."><meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png"><link rel="stylesheet" href="../consent.css"><script src="../consent.js" type="text/javascript" charset="utf-8"></script></head><body>
+This function assumes that df has been filtered to only include post-baseline records.">
+<meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png">
+<link rel="stylesheet" href="../consent.css">
+<script src="../consent.js" type="text/javascript" charset="utf-8"></script>
+</head>
+<body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
 
 
@@ -67,26 +90,66 @@
     </button>
 
     <div id="navbar" class="collapse navbar-collapse ms-3">
-      <ul class="navbar-nav me-auto"><li class="nav-item"><a class="nav-link" href="../articles/tern.html">Get started</a></li>
+      <ul class="navbar-nav me-auto">
+<li class="nav-item"><a class="nav-link" href="../articles/tern.html">Get started</a></li>
 <li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
 <li class="nav-item dropdown">
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-articles" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Articles</button>
-  <ul class="dropdown-menu" aria-labelledby="dropdown-articles"><li><a class="dropdown-item" href="../articles/missing_values.html">Missing Values in Tern</a></li>
+  <ul class="dropdown-menu" aria-labelledby="dropdown-articles">
+<li><a class="dropdown-item" href="../articles/missing_values.html">Missing Values in Tern</a></li>
     <li><a class="dropdown-item" href="../articles/tables.html">Tabulation</a></li>
     <li><a class="dropdown-item" href="../articles/tern_formats.html">Formatting Functions</a></li>
     <li><a class="dropdown-item" href="../articles/tern_functions_guide.html">Understanding `tern` functions</a></li>
-  </ul></li>
+  </ul>
+</li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
-  <ul class="dropdown-menu" aria-labelledby="dropdown-reports"><li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
+  <ul class="dropdown-menu" aria-labelledby="dropdown-reports">
+<li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
     <li><a class="dropdown-item" href="../unit-test-report/">Unit test report</a></li>
     <li><a class="dropdown-item" href="../unit-test-report-non-cran/">Non-CRAN unit test report</a></li>
-  </ul></li>
-      </ul><ul class="navbar-nav"><li class="nav-item"><form class="form-inline" role="search">
- <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json"></form></li>
+  </ul>
+</li>
+      <div><li class="nav-item dropdown">
+    <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-versions">Versions</a>
+    <div class="dropdown-menu" aria-labelledby="dropdown-versions">
+    <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/main">main</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.5">v0.9.5</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.4">v0.9.4</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.3">v0.9.3</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1-rc3">v0.9.1-rc3</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a>
+</div>
+</li></div>
+</ul>
+<ul class="navbar-nav">
+<li class="nav-item"><form class="form-inline" role="search">
+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json">
+</form></li>
 <li class="nav-item"><a class="external-link nav-link" href="https://github.com/insightsengineering/tern" aria-label="GitHub"><span class="fa fa-github"></span></a></li>
-      </ul></div>
+      </ul>
+</div>
 
 
   </div>
@@ -108,22 +171,38 @@
 variable to indicate baseline reference ranges.</p>
 <p>For each direction specified via the <code>abnormal</code> parameter (e.g. High or Low), we condition on baseline
 range result and count patients in the numerator and denominator as follows for each of the following
-categories:</p><ul><li><p><code>Not &lt;abnormality&gt;</code></p><ul><li><p><code>num</code>:  The number of patients without abnormality at baseline (excluding those with missing baseline)
+categories:</p>
+<ul>
+<li>
+<p><code>Not &lt;abnormality&gt;</code></p>
+<ul>
+<li><p><code>num</code>:  The number of patients without abnormality at baseline (excluding those with missing baseline)
 and with at least one abnormality post-baseline.</p></li>
 <li><p><code>denom</code>: The number of patients without abnormality at baseline (excluding those with missing baseline).</p></li>
-</ul></li>
-<li><p><code>&lt;Abnormality&gt;</code></p><ul><li><p><code>num</code>: The number of patients with abnormality as baseline and at least one abnormality post-baseline.</p></li>
+</ul>
+</li>
+<li>
+<p><code>&lt;Abnormality&gt;</code></p>
+<ul>
+<li><p><code>num</code>: The number of patients with abnormality as baseline and at least one abnormality post-baseline.</p></li>
 <li><p><code>denom</code>: The number of patients with abnormality at baseline.</p></li>
-</ul></li>
-<li><p><code>Total</code></p><ul><li><p><code>num</code>: The number of patients with at least one post-baseline record and at least one abnormality
+</ul>
+</li>
+<li>
+<p><code>Total</code></p>
+<ul>
+<li><p><code>num</code>: The number of patients with at least one post-baseline record and at least one abnormality
 post-baseline.</p></li>
 <li><p><code>denom</code>: The number of patients with at least one post-baseline record.</p></li>
-</ul></li>
-</ul><p>This function assumes that <code>df</code> has been filtered to only include post-baseline records.</p>
+</ul>
+</li>
+</ul>
+<p>This function assumes that <code>df</code> has been filtered to only include post-baseline records.</p>
     </div>
 
     <div class="section level2">
-    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
+    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">count_abnormal_by_baseline</span><span class="op">(</span></span>
 <span>  <span class="va">lyt</span>,</span>
 <span>  <span class="va">var</span>,</span>
@@ -157,102 +236,135 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
     </div>
 
     <div class="section level2">
-    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
+    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a>
+</h2>
 
 
-<dl><dt id="arg-lyt">lyt<a class="anchor" aria-label="anchor" href="#arg-lyt"></a></dt>
+<dl>
+<dt id="arg-lyt">lyt<a class="anchor" aria-label="anchor" href="#arg-lyt"></a>
+</dt>
 <dd><p>(<code>PreDataTableLayouts</code>)<br> layout that analyses will be added to.</p></dd>
 
 
-<dt id="arg-abnormal">abnormal<a class="anchor" aria-label="anchor" href="#arg-abnormal"></a></dt>
+<dt id="arg-abnormal">abnormal<a class="anchor" aria-label="anchor" href="#arg-abnormal"></a>
+</dt>
 <dd><p>(<code>character</code>)<br> values identifying the abnormal range level(s) in <code>.var</code>.</p></dd>
 
 
-<dt id="arg-variables">variables<a class="anchor" aria-label="anchor" href="#arg-variables"></a></dt>
+<dt id="arg-variables">variables<a class="anchor" aria-label="anchor" href="#arg-variables"></a>
+</dt>
 <dd><p>(named <code>list</code> of <code>string</code>)<br> list of additional analysis variables.</p></dd>
 
 
-<dt id="arg-na-str">na_str<a class="anchor" aria-label="anchor" href="#arg-na-str"></a></dt>
+<dt id="arg-na-str">na_str<a class="anchor" aria-label="anchor" href="#arg-na-str"></a>
+</dt>
 <dd><p>(<code>string</code>)<br> the explicit <code>na_level</code> argument you used in the pre-processing steps (maybe with
 <code><a href="df_explicit_na.html">df_explicit_na()</a></code>). The default is <code>"&lt;Missing&gt;"</code>.</p></dd>
 
 
-<dt id="arg-nested">nested<a class="anchor" aria-label="anchor" href="#arg-nested"></a></dt>
+<dt id="arg-nested">nested<a class="anchor" aria-label="anchor" href="#arg-nested"></a>
+</dt>
 <dd><p>(<code>flag</code>)<br> whether this layout instruction should be applied within the existing layout structure _if
 possible (<code>TRUE</code>, the default) or as a new top-level element (<code>FALSE</code>). Ignored if it would nest a split.
 underneath analyses, which is not allowed.</p></dd>
 
 
-<dt id="arg--">...<a class="anchor" aria-label="anchor" href="#arg--"></a></dt>
+<dt id="arg--">...<a class="anchor" aria-label="anchor" href="#arg--"></a>
+</dt>
 <dd><p>additional arguments for the lower level functions.</p></dd>
 
 
-<dt id="arg-table-names">table_names<a class="anchor" aria-label="anchor" href="#arg-table-names"></a></dt>
+<dt id="arg-table-names">table_names<a class="anchor" aria-label="anchor" href="#arg-table-names"></a>
+</dt>
 <dd><p>(<code>character</code>)<br> this can be customized in the case that the same <code>vars</code> are analyzed multiple
 times, to avoid warnings from <code>rtables</code>.</p></dd>
 
 
-<dt id="arg--stats">.stats<a class="anchor" aria-label="anchor" href="#arg--stats"></a></dt>
-<dd><p>(<code>character</code>)<br> statistics to select for the table.</p>
-<p>Options are: <code>'fraction'</code></p></dd>
+<dt id="arg--stats">.stats<a class="anchor" aria-label="anchor" href="#arg--stats"></a>
+</dt>
+<dd>
+<p>(<code>character</code>)<br> statistics to select for the table.</p>
+<p>Options are: <code>'fraction'</code></p>
+</dd>
 
 
-<dt id="arg--formats">.formats<a class="anchor" aria-label="anchor" href="#arg--formats"></a></dt>
+<dt id="arg--formats">.formats<a class="anchor" aria-label="anchor" href="#arg--formats"></a>
+</dt>
 <dd><p>(named <code>character</code> or <code>list</code>)<br> formats for the statistics. See Details in <code>analyze_vars</code> for more
 information on the <code>"auto"</code> setting.</p></dd>
 
 
-<dt id="arg--labels">.labels<a class="anchor" aria-label="anchor" href="#arg--labels"></a></dt>
+<dt id="arg--labels">.labels<a class="anchor" aria-label="anchor" href="#arg--labels"></a>
+</dt>
 <dd><p>(named <code>character</code>)<br> labels for the statistics (without indent).</p></dd>
 
 
-<dt id="arg--indent-mods">.indent_mods<a class="anchor" aria-label="anchor" href="#arg--indent-mods"></a></dt>
+<dt id="arg--indent-mods">.indent_mods<a class="anchor" aria-label="anchor" href="#arg--indent-mods"></a>
+</dt>
 <dd><p>(named <code>integer</code>)<br> indent modifiers for the labels. Defaults to 0, which corresponds to the
 unmodified default behavior. Can be negative.</p></dd>
 
 
-<dt id="arg-df">df<a class="anchor" aria-label="anchor" href="#arg-df"></a></dt>
+<dt id="arg-df">df<a class="anchor" aria-label="anchor" href="#arg-df"></a>
+</dt>
 <dd><p>(<code>data.frame</code>)<br> data set containing all analysis variables.</p></dd>
 
 
-<dt id="arg--var-var">.var, var<a class="anchor" aria-label="anchor" href="#arg--var-var"></a></dt>
+<dt id="arg--var-var">.var, var<a class="anchor" aria-label="anchor" href="#arg--var-var"></a>
+</dt>
 <dd><p>(<code>string</code>)<br> single variable name that is passed by <code>rtables</code> when requested
 by a statistics function.</p></dd>
 
-</dl></div>
+</dl>
+</div>
     <div class="section level2">
-    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
+    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a>
+</h2>
 
-<ul><li><p><code>count_abnormal_by_baseline()</code> returns a layout object suitable for passing to further layouting functions,
+<ul>
+<li><p><code>count_abnormal_by_baseline()</code> returns a layout object suitable for passing to further layouting functions,
 or to <code><a href="https://insightsengineering.github.io/rtables/latest-tag/reference/build_table.html" class="external-link">rtables::build_table()</a></code>. Adding this function to an <code>rtable</code> layout will add formatted rows containing
 the statistics from <code>s_count_abnormal_by_baseline()</code> to the table layout.</p></li>
-</ul><ul><li><p><code>s_count_abnormal_by_baseline()</code> returns statistic <code>fraction</code> which is a named list with 3 labeled elements:
+</ul>
+<ul>
+<li><p><code>s_count_abnormal_by_baseline()</code> returns statistic <code>fraction</code> which is a named list with 3 labeled elements:
 <code>not_abnormal</code>, <code>abnormal</code>, and <code>total</code>. Each element contains a vector with <code>num</code> and <code>denom</code> patient counts.</p></li>
-</ul><ul><li><p><code>a_count_abnormal_by_baseline()</code> returns the corresponding list with formatted <code><a href="https://insightsengineering.github.io/rtables/latest-tag/reference/CellValue.html" class="external-link">rtables::CellValue()</a></code>.</p></li>
-</ul></div>
+</ul>
+<ul>
+<li><p><code>a_count_abnormal_by_baseline()</code> returns the corresponding list with formatted <code><a href="https://insightsengineering.github.io/rtables/latest-tag/reference/CellValue.html" class="external-link">rtables::CellValue()</a></code>.</p></li>
+</ul>
+</div>
     <div class="section level2">
-    <h2 id="functions">Functions<a class="anchor" aria-label="anchor" href="#functions"></a></h2>
+    <h2 id="functions">Functions<a class="anchor" aria-label="anchor" href="#functions"></a>
+</h2>
 
-<ul><li><p><code>count_abnormal_by_baseline()</code>: Layout-creating function which can take statistics function arguments
+<ul>
+<li><p><code>count_abnormal_by_baseline()</code>: Layout-creating function which can take statistics function arguments
 and additional format arguments. This function is a wrapper for <code><a href="https://insightsengineering.github.io/rtables/latest-tag/reference/analyze.html" class="external-link">rtables::analyze()</a></code>.</p></li>
 <li><p><code>s_count_abnormal_by_baseline()</code>: Statistics function for a single <code>abnormal</code> level.</p></li>
 <li><p><code>a_count_abnormal_by_baseline()</code>: Formatted analysis function which is used as <code>afun</code>
 in <code>count_abnormal_by_baseline()</code>.</p></li>
-</ul></div>
+</ul>
+</div>
     <div class="section level2">
-    <h2 id="note">Note<a class="anchor" aria-label="anchor" href="#note"></a></h2>
+    <h2 id="note">Note<a class="anchor" aria-label="anchor" href="#note"></a>
+</h2>
 
-<ul><li><p><code>df</code> should be filtered to include only post-baseline records.</p></li>
+<ul>
+<li><p><code>df</code> should be filtered to include only post-baseline records.</p></li>
 <li><p>If the baseline variable or analysis variable contains <code>NA</code> records, it is expected that <code>df</code> has been
 pre-processed using <code><a href="df_explicit_na.html">df_explicit_na()</a></code> or <code><a href="explicit_na.html">explicit_na()</a></code>.</p></li>
-</ul></div>
+</ul>
+</div>
     <div class="section level2">
-    <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"></a></h2>
+    <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"></a>
+</h2>
     <div class="dont-index"><p>Relevant description function <code><a href="d_count_abnormal_by_baseline.html">d_count_abnormal_by_baseline()</a></code>.</p></div>
     </div>
 
     <div class="section level2">
-    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
+    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">df</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a></span><span class="op">(</span></span></span>
 <span class="r-in"><span>  USUBJID <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/character.html" class="external-link">as.character</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">1</span><span class="op">:</span><span class="fl">6</span><span class="op">)</span><span class="op">)</span>,</span></span>
 <span class="r-in"><span>  ANRIND <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/factor.html" class="external-link">factor</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/rep.html" class="external-link">rep</a></span><span class="op">(</span><span class="st">"LOW"</span>, <span class="fl">4</span><span class="op">)</span>, <span class="st">"NORMAL"</span>, <span class="st">"HIGH"</span><span class="op">)</span><span class="op">)</span>,</span></span>
@@ -297,17 +409,19 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 </code></pre></div>
     </div>
   </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
-    </nav></aside></div>
+    </nav></aside>
+</div>
 
 
     <footer><div class="nest">
   <p>tern is a part of the <strong>NEST</strong> and <a href="https://pharmaverse.org/" class="external-link"><strong>pharmaverse</strong></a>.</p>
 </div>
-<script type="text/javascript" src="../analytics.js"></script></footer></div>
-
+<script type="text/javascript" src="../analytics.js"></script></footer>
+</div>
 
 
 
 
-  </body></html>
 
+  </body>
+</html>
diff --git a/main/reference/abnormal_by_marked.html b/main/reference/abnormal_by_marked.html
index 5b78aed841..b797891b8d 100644
--- a/main/reference/abnormal_by_marked.html
+++ b/main/reference/abnormal_by_marked.html
@@ -1,5 +1,22 @@
-<!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Count patients with marked laboratory abnormalities — abnormal_by_marked • tern</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Count patients with marked laboratory abnormalities — abnormal_by_marked"><meta name="description" content="
+<html lang="en">
+<head>
+<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+<meta charset="utf-8">
+<meta http-equiv="X-UA-Compatible" content="IE=edge">
+<meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<title>Count patients with marked laboratory abnormalities — abnormal_by_marked • tern</title>
+<!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png">
+<link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png">
+<link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png">
+<link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png">
+<link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png">
+<link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png">
+<script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet">
+<script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet">
+<link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet">
+<script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Count patients with marked laboratory abnormalities — abnormal_by_marked">
+<meta name="description" content="
 The analyze function count_abnormal_by_marked() creates a layout element to count patients with marked laboratory
 abnormalities for each direction of abnormality, categorized by parameter value.
 This function analyzes primary analysis variable var which indicates whether a single, replicated,
@@ -19,7 +36,8 @@
 Fractions are calculated by dividing the above counts by the number of patients with at least one
 valid measurement recorded during the analysis.
 Prior to using this function in your table layout you must use rtables::split_rows_by() to create two
-row splits, one on variable param and one on variable direction."><meta property="og:description" content="
+row splits, one on variable param and one on variable direction.">
+<meta property="og:description" content="
 The analyze function count_abnormal_by_marked() creates a layout element to count patients with marked laboratory
 abnormalities for each direction of abnormality, categorized by parameter value.
 This function analyzes primary analysis variable var which indicates whether a single, replicated,
@@ -39,7 +57,12 @@
 Fractions are calculated by dividing the above counts by the number of patients with at least one
 valid measurement recorded during the analysis.
 Prior to using this function in your table layout you must use rtables::split_rows_by() to create two
-row splits, one on variable param and one on variable direction."><meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png"><link rel="stylesheet" href="../consent.css"><script src="../consent.js" type="text/javascript" charset="utf-8"></script></head><body>
+row splits, one on variable param and one on variable direction.">
+<meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png">
+<link rel="stylesheet" href="../consent.css">
+<script src="../consent.js" type="text/javascript" charset="utf-8"></script>
+</head>
+<body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
 
 
@@ -55,26 +78,66 @@
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-      <ul class="navbar-nav me-auto"><li class="nav-item"><a class="nav-link" href="../articles/tern.html">Get started</a></li>
+      <ul class="navbar-nav me-auto">
+<li class="nav-item"><a class="nav-link" href="../articles/tern.html">Get started</a></li>
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   <button class="nav-link dropdown-toggle" type="button" id="dropdown-articles" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Articles</button>
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+  <ul class="dropdown-menu" aria-labelledby="dropdown-articles">
+<li><a class="dropdown-item" href="../articles/missing_values.html">Missing Values in Tern</a></li>
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+</ul>
+<ul class="navbar-nav">
+<li class="nav-item"><form class="form-inline" role="search">
+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json">
+</form></li>
 <li class="nav-item"><a class="external-link nav-link" href="https://github.com/insightsengineering/tern" aria-label="GitHub"><span class="fa fa-github"></span></a></li>
-      </ul></div>
+      </ul>
+</div>
 
 
   </div>
@@ -98,17 +161,21 @@
 variable to indicate parameter values, and <code>direction</code> (defaults to <code>abn_dir</code>), a variable to indicate
 abnormality directions.</p>
 <p>For each combination of <code>param</code> and <code>direction</code> levels, marked lab abnormality counts are calculated
-as follows:</p><ul><li><p><code>Single, not last</code> &amp; <code>Last or replicated</code>: The number of patients with <code>Single, not last</code>
+as follows:</p>
+<ul>
+<li><p><code>Single, not last</code> &amp; <code>Last or replicated</code>: The number of patients with <code>Single, not last</code>
 and <code>Last or replicated</code> values, respectively.</p></li>
 <li><p><code>Any</code>: The number of patients with either single or replicated marked abnormalities.</p></li>
-</ul><p>Fractions are calculated by dividing the above counts by the number of patients with at least one
+</ul>
+<p>Fractions are calculated by dividing the above counts by the number of patients with at least one
 valid measurement recorded during the analysis.</p>
 <p>Prior to using this function in your table layout you must use <code><a href="https://insightsengineering.github.io/rtables/latest-tag/reference/split_rows_by.html" class="external-link">rtables::split_rows_by()</a></code> to create two
 row splits, one on variable <code>param</code> and one on variable <code>direction</code>.</p>
     </div>
 
     <div class="section level2">
-    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
+    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">count_abnormal_by_marked</span><span class="op">(</span></span>
 <span>  <span class="va">lyt</span>,</span>
 <span>  <span class="va">var</span>,</span>
@@ -141,97 +208,127 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
     </div>
 
     <div class="section level2">
-    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
+    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a>
+</h2>
 
 
-<dl><dt id="arg-lyt">lyt<a class="anchor" aria-label="anchor" href="#arg-lyt"></a></dt>
+<dl>
+<dt id="arg-lyt">lyt<a class="anchor" aria-label="anchor" href="#arg-lyt"></a>
+</dt>
 <dd><p>(<code>PreDataTableLayouts</code>)<br> layout that analyses will be added to.</p></dd>
 
 
-<dt id="arg-category">category<a class="anchor" aria-label="anchor" href="#arg-category"></a></dt>
+<dt id="arg-category">category<a class="anchor" aria-label="anchor" href="#arg-category"></a>
+</dt>
 <dd><p>(<code>list</code>)<br> a list with different marked category names for single
 and last or replicated.</p></dd>
 
 
-<dt id="arg-variables">variables<a class="anchor" aria-label="anchor" href="#arg-variables"></a></dt>
+<dt id="arg-variables">variables<a class="anchor" aria-label="anchor" href="#arg-variables"></a>
+</dt>
 <dd><p>(named <code>list</code> of <code>string</code>)<br> list of additional analysis variables.</p></dd>
 
 
-<dt id="arg-na-str">na_str<a class="anchor" aria-label="anchor" href="#arg-na-str"></a></dt>
+<dt id="arg-na-str">na_str<a class="anchor" aria-label="anchor" href="#arg-na-str"></a>
+</dt>
 <dd><p>(<code>string</code>)<br> string used to replace all <code>NA</code> or empty values in the output.</p></dd>
 
 
-<dt id="arg-nested">nested<a class="anchor" aria-label="anchor" href="#arg-nested"></a></dt>
+<dt id="arg-nested">nested<a class="anchor" aria-label="anchor" href="#arg-nested"></a>
+</dt>
 <dd><p>(<code>flag</code>)<br> whether this layout instruction should be applied within the existing layout structure _if
 possible (<code>TRUE</code>, the default) or as a new top-level element (<code>FALSE</code>). Ignored if it would nest a split.
 underneath analyses, which is not allowed.</p></dd>
 
 
-<dt id="arg--">...<a class="anchor" aria-label="anchor" href="#arg--"></a></dt>
+<dt id="arg--">...<a class="anchor" aria-label="anchor" href="#arg--"></a>
+</dt>
 <dd><p>additional arguments for the lower level functions.</p></dd>
 
 
-<dt id="arg--stats">.stats<a class="anchor" aria-label="anchor" href="#arg--stats"></a></dt>
-<dd><p>(<code>character</code>)<br> statistics to select for the table.</p>
-<p>Options are: <code>'count_fraction', 'count_fraction_fixed_dp'</code></p></dd>
+<dt id="arg--stats">.stats<a class="anchor" aria-label="anchor" href="#arg--stats"></a>
+</dt>
+<dd>
+<p>(<code>character</code>)<br> statistics to select for the table.</p>
+<p>Options are: <code>'count_fraction', 'count_fraction_fixed_dp'</code></p>
+</dd>
 
 
-<dt id="arg--formats">.formats<a class="anchor" aria-label="anchor" href="#arg--formats"></a></dt>
+<dt id="arg--formats">.formats<a class="anchor" aria-label="anchor" href="#arg--formats"></a>
+</dt>
 <dd><p>(named <code>character</code> or <code>list</code>)<br> formats for the statistics. See Details in <code>analyze_vars</code> for more
 information on the <code>"auto"</code> setting.</p></dd>
 
 
-<dt id="arg--labels">.labels<a class="anchor" aria-label="anchor" href="#arg--labels"></a></dt>
+<dt id="arg--labels">.labels<a class="anchor" aria-label="anchor" href="#arg--labels"></a>
+</dt>
 <dd><p>(named <code>character</code>)<br> labels for the statistics (without indent).</p></dd>
 
 
-<dt id="arg--indent-mods">.indent_mods<a class="anchor" aria-label="anchor" href="#arg--indent-mods"></a></dt>
+<dt id="arg--indent-mods">.indent_mods<a class="anchor" aria-label="anchor" href="#arg--indent-mods"></a>
+</dt>
 <dd><p>(named <code>integer</code>)<br> indent modifiers for the labels. Defaults to 0, which corresponds to the
 unmodified default behavior. Can be negative.</p></dd>
 
 
-<dt id="arg-df">df<a class="anchor" aria-label="anchor" href="#arg-df"></a></dt>
+<dt id="arg-df">df<a class="anchor" aria-label="anchor" href="#arg-df"></a>
+</dt>
 <dd><p>(<code>data.frame</code>)<br> data set containing all analysis variables.</p></dd>
 
 
-<dt id="arg--var-var">.var, var<a class="anchor" aria-label="anchor" href="#arg--var-var"></a></dt>
+<dt id="arg--var-var">.var, var<a class="anchor" aria-label="anchor" href="#arg--var-var"></a>
+</dt>
 <dd><p>(<code>string</code>)<br> single variable name that is passed by <code>rtables</code> when requested
 by a statistics function.</p></dd>
 
 
-<dt id="arg--spl-context">.spl_context<a class="anchor" aria-label="anchor" href="#arg--spl-context"></a></dt>
+<dt id="arg--spl-context">.spl_context<a class="anchor" aria-label="anchor" href="#arg--spl-context"></a>
+</dt>
 <dd><p>(<code>data.frame</code>)<br> gives information about ancestor split states
 that is passed by <code>rtables</code>.</p></dd>
 
-</dl></div>
+</dl>
+</div>
     <div class="section level2">
-    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
+    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a>
+</h2>
 
-<ul><li><p><code>count_abnormal_by_marked()</code> returns a layout object suitable for passing to further layouting functions,
+<ul>
+<li><p><code>count_abnormal_by_marked()</code> returns a layout object suitable for passing to further layouting functions,
 or to <code><a href="https://insightsengineering.github.io/rtables/latest-tag/reference/build_table.html" class="external-link">rtables::build_table()</a></code>. Adding this function to an <code>rtable</code> layout will add formatted rows containing
 the statistics from <code>s_count_abnormal_by_marked()</code> to the table layout.</p></li>
-</ul><ul><li><p><code>s_count_abnormal_by_marked()</code> returns statistic <code>count_fraction</code> with <code>Single, not last</code>,
+</ul>
+<ul>
+<li><p><code>s_count_abnormal_by_marked()</code> returns statistic <code>count_fraction</code> with <code>Single, not last</code>,
 <code>Last or replicated</code>, and <code>Any</code> results.</p></li>
-</ul><ul><li><p><code>a_count_abnormal_by_marked()</code> returns the corresponding list with formatted <code><a href="https://insightsengineering.github.io/rtables/latest-tag/reference/CellValue.html" class="external-link">rtables::CellValue()</a></code>.</p></li>
-</ul></div>
+</ul>
+<ul>
+<li><p><code>a_count_abnormal_by_marked()</code> returns the corresponding list with formatted <code><a href="https://insightsengineering.github.io/rtables/latest-tag/reference/CellValue.html" class="external-link">rtables::CellValue()</a></code>.</p></li>
+</ul>
+</div>
     <div class="section level2">
-    <h2 id="functions">Functions<a class="anchor" aria-label="anchor" href="#functions"></a></h2>
+    <h2 id="functions">Functions<a class="anchor" aria-label="anchor" href="#functions"></a>
+</h2>
 
-<ul><li><p><code>count_abnormal_by_marked()</code>: Layout-creating function which can take statistics function arguments
+<ul>
+<li><p><code>count_abnormal_by_marked()</code>: Layout-creating function which can take statistics function arguments
 and additional format arguments. This function is a wrapper for <code><a href="https://insightsengineering.github.io/rtables/latest-tag/reference/analyze.html" class="external-link">rtables::analyze()</a></code>.</p></li>
 <li><p><code>s_count_abnormal_by_marked()</code>: Statistics function for patients with marked lab abnormalities.</p></li>
 <li><p><code>a_count_abnormal_by_marked()</code>: Formatted analysis function which is used as <code>afun</code>
 in <code>count_abnormal_by_marked()</code>.</p></li>
-</ul></div>
+</ul>
+</div>
     <div class="section level2">
-    <h2 id="note">Note<a class="anchor" aria-label="anchor" href="#note"></a></h2>
+    <h2 id="note">Note<a class="anchor" aria-label="anchor" href="#note"></a>
+</h2>
     <p><code>Single, not last</code> and <code>Last or replicated</code> levels are mutually exclusive. If a patient has
 abnormalities that meet both the <code>Single, not last</code> and <code>Last or replicated</code> criteria, then the
 patient will be counted only under the <code>Last or replicated</code> category.</p>
     </div>
 
     <div class="section level2">
-    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
+    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://dplyr.tidyverse.org" class="external-link">dplyr</a></span><span class="op">)</span></span></span>
 <span class="r-in"><span></span></span>
 <span class="r-in"><span><span class="va">df</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a></span><span class="op">(</span></span></span>
@@ -347,17 +444,19 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 </code></pre></div>
     </div>
   </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
-    </nav></aside></div>
+    </nav></aside>
+</div>
 
 
     <footer><div class="nest">
   <p>tern is a part of the <strong>NEST</strong> and <a href="https://pharmaverse.org/" class="external-link"><strong>pharmaverse</strong></a>.</p>
 </div>
-<script type="text/javascript" src="../analytics.js"></script></footer></div>
-
+<script type="text/javascript" src="../analytics.js"></script></footer>
+</div>
 
 
 
 
-  </body></html>
 
+  </body>
+</html>
diff --git a/main/reference/abnormal_by_worst_grade.html b/main/reference/abnormal_by_worst_grade.html
index 459ef94de9..ee7163e51f 100644
--- a/main/reference/abnormal_by_worst_grade.html
+++ b/main/reference/abnormal_by_worst_grade.html
@@ -1,5 +1,22 @@
-<!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Count patients by most extreme post-baseline toxicity grade per direction of abnormality — abnormal_by_worst_grade • tern</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Count patients by most extreme post-baseline toxicity grade per direction of abnormality — abnormal_by_worst_grade"><meta name="description" content="
+<html lang="en">
+<head>
+<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+<meta charset="utf-8">
+<meta http-equiv="X-UA-Compatible" content="IE=edge">
+<meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<title>Count patients by most extreme post-baseline toxicity grade per direction of abnormality — abnormal_by_worst_grade • tern</title>
+<!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png">
+<link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png">
+<link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png">
+<link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png">
+<link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png">
+<link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png">
+<script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet">
+<script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet">
+<link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet">
+<script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Count patients by most extreme post-baseline toxicity grade per direction of abnormality — abnormal_by_worst_grade">
+<meta name="description" content="
 The analyze function count_abnormal_by_worst_grade() creates a layout element to count patients by highest (worst)
 analysis toxicity grade post-baseline for each direction, categorized by parameter value.
 This function analyzes primary analysis variable var which indicates toxicity grades. Additional
@@ -19,7 +36,8 @@
 h_adlb_abnormal_by_worst_grade() helper function. See the description of this function for details on the
 necessary pre-processing steps.
 Prior to using this function in your table layout you must use rtables::split_rows_by() to create two row
-splits, one on variable param and one on variable grade_dir."><meta property="og:description" content="
+splits, one on variable param and one on variable grade_dir.">
+<meta property="og:description" content="
 The analyze function count_abnormal_by_worst_grade() creates a layout element to count patients by highest (worst)
 analysis toxicity grade post-baseline for each direction, categorized by parameter value.
 This function analyzes primary analysis variable var which indicates toxicity grades. Additional
@@ -39,7 +57,12 @@
 h_adlb_abnormal_by_worst_grade() helper function. See the description of this function for details on the
 necessary pre-processing steps.
 Prior to using this function in your table layout you must use rtables::split_rows_by() to create two row
-splits, one on variable param and one on variable grade_dir."><meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png"><link rel="stylesheet" href="../consent.css"><script src="../consent.js" type="text/javascript" charset="utf-8"></script></head><body>
+splits, one on variable param and one on variable grade_dir.">
+<meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png">
+<link rel="stylesheet" href="../consent.css">
+<script src="../consent.js" type="text/javascript" charset="utf-8"></script>
+</head>
+<body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
 
 
@@ -55,26 +78,66 @@
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     <div id="navbar" class="collapse navbar-collapse ms-3">
-      <ul class="navbar-nav me-auto"><li class="nav-item"><a class="nav-link" href="../articles/tern.html">Get started</a></li>
+      <ul class="navbar-nav me-auto">
+<li class="nav-item"><a class="nav-link" href="../articles/tern.html">Get started</a></li>
 <li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
 <li class="nav-item dropdown">
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-articles" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Articles</button>
-  <ul class="dropdown-menu" aria-labelledby="dropdown-articles"><li><a class="dropdown-item" href="../articles/missing_values.html">Missing Values in Tern</a></li>
+  <ul class="dropdown-menu" aria-labelledby="dropdown-articles">
+<li><a class="dropdown-item" href="../articles/missing_values.html">Missing Values in Tern</a></li>
     <li><a class="dropdown-item" href="../articles/tables.html">Tabulation</a></li>
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     <li><a class="dropdown-item" href="../articles/tern_functions_guide.html">Understanding `tern` functions</a></li>
-  </ul></li>
+  </ul>
+</li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
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+  <ul class="dropdown-menu" aria-labelledby="dropdown-reports">
+<li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
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- <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json"></form></li>
+  </ul>
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+      <div><li class="nav-item dropdown">
+    <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-versions">Versions</a>
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+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a>
+</div>
+</li></div>
+</ul>
+<ul class="navbar-nav">
+<li class="nav-item"><form class="form-inline" role="search">
+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json">
+</form></li>
 <li class="nav-item"><a class="external-link nav-link" href="https://github.com/insightsengineering/tern" aria-label="GitHub"><span class="fa fa-github"></span></a></li>
-      </ul></div>
+      </ul>
+</div>
 
 
   </div>
@@ -96,9 +159,12 @@
 to indicate parameter values, and <code>grade_dir</code> (defaults to <code>GRADE_DIR</code>), a variable to indicate directions
 (e.g. High or Low) for each toxicity grade supplied in <code>var</code>.</p>
 <p>For each combination of <code>param</code> and <code>grade_dir</code> levels, patient counts by worst
-grade are calculated as follows:</p><ul><li><p><code>1</code> to <code>4</code>: The number of patients with worst grades 1-4, respectively.</p></li>
+grade are calculated as follows:</p>
+<ul>
+<li><p><code>1</code> to <code>4</code>: The number of patients with worst grades 1-4, respectively.</p></li>
 <li><p><code>Any</code>: The number of patients with at least one abnormality (i.e. grade is not 0).</p></li>
-</ul><p>Fractions are calculated by dividing the above counts by the number of patients with at least one
+</ul>
+<p>Fractions are calculated by dividing the above counts by the number of patients with at least one
 valid measurement recorded during treatment.</p>
 <p>Pre-processing is crucial when using this function and can be done automatically using the
 <code><a href="h_adlb_abnormal_by_worst_grade.html">h_adlb_abnormal_by_worst_grade()</a></code> helper function. See the description of this function for details on the
@@ -108,7 +174,8 @@
     </div>
 
     <div class="section level2">
-    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
+    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">count_abnormal_by_worst_grade</span><span class="op">(</span></span>
 <span>  <span class="va">lyt</span>,</span>
 <span>  <span class="va">var</span>,</span>
@@ -138,91 +205,120 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
     </div>
 
     <div class="section level2">
-    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
+    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a>
+</h2>
 
 
-<dl><dt id="arg-lyt">lyt<a class="anchor" aria-label="anchor" href="#arg-lyt"></a></dt>
+<dl>
+<dt id="arg-lyt">lyt<a class="anchor" aria-label="anchor" href="#arg-lyt"></a>
+</dt>
 <dd><p>(<code>PreDataTableLayouts</code>)<br> layout that analyses will be added to.</p></dd>
 
 
-<dt id="arg-variables">variables<a class="anchor" aria-label="anchor" href="#arg-variables"></a></dt>
+<dt id="arg-variables">variables<a class="anchor" aria-label="anchor" href="#arg-variables"></a>
+</dt>
 <dd><p>(named <code>list</code> of <code>string</code>)<br> list of additional analysis variables.</p></dd>
 
 
-<dt id="arg-na-str">na_str<a class="anchor" aria-label="anchor" href="#arg-na-str"></a></dt>
+<dt id="arg-na-str">na_str<a class="anchor" aria-label="anchor" href="#arg-na-str"></a>
+</dt>
 <dd><p>(<code>string</code>)<br> string used to replace all <code>NA</code> or empty values in the output.</p></dd>
 
 
-<dt id="arg-nested">nested<a class="anchor" aria-label="anchor" href="#arg-nested"></a></dt>
+<dt id="arg-nested">nested<a class="anchor" aria-label="anchor" href="#arg-nested"></a>
+</dt>
 <dd><p>(<code>flag</code>)<br> whether this layout instruction should be applied within the existing layout structure _if
 possible (<code>TRUE</code>, the default) or as a new top-level element (<code>FALSE</code>). Ignored if it would nest a split.
 underneath analyses, which is not allowed.</p></dd>
 
 
-<dt id="arg--">...<a class="anchor" aria-label="anchor" href="#arg--"></a></dt>
+<dt id="arg--">...<a class="anchor" aria-label="anchor" href="#arg--"></a>
+</dt>
 <dd><p>additional arguments for the lower level functions.</p></dd>
 
 
-<dt id="arg--stats">.stats<a class="anchor" aria-label="anchor" href="#arg--stats"></a></dt>
-<dd><p>(<code>character</code>)<br> statistics to select for the table.</p>
-<p>Options are: <code>'count_fraction', 'count_fraction_fixed_dp'</code></p></dd>
+<dt id="arg--stats">.stats<a class="anchor" aria-label="anchor" href="#arg--stats"></a>
+</dt>
+<dd>
+<p>(<code>character</code>)<br> statistics to select for the table.</p>
+<p>Options are: <code>'count_fraction', 'count_fraction_fixed_dp'</code></p>
+</dd>
 
 
-<dt id="arg--formats">.formats<a class="anchor" aria-label="anchor" href="#arg--formats"></a></dt>
+<dt id="arg--formats">.formats<a class="anchor" aria-label="anchor" href="#arg--formats"></a>
+</dt>
 <dd><p>(named <code>character</code> or <code>list</code>)<br> formats for the statistics. See Details in <code>analyze_vars</code> for more
 information on the <code>"auto"</code> setting.</p></dd>
 
 
-<dt id="arg--labels">.labels<a class="anchor" aria-label="anchor" href="#arg--labels"></a></dt>
+<dt id="arg--labels">.labels<a class="anchor" aria-label="anchor" href="#arg--labels"></a>
+</dt>
 <dd><p>(named <code>character</code>)<br> labels for the statistics (without indent).</p></dd>
 
 
-<dt id="arg--indent-mods">.indent_mods<a class="anchor" aria-label="anchor" href="#arg--indent-mods"></a></dt>
+<dt id="arg--indent-mods">.indent_mods<a class="anchor" aria-label="anchor" href="#arg--indent-mods"></a>
+</dt>
 <dd><p>(named <code>integer</code>)<br> indent modifiers for the labels. Defaults to 0, which corresponds to the
 unmodified default behavior. Can be negative.</p></dd>
 
 
-<dt id="arg-df">df<a class="anchor" aria-label="anchor" href="#arg-df"></a></dt>
+<dt id="arg-df">df<a class="anchor" aria-label="anchor" href="#arg-df"></a>
+</dt>
 <dd><p>(<code>data.frame</code>)<br> data set containing all analysis variables.</p></dd>
 
 
-<dt id="arg--var-var">.var, var<a class="anchor" aria-label="anchor" href="#arg--var-var"></a></dt>
+<dt id="arg--var-var">.var, var<a class="anchor" aria-label="anchor" href="#arg--var-var"></a>
+</dt>
 <dd><p>(<code>string</code>)<br> single variable name that is passed by <code>rtables</code> when requested
 by a statistics function.</p></dd>
 
 
-<dt id="arg--spl-context">.spl_context<a class="anchor" aria-label="anchor" href="#arg--spl-context"></a></dt>
+<dt id="arg--spl-context">.spl_context<a class="anchor" aria-label="anchor" href="#arg--spl-context"></a>
+</dt>
 <dd><p>(<code>data.frame</code>)<br> gives information about ancestor split states
 that is passed by <code>rtables</code>.</p></dd>
 
-</dl></div>
+</dl>
+</div>
     <div class="section level2">
-    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
+    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a>
+</h2>
 
-<ul><li><p><code>count_abnormal_by_worst_grade()</code> returns a layout object suitable for passing to further layouting functions,
+<ul>
+<li><p><code>count_abnormal_by_worst_grade()</code> returns a layout object suitable for passing to further layouting functions,
 or to <code><a href="https://insightsengineering.github.io/rtables/latest-tag/reference/build_table.html" class="external-link">rtables::build_table()</a></code>. Adding this function to an <code>rtable</code> layout will add formatted rows containing
 the statistics from <code>s_count_abnormal_by_worst_grade()</code> to the table layout.</p></li>
-</ul><ul><li><p><code>s_count_abnormal_by_worst_grade()</code> returns the single statistic <code>count_fraction</code> with grades 1 to 4 and
+</ul>
+<ul>
+<li><p><code>s_count_abnormal_by_worst_grade()</code> returns the single statistic <code>count_fraction</code> with grades 1 to 4 and
 "Any" results.</p></li>
-</ul><ul><li><p><code>a_count_abnormal_by_worst_grade()</code> returns the corresponding list with formatted <code><a href="https://insightsengineering.github.io/rtables/latest-tag/reference/CellValue.html" class="external-link">rtables::CellValue()</a></code>.</p></li>
-</ul></div>
+</ul>
+<ul>
+<li><p><code>a_count_abnormal_by_worst_grade()</code> returns the corresponding list with formatted <code><a href="https://insightsengineering.github.io/rtables/latest-tag/reference/CellValue.html" class="external-link">rtables::CellValue()</a></code>.</p></li>
+</ul>
+</div>
     <div class="section level2">
-    <h2 id="functions">Functions<a class="anchor" aria-label="anchor" href="#functions"></a></h2>
+    <h2 id="functions">Functions<a class="anchor" aria-label="anchor" href="#functions"></a>
+</h2>
 
-<ul><li><p><code>count_abnormal_by_worst_grade()</code>: Layout-creating function which can take statistics function arguments
+<ul>
+<li><p><code>count_abnormal_by_worst_grade()</code>: Layout-creating function which can take statistics function arguments
 and additional format arguments. This function is a wrapper for <code><a href="https://insightsengineering.github.io/rtables/latest-tag/reference/analyze.html" class="external-link">rtables::analyze()</a></code>.</p></li>
 <li><p><code>s_count_abnormal_by_worst_grade()</code>: Statistics function which counts patients by worst grade.</p></li>
 <li><p><code>a_count_abnormal_by_worst_grade()</code>: Formatted analysis function which is used as <code>afun</code>
 in <code>count_abnormal_by_worst_grade()</code>.</p></li>
-</ul></div>
+</ul>
+</div>
     <div class="section level2">
-    <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"></a></h2>
+    <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"></a>
+</h2>
     <div class="dont-index"><p><code><a href="h_adlb_abnormal_by_worst_grade.html">h_adlb_abnormal_by_worst_grade()</a></code> which pre-processes ADLB data frames to be used in
 <code>count_abnormal_by_worst_grade()</code>.</p></div>
     </div>
 
     <div class="section level2">
-    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
+    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://dplyr.tidyverse.org" class="external-link">dplyr</a></span><span class="op">)</span></span></span>
 <span class="r-in"><span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://forcats.tidyverse.org/" class="external-link">forcats</a></span><span class="op">)</span></span></span>
 <span class="r-in"><span><span class="va">adlb</span> <span class="op">&lt;-</span> <span class="va">tern_ex_adlb</span></span></span>
@@ -289,17 +385,19 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 </code></pre></div>
     </div>
   </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
-    </nav></aside></div>
+    </nav></aside>
+</div>
 
 
     <footer><div class="nest">
   <p>tern is a part of the <strong>NEST</strong> and <a href="https://pharmaverse.org/" class="external-link"><strong>pharmaverse</strong></a>.</p>
 </div>
-<script type="text/javascript" src="../analytics.js"></script></footer></div>
-
+<script type="text/javascript" src="../analytics.js"></script></footer>
+</div>
 
 
 
 
-  </body></html>
 
+  </body>
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diff --git a/main/reference/abnormal_by_worst_grade_worsen.html b/main/reference/abnormal_by_worst_grade_worsen.html
index d76919989e..22a4bae51d 100644
--- a/main/reference/abnormal_by_worst_grade_worsen.html
+++ b/main/reference/abnormal_by_worst_grade_worsen.html
@@ -1,5 +1,22 @@
-<!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Count patients with toxicity grades that have worsened from baseline by highest grade post-baseline — abnormal_by_worst_grade_worsen • tern</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Count patients with toxicity grades that have worsened from baseline by highest grade post-baseline — abnormal_by_worst_grade_worsen"><meta name="description" content="
+<html lang="en">
+<head>
+<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+<meta charset="utf-8">
+<meta http-equiv="X-UA-Compatible" content="IE=edge">
+<meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<title>Count patients with toxicity grades that have worsened from baseline by highest grade post-baseline — abnormal_by_worst_grade_worsen • tern</title>
+<!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png">
+<link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png">
+<link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png">
+<link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png">
+<link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png">
+<link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png">
+<script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet">
+<script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet">
+<link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet">
+<script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Count patients with toxicity grades that have worsened from baseline by highest grade post-baseline — abnormal_by_worst_grade_worsen">
+<meta name="description" content="
 The analyze function count_abnormal_lab_worsen_by_baseline() creates a layout element to count patients with
 analysis toxicity grades which have worsened from baseline, categorized by highest (worst) grade post-baseline.
 This function analyzes primary analysis variable var which indicates analysis toxicity grades. Additional
@@ -17,7 +34,8 @@
 Fractions are calculated by dividing the above counts by the number of patients who's analysis toxicity grades
 have worsened from baseline toxicity grades during treatment.
 Prior to using this function in your table layout you must use rtables::split_rows_by() to create a row
-split on variable direction_var."><meta property="og:description" content="
+split on variable direction_var.">
+<meta property="og:description" content="
 The analyze function count_abnormal_lab_worsen_by_baseline() creates a layout element to count patients with
 analysis toxicity grades which have worsened from baseline, categorized by highest (worst) grade post-baseline.
 This function analyzes primary analysis variable var which indicates analysis toxicity grades. Additional
@@ -35,7 +53,12 @@
 Fractions are calculated by dividing the above counts by the number of patients who's analysis toxicity grades
 have worsened from baseline toxicity grades during treatment.
 Prior to using this function in your table layout you must use rtables::split_rows_by() to create a row
-split on variable direction_var."><meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png"><link rel="stylesheet" href="../consent.css"><script src="../consent.js" type="text/javascript" charset="utf-8"></script></head><body>
+split on variable direction_var.">
+<meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png">
+<link rel="stylesheet" href="../consent.css">
+<script src="../consent.js" type="text/javascript" charset="utf-8"></script>
+</head>
+<body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
 
 
@@ -51,26 +74,66 @@
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     <div id="navbar" class="collapse navbar-collapse ms-3">
-      <ul class="navbar-nav me-auto"><li class="nav-item"><a class="nav-link" href="../articles/tern.html">Get started</a></li>
+      <ul class="navbar-nav me-auto">
+<li class="nav-item"><a class="nav-link" href="../articles/tern.html">Get started</a></li>
 <li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
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   <button class="nav-link dropdown-toggle" type="button" id="dropdown-articles" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Articles</button>
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+  <ul class="dropdown-menu" aria-labelledby="dropdown-articles">
+<li><a class="dropdown-item" href="../articles/missing_values.html">Missing Values in Tern</a></li>
     <li><a class="dropdown-item" href="../articles/tables.html">Tabulation</a></li>
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     <li><a class="dropdown-item" href="../articles/tern_functions_guide.html">Understanding `tern` functions</a></li>
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+  </ul>
+</li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
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+    <div class="dropdown-menu" aria-labelledby="dropdown-versions">
+    <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
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+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.5">v0.9.5</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.4">v0.9.4</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.3">v0.9.3</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1-rc3">v0.9.1-rc3</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a>
+</div>
+</li></div>
+</ul>
+<ul class="navbar-nav">
+<li class="nav-item"><form class="form-inline" role="search">
+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json">
+</form></li>
 <li class="nav-item"><a class="external-link nav-link" href="https://github.com/insightsengineering/tern" aria-label="GitHub"><span class="fa fa-github"></span></a></li>
-      </ul></div>
+      </ul>
+</div>
 
 
   </div>
@@ -92,17 +155,21 @@
 baseline toxicity grades, and <code>direction_var</code> (defaults to <code>GRADDIR</code>), a variable to indicate toxicity grade
 directions of interest to include (e.g. <code>"H"</code> (high), <code>"L"</code> (low), or <code>"B"</code> (both)).</p>
 <p>For the direction(s) specified in <code>direction_var</code>, patient counts by worst grade for patients who have
-worsened from baseline are calculated as follows:</p><ul><li><p><code>1</code> to <code>4</code>: The number of patients who have worsened from their baseline grades with worst
+worsened from baseline are calculated as follows:</p>
+<ul>
+<li><p><code>1</code> to <code>4</code>: The number of patients who have worsened from their baseline grades with worst
 grades 1-4, respectively.</p></li>
 <li><p><code>Any</code>: The total number of patients who have worsened from their baseline grades.</p></li>
-</ul><p>Fractions are calculated by dividing the above counts by the number of patients who's analysis toxicity grades
+</ul>
+<p>Fractions are calculated by dividing the above counts by the number of patients who's analysis toxicity grades
 have worsened from baseline toxicity grades during treatment.</p>
 <p>Prior to using this function in your table layout you must use <code><a href="https://insightsengineering.github.io/rtables/latest-tag/reference/split_rows_by.html" class="external-link">rtables::split_rows_by()</a></code> to create a row
 split on variable <code>direction_var</code>.</p>
     </div>
 
     <div class="section level2">
-    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
+    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">count_abnormal_lab_worsen_by_baseline</span><span class="op">(</span></span>
 <span>  <span class="va">lyt</span>,</span>
 <span>  <span class="va">var</span>,</span>
@@ -131,97 +198,130 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
     </div>
 
     <div class="section level2">
-    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
+    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a>
+</h2>
 
 
-<dl><dt id="arg-lyt">lyt<a class="anchor" aria-label="anchor" href="#arg-lyt"></a></dt>
+<dl>
+<dt id="arg-lyt">lyt<a class="anchor" aria-label="anchor" href="#arg-lyt"></a>
+</dt>
 <dd><p>(<code>PreDataTableLayouts</code>)<br> layout that analyses will be added to.</p></dd>
 
 
-<dt id="arg-variables">variables<a class="anchor" aria-label="anchor" href="#arg-variables"></a></dt>
-<dd><p>(named <code>list</code> of <code>string</code>)<br> list of additional analysis variables including:</p><ul><li><p><code>id</code> (<code>string</code>)<br> subject variable name.</p></li>
+<dt id="arg-variables">variables<a class="anchor" aria-label="anchor" href="#arg-variables"></a>
+</dt>
+<dd>
+<p>(named <code>list</code> of <code>string</code>)<br> list of additional analysis variables including:</p>
+<ul>
+<li><p><code>id</code> (<code>string</code>)<br> subject variable name.</p></li>
 <li><p><code>baseline_var</code> (<code>string</code>)<br> name of the data column containing baseline toxicity variable.</p></li>
 <li><p><code>direction_var</code> (<code>string</code>)<br> see <code>direction_var</code> for more details.</p></li>
-</ul></dd>
+</ul>
+</dd>
 
 
-<dt id="arg-na-str">na_str<a class="anchor" aria-label="anchor" href="#arg-na-str"></a></dt>
+<dt id="arg-na-str">na_str<a class="anchor" aria-label="anchor" href="#arg-na-str"></a>
+</dt>
 <dd><p>(<code>string</code>)<br> string used to replace all <code>NA</code> or empty values in the output.</p></dd>
 
 
-<dt id="arg-nested">nested<a class="anchor" aria-label="anchor" href="#arg-nested"></a></dt>
+<dt id="arg-nested">nested<a class="anchor" aria-label="anchor" href="#arg-nested"></a>
+</dt>
 <dd><p>(<code>flag</code>)<br> whether this layout instruction should be applied within the existing layout structure _if
 possible (<code>TRUE</code>, the default) or as a new top-level element (<code>FALSE</code>). Ignored if it would nest a split.
 underneath analyses, which is not allowed.</p></dd>
 
 
-<dt id="arg--">...<a class="anchor" aria-label="anchor" href="#arg--"></a></dt>
+<dt id="arg--">...<a class="anchor" aria-label="anchor" href="#arg--"></a>
+</dt>
 <dd><p>additional arguments for the lower level functions.</p></dd>
 
 
-<dt id="arg-table-names">table_names<a class="anchor" aria-label="anchor" href="#arg-table-names"></a></dt>
+<dt id="arg-table-names">table_names<a class="anchor" aria-label="anchor" href="#arg-table-names"></a>
+</dt>
 <dd><p>(<code>character</code>)<br> this can be customized in the case that the same <code>vars</code> are analyzed multiple
 times, to avoid warnings from <code>rtables</code>.</p></dd>
 
 
-<dt id="arg--stats">.stats<a class="anchor" aria-label="anchor" href="#arg--stats"></a></dt>
-<dd><p>(<code>character</code>)<br> statistics to select for the table.</p>
-<p>Options are: <code>'fraction'</code></p></dd>
+<dt id="arg--stats">.stats<a class="anchor" aria-label="anchor" href="#arg--stats"></a>
+</dt>
+<dd>
+<p>(<code>character</code>)<br> statistics to select for the table.</p>
+<p>Options are: <code>'fraction'</code></p>
+</dd>
 
 
-<dt id="arg--formats">.formats<a class="anchor" aria-label="anchor" href="#arg--formats"></a></dt>
+<dt id="arg--formats">.formats<a class="anchor" aria-label="anchor" href="#arg--formats"></a>
+</dt>
 <dd><p>(named <code>character</code> or <code>list</code>)<br> formats for the statistics. See Details in <code>analyze_vars</code> for more
 information on the <code>"auto"</code> setting.</p></dd>
 
 
-<dt id="arg--labels">.labels<a class="anchor" aria-label="anchor" href="#arg--labels"></a></dt>
+<dt id="arg--labels">.labels<a class="anchor" aria-label="anchor" href="#arg--labels"></a>
+</dt>
 <dd><p>(named <code>character</code>)<br> labels for the statistics (without indent).</p></dd>
 
 
-<dt id="arg--indent-mods">.indent_mods<a class="anchor" aria-label="anchor" href="#arg--indent-mods"></a></dt>
+<dt id="arg--indent-mods">.indent_mods<a class="anchor" aria-label="anchor" href="#arg--indent-mods"></a>
+</dt>
 <dd><p>(named <code>integer</code>)<br> indent modifiers for the labels. Defaults to 0, which corresponds to the
 unmodified default behavior. Can be negative.</p></dd>
 
 
-<dt id="arg-df">df<a class="anchor" aria-label="anchor" href="#arg-df"></a></dt>
+<dt id="arg-df">df<a class="anchor" aria-label="anchor" href="#arg-df"></a>
+</dt>
 <dd><p>(<code>data.frame</code>)<br> data set containing all analysis variables.</p></dd>
 
 
-<dt id="arg--var-var">.var, var<a class="anchor" aria-label="anchor" href="#arg--var-var"></a></dt>
+<dt id="arg--var-var">.var, var<a class="anchor" aria-label="anchor" href="#arg--var-var"></a>
+</dt>
 <dd><p>(<code>string</code>)<br> single variable name that is passed by <code>rtables</code> when requested
 by a statistics function.</p></dd>
 
-</dl></div>
+</dl>
+</div>
     <div class="section level2">
-    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
+    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a>
+</h2>
 
-<ul><li><p><code>count_abnormal_lab_worsen_by_baseline()</code> returns a layout object suitable for passing to further layouting
+<ul>
+<li><p><code>count_abnormal_lab_worsen_by_baseline()</code> returns a layout object suitable for passing to further layouting
 functions, or to <code><a href="https://insightsengineering.github.io/rtables/latest-tag/reference/build_table.html" class="external-link">rtables::build_table()</a></code>. Adding this function to an <code>rtable</code> layout will add formatted
 rows containing the statistics from <code>s_count_abnormal_lab_worsen_by_baseline()</code> to the table layout.</p></li>
-</ul><ul><li><p><code>s_count_abnormal_lab_worsen_by_baseline()</code> returns the counts and fraction of patients whose worst
+</ul>
+<ul>
+<li><p><code>s_count_abnormal_lab_worsen_by_baseline()</code> returns the counts and fraction of patients whose worst
 post-baseline lab grades are worse than their baseline grades, for post-baseline worst grades
 "1", "2", "3", "4" and "Any".</p></li>
-</ul><ul><li><p><code>a_count_abnormal_lab_worsen_by_baseline()</code> returns the corresponding list with
+</ul>
+<ul>
+<li><p><code>a_count_abnormal_lab_worsen_by_baseline()</code> returns the corresponding list with
 formatted <code><a href="https://insightsengineering.github.io/rtables/latest-tag/reference/CellValue.html" class="external-link">rtables::CellValue()</a></code>.</p></li>
-</ul></div>
+</ul>
+</div>
     <div class="section level2">
-    <h2 id="functions">Functions<a class="anchor" aria-label="anchor" href="#functions"></a></h2>
+    <h2 id="functions">Functions<a class="anchor" aria-label="anchor" href="#functions"></a>
+</h2>
 
-<ul><li><p><code>count_abnormal_lab_worsen_by_baseline()</code>: Layout-creating function which can take statistics function
+<ul>
+<li><p><code>count_abnormal_lab_worsen_by_baseline()</code>: Layout-creating function which can take statistics function
 arguments and additional format arguments. This function is a wrapper for <code><a href="https://insightsengineering.github.io/rtables/latest-tag/reference/analyze.html" class="external-link">rtables::analyze()</a></code>.</p></li>
 <li><p><code>s_count_abnormal_lab_worsen_by_baseline()</code>: Statistics function for patients whose worst post-baseline
 lab grades are worse than their baseline grades.</p></li>
 <li><p><code>a_count_abnormal_lab_worsen_by_baseline()</code>: Formatted analysis function which is used as <code>afun</code>
 in <code>count_abnormal_lab_worsen_by_baseline()</code>.</p></li>
-</ul></div>
+</ul>
+</div>
     <div class="section level2">
-    <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"></a></h2>
+    <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"></a>
+</h2>
     <div class="dont-index"><p>Relevant helper functions <code><a href="h_adlb_worsen.html">h_adlb_worsen()</a></code> and <code><a href="h_worsen_counter.html">h_worsen_counter()</a></code> which are used within
 <code>s_count_abnormal_lab_worsen_by_baseline()</code> to process input data.</p></div>
     </div>
 
     <div class="section level2">
-    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
+    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://dplyr.tidyverse.org" class="external-link">dplyr</a></span><span class="op">)</span></span></span>
 <span class="r-in"><span></span></span>
 <span class="r-in"><span><span class="co"># The direction variable, GRADDR, is based on metadata</span></span></span>
@@ -291,17 +391,19 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 </code></pre></div>
     </div>
   </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
-    </nav></aside></div>
+    </nav></aside>
+</div>
 
 
     <footer><div class="nest">
   <p>tern is a part of the <strong>NEST</strong> and <a href="https://pharmaverse.org/" class="external-link"><strong>pharmaverse</strong></a>.</p>
 </div>
-<script type="text/javascript" src="../analytics.js"></script></footer></div>
-
+<script type="text/javascript" src="../analytics.js"></script></footer>
+</div>
 
 
 
 
-  </body></html>
 
+  </body>
+</html>
diff --git a/main/reference/add_riskdiff.html b/main/reference/add_riskdiff.html
index d865970eba..b86bffc5d7 100644
--- a/main/reference/add_riskdiff.html
+++ b/main/reference/add_riskdiff.html
@@ -1,13 +1,36 @@
-<!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Split function to configure risk difference column — add_riskdiff • tern</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Split function to configure risk difference column — add_riskdiff"><meta name="description" content="
+<html lang="en">
+<head>
+<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+<meta charset="utf-8">
+<meta http-equiv="X-UA-Compatible" content="IE=edge">
+<meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<title>Split function to configure risk difference column — add_riskdiff • tern</title>
+<!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png">
+<link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png">
+<link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png">
+<link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png">
+<link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png">
+<link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png">
+<script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet">
+<script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet">
+<link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet">
+<script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Split function to configure risk difference column — add_riskdiff">
+<meta name="description" content="
 Wrapper function for rtables::add_combo_levels() which configures settings for the risk difference
 column to be added to an rtables object. To add a risk difference column to a table, this function
 should be used as split_fun in calls to rtables::split_cols_by(), followed by setting argument
-riskdiff to TRUE in all following analyze function calls."><meta property="og:description" content="
+riskdiff to TRUE in all following analyze function calls.">
+<meta property="og:description" content="
 Wrapper function for rtables::add_combo_levels() which configures settings for the risk difference
 column to be added to an rtables object. To add a risk difference column to a table, this function
 should be used as split_fun in calls to rtables::split_cols_by(), followed by setting argument
-riskdiff to TRUE in all following analyze function calls."><meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png"><link rel="stylesheet" href="../consent.css"><script src="../consent.js" type="text/javascript" charset="utf-8"></script></head><body>
+riskdiff to TRUE in all following analyze function calls.">
+<meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png">
+<link rel="stylesheet" href="../consent.css">
+<script src="../consent.js" type="text/javascript" charset="utf-8"></script>
+</head>
+<body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
 
 
@@ -23,26 +46,66 @@
     </button>
 
     <div id="navbar" class="collapse navbar-collapse ms-3">
-      <ul class="navbar-nav me-auto"><li class="nav-item"><a class="nav-link" href="../articles/tern.html">Get started</a></li>
+      <ul class="navbar-nav me-auto">
+<li class="nav-item"><a class="nav-link" href="../articles/tern.html">Get started</a></li>
 <li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
 <li class="nav-item dropdown">
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-articles" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Articles</button>
-  <ul class="dropdown-menu" aria-labelledby="dropdown-articles"><li><a class="dropdown-item" href="../articles/missing_values.html">Missing Values in Tern</a></li>
+  <ul class="dropdown-menu" aria-labelledby="dropdown-articles">
+<li><a class="dropdown-item" href="../articles/missing_values.html">Missing Values in Tern</a></li>
     <li><a class="dropdown-item" href="../articles/tables.html">Tabulation</a></li>
     <li><a class="dropdown-item" href="../articles/tern_formats.html">Formatting Functions</a></li>
     <li><a class="dropdown-item" href="../articles/tern_functions_guide.html">Understanding `tern` functions</a></li>
-  </ul></li>
+  </ul>
+</li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
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   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
-  <ul class="dropdown-menu" aria-labelledby="dropdown-reports"><li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
+  <ul class="dropdown-menu" aria-labelledby="dropdown-reports">
+<li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
     <li><a class="dropdown-item" href="../unit-test-report/">Unit test report</a></li>
     <li><a class="dropdown-item" href="../unit-test-report-non-cran/">Non-CRAN unit test report</a></li>
-  </ul></li>
-      </ul><ul class="navbar-nav"><li class="nav-item"><form class="form-inline" role="search">
- <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json"></form></li>
+  </ul>
+</li>
+      <div><li class="nav-item dropdown">
+    <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-versions">Versions</a>
+    <div class="dropdown-menu" aria-labelledby="dropdown-versions">
+    <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/main">main</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.5">v0.9.5</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.4">v0.9.4</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.3">v0.9.3</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1-rc3">v0.9.1-rc3</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a>
+</div>
+</li></div>
+</ul>
+<ul class="navbar-nav">
+<li class="nav-item"><form class="form-inline" role="search">
+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json">
+</form></li>
 <li class="nav-item"><a class="external-link nav-link" href="https://github.com/insightsengineering/tern" aria-label="GitHub"><span class="fa fa-github"></span></a></li>
-      </ul></div>
+      </ul>
+</div>
 
 
   </div>
@@ -63,7 +126,8 @@
     </div>
 
     <div class="section level2">
-    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
+    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">add_riskdiff</span><span class="op">(</span></span>
 <span>  <span class="va">arm_x</span>,</span>
 <span>  <span class="va">arm_y</span>,</span>
@@ -74,40 +138,50 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
     </div>
 
     <div class="section level2">
-    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
+    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a>
+</h2>
 
 
-<dl><dt id="arg-arm-x">arm_x<a class="anchor" aria-label="anchor" href="#arg-arm-x"></a></dt>
+<dl>
+<dt id="arg-arm-x">arm_x<a class="anchor" aria-label="anchor" href="#arg-arm-x"></a>
+</dt>
 <dd><p>(<code>string</code>)<br> name of reference arm to use in risk difference calculations.</p></dd>
 
 
-<dt id="arg-arm-y">arm_y<a class="anchor" aria-label="anchor" href="#arg-arm-y"></a></dt>
+<dt id="arg-arm-y">arm_y<a class="anchor" aria-label="anchor" href="#arg-arm-y"></a>
+</dt>
 <dd><p>(<code>character</code>)<br> names of one or more arms to compare to reference arm in risk difference
 calculations. A new column will be added for each value of <code>arm_y</code>.</p></dd>
 
 
-<dt id="arg-col-label">col_label<a class="anchor" aria-label="anchor" href="#arg-col-label"></a></dt>
+<dt id="arg-col-label">col_label<a class="anchor" aria-label="anchor" href="#arg-col-label"></a>
+</dt>
 <dd><p>(<code>character</code>)<br> labels to use when rendering the risk difference column within the table.
 If more than one comparison arm is specified in <code>arm_y</code>, default labels will specify which two arms are
 being compared (reference arm vs. comparison arm).</p></dd>
 
 
-<dt id="arg-pct">pct<a class="anchor" aria-label="anchor" href="#arg-pct"></a></dt>
+<dt id="arg-pct">pct<a class="anchor" aria-label="anchor" href="#arg-pct"></a>
+</dt>
 <dd><p>(<code>flag</code>)<br> whether output should be returned as percentages. Defaults to <code>TRUE</code>.</p></dd>
 
-</dl></div>
+</dl>
+</div>
     <div class="section level2">
-    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
+    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a>
+</h2>
     <p>A closure suitable for use as a split function (<code>split_fun</code>) within <code><a href="https://insightsengineering.github.io/rtables/latest-tag/reference/split_cols_by.html" class="external-link">rtables::split_cols_by()</a></code>
 when creating a table layout.</p>
     </div>
     <div class="section level2">
-    <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"></a></h2>
+    <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"></a>
+</h2>
     <div class="dont-index"><p><code><a href="stat_propdiff_ci.html">stat_propdiff_ci()</a></code> for details on risk difference calculation.</p></div>
     </div>
 
     <div class="section level2">
-    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
+    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">adae</span> <span class="op">&lt;-</span> <span class="va">tern_ex_adae</span></span></span>
 <span class="r-in"><span><span class="va">adae</span><span class="op">$</span><span class="va">AESEV</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/factor.html" class="external-link">factor</a></span><span class="op">(</span><span class="va">adae</span><span class="op">$</span><span class="va">AESEV</span><span class="op">)</span></span></span>
 <span class="r-in"><span></span></span>
@@ -130,17 +204,19 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 </code></pre></div>
     </div>
   </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
-    </nav></aside></div>
+    </nav></aside>
+</div>
 
 
     <footer><div class="nest">
   <p>tern is a part of the <strong>NEST</strong> and <a href="https://pharmaverse.org/" class="external-link"><strong>pharmaverse</strong></a>.</p>
 </div>
-<script type="text/javascript" src="../analytics.js"></script></footer></div>
-
+<script type="text/javascript" src="../analytics.js"></script></footer>
+</div>
 
 
 
 
-  </body></html>
 
+  </body>
+</html>
diff --git a/main/reference/add_rowcounts.html b/main/reference/add_rowcounts.html
index 6881c60514..1c4918ccb1 100644
--- a/main/reference/add_rowcounts.html
+++ b/main/reference/add_rowcounts.html
@@ -1,9 +1,32 @@
-<!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Layout-creating function to add row total counts — add_rowcounts • tern</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Layout-creating function to add row total counts — add_rowcounts"><meta name="description" content="
+<html lang="en">
+<head>
+<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+<meta charset="utf-8">
+<meta http-equiv="X-UA-Compatible" content="IE=edge">
+<meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<title>Layout-creating function to add row total counts — add_rowcounts • tern</title>
+<!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png">
+<link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png">
+<link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png">
+<link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png">
+<link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png">
+<link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png">
+<script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet">
+<script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet">
+<link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet">
+<script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Layout-creating function to add row total counts — add_rowcounts">
+<meta name="description" content="
 This works analogously to rtables::add_colcounts() but on the rows. This function
-is a wrapper for rtables::summarize_row_groups()."><meta property="og:description" content="
+is a wrapper for rtables::summarize_row_groups().">
+<meta property="og:description" content="
 This works analogously to rtables::add_colcounts() but on the rows. This function
-is a wrapper for rtables::summarize_row_groups()."><meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png"><link rel="stylesheet" href="../consent.css"><script src="../consent.js" type="text/javascript" charset="utf-8"></script></head><body>
+is a wrapper for rtables::summarize_row_groups().">
+<meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png">
+<link rel="stylesheet" href="../consent.css">
+<script src="../consent.js" type="text/javascript" charset="utf-8"></script>
+</head>
+<body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
 
 
@@ -19,26 +42,66 @@
     </button>
 
     <div id="navbar" class="collapse navbar-collapse ms-3">
-      <ul class="navbar-nav me-auto"><li class="nav-item"><a class="nav-link" href="../articles/tern.html">Get started</a></li>
+      <ul class="navbar-nav me-auto">
+<li class="nav-item"><a class="nav-link" href="../articles/tern.html">Get started</a></li>
 <li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
 <li class="nav-item dropdown">
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-articles" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Articles</button>
-  <ul class="dropdown-menu" aria-labelledby="dropdown-articles"><li><a class="dropdown-item" href="../articles/missing_values.html">Missing Values in Tern</a></li>
+  <ul class="dropdown-menu" aria-labelledby="dropdown-articles">
+<li><a class="dropdown-item" href="../articles/missing_values.html">Missing Values in Tern</a></li>
     <li><a class="dropdown-item" href="../articles/tables.html">Tabulation</a></li>
     <li><a class="dropdown-item" href="../articles/tern_formats.html">Formatting Functions</a></li>
     <li><a class="dropdown-item" href="../articles/tern_functions_guide.html">Understanding `tern` functions</a></li>
-  </ul></li>
+  </ul>
+</li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
-  <ul class="dropdown-menu" aria-labelledby="dropdown-reports"><li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
+  <ul class="dropdown-menu" aria-labelledby="dropdown-reports">
+<li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
     <li><a class="dropdown-item" href="../unit-test-report/">Unit test report</a></li>
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-      </ul><ul class="navbar-nav"><li class="nav-item"><form class="form-inline" role="search">
- <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json"></form></li>
+  </ul>
+</li>
+      <div><li class="nav-item dropdown">
+    <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-versions">Versions</a>
+    <div class="dropdown-menu" aria-labelledby="dropdown-versions">
+    <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/main">main</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.5">v0.9.5</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.4">v0.9.4</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.3">v0.9.3</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1-rc3">v0.9.1-rc3</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a>
+</div>
+</li></div>
+</ul>
+<ul class="navbar-nav">
+<li class="nav-item"><form class="form-inline" role="search">
+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json">
+</form></li>
 <li class="nav-item"><a class="external-link nav-link" href="https://github.com/insightsengineering/tern" aria-label="GitHub"><span class="fa fa-github"></span></a></li>
-      </ul></div>
+      </ul>
+</div>
 
 
   </div>
@@ -57,36 +120,45 @@
     </div>
 
     <div class="section level2">
-    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
+    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">add_rowcounts</span><span class="op">(</span><span class="va">lyt</span>, alt_counts <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span></code></pre></div>
     </div>
 
     <div class="section level2">
-    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
+    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a>
+</h2>
 
 
-<dl><dt id="arg-lyt">lyt<a class="anchor" aria-label="anchor" href="#arg-lyt"></a></dt>
+<dl>
+<dt id="arg-lyt">lyt<a class="anchor" aria-label="anchor" href="#arg-lyt"></a>
+</dt>
 <dd><p>(<code>PreDataTableLayouts</code>)<br> layout that analyses will be added to.</p></dd>
 
 
-<dt id="arg-alt-counts">alt_counts<a class="anchor" aria-label="anchor" href="#arg-alt-counts"></a></dt>
+<dt id="arg-alt-counts">alt_counts<a class="anchor" aria-label="anchor" href="#arg-alt-counts"></a>
+</dt>
 <dd><p>(<code>flag</code>)<br> whether row counts should be taken from <code>alt_counts_df</code> (<code>TRUE</code>)
 or from <code>df</code> (<code>FALSE</code>). Defaults to <code>FALSE</code>.</p></dd>
 
-</dl></div>
+</dl>
+</div>
     <div class="section level2">
-    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
+    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a>
+</h2>
     <p>A modified layout where the latest row split labels now have the row-wise
 total counts (i.e. without column-based subsetting) attached in parentheses.</p>
     </div>
     <div class="section level2">
-    <h2 id="note">Note<a class="anchor" aria-label="anchor" href="#note"></a></h2>
+    <h2 id="note">Note<a class="anchor" aria-label="anchor" href="#note"></a>
+</h2>
     <p>Row count values are contained in these row count rows but are not displayed
 so that they are not considered zero rows by default when pruning.</p>
     </div>
 
     <div class="section level2">
-    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
+    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="fu">basic_table</span><span class="op">(</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span></span>
 <span class="r-in"><span>  <span class="fu">split_cols_by</span><span class="op">(</span><span class="st">"ARM"</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span></span>
 <span class="r-in"><span>  <span class="fu">add_colcounts</span><span class="op">(</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span></span>
@@ -122,17 +194,19 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 </code></pre></div>
     </div>
   </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
-    </nav></aside></div>
+    </nav></aside>
+</div>
 
 
     <footer><div class="nest">
   <p>tern is a part of the <strong>NEST</strong> and <a href="https://pharmaverse.org/" class="external-link"><strong>pharmaverse</strong></a>.</p>
 </div>
-<script type="text/javascript" src="../analytics.js"></script></footer></div>
-
+<script type="text/javascript" src="../analytics.js"></script></footer>
+</div>
 
 
 
 
-  </body></html>
 
+  </body>
+</html>
diff --git a/main/reference/aesi_label.html b/main/reference/aesi_label.html
index be2a106aa9..f8ccbf85fc 100644
--- a/main/reference/aesi_label.html
+++ b/main/reference/aesi_label.html
@@ -1,5 +1,28 @@
-<!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Labels for adverse event baskets — aesi_label • tern</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Labels for adverse event baskets — aesi_label"><meta name="description" content=""><meta property="og:description" content=""><meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png"><link rel="stylesheet" href="../consent.css"><script src="../consent.js" type="text/javascript" charset="utf-8"></script></head><body>
+<html lang="en">
+<head>
+<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+<meta charset="utf-8">
+<meta http-equiv="X-UA-Compatible" content="IE=edge">
+<meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<title>Labels for adverse event baskets — aesi_label • tern</title>
+<!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png">
+<link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png">
+<link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png">
+<link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png">
+<link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png">
+<link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png">
+<script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet">
+<script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet">
+<link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet">
+<script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Labels for adverse event baskets — aesi_label">
+<meta name="description" content="">
+<meta property="og:description" content="">
+<meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png">
+<link rel="stylesheet" href="../consent.css">
+<script src="../consent.js" type="text/javascript" charset="utf-8"></script>
+</head>
+<body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
 
 
@@ -15,26 +38,66 @@
     </button>
 
     <div id="navbar" class="collapse navbar-collapse ms-3">
-      <ul class="navbar-nav me-auto"><li class="nav-item"><a class="nav-link" href="../articles/tern.html">Get started</a></li>
+      <ul class="navbar-nav me-auto">
+<li class="nav-item"><a class="nav-link" href="../articles/tern.html">Get started</a></li>
 <li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
 <li class="nav-item dropdown">
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-articles" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Articles</button>
-  <ul class="dropdown-menu" aria-labelledby="dropdown-articles"><li><a class="dropdown-item" href="../articles/missing_values.html">Missing Values in Tern</a></li>
+  <ul class="dropdown-menu" aria-labelledby="dropdown-articles">
+<li><a class="dropdown-item" href="../articles/missing_values.html">Missing Values in Tern</a></li>
     <li><a class="dropdown-item" href="../articles/tables.html">Tabulation</a></li>
     <li><a class="dropdown-item" href="../articles/tern_formats.html">Formatting Functions</a></li>
     <li><a class="dropdown-item" href="../articles/tern_functions_guide.html">Understanding `tern` functions</a></li>
-  </ul></li>
+  </ul>
+</li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
-  <ul class="dropdown-menu" aria-labelledby="dropdown-reports"><li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
+  <ul class="dropdown-menu" aria-labelledby="dropdown-reports">
+<li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
     <li><a class="dropdown-item" href="../unit-test-report/">Unit test report</a></li>
     <li><a class="dropdown-item" href="../unit-test-report-non-cran/">Non-CRAN unit test report</a></li>
-  </ul></li>
-      </ul><ul class="navbar-nav"><li class="nav-item"><form class="form-inline" role="search">
- <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json"></form></li>
+  </ul>
+</li>
+      <div><li class="nav-item dropdown">
+    <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-versions">Versions</a>
+    <div class="dropdown-menu" aria-labelledby="dropdown-versions">
+    <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/main">main</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.5">v0.9.5</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.4">v0.9.4</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.3">v0.9.3</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1-rc3">v0.9.1-rc3</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a>
+</div>
+</li></div>
+</ul>
+<ul class="navbar-nav">
+<li class="nav-item"><form class="form-inline" role="search">
+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json">
+</form></li>
 <li class="nav-item"><a class="external-link nav-link" href="https://github.com/insightsengineering/tern" aria-label="GitHub"><span class="fa fa-github"></span></a></li>
-      </ul></div>
+      </ul>
+</div>
 
 
   </div>
@@ -51,30 +114,38 @@
     </div>
 
     <div class="section level2">
-    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
+    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">aesi_label</span><span class="op">(</span><span class="va">aesi</span>, scope <span class="op">=</span> <span class="cn">NULL</span><span class="op">)</span></span></code></pre></div>
     </div>
 
     <div class="section level2">
-    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
+    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a>
+</h2>
 
 
-<dl><dt id="arg-aesi">aesi<a class="anchor" aria-label="anchor" href="#arg-aesi"></a></dt>
+<dl>
+<dt id="arg-aesi">aesi<a class="anchor" aria-label="anchor" href="#arg-aesi"></a>
+</dt>
 <dd><p>(<code>character</code>)<br> vector with standardized MedDRA query name (e.g. <code>SMQxxNAM</code>) or customized query
 name (e.g. <code>CQxxNAM</code>).</p></dd>
 
 
-<dt id="arg-scope">scope<a class="anchor" aria-label="anchor" href="#arg-scope"></a></dt>
+<dt id="arg-scope">scope<a class="anchor" aria-label="anchor" href="#arg-scope"></a>
+</dt>
 <dd><p>(<code>character</code>)<br> vector with scope of query (e.g. <code>SMQxxSC</code>).</p></dd>
 
-</dl></div>
+</dl>
+</div>
     <div class="section level2">
-    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
+    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a>
+</h2>
     <p>A <code>string</code> with the standard label for the AE basket.</p>
     </div>
 
     <div class="section level2">
-    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
+    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">adae</span> <span class="op">&lt;-</span> <span class="va">tern_ex_adae</span></span></span>
 <span class="r-in"><span></span></span>
 <span class="r-in"><span><span class="co"># Standardized query label includes scope.</span></span></span>
@@ -88,17 +159,19 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 </code></pre></div>
     </div>
   </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
-    </nav></aside></div>
+    </nav></aside>
+</div>
 
 
     <footer><div class="nest">
   <p>tern is a part of the <strong>NEST</strong> and <a href="https://pharmaverse.org/" class="external-link"><strong>pharmaverse</strong></a>.</p>
 </div>
-<script type="text/javascript" src="../analytics.js"></script></footer></div>
-
+<script type="text/javascript" src="../analytics.js"></script></footer>
+</div>
 
 
 
 
-  </body></html>
 
+  </body>
+</html>
diff --git a/main/reference/afun_riskdiff.html b/main/reference/afun_riskdiff.html
index 4df23f432c..ee237aa792 100644
--- a/main/reference/afun_riskdiff.html
+++ b/main/reference/afun_riskdiff.html
@@ -1,13 +1,36 @@
-<!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Analysis function to calculate risk difference column values — afun_riskdiff • tern</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Analysis function to calculate risk difference column values — afun_riskdiff"><meta name="description" content="In the risk difference column, this function uses the statistics function associated with afun to
+<html lang="en">
+<head>
+<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+<meta charset="utf-8">
+<meta http-equiv="X-UA-Compatible" content="IE=edge">
+<meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<title>Analysis function to calculate risk difference column values — afun_riskdiff • tern</title>
+<!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png">
+<link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png">
+<link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png">
+<link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png">
+<link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png">
+<link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png">
+<script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet">
+<script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet">
+<link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet">
+<script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Analysis function to calculate risk difference column values — afun_riskdiff">
+<meta name="description" content="In the risk difference column, this function uses the statistics function associated with afun to
 calculates risk difference values from arm X (reference group) and arm Y. These arms are specified
 when configuring the risk difference column which is done using the add_riskdiff() split function in
 the previous call to rtables::split_cols_by(). For all other columns, applies afun as usual. This
-function utilizes the stat_propdiff_ci() function to perform risk difference calculations."><meta property="og:description" content="In the risk difference column, this function uses the statistics function associated with afun to
+function utilizes the stat_propdiff_ci() function to perform risk difference calculations.">
+<meta property="og:description" content="In the risk difference column, this function uses the statistics function associated with afun to
 calculates risk difference values from arm X (reference group) and arm Y. These arms are specified
 when configuring the risk difference column which is done using the add_riskdiff() split function in
 the previous call to rtables::split_cols_by(). For all other columns, applies afun as usual. This
-function utilizes the stat_propdiff_ci() function to perform risk difference calculations."><meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png"><link rel="stylesheet" href="../consent.css"><script src="../consent.js" type="text/javascript" charset="utf-8"></script></head><body>
+function utilizes the stat_propdiff_ci() function to perform risk difference calculations.">
+<meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png">
+<link rel="stylesheet" href="../consent.css">
+<script src="../consent.js" type="text/javascript" charset="utf-8"></script>
+</head>
+<body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
 
 
@@ -23,26 +46,66 @@
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     <div id="navbar" class="collapse navbar-collapse ms-3">
-      <ul class="navbar-nav me-auto"><li class="nav-item"><a class="nav-link" href="../articles/tern.html">Get started</a></li>
+      <ul class="navbar-nav me-auto">
+<li class="nav-item"><a class="nav-link" href="../articles/tern.html">Get started</a></li>
 <li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
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-  <ul class="dropdown-menu" aria-labelledby="dropdown-articles"><li><a class="dropdown-item" href="../articles/missing_values.html">Missing Values in Tern</a></li>
+  <ul class="dropdown-menu" aria-labelledby="dropdown-articles">
+<li><a class="dropdown-item" href="../articles/missing_values.html">Missing Values in Tern</a></li>
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+  </ul>
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+  <ul class="dropdown-menu" aria-labelledby="dropdown-reports">
+<li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
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- <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json"></form></li>
+  </ul>
+</li>
+      <div><li class="nav-item dropdown">
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+    <div class="dropdown-menu" aria-labelledby="dropdown-versions">
+    <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/main">main</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.5">v0.9.5</a>
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+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.3">v0.9.3</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
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+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
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+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a>
+</div>
+</li></div>
+</ul>
+<ul class="navbar-nav">
+<li class="nav-item"><form class="form-inline" role="search">
+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json">
+</form></li>
 <li class="nav-item"><a class="external-link nav-link" href="https://github.com/insightsengineering/tern" aria-label="GitHub"><span class="fa fa-github"></span></a></li>
-      </ul></div>
+      </ul>
+</div>
 
 
   </div>
@@ -63,7 +126,8 @@
     </div>
 
     <div class="section level2">
-    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
+    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">afun_riskdiff</span><span class="op">(</span></span>
 <span>  <span class="va">df</span>,</span>
 <span>  labelstr <span class="op">=</span> <span class="st">""</span>,</span>
@@ -84,107 +148,131 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
     </div>
 
     <div class="section level2">
-    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
+    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a>
+</h2>
 
 
-<dl><dt id="arg-df">df<a class="anchor" aria-label="anchor" href="#arg-df"></a></dt>
+<dl>
+<dt id="arg-df">df<a class="anchor" aria-label="anchor" href="#arg-df"></a>
+</dt>
 <dd><p>(<code>data.frame</code>)<br> data set containing all analysis variables.</p></dd>
 
 
-<dt id="arg-labelstr">labelstr<a class="anchor" aria-label="anchor" href="#arg-labelstr"></a></dt>
+<dt id="arg-labelstr">labelstr<a class="anchor" aria-label="anchor" href="#arg-labelstr"></a>
+</dt>
 <dd><p>(<code>string</code>)<br> label of the level of the parent split currently being summarized
 (must be present as second argument in Content Row Functions). See <code><a href="https://insightsengineering.github.io/rtables/latest-tag/reference/summarize_row_groups.html" class="external-link">rtables::summarize_row_groups()</a></code>
 for more information.</p></dd>
 
 
-<dt id="arg--var">.var<a class="anchor" aria-label="anchor" href="#arg--var"></a></dt>
+<dt id="arg--var">.var<a class="anchor" aria-label="anchor" href="#arg--var"></a>
+</dt>
 <dd><p>(<code>string</code>)<br> single variable name that is passed by <code>rtables</code> when requested
 by a statistics function.</p></dd>
 
 
-<dt id="arg--n-col">.N_col<a class="anchor" aria-label="anchor" href="#arg--n-col"></a></dt>
+<dt id="arg--n-col">.N_col<a class="anchor" aria-label="anchor" href="#arg--n-col"></a>
+</dt>
 <dd><p>(<code>integer(1)</code>)<br> column-wise N (column count) for the full column being analyzed that is typically
 passed by <code>rtables</code>.</p></dd>
 
 
-<dt id="arg--n-row">.N_row<a class="anchor" aria-label="anchor" href="#arg--n-row"></a></dt>
+<dt id="arg--n-row">.N_row<a class="anchor" aria-label="anchor" href="#arg--n-row"></a>
+</dt>
 <dd><p>(<code>integer(1)</code>)<br> row-wise N (row group count) for the group of observations being analyzed
 (i.e. with no column-based subsetting) that is typically passed by <code>rtables</code>.</p></dd>
 
 
-<dt id="arg--df-row">.df_row<a class="anchor" aria-label="anchor" href="#arg--df-row"></a></dt>
+<dt id="arg--df-row">.df_row<a class="anchor" aria-label="anchor" href="#arg--df-row"></a>
+</dt>
 <dd><p>(<code>data.frame</code>)<br> data frame across all of the columns for the given row split.</p></dd>
 
 
-<dt id="arg--spl-context">.spl_context<a class="anchor" aria-label="anchor" href="#arg--spl-context"></a></dt>
+<dt id="arg--spl-context">.spl_context<a class="anchor" aria-label="anchor" href="#arg--spl-context"></a>
+</dt>
 <dd><p>(<code>data.frame</code>)<br> gives information about ancestor split states
 that is passed by <code>rtables</code>.</p></dd>
 
 
-<dt id="arg--all-col-counts">.all_col_counts<a class="anchor" aria-label="anchor" href="#arg--all-col-counts"></a></dt>
+<dt id="arg--all-col-counts">.all_col_counts<a class="anchor" aria-label="anchor" href="#arg--all-col-counts"></a>
+</dt>
 <dd><p>(<code>integer</code>)<br> vector where each value represents a global count for a column. Values are
 taken from <code>alt_counts_df</code> if specified (see <code><a href="https://insightsengineering.github.io/rtables/latest-tag/reference/build_table.html" class="external-link">rtables::build_table()</a></code>).</p></dd>
 
 
-<dt id="arg--stats">.stats<a class="anchor" aria-label="anchor" href="#arg--stats"></a></dt>
+<dt id="arg--stats">.stats<a class="anchor" aria-label="anchor" href="#arg--stats"></a>
+</dt>
 <dd><p>(<code>character</code>)<br> statistics to select for the table.</p></dd>
 
 
-<dt id="arg--formats">.formats<a class="anchor" aria-label="anchor" href="#arg--formats"></a></dt>
+<dt id="arg--formats">.formats<a class="anchor" aria-label="anchor" href="#arg--formats"></a>
+</dt>
 <dd><p>(named <code>character</code> or <code>list</code>)<br> formats for the statistics. See Details in <code>analyze_vars</code> for more
 information on the <code>"auto"</code> setting.</p></dd>
 
 
-<dt id="arg--labels">.labels<a class="anchor" aria-label="anchor" href="#arg--labels"></a></dt>
+<dt id="arg--labels">.labels<a class="anchor" aria-label="anchor" href="#arg--labels"></a>
+</dt>
 <dd><p>(named <code>character</code>)<br> labels for the statistics (without indent).</p></dd>
 
 
-<dt id="arg--indent-mods">.indent_mods<a class="anchor" aria-label="anchor" href="#arg--indent-mods"></a></dt>
+<dt id="arg--indent-mods">.indent_mods<a class="anchor" aria-label="anchor" href="#arg--indent-mods"></a>
+</dt>
 <dd><p>(named <code>integer</code>)<br> indent modifiers for the labels. Defaults to 0, which corresponds to the
 unmodified default behavior. Can be negative.</p></dd>
 
 
-<dt id="arg-na-str">na_str<a class="anchor" aria-label="anchor" href="#arg-na-str"></a></dt>
+<dt id="arg-na-str">na_str<a class="anchor" aria-label="anchor" href="#arg-na-str"></a>
+</dt>
 <dd><p>(<code>string</code>)<br> string used to replace all <code>NA</code> or empty values in the output.</p></dd>
 
 
-<dt id="arg-afun">afun<a class="anchor" aria-label="anchor" href="#arg-afun"></a></dt>
+<dt id="arg-afun">afun<a class="anchor" aria-label="anchor" href="#arg-afun"></a>
+</dt>
 <dd><p>(named <code>list</code>)<br> a named list containing one name-value pair where the name corresponds to
 the name of the statistics function that should be used in calculations and the value is the corresponding
 analysis function.</p></dd>
 
 
-<dt id="arg-s-args">s_args<a class="anchor" aria-label="anchor" href="#arg-s-args"></a></dt>
+<dt id="arg-s-args">s_args<a class="anchor" aria-label="anchor" href="#arg-s-args"></a>
+</dt>
 <dd><p>(named <code>list</code>)<br> additional arguments to be passed to the statistics function and analysis
 function supplied in <code>afun</code>.</p></dd>
 
-</dl></div>
+</dl>
+</div>
     <div class="section level2">
-    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
+    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a>
+</h2>
     <p>A list of formatted <code><a href="https://insightsengineering.github.io/rtables/latest-tag/reference/CellValue.html" class="external-link">rtables::CellValue()</a></code>.</p>
     </div>
     <div class="section level2">
-    <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"></a></h2>
+    <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"></a>
+</h2>
     <div class="dont-index">
-<ul><li><p><code><a href="stat_propdiff_ci.html">stat_propdiff_ci()</a></code> for details on risk difference calculation.</p></li>
+<ul>
+<li><p><code><a href="stat_propdiff_ci.html">stat_propdiff_ci()</a></code> for details on risk difference calculation.</p></li>
 <li><p>Split function <code><a href="add_riskdiff.html">add_riskdiff()</a></code> which, when used as <code>split_fun</code> within <code><a href="https://insightsengineering.github.io/rtables/latest-tag/reference/split_cols_by.html" class="external-link">rtables::split_cols_by()</a></code> with
 <code>riskdiff</code> argument set to <code>TRUE</code> in subsequent analyze functions calls, adds a risk difference column
 to a table layout.</p></li>
-</ul></div>
+</ul>
+</div>
     </div>
 
   </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
-    </nav></aside></div>
+    </nav></aside>
+</div>
 
 
     <footer><div class="nest">
   <p>tern is a part of the <strong>NEST</strong> and <a href="https://pharmaverse.org/" class="external-link"><strong>pharmaverse</strong></a>.</p>
 </div>
-<script type="text/javascript" src="../analytics.js"></script></footer></div>
-
+<script type="text/javascript" src="../analytics.js"></script></footer>
+</div>
 
 
 
 
-  </body></html>
 
+  </body>
+</html>
diff --git a/main/reference/afun_selected_stats.html b/main/reference/afun_selected_stats.html
index 5e182cec17..4760784f9c 100644
--- a/main/reference/afun_selected_stats.html
+++ b/main/reference/afun_selected_stats.html
@@ -1,5 +1,28 @@
-<!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Get selected statistics names — afun_selected_stats • tern</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Get selected statistics names — afun_selected_stats"><meta name="description" content="Helper function to be used for creating afun."><meta property="og:description" content="Helper function to be used for creating afun."><meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png"><link rel="stylesheet" href="../consent.css"><script src="../consent.js" type="text/javascript" charset="utf-8"></script></head><body>
+<html lang="en">
+<head>
+<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+<meta charset="utf-8">
+<meta http-equiv="X-UA-Compatible" content="IE=edge">
+<meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<title>Get selected statistics names — afun_selected_stats • tern</title>
+<!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png">
+<link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png">
+<link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png">
+<link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png">
+<link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png">
+<link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png">
+<script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet">
+<script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet">
+<link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet">
+<script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Get selected statistics names — afun_selected_stats">
+<meta name="description" content="Helper function to be used for creating afun.">
+<meta property="og:description" content="Helper function to be used for creating afun.">
+<meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png">
+<link rel="stylesheet" href="../consent.css">
+<script src="../consent.js" type="text/javascript" charset="utf-8"></script>
+</head>
+<body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
 
 
@@ -15,26 +38,66 @@
     </button>
 
     <div id="navbar" class="collapse navbar-collapse ms-3">
-      <ul class="navbar-nav me-auto"><li class="nav-item"><a class="nav-link" href="../articles/tern.html">Get started</a></li>
+      <ul class="navbar-nav me-auto">
+<li class="nav-item"><a class="nav-link" href="../articles/tern.html">Get started</a></li>
 <li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
 <li class="nav-item dropdown">
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-articles" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Articles</button>
-  <ul class="dropdown-menu" aria-labelledby="dropdown-articles"><li><a class="dropdown-item" href="../articles/missing_values.html">Missing Values in Tern</a></li>
+  <ul class="dropdown-menu" aria-labelledby="dropdown-articles">
+<li><a class="dropdown-item" href="../articles/missing_values.html">Missing Values in Tern</a></li>
     <li><a class="dropdown-item" href="../articles/tables.html">Tabulation</a></li>
     <li><a class="dropdown-item" href="../articles/tern_formats.html">Formatting Functions</a></li>
     <li><a class="dropdown-item" href="../articles/tern_functions_guide.html">Understanding `tern` functions</a></li>
-  </ul></li>
+  </ul>
+</li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
-  <ul class="dropdown-menu" aria-labelledby="dropdown-reports"><li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
+  <ul class="dropdown-menu" aria-labelledby="dropdown-reports">
+<li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
     <li><a class="dropdown-item" href="../unit-test-report/">Unit test report</a></li>
     <li><a class="dropdown-item" href="../unit-test-report-non-cran/">Non-CRAN unit test report</a></li>
-  </ul></li>
-      </ul><ul class="navbar-nav"><li class="nav-item"><form class="form-inline" role="search">
- <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json"></form></li>
+  </ul>
+</li>
+      <div><li class="nav-item dropdown">
+    <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-versions">Versions</a>
+    <div class="dropdown-menu" aria-labelledby="dropdown-versions">
+    <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/main">main</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.5">v0.9.5</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.4">v0.9.4</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.3">v0.9.3</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1-rc3">v0.9.1-rc3</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a>
+</div>
+</li></div>
+</ul>
+<ul class="navbar-nav">
+<li class="nav-item"><form class="form-inline" role="search">
+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json">
+</form></li>
 <li class="nav-item"><a class="external-link nav-link" href="https://github.com/insightsengineering/tern" aria-label="GitHub"><span class="fa fa-github"></span></a></li>
-      </ul></div>
+      </ul>
+</div>
 
 
   </div>
@@ -51,40 +114,49 @@
     </div>
 
     <div class="section level2">
-    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
+    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">afun_selected_stats</span><span class="op">(</span><span class="va">.stats</span>, <span class="va">all_stats</span><span class="op">)</span></span></code></pre></div>
     </div>
 
     <div class="section level2">
-    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
+    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a>
+</h2>
 
 
-<dl><dt id="arg--stats">.stats<a class="anchor" aria-label="anchor" href="#arg--stats"></a></dt>
+<dl>
+<dt id="arg--stats">.stats<a class="anchor" aria-label="anchor" href="#arg--stats"></a>
+</dt>
 <dd><p>(<code>vector</code> or <code>NULL</code>)<br> input to the layout creating function. Note that <code>NULL</code> means
 in this context that all default statistics should be used.</p></dd>
 
 
-<dt id="arg-all-stats">all_stats<a class="anchor" aria-label="anchor" href="#arg-all-stats"></a></dt>
+<dt id="arg-all-stats">all_stats<a class="anchor" aria-label="anchor" href="#arg-all-stats"></a>
+</dt>
 <dd><p>(<code>character</code>)<br> all statistics which can be selected here potentially.</p></dd>
 
-</dl></div>
+</dl>
+</div>
     <div class="section level2">
-    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
+    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a>
+</h2>
     <p>A <code>character</code> vector with the selected statistics.</p>
     </div>
 
   </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
-    </nav></aside></div>
+    </nav></aside>
+</div>
 
 
     <footer><div class="nest">
   <p>tern is a part of the <strong>NEST</strong> and <a href="https://pharmaverse.org/" class="external-link"><strong>pharmaverse</strong></a>.</p>
 </div>
-<script type="text/javascript" src="../analytics.js"></script></footer></div>
-
+<script type="text/javascript" src="../analytics.js"></script></footer>
+</div>
 
 
 
 
-  </body></html>
 
+  </body>
+</html>
diff --git a/main/reference/analyze_colvars_functions.html b/main/reference/analyze_colvars_functions.html
index 281b6f728a..58bbea23dc 100644
--- a/main/reference/analyze_colvars_functions.html
+++ b/main/reference/analyze_colvars_functions.html
@@ -1,5 +1,22 @@
-<!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Analyze functions in columns — analyze_colvars_functions • tern</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Analyze functions in columns — analyze_colvars_functions"><meta name="description" content="These functions are wrappers of rtables::analyze_colvars() which apply corresponding tern
+<html lang="en">
+<head>
+<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+<meta charset="utf-8">
+<meta http-equiv="X-UA-Compatible" content="IE=edge">
+<meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<title>Analyze functions in columns — analyze_colvars_functions • tern</title>
+<!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png">
+<link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png">
+<link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png">
+<link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png">
+<link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png">
+<link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png">
+<script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet">
+<script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet">
+<link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet">
+<script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Analyze functions in columns — analyze_colvars_functions">
+<meta name="description" content="These functions are wrappers of rtables::analyze_colvars() which apply corresponding tern
 statistics functions to add an analysis to a given table layout. In particular, these functions
 where designed to have the analysis methods split into different columns.
 analyze_vars_in_cols(): fundamental tabulation of analysis methods onto columns.
@@ -19,7 +36,8 @@
 specific standard tables that may contain nested structure with a combination of
 summarize_row_groups() and rtables::analyze_colvars().
 
-"><meta property="og:description" content="These functions are wrappers of rtables::analyze_colvars() which apply corresponding tern
+">
+<meta property="og:description" content="These functions are wrappers of rtables::analyze_colvars() which apply corresponding tern
 statistics functions to add an analysis to a given table layout. In particular, these functions
 where designed to have the analysis methods split into different columns.
 analyze_vars_in_cols(): fundamental tabulation of analysis methods onto columns.
@@ -39,7 +57,12 @@
 specific standard tables that may contain nested structure with a combination of
 summarize_row_groups() and rtables::analyze_colvars().
 
-"><meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png"><link rel="stylesheet" href="../consent.css"><script src="../consent.js" type="text/javascript" charset="utf-8"></script></head><body>
+">
+<meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png">
+<link rel="stylesheet" href="../consent.css">
+<script src="../consent.js" type="text/javascript" charset="utf-8"></script>
+</head>
+<body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
 
 
@@ -55,26 +78,66 @@
     </button>
 
     <div id="navbar" class="collapse navbar-collapse ms-3">
-      <ul class="navbar-nav me-auto"><li class="nav-item"><a class="nav-link" href="../articles/tern.html">Get started</a></li>
+      <ul class="navbar-nav me-auto">
+<li class="nav-item"><a class="nav-link" href="../articles/tern.html">Get started</a></li>
 <li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
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   <button class="nav-link dropdown-toggle" type="button" id="dropdown-articles" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Articles</button>
-  <ul class="dropdown-menu" aria-labelledby="dropdown-articles"><li><a class="dropdown-item" href="../articles/missing_values.html">Missing Values in Tern</a></li>
+  <ul class="dropdown-menu" aria-labelledby="dropdown-articles">
+<li><a class="dropdown-item" href="../articles/missing_values.html">Missing Values in Tern</a></li>
     <li><a class="dropdown-item" href="../articles/tables.html">Tabulation</a></li>
     <li><a class="dropdown-item" href="../articles/tern_formats.html">Formatting Functions</a></li>
     <li><a class="dropdown-item" href="../articles/tern_functions_guide.html">Understanding `tern` functions</a></li>
-  </ul></li>
+  </ul>
+</li>
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+  <ul class="dropdown-menu" aria-labelledby="dropdown-reports">
+<li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
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+  </ul>
+</li>
+      <div><li class="nav-item dropdown">
+    <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-versions">Versions</a>
+    <div class="dropdown-menu" aria-labelledby="dropdown-versions">
+    <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/main">main</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.5">v0.9.5</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.4">v0.9.4</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.3">v0.9.3</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1-rc3">v0.9.1-rc3</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a>
+</div>
+</li></div>
+</ul>
+<ul class="navbar-nav">
+<li class="nav-item"><form class="form-inline" role="search">
+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json">
+</form></li>
 <li class="nav-item"><a class="external-link nav-link" href="https://github.com/insightsengineering/tern" aria-label="GitHub"><span class="fa fa-github"></span></a></li>
-      </ul></div>
+      </ul>
+</div>
 
 
   </div>
@@ -89,7 +152,9 @@
     <div class="ref-description section level2">
     <p>These functions are wrappers of <code><a href="https://insightsengineering.github.io/rtables/latest-tag/reference/analyze_colvars.html" class="external-link">rtables::analyze_colvars()</a></code> which apply corresponding <code>tern</code>
 statistics functions to add an analysis to a given table layout. In particular, these functions
-where designed to have the analysis methods split into different columns.</p><ul><li><p><code><a href="analyze_vars_in_cols.html">analyze_vars_in_cols()</a></code>: fundamental tabulation of analysis methods onto columns.
+where designed to have the analysis methods split into different columns.</p>
+<ul>
+<li><p><code><a href="analyze_vars_in_cols.html">analyze_vars_in_cols()</a></code>: fundamental tabulation of analysis methods onto columns.
 In other words, the analysis methods are defined in the column space, i.e. they become
 column labels. By changing the variable vector, the list of functions can be applied on
 different variables, with the caveat of having the same number of statistical functions.</p></li>
@@ -105,28 +170,34 @@
 similarly to <code>tabulate_*</code> functions described above as it is designed to provide
 specific standard tables that may contain nested structure with a combination of
 <code>summarize_row_groups()</code> and <code><a href="https://insightsengineering.github.io/rtables/latest-tag/reference/analyze_colvars.html" class="external-link">rtables::analyze_colvars()</a></code>.</p></li>
-</ul></div>
+</ul>
+</div>
 
 
     <div class="section level2">
-    <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"></a></h2>
+    <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"></a>
+</h2>
     <div class="dont-index">
-<ul><li><p><a href="summarize_functions.html">summarize_functions</a> for functions which are wrappers for <code><a href="https://insightsengineering.github.io/rtables/latest-tag/reference/summarize_row_groups.html" class="external-link">rtables::summarize_row_groups()</a></code>.</p></li>
+<ul>
+<li><p><a href="summarize_functions.html">summarize_functions</a> for functions which are wrappers for <code><a href="https://insightsengineering.github.io/rtables/latest-tag/reference/summarize_row_groups.html" class="external-link">rtables::summarize_row_groups()</a></code>.</p></li>
 <li><p><a href="analyze_functions.html">analyze_functions</a> for functions which are wrappers for <code><a href="https://insightsengineering.github.io/rtables/latest-tag/reference/analyze.html" class="external-link">rtables::analyze()</a></code>.</p></li>
-</ul></div>
+</ul>
+</div>
     </div>
 
-  </main></div>
+  </main>
+</div>
 
 
     <footer><div class="nest">
   <p>tern is a part of the <strong>NEST</strong> and <a href="https://pharmaverse.org/" class="external-link"><strong>pharmaverse</strong></a>.</p>
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-
+<script type="text/javascript" src="../analytics.js"></script></footer>
+</div>
 
 
 
 
-  </body></html>
 
+  </body>
+</html>
diff --git a/main/reference/analyze_functions.html b/main/reference/analyze_functions.html
index 61df0be781..904173ee47 100644
--- a/main/reference/analyze_functions.html
+++ b/main/reference/analyze_functions.html
@@ -1,5 +1,22 @@
-<!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Analyze functions — analyze_functions • tern</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Analyze functions — analyze_functions"><meta name="description" content="These functions are wrappers of rtables::analyze() which apply corresponding tern statistics functions
+<html lang="en">
+<head>
+<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+<meta charset="utf-8">
+<meta http-equiv="X-UA-Compatible" content="IE=edge">
+<meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<title>Analyze functions — analyze_functions • tern</title>
+<!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png">
+<link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png">
+<link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png">
+<link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png">
+<link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png">
+<link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png">
+<script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet">
+<script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet">
+<link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet">
+<script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Analyze functions — analyze_functions">
+<meta name="description" content="These functions are wrappers of rtables::analyze() which apply corresponding tern statistics functions
 to add an analysis to a given table layout:
 analyze_num_patients()
 analyze_vars()
@@ -33,7 +50,8 @@
 surv_timepoint()
 test_proportion_diff()
 
-"><meta property="og:description" content="These functions are wrappers of rtables::analyze() which apply corresponding tern statistics functions
+">
+<meta property="og:description" content="These functions are wrappers of rtables::analyze() which apply corresponding tern statistics functions
 to add an analysis to a given table layout:
 analyze_num_patients()
 analyze_vars()
@@ -67,7 +85,12 @@
 surv_timepoint()
 test_proportion_diff()
 
-"><meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png"><link rel="stylesheet" href="../consent.css"><script src="../consent.js" type="text/javascript" charset="utf-8"></script></head><body>
+">
+<meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png">
+<link rel="stylesheet" href="../consent.css">
+<script src="../consent.js" type="text/javascript" charset="utf-8"></script>
+</head>
+<body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
 
 
@@ -83,26 +106,66 @@
     </button>
 
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-      <ul class="navbar-nav me-auto"><li class="nav-item"><a class="nav-link" href="../articles/tern.html">Get started</a></li>
+      <ul class="navbar-nav me-auto">
+<li class="nav-item"><a class="nav-link" href="../articles/tern.html">Get started</a></li>
 <li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
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   <button class="nav-link dropdown-toggle" type="button" id="dropdown-articles" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Articles</button>
-  <ul class="dropdown-menu" aria-labelledby="dropdown-articles"><li><a class="dropdown-item" href="../articles/missing_values.html">Missing Values in Tern</a></li>
+  <ul class="dropdown-menu" aria-labelledby="dropdown-articles">
+<li><a class="dropdown-item" href="../articles/missing_values.html">Missing Values in Tern</a></li>
     <li><a class="dropdown-item" href="../articles/tables.html">Tabulation</a></li>
     <li><a class="dropdown-item" href="../articles/tern_formats.html">Formatting Functions</a></li>
     <li><a class="dropdown-item" href="../articles/tern_functions_guide.html">Understanding `tern` functions</a></li>
-  </ul></li>
+  </ul>
+</li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
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   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
-  <ul class="dropdown-menu" aria-labelledby="dropdown-reports"><li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
+  <ul class="dropdown-menu" aria-labelledby="dropdown-reports">
+<li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
     <li><a class="dropdown-item" href="../unit-test-report/">Unit test report</a></li>
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-      </ul><ul class="navbar-nav"><li class="nav-item"><form class="form-inline" role="search">
- <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json"></form></li>
+  </ul>
+</li>
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+    <div class="dropdown-menu" aria-labelledby="dropdown-versions">
+    <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
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+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.5">v0.9.5</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.4">v0.9.4</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.3">v0.9.3</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1-rc3">v0.9.1-rc3</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a>
+</div>
+</li></div>
+</ul>
+<ul class="navbar-nav">
+<li class="nav-item"><form class="form-inline" role="search">
+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json">
+</form></li>
 <li class="nav-item"><a class="external-link nav-link" href="https://github.com/insightsengineering/tern" aria-label="GitHub"><span class="fa fa-github"></span></a></li>
-      </ul></div>
+      </ul>
+</div>
 
 
   </div>
@@ -116,7 +179,9 @@
 
     <div class="ref-description section level2">
     <p>These functions are wrappers of <code><a href="https://insightsengineering.github.io/rtables/latest-tag/reference/analyze.html" class="external-link">rtables::analyze()</a></code> which apply corresponding <code>tern</code> statistics functions
-to add an analysis to a given table layout:</p><ul><li><p><code><a href="summarize_num_patients.html">analyze_num_patients()</a></code></p></li>
+to add an analysis to a given table layout:</p>
+<ul>
+<li><p><code><a href="summarize_num_patients.html">analyze_num_patients()</a></code></p></li>
 <li><p><code><a href="analyze_variables.html">analyze_vars()</a></code></p></li>
 <li><p><code><a href="compare_variables.html">compare_vars()</a></code></p></li>
 <li><p><code><a href="abnormal.html">count_abnormal()</a></code></p></li>
@@ -147,28 +212,34 @@
 <li><p><code><a href="survival_time.html">surv_time()</a></code></p></li>
 <li><p><code><a href="survival_timepoint.html">surv_timepoint()</a></code></p></li>
 <li><p><code><a href="prop_diff_test.html">test_proportion_diff()</a></code></p></li>
-</ul></div>
+</ul>
+</div>
 
 
     <div class="section level2">
-    <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"></a></h2>
+    <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"></a>
+</h2>
     <div class="dont-index">
-<ul><li><p><a href="analyze_colvars_functions.html">analyze_colvars_functions</a> for functions that are wrappers for <code><a href="https://insightsengineering.github.io/rtables/latest-tag/reference/analyze_colvars.html" class="external-link">rtables::analyze_colvars()</a></code>.</p></li>
+<ul>
+<li><p><a href="analyze_colvars_functions.html">analyze_colvars_functions</a> for functions that are wrappers for <code><a href="https://insightsengineering.github.io/rtables/latest-tag/reference/analyze_colvars.html" class="external-link">rtables::analyze_colvars()</a></code>.</p></li>
 <li><p><a href="summarize_functions.html">summarize_functions</a> for functions which are wrappers for <code><a href="https://insightsengineering.github.io/rtables/latest-tag/reference/summarize_row_groups.html" class="external-link">rtables::summarize_row_groups()</a></code>.</p></li>
-</ul></div>
+</ul>
+</div>
     </div>
 
-  </main></div>
+  </main>
+</div>
 
 
     <footer><div class="nest">
   <p>tern is a part of the <strong>NEST</strong> and <a href="https://pharmaverse.org/" class="external-link"><strong>pharmaverse</strong></a>.</p>
 </div>
-<script type="text/javascript" src="../analytics.js"></script></footer></div>
-
+<script type="text/javascript" src="../analytics.js"></script></footer>
+</div>
 
 
 
 
-  </body></html>
 
+  </body>
+</html>
diff --git a/main/reference/analyze_variables.html b/main/reference/analyze_variables.html
index 8abb6152b0..59befade06 100644
--- a/main/reference/analyze_variables.html
+++ b/main/reference/analyze_variables.html
@@ -1,15 +1,38 @@
-<!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Analyze variables — analyze_variables • tern</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Analyze variables — analyze_variables"><meta name="description" content='
+<html lang="en">
+<head>
+<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+<meta charset="utf-8">
+<meta http-equiv="X-UA-Compatible" content="IE=edge">
+<meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<title>Analyze variables — analyze_variables • tern</title>
+<!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png">
+<link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png">
+<link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png">
+<link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png">
+<link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png">
+<link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png">
+<script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet">
+<script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet">
+<link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet">
+<script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Analyze variables — analyze_variables">
+<meta name="description" content='
 The analyze function analyze_vars() creates a layout element to summarize one or more variables, using the S3
 generic function s_summary() to calculate a list of summary statistics. A list of all available statistics for
 numeric variables can be viewed by running get_stats("analyze_vars_numeric") and for non-numeric variables by
 running get_stats("analyze_vars_counts"). Use the .stats parameter to specify the statistics to include in your
-output summary table.'><meta property="og:description" content='
+output summary table.'>
+<meta property="og:description" content='
 The analyze function analyze_vars() creates a layout element to summarize one or more variables, using the S3
 generic function s_summary() to calculate a list of summary statistics. A list of all available statistics for
 numeric variables can be viewed by running get_stats("analyze_vars_numeric") and for non-numeric variables by
 running get_stats("analyze_vars_counts"). Use the .stats parameter to specify the statistics to include in your
-output summary table.'><meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png"><link rel="stylesheet" href="../consent.css"><script src="../consent.js" type="text/javascript" charset="utf-8"></script></head><body>
+output summary table.'>
+<meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png">
+<link rel="stylesheet" href="../consent.css">
+<script src="../consent.js" type="text/javascript" charset="utf-8"></script>
+</head>
+<body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
 
 
@@ -25,26 +48,66 @@
     </button>
 
     <div id="navbar" class="collapse navbar-collapse ms-3">
-      <ul class="navbar-nav me-auto"><li class="nav-item"><a class="nav-link" href="../articles/tern.html">Get started</a></li>
+      <ul class="navbar-nav me-auto">
+<li class="nav-item"><a class="nav-link" href="../articles/tern.html">Get started</a></li>
 <li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
 <li class="nav-item dropdown">
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-articles" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Articles</button>
-  <ul class="dropdown-menu" aria-labelledby="dropdown-articles"><li><a class="dropdown-item" href="../articles/missing_values.html">Missing Values in Tern</a></li>
+  <ul class="dropdown-menu" aria-labelledby="dropdown-articles">
+<li><a class="dropdown-item" href="../articles/missing_values.html">Missing Values in Tern</a></li>
     <li><a class="dropdown-item" href="../articles/tables.html">Tabulation</a></li>
     <li><a class="dropdown-item" href="../articles/tern_formats.html">Formatting Functions</a></li>
     <li><a class="dropdown-item" href="../articles/tern_functions_guide.html">Understanding `tern` functions</a></li>
-  </ul></li>
+  </ul>
+</li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
-  <ul class="dropdown-menu" aria-labelledby="dropdown-reports"><li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
+  <ul class="dropdown-menu" aria-labelledby="dropdown-reports">
+<li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
     <li><a class="dropdown-item" href="../unit-test-report/">Unit test report</a></li>
     <li><a class="dropdown-item" href="../unit-test-report-non-cran/">Non-CRAN unit test report</a></li>
-  </ul></li>
-      </ul><ul class="navbar-nav"><li class="nav-item"><form class="form-inline" role="search">
- <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json"></form></li>
+  </ul>
+</li>
+      <div><li class="nav-item dropdown">
+    <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-versions">Versions</a>
+    <div class="dropdown-menu" aria-labelledby="dropdown-versions">
+    <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/main">main</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.5">v0.9.5</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.4">v0.9.4</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.3">v0.9.3</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1-rc3">v0.9.1-rc3</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a>
+</div>
+</li></div>
+</ul>
+<ul class="navbar-nav">
+<li class="nav-item"><form class="form-inline" role="search">
+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json">
+</form></li>
 <li class="nav-item"><a class="external-link nav-link" href="https://github.com/insightsengineering/tern" aria-label="GitHub"><span class="fa fa-github"></span></a></li>
-      </ul></div>
+      </ul>
+</div>
 
 
   </div>
@@ -66,7 +129,8 @@
     </div>
 
     <div class="section level2">
-    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
+    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">analyze_vars</span><span class="op">(</span></span>
 <span>  <span class="va">lyt</span>,</span>
 <span>  <span class="va">vars</span>,</span>
@@ -150,140 +214,187 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
     </div>
 
     <div class="section level2">
-    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
+    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a>
+</h2>
 
 
-<dl><dt id="arg-lyt">lyt<a class="anchor" aria-label="anchor" href="#arg-lyt"></a></dt>
+<dl>
+<dt id="arg-lyt">lyt<a class="anchor" aria-label="anchor" href="#arg-lyt"></a>
+</dt>
 <dd><p>(<code>PreDataTableLayouts</code>)<br> layout that analyses will be added to.</p></dd>
 
 
-<dt id="arg-vars">vars<a class="anchor" aria-label="anchor" href="#arg-vars"></a></dt>
+<dt id="arg-vars">vars<a class="anchor" aria-label="anchor" href="#arg-vars"></a>
+</dt>
 <dd><p>(<code>character</code>)<br> variable names for the primary analysis variable to be iterated over.</p></dd>
 
 
-<dt id="arg-var-labels">var_labels<a class="anchor" aria-label="anchor" href="#arg-var-labels"></a></dt>
+<dt id="arg-var-labels">var_labels<a class="anchor" aria-label="anchor" href="#arg-var-labels"></a>
+</dt>
 <dd><p>(<code>character</code>)<br> variable labels.</p></dd>
 
 
-<dt id="arg-na-str">na_str<a class="anchor" aria-label="anchor" href="#arg-na-str"></a></dt>
+<dt id="arg-na-str">na_str<a class="anchor" aria-label="anchor" href="#arg-na-str"></a>
+</dt>
 <dd><p>(<code>string</code>)<br> string used to replace all <code>NA</code> or empty values in the output.</p></dd>
 
 
-<dt id="arg-nested">nested<a class="anchor" aria-label="anchor" href="#arg-nested"></a></dt>
+<dt id="arg-nested">nested<a class="anchor" aria-label="anchor" href="#arg-nested"></a>
+</dt>
 <dd><p>(<code>flag</code>)<br> whether this layout instruction should be applied within the existing layout structure _if
 possible (<code>TRUE</code>, the default) or as a new top-level element (<code>FALSE</code>). Ignored if it would nest a split.
 underneath analyses, which is not allowed.</p></dd>
 
 
-<dt id="arg--">...<a class="anchor" aria-label="anchor" href="#arg--"></a></dt>
+<dt id="arg--">...<a class="anchor" aria-label="anchor" href="#arg--"></a>
+</dt>
 <dd><p>arguments passed to <code>s_summary()</code>.</p></dd>
 
 
-<dt id="arg-na-rm">na.rm<a class="anchor" aria-label="anchor" href="#arg-na-rm"></a></dt>
+<dt id="arg-na-rm">na.rm<a class="anchor" aria-label="anchor" href="#arg-na-rm"></a>
+</dt>
 <dd><p>(<code>flag</code>)<br> whether <code>NA</code> values should be removed from <code>x</code> prior to analysis.</p></dd>
 
 
-<dt id="arg-show-labels">show_labels<a class="anchor" aria-label="anchor" href="#arg-show-labels"></a></dt>
+<dt id="arg-show-labels">show_labels<a class="anchor" aria-label="anchor" href="#arg-show-labels"></a>
+</dt>
 <dd><p>(<code>string</code>)<br> label visibility: one of "default", "visible" and "hidden".</p></dd>
 
 
-<dt id="arg-table-names">table_names<a class="anchor" aria-label="anchor" href="#arg-table-names"></a></dt>
+<dt id="arg-table-names">table_names<a class="anchor" aria-label="anchor" href="#arg-table-names"></a>
+</dt>
 <dd><p>(<code>character</code>)<br> this can be customized in the case that the same <code>vars</code> are analyzed multiple
 times, to avoid warnings from <code>rtables</code>.</p></dd>
 
 
-<dt id="arg-section-div">section_div<a class="anchor" aria-label="anchor" href="#arg-section-div"></a></dt>
+<dt id="arg-section-div">section_div<a class="anchor" aria-label="anchor" href="#arg-section-div"></a>
+</dt>
 <dd><p>(<code>string</code>)<br> string which should be repeated as a section divider after each group
 defined by this split instruction, or <code>NA_character_</code> (the default) for no section divider.</p></dd>
 
 
-<dt id="arg--stats">.stats<a class="anchor" aria-label="anchor" href="#arg--stats"></a></dt>
-<dd><p>(<code>character</code>)<br> statistics to select for the table.</p>
+<dt id="arg--stats">.stats<a class="anchor" aria-label="anchor" href="#arg--stats"></a>
+</dt>
+<dd>
+<p>(<code>character</code>)<br> statistics to select for the table.</p>
 <p>Options for numeric variables are: <code>'n', 'sum', 'mean', 'sd', 'se', 'mean_sd', 'mean_se', 'mean_ci', 'mean_sei', 'mean_sdi', 'mean_pval', 'median', 'mad', 'median_ci', 'quantiles', 'iqr', 'range', 'min', 'max', 'median_range', 'cv', 'geom_mean', 'geom_mean_ci', 'geom_cv', 'median_ci_3d', 'mean_ci_3d', 'geom_mean_ci_3d'</code></p>
-<p>Options for non-numeric variables are: <code>'n', 'count', 'count_fraction', 'count_fraction_fixed_dp', 'fraction', 'n_blq'</code></p></dd>
+<p>Options for non-numeric variables are: <code>'n', 'count', 'count_fraction', 'count_fraction_fixed_dp', 'fraction', 'n_blq'</code></p>
+</dd>
 
 
-<dt id="arg--formats">.formats<a class="anchor" aria-label="anchor" href="#arg--formats"></a></dt>
+<dt id="arg--formats">.formats<a class="anchor" aria-label="anchor" href="#arg--formats"></a>
+</dt>
 <dd><p>(named <code>character</code> or <code>list</code>)<br> formats for the statistics. See Details in <code>analyze_vars</code> for more
 information on the <code>"auto"</code> setting.</p></dd>
 
 
-<dt id="arg--labels">.labels<a class="anchor" aria-label="anchor" href="#arg--labels"></a></dt>
+<dt id="arg--labels">.labels<a class="anchor" aria-label="anchor" href="#arg--labels"></a>
+</dt>
 <dd><p>(named <code>character</code>)<br> labels for the statistics (without indent).</p></dd>
 
 
-<dt id="arg--indent-mods">.indent_mods<a class="anchor" aria-label="anchor" href="#arg--indent-mods"></a></dt>
+<dt id="arg--indent-mods">.indent_mods<a class="anchor" aria-label="anchor" href="#arg--indent-mods"></a>
+</dt>
 <dd><p>(named <code>integer</code>)<br> indent modifiers for the labels. Each element of the vector
 should be a name-value pair with name corresponding to a statistic specified in <code>.stats</code> and value the indentation
 for that statistic's row label.</p></dd>
 
 
-<dt id="arg-x">x<a class="anchor" aria-label="anchor" href="#arg-x"></a></dt>
+<dt id="arg-x">x<a class="anchor" aria-label="anchor" href="#arg-x"></a>
+</dt>
 <dd><p>(<code>numeric</code>)<br> vector of numbers we want to analyze.</p></dd>
 
 
-<dt id="arg-denom">denom<a class="anchor" aria-label="anchor" href="#arg-denom"></a></dt>
-<dd><p>(<code>string</code>)<br> choice of denominator for proportion. Options are:</p><ul><li><p><code>n</code>: number of values in this row and column intersection.</p></li>
+<dt id="arg-denom">denom<a class="anchor" aria-label="anchor" href="#arg-denom"></a>
+</dt>
+<dd>
+<p>(<code>string</code>)<br> choice of denominator for proportion. Options are:</p>
+<ul>
+<li><p><code>n</code>: number of values in this row and column intersection.</p></li>
 <li><p><code>N_row</code>: total number of values in this row across columns.</p></li>
 <li><p><code>N_col</code>: total number of values in this column across rows.</p></li>
-</ul></dd>
+</ul>
+</dd>
 
 
-<dt id="arg--n-row">.N_row<a class="anchor" aria-label="anchor" href="#arg--n-row"></a></dt>
+<dt id="arg--n-row">.N_row<a class="anchor" aria-label="anchor" href="#arg--n-row"></a>
+</dt>
 <dd><p>(<code>integer(1)</code>)<br> row-wise N (row group count) for the group of observations being analyzed
 (i.e. with no column-based subsetting) that is typically passed by <code>rtables</code>.</p></dd>
 
 
-<dt id="arg--n-col">.N_col<a class="anchor" aria-label="anchor" href="#arg--n-col"></a></dt>
+<dt id="arg--n-col">.N_col<a class="anchor" aria-label="anchor" href="#arg--n-col"></a>
+</dt>
 <dd><p>(<code>integer(1)</code>)<br> column-wise N (column count) for the full column being analyzed that is typically
 passed by <code>rtables</code>.</p></dd>
 
 
-<dt id="arg--var">.var<a class="anchor" aria-label="anchor" href="#arg--var"></a></dt>
+<dt id="arg--var">.var<a class="anchor" aria-label="anchor" href="#arg--var"></a>
+</dt>
 <dd><p>(<code>string</code>)<br> single variable name that is passed by <code>rtables</code> when requested
 by a statistics function.</p></dd>
 
 
-<dt id="arg-control">control<a class="anchor" aria-label="anchor" href="#arg-control"></a></dt>
-<dd><p>(<code>list</code>)<br> parameters for descriptive statistics details, specified by using
-the helper function <code><a href="control_analyze_vars.html">control_analyze_vars()</a></code>. Some possible parameter options are:</p><ul><li><p><code>conf_level</code> (<code>proportion</code>)<br> confidence level of the interval for mean and median.</p></li>
+<dt id="arg-control">control<a class="anchor" aria-label="anchor" href="#arg-control"></a>
+</dt>
+<dd>
+<p>(<code>list</code>)<br> parameters for descriptive statistics details, specified by using
+the helper function <code><a href="control_analyze_vars.html">control_analyze_vars()</a></code>. Some possible parameter options are:</p>
+<ul>
+<li><p><code>conf_level</code> (<code>proportion</code>)<br> confidence level of the interval for mean and median.</p></li>
 <li><p><code>quantiles</code> (<code>numeric(2)</code>)<br> vector of length two to specify the quantiles.</p></li>
 <li><p><code>quantile_type</code> (<code>numeric(1)</code>)<br> between 1 and 9 selecting quantile algorithms to be used.
 See more about <code>type</code> in <code><a href="https://rdrr.io/r/stats/quantile.html" class="external-link">stats::quantile()</a></code>.</p></li>
 <li><p><code>test_mean</code> (<code>numeric(1)</code>)<br> value to test against the mean under the null hypothesis when calculating p-value.</p></li>
-</ul></dd>
+</ul>
+</dd>
 
 
-<dt id="arg-verbose">verbose<a class="anchor" aria-label="anchor" href="#arg-verbose"></a></dt>
+<dt id="arg-verbose">verbose<a class="anchor" aria-label="anchor" href="#arg-verbose"></a>
+</dt>
 <dd><p>(<code>flag</code>)<br> defaults to <code>TRUE</code>, which prints out warnings and messages. It is mainly used
 to print out information about factor casting.</p></dd>
 
 
-<dt id="arg--df-row">.df_row<a class="anchor" aria-label="anchor" href="#arg--df-row"></a></dt>
+<dt id="arg--df-row">.df_row<a class="anchor" aria-label="anchor" href="#arg--df-row"></a>
+</dt>
 <dd><p>(<code>data.frame</code>)<br> data frame across all of the columns for the given row split.</p></dd>
 
 
-<dt id="arg--ref-group">.ref_group<a class="anchor" aria-label="anchor" href="#arg--ref-group"></a></dt>
+<dt id="arg--ref-group">.ref_group<a class="anchor" aria-label="anchor" href="#arg--ref-group"></a>
+</dt>
 <dd><p>(<code>data.frame</code> or <code>vector</code>)<br> the data corresponding to the reference group.</p></dd>
 
 
-<dt id="arg--in-ref-col">.in_ref_col<a class="anchor" aria-label="anchor" href="#arg--in-ref-col"></a></dt>
+<dt id="arg--in-ref-col">.in_ref_col<a class="anchor" aria-label="anchor" href="#arg--in-ref-col"></a>
+</dt>
 <dd><p>(<code>flag</code>)<br><code>TRUE</code> when working with the reference level, <code>FALSE</code> otherwise.</p></dd>
 
 
-<dt id="arg-compare">compare<a class="anchor" aria-label="anchor" href="#arg-compare"></a></dt>
+<dt id="arg-compare">compare<a class="anchor" aria-label="anchor" href="#arg-compare"></a>
+</dt>
 <dd><p>(<code>flag</code>)<br> whether comparison statistics should be analyzed instead of summary statistics
 (<code>compare = TRUE</code> adds <code>pval</code> statistic comparing against reference group).</p></dd>
 
-</dl></div>
+</dl>
+</div>
     <div class="section level2">
-    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
+    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a>
+</h2>
 
-<ul><li><p><code>analyze_vars()</code> returns a layout object suitable for passing to further layouting functions,
+<ul>
+<li><p><code>analyze_vars()</code> returns a layout object suitable for passing to further layouting functions,
 or to <code><a href="https://insightsengineering.github.io/rtables/latest-tag/reference/build_table.html" class="external-link">rtables::build_table()</a></code>. Adding this function to an <code>rtable</code> layout will add formatted rows containing
 the statistics from <code>s_summary()</code> to the table layout.</p></li>
-</ul><ul><li><p><code>s_summary()</code> returns different statistics depending on the class of <code>x</code>.</p></li>
-</ul><ul><li><p>If <code>x</code> is of class <code>numeric</code>, returns a <code>list</code> with the following named <code>numeric</code> items:</p><ul><li><p><code>n</code>: The <code><a href="https://rdrr.io/r/base/length.html" class="external-link">length()</a></code> of <code>x</code>.</p></li>
+</ul>
+<ul>
+<li><p><code>s_summary()</code> returns different statistics depending on the class of <code>x</code>.</p></li>
+</ul>
+<ul>
+<li>
+<p>If <code>x</code> is of class <code>numeric</code>, returns a <code>list</code> with the following named <code>numeric</code> items:</p>
+<ul>
+<li><p><code>n</code>: The <code><a href="https://rdrr.io/r/base/length.html" class="external-link">length()</a></code> of <code>x</code>.</p></li>
 <li><p><code>sum</code>: The <code><a href="https://rdrr.io/r/base/sum.html" class="external-link">sum()</a></code> of <code>x</code>.</p></li>
 <li><p><code>mean</code>: The <code><a href="https://rdrr.io/r/base/mean.html" class="external-link">mean()</a></code> of <code>x</code>.</p></li>
 <li><p><code>sd</code>: The <code><a href="https://rdrr.io/r/stats/sd.html" class="external-link">stats::sd()</a></code> of <code>x</code>.</p></li>
@@ -307,30 +418,49 @@ <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2
 <li><p><code>cv</code>: The coefficient of variation of <code>x</code>, i.e.: (<code><a href="https://rdrr.io/r/stats/sd.html" class="external-link">stats::sd()</a></code> / <code><a href="https://rdrr.io/r/base/mean.html" class="external-link">mean()</a></code> * 100).</p></li>
 <li><p><code>geom_mean</code>: The geometric mean of <code>x</code>, i.e.: (<code>exp(mean(log(x)))</code>).</p></li>
 <li><p><code>geom_cv</code>: The geometric coefficient of variation of <code>x</code>, i.e.: (<code>sqrt(exp(sd(log(x)) ^ 2) - 1) * 100</code>).</p></li>
-</ul></li>
-</ul><ul><li><p>If <code>x</code> is of class <code>factor</code> or converted from <code>character</code>, returns a <code>list</code> with named <code>numeric</code> items:</p><ul><li><p><code>n</code>: The <code><a href="https://rdrr.io/r/base/length.html" class="external-link">length()</a></code> of <code>x</code>.</p></li>
+</ul>
+</li>
+</ul>
+<ul>
+<li>
+<p>If <code>x</code> is of class <code>factor</code> or converted from <code>character</code>, returns a <code>list</code> with named <code>numeric</code> items:</p>
+<ul>
+<li><p><code>n</code>: The <code><a href="https://rdrr.io/r/base/length.html" class="external-link">length()</a></code> of <code>x</code>.</p></li>
 <li><p><code>count</code>: A list with the number of cases for each level of the factor <code>x</code>.</p></li>
 <li><p><code>count_fraction</code>: Similar to <code>count</code> but also includes the proportion of cases for each level of the
 factor <code>x</code> relative to the denominator, or <code>NA</code> if the denominator is zero.</p></li>
-</ul></li>
-</ul><ul><li><p>If <code>x</code> is of class <code>logical</code>, returns a <code>list</code> with named <code>numeric</code> items:</p><ul><li><p><code>n</code>: The <code><a href="https://rdrr.io/r/base/length.html" class="external-link">length()</a></code> of <code>x</code> (possibly after removing <code>NA</code>s).</p></li>
+</ul>
+</li>
+</ul>
+<ul>
+<li>
+<p>If <code>x</code> is of class <code>logical</code>, returns a <code>list</code> with named <code>numeric</code> items:</p>
+<ul>
+<li><p><code>n</code>: The <code><a href="https://rdrr.io/r/base/length.html" class="external-link">length()</a></code> of <code>x</code> (possibly after removing <code>NA</code>s).</p></li>
 <li><p><code>count</code>: Count of <code>TRUE</code> in <code>x</code>.</p></li>
 <li><p><code>count_fraction</code>: Count and proportion of <code>TRUE</code> in <code>x</code> relative to the denominator, or <code>NA</code> if the
 denominator is zero. Note that <code>NA</code>s in <code>x</code> are never counted or leading to <code>NA</code> here.</p></li>
-</ul></li>
-</ul><ul><li><p><code>a_summary()</code> returns the corresponding list with formatted <code><a href="https://insightsengineering.github.io/rtables/latest-tag/reference/CellValue.html" class="external-link">rtables::CellValue()</a></code>.</p></li>
-</ul></div>
+</ul>
+</li>
+</ul>
+<ul>
+<li><p><code>a_summary()</code> returns the corresponding list with formatted <code><a href="https://insightsengineering.github.io/rtables/latest-tag/reference/CellValue.html" class="external-link">rtables::CellValue()</a></code>.</p></li>
+</ul>
+</div>
     <div class="section level2">
-    <h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a></h2>
+    <h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a>
+</h2>
     <p><strong>Automatic digit formatting:</strong> The number of digits to display can be automatically determined from the analyzed
 variable(s) (<code>vars</code>) for certain statistics by setting the statistic format to <code>"auto"</code> in <code>.formats</code>.
 This utilizes the <code><a href="format_auto.html">format_auto()</a></code> formatting function. Note that only data for the current row &amp; variable (for all
 columns) will be considered (<code>.df_row[[.var]]</code>, see <code><a href="https://insightsengineering.github.io/rtables/latest-tag/reference/additional_fun_params.html" class="external-link">rtables::additional_fun_params</a></code>) and not the whole dataset.</p>
     </div>
     <div class="section level2">
-    <h2 id="functions">Functions<a class="anchor" aria-label="anchor" href="#functions"></a></h2>
+    <h2 id="functions">Functions<a class="anchor" aria-label="anchor" href="#functions"></a>
+</h2>
 
-<ul><li><p><code>analyze_vars()</code>: Layout-creating function which can take statistics function arguments
+<ul>
+<li><p><code>analyze_vars()</code>: Layout-creating function which can take statistics function arguments
 and additional format arguments. This function is a wrapper for <code><a href="https://insightsengineering.github.io/rtables/latest-tag/reference/analyze.html" class="external-link">rtables::analyze()</a></code>.</p></li>
 <li><p><code>s_summary()</code>: S3 generic function to produces a variable summary.</p></li>
 <li><p><code>s_summary(numeric)</code>: Method for <code>numeric</code> class.</p></li>
@@ -340,30 +470,41 @@ <h2 id="functions">Functions<a class="anchor" aria-label="anchor" href="#functio
 <li><p><code>s_summary(logical)</code>: Method for <code>logical</code> class.</p></li>
 <li><p><code>a_summary()</code>: Formatted analysis function which is used as <code>afun</code> in <code>analyze_vars()</code> and
 <code><a href="compare_variables.html">compare_vars()</a></code> and as <code>cfun</code> in <code><a href="summarize_colvars.html">summarize_colvars()</a></code>.</p></li>
-</ul></div>
+</ul>
+</div>
     <div class="section level2">
-    <h2 id="note">Note<a class="anchor" aria-label="anchor" href="#note"></a></h2>
+    <h2 id="note">Note<a class="anchor" aria-label="anchor" href="#note"></a>
+</h2>
 
-<ul><li><p>If <code>x</code> is an empty vector, <code>NA</code> is returned. This is the expected feature so as to return <code>rcell</code> content in
+<ul>
+<li><p>If <code>x</code> is an empty vector, <code>NA</code> is returned. This is the expected feature so as to return <code>rcell</code> content in
 <code>rtables</code> when the intersection of a column and a row delimits an empty data selection.</p></li>
 <li><p>When the <code>mean</code> function is applied to an empty vector, <code>NA</code> will be returned instead of <code>NaN</code>, the latter
 being standard behavior in R.</p></li>
-</ul><ul><li><p>If <code>x</code> is an empty <code>factor</code>, a list is still returned for <code>counts</code> with one element
+</ul>
+<ul>
+<li><p>If <code>x</code> is an empty <code>factor</code>, a list is still returned for <code>counts</code> with one element
 per factor level. If there are no levels in <code>x</code>, the function fails.</p></li>
 <li><p>If factor variables contain <code>NA</code>, these <code>NA</code> values are excluded by default. To include <code>NA</code> values
 set <code>na.rm = FALSE</code> and missing values will be displayed as an <code>NA</code> level. Alternatively, an explicit
 factor level can be defined for <code>NA</code> values during pre-processing via <code><a href="df_explicit_na.html">df_explicit_na()</a></code> - the
 default <code>na_level</code> (<code>"&lt;Missing&gt;"</code>) will also be excluded when <code>na.rm</code> is set to <code>TRUE</code>.</p></li>
-</ul><ul><li><p>Automatic conversion of character to factor does not guarantee that the table
+</ul>
+<ul>
+<li><p>Automatic conversion of character to factor does not guarantee that the table
 can be generated correctly. In particular for sparse tables this very likely can fail.
 It is therefore better to always pre-process the dataset such that factors are manually
 created from character variables before passing the dataset to <code><a href="https://insightsengineering.github.io/rtables/latest-tag/reference/build_table.html" class="external-link">rtables::build_table()</a></code>.</p></li>
-</ul><ul><li><p>To use for comparison (with additional p-value statistic), parameter <code>compare</code> must be set to <code>TRUE</code>.</p></li>
+</ul>
+<ul>
+<li><p>To use for comparison (with additional p-value statistic), parameter <code>compare</code> must be set to <code>TRUE</code>.</p></li>
 <li><p>Ensure that either all <code>NA</code> values are converted to an explicit <code>NA</code> level or all <code>NA</code> values are left as is.</p></li>
-</ul></div>
+</ul>
+</div>
 
     <div class="section level2">
-    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
+    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="co">## Fabricated dataset.</span></span></span>
 <span class="r-in"><span><span class="va">dta_test</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a></span><span class="op">(</span></span></span>
 <span class="r-in"><span>  USUBJID <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/rep.html" class="external-link">rep</a></span><span class="op">(</span><span class="fl">1</span><span class="op">:</span><span class="fl">6</span>, each <span class="op">=</span> <span class="fl">3</span><span class="op">)</span>,</span></span>
@@ -2538,17 +2679,19 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 </code></pre></div>
     </div>
   </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
-    </nav></aside></div>
+    </nav></aside>
+</div>
 
 
     <footer><div class="nest">
   <p>tern is a part of the <strong>NEST</strong> and <a href="https://pharmaverse.org/" class="external-link"><strong>pharmaverse</strong></a>.</p>
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-<script type="text/javascript" src="../analytics.js"></script></footer></div>
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+<script type="text/javascript" src="../analytics.js"></script></footer>
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diff --git a/main/reference/analyze_vars_in_cols.html b/main/reference/analyze_vars_in_cols.html
index 62295bb1d0..cc2afba829 100644
--- a/main/reference/analyze_vars_in_cols.html
+++ b/main/reference/analyze_vars_in_cols.html
@@ -1,13 +1,36 @@
-<!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Analyze numeric variables in columns — analyze_vars_in_cols • tern</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Analyze numeric variables in columns — analyze_vars_in_cols"><meta name="description" content="
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+<title>Analyze numeric variables in columns — analyze_vars_in_cols • tern</title>
+<!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png">
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+<script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet">
+<script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet">
+<link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet">
+<script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Analyze numeric variables in columns — analyze_vars_in_cols">
+<meta name="description" content="
 The layout-creating function analyze_vars_in_cols() creates a layout element to generate a column-wise
 analysis table.
 This function sets the analysis methods as column labels and is a wrapper for rtables::analyze_colvars().
-It was designed principally for PK tables."><meta property="og:description" content="
+It was designed principally for PK tables.">
+<meta property="og:description" content="
 The layout-creating function analyze_vars_in_cols() creates a layout element to generate a column-wise
 analysis table.
 This function sets the analysis methods as column labels and is a wrapper for rtables::analyze_colvars().
-It was designed principally for PK tables."><meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png"><link rel="stylesheet" href="../consent.css"><script src="../consent.js" type="text/javascript" charset="utf-8"></script></head><body>
+It was designed principally for PK tables.">
+<meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png">
+<link rel="stylesheet" href="../consent.css">
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+</head>
+<body>
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+  <ul class="dropdown-menu" aria-labelledby="dropdown-articles">
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+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
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+</div>
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+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json">
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+</div>
 
 
   </div>
@@ -63,7 +126,8 @@
     </div>
 
     <div class="section level2">
-    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
+    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">analyze_vars_in_cols</span><span class="op">(</span></span>
 <span>  <span class="va">lyt</span>,</span>
 <span>  <span class="va">vars</span>,</span>
@@ -86,116 +150,141 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
     </div>
 
     <div class="section level2">
-    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
+    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a>
+</h2>
 
 
-<dl><dt id="arg-lyt">lyt<a class="anchor" aria-label="anchor" href="#arg-lyt"></a></dt>
+<dl>
+<dt id="arg-lyt">lyt<a class="anchor" aria-label="anchor" href="#arg-lyt"></a>
+</dt>
 <dd><p>(<code>PreDataTableLayouts</code>)<br> layout that analyses will be added to.</p></dd>
 
 
-<dt id="arg-vars">vars<a class="anchor" aria-label="anchor" href="#arg-vars"></a></dt>
+<dt id="arg-vars">vars<a class="anchor" aria-label="anchor" href="#arg-vars"></a>
+</dt>
 <dd><p>(<code>character</code>)<br> variable names for the primary analysis variable to be iterated over.</p></dd>
 
 
-<dt id="arg--">...<a class="anchor" aria-label="anchor" href="#arg--"></a></dt>
+<dt id="arg--">...<a class="anchor" aria-label="anchor" href="#arg--"></a>
+</dt>
 <dd><p>additional arguments for the lower level functions.</p></dd>
 
 
-<dt id="arg--stats">.stats<a class="anchor" aria-label="anchor" href="#arg--stats"></a></dt>
+<dt id="arg--stats">.stats<a class="anchor" aria-label="anchor" href="#arg--stats"></a>
+</dt>
 <dd><p>(<code>character</code>)<br> statistics to select for the table.</p></dd>
 
 
-<dt id="arg--labels">.labels<a class="anchor" aria-label="anchor" href="#arg--labels"></a></dt>
+<dt id="arg--labels">.labels<a class="anchor" aria-label="anchor" href="#arg--labels"></a>
+</dt>
 <dd><p>(named <code>character</code>)<br> labels for the statistics (without indent).</p></dd>
 
 
-<dt id="arg-row-labels">row_labels<a class="anchor" aria-label="anchor" href="#arg-row-labels"></a></dt>
+<dt id="arg-row-labels">row_labels<a class="anchor" aria-label="anchor" href="#arg-row-labels"></a>
+</dt>
 <dd><p>(<code>character</code>)<br> as this function works in columns space, usually <code>.labels</code>
 character vector applies on the column space. You can change the row labels by defining this
 parameter to a named character vector with names corresponding to the split values. It defaults
 to <code>NULL</code> and if it contains only one <code>string</code>, it will duplicate that as a row label.</p></dd>
 
 
-<dt id="arg-do-summarize-row-groups">do_summarize_row_groups<a class="anchor" aria-label="anchor" href="#arg-do-summarize-row-groups"></a></dt>
+<dt id="arg-do-summarize-row-groups">do_summarize_row_groups<a class="anchor" aria-label="anchor" href="#arg-do-summarize-row-groups"></a>
+</dt>
 <dd><p>(<code>flag</code>)<br> defaults to <code>FALSE</code> and applies the analysis to the current
 label rows. This is a wrapper of <code><a href="https://insightsengineering.github.io/rtables/latest-tag/reference/summarize_row_groups.html" class="external-link">rtables::summarize_row_groups()</a></code> and it can accept <code>labelstr</code>
 to define row labels. This behavior is not supported as we never need to overload row labels.</p></dd>
 
 
-<dt id="arg-split-col-vars">split_col_vars<a class="anchor" aria-label="anchor" href="#arg-split-col-vars"></a></dt>
+<dt id="arg-split-col-vars">split_col_vars<a class="anchor" aria-label="anchor" href="#arg-split-col-vars"></a>
+</dt>
 <dd><p>(<code>flag</code>)<br> defaults to <code>TRUE</code> and puts the analysis results onto the columns.
 This option allows you to add multiple instances of this functions, also in a nested fashion,
 without adding more splits. This split must happen only one time on a single layout.</p></dd>
 
 
-<dt id="arg-imp-rule">imp_rule<a class="anchor" aria-label="anchor" href="#arg-imp-rule"></a></dt>
+<dt id="arg-imp-rule">imp_rule<a class="anchor" aria-label="anchor" href="#arg-imp-rule"></a>
+</dt>
 <dd><p>(<code>string</code> or <code>NULL</code>)<br> imputation rule setting. Defaults to <code>NULL</code> for no imputation rule. Can
 also be <code>"1/3"</code> to implement 1/3 imputation rule or <code>"1/2"</code> to implement 1/2 imputation rule. In order
 to use an imputation rule, the <code>avalcat_var</code> argument must be specified. See <code><a href="imputation_rule.html">imputation_rule()</a></code>
 for more details on imputation.</p></dd>
 
 
-<dt id="arg-avalcat-var">avalcat_var<a class="anchor" aria-label="anchor" href="#arg-avalcat-var"></a></dt>
+<dt id="arg-avalcat-var">avalcat_var<a class="anchor" aria-label="anchor" href="#arg-avalcat-var"></a>
+</dt>
 <dd><p>(<code>string</code>)<br> if <code>imp_rule</code> is not <code>NULL</code>, name of variable that indicates whether a
 row in the data corresponds to an analysis value in category <code>"BLQ"</code>, <code>"LTR"</code>, <code>"&lt;PCLLOQ"</code>, or none of
 the above (defaults to <code>"AVALCAT1"</code>). Variable must be present in the data and should match the variable
 used to calculate the <code>n_blq</code> statistic (if included in <code>.stats</code>).</p></dd>
 
 
-<dt id="arg-cache">cache<a class="anchor" aria-label="anchor" href="#arg-cache"></a></dt>
+<dt id="arg-cache">cache<a class="anchor" aria-label="anchor" href="#arg-cache"></a>
+</dt>
 <dd><p>(<code>flag</code>)<br> whether to store computed values in a temporary caching environment. This will
 speed up calculations in large tables, but should be set to <code>FALSE</code> if the same <code>rtable</code> layout is
 used for multiple tables with different data. Defaults to <code>FALSE</code>.</p></dd>
 
 
-<dt id="arg--indent-mods">.indent_mods<a class="anchor" aria-label="anchor" href="#arg--indent-mods"></a></dt>
+<dt id="arg--indent-mods">.indent_mods<a class="anchor" aria-label="anchor" href="#arg--indent-mods"></a>
+</dt>
 <dd><p>(named <code>integer</code>)<br> indent modifiers for the labels. Defaults to 0, which corresponds to the
 unmodified default behavior. Can be negative.</p></dd>
 
 
-<dt id="arg-na-str">na_str<a class="anchor" aria-label="anchor" href="#arg-na-str"></a></dt>
+<dt id="arg-na-str">na_str<a class="anchor" aria-label="anchor" href="#arg-na-str"></a>
+</dt>
 <dd><p>(<code>string</code>)<br> string used to replace all <code>NA</code> or empty values in the output.</p></dd>
 
 
-<dt id="arg-nested">nested<a class="anchor" aria-label="anchor" href="#arg-nested"></a></dt>
+<dt id="arg-nested">nested<a class="anchor" aria-label="anchor" href="#arg-nested"></a>
+</dt>
 <dd><p>(<code>flag</code>)<br> whether this layout instruction should be applied within the existing layout structure _if
 possible (<code>TRUE</code>, the default) or as a new top-level element (<code>FALSE</code>). Ignored if it would nest a split.
 underneath analyses, which is not allowed.</p></dd>
 
 
-<dt id="arg--formats">.formats<a class="anchor" aria-label="anchor" href="#arg--formats"></a></dt>
+<dt id="arg--formats">.formats<a class="anchor" aria-label="anchor" href="#arg--formats"></a>
+</dt>
 <dd><p>(named <code>character</code> or <code>list</code>)<br> formats for the statistics. See Details in <code>analyze_vars</code> for more
 information on the <code>"auto"</code> setting.</p></dd>
 
 
-<dt id="arg--aligns">.aligns<a class="anchor" aria-label="anchor" href="#arg--aligns"></a></dt>
+<dt id="arg--aligns">.aligns<a class="anchor" aria-label="anchor" href="#arg--aligns"></a>
+</dt>
 <dd><p>(<code>character</code> or <code>NULL</code>)<br> alignment for table contents (not including labels). When <code>NULL</code>,
 <code>"center"</code> is applied. See <code><a href="https://insightsengineering.github.io/formatters/latest-tag/reference/list_formats.html" class="external-link">formatters::list_valid_aligns()</a></code> for a list of all currently supported alignments.</p></dd>
 
-</dl></div>
+</dl>
+</div>
     <div class="section level2">
-    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
+    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a>
+</h2>
     <p>A layout object suitable for passing to further layouting functions, or to <code><a href="https://insightsengineering.github.io/rtables/latest-tag/reference/build_table.html" class="external-link">rtables::build_table()</a></code>.
 Adding this function to an <code>rtable</code> layout will summarize the given variables, arrange the output
 in columns, and add it to the table layout.</p>
     </div>
     <div class="section level2">
-    <h2 id="note">Note<a class="anchor" aria-label="anchor" href="#note"></a></h2>
+    <h2 id="note">Note<a class="anchor" aria-label="anchor" href="#note"></a>
+</h2>
 
-<ul><li><p>This is an experimental implementation of <code><a href="https://insightsengineering.github.io/rtables/latest-tag/reference/summarize_row_groups.html" class="external-link">rtables::summarize_row_groups()</a></code> and <code><a href="https://insightsengineering.github.io/rtables/latest-tag/reference/analyze_colvars.html" class="external-link">rtables::analyze_colvars()</a></code>
+<ul>
+<li><p>This is an experimental implementation of <code><a href="https://insightsengineering.github.io/rtables/latest-tag/reference/summarize_row_groups.html" class="external-link">rtables::summarize_row_groups()</a></code> and <code><a href="https://insightsengineering.github.io/rtables/latest-tag/reference/analyze_colvars.html" class="external-link">rtables::analyze_colvars()</a></code>
 that may be subjected to changes as <code>rtables</code> extends its support to more complex analysis pipelines in the
 column space. We encourage users to read the examples carefully and file issues for different use cases.</p></li>
 <li><p>In this function, <code>labelstr</code> behaves atypically. If <code>labelstr = NULL</code> (the default), row labels are assigned
 automatically as the split values if <code>do_summarize_row_groups = FALSE</code> (the default), and as the group label
 if <code>do_summarize_row_groups = TRUE</code>.</p></li>
-</ul></div>
+</ul>
+</div>
     <div class="section level2">
-    <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"></a></h2>
+    <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"></a>
+</h2>
     <div class="dont-index"><p><code><a href="analyze_variables.html">analyze_vars()</a></code>, <code><a href="https://insightsengineering.github.io/rtables/latest-tag/reference/analyze_colvars.html" class="external-link">rtables::analyze_colvars()</a></code>.</p></div>
     </div>
 
     <div class="section level2">
-    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
+    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://dplyr.tidyverse.org" class="external-link">dplyr</a></span><span class="op">)</span></span></span>
 <span class="r-in"><span></span></span>
 <span class="r-in"><span><span class="co"># Data preparation</span></span></span>
@@ -345,17 +434,19 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 </code></pre></div>
     </div>
   </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
-    </nav></aside></div>
+    </nav></aside>
+</div>
 
 
     <footer><div class="nest">
   <p>tern is a part of the <strong>NEST</strong> and <a href="https://pharmaverse.org/" class="external-link"><strong>pharmaverse</strong></a>.</p>
 </div>
-<script type="text/javascript" src="../analytics.js"></script></footer></div>
-
+<script type="text/javascript" src="../analytics.js"></script></footer>
+</div>
 
 
 
 
-  </body></html>
 
+  </body>
+</html>
diff --git a/main/reference/append_varlabels.html b/main/reference/append_varlabels.html
index 43219749d1..f9b6084e25 100644
--- a/main/reference/append_varlabels.html
+++ b/main/reference/append_varlabels.html
@@ -1,11 +1,34 @@
-<!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Add variable labels to top left corner in table — append_varlabels • tern</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Add variable labels to top left corner in table — append_varlabels"><meta name="description" content="
+<html lang="en">
+<head>
+<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+<meta charset="utf-8">
+<meta http-equiv="X-UA-Compatible" content="IE=edge">
+<meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<title>Add variable labels to top left corner in table — append_varlabels • tern</title>
+<!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png">
+<link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png">
+<link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png">
+<link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png">
+<link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png">
+<link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png">
+<script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet">
+<script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet">
+<link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet">
+<script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Add variable labels to top left corner in table — append_varlabels">
+<meta name="description" content="
 Helper layout-creating function to append the variable labels of a given variables vector
 from a given dataset in the top left corner. If a variable label is not found then the
-variable name itself is used instead. Multiple variable labels are concatenated with slashes."><meta property="og:description" content="
+variable name itself is used instead. Multiple variable labels are concatenated with slashes.">
+<meta property="og:description" content="
 Helper layout-creating function to append the variable labels of a given variables vector
 from a given dataset in the top left corner. If a variable label is not found then the
-variable name itself is used instead. Multiple variable labels are concatenated with slashes."><meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png"><link rel="stylesheet" href="../consent.css"><script src="../consent.js" type="text/javascript" charset="utf-8"></script></head><body>
+variable name itself is used instead. Multiple variable labels are concatenated with slashes.">
+<meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png">
+<link rel="stylesheet" href="../consent.css">
+<script src="../consent.js" type="text/javascript" charset="utf-8"></script>
+</head>
+<body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
 
 
@@ -21,26 +44,66 @@
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     <div id="navbar" class="collapse navbar-collapse ms-3">
-      <ul class="navbar-nav me-auto"><li class="nav-item"><a class="nav-link" href="../articles/tern.html">Get started</a></li>
+      <ul class="navbar-nav me-auto">
+<li class="nav-item"><a class="nav-link" href="../articles/tern.html">Get started</a></li>
 <li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
 <li class="nav-item dropdown">
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-articles" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Articles</button>
-  <ul class="dropdown-menu" aria-labelledby="dropdown-articles"><li><a class="dropdown-item" href="../articles/missing_values.html">Missing Values in Tern</a></li>
+  <ul class="dropdown-menu" aria-labelledby="dropdown-articles">
+<li><a class="dropdown-item" href="../articles/missing_values.html">Missing Values in Tern</a></li>
     <li><a class="dropdown-item" href="../articles/tables.html">Tabulation</a></li>
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     <li><a class="dropdown-item" href="../articles/tern_functions_guide.html">Understanding `tern` functions</a></li>
-  </ul></li>
+  </ul>
+</li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
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+  <ul class="dropdown-menu" aria-labelledby="dropdown-reports">
+<li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
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- <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json"></form></li>
+  </ul>
+</li>
+      <div><li class="nav-item dropdown">
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+    <div class="dropdown-menu" aria-labelledby="dropdown-versions">
+    <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/main">main</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.5">v0.9.5</a>
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+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.3">v0.9.3</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1-rc3">v0.9.1-rc3</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a>
+</div>
+</li></div>
+</ul>
+<ul class="navbar-nav">
+<li class="nav-item"><form class="form-inline" role="search">
+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json">
+</form></li>
 <li class="nav-item"><a class="external-link nav-link" href="https://github.com/insightsengineering/tern" aria-label="GitHub"><span class="fa fa-github"></span></a></li>
-      </ul></div>
+      </ul>
+</div>
 
 
   </div>
@@ -60,44 +123,55 @@
     </div>
 
     <div class="section level2">
-    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
+    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">append_varlabels</span><span class="op">(</span><span class="va">lyt</span>, <span class="va">df</span>, <span class="va">vars</span>, indent <span class="op">=</span> <span class="fl">0L</span><span class="op">)</span></span></code></pre></div>
     </div>
 
     <div class="section level2">
-    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
+    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a>
+</h2>
 
 
-<dl><dt id="arg-lyt">lyt<a class="anchor" aria-label="anchor" href="#arg-lyt"></a></dt>
+<dl>
+<dt id="arg-lyt">lyt<a class="anchor" aria-label="anchor" href="#arg-lyt"></a>
+</dt>
 <dd><p>(<code>PreDataTableLayouts</code>)<br> layout that analyses will be added to.</p></dd>
 
 
-<dt id="arg-df">df<a class="anchor" aria-label="anchor" href="#arg-df"></a></dt>
+<dt id="arg-df">df<a class="anchor" aria-label="anchor" href="#arg-df"></a>
+</dt>
 <dd><p>(<code>data.frame</code>)<br> data set containing all analysis variables.</p></dd>
 
 
-<dt id="arg-vars">vars<a class="anchor" aria-label="anchor" href="#arg-vars"></a></dt>
+<dt id="arg-vars">vars<a class="anchor" aria-label="anchor" href="#arg-vars"></a>
+</dt>
 <dd><p>(<code>character</code>)<br> variable names of which the labels are to be looked up in <code>df</code>.</p></dd>
 
 
-<dt id="arg-indent">indent<a class="anchor" aria-label="anchor" href="#arg-indent"></a></dt>
+<dt id="arg-indent">indent<a class="anchor" aria-label="anchor" href="#arg-indent"></a>
+</dt>
 <dd><p>(<code>integer(1)</code>)<br> non-negative number of nested indent space, default to 0L which means no indent.
 1L means two spaces indent, 2L means four spaces indent and so on.</p></dd>
 
-</dl></div>
+</dl>
+</div>
     <div class="section level2">
-    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
+    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a>
+</h2>
     <p>A modified layout with the new variable label(s) added to the top-left material.</p>
     </div>
     <div class="section level2">
-    <h2 id="note">Note<a class="anchor" aria-label="anchor" href="#note"></a></h2>
+    <h2 id="note">Note<a class="anchor" aria-label="anchor" href="#note"></a>
+</h2>
     <p>This is not an optimal implementation of course, since we are using here the data set
 itself during the layout creation. When we have a more mature <code>rtables</code> implementation then
 this will also be improved or not necessary anymore.</p>
     </div>
 
     <div class="section level2">
-    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
+    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">lyt</span> <span class="op">&lt;-</span> <span class="fu">basic_table</span><span class="op">(</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span></span>
 <span class="r-in"><span>  <span class="fu">split_cols_by</span><span class="op">(</span><span class="st">"ARM"</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span></span>
 <span class="r-in"><span>  <span class="fu">add_colcounts</span><span class="op">(</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span></span>
@@ -138,17 +212,19 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 </code></pre></div>
     </div>
   </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
-    </nav></aside></div>
+    </nav></aside>
+</div>
 
 
     <footer><div class="nest">
   <p>tern is a part of the <strong>NEST</strong> and <a href="https://pharmaverse.org/" class="external-link"><strong>pharmaverse</strong></a>.</p>
 </div>
-<script type="text/javascript" src="../analytics.js"></script></footer></div>
-
+<script type="text/javascript" src="../analytics.js"></script></footer>
+</div>
 
 
 
 
-  </body></html>
 
+  </body>
+</html>
diff --git a/main/reference/apply_auto_formatting.html b/main/reference/apply_auto_formatting.html
index f94118191e..978659205f 100644
--- a/main/reference/apply_auto_formatting.html
+++ b/main/reference/apply_auto_formatting.html
@@ -1,7 +1,30 @@
-<!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Apply automatic formatting — apply_auto_formatting • tern</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Apply automatic formatting — apply_auto_formatting"><meta name="description" content='Checks if any of the listed formats in .formats are "auto", and replaces "auto" with
-the correct implementation of format_auto for the given statistics, data, and variable.'><meta property="og:description" content='Checks if any of the listed formats in .formats are "auto", and replaces "auto" with
-the correct implementation of format_auto for the given statistics, data, and variable.'><meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png"><link rel="stylesheet" href="../consent.css"><script src="../consent.js" type="text/javascript" charset="utf-8"></script></head><body>
+<html lang="en">
+<head>
+<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+<meta charset="utf-8">
+<meta http-equiv="X-UA-Compatible" content="IE=edge">
+<meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<title>Apply automatic formatting — apply_auto_formatting • tern</title>
+<!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png">
+<link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png">
+<link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png">
+<link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png">
+<link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png">
+<link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png">
+<script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet">
+<script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet">
+<link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet">
+<script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Apply automatic formatting — apply_auto_formatting">
+<meta name="description" content='Checks if any of the listed formats in .formats are "auto", and replaces "auto" with
+the correct implementation of format_auto for the given statistics, data, and variable.'>
+<meta property="og:description" content='Checks if any of the listed formats in .formats are "auto", and replaces "auto" with
+the correct implementation of format_auto for the given statistics, data, and variable.'>
+<meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png">
+<link rel="stylesheet" href="../consent.css">
+<script src="../consent.js" type="text/javascript" charset="utf-8"></script>
+</head>
+<body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
 
 
@@ -17,26 +40,66 @@
     </button>
 
     <div id="navbar" class="collapse navbar-collapse ms-3">
-      <ul class="navbar-nav me-auto"><li class="nav-item"><a class="nav-link" href="../articles/tern.html">Get started</a></li>
+      <ul class="navbar-nav me-auto">
+<li class="nav-item"><a class="nav-link" href="../articles/tern.html">Get started</a></li>
 <li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
 <li class="nav-item dropdown">
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-articles" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Articles</button>
-  <ul class="dropdown-menu" aria-labelledby="dropdown-articles"><li><a class="dropdown-item" href="../articles/missing_values.html">Missing Values in Tern</a></li>
+  <ul class="dropdown-menu" aria-labelledby="dropdown-articles">
+<li><a class="dropdown-item" href="../articles/missing_values.html">Missing Values in Tern</a></li>
     <li><a class="dropdown-item" href="../articles/tables.html">Tabulation</a></li>
     <li><a class="dropdown-item" href="../articles/tern_formats.html">Formatting Functions</a></li>
     <li><a class="dropdown-item" href="../articles/tern_functions_guide.html">Understanding `tern` functions</a></li>
-  </ul></li>
+  </ul>
+</li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
-  <ul class="dropdown-menu" aria-labelledby="dropdown-reports"><li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
+  <ul class="dropdown-menu" aria-labelledby="dropdown-reports">
+<li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
     <li><a class="dropdown-item" href="../unit-test-report/">Unit test report</a></li>
     <li><a class="dropdown-item" href="../unit-test-report-non-cran/">Non-CRAN unit test report</a></li>
-  </ul></li>
-      </ul><ul class="navbar-nav"><li class="nav-item"><form class="form-inline" role="search">
- <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json"></form></li>
+  </ul>
+</li>
+      <div><li class="nav-item dropdown">
+    <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-versions">Versions</a>
+    <div class="dropdown-menu" aria-labelledby="dropdown-versions">
+    <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/main">main</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.5">v0.9.5</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.4">v0.9.4</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.3">v0.9.3</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1-rc3">v0.9.1-rc3</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a>
+</div>
+</li></div>
+</ul>
+<ul class="navbar-nav">
+<li class="nav-item"><form class="form-inline" role="search">
+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json">
+</form></li>
 <li class="nav-item"><a class="external-link nav-link" href="https://github.com/insightsengineering/tern" aria-label="GitHub"><span class="fa fa-github"></span></a></li>
-      </ul></div>
+      </ul>
+</div>
 
 
   </div>
@@ -54,46 +117,56 @@
     </div>
 
     <div class="section level2">
-    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
+    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">apply_auto_formatting</span><span class="op">(</span><span class="va">.formats</span>, <span class="va">x_stats</span>, <span class="va">.df_row</span>, <span class="va">.var</span><span class="op">)</span></span></code></pre></div>
     </div>
 
     <div class="section level2">
-    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
+    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a>
+</h2>
 
 
-<dl><dt id="arg--formats">.formats<a class="anchor" aria-label="anchor" href="#arg--formats"></a></dt>
+<dl>
+<dt id="arg--formats">.formats<a class="anchor" aria-label="anchor" href="#arg--formats"></a>
+</dt>
 <dd><p>(named <code>character</code> or <code>list</code>)<br> formats for the statistics. See Details in <code>analyze_vars</code> for more
 information on the <code>"auto"</code> setting.</p></dd>
 
 
-<dt id="arg-x-stats">x_stats<a class="anchor" aria-label="anchor" href="#arg-x-stats"></a></dt>
+<dt id="arg-x-stats">x_stats<a class="anchor" aria-label="anchor" href="#arg-x-stats"></a>
+</dt>
 <dd><p>(named <code>list</code>)<br> a named list of statistics where each element corresponds
 to an element in <code>.formats</code>, with matching names.</p></dd>
 
 
-<dt id="arg--df-row">.df_row<a class="anchor" aria-label="anchor" href="#arg--df-row"></a></dt>
+<dt id="arg--df-row">.df_row<a class="anchor" aria-label="anchor" href="#arg--df-row"></a>
+</dt>
 <dd><p>(<code>data.frame</code>)<br> data frame across all of the columns for the given row split.</p></dd>
 
 
-<dt id="arg--var">.var<a class="anchor" aria-label="anchor" href="#arg--var"></a></dt>
+<dt id="arg--var">.var<a class="anchor" aria-label="anchor" href="#arg--var"></a>
+</dt>
 <dd><p>(<code>string</code>)<br> single variable name that is passed by <code>rtables</code> when requested
 by a statistics function.</p></dd>
 
-</dl></div>
+</dl>
+</div>
 
   </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
-    </nav></aside></div>
+    </nav></aside>
+</div>
 
 
     <footer><div class="nest">
   <p>tern is a part of the <strong>NEST</strong> and <a href="https://pharmaverse.org/" class="external-link"><strong>pharmaverse</strong></a>.</p>
 </div>
-<script type="text/javascript" src="../analytics.js"></script></footer></div>
-
+<script type="text/javascript" src="../analytics.js"></script></footer>
+</div>
 
 
 
 
-  </body></html>
 
+  </body>
+</html>
diff --git a/main/reference/argument_convention.html b/main/reference/argument_convention.html
index 66085d884f..c82d790eab 100644
--- a/main/reference/argument_convention.html
+++ b/main/reference/argument_convention.html
@@ -1,7 +1,30 @@
-<!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Standard arguments — argument_convention • tern</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Standard arguments — argument_convention"><meta name="description" content="The documentation to this function lists all the arguments in tern
-that are used repeatedly to express an analysis."><meta property="og:description" content="The documentation to this function lists all the arguments in tern
-that are used repeatedly to express an analysis."><meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png"><link rel="stylesheet" href="../consent.css"><script src="../consent.js" type="text/javascript" charset="utf-8"></script></head><body>
+<html lang="en">
+<head>
+<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+<meta charset="utf-8">
+<meta http-equiv="X-UA-Compatible" content="IE=edge">
+<meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<title>Standard arguments — argument_convention • tern</title>
+<!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png">
+<link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png">
+<link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png">
+<link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png">
+<link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png">
+<link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png">
+<script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet">
+<script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet">
+<link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet">
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+<meta name="description" content="The documentation to this function lists all the arguments in tern
+that are used repeatedly to express an analysis.">
+<meta property="og:description" content="The documentation to this function lists all the arguments in tern
+that are used repeatedly to express an analysis.">
+<meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png">
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@@ -17,26 +40,66 @@
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+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json">
+</form></li>
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-      </ul></div>
+      </ul>
+</div>
 
 
   </div>
@@ -55,212 +118,264 @@
 
 
     <div class="section level2">
-    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
+    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a>
+</h2>
 
 
-<dl><dt id="arg--">...<a class="anchor" aria-label="anchor" href="#arg--"></a></dt>
+<dl>
+<dt id="arg--">...<a class="anchor" aria-label="anchor" href="#arg--"></a>
+</dt>
 <dd><p>additional arguments for the lower level functions.</p></dd>
 
 
-<dt id="arg--aligns">.aligns<a class="anchor" aria-label="anchor" href="#arg--aligns"></a></dt>
+<dt id="arg--aligns">.aligns<a class="anchor" aria-label="anchor" href="#arg--aligns"></a>
+</dt>
 <dd><p>(<code>character</code> or <code>NULL</code>)<br> alignment for table contents (not including labels). When <code>NULL</code>,
 <code>"center"</code> is applied. See <code><a href="https://insightsengineering.github.io/formatters/latest-tag/reference/list_formats.html" class="external-link">formatters::list_valid_aligns()</a></code> for a list of all currently supported alignments.</p></dd>
 
 
-<dt id="arg--all-col-counts">.all_col_counts<a class="anchor" aria-label="anchor" href="#arg--all-col-counts"></a></dt>
+<dt id="arg--all-col-counts">.all_col_counts<a class="anchor" aria-label="anchor" href="#arg--all-col-counts"></a>
+</dt>
 <dd><p>(<code>integer</code>)<br> vector where each value represents a global count for a column. Values are
 taken from <code>alt_counts_df</code> if specified (see <code><a href="https://insightsengineering.github.io/rtables/latest-tag/reference/build_table.html" class="external-link">rtables::build_table()</a></code>).</p></dd>
 
 
-<dt id="arg--df-row">.df_row<a class="anchor" aria-label="anchor" href="#arg--df-row"></a></dt>
+<dt id="arg--df-row">.df_row<a class="anchor" aria-label="anchor" href="#arg--df-row"></a>
+</dt>
 <dd><p>(<code>data.frame</code>)<br> data frame across all of the columns for the given row split.</p></dd>
 
 
-<dt id="arg--formats">.formats<a class="anchor" aria-label="anchor" href="#arg--formats"></a></dt>
+<dt id="arg--formats">.formats<a class="anchor" aria-label="anchor" href="#arg--formats"></a>
+</dt>
 <dd><p>(named <code>character</code> or <code>list</code>)<br> formats for the statistics. See Details in <code>analyze_vars</code> for more
 information on the <code>"auto"</code> setting.</p></dd>
 
 
-<dt id="arg--in-ref-col">.in_ref_col<a class="anchor" aria-label="anchor" href="#arg--in-ref-col"></a></dt>
+<dt id="arg--in-ref-col">.in_ref_col<a class="anchor" aria-label="anchor" href="#arg--in-ref-col"></a>
+</dt>
 <dd><p>(<code>flag</code>)<br><code>TRUE</code> when working with the reference level, <code>FALSE</code> otherwise.</p></dd>
 
 
-<dt id="arg--indent-mods">.indent_mods<a class="anchor" aria-label="anchor" href="#arg--indent-mods"></a></dt>
+<dt id="arg--indent-mods">.indent_mods<a class="anchor" aria-label="anchor" href="#arg--indent-mods"></a>
+</dt>
 <dd><p>(named <code>integer</code>)<br> indent modifiers for the labels. Defaults to 0, which corresponds to the
 unmodified default behavior. Can be negative.</p></dd>
 
 
-<dt id="arg--labels">.labels<a class="anchor" aria-label="anchor" href="#arg--labels"></a></dt>
+<dt id="arg--labels">.labels<a class="anchor" aria-label="anchor" href="#arg--labels"></a>
+</dt>
 <dd><p>(named <code>character</code>)<br> labels for the statistics (without indent).</p></dd>
 
 
-<dt id="arg--n-col">.N_col<a class="anchor" aria-label="anchor" href="#arg--n-col"></a></dt>
+<dt id="arg--n-col">.N_col<a class="anchor" aria-label="anchor" href="#arg--n-col"></a>
+</dt>
 <dd><p>(<code>integer(1)</code>)<br> column-wise N (column count) for the full column being analyzed that is typically
 passed by <code>rtables</code>.</p></dd>
 
 
-<dt id="arg--n-row">.N_row<a class="anchor" aria-label="anchor" href="#arg--n-row"></a></dt>
+<dt id="arg--n-row">.N_row<a class="anchor" aria-label="anchor" href="#arg--n-row"></a>
+</dt>
 <dd><p>(<code>integer(1)</code>)<br> row-wise N (row group count) for the group of observations being analyzed
 (i.e. with no column-based subsetting) that is typically passed by <code>rtables</code>.</p></dd>
 
 
-<dt id="arg--ref-group">.ref_group<a class="anchor" aria-label="anchor" href="#arg--ref-group"></a></dt>
+<dt id="arg--ref-group">.ref_group<a class="anchor" aria-label="anchor" href="#arg--ref-group"></a>
+</dt>
 <dd><p>(<code>data.frame</code> or <code>vector</code>)<br> the data corresponding to the reference group.</p></dd>
 
 
-<dt id="arg--spl-context">.spl_context<a class="anchor" aria-label="anchor" href="#arg--spl-context"></a></dt>
+<dt id="arg--spl-context">.spl_context<a class="anchor" aria-label="anchor" href="#arg--spl-context"></a>
+</dt>
 <dd><p>(<code>data.frame</code>)<br> gives information about ancestor split states
 that is passed by <code>rtables</code>.</p></dd>
 
 
-<dt id="arg--stats">.stats<a class="anchor" aria-label="anchor" href="#arg--stats"></a></dt>
+<dt id="arg--stats">.stats<a class="anchor" aria-label="anchor" href="#arg--stats"></a>
+</dt>
 <dd><p>(<code>character</code>)<br> statistics to select for the table.</p></dd>
 
 
-<dt id="arg--var">.var<a class="anchor" aria-label="anchor" href="#arg--var"></a></dt>
+<dt id="arg--var">.var<a class="anchor" aria-label="anchor" href="#arg--var"></a>
+</dt>
 <dd><p>(<code>string</code>)<br> single variable name that is passed by <code>rtables</code> when requested
 by a statistics function.</p></dd>
 
 
-<dt id="arg-add-total-level">add_total_level<a class="anchor" aria-label="anchor" href="#arg-add-total-level"></a></dt>
+<dt id="arg-add-total-level">add_total_level<a class="anchor" aria-label="anchor" href="#arg-add-total-level"></a>
+</dt>
 <dd><p>(<code>flag</code>)<br> adds a "total" level after the others which includes all the levels
 that constitute the split. A custom label can be set for this level via the <code>custom_label</code> argument.</p></dd>
 
 
-<dt id="arg-col-by">col_by<a class="anchor" aria-label="anchor" href="#arg-col-by"></a></dt>
+<dt id="arg-col-by">col_by<a class="anchor" aria-label="anchor" href="#arg-col-by"></a>
+</dt>
 <dd><p>(<code>factor</code>)<br> defining column groups.</p></dd>
 
 
-<dt id="arg-conf-level">conf_level<a class="anchor" aria-label="anchor" href="#arg-conf-level"></a></dt>
+<dt id="arg-conf-level">conf_level<a class="anchor" aria-label="anchor" href="#arg-conf-level"></a>
+</dt>
 <dd><p>(<code>proportion</code>)<br> confidence level of the interval.</p></dd>
 
 
-<dt id="arg-data">data<a class="anchor" aria-label="anchor" href="#arg-data"></a></dt>
+<dt id="arg-data">data<a class="anchor" aria-label="anchor" href="#arg-data"></a>
+</dt>
 <dd><p>(<code>data.frame</code>)<br> the dataset containing the variables to summarize.</p></dd>
 
 
-<dt id="arg-denom">denom<a class="anchor" aria-label="anchor" href="#arg-denom"></a></dt>
-<dd><p>(<code>string</code>)<br> choice of denominator for proportion. Options are:</p><ul><li><p><code>n</code>: number of values in this row and column intersection.</p></li>
+<dt id="arg-denom">denom<a class="anchor" aria-label="anchor" href="#arg-denom"></a>
+</dt>
+<dd>
+<p>(<code>string</code>)<br> choice of denominator for proportion. Options are:</p>
+<ul>
+<li><p><code>n</code>: number of values in this row and column intersection.</p></li>
 <li><p><code>N_row</code>: total number of values in this row across columns.</p></li>
 <li><p><code>N_col</code>: total number of values in this column across rows.</p></li>
-</ul></dd>
+</ul>
+</dd>
 
 
-<dt id="arg-df">df<a class="anchor" aria-label="anchor" href="#arg-df"></a></dt>
+<dt id="arg-df">df<a class="anchor" aria-label="anchor" href="#arg-df"></a>
+</dt>
 <dd><p>(<code>data.frame</code>)<br> data set containing all analysis variables.</p></dd>
 
 
-<dt id="arg-groups-lists">groups_lists<a class="anchor" aria-label="anchor" href="#arg-groups-lists"></a></dt>
+<dt id="arg-groups-lists">groups_lists<a class="anchor" aria-label="anchor" href="#arg-groups-lists"></a>
+</dt>
 <dd><p>(named <code>list</code> of <code>list</code>)<br> optionally contains for each <code>subgroups</code> variable a
 list, which specifies the new group levels via the names and the
 levels that belong to it in the character vectors that are elements of the list.</p></dd>
 
 
-<dt id="arg-id">id<a class="anchor" aria-label="anchor" href="#arg-id"></a></dt>
+<dt id="arg-id">id<a class="anchor" aria-label="anchor" href="#arg-id"></a>
+</dt>
 <dd><p>(<code>string</code>)<br> subject variable name.</p></dd>
 
 
-<dt id="arg-is-event">is_event<a class="anchor" aria-label="anchor" href="#arg-is-event"></a></dt>
+<dt id="arg-is-event">is_event<a class="anchor" aria-label="anchor" href="#arg-is-event"></a>
+</dt>
 <dd><p>(<code>flag</code>)<br><code>TRUE</code> if event, <code>FALSE</code> if time to event is censored.</p></dd>
 
 
-<dt id="arg-label-all">label_all<a class="anchor" aria-label="anchor" href="#arg-label-all"></a></dt>
+<dt id="arg-label-all">label_all<a class="anchor" aria-label="anchor" href="#arg-label-all"></a>
+</dt>
 <dd><p>(<code>string</code>)<br> label for the total population analysis.</p></dd>
 
 
-<dt id="arg-labelstr">labelstr<a class="anchor" aria-label="anchor" href="#arg-labelstr"></a></dt>
+<dt id="arg-labelstr">labelstr<a class="anchor" aria-label="anchor" href="#arg-labelstr"></a>
+</dt>
 <dd><p>(<code>string</code>)<br> label of the level of the parent split currently being summarized
 (must be present as second argument in Content Row Functions). See <code><a href="https://insightsengineering.github.io/rtables/latest-tag/reference/summarize_row_groups.html" class="external-link">rtables::summarize_row_groups()</a></code>
 for more information.</p></dd>
 
 
-<dt id="arg-lyt">lyt<a class="anchor" aria-label="anchor" href="#arg-lyt"></a></dt>
+<dt id="arg-lyt">lyt<a class="anchor" aria-label="anchor" href="#arg-lyt"></a>
+</dt>
 <dd><p>(<code>PreDataTableLayouts</code>)<br> layout that analyses will be added to.</p></dd>
 
 
-<dt id="arg-method">method<a class="anchor" aria-label="anchor" href="#arg-method"></a></dt>
+<dt id="arg-method">method<a class="anchor" aria-label="anchor" href="#arg-method"></a>
+</dt>
 <dd><p>(<code>string</code> or <code>NULL</code>)<br> specifies the test used to calculate the p-value for the difference between
 two proportions. For options, see <code><a href="prop_diff_test.html">test_proportion_diff()</a></code>. Default is <code>NULL</code> so no test is performed.</p></dd>
 
 
-<dt id="arg-na-rm">na.rm<a class="anchor" aria-label="anchor" href="#arg-na-rm"></a></dt>
+<dt id="arg-na-rm">na.rm<a class="anchor" aria-label="anchor" href="#arg-na-rm"></a>
+</dt>
 <dd><p>(<code>flag</code>)<br> whether <code>NA</code> values should be removed from <code>x</code> prior to analysis.</p></dd>
 
 
-<dt id="arg-na-str">na_str<a class="anchor" aria-label="anchor" href="#arg-na-str"></a></dt>
+<dt id="arg-na-str">na_str<a class="anchor" aria-label="anchor" href="#arg-na-str"></a>
+</dt>
 <dd><p>(<code>string</code>)<br> string used to replace all <code>NA</code> or empty values in the output.</p></dd>
 
 
-<dt id="arg-nested">nested<a class="anchor" aria-label="anchor" href="#arg-nested"></a></dt>
+<dt id="arg-nested">nested<a class="anchor" aria-label="anchor" href="#arg-nested"></a>
+</dt>
 <dd><p>(<code>flag</code>)<br> whether this layout instruction should be applied within the existing layout structure _if
 possible (<code>TRUE</code>, the default) or as a new top-level element (<code>FALSE</code>). Ignored if it would nest a split.
 underneath analyses, which is not allowed.</p></dd>
 
 
-<dt id="arg-prune-zero-rows">prune_zero_rows<a class="anchor" aria-label="anchor" href="#arg-prune-zero-rows"></a></dt>
+<dt id="arg-prune-zero-rows">prune_zero_rows<a class="anchor" aria-label="anchor" href="#arg-prune-zero-rows"></a>
+</dt>
 <dd><p>(<code>flag</code>)<br> whether to prune all zero rows.</p></dd>
 
 
-<dt id="arg-riskdiff">riskdiff<a class="anchor" aria-label="anchor" href="#arg-riskdiff"></a></dt>
+<dt id="arg-riskdiff">riskdiff<a class="anchor" aria-label="anchor" href="#arg-riskdiff"></a>
+</dt>
 <dd><p>(<code>flag</code>)<br> whether a risk difference column is present. When set to <code>TRUE</code>, <code><a href="add_riskdiff.html">add_riskdiff()</a></code> must be
 used as <code>split_fun</code> in the prior column split of the table layout, specifying which columns should be compared.
 See <code><a href="stat_propdiff_ci.html">stat_propdiff_ci()</a></code> for details on risk difference calculation.</p></dd>
 
 
-<dt id="arg-rsp">rsp<a class="anchor" aria-label="anchor" href="#arg-rsp"></a></dt>
+<dt id="arg-rsp">rsp<a class="anchor" aria-label="anchor" href="#arg-rsp"></a>
+</dt>
 <dd><p>(<code>logical</code>)<br> vector indicating whether each subject is a responder or not.</p></dd>
 
 
-<dt id="arg-show-labels">show_labels<a class="anchor" aria-label="anchor" href="#arg-show-labels"></a></dt>
+<dt id="arg-show-labels">show_labels<a class="anchor" aria-label="anchor" href="#arg-show-labels"></a>
+</dt>
 <dd><p>(<code>string</code>)<br> label visibility: one of "default", "visible" and "hidden".</p></dd>
 
 
-<dt id="arg-section-div">section_div<a class="anchor" aria-label="anchor" href="#arg-section-div"></a></dt>
+<dt id="arg-section-div">section_div<a class="anchor" aria-label="anchor" href="#arg-section-div"></a>
+</dt>
 <dd><p>(<code>string</code>)<br> string which should be repeated as a section divider after each group
 defined by this split instruction, or <code>NA_character_</code> (the default) for no section divider.</p></dd>
 
 
-<dt id="arg-table-names">table_names<a class="anchor" aria-label="anchor" href="#arg-table-names"></a></dt>
+<dt id="arg-table-names">table_names<a class="anchor" aria-label="anchor" href="#arg-table-names"></a>
+</dt>
 <dd><p>(<code>character</code>)<br> this can be customized in the case that the same <code>vars</code> are analyzed multiple
 times, to avoid warnings from <code>rtables</code>.</p></dd>
 
 
-<dt id="arg-tte">tte<a class="anchor" aria-label="anchor" href="#arg-tte"></a></dt>
+<dt id="arg-tte">tte<a class="anchor" aria-label="anchor" href="#arg-tte"></a>
+</dt>
 <dd><p>(<code>numeric</code>)<br> vector of time-to-event duration values.</p></dd>
 
 
-<dt id="arg-var-labels">var_labels<a class="anchor" aria-label="anchor" href="#arg-var-labels"></a></dt>
+<dt id="arg-var-labels">var_labels<a class="anchor" aria-label="anchor" href="#arg-var-labels"></a>
+</dt>
 <dd><p>(<code>character</code>)<br> variable labels.</p></dd>
 
 
-<dt id="arg-variables">variables<a class="anchor" aria-label="anchor" href="#arg-variables"></a></dt>
+<dt id="arg-variables">variables<a class="anchor" aria-label="anchor" href="#arg-variables"></a>
+</dt>
 <dd><p>(named <code>list</code> of <code>string</code>)<br> list of additional analysis variables.</p></dd>
 
 
-<dt id="arg-vars">vars<a class="anchor" aria-label="anchor" href="#arg-vars"></a></dt>
+<dt id="arg-vars">vars<a class="anchor" aria-label="anchor" href="#arg-vars"></a>
+</dt>
 <dd><p>(<code>character</code>)<br> variable names for the primary analysis variable to be iterated over.</p></dd>
 
 
-<dt id="arg-var">var<a class="anchor" aria-label="anchor" href="#arg-var"></a></dt>
+<dt id="arg-var">var<a class="anchor" aria-label="anchor" href="#arg-var"></a>
+</dt>
 <dd><p>(<code>string</code>)<br> single variable name for the primary analysis variable.</p></dd>
 
 
-<dt id="arg-x">x<a class="anchor" aria-label="anchor" href="#arg-x"></a></dt>
+<dt id="arg-x">x<a class="anchor" aria-label="anchor" href="#arg-x"></a>
+</dt>
 <dd><p>(<code>numeric</code>)<br> vector of numbers we want to analyze.</p></dd>
 
 
-<dt id="arg-xlim">xlim<a class="anchor" aria-label="anchor" href="#arg-xlim"></a></dt>
+<dt id="arg-xlim">xlim<a class="anchor" aria-label="anchor" href="#arg-xlim"></a>
+</dt>
 <dd><p>(<code>numeric(2)</code>)<br> vector containing lower and upper limits for the x-axis, respectively.
 If <code>NULL</code> (default), the default scale range is used.</p></dd>
 
 
-<dt id="arg-ylim">ylim<a class="anchor" aria-label="anchor" href="#arg-ylim"></a></dt>
+<dt id="arg-ylim">ylim<a class="anchor" aria-label="anchor" href="#arg-ylim"></a>
+</dt>
 <dd><p>(<code>numeric(2)</code>)<br> vector containing lower and upper limits for the y-axis, respectively.
 If <code>NULL</code> (default), the default scale range is used.</p></dd>
 
-</dl></div>
+</dl>
+</div>
     <div class="section level2">
-    <h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a></h2>
+    <h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a>
+</h2>
     <p>Although this function just returns <code>NULL</code> it has two uses, for
 the <code>tern</code> users it provides a documentation of arguments that are
 commonly and consistently used in the framework. For the developer it adds a
@@ -269,17 +384,19 @@ <h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></
     </div>
 
   </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
-    </nav></aside></div>
+    </nav></aside>
+</div>
 
 
     <footer><div class="nest">
   <p>tern is a part of the <strong>NEST</strong> and <a href="https://pharmaverse.org/" class="external-link"><strong>pharmaverse</strong></a>.</p>
 </div>
-<script type="text/javascript" src="../analytics.js"></script></footer></div>
-
+<script type="text/javascript" src="../analytics.js"></script></footer>
+</div>
 
 
 
 
-  </body></html>
 
+  </body>
+</html>
diff --git a/main/reference/arrange_grobs.html b/main/reference/arrange_grobs.html
index b5f18ca1b3..1ef2a4312c 100644
--- a/main/reference/arrange_grobs.html
+++ b/main/reference/arrange_grobs.html
@@ -1,7 +1,30 @@
-<!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Arrange multiple grobs — arrange_grobs • tern</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Arrange multiple grobs — arrange_grobs"><meta name="description" content="
-Arrange grobs as a new grob with n * m (rows * cols) layout."><meta property="og:description" content="
-Arrange grobs as a new grob with n * m (rows * cols) layout."><meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png"><link rel="stylesheet" href="../consent.css"><script src="../consent.js" type="text/javascript" charset="utf-8"></script></head><body>
+<html lang="en">
+<head>
+<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+<meta charset="utf-8">
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+<meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<title>Arrange multiple grobs — arrange_grobs • tern</title>
+<!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png">
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+<link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png">
+<link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png">
+<script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet">
+<script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet">
+<link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet">
+<script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Arrange multiple grobs — arrange_grobs">
+<meta name="description" content="
+Arrange grobs as a new grob with n * m (rows * cols) layout.">
+<meta property="og:description" content="
+Arrange grobs as a new grob with n * m (rows * cols) layout.">
+<meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png">
+<link rel="stylesheet" href="../consent.css">
+<script src="../consent.js" type="text/javascript" charset="utf-8"></script>
+</head>
+<body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
 
 
@@ -17,26 +40,66 @@
     </button>
 
     <div id="navbar" class="collapse navbar-collapse ms-3">
-      <ul class="navbar-nav me-auto"><li class="nav-item"><a class="nav-link" href="../articles/tern.html">Get started</a></li>
+      <ul class="navbar-nav me-auto">
+<li class="nav-item"><a class="nav-link" href="../articles/tern.html">Get started</a></li>
 <li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
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-  <ul class="dropdown-menu" aria-labelledby="dropdown-articles"><li><a class="dropdown-item" href="../articles/missing_values.html">Missing Values in Tern</a></li>
+  <ul class="dropdown-menu" aria-labelledby="dropdown-articles">
+<li><a class="dropdown-item" href="../articles/missing_values.html">Missing Values in Tern</a></li>
     <li><a class="dropdown-item" href="../articles/tables.html">Tabulation</a></li>
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     <li><a class="dropdown-item" href="../articles/tern_functions_guide.html">Understanding `tern` functions</a></li>
-  </ul></li>
+  </ul>
+</li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
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+  <ul class="dropdown-menu" aria-labelledby="dropdown-reports">
+<li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
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-      </ul><ul class="navbar-nav"><li class="nav-item"><form class="form-inline" role="search">
- <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json"></form></li>
+  </ul>
+</li>
+      <div><li class="nav-item dropdown">
+    <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-versions">Versions</a>
+    <div class="dropdown-menu" aria-labelledby="dropdown-versions">
+    <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/main">main</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.5">v0.9.5</a>
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+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.3">v0.9.3</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1-rc3">v0.9.1-rc3</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a>
+</div>
+</li></div>
+</ul>
+<ul class="navbar-nav">
+<li class="nav-item"><form class="form-inline" role="search">
+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json">
+</form></li>
 <li class="nav-item"><a class="external-link nav-link" href="https://github.com/insightsengineering/tern" aria-label="GitHub"><span class="fa fa-github"></span></a></li>
-      </ul></div>
+      </ul>
+</div>
 
 
   </div>
@@ -54,7 +117,8 @@
     </div>
 
     <div class="section level2">
-    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
+    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">arrange_grobs</span><span class="op">(</span></span>
 <span>  <span class="va">...</span>,</span>
 <span>  grobs <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span><span class="va">...</span><span class="op">)</span>,</span>
@@ -69,52 +133,66 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
     </div>
 
     <div class="section level2">
-    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
+    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a>
+</h2>
 
 
-<dl><dt id="arg--">...<a class="anchor" aria-label="anchor" href="#arg--"></a></dt>
+<dl>
+<dt id="arg--">...<a class="anchor" aria-label="anchor" href="#arg--"></a>
+</dt>
 <dd><p>grobs.</p></dd>
 
 
-<dt id="arg-grobs">grobs<a class="anchor" aria-label="anchor" href="#arg-grobs"></a></dt>
+<dt id="arg-grobs">grobs<a class="anchor" aria-label="anchor" href="#arg-grobs"></a>
+</dt>
 <dd><p>(<code>list</code> of <code>grob</code>)<br> a list of grobs.</p></dd>
 
 
-<dt id="arg-ncol">ncol<a class="anchor" aria-label="anchor" href="#arg-ncol"></a></dt>
+<dt id="arg-ncol">ncol<a class="anchor" aria-label="anchor" href="#arg-ncol"></a>
+</dt>
 <dd><p>(<code>integer(1)</code>)<br> number of columns in layout.</p></dd>
 
 
-<dt id="arg-nrow">nrow<a class="anchor" aria-label="anchor" href="#arg-nrow"></a></dt>
+<dt id="arg-nrow">nrow<a class="anchor" aria-label="anchor" href="#arg-nrow"></a>
+</dt>
 <dd><p>(<code>integer(1)</code>)<br> number of rows in layout.</p></dd>
 
 
-<dt id="arg-padding-ht">padding_ht<a class="anchor" aria-label="anchor" href="#arg-padding-ht"></a></dt>
+<dt id="arg-padding-ht">padding_ht<a class="anchor" aria-label="anchor" href="#arg-padding-ht"></a>
+</dt>
 <dd><p>(<code><a href="https://rdrr.io/r/grid/unit.html" class="external-link">grid::unit</a></code>)<br> unit of length 1, vertical space between each grob.</p></dd>
 
 
-<dt id="arg-padding-wt">padding_wt<a class="anchor" aria-label="anchor" href="#arg-padding-wt"></a></dt>
+<dt id="arg-padding-wt">padding_wt<a class="anchor" aria-label="anchor" href="#arg-padding-wt"></a>
+</dt>
 <dd><p>(<code><a href="https://rdrr.io/r/grid/unit.html" class="external-link">grid::unit</a></code>)<br> unit of length 1, horizontal space between each grob.</p></dd>
 
 
-<dt id="arg-vp">vp<a class="anchor" aria-label="anchor" href="#arg-vp"></a></dt>
+<dt id="arg-vp">vp<a class="anchor" aria-label="anchor" href="#arg-vp"></a>
+</dt>
 <dd><p>(<code>viewport</code> or <code>NULL</code>)<br> a <code><a href="https://rdrr.io/r/grid/viewport.html" class="external-link">viewport()</a></code> object (or <code>NULL</code>).</p></dd>
 
 
-<dt id="arg-gp">gp<a class="anchor" aria-label="anchor" href="#arg-gp"></a></dt>
+<dt id="arg-gp">gp<a class="anchor" aria-label="anchor" href="#arg-gp"></a>
+</dt>
 <dd><p>(<code>gpar</code>)<br> a <code><a href="https://rdrr.io/r/grid/gpar.html" class="external-link">gpar()</a></code> object.</p></dd>
 
 
-<dt id="arg-name">name<a class="anchor" aria-label="anchor" href="#arg-name"></a></dt>
+<dt id="arg-name">name<a class="anchor" aria-label="anchor" href="#arg-name"></a>
+</dt>
 <dd><p>(<code>string</code>)<br> a character identifier for the grob.</p></dd>
 
-</dl></div>
+</dl>
+</div>
     <div class="section level2">
-    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
+    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a>
+</h2>
     <p>A <code>grob</code>.</p>
     </div>
 
     <div class="section level2">
-    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
+    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va">grid</span><span class="op">)</span></span></span>
 <span class="r-in"><span></span></span>
 <span class="r-in"><span><span class="co"># \donttest{</span></span></span>
@@ -151,17 +229,19 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 </code></pre></div>
     </div>
   </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
-    </nav></aside></div>
+    </nav></aside>
+</div>
 
 
     <footer><div class="nest">
   <p>tern is a part of the <strong>NEST</strong> and <a href="https://pharmaverse.org/" class="external-link"><strong>pharmaverse</strong></a>.</p>
 </div>
-<script type="text/javascript" src="../analytics.js"></script></footer></div>
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+<script type="text/javascript" src="../analytics.js"></script></footer>
+</div>
 
 
 
 
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+  </body>
+</html>
diff --git a/main/reference/as.rtable.html b/main/reference/as.rtable.html
index 8d6b1571a8..3f4dc767a4 100644
--- a/main/reference/as.rtable.html
+++ b/main/reference/as.rtable.html
@@ -1,7 +1,30 @@
-<!DOCTYPE html>
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-This is a new generic function to convert objects to rtable tables."><meta property="og:description" content="
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+<meta name="description" content="
+This is a new generic function to convert objects to rtable tables.">
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+This is a new generic function to convert objects to rtable tables.">
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+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
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+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a>
+</div>
+</li></div>
+</ul>
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+<li class="nav-item"><form class="form-inline" role="search">
+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json">
+</form></li>
 <li class="nav-item"><a class="external-link nav-link" href="https://github.com/insightsengineering/tern" aria-label="GitHub"><span class="fa fa-github"></span></a></li>
-      </ul></div>
+      </ul>
+</div>
 
 
   </div>
 </nav><div class="container template-reference-topic">
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
-      <img src="../logo.png" class="logo" alt=""><h1>Convert to <code>rtable</code></h1>
+      <img src="../logo.png" class="logo" alt=""><h1>Convert to <code>rtable</code>
+</h1>
       <small class="dont-index">Source: <a href="https://github.com/insightsengineering/tern/blob/main/R/utils_rtables.R" class="external-link"><code>R/utils_rtables.R</code></a></small>
       <div class="d-none name"><code>as.rtable.Rd</code></div>
     </div>
@@ -54,7 +118,8 @@
     </div>
 
     <div class="section level2">
-    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
+    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">as.rtable</span><span class="op">(</span><span class="va">x</span>, <span class="va">...</span><span class="op">)</span></span>
 <span></span>
 <span><span class="co"># S3 method for class 'data.frame'</span></span>
@@ -62,33 +127,44 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
     </div>
 
     <div class="section level2">
-    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
+    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a>
+</h2>
 
 
-<dl><dt id="arg-x">x<a class="anchor" aria-label="anchor" href="#arg-x"></a></dt>
+<dl>
+<dt id="arg-x">x<a class="anchor" aria-label="anchor" href="#arg-x"></a>
+</dt>
 <dd><p>(<code>data.frame</code>)<br> the object which should be converted to an <code>rtable</code>.</p></dd>
 
 
-<dt id="arg--">...<a class="anchor" aria-label="anchor" href="#arg--"></a></dt>
+<dt id="arg--">...<a class="anchor" aria-label="anchor" href="#arg--"></a>
+</dt>
 <dd><p>additional arguments for methods.</p></dd>
 
 
-<dt id="arg-format">format<a class="anchor" aria-label="anchor" href="#arg-format"></a></dt>
+<dt id="arg-format">format<a class="anchor" aria-label="anchor" href="#arg-format"></a>
+</dt>
 <dd><p>(<code>string</code> or <code>function</code>)<br> the format which should be used for the columns.</p></dd>
 
-</dl></div>
+</dl>
+</div>
     <div class="section level2">
-    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
+    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a>
+</h2>
     <p>An <code>rtables</code> table object. Note that the concrete class will depend on the method used.</p>
     </div>
     <div class="section level2">
-    <h2 id="methods-by-class-">Methods (by class)<a class="anchor" aria-label="anchor" href="#methods-by-class-"></a></h2>
+    <h2 id="methods-by-class-">Methods (by class)<a class="anchor" aria-label="anchor" href="#methods-by-class-"></a>
+</h2>
 
-<ul><li><p><code>as.rtable(data.frame)</code>: Method for converting a <code>data.frame</code> that contains numeric columns to <code>rtable</code>.</p></li>
-</ul></div>
+<ul>
+<li><p><code>as.rtable(data.frame)</code>: Method for converting a <code>data.frame</code> that contains numeric columns to <code>rtable</code>.</p></li>
+</ul>
+</div>
 
     <div class="section level2">
-    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
+    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">x</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a></span><span class="op">(</span></span></span>
 <span class="r-in"><span>  a <span class="op">=</span> <span class="fl">1</span><span class="op">:</span><span class="fl">10</span>,</span></span>
 <span class="r-in"><span>  b <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/stats/Normal.html" class="external-link">rnorm</a></span><span class="op">(</span><span class="fl">10</span><span class="op">)</span></span></span>
@@ -110,17 +186,19 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 </code></pre></div>
     </div>
   </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
-    </nav></aside></div>
+    </nav></aside>
+</div>
 
 
     <footer><div class="nest">
   <p>tern is a part of the <strong>NEST</strong> and <a href="https://pharmaverse.org/" class="external-link"><strong>pharmaverse</strong></a>.</p>
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-<script type="text/javascript" src="../analytics.js"></script></footer></div>
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+<script type="text/javascript" src="../analytics.js"></script></footer>
+</div>
 
 
 
 
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diff --git a/main/reference/as_factor_keep_attributes.html b/main/reference/as_factor_keep_attributes.html
index edbf09c265..78e1e9005d 100644
--- a/main/reference/as_factor_keep_attributes.html
+++ b/main/reference/as_factor_keep_attributes.html
@@ -1,9 +1,32 @@
-<!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Conversion of a vector to a factor — as_factor_keep_attributes • tern</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Conversion of a vector to a factor — as_factor_keep_attributes"><meta name="description" content="Converts x to a factor and keeps its attributes. Warns appropriately such that the user
+<html lang="en">
+<head>
+<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+<meta charset="utf-8">
+<meta http-equiv="X-UA-Compatible" content="IE=edge">
+<meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<title>Conversion of a vector to a factor — as_factor_keep_attributes • tern</title>
+<!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png">
+<link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png">
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+<link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png">
+<link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png">
+<script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet">
+<script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet">
+<link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet">
+<script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Conversion of a vector to a factor — as_factor_keep_attributes">
+<meta name="description" content="Converts x to a factor and keeps its attributes. Warns appropriately such that the user
 can decide whether they prefer converting to factor manually (e.g. for full control of
-factor levels)."><meta property="og:description" content="Converts x to a factor and keeps its attributes. Warns appropriately such that the user
+factor levels).">
+<meta property="og:description" content="Converts x to a factor and keeps its attributes. Warns appropriately such that the user
 can decide whether they prefer converting to factor manually (e.g. for full control of
-factor levels)."><meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png"><link rel="stylesheet" href="../consent.css"><script src="../consent.js" type="text/javascript" charset="utf-8"></script></head><body>
+factor levels).">
+<meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png">
+<link rel="stylesheet" href="../consent.css">
+<script src="../consent.js" type="text/javascript" charset="utf-8"></script>
+</head>
+<body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
 
 
@@ -19,26 +42,66 @@
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-      <ul class="navbar-nav me-auto"><li class="nav-item"><a class="nav-link" href="../articles/tern.html">Get started</a></li>
+      <ul class="navbar-nav me-auto">
+<li class="nav-item"><a class="nav-link" href="../articles/tern.html">Get started</a></li>
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+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
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+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a>
+</div>
+</li></div>
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+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json">
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-      </ul></div>
+      </ul>
+</div>
 
 
   </div>
@@ -57,7 +120,8 @@
     </div>
 
     <div class="section level2">
-    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
+    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">as_factor_keep_attributes</span><span class="op">(</span></span>
 <span>  <span class="va">x</span>,</span>
 <span>  x_name <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/deparse.html" class="external-link">deparse</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/substitute.html" class="external-link">substitute</a></span><span class="op">(</span><span class="va">x</span><span class="op">)</span><span class="op">)</span>,</span>
@@ -67,42 +131,52 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
     </div>
 
     <div class="section level2">
-    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
+    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a>
+</h2>
 
 
-<dl><dt id="arg-x">x<a class="anchor" aria-label="anchor" href="#arg-x"></a></dt>
+<dl>
+<dt id="arg-x">x<a class="anchor" aria-label="anchor" href="#arg-x"></a>
+</dt>
 <dd><p>(<code>vector</code>)<br> object to convert.</p></dd>
 
 
-<dt id="arg-x-name">x_name<a class="anchor" aria-label="anchor" href="#arg-x-name"></a></dt>
+<dt id="arg-x-name">x_name<a class="anchor" aria-label="anchor" href="#arg-x-name"></a>
+</dt>
 <dd><p>(<code>string</code>)<br> name of <code>x</code>.</p></dd>
 
 
-<dt id="arg-na-level">na_level<a class="anchor" aria-label="anchor" href="#arg-na-level"></a></dt>
+<dt id="arg-na-level">na_level<a class="anchor" aria-label="anchor" href="#arg-na-level"></a>
+</dt>
 <dd><p>(<code>string</code>)<br> the explicit missing level which should be used when converting a character vector.</p></dd>
 
 
-<dt id="arg-verbose">verbose<a class="anchor" aria-label="anchor" href="#arg-verbose"></a></dt>
+<dt id="arg-verbose">verbose<a class="anchor" aria-label="anchor" href="#arg-verbose"></a>
+</dt>
 <dd><p>(<code>flag</code>)<br> defaults to <code>TRUE</code>. It prints out warnings and messages.</p></dd>
 
-</dl></div>
+</dl>
+</div>
     <div class="section level2">
-    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
+    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a>
+</h2>
     <p>A <code>factor</code> with same attributes (except class) as <code>x</code>. Does not modify <code>x</code> if already a <code>factor</code>.</p>
     </div>
 
   </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
-    </nav></aside></div>
+    </nav></aside>
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     <footer><div class="nest">
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diff --git a/main/reference/assertions.html b/main/reference/assertions.html
index a315dbd24c..7df0d4a0eb 100644
--- a/main/reference/assertions.html
+++ b/main/reference/assertions.html
@@ -1,5 +1,28 @@
-<!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Additional assertions to use with checkmate — assertions • tern</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Additional assertions to use with checkmate — assertions"><meta name="description" content="Additional assertion functions which can be used together with the checkmate package."><meta property="og:description" content="Additional assertion functions which can be used together with the checkmate package."><meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png"><link rel="stylesheet" href="../consent.css"><script src="../consent.js" type="text/javascript" charset="utf-8"></script></head><body>
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+<script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Additional assertions to use with checkmate — assertions">
+<meta name="description" content="Additional assertion functions which can be used together with the checkmate package.">
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@@ -15,33 +38,74 @@
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 </nav><div class="container template-reference-topic">
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   <main id="main" class="col-md-9"><div class="page-header">
-      <img src="../logo.png" class="logo" alt=""><h1>Additional assertions to use with <code>checkmate</code></h1>
+      <img src="../logo.png" class="logo" alt=""><h1>Additional assertions to use with <code>checkmate</code>
+</h1>
       <small class="dont-index">Source: <a href="https://github.com/insightsengineering/tern/blob/main/R/utils_checkmate.R" class="external-link"><code>R/utils_checkmate.R</code></a></small>
       <div class="d-none name"><code>assertions.Rd</code></div>
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@@ -51,7 +115,8 @@
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-    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
+    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">assert_list_of_variables</span><span class="op">(</span><span class="va">x</span>, .var.name <span class="op">=</span> <span class="fu">checkmate</span><span class="fu">::</span><span class="fu"><a href="https://mllg.github.io/checkmate/reference/vname.html" class="external-link">vname</a></span><span class="op">(</span><span class="va">x</span><span class="op">)</span>, add <span class="op">=</span> <span class="cn">NULL</span><span class="op">)</span></span>
 <span></span>
 <span><span class="fu">assert_df_with_variables</span><span class="op">(</span></span>
@@ -89,85 +154,104 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
     </div>
 
     <div class="section level2">
-    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
+    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a>
+</h2>
 
 
-<dl><dt id="arg-x">x<a class="anchor" aria-label="anchor" href="#arg-x"></a></dt>
+<dl>
+<dt id="arg-x">x<a class="anchor" aria-label="anchor" href="#arg-x"></a>
+</dt>
 <dd><p>(<code>any</code>)<br> object to test.</p></dd>
 
 
-<dt id="arg--var-name">.var.name<a class="anchor" aria-label="anchor" href="#arg--var-name"></a></dt>
+<dt id="arg--var-name">.var.name<a class="anchor" aria-label="anchor" href="#arg--var-name"></a>
+</dt>
 <dd><p>[<code>character(1)</code>]<br>
 Name of the checked object to print in assertions. Defaults to
 the heuristic implemented in <code><a href="https://mllg.github.io/checkmate/reference/vname.html" class="external-link">vname</a></code>.</p></dd>
 
 
-<dt id="arg-add">add<a class="anchor" aria-label="anchor" href="#arg-add"></a></dt>
+<dt id="arg-add">add<a class="anchor" aria-label="anchor" href="#arg-add"></a>
+</dt>
 <dd><p>[<code>AssertCollection</code>]<br>
 Collection to store assertion messages. See <code><a href="https://mllg.github.io/checkmate/reference/AssertCollection.html" class="external-link">AssertCollection</a></code>.</p></dd>
 
 
-<dt id="arg-df">df<a class="anchor" aria-label="anchor" href="#arg-df"></a></dt>
+<dt id="arg-df">df<a class="anchor" aria-label="anchor" href="#arg-df"></a>
+</dt>
 <dd><p>(<code>data.frame</code>)<br> data set to test.</p></dd>
 
 
-<dt id="arg-variables">variables<a class="anchor" aria-label="anchor" href="#arg-variables"></a></dt>
+<dt id="arg-variables">variables<a class="anchor" aria-label="anchor" href="#arg-variables"></a>
+</dt>
 <dd><p>(named <code>list</code> of <code>character</code>)<br> list of variables to test.</p></dd>
 
 
-<dt id="arg-na-level">na_level<a class="anchor" aria-label="anchor" href="#arg-na-level"></a></dt>
+<dt id="arg-na-level">na_level<a class="anchor" aria-label="anchor" href="#arg-na-level"></a>
+</dt>
 <dd><p>(<code>string</code>)<br> the string you have been using to represent NA or
 missing data. For <code>NA</code> values please consider using directly <code><a href="https://rdrr.io/r/base/NA.html" class="external-link">is.na()</a></code> or
 similar approaches.</p></dd>
 
 
-<dt id="arg-min-levels">min.levels<a class="anchor" aria-label="anchor" href="#arg-min-levels"></a></dt>
+<dt id="arg-min-levels">min.levels<a class="anchor" aria-label="anchor" href="#arg-min-levels"></a>
+</dt>
 <dd><p>[<code>integer(1)</code>]<br>
 Minimum number of factor levels.
 Default is <code>NULL</code> (no check).</p></dd>
 
 
-<dt id="arg-max-levels">max.levels<a class="anchor" aria-label="anchor" href="#arg-max-levels"></a></dt>
+<dt id="arg-max-levels">max.levels<a class="anchor" aria-label="anchor" href="#arg-max-levels"></a>
+</dt>
 <dd><p>[<code>integer(1)</code>]<br>
 Maximum number of factor levels.
 Default is <code>NULL</code> (no check).</p></dd>
 
 
-<dt id="arg-null-ok">null.ok<a class="anchor" aria-label="anchor" href="#arg-null-ok"></a></dt>
+<dt id="arg-null-ok">null.ok<a class="anchor" aria-label="anchor" href="#arg-null-ok"></a>
+</dt>
 <dd><p>[<code>logical(1)</code>]<br>
 If set to <code>TRUE</code>, <code>x</code> may also be <code>NULL</code>.
 In this case only a type check of <code>x</code> is performed, all additional checks are disabled.</p></dd>
 
 
-<dt id="arg-any-missing">any.missing<a class="anchor" aria-label="anchor" href="#arg-any-missing"></a></dt>
+<dt id="arg-any-missing">any.missing<a class="anchor" aria-label="anchor" href="#arg-any-missing"></a>
+</dt>
 <dd><p>[<code>logical(1)</code>]<br>
 Are vectors with missing values allowed? Default is <code>TRUE</code>.</p></dd>
 
 
-<dt id="arg-n-levels">n.levels<a class="anchor" aria-label="anchor" href="#arg-n-levels"></a></dt>
+<dt id="arg-n-levels">n.levels<a class="anchor" aria-label="anchor" href="#arg-n-levels"></a>
+</dt>
 <dd><p>[<code>integer(1)</code>]<br>
 Exact number of factor levels.
 Default is <code>NULL</code> (no check).</p></dd>
 
 
-<dt id="arg-len">len<a class="anchor" aria-label="anchor" href="#arg-len"></a></dt>
+<dt id="arg-len">len<a class="anchor" aria-label="anchor" href="#arg-len"></a>
+</dt>
 <dd><p>[<code>integer(1)</code>]<br>
 Exact expected length of <code>x</code>.</p></dd>
 
 
-<dt id="arg-include-boundaries">include_boundaries<a class="anchor" aria-label="anchor" href="#arg-include-boundaries"></a></dt>
+<dt id="arg-include-boundaries">include_boundaries<a class="anchor" aria-label="anchor" href="#arg-include-boundaries"></a>
+</dt>
 <dd><p>(<code>flag</code>)<br> whether to include boundaries when testing
 for proportions.</p></dd>
 
-</dl></div>
+</dl>
+</div>
     <div class="section level2">
-    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
+    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a>
+</h2>
     <p>Nothing if assertion passes, otherwise prints the error message.</p>
     </div>
     <div class="section level2">
-    <h2 id="functions">Functions<a class="anchor" aria-label="anchor" href="#functions"></a></h2>
+    <h2 id="functions">Functions<a class="anchor" aria-label="anchor" href="#functions"></a>
+</h2>
 
-<ul><li><p><code>assert_list_of_variables()</code>: Checks whether <code>x</code> is a valid list of variable names.
+<ul>
+<li><p><code>assert_list_of_variables()</code>: Checks whether <code>x</code> is a valid list of variable names.
 <code>NULL</code> elements of the list <code>x</code> are dropped with <code>Filter(Negate(is.null), x)</code>.</p></li>
 <li><p><code>assert_df_with_variables()</code>: Check whether <code>df</code> is a data frame with the analysis <code>variables</code>.
 Please notice how this produces an error when not all variables are present in the
@@ -178,20 +262,23 @@ <h2 id="functions">Functions<a class="anchor" aria-label="anchor" href="#functio
 are all factors. Note that the creation of <code>NA</code> by direct call of <code><a href="https://rdrr.io/r/base/factor.html" class="external-link">factor()</a></code> will
 trim <code>NA</code> levels out of the vector list itself.</p></li>
 <li><p><code>assert_proportion_value()</code>: Check whether <code>x</code> is a proportion: number between 0 and 1.</p></li>
-</ul></div>
+</ul>
+</div>
 
   </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
-    </nav></aside></div>
+    </nav></aside>
+</div>
 
 
     <footer><div class="nest">
   <p>tern is a part of the <strong>NEST</strong> and <a href="https://pharmaverse.org/" class="external-link"><strong>pharmaverse</strong></a>.</p>
 </div>
-<script type="text/javascript" src="../analytics.js"></script></footer></div>
-
+<script type="text/javascript" src="../analytics.js"></script></footer>
+</div>
 
 
 
 
-  </body></html>
 
+  </body>
+</html>
diff --git a/main/reference/bins_percent_labels.html b/main/reference/bins_percent_labels.html
index 7ced1378ce..660c68c293 100644
--- a/main/reference/bins_percent_labels.html
+++ b/main/reference/bins_percent_labels.html
@@ -1,7 +1,30 @@
-<!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Labels for bins in percent — bins_percent_labels • tern</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Labels for bins in percent — bins_percent_labels"><meta name="description" content="This creates labels for quantile based bins in percent. This assumes the right-closed
-intervals as produced by cut_quantile_bins()."><meta property="og:description" content="This creates labels for quantile based bins in percent. This assumes the right-closed
-intervals as produced by cut_quantile_bins()."><meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png"><link rel="stylesheet" href="../consent.css"><script src="../consent.js" type="text/javascript" charset="utf-8"></script></head><body>
+<html lang="en">
+<head>
+<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+<meta charset="utf-8">
+<meta http-equiv="X-UA-Compatible" content="IE=edge">
+<meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<title>Labels for bins in percent — bins_percent_labels • tern</title>
+<!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png">
+<link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png">
+<link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png">
+<link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png">
+<link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png">
+<link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png">
+<script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet">
+<script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet">
+<link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet">
+<script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Labels for bins in percent — bins_percent_labels">
+<meta name="description" content="This creates labels for quantile based bins in percent. This assumes the right-closed
+intervals as produced by cut_quantile_bins().">
+<meta property="og:description" content="This creates labels for quantile based bins in percent. This assumes the right-closed
+intervals as produced by cut_quantile_bins().">
+<meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png">
+<link rel="stylesheet" href="../consent.css">
+<script src="../consent.js" type="text/javascript" charset="utf-8"></script>
+</head>
+<body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
 
 
@@ -17,26 +40,66 @@
     </button>
 
     <div id="navbar" class="collapse navbar-collapse ms-3">
-      <ul class="navbar-nav me-auto"><li class="nav-item"><a class="nav-link" href="../articles/tern.html">Get started</a></li>
+      <ul class="navbar-nav me-auto">
+<li class="nav-item"><a class="nav-link" href="../articles/tern.html">Get started</a></li>
 <li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
 <li class="nav-item dropdown">
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-articles" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Articles</button>
-  <ul class="dropdown-menu" aria-labelledby="dropdown-articles"><li><a class="dropdown-item" href="../articles/missing_values.html">Missing Values in Tern</a></li>
+  <ul class="dropdown-menu" aria-labelledby="dropdown-articles">
+<li><a class="dropdown-item" href="../articles/missing_values.html">Missing Values in Tern</a></li>
     <li><a class="dropdown-item" href="../articles/tables.html">Tabulation</a></li>
     <li><a class="dropdown-item" href="../articles/tern_formats.html">Formatting Functions</a></li>
     <li><a class="dropdown-item" href="../articles/tern_functions_guide.html">Understanding `tern` functions</a></li>
-  </ul></li>
+  </ul>
+</li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
-  <ul class="dropdown-menu" aria-labelledby="dropdown-reports"><li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
+  <ul class="dropdown-menu" aria-labelledby="dropdown-reports">
+<li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
     <li><a class="dropdown-item" href="../unit-test-report/">Unit test report</a></li>
     <li><a class="dropdown-item" href="../unit-test-report-non-cran/">Non-CRAN unit test report</a></li>
-  </ul></li>
-      </ul><ul class="navbar-nav"><li class="nav-item"><form class="form-inline" role="search">
- <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json"></form></li>
+  </ul>
+</li>
+      <div><li class="nav-item dropdown">
+    <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-versions">Versions</a>
+    <div class="dropdown-menu" aria-labelledby="dropdown-versions">
+    <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/main">main</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.5">v0.9.5</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.4">v0.9.4</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.3">v0.9.3</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1-rc3">v0.9.1-rc3</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a>
+</div>
+</li></div>
+</ul>
+<ul class="navbar-nav">
+<li class="nav-item"><form class="form-inline" role="search">
+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json">
+</form></li>
 <li class="nav-item"><a class="external-link nav-link" href="https://github.com/insightsengineering/tern" aria-label="GitHub"><span class="fa fa-github"></span></a></li>
-      </ul></div>
+      </ul>
+</div>
 
 
   </div>
@@ -54,41 +117,50 @@
     </div>
 
     <div class="section level2">
-    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
+    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">bins_percent_labels</span><span class="op">(</span><span class="va">probs</span>, digits <span class="op">=</span> <span class="fl">0</span><span class="op">)</span></span></code></pre></div>
     </div>
 
     <div class="section level2">
-    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
+    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a>
+</h2>
 
 
-<dl><dt id="arg-probs">probs<a class="anchor" aria-label="anchor" href="#arg-probs"></a></dt>
+<dl>
+<dt id="arg-probs">probs<a class="anchor" aria-label="anchor" href="#arg-probs"></a>
+</dt>
 <dd><p>(<code>numeric</code>)<br> the probabilities identifying the quantiles.
 This is a sorted vector of unique <code>proportion</code> values, i.e. between 0 and 1, where
 the boundaries 0 and 1 must not be included.</p></dd>
 
 
-<dt id="arg-digits">digits<a class="anchor" aria-label="anchor" href="#arg-digits"></a></dt>
+<dt id="arg-digits">digits<a class="anchor" aria-label="anchor" href="#arg-digits"></a>
+</dt>
 <dd><p>(<code>integer(1)</code>)<br> number of decimal places to round the percent numbers.</p></dd>
 
-</dl></div>
+</dl>
+</div>
     <div class="section level2">
-    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
+    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a>
+</h2>
     <p>A <code>character</code> vector with labels in the format <code>[0%,20%]</code>, <code>(20%,50%]</code>, etc.</p>
     </div>
 
   </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
-    </nav></aside></div>
+    </nav></aside>
+</div>
 
 
     <footer><div class="nest">
   <p>tern is a part of the <strong>NEST</strong> and <a href="https://pharmaverse.org/" class="external-link"><strong>pharmaverse</strong></a>.</p>
 </div>
-<script type="text/javascript" src="../analytics.js"></script></footer></div>
-
+<script type="text/javascript" src="../analytics.js"></script></footer>
+</div>
 
 
 
 
-  </body></html>
 
+  </body>
+</html>
diff --git a/main/reference/c_label_n.html b/main/reference/c_label_n.html
index 4fa1a6a1b5..ded5192be3 100644
--- a/main/reference/c_label_n.html
+++ b/main/reference/c_label_n.html
@@ -1,9 +1,32 @@
-<!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Content row function to add row total to labels — c_label_n • tern</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Content row function to add row total to labels — c_label_n"><meta name="description" content="This takes the label of the latest row split level and adds the row total from df in parentheses.
+<html lang="en">
+<head>
+<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
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+<meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<title>Content row function to add row total to labels — c_label_n • tern</title>
+<!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png">
+<link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png">
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+<link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet">
+<script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet">
+<link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet">
+<script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Content row function to add row total to labels — c_label_n">
+<meta name="description" content="This takes the label of the latest row split level and adds the row total from df in parentheses.
 This function differs from c_label_n_alt() by taking row counts from df rather than
-alt_counts_df, and is used by add_rowcounts() when alt_counts is set to FALSE."><meta property="og:description" content="This takes the label of the latest row split level and adds the row total from df in parentheses.
+alt_counts_df, and is used by add_rowcounts() when alt_counts is set to FALSE.">
+<meta property="og:description" content="This takes the label of the latest row split level and adds the row total from df in parentheses.
 This function differs from c_label_n_alt() by taking row counts from df rather than
-alt_counts_df, and is used by add_rowcounts() when alt_counts is set to FALSE."><meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png"><link rel="stylesheet" href="../consent.css"><script src="../consent.js" type="text/javascript" charset="utf-8"></script></head><body>
+alt_counts_df, and is used by add_rowcounts() when alt_counts is set to FALSE.">
+<meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png">
+<link rel="stylesheet" href="../consent.css">
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@@ -19,26 +42,66 @@
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+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
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+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a>
+</div>
+</li></div>
+</ul>
+<ul class="navbar-nav">
+<li class="nav-item"><form class="form-inline" role="search">
+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json">
+</form></li>
 <li class="nav-item"><a class="external-link nav-link" href="https://github.com/insightsengineering/tern" aria-label="GitHub"><span class="fa fa-github"></span></a></li>
-      </ul></div>
+      </ul>
+</div>
 
 
   </div>
@@ -57,56 +120,68 @@
     </div>
 
     <div class="section level2">
-    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
+    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">c_label_n</span><span class="op">(</span><span class="va">df</span>, <span class="va">labelstr</span>, <span class="va">.N_row</span><span class="op">)</span></span></code></pre></div>
     </div>
 
     <div class="section level2">
-    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
+    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a>
+</h2>
 
 
-<dl><dt id="arg-df">df<a class="anchor" aria-label="anchor" href="#arg-df"></a></dt>
+<dl>
+<dt id="arg-df">df<a class="anchor" aria-label="anchor" href="#arg-df"></a>
+</dt>
 <dd><p>(<code>data.frame</code>)<br> data set containing all analysis variables.</p></dd>
 
 
-<dt id="arg-labelstr">labelstr<a class="anchor" aria-label="anchor" href="#arg-labelstr"></a></dt>
+<dt id="arg-labelstr">labelstr<a class="anchor" aria-label="anchor" href="#arg-labelstr"></a>
+</dt>
 <dd><p>(<code>string</code>)<br> label of the level of the parent split currently being summarized
 (must be present as second argument in Content Row Functions). See <code><a href="https://insightsengineering.github.io/rtables/latest-tag/reference/summarize_row_groups.html" class="external-link">rtables::summarize_row_groups()</a></code>
 for more information.</p></dd>
 
 
-<dt id="arg--n-row">.N_row<a class="anchor" aria-label="anchor" href="#arg--n-row"></a></dt>
+<dt id="arg--n-row">.N_row<a class="anchor" aria-label="anchor" href="#arg--n-row"></a>
+</dt>
 <dd><p>(<code>integer(1)</code>)<br> row-wise N (row group count) for the group of observations being analyzed
 (i.e. with no column-based subsetting) that is typically passed by <code>rtables</code>.</p></dd>
 
-</dl></div>
+</dl>
+</div>
     <div class="section level2">
-    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
+    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a>
+</h2>
     <p>A list with formatted <code><a href="https://insightsengineering.github.io/rtables/latest-tag/reference/CellValue.html" class="external-link">rtables::CellValue()</a></code> with the row count value and the correct label.</p>
     </div>
     <div class="section level2">
-    <h2 id="note">Note<a class="anchor" aria-label="anchor" href="#note"></a></h2>
+    <h2 id="note">Note<a class="anchor" aria-label="anchor" href="#note"></a>
+</h2>
     <p>It is important here to not use <code>df</code> but rather <code>.N_row</code> in the implementation, because
 the former is already split by columns and will refer to the first column of the data only.</p>
     </div>
     <div class="section level2">
-    <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"></a></h2>
+    <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"></a>
+</h2>
     <div class="dont-index"><p><code><a href="c_label_n_alt.html">c_label_n_alt()</a></code> which performs the same function but retrieves row counts from
 <code>alt_counts_df</code> instead of <code>df</code>.</p></div>
     </div>
 
   </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
-    </nav></aside></div>
+    </nav></aside>
+</div>
 
 
     <footer><div class="nest">
   <p>tern is a part of the <strong>NEST</strong> and <a href="https://pharmaverse.org/" class="external-link"><strong>pharmaverse</strong></a>.</p>
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-<script type="text/javascript" src="../analytics.js"></script></footer></div>
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+<script type="text/javascript" src="../analytics.js"></script></footer>
+</div>
 
 
 
 
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diff --git a/main/reference/c_label_n_alt.html b/main/reference/c_label_n_alt.html
index b530ab79f3..caaaa548c8 100644
--- a/main/reference/c_label_n_alt.html
+++ b/main/reference/c_label_n_alt.html
@@ -1,9 +1,32 @@
-<!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Content row function to add alt_counts_df row total to labels — c_label_n_alt • tern</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Content row function to add alt_counts_df row total to labels — c_label_n_alt"><meta name="description" content="This takes the label of the latest row split level and adds the row total from alt_counts_df
+<html lang="en">
+<head>
+<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+<meta charset="utf-8">
+<meta http-equiv="X-UA-Compatible" content="IE=edge">
+<meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<title>Content row function to add alt_counts_df row total to labels — c_label_n_alt • tern</title>
+<!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png">
+<link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png">
+<link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png">
+<link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png">
+<link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png">
+<link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png">
+<script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet">
+<script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet">
+<link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet">
+<script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Content row function to add alt_counts_df row total to labels — c_label_n_alt">
+<meta name="description" content="This takes the label of the latest row split level and adds the row total from alt_counts_df
 in parentheses. This function differs from c_label_n() by taking row counts from alt_counts_df
-rather than df, and is used by add_rowcounts() when alt_counts is set to TRUE."><meta property="og:description" content="This takes the label of the latest row split level and adds the row total from alt_counts_df
+rather than df, and is used by add_rowcounts() when alt_counts is set to TRUE.">
+<meta property="og:description" content="This takes the label of the latest row split level and adds the row total from alt_counts_df
 in parentheses. This function differs from c_label_n() by taking row counts from alt_counts_df
-rather than df, and is used by add_rowcounts() when alt_counts is set to TRUE."><meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png"><link rel="stylesheet" href="../consent.css"><script src="../consent.js" type="text/javascript" charset="utf-8"></script></head><body>
+rather than df, and is used by add_rowcounts() when alt_counts is set to TRUE.">
+<meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png">
+<link rel="stylesheet" href="../consent.css">
+<script src="../consent.js" type="text/javascript" charset="utf-8"></script>
+</head>
+<body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
 
 
@@ -19,26 +42,66 @@
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-  <ul class="dropdown-menu" aria-labelledby="dropdown-articles"><li><a class="dropdown-item" href="../articles/missing_values.html">Missing Values in Tern</a></li>
+  <ul class="dropdown-menu" aria-labelledby="dropdown-articles">
+<li><a class="dropdown-item" href="../articles/missing_values.html">Missing Values in Tern</a></li>
     <li><a class="dropdown-item" href="../articles/tables.html">Tabulation</a></li>
     <li><a class="dropdown-item" href="../articles/tern_formats.html">Formatting Functions</a></li>
     <li><a class="dropdown-item" href="../articles/tern_functions_guide.html">Understanding `tern` functions</a></li>
-  </ul></li>
+  </ul>
+</li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
-  <ul class="dropdown-menu" aria-labelledby="dropdown-reports"><li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
+  <ul class="dropdown-menu" aria-labelledby="dropdown-reports">
+<li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
     <li><a class="dropdown-item" href="../unit-test-report/">Unit test report</a></li>
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-      </ul><ul class="navbar-nav"><li class="nav-item"><form class="form-inline" role="search">
- <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json"></form></li>
+  </ul>
+</li>
+      <div><li class="nav-item dropdown">
+    <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-versions">Versions</a>
+    <div class="dropdown-menu" aria-labelledby="dropdown-versions">
+    <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/main">main</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.5">v0.9.5</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.4">v0.9.4</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.3">v0.9.3</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1-rc3">v0.9.1-rc3</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a>
+</div>
+</li></div>
+</ul>
+<ul class="navbar-nav">
+<li class="nav-item"><form class="form-inline" role="search">
+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json">
+</form></li>
 <li class="nav-item"><a class="external-link nav-link" href="https://github.com/insightsengineering/tern" aria-label="GitHub"><span class="fa fa-github"></span></a></li>
-      </ul></div>
+      </ul>
+</div>
 
 
   </div>
@@ -57,46 +120,56 @@
     </div>
 
     <div class="section level2">
-    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
+    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">c_label_n_alt</span><span class="op">(</span><span class="va">df</span>, <span class="va">labelstr</span>, <span class="va">.alt_df_row</span><span class="op">)</span></span></code></pre></div>
     </div>
 
     <div class="section level2">
-    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
+    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a>
+</h2>
 
 
-<dl><dt id="arg-df">df<a class="anchor" aria-label="anchor" href="#arg-df"></a></dt>
+<dl>
+<dt id="arg-df">df<a class="anchor" aria-label="anchor" href="#arg-df"></a>
+</dt>
 <dd><p>(<code>data.frame</code>)<br> data set containing all analysis variables.</p></dd>
 
 
-<dt id="arg-labelstr">labelstr<a class="anchor" aria-label="anchor" href="#arg-labelstr"></a></dt>
+<dt id="arg-labelstr">labelstr<a class="anchor" aria-label="anchor" href="#arg-labelstr"></a>
+</dt>
 <dd><p>(<code>string</code>)<br> label of the level of the parent split currently being summarized
 (must be present as second argument in Content Row Functions). See <code><a href="https://insightsengineering.github.io/rtables/latest-tag/reference/summarize_row_groups.html" class="external-link">rtables::summarize_row_groups()</a></code>
 for more information.</p></dd>
 
-</dl></div>
+</dl>
+</div>
     <div class="section level2">
-    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
+    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a>
+</h2>
     <p>A list with formatted <code><a href="https://insightsengineering.github.io/rtables/latest-tag/reference/CellValue.html" class="external-link">rtables::CellValue()</a></code> with the row count value and the correct label.</p>
     </div>
     <div class="section level2">
-    <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"></a></h2>
+    <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"></a>
+</h2>
     <div class="dont-index"><p><code><a href="c_label_n.html">c_label_n()</a></code> which performs the same function but retrieves row counts from <code>df</code> instead
 of <code>alt_counts_df</code>.</p></div>
     </div>
 
   </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
-    </nav></aside></div>
+    </nav></aside>
+</div>
 
 
     <footer><div class="nest">
   <p>tern is a part of the <strong>NEST</strong> and <a href="https://pharmaverse.org/" class="external-link"><strong>pharmaverse</strong></a>.</p>
 </div>
-<script type="text/javascript" src="../analytics.js"></script></footer></div>
-
+<script type="text/javascript" src="../analytics.js"></script></footer>
+</div>
 
 
 
 
-  </body></html>
 
+  </body>
+</html>
diff --git a/main/reference/cfun_by_flag.html b/main/reference/cfun_by_flag.html
index 4960b09e51..96772efa77 100644
--- a/main/reference/cfun_by_flag.html
+++ b/main/reference/cfun_by_flag.html
@@ -1,5 +1,28 @@
-<!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Constructor for content functions given a data frame with flag input — cfun_by_flag • tern</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Constructor for content functions given a data frame with flag input — cfun_by_flag"><meta name="description" content="This can be useful for tabulating model results."><meta property="og:description" content="This can be useful for tabulating model results."><meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png"><link rel="stylesheet" href="../consent.css"><script src="../consent.js" type="text/javascript" charset="utf-8"></script></head><body>
+<html lang="en">
+<head>
+<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+<meta charset="utf-8">
+<meta http-equiv="X-UA-Compatible" content="IE=edge">
+<meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<title>Constructor for content functions given a data frame with flag input — cfun_by_flag • tern</title>
+<!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png">
+<link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png">
+<link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png">
+<link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png">
+<link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png">
+<link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png">
+<script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet">
+<script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet">
+<link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet">
+<script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Constructor for content functions given a data frame with flag input — cfun_by_flag">
+<meta name="description" content="This can be useful for tabulating model results.">
+<meta property="og:description" content="This can be useful for tabulating model results.">
+<meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png">
+<link rel="stylesheet" href="../consent.css">
+<script src="../consent.js" type="text/javascript" charset="utf-8"></script>
+</head>
+<body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
 
 
@@ -15,26 +38,66 @@
     </button>
 
     <div id="navbar" class="collapse navbar-collapse ms-3">
-      <ul class="navbar-nav me-auto"><li class="nav-item"><a class="nav-link" href="../articles/tern.html">Get started</a></li>
+      <ul class="navbar-nav me-auto">
+<li class="nav-item"><a class="nav-link" href="../articles/tern.html">Get started</a></li>
 <li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
 <li class="nav-item dropdown">
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-articles" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Articles</button>
-  <ul class="dropdown-menu" aria-labelledby="dropdown-articles"><li><a class="dropdown-item" href="../articles/missing_values.html">Missing Values in Tern</a></li>
+  <ul class="dropdown-menu" aria-labelledby="dropdown-articles">
+<li><a class="dropdown-item" href="../articles/missing_values.html">Missing Values in Tern</a></li>
     <li><a class="dropdown-item" href="../articles/tables.html">Tabulation</a></li>
     <li><a class="dropdown-item" href="../articles/tern_formats.html">Formatting Functions</a></li>
     <li><a class="dropdown-item" href="../articles/tern_functions_guide.html">Understanding `tern` functions</a></li>
-  </ul></li>
+  </ul>
+</li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
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   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
-  <ul class="dropdown-menu" aria-labelledby="dropdown-reports"><li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
+  <ul class="dropdown-menu" aria-labelledby="dropdown-reports">
+<li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
     <li><a class="dropdown-item" href="../unit-test-report/">Unit test report</a></li>
     <li><a class="dropdown-item" href="../unit-test-report-non-cran/">Non-CRAN unit test report</a></li>
-  </ul></li>
-      </ul><ul class="navbar-nav"><li class="nav-item"><form class="form-inline" role="search">
- <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json"></form></li>
+  </ul>
+</li>
+      <div><li class="nav-item dropdown">
+    <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-versions">Versions</a>
+    <div class="dropdown-menu" aria-labelledby="dropdown-versions">
+    <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/main">main</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.5">v0.9.5</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.4">v0.9.4</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.3">v0.9.3</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1-rc3">v0.9.1-rc3</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a>
+</div>
+</li></div>
+</ul>
+<ul class="navbar-nav">
+<li class="nav-item"><form class="form-inline" role="search">
+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json">
+</form></li>
 <li class="nav-item"><a class="external-link nav-link" href="https://github.com/insightsengineering/tern" aria-label="GitHub"><span class="fa fa-github"></span></a></li>
-      </ul></div>
+      </ul>
+</div>
 
 
   </div>
@@ -51,45 +114,55 @@
     </div>
 
     <div class="section level2">
-    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
+    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">cfun_by_flag</span><span class="op">(</span><span class="va">analysis_var</span>, <span class="va">flag_var</span>, format <span class="op">=</span> <span class="st">"xx"</span>, .indent_mods <span class="op">=</span> <span class="cn">NULL</span><span class="op">)</span></span></code></pre></div>
     </div>
 
     <div class="section level2">
-    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
+    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a>
+</h2>
 
 
-<dl><dt id="arg-analysis-var">analysis_var<a class="anchor" aria-label="anchor" href="#arg-analysis-var"></a></dt>
+<dl>
+<dt id="arg-analysis-var">analysis_var<a class="anchor" aria-label="anchor" href="#arg-analysis-var"></a>
+</dt>
 <dd><p>(<code>string</code>)<br> variable name for the column containing values to be returned by the
 content function.</p></dd>
 
 
-<dt id="arg-flag-var">flag_var<a class="anchor" aria-label="anchor" href="#arg-flag-var"></a></dt>
+<dt id="arg-flag-var">flag_var<a class="anchor" aria-label="anchor" href="#arg-flag-var"></a>
+</dt>
 <dd><p>(<code>string</code>)<br> variable name for the logical column identifying which row should be returned.</p></dd>
 
 
-<dt id="arg-format">format<a class="anchor" aria-label="anchor" href="#arg-format"></a></dt>
+<dt id="arg-format">format<a class="anchor" aria-label="anchor" href="#arg-format"></a>
+</dt>
 <dd><p>(<code>string</code>)<br><code>rtables</code> format to use.</p></dd>
 
-</dl></div>
+</dl>
+</div>
     <div class="section level2">
-    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
+    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a>
+</h2>
     <p>A content function which gives <code>df$analysis_var</code> at the row identified by
 <code>.df_row$flag</code> in the given format.</p>
     </div>
 
   </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
-    </nav></aside></div>
+    </nav></aside>
+</div>
 
 
     <footer><div class="nest">
   <p>tern is a part of the <strong>NEST</strong> and <a href="https://pharmaverse.org/" class="external-link"><strong>pharmaverse</strong></a>.</p>
 </div>
-<script type="text/javascript" src="../analytics.js"></script></footer></div>
-
+<script type="text/javascript" src="../analytics.js"></script></footer>
+</div>
 
 
 
 
-  </body></html>
 
+  </body>
+</html>
diff --git a/main/reference/check_diff_prop_ci.html b/main/reference/check_diff_prop_ci.html
index 08425d2b06..281cfab8de 100644
--- a/main/reference/check_diff_prop_ci.html
+++ b/main/reference/check_diff_prop_ci.html
@@ -1,7 +1,30 @@
-<!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Check proportion difference arguments — check_diff_prop_ci • tern</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Check proportion difference arguments — check_diff_prop_ci"><meta name="description" content="Verifies that and/or convert arguments into valid values to be used in the
-estimation of difference in responder proportions."><meta property="og:description" content="Verifies that and/or convert arguments into valid values to be used in the
-estimation of difference in responder proportions."><meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png"><link rel="stylesheet" href="../consent.css"><script src="../consent.js" type="text/javascript" charset="utf-8"></script></head><body>
+<html lang="en">
+<head>
+<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+<meta charset="utf-8">
+<meta http-equiv="X-UA-Compatible" content="IE=edge">
+<meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<title>Check proportion difference arguments — check_diff_prop_ci • tern</title>
+<!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png">
+<link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png">
+<link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png">
+<link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png">
+<link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png">
+<link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png">
+<script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet">
+<script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet">
+<link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet">
+<script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Check proportion difference arguments — check_diff_prop_ci">
+<meta name="description" content="Verifies that and/or convert arguments into valid values to be used in the
+estimation of difference in responder proportions.">
+<meta property="og:description" content="Verifies that and/or convert arguments into valid values to be used in the
+estimation of difference in responder proportions.">
+<meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png">
+<link rel="stylesheet" href="../consent.css">
+<script src="../consent.js" type="text/javascript" charset="utf-8"></script>
+</head>
+<body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
 
 
@@ -17,26 +40,66 @@
     </button>
 
     <div id="navbar" class="collapse navbar-collapse ms-3">
-      <ul class="navbar-nav me-auto"><li class="nav-item"><a class="nav-link" href="../articles/tern.html">Get started</a></li>
+      <ul class="navbar-nav me-auto">
+<li class="nav-item"><a class="nav-link" href="../articles/tern.html">Get started</a></li>
 <li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
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   <button class="nav-link dropdown-toggle" type="button" id="dropdown-articles" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Articles</button>
-  <ul class="dropdown-menu" aria-labelledby="dropdown-articles"><li><a class="dropdown-item" href="../articles/missing_values.html">Missing Values in Tern</a></li>
+  <ul class="dropdown-menu" aria-labelledby="dropdown-articles">
+<li><a class="dropdown-item" href="../articles/missing_values.html">Missing Values in Tern</a></li>
     <li><a class="dropdown-item" href="../articles/tables.html">Tabulation</a></li>
     <li><a class="dropdown-item" href="../articles/tern_formats.html">Formatting Functions</a></li>
     <li><a class="dropdown-item" href="../articles/tern_functions_guide.html">Understanding `tern` functions</a></li>
-  </ul></li>
+  </ul>
+</li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
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   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
-  <ul class="dropdown-menu" aria-labelledby="dropdown-reports"><li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
+  <ul class="dropdown-menu" aria-labelledby="dropdown-reports">
+<li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
     <li><a class="dropdown-item" href="../unit-test-report/">Unit test report</a></li>
     <li><a class="dropdown-item" href="../unit-test-report-non-cran/">Non-CRAN unit test report</a></li>
-  </ul></li>
-      </ul><ul class="navbar-nav"><li class="nav-item"><form class="form-inline" role="search">
- <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json"></form></li>
+  </ul>
+</li>
+      <div><li class="nav-item dropdown">
+    <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-versions">Versions</a>
+    <div class="dropdown-menu" aria-labelledby="dropdown-versions">
+    <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/main">main</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.5">v0.9.5</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.4">v0.9.4</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.3">v0.9.3</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1-rc3">v0.9.1-rc3</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a>
+</div>
+</li></div>
+</ul>
+<ul class="navbar-nav">
+<li class="nav-item"><form class="form-inline" role="search">
+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json">
+</form></li>
 <li class="nav-item"><a class="external-link nav-link" href="https://github.com/insightsengineering/tern" aria-label="GitHub"><span class="fa fa-github"></span></a></li>
-      </ul></div>
+      </ul>
+</div>
 
 
   </div>
@@ -54,49 +117,60 @@
     </div>
 
     <div class="section level2">
-    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
+    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">check_diff_prop_ci</span><span class="op">(</span><span class="va">rsp</span>, <span class="va">grp</span>, strata <span class="op">=</span> <span class="cn">NULL</span>, <span class="va">conf_level</span>, correct <span class="op">=</span> <span class="cn">NULL</span><span class="op">)</span></span></code></pre></div>
     </div>
 
     <div class="section level2">
-    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
+    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a>
+</h2>
 
 
-<dl><dt id="arg-rsp">rsp<a class="anchor" aria-label="anchor" href="#arg-rsp"></a></dt>
+<dl>
+<dt id="arg-rsp">rsp<a class="anchor" aria-label="anchor" href="#arg-rsp"></a>
+</dt>
 <dd><p>(<code>logical</code>)<br> vector indicating whether each subject is a responder or not.</p></dd>
 
 
-<dt id="arg-grp">grp<a class="anchor" aria-label="anchor" href="#arg-grp"></a></dt>
+<dt id="arg-grp">grp<a class="anchor" aria-label="anchor" href="#arg-grp"></a>
+</dt>
 <dd><p>(<code>factor</code>)<br> vector assigning observations to one out of two groups
 (e.g. reference and treatment group).</p></dd>
 
 
-<dt id="arg-strata">strata<a class="anchor" aria-label="anchor" href="#arg-strata"></a></dt>
+<dt id="arg-strata">strata<a class="anchor" aria-label="anchor" href="#arg-strata"></a>
+</dt>
 <dd><p>(<code>factor</code>)<br> variable with one level per stratum and same length as <code>rsp</code>.</p></dd>
 
 
-<dt id="arg-conf-level">conf_level<a class="anchor" aria-label="anchor" href="#arg-conf-level"></a></dt>
+<dt id="arg-conf-level">conf_level<a class="anchor" aria-label="anchor" href="#arg-conf-level"></a>
+</dt>
 <dd><p>(<code>proportion</code>)<br> confidence level of the interval.</p></dd>
 
 
-<dt id="arg-correct">correct<a class="anchor" aria-label="anchor" href="#arg-correct"></a></dt>
+<dt id="arg-correct">correct<a class="anchor" aria-label="anchor" href="#arg-correct"></a>
+</dt>
 <dd><p>(<code>flag</code>)<br> whether to include the continuity correction. For further
 information, see <code><a href="https://rdrr.io/r/stats/prop.test.html" class="external-link">stats::prop.test()</a></code>.</p></dd>
 
-</dl></div>
+</dl>
+</div>
 
   </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
-    </nav></aside></div>
+    </nav></aside>
+</div>
 
 
     <footer><div class="nest">
   <p>tern is a part of the <strong>NEST</strong> and <a href="https://pharmaverse.org/" class="external-link"><strong>pharmaverse</strong></a>.</p>
 </div>
-<script type="text/javascript" src="../analytics.js"></script></footer></div>
-
+<script type="text/javascript" src="../analytics.js"></script></footer>
+</div>
 
 
 
 
-  </body></html>
 
+  </body>
+</html>
diff --git a/main/reference/check_same_n.html b/main/reference/check_same_n.html
index bac22c5d86..8c8983b72f 100644
--- a/main/reference/check_same_n.html
+++ b/main/reference/check_same_n.html
@@ -1,5 +1,28 @@
-<!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Check element dimension — check_same_n • tern</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Check element dimension — check_same_n"><meta name="description" content="Checks if the elements in ... have the same dimension."><meta property="og:description" content="Checks if the elements in ... have the same dimension."><meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png"><link rel="stylesheet" href="../consent.css"><script src="../consent.js" type="text/javascript" charset="utf-8"></script></head><body>
+<html lang="en">
+<head>
+<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+<meta charset="utf-8">
+<meta http-equiv="X-UA-Compatible" content="IE=edge">
+<meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<title>Check element dimension — check_same_n • tern</title>
+<!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png">
+<link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png">
+<link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png">
+<link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png">
+<link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png">
+<link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png">
+<script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet">
+<script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet">
+<link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet">
+<script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Check element dimension — check_same_n">
+<meta name="description" content="Checks if the elements in ... have the same dimension.">
+<meta property="og:description" content="Checks if the elements in ... have the same dimension.">
+<meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png">
+<link rel="stylesheet" href="../consent.css">
+<script src="../consent.js" type="text/javascript" charset="utf-8"></script>
+</head>
+<body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
 
 
@@ -15,26 +38,66 @@
     </button>
 
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-      <ul class="navbar-nav me-auto"><li class="nav-item"><a class="nav-link" href="../articles/tern.html">Get started</a></li>
+      <ul class="navbar-nav me-auto">
+<li class="nav-item"><a class="nav-link" href="../articles/tern.html">Get started</a></li>
 <li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
 <li class="nav-item dropdown">
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-articles" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Articles</button>
-  <ul class="dropdown-menu" aria-labelledby="dropdown-articles"><li><a class="dropdown-item" href="../articles/missing_values.html">Missing Values in Tern</a></li>
+  <ul class="dropdown-menu" aria-labelledby="dropdown-articles">
+<li><a class="dropdown-item" href="../articles/missing_values.html">Missing Values in Tern</a></li>
     <li><a class="dropdown-item" href="../articles/tables.html">Tabulation</a></li>
     <li><a class="dropdown-item" href="../articles/tern_formats.html">Formatting Functions</a></li>
     <li><a class="dropdown-item" href="../articles/tern_functions_guide.html">Understanding `tern` functions</a></li>
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+</li>
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+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.5">v0.9.5</a>
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+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a>
+</div>
+</li></div>
+</ul>
+<ul class="navbar-nav">
+<li class="nav-item"><form class="form-inline" role="search">
+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json">
+</form></li>
 <li class="nav-item"><a class="external-link nav-link" href="https://github.com/insightsengineering/tern" aria-label="GitHub"><span class="fa fa-github"></span></a></li>
-      </ul></div>
+      </ul>
+</div>
 
 
   </div>
@@ -51,39 +114,48 @@
     </div>
 
     <div class="section level2">
-    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
+    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">check_same_n</span><span class="op">(</span><span class="va">...</span>, omit_null <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></code></pre></div>
     </div>
 
     <div class="section level2">
-    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
+    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a>
+</h2>
 
 
-<dl><dt id="arg--">...<a class="anchor" aria-label="anchor" href="#arg--"></a></dt>
+<dl>
+<dt id="arg--">...<a class="anchor" aria-label="anchor" href="#arg--"></a>
+</dt>
 <dd><p>(<code>data.frame</code> or <code>vector</code>)<br> any data frames or vectors.</p></dd>
 
 
-<dt id="arg-omit-null">omit_null<a class="anchor" aria-label="anchor" href="#arg-omit-null"></a></dt>
+<dt id="arg-omit-null">omit_null<a class="anchor" aria-label="anchor" href="#arg-omit-null"></a>
+</dt>
 <dd><p>(<code>flag</code>)<br> whether <code>NULL</code> elements in <code>...</code> should be omitted from the check.</p></dd>
 
-</dl></div>
+</dl>
+</div>
     <div class="section level2">
-    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
+    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a>
+</h2>
     <p>A <code>logical</code> value.</p>
     </div>
 
   </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
-    </nav></aside></div>
+    </nav></aside>
+</div>
 
 
     <footer><div class="nest">
   <p>tern is a part of the <strong>NEST</strong> and <a href="https://pharmaverse.org/" class="external-link"><strong>pharmaverse</strong></a>.</p>
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diff --git a/main/reference/combination_function.html b/main/reference/combination_function.html
index bce4988d87..0bbf866fb7 100644
--- a/main/reference/combination_function.html
+++ b/main/reference/combination_function.html
@@ -1,9 +1,32 @@
-<!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Class for CombinationFunction — combination_function • tern</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Class for CombinationFunction — combination_function"><meta name="description" content="
+<html lang="en">
+<head>
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+<meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<title>Class for CombinationFunction — combination_function • tern</title>
+<!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png">
+<link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png">
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+<link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet">
+<script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet">
+<link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet">
+<script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Class for CombinationFunction — combination_function">
+<meta name="description" content="
 CombinationFunction is an S4 class which extends standard functions. These are special functions that
-can be combined and negated with the logical operators."><meta property="og:description" content="
+can be combined and negated with the logical operators.">
+<meta property="og:description" content="
 CombinationFunction is an S4 class which extends standard functions. These are special functions that
-can be combined and negated with the logical operators."><meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png"><link rel="stylesheet" href="../consent.css"><script src="../consent.js" type="text/javascript" charset="utf-8"></script></head><body>
+can be combined and negated with the logical operators.">
+<meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png">
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@@ -19,33 +42,74 @@
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- <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json"></form></li>
+  </ul>
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+    <div class="dropdown-menu" aria-labelledby="dropdown-versions">
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+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
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+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
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+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a>
+</div>
+</li></div>
+</ul>
+<ul class="navbar-nav">
+<li class="nav-item"><form class="form-inline" role="search">
+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json">
+</form></li>
 <li class="nav-item"><a class="external-link nav-link" href="https://github.com/insightsengineering/tern" aria-label="GitHub"><span class="fa fa-github"></span></a></li>
-      </ul></div>
+      </ul>
+</div>
 
 
   </div>
 </nav><div class="container template-reference-topic">
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
-      <img src="../logo.png" class="logo" alt=""><h1>Class for <code>CombinationFunction</code></h1>
+      <img src="../logo.png" class="logo" alt=""><h1>Class for <code>CombinationFunction</code>
+</h1>
       <small class="dont-index">Source: <a href="https://github.com/insightsengineering/tern/blob/main/R/combination_function.R" class="external-link"><code>R/combination_function.R</code></a></small>
       <div class="d-none name"><code>combination_function.Rd</code></div>
     </div>
@@ -57,7 +121,8 @@
     </div>
 
     <div class="section level2">
-    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
+    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="co"># S4 method for class 'CombinationFunction,CombinationFunction'</span></span>
 <span><span class="va">e1</span> <span class="op">&amp;</span> <span class="va">e2</span></span>
 <span></span>
@@ -69,29 +134,38 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
     </div>
 
     <div class="section level2">
-    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
+    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a>
+</h2>
 
 
-<dl><dt id="arg-e-">e1<a class="anchor" aria-label="anchor" href="#arg-e-"></a></dt>
+<dl>
+<dt id="arg-e-">e1<a class="anchor" aria-label="anchor" href="#arg-e-"></a>
+</dt>
 <dd><p>(<code>CombinationFunction</code>)<br> left hand side of logical operator.</p></dd>
 
 
-<dt id="arg-e-">e2<a class="anchor" aria-label="anchor" href="#arg-e-"></a></dt>
+<dt id="arg-e-">e2<a class="anchor" aria-label="anchor" href="#arg-e-"></a>
+</dt>
 <dd><p>(<code>CombinationFunction</code>)<br> right hand side of logical operator.</p></dd>
 
 
-<dt id="arg-x">x<a class="anchor" aria-label="anchor" href="#arg-x"></a></dt>
+<dt id="arg-x">x<a class="anchor" aria-label="anchor" href="#arg-x"></a>
+</dt>
 <dd><p>(<code>CombinationFunction</code>)<br> the function which should be negated.</p></dd>
 
-</dl></div>
+</dl>
+</div>
     <div class="section level2">
-    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
+    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a>
+</h2>
     <p>A logical value indicating whether the left hand side of the equation equals the right hand side.</p>
     </div>
     <div class="section level2">
-    <h2 id="functions">Functions<a class="anchor" aria-label="anchor" href="#functions"></a></h2>
+    <h2 id="functions">Functions<a class="anchor" aria-label="anchor" href="#functions"></a>
+</h2>
 
-<ul><li><p><code>e1 &amp; e2</code>: Logical "AND" combination of <code>CombinationFunction</code> functions.
+<ul>
+<li><p><code>e1 &amp; e2</code>: Logical "AND" combination of <code>CombinationFunction</code> functions.
 The resulting object is of the same class, and evaluates the two argument functions. The result
 is then the "AND" of the two individual results.</p></li>
 <li><p><code>e1 | e2</code>: Logical "OR" combination of <code>CombinationFunction</code> functions.
@@ -100,10 +174,12 @@ <h2 id="functions">Functions<a class="anchor" aria-label="anchor" href="#functio
 <li><p><code>`!`(CombinationFunction)</code>: Logical negation of <code>CombinationFunction</code> functions.
 The resulting object is of the same class, and evaluates the original function. The result
 is then the opposite of this results.</p></li>
-</ul></div>
+</ul>
+</div>
 
     <div class="section level2">
-    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
+    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">higher</span> <span class="op">&lt;-</span> <span class="kw">function</span><span class="op">(</span><span class="va">a</span><span class="op">)</span> <span class="op">{</span></span></span>
 <span class="r-in"><span>  <span class="fu"><a href="https://rdrr.io/r/base/force.html" class="external-link">force</a></span><span class="op">(</span><span class="va">a</span><span class="op">)</span></span></span>
 <span class="r-in"><span>  <span class="fu">CombinationFunction</span><span class="op">(</span></span></span>
@@ -131,17 +207,19 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 </code></pre></div>
     </div>
   </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
-    </nav></aside></div>
+    </nav></aside>
+</div>
 
 
     <footer><div class="nest">
   <p>tern is a part of the <strong>NEST</strong> and <a href="https://pharmaverse.org/" class="external-link"><strong>pharmaverse</strong></a>.</p>
 </div>
-<script type="text/javascript" src="../analytics.js"></script></footer></div>
-
+<script type="text/javascript" src="../analytics.js"></script></footer>
+</div>
 
 
 
 
-  </body></html>
 
+  </body>
+</html>
diff --git a/main/reference/combine_counts.html b/main/reference/combine_counts.html
index 394c4cd116..90c7a5c161 100644
--- a/main/reference/combine_counts.html
+++ b/main/reference/combine_counts.html
@@ -1,5 +1,28 @@
-<!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Combine counts — combine_counts • tern</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Combine counts — combine_counts"><meta name="description" content="Simplifies the estimation of column counts, especially when group combination is required."><meta property="og:description" content="Simplifies the estimation of column counts, especially when group combination is required."><meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png"><link rel="stylesheet" href="../consent.css"><script src="../consent.js" type="text/javascript" charset="utf-8"></script></head><body>
+<html lang="en">
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+<script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
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+<script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet">
+<link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet">
+<script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Combine counts — combine_counts">
+<meta name="description" content="Simplifies the estimation of column counts, especially when group combination is required.">
+<meta property="og:description" content="Simplifies the estimation of column counts, especially when group combination is required.">
+<meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png">
+<link rel="stylesheet" href="../consent.css">
+<script src="../consent.js" type="text/javascript" charset="utf-8"></script>
+</head>
+<body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
 
 
@@ -15,26 +38,66 @@
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-      <ul class="navbar-nav me-auto"><li class="nav-item"><a class="nav-link" href="../articles/tern.html">Get started</a></li>
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 <li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
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+  <ul class="dropdown-menu" aria-labelledby="dropdown-articles">
+<li><a class="dropdown-item" href="../articles/missing_values.html">Missing Values in Tern</a></li>
     <li><a class="dropdown-item" href="../articles/tables.html">Tabulation</a></li>
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     <li><a class="dropdown-item" href="../articles/tern_functions_guide.html">Understanding `tern` functions</a></li>
-  </ul></li>
+  </ul>
+</li>
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+  <ul class="dropdown-menu" aria-labelledby="dropdown-reports">
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+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
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+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a>
+</div>
+</li></div>
+</ul>
+<ul class="navbar-nav">
+<li class="nav-item"><form class="form-inline" role="search">
+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json">
+</form></li>
 <li class="nav-item"><a class="external-link nav-link" href="https://github.com/insightsengineering/tern" aria-label="GitHub"><span class="fa fa-github"></span></a></li>
-      </ul></div>
+      </ul>
+</div>
 
 
   </div>
@@ -51,34 +114,43 @@
     </div>
 
     <div class="section level2">
-    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
+    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">combine_counts</span><span class="op">(</span><span class="va">fct</span>, groups_list <span class="op">=</span> <span class="cn">NULL</span><span class="op">)</span></span></code></pre></div>
     </div>
 
     <div class="section level2">
-    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
+    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a>
+</h2>
 
 
-<dl><dt id="arg-fct">fct<a class="anchor" aria-label="anchor" href="#arg-fct"></a></dt>
+<dl>
+<dt id="arg-fct">fct<a class="anchor" aria-label="anchor" href="#arg-fct"></a>
+</dt>
 <dd><p>(<code>factor</code>)<br> the variable with levels which needs to be grouped.</p></dd>
 
 
-<dt id="arg-groups-list">groups_list<a class="anchor" aria-label="anchor" href="#arg-groups-list"></a></dt>
+<dt id="arg-groups-list">groups_list<a class="anchor" aria-label="anchor" href="#arg-groups-list"></a>
+</dt>
 <dd><p>(named <code>list</code> of <code>character</code>)<br> specifies the new group levels via the names and the
 levels that belong to it in the character vectors that are elements of the list.</p></dd>
 
-</dl></div>
+</dl>
+</div>
     <div class="section level2">
-    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
+    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a>
+</h2>
     <p>A <code>vector</code> of column counts.</p>
     </div>
     <div class="section level2">
-    <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"></a></h2>
+    <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"></a>
+</h2>
     <div class="dont-index"><p><code><a href="combine_groups.html">combine_groups()</a></code></p></div>
     </div>
 
     <div class="section level2">
-    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
+    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">ref</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"A: Drug X"</span>, <span class="st">"B: Placebo"</span><span class="op">)</span></span></span>
 <span class="r-in"><span><span class="va">groups</span> <span class="op">&lt;-</span> <span class="fu"><a href="combine_groups.html">combine_groups</a></span><span class="op">(</span>fct <span class="op">=</span> <span class="va">DM</span><span class="op">$</span><span class="va">ARM</span>, ref <span class="op">=</span> <span class="va">ref</span><span class="op">)</span></span></span>
 <span class="r-in"><span></span></span>
@@ -123,17 +195,19 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 </code></pre></div>
     </div>
   </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
-    </nav></aside></div>
+    </nav></aside>
+</div>
 
 
     <footer><div class="nest">
   <p>tern is a part of the <strong>NEST</strong> and <a href="https://pharmaverse.org/" class="external-link"><strong>pharmaverse</strong></a>.</p>
 </div>
-<script type="text/javascript" src="../analytics.js"></script></footer></div>
-
+<script type="text/javascript" src="../analytics.js"></script></footer>
+</div>
 
 
 
 
-  </body></html>
 
+  </body>
+</html>
diff --git a/main/reference/combine_groups.html b/main/reference/combine_groups.html
index 7a86a29247..06554eb18c 100644
--- a/main/reference/combine_groups.html
+++ b/main/reference/combine_groups.html
@@ -1,9 +1,32 @@
-<!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Reference and treatment group combination — combine_groups • tern</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Reference and treatment group combination — combine_groups"><meta name="description" content="
+<html lang="en">
+<head>
+<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+<meta charset="utf-8">
+<meta http-equiv="X-UA-Compatible" content="IE=edge">
+<meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<title>Reference and treatment group combination — combine_groups • tern</title>
+<!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png">
+<link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png">
+<link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png">
+<link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png">
+<link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png">
+<link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png">
+<script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet">
+<script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet">
+<link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet">
+<script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Reference and treatment group combination — combine_groups">
+<meta name="description" content="
 Facilitate the re-combination of groups divided as reference and treatment groups; it helps in arranging groups of
-columns in the rtables framework and teal modules."><meta property="og:description" content="
+columns in the rtables framework and teal modules.">
+<meta property="og:description" content="
 Facilitate the re-combination of groups divided as reference and treatment groups; it helps in arranging groups of
-columns in the rtables framework and teal modules."><meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png"><link rel="stylesheet" href="../consent.css"><script src="../consent.js" type="text/javascript" charset="utf-8"></script></head><body>
+columns in the rtables framework and teal modules.">
+<meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png">
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+</head>
+<body>
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@@ -19,26 +42,66 @@
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+      <ul class="navbar-nav me-auto">
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-  <ul class="dropdown-menu" aria-labelledby="dropdown-articles"><li><a class="dropdown-item" href="../articles/missing_values.html">Missing Values in Tern</a></li>
+  <ul class="dropdown-menu" aria-labelledby="dropdown-articles">
+<li><a class="dropdown-item" href="../articles/missing_values.html">Missing Values in Tern</a></li>
     <li><a class="dropdown-item" href="../articles/tables.html">Tabulation</a></li>
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     <li><a class="dropdown-item" href="../articles/tern_functions_guide.html">Understanding `tern` functions</a></li>
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+  </ul>
+</li>
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   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
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+  <ul class="dropdown-menu" aria-labelledby="dropdown-reports">
+<li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
     <li><a class="dropdown-item" href="../unit-test-report/">Unit test report</a></li>
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- <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json"></form></li>
+  </ul>
+</li>
+      <div><li class="nav-item dropdown">
+    <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-versions">Versions</a>
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+    <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/main">main</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.5">v0.9.5</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.4">v0.9.4</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.3">v0.9.3</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1-rc3">v0.9.1-rc3</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a>
+</div>
+</li></div>
+</ul>
+<ul class="navbar-nav">
+<li class="nav-item"><form class="form-inline" role="search">
+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json">
+</form></li>
 <li class="nav-item"><a class="external-link nav-link" href="https://github.com/insightsengineering/tern" aria-label="GitHub"><span class="fa fa-github"></span></a></li>
-      </ul></div>
+      </ul>
+</div>
 
 
   </div>
@@ -57,33 +120,42 @@
     </div>
 
     <div class="section level2">
-    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
+    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">combine_groups</span><span class="op">(</span><span class="va">fct</span>, ref <span class="op">=</span> <span class="cn">NULL</span>, collapse <span class="op">=</span> <span class="st">"/"</span><span class="op">)</span></span></code></pre></div>
     </div>
 
     <div class="section level2">
-    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
+    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a>
+</h2>
 
 
-<dl><dt id="arg-fct">fct<a class="anchor" aria-label="anchor" href="#arg-fct"></a></dt>
+<dl>
+<dt id="arg-fct">fct<a class="anchor" aria-label="anchor" href="#arg-fct"></a>
+</dt>
 <dd><p>(<code>factor</code>)<br> the variable with levels which needs to be grouped.</p></dd>
 
 
-<dt id="arg-ref">ref<a class="anchor" aria-label="anchor" href="#arg-ref"></a></dt>
+<dt id="arg-ref">ref<a class="anchor" aria-label="anchor" href="#arg-ref"></a>
+</dt>
 <dd><p>(<code>character</code>)<br> the reference level(s).</p></dd>
 
 
-<dt id="arg-collapse">collapse<a class="anchor" aria-label="anchor" href="#arg-collapse"></a></dt>
+<dt id="arg-collapse">collapse<a class="anchor" aria-label="anchor" href="#arg-collapse"></a>
+</dt>
 <dd><p>(<code>string</code>)<br> a character string to separate <code>fct</code> and <code>ref</code>.</p></dd>
 
-</dl></div>
+</dl>
+</div>
     <div class="section level2">
-    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
+    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a>
+</h2>
     <p>A <code>list</code> with first item <code>ref</code> (reference) and second item <code>trt</code> (treatment).</p>
     </div>
 
     <div class="section level2">
-    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
+    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">groups</span> <span class="op">&lt;-</span> <span class="fu">combine_groups</span><span class="op">(</span></span></span>
 <span class="r-in"><span>  fct <span class="op">=</span> <span class="va">DM</span><span class="op">$</span><span class="va">ARM</span>,</span></span>
 <span class="r-in"><span>  ref <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"B: Placebo"</span><span class="op">)</span></span></span>
@@ -105,17 +177,19 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 </code></pre></div>
     </div>
   </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
-    </nav></aside></div>
+    </nav></aside>
+</div>
 
 
     <footer><div class="nest">
   <p>tern is a part of the <strong>NEST</strong> and <a href="https://pharmaverse.org/" class="external-link"><strong>pharmaverse</strong></a>.</p>
 </div>
-<script type="text/javascript" src="../analytics.js"></script></footer></div>
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+<script type="text/javascript" src="../analytics.js"></script></footer>
+</div>
 
 
 
 
-  </body></html>
 
+  </body>
+</html>
diff --git a/main/reference/combine_levels.html b/main/reference/combine_levels.html
index bfb8b34a80..02e05849d2 100644
--- a/main/reference/combine_levels.html
+++ b/main/reference/combine_levels.html
@@ -1,7 +1,30 @@
-<!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Combine factor levels — combine_levels • tern</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Combine factor levels — combine_levels"><meta name="description" content="
-Combine specified old factor Levels in a single new level."><meta property="og:description" content="
-Combine specified old factor Levels in a single new level."><meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png"><link rel="stylesheet" href="../consent.css"><script src="../consent.js" type="text/javascript" charset="utf-8"></script></head><body>
+<html lang="en">
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+<link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png">
+<link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png">
+<script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet">
+<script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet">
+<link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet">
+<script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Combine factor levels — combine_levels">
+<meta name="description" content="
+Combine specified old factor Levels in a single new level.">
+<meta property="og:description" content="
+Combine specified old factor Levels in a single new level.">
+<meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png">
+<link rel="stylesheet" href="../consent.css">
+<script src="../consent.js" type="text/javascript" charset="utf-8"></script>
+</head>
+<body>
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@@ -17,26 +40,66 @@
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+</li>
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+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
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+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
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+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a>
+</div>
+</li></div>
+</ul>
+<ul class="navbar-nav">
+<li class="nav-item"><form class="form-inline" role="search">
+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json">
+</form></li>
 <li class="nav-item"><a class="external-link nav-link" href="https://github.com/insightsengineering/tern" aria-label="GitHub"><span class="fa fa-github"></span></a></li>
-      </ul></div>
+      </ul>
+</div>
 
 
   </div>
@@ -54,33 +117,42 @@
     </div>
 
     <div class="section level2">
-    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
+    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">combine_levels</span><span class="op">(</span><span class="va">x</span>, <span class="va">levels</span>, new_level <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/paste.html" class="external-link">paste</a></span><span class="op">(</span><span class="va">levels</span>, collapse <span class="op">=</span> <span class="st">"/"</span><span class="op">)</span><span class="op">)</span></span></code></pre></div>
     </div>
 
     <div class="section level2">
-    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
+    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a>
+</h2>
 
 
-<dl><dt id="arg-x">x<a class="anchor" aria-label="anchor" href="#arg-x"></a></dt>
+<dl>
+<dt id="arg-x">x<a class="anchor" aria-label="anchor" href="#arg-x"></a>
+</dt>
 <dd><p>(<code>factor</code>)<br> factor variable.</p></dd>
 
 
-<dt id="arg-levels">levels<a class="anchor" aria-label="anchor" href="#arg-levels"></a></dt>
+<dt id="arg-levels">levels<a class="anchor" aria-label="anchor" href="#arg-levels"></a>
+</dt>
 <dd><p>(<code>character</code>)<br> level names to be combined.</p></dd>
 
 
-<dt id="arg-new-level">new_level<a class="anchor" aria-label="anchor" href="#arg-new-level"></a></dt>
+<dt id="arg-new-level">new_level<a class="anchor" aria-label="anchor" href="#arg-new-level"></a>
+</dt>
 <dd><p>(<code>string</code>)<br> name of new level.</p></dd>
 
-</dl></div>
+</dl>
+</div>
     <div class="section level2">
-    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
+    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a>
+</h2>
     <p>A <code>factor</code> with the new levels.</p>
     </div>
 
     <div class="section level2">
-    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
+    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">x</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/factor.html" class="external-link">factor</a></span><span class="op">(</span><span class="va">letters</span><span class="op">[</span><span class="fl">1</span><span class="op">:</span><span class="fl">5</span><span class="op">]</span>, levels <span class="op">=</span> <span class="va">letters</span><span class="op">[</span><span class="fl">5</span><span class="op">:</span><span class="fl">1</span><span class="op">]</span><span class="op">)</span></span></span>
 <span class="r-in"><span><span class="fu">combine_levels</span><span class="op">(</span><span class="va">x</span>, levels <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"a"</span>, <span class="st">"b"</span><span class="op">)</span><span class="op">)</span></span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> [1] a/b a/b c   d   e  </span>
@@ -93,17 +165,19 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 </code></pre></div>
     </div>
   </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
-    </nav></aside></div>
+    </nav></aside>
+</div>
 
 
     <footer><div class="nest">
   <p>tern is a part of the <strong>NEST</strong> and <a href="https://pharmaverse.org/" class="external-link"><strong>pharmaverse</strong></a>.</p>
 </div>
-<script type="text/javascript" src="../analytics.js"></script></footer></div>
-
+<script type="text/javascript" src="../analytics.js"></script></footer>
+</div>
 
 
 
 
-  </body></html>
 
+  </body>
+</html>
diff --git a/main/reference/combine_vectors.html b/main/reference/combine_vectors.html
index c6b6386c20..4760cd0338 100644
--- a/main/reference/combine_vectors.html
+++ b/main/reference/combine_vectors.html
@@ -1,5 +1,28 @@
-<!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Element-wise combination of two vectors — combine_vectors • tern</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Element-wise combination of two vectors — combine_vectors"><meta name="description" content="Element-wise combination of two vectors"><meta property="og:description" content="Element-wise combination of two vectors"><meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png"><link rel="stylesheet" href="../consent.css"><script src="../consent.js" type="text/javascript" charset="utf-8"></script></head><body>
+<html lang="en">
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+<meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<title>Element-wise combination of two vectors — combine_vectors • tern</title>
+<!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png">
+<link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png">
+<link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png">
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+<link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png">
+<link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png">
+<script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet">
+<script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet">
+<link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet">
+<script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Element-wise combination of two vectors — combine_vectors">
+<meta name="description" content="Element-wise combination of two vectors">
+<meta property="og:description" content="Element-wise combination of two vectors">
+<meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png">
+<link rel="stylesheet" href="../consent.css">
+<script src="../consent.js" type="text/javascript" charset="utf-8"></script>
+</head>
+<body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
 
 
@@ -15,26 +38,66 @@
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-      <ul class="navbar-nav me-auto"><li class="nav-item"><a class="nav-link" href="../articles/tern.html">Get started</a></li>
+      <ul class="navbar-nav me-auto">
+<li class="nav-item"><a class="nav-link" href="../articles/tern.html">Get started</a></li>
 <li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
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   <button class="nav-link dropdown-toggle" type="button" id="dropdown-articles" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Articles</button>
-  <ul class="dropdown-menu" aria-labelledby="dropdown-articles"><li><a class="dropdown-item" href="../articles/missing_values.html">Missing Values in Tern</a></li>
+  <ul class="dropdown-menu" aria-labelledby="dropdown-articles">
+<li><a class="dropdown-item" href="../articles/missing_values.html">Missing Values in Tern</a></li>
     <li><a class="dropdown-item" href="../articles/tables.html">Tabulation</a></li>
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     <li><a class="dropdown-item" href="../articles/tern_functions_guide.html">Understanding `tern` functions</a></li>
-  </ul></li>
+  </ul>
+</li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
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+<li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
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- <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json"></form></li>
+  </ul>
+</li>
+      <div><li class="nav-item dropdown">
+    <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-versions">Versions</a>
+    <div class="dropdown-menu" aria-labelledby="dropdown-versions">
+    <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/main">main</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.5">v0.9.5</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.4">v0.9.4</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.3">v0.9.3</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1-rc3">v0.9.1-rc3</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a>
+</div>
+</li></div>
+</ul>
+<ul class="navbar-nav">
+<li class="nav-item"><form class="form-inline" role="search">
+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json">
+</form></li>
 <li class="nav-item"><a class="external-link nav-link" href="https://github.com/insightsengineering/tern" aria-label="GitHub"><span class="fa fa-github"></span></a></li>
-      </ul></div>
+      </ul>
+</div>
 
 
   </div>
@@ -51,29 +114,37 @@
     </div>
 
     <div class="section level2">
-    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
+    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">combine_vectors</span><span class="op">(</span><span class="va">x</span>, <span class="va">y</span><span class="op">)</span></span></code></pre></div>
     </div>
 
     <div class="section level2">
-    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
+    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a>
+</h2>
 
 
-<dl><dt id="arg-x">x<a class="anchor" aria-label="anchor" href="#arg-x"></a></dt>
+<dl>
+<dt id="arg-x">x<a class="anchor" aria-label="anchor" href="#arg-x"></a>
+</dt>
 <dd><p>(<code>vector</code>)<br> first vector to combine.</p></dd>
 
 
-<dt id="arg-y">y<a class="anchor" aria-label="anchor" href="#arg-y"></a></dt>
+<dt id="arg-y">y<a class="anchor" aria-label="anchor" href="#arg-y"></a>
+</dt>
 <dd><p>(<code>vector</code>)<br> second vector to combine.</p></dd>
 
-</dl></div>
+</dl>
+</div>
     <div class="section level2">
-    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
+    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a>
+</h2>
     <p>A <code>list</code> where each element combines corresponding elements of <code>x</code> and <code>y</code>.</p>
     </div>
 
     <div class="section level2">
-    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
+    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="fu">combine_vectors</span><span class="op">(</span><span class="fl">1</span><span class="op">:</span><span class="fl">3</span>, <span class="fl">4</span><span class="op">:</span><span class="fl">6</span><span class="op">)</span></span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> [[1]]</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> [1] 1 4</span>
@@ -88,17 +159,19 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 </code></pre></div>
     </div>
   </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
-    </nav></aside></div>
+    </nav></aside>
+</div>
 
 
     <footer><div class="nest">
   <p>tern is a part of the <strong>NEST</strong> and <a href="https://pharmaverse.org/" class="external-link"><strong>pharmaverse</strong></a>.</p>
 </div>
-<script type="text/javascript" src="../analytics.js"></script></footer></div>
-
+<script type="text/javascript" src="../analytics.js"></script></footer>
+</div>
 
 
 
 
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+  </body>
+</html>
diff --git a/main/reference/compare_variables.html b/main/reference/compare_variables.html
index 41779bc48f..b6dd9953e9 100644
--- a/main/reference/compare_variables.html
+++ b/main/reference/compare_variables.html
@@ -1,5 +1,22 @@
-<!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Compare variables between groups — compare_variables • tern</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Compare variables between groups — compare_variables"><meta name="description" content='
+<html lang="en">
+<head>
+<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+<meta charset="utf-8">
+<meta http-equiv="X-UA-Compatible" content="IE=edge">
+<meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<title>Compare variables between groups — compare_variables • tern</title>
+<!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png">
+<link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png">
+<link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png">
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+<meta name="description" content='
 The analyze function compare_vars() creates a layout element to summarize and compare one or more variables, using
 the S3 generic function s_summary() to calculate a list of summary statistics. A list of all available statistics
 for numeric variables can be viewed by running get_stats("analyze_vars_numeric", add_pval = TRUE) and for
@@ -8,7 +25,8 @@
 Prior to using this function in your table layout you must use rtables::split_cols_by() to create a column
 split on the variable to be used in comparisons, and specify a reference group via the ref_group parameter.
 Comparisons can be performed for each group (column) against the specified reference group by including the p-value
-statistic.'><meta property="og:description" content='
+statistic.'>
+<meta property="og:description" content='
 The analyze function compare_vars() creates a layout element to summarize and compare one or more variables, using
 the S3 generic function s_summary() to calculate a list of summary statistics. A list of all available statistics
 for numeric variables can be viewed by running get_stats("analyze_vars_numeric", add_pval = TRUE) and for
@@ -17,7 +35,12 @@
 Prior to using this function in your table layout you must use rtables::split_cols_by() to create a column
 split on the variable to be used in comparisons, and specify a reference group via the ref_group parameter.
 Comparisons can be performed for each group (column) against the specified reference group by including the p-value
-statistic.'><meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png"><link rel="stylesheet" href="../consent.css"><script src="../consent.js" type="text/javascript" charset="utf-8"></script></head><body>
+statistic.'>
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+</form></li>
 <li class="nav-item"><a class="external-link nav-link" href="https://github.com/insightsengineering/tern" aria-label="GitHub"><span class="fa fa-github"></span></a></li>
-      </ul></div>
+      </ul>
+</div>
 
 
   </div>
@@ -78,7 +141,8 @@
     </div>
 
     <div class="section level2">
-    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
+    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">compare_vars</span><span class="op">(</span></span>
 <span>  <span class="va">lyt</span>,</span>
 <span>  <span class="va">vars</span>,</span>
@@ -121,113 +185,145 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
     </div>
 
     <div class="section level2">
-    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
+    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a>
+</h2>
 
 
-<dl><dt id="arg-lyt">lyt<a class="anchor" aria-label="anchor" href="#arg-lyt"></a></dt>
+<dl>
+<dt id="arg-lyt">lyt<a class="anchor" aria-label="anchor" href="#arg-lyt"></a>
+</dt>
 <dd><p>(<code>PreDataTableLayouts</code>)<br> layout that analyses will be added to.</p></dd>
 
 
-<dt id="arg-vars">vars<a class="anchor" aria-label="anchor" href="#arg-vars"></a></dt>
+<dt id="arg-vars">vars<a class="anchor" aria-label="anchor" href="#arg-vars"></a>
+</dt>
 <dd><p>(<code>character</code>)<br> variable names for the primary analysis variable to be iterated over.</p></dd>
 
 
-<dt id="arg-var-labels">var_labels<a class="anchor" aria-label="anchor" href="#arg-var-labels"></a></dt>
+<dt id="arg-var-labels">var_labels<a class="anchor" aria-label="anchor" href="#arg-var-labels"></a>
+</dt>
 <dd><p>(<code>character</code>)<br> variable labels.</p></dd>
 
 
-<dt id="arg-na-str">na_str<a class="anchor" aria-label="anchor" href="#arg-na-str"></a></dt>
+<dt id="arg-na-str">na_str<a class="anchor" aria-label="anchor" href="#arg-na-str"></a>
+</dt>
 <dd><p>(<code>string</code>)<br> string used to replace all <code>NA</code> or empty values in the output.</p></dd>
 
 
-<dt id="arg-nested">nested<a class="anchor" aria-label="anchor" href="#arg-nested"></a></dt>
+<dt id="arg-nested">nested<a class="anchor" aria-label="anchor" href="#arg-nested"></a>
+</dt>
 <dd><p>(<code>flag</code>)<br> whether this layout instruction should be applied within the existing layout structure _if
 possible (<code>TRUE</code>, the default) or as a new top-level element (<code>FALSE</code>). Ignored if it would nest a split.
 underneath analyses, which is not allowed.</p></dd>
 
 
-<dt id="arg--">...<a class="anchor" aria-label="anchor" href="#arg--"></a></dt>
+<dt id="arg--">...<a class="anchor" aria-label="anchor" href="#arg--"></a>
+</dt>
 <dd><p>arguments passed to <code>s_compare()</code>.</p></dd>
 
 
-<dt id="arg-na-rm">na.rm<a class="anchor" aria-label="anchor" href="#arg-na-rm"></a></dt>
+<dt id="arg-na-rm">na.rm<a class="anchor" aria-label="anchor" href="#arg-na-rm"></a>
+</dt>
 <dd><p>(<code>flag</code>)<br> whether <code>NA</code> values should be removed from <code>x</code> prior to analysis.</p></dd>
 
 
-<dt id="arg-show-labels">show_labels<a class="anchor" aria-label="anchor" href="#arg-show-labels"></a></dt>
+<dt id="arg-show-labels">show_labels<a class="anchor" aria-label="anchor" href="#arg-show-labels"></a>
+</dt>
 <dd><p>(<code>string</code>)<br> label visibility: one of "default", "visible" and "hidden".</p></dd>
 
 
-<dt id="arg-table-names">table_names<a class="anchor" aria-label="anchor" href="#arg-table-names"></a></dt>
+<dt id="arg-table-names">table_names<a class="anchor" aria-label="anchor" href="#arg-table-names"></a>
+</dt>
 <dd><p>(<code>character</code>)<br> this can be customized in the case that the same <code>vars</code> are analyzed multiple
 times, to avoid warnings from <code>rtables</code>.</p></dd>
 
 
-<dt id="arg-section-div">section_div<a class="anchor" aria-label="anchor" href="#arg-section-div"></a></dt>
+<dt id="arg-section-div">section_div<a class="anchor" aria-label="anchor" href="#arg-section-div"></a>
+</dt>
 <dd><p>(<code>string</code>)<br> string which should be repeated as a section divider after each group
 defined by this split instruction, or <code>NA_character_</code> (the default) for no section divider.</p></dd>
 
 
-<dt id="arg--stats">.stats<a class="anchor" aria-label="anchor" href="#arg--stats"></a></dt>
-<dd><p>(<code>character</code>)<br> statistics to select for the table.</p>
+<dt id="arg--stats">.stats<a class="anchor" aria-label="anchor" href="#arg--stats"></a>
+</dt>
+<dd>
+<p>(<code>character</code>)<br> statistics to select for the table.</p>
 <p>Options for numeric variables are: <code>'n', 'sum', 'mean', 'sd', 'se', 'mean_sd', 'mean_se', 'mean_ci', 'mean_sei', 'mean_sdi', 'mean_pval', 'median', 'mad', 'median_ci', 'quantiles', 'iqr', 'range', 'min', 'max', 'median_range', 'cv', 'geom_mean', 'geom_mean_ci', 'geom_cv', 'median_ci_3d', 'mean_ci_3d', 'geom_mean_ci_3d', 'pval'</code></p>
-<p>Options for non-numeric variables are: <code>'n', 'count', 'count_fraction', 'count_fraction_fixed_dp', 'fraction', 'n_blq', 'pval_counts'</code></p></dd>
+<p>Options for non-numeric variables are: <code>'n', 'count', 'count_fraction', 'count_fraction_fixed_dp', 'fraction', 'n_blq', 'pval_counts'</code></p>
+</dd>
 
 
-<dt id="arg--formats">.formats<a class="anchor" aria-label="anchor" href="#arg--formats"></a></dt>
+<dt id="arg--formats">.formats<a class="anchor" aria-label="anchor" href="#arg--formats"></a>
+</dt>
 <dd><p>(named <code>character</code> or <code>list</code>)<br> formats for the statistics. See Details in <code>analyze_vars</code> for more
 information on the <code>"auto"</code> setting.</p></dd>
 
 
-<dt id="arg--labels">.labels<a class="anchor" aria-label="anchor" href="#arg--labels"></a></dt>
+<dt id="arg--labels">.labels<a class="anchor" aria-label="anchor" href="#arg--labels"></a>
+</dt>
 <dd><p>(named <code>character</code>)<br> labels for the statistics (without indent).</p></dd>
 
 
-<dt id="arg--indent-mods">.indent_mods<a class="anchor" aria-label="anchor" href="#arg--indent-mods"></a></dt>
+<dt id="arg--indent-mods">.indent_mods<a class="anchor" aria-label="anchor" href="#arg--indent-mods"></a>
+</dt>
 <dd><p>(named <code>integer</code>)<br> indent modifiers for the labels. Each element of the vector
 should be a name-value pair with name corresponding to a statistic specified in <code>.stats</code> and value the indentation
 for that statistic's row label.</p></dd>
 
 
-<dt id="arg-x">x<a class="anchor" aria-label="anchor" href="#arg-x"></a></dt>
+<dt id="arg-x">x<a class="anchor" aria-label="anchor" href="#arg-x"></a>
+</dt>
 <dd><p>(<code>numeric</code>)<br> vector of numbers we want to analyze.</p></dd>
 
 
-<dt id="arg--ref-group">.ref_group<a class="anchor" aria-label="anchor" href="#arg--ref-group"></a></dt>
+<dt id="arg--ref-group">.ref_group<a class="anchor" aria-label="anchor" href="#arg--ref-group"></a>
+</dt>
 <dd><p>(<code>data.frame</code> or <code>vector</code>)<br> the data corresponding to the reference group.</p></dd>
 
 
-<dt id="arg--in-ref-col">.in_ref_col<a class="anchor" aria-label="anchor" href="#arg--in-ref-col"></a></dt>
+<dt id="arg--in-ref-col">.in_ref_col<a class="anchor" aria-label="anchor" href="#arg--in-ref-col"></a>
+</dt>
 <dd><p>(<code>flag</code>)<br><code>TRUE</code> when working with the reference level, <code>FALSE</code> otherwise.</p></dd>
 
 
-<dt id="arg-denom">denom<a class="anchor" aria-label="anchor" href="#arg-denom"></a></dt>
+<dt id="arg-denom">denom<a class="anchor" aria-label="anchor" href="#arg-denom"></a>
+</dt>
 <dd><p>(<code>string</code>)<br> choice of denominator for factor proportions,
 can only be <code>n</code> (number of values in this row and column intersection).</p></dd>
 
 
-<dt id="arg--var">.var<a class="anchor" aria-label="anchor" href="#arg--var"></a></dt>
+<dt id="arg--var">.var<a class="anchor" aria-label="anchor" href="#arg--var"></a>
+</dt>
 <dd><p>(<code>string</code>)<br> single variable name that is passed by <code>rtables</code> when requested
 by a statistics function.</p></dd>
 
 
-<dt id="arg-verbose">verbose<a class="anchor" aria-label="anchor" href="#arg-verbose"></a></dt>
+<dt id="arg-verbose">verbose<a class="anchor" aria-label="anchor" href="#arg-verbose"></a>
+</dt>
 <dd><p>(<code>flag</code>)<br> whether warnings and messages should be printed. Mainly used
 to print out information about factor casting. Defaults to <code>TRUE</code>.</p></dd>
 
-</dl></div>
+</dl>
+</div>
     <div class="section level2">
-    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
+    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a>
+</h2>
 
-<ul><li><p><code>compare_vars()</code> returns a layout object suitable for passing to further layouting functions,
+<ul>
+<li><p><code>compare_vars()</code> returns a layout object suitable for passing to further layouting functions,
 or to <code><a href="https://insightsengineering.github.io/rtables/latest-tag/reference/build_table.html" class="external-link">rtables::build_table()</a></code>. Adding this function to an <code>rtable</code> layout will add formatted rows containing
 the statistics from <code>s_compare()</code> to the table layout.</p></li>
-</ul><ul><li><p><code>s_compare()</code> returns output of <code><a href="analyze_variables.html">s_summary()</a></code> and comparisons versus the reference group in the form of p-values.</p></li>
-</ul></div>
+</ul>
+<ul>
+<li><p><code>s_compare()</code> returns output of <code><a href="analyze_variables.html">s_summary()</a></code> and comparisons versus the reference group in the form of p-values.</p></li>
+</ul>
+</div>
     <div class="section level2">
-    <h2 id="functions">Functions<a class="anchor" aria-label="anchor" href="#functions"></a></h2>
+    <h2 id="functions">Functions<a class="anchor" aria-label="anchor" href="#functions"></a>
+</h2>
 
-<ul><li><p><code>compare_vars()</code>: Layout-creating function which can take statistics function arguments
+<ul>
+<li><p><code>compare_vars()</code>: Layout-creating function which can take statistics function arguments
 and additional format arguments. This function is a wrapper for <code><a href="https://insightsengineering.github.io/rtables/latest-tag/reference/analyze.html" class="external-link">rtables::analyze()</a></code>.</p></li>
 <li><p><code>s_compare()</code>: S3 generic function to produce a comparison summary.</p></li>
 <li><p><code>s_compare(numeric)</code>: Method for <code>numeric</code> class. This uses the standard t-test
@@ -238,11 +334,14 @@ <h2 id="functions">Functions<a class="anchor" aria-label="anchor" href="#functio
 conversion to <code>factor</code> (with a warning) and then forwards to the method for factors.</p></li>
 <li><p><code>s_compare(logical)</code>: Method for <code>logical</code> class. A chi-squared test
 is used. If missing values are not removed, then they are counted as <code>FALSE</code>.</p></li>
-</ul></div>
+</ul>
+</div>
     <div class="section level2">
-    <h2 id="note">Note<a class="anchor" aria-label="anchor" href="#note"></a></h2>
+    <h2 id="note">Note<a class="anchor" aria-label="anchor" href="#note"></a>
+</h2>
 
-<ul><li><p>For factor variables, <code>denom</code> for factor proportions can only be <code>n</code> since the purpose is to compare proportions
+<ul>
+<li><p>For factor variables, <code>denom</code> for factor proportions can only be <code>n</code> since the purpose is to compare proportions
 between columns, therefore a row-based proportion would not make sense. Proportion based on <code>N_col</code> would
 be difficult since we use counts for the chi-squared test statistic, therefore missing values should be accounted
 for as explicit factor levels.</p></li>
@@ -255,15 +354,18 @@ <h2 id="note">Note<a class="anchor" aria-label="anchor" href="#note"></a></h2>
 Therefore it is always better to manually convert character variables to factors during pre-processing.</p></li>
 <li><p>For <code>compare_vars()</code>, the column split must define a reference group via <code>ref_group</code> so that the comparison
 is well defined.</p></li>
-</ul></div>
+</ul>
+</div>
     <div class="section level2">
-    <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"></a></h2>
+    <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"></a>
+</h2>
     <div class="dont-index"><p><code><a href="analyze_variables.html">s_summary()</a></code> which is used internally to compute a summary within <code>s_compare()</code>, and <code><a href="analyze_variables.html">a_summary()</a></code>
 which is used (with <code>compare = TRUE</code>) as the analysis function for <code>compare_vars()</code>.</p></div>
     </div>
 
     <div class="section level2">
-    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
+    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="co"># `compare_vars()` in `rtables` pipelines</span></span></span>
 <span class="r-in"><span></span></span>
 <span class="r-in"><span><span class="co">## Default output within a `rtables` pipeline.</span></span></span>
@@ -1097,17 +1199,19 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 </code></pre></div>
     </div>
   </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
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+    </nav></aside>
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diff --git a/main/reference/control_analyze_vars.html b/main/reference/control_analyze_vars.html
index c0f098060f..cc7211a740 100644
--- a/main/reference/control_analyze_vars.html
+++ b/main/reference/control_analyze_vars.html
@@ -1,9 +1,32 @@
-<!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Control function for descriptive statistics — control_analyze_vars • tern</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Control function for descriptive statistics — control_analyze_vars"><meta name="description" content="
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+<link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet">
+<script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Control function for descriptive statistics — control_analyze_vars">
+<meta name="description" content="
 Sets a list of parameters for summaries of descriptive statistics. Typically used internally to specify
-details for s_summary(). This function family is mainly used by analyze_vars()."><meta property="og:description" content="
+details for s_summary(). This function family is mainly used by analyze_vars().">
+<meta property="og:description" content="
 Sets a list of parameters for summaries of descriptive statistics. Typically used internally to specify
-details for s_summary(). This function family is mainly used by analyze_vars()."><meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png"><link rel="stylesheet" href="../consent.css"><script src="../consent.js" type="text/javascript" charset="utf-8"></script></head><body>
+details for s_summary(). This function family is mainly used by analyze_vars().">
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+</div>
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+</div>
 
 
   </div>
@@ -57,7 +120,8 @@
     </div>
 
     <div class="section level2">
-    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
+    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">control_analyze_vars</span><span class="op">(</span></span>
 <span>  conf_level <span class="op">=</span> <span class="fl">0.95</span>,</span>
 <span>  quantiles <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">0.25</span>, <span class="fl">0.75</span><span class="op">)</span>,</span>
@@ -67,45 +131,55 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
     </div>
 
     <div class="section level2">
-    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
+    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a>
+</h2>
 
 
-<dl><dt id="arg-conf-level">conf_level<a class="anchor" aria-label="anchor" href="#arg-conf-level"></a></dt>
+<dl>
+<dt id="arg-conf-level">conf_level<a class="anchor" aria-label="anchor" href="#arg-conf-level"></a>
+</dt>
 <dd><p>(<code>proportion</code>)<br> confidence level of the interval.</p></dd>
 
 
-<dt id="arg-quantiles">quantiles<a class="anchor" aria-label="anchor" href="#arg-quantiles"></a></dt>
+<dt id="arg-quantiles">quantiles<a class="anchor" aria-label="anchor" href="#arg-quantiles"></a>
+</dt>
 <dd><p>(<code>numeric(2)</code>)<br> vector of length two to specify the quantiles to calculate.</p></dd>
 
 
-<dt id="arg-quantile-type">quantile_type<a class="anchor" aria-label="anchor" href="#arg-quantile-type"></a></dt>
+<dt id="arg-quantile-type">quantile_type<a class="anchor" aria-label="anchor" href="#arg-quantile-type"></a>
+</dt>
 <dd><p>(<code>numeric(1)</code>)<br> number between 1 and 9 selecting quantile algorithms to be used.
 Default is set to 2 as this matches the default quantile algorithm in SAS <code>proc univariate</code> set by <code>QNTLDEF=5</code>.
 This differs from R's default. See more about <code>type</code> in <code><a href="https://rdrr.io/r/stats/quantile.html" class="external-link">stats::quantile()</a></code>.</p></dd>
 
 
-<dt id="arg-test-mean">test_mean<a class="anchor" aria-label="anchor" href="#arg-test-mean"></a></dt>
+<dt id="arg-test-mean">test_mean<a class="anchor" aria-label="anchor" href="#arg-test-mean"></a>
+</dt>
 <dd><p>(<code>numeric(1)</code>)<br> number to test against the mean under the null hypothesis when calculating
 p-value.</p></dd>
 
-</dl></div>
+</dl>
+</div>
     <div class="section level2">
-    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
+    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a>
+</h2>
     <p>A list of components with the same names as the arguments.</p>
     </div>
 
   </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
-    </nav></aside></div>
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diff --git a/main/reference/control_annot.html b/main/reference/control_annot.html
index 47671d9dee..3ccaaab269 100644
--- a/main/reference/control_annot.html
+++ b/main/reference/control_annot.html
@@ -1,9 +1,32 @@
-<!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Control functions for Kaplan-Meier plot annotation tables — control_annot • tern</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Control functions for Kaplan-Meier plot annotation tables — control_annot"><meta name="description" content="
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+<script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Control functions for Kaplan-Meier plot annotation tables — control_annot">
+<meta name="description" content="
 Auxiliary functions for controlling arguments for formatting the annotation tables that can be added to plots
-generated via g_km()."><meta property="og:description" content="
+generated via g_km().">
+<meta property="og:description" content="
 Auxiliary functions for controlling arguments for formatting the annotation tables that can be added to plots
-generated via g_km()."><meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png"><link rel="stylesheet" href="../consent.css"><script src="../consent.js" type="text/javascript" charset="utf-8"></script></head><body>
+generated via g_km().">
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+</head>
+<body>
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@@ -19,26 +42,66 @@
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     <li><a class="dropdown-item" href="../articles/tern_functions_guide.html">Understanding `tern` functions</a></li>
-  </ul></li>
+  </ul>
+</li>
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- <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json"></form></li>
+  </ul>
+</li>
+      <div><li class="nav-item dropdown">
+    <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-versions">Versions</a>
+    <div class="dropdown-menu" aria-labelledby="dropdown-versions">
+    <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/main">main</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.5">v0.9.5</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.4">v0.9.4</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.3">v0.9.3</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1-rc3">v0.9.1-rc3</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a>
+</div>
+</li></div>
+</ul>
+<ul class="navbar-nav">
+<li class="nav-item"><form class="form-inline" role="search">
+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json">
+</form></li>
 <li class="nav-item"><a class="external-link nav-link" href="https://github.com/insightsengineering/tern" aria-label="GitHub"><span class="fa fa-github"></span></a></li>
-      </ul></div>
+      </ul>
+</div>
 
 
   </div>
@@ -57,7 +120,8 @@
     </div>
 
     <div class="section level2">
-    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
+    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">control_surv_med_annot</span><span class="op">(</span>x <span class="op">=</span> <span class="fl">0.8</span>, y <span class="op">=</span> <span class="fl">0.85</span>, w <span class="op">=</span> <span class="fl">0.32</span>, h <span class="op">=</span> <span class="fl">0.16</span>, fill <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span>
 <span></span>
 <span><span class="fu">control_coxph_annot</span><span class="op">(</span></span>
@@ -71,56 +135,71 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
     </div>
 
     <div class="section level2">
-    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
+    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a>
+</h2>
 
 
-<dl><dt id="arg-x">x<a class="anchor" aria-label="anchor" href="#arg-x"></a></dt>
+<dl>
+<dt id="arg-x">x<a class="anchor" aria-label="anchor" href="#arg-x"></a>
+</dt>
 <dd><p>(<code>proportion</code>)<br> x-coordinate for center of annotation table.</p></dd>
 
 
-<dt id="arg-y">y<a class="anchor" aria-label="anchor" href="#arg-y"></a></dt>
+<dt id="arg-y">y<a class="anchor" aria-label="anchor" href="#arg-y"></a>
+</dt>
 <dd><p>(<code>proportion</code>)<br> y-coordinate for center of annotation table.</p></dd>
 
 
-<dt id="arg-w">w<a class="anchor" aria-label="anchor" href="#arg-w"></a></dt>
+<dt id="arg-w">w<a class="anchor" aria-label="anchor" href="#arg-w"></a>
+</dt>
 <dd><p>(<code>proportion</code>)<br> relative width of the annotation table.</p></dd>
 
 
-<dt id="arg-h">h<a class="anchor" aria-label="anchor" href="#arg-h"></a></dt>
+<dt id="arg-h">h<a class="anchor" aria-label="anchor" href="#arg-h"></a>
+</dt>
 <dd><p>(<code>proportion</code>)<br> relative height of the annotation table.</p></dd>
 
 
-<dt id="arg-fill">fill<a class="anchor" aria-label="anchor" href="#arg-fill"></a></dt>
+<dt id="arg-fill">fill<a class="anchor" aria-label="anchor" href="#arg-fill"></a>
+</dt>
 <dd><p>(<code>flag</code> or <code>character</code>)<br> whether the annotation table should have a background fill color.
 Can also be a color code to use as the background fill color. If <code>TRUE</code>, color code defaults to <code>"#00000020"</code>.</p></dd>
 
 
-<dt id="arg-ref-lbls">ref_lbls<a class="anchor" aria-label="anchor" href="#arg-ref-lbls"></a></dt>
+<dt id="arg-ref-lbls">ref_lbls<a class="anchor" aria-label="anchor" href="#arg-ref-lbls"></a>
+</dt>
 <dd><p>(<code>flag</code>)<br> whether the reference group should be explicitly printed in labels for the
 annotation table. If <code>FALSE</code> (default), only comparison groups will be printed in the table labels.</p></dd>
 
-</dl></div>
+</dl>
+</div>
     <div class="section level2">
-    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
+    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a>
+</h2>
     <p>A list of components with the same names as the arguments.</p>
     </div>
     <div class="section level2">
-    <h2 id="functions">Functions<a class="anchor" aria-label="anchor" href="#functions"></a></h2>
+    <h2 id="functions">Functions<a class="anchor" aria-label="anchor" href="#functions"></a>
+</h2>
 
-<ul><li><p><code>control_surv_med_annot()</code>: Control function for formatting the median survival time annotation table. This annotation
+<ul>
+<li><p><code>control_surv_med_annot()</code>: Control function for formatting the median survival time annotation table. This annotation
 table can be added in <code><a href="g_km.html">g_km()</a></code> by setting <code>annot_surv_med=TRUE</code>, and can be configured using the
 <code>control_surv_med_annot()</code> function by setting it as the <code>control_annot_surv_med</code> argument.</p></li>
 <li><p><code>control_coxph_annot()</code>: Control function for formatting the Cox-PH annotation table. This annotation table can be
 added in <code><a href="g_km.html">g_km()</a></code> by setting <code>annot_coxph=TRUE</code>, and can be configured using the <code>control_coxph_annot()</code> function
 by setting it as the <code>control_annot_coxph</code> argument.</p></li>
-</ul></div>
+</ul>
+</div>
     <div class="section level2">
-    <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"></a></h2>
+    <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"></a>
+</h2>
     <div class="dont-index"><p><code><a href="g_km.html">g_km()</a></code></p></div>
     </div>
 
     <div class="section level2">
-    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
+    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="fu">control_surv_med_annot</span><span class="op">(</span><span class="op">)</span></span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> $x</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0.8</span>
@@ -161,17 +240,19 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 </code></pre></div>
     </div>
   </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
-    </nav></aside></div>
+    </nav></aside>
+</div>
 
 
     <footer><div class="nest">
   <p>tern is a part of the <strong>NEST</strong> and <a href="https://pharmaverse.org/" class="external-link"><strong>pharmaverse</strong></a>.</p>
 </div>
-<script type="text/javascript" src="../analytics.js"></script></footer></div>
-
+<script type="text/javascript" src="../analytics.js"></script></footer>
+</div>
 
 
 
 
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+  </body>
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diff --git a/main/reference/control_coxph.html b/main/reference/control_coxph.html
index 5331019b92..6c1dd07dfc 100644
--- a/main/reference/control_coxph.html
+++ b/main/reference/control_coxph.html
@@ -1,9 +1,32 @@
-<!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Control function for Cox-PH model — control_coxph • tern</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Control function for Cox-PH model — control_coxph"><meta name="description" content="
+<html lang="en">
+<head>
+<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+<meta charset="utf-8">
+<meta http-equiv="X-UA-Compatible" content="IE=edge">
+<meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<title>Control function for Cox-PH model — control_coxph • tern</title>
+<!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png">
+<link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png">
+<link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png">
+<link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png">
+<link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png">
+<link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png">
+<script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet">
+<script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet">
+<link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet">
+<script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Control function for Cox-PH model — control_coxph">
+<meta name="description" content="
 This is an auxiliary function for controlling arguments for Cox-PH model, typically used internally to specify
-details of Cox-PH model for s_coxph_pairwise(). conf_level refers to Hazard Ratio estimation."><meta property="og:description" content="
+details of Cox-PH model for s_coxph_pairwise(). conf_level refers to Hazard Ratio estimation.">
+<meta property="og:description" content="
 This is an auxiliary function for controlling arguments for Cox-PH model, typically used internally to specify
-details of Cox-PH model for s_coxph_pairwise(). conf_level refers to Hazard Ratio estimation."><meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png"><link rel="stylesheet" href="../consent.css"><script src="../consent.js" type="text/javascript" charset="utf-8"></script></head><body>
+details of Cox-PH model for s_coxph_pairwise(). conf_level refers to Hazard Ratio estimation.">
+<meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png">
+<link rel="stylesheet" href="../consent.css">
+<script src="../consent.js" type="text/javascript" charset="utf-8"></script>
+</head>
+<body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
 
 
@@ -19,26 +42,66 @@
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+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a>
+</div>
+</li></div>
+</ul>
+<ul class="navbar-nav">
+<li class="nav-item"><form class="form-inline" role="search">
+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json">
+</form></li>
 <li class="nav-item"><a class="external-link nav-link" href="https://github.com/insightsengineering/tern" aria-label="GitHub"><span class="fa fa-github"></span></a></li>
-      </ul></div>
+      </ul>
+</div>
 
 
   </div>
@@ -57,7 +120,8 @@
     </div>
 
     <div class="section level2">
-    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
+    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">control_coxph</span><span class="op">(</span></span>
 <span>  pval_method <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"log-rank"</span>, <span class="st">"wald"</span>, <span class="st">"likelihood"</span><span class="op">)</span>,</span>
 <span>  ties <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"efron"</span>, <span class="st">"breslow"</span>, <span class="st">"exact"</span><span class="op">)</span>,</span>
@@ -66,40 +130,49 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
     </div>
 
     <div class="section level2">
-    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
+    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a>
+</h2>
 
 
-<dl><dt id="arg-pval-method">pval_method<a class="anchor" aria-label="anchor" href="#arg-pval-method"></a></dt>
+<dl>
+<dt id="arg-pval-method">pval_method<a class="anchor" aria-label="anchor" href="#arg-pval-method"></a>
+</dt>
 <dd><p>(<code>string</code>)<br> p-value method for testing hazard ratio = 1.
 Default method is <code>"log-rank"</code>, can also be set to <code>"wald"</code> or <code>"likelihood"</code>.</p></dd>
 
 
-<dt id="arg-ties">ties<a class="anchor" aria-label="anchor" href="#arg-ties"></a></dt>
+<dt id="arg-ties">ties<a class="anchor" aria-label="anchor" href="#arg-ties"></a>
+</dt>
 <dd><p>(<code>string</code>)<br> string specifying the method for tie handling. Default is <code>"efron"</code>,
 can also be set to <code>"breslow"</code> or <code>"exact"</code>. See more in <code><a href="https://rdrr.io/pkg/survival/man/coxph.html" class="external-link">survival::coxph()</a></code>.</p></dd>
 
 
-<dt id="arg-conf-level">conf_level<a class="anchor" aria-label="anchor" href="#arg-conf-level"></a></dt>
+<dt id="arg-conf-level">conf_level<a class="anchor" aria-label="anchor" href="#arg-conf-level"></a>
+</dt>
 <dd><p>(<code>proportion</code>)<br> confidence level of the interval.</p></dd>
 
-</dl></div>
+</dl>
+</div>
     <div class="section level2">
-    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
+    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a>
+</h2>
     <p>A list of components with the same names as the arguments.</p>
     </div>
 
   </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
-    </nav></aside></div>
+    </nav></aside>
+</div>
 
 
     <footer><div class="nest">
   <p>tern is a part of the <strong>NEST</strong> and <a href="https://pharmaverse.org/" class="external-link"><strong>pharmaverse</strong></a>.</p>
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-<script type="text/javascript" src="../analytics.js"></script></footer></div>
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+  </body>
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diff --git a/main/reference/control_coxreg.html b/main/reference/control_coxreg.html
index 89189f7f61..195ce5854e 100644
--- a/main/reference/control_coxreg.html
+++ b/main/reference/control_coxreg.html
@@ -1,7 +1,30 @@
-<!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Control function for Cox regression — control_coxreg • tern</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Control function for Cox regression — control_coxreg"><meta name="description" content="
-Sets a list of parameters for Cox regression fit. Used internally."><meta property="og:description" content="
-Sets a list of parameters for Cox regression fit. Used internally."><meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png"><link rel="stylesheet" href="../consent.css"><script src="../consent.js" type="text/javascript" charset="utf-8"></script></head><body>
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+<script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet">
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+<script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Control function for Cox regression — control_coxreg">
+<meta name="description" content="
+Sets a list of parameters for Cox regression fit. Used internally.">
+<meta property="og:description" content="
+Sets a list of parameters for Cox regression fit. Used internally.">
+<meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png">
+<link rel="stylesheet" href="../consent.css">
+<script src="../consent.js" type="text/javascript" charset="utf-8"></script>
+</head>
+<body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
 
 
@@ -17,26 +40,66 @@
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+  </ul>
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+  </ul>
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+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
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+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a>
+</div>
+</li></div>
+</ul>
+<ul class="navbar-nav">
+<li class="nav-item"><form class="form-inline" role="search">
+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json">
+</form></li>
 <li class="nav-item"><a class="external-link nav-link" href="https://github.com/insightsengineering/tern" aria-label="GitHub"><span class="fa fa-github"></span></a></li>
-      </ul></div>
+      </ul>
+</div>
 
 
   </div>
@@ -54,7 +117,8 @@
     </div>
 
     <div class="section level2">
-    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
+    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">control_coxreg</span><span class="op">(</span></span>
 <span>  pval_method <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"wald"</span>, <span class="st">"likelihood"</span><span class="op">)</span>,</span>
 <span>  ties <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"exact"</span>, <span class="st">"efron"</span>, <span class="st">"breslow"</span><span class="op">)</span>,</span>
@@ -64,39 +128,49 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
     </div>
 
     <div class="section level2">
-    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
+    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a>
+</h2>
 
 
-<dl><dt id="arg-pval-method">pval_method<a class="anchor" aria-label="anchor" href="#arg-pval-method"></a></dt>
+<dl>
+<dt id="arg-pval-method">pval_method<a class="anchor" aria-label="anchor" href="#arg-pval-method"></a>
+</dt>
 <dd><p>(<code>string</code>)<br> the method used for estimation of p.values; <code>wald</code> (default) or <code>likelihood</code>.</p></dd>
 
 
-<dt id="arg-ties">ties<a class="anchor" aria-label="anchor" href="#arg-ties"></a></dt>
+<dt id="arg-ties">ties<a class="anchor" aria-label="anchor" href="#arg-ties"></a>
+</dt>
 <dd><p>(<code>string</code>)<br> among <code>exact</code> (equivalent to <code>DISCRETE</code> in SAS), <code>efron</code> and <code>breslow</code>,
 see <code><a href="https://rdrr.io/pkg/survival/man/coxph.html" class="external-link">survival::coxph()</a></code>. Note: there is no equivalent of SAS <code>EXACT</code> method in R.</p></dd>
 
 
-<dt id="arg-conf-level">conf_level<a class="anchor" aria-label="anchor" href="#arg-conf-level"></a></dt>
+<dt id="arg-conf-level">conf_level<a class="anchor" aria-label="anchor" href="#arg-conf-level"></a>
+</dt>
 <dd><p>(<code>proportion</code>)<br> confidence level of the interval.</p></dd>
 
 
-<dt id="arg-interaction">interaction<a class="anchor" aria-label="anchor" href="#arg-interaction"></a></dt>
+<dt id="arg-interaction">interaction<a class="anchor" aria-label="anchor" href="#arg-interaction"></a>
+</dt>
 <dd><p>(<code>flag</code>)<br> if <code>TRUE</code>, the model includes the interaction between the studied
 treatment and candidate covariate. Note that for univariate models without treatment arm, and
 multivariate models, no interaction can be used so that this needs to be <code>FALSE</code>.</p></dd>
 
-</dl></div>
+</dl>
+</div>
     <div class="section level2">
-    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
+    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a>
+</h2>
     <p>A <code>list</code> of items with names corresponding to the arguments.</p>
     </div>
     <div class="section level2">
-    <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"></a></h2>
+    <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"></a>
+</h2>
     <div class="dont-index"><p><code><a href="fit_coxreg.html">fit_coxreg_univar()</a></code> and <code><a href="fit_coxreg.html">fit_coxreg_multivar()</a></code>.</p></div>
     </div>
 
     <div class="section level2">
-    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
+    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="fu">control_coxreg</span><span class="op">(</span><span class="op">)</span></span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> $pval_method</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> [1] "wald"</span>
@@ -114,17 +188,19 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 </code></pre></div>
     </div>
   </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
-    </nav></aside></div>
+    </nav></aside>
+</div>
 
 
     <footer><div class="nest">
   <p>tern is a part of the <strong>NEST</strong> and <a href="https://pharmaverse.org/" class="external-link"><strong>pharmaverse</strong></a>.</p>
 </div>
-<script type="text/javascript" src="../analytics.js"></script></footer></div>
-
+<script type="text/javascript" src="../analytics.js"></script></footer>
+</div>
 
 
 
 
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+</html>
diff --git a/main/reference/control_incidence_rate.html b/main/reference/control_incidence_rate.html
index c27c4122fc..b1a322adf0 100644
--- a/main/reference/control_incidence_rate.html
+++ b/main/reference/control_incidence_rate.html
@@ -1,9 +1,32 @@
-<!DOCTYPE html>
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+<title>Control function for incidence rate — control_incidence_rate • tern</title>
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+<script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Control function for incidence rate — control_incidence_rate">
+<meta name="description" content="
 This is an auxiliary function for controlling arguments for the incidence rate, used
-internally to specify details in s_incidence_rate()."><meta property="og:description" content="
+internally to specify details in s_incidence_rate().">
+<meta property="og:description" content="
 This is an auxiliary function for controlling arguments for the incidence rate, used
-internally to specify details in s_incidence_rate()."><meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png"><link rel="stylesheet" href="../consent.css"><script src="../consent.js" type="text/javascript" charset="utf-8"></script></head><body>
+internally to specify details in s_incidence_rate().">
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+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
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+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a>
+</div>
+</li></div>
+</ul>
+<ul class="navbar-nav">
+<li class="nav-item"><form class="form-inline" role="search">
+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json">
+</form></li>
 <li class="nav-item"><a class="external-link nav-link" href="https://github.com/insightsengineering/tern" aria-label="GitHub"><span class="fa fa-github"></span></a></li>
-      </ul></div>
+      </ul>
+</div>
 
 
   </div>
@@ -57,7 +120,8 @@
     </div>
 
     <div class="section level2">
-    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
+    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">control_incidence_rate</span><span class="op">(</span></span>
 <span>  conf_level <span class="op">=</span> <span class="fl">0.95</span>,</span>
 <span>  conf_type <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"normal"</span>, <span class="st">"normal_log"</span>, <span class="st">"exact"</span>, <span class="st">"byar"</span><span class="op">)</span>,</span>
@@ -67,38 +131,48 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
     </div>
 
     <div class="section level2">
-    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
+    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a>
+</h2>
 
 
-<dl><dt id="arg-conf-level">conf_level<a class="anchor" aria-label="anchor" href="#arg-conf-level"></a></dt>
+<dl>
+<dt id="arg-conf-level">conf_level<a class="anchor" aria-label="anchor" href="#arg-conf-level"></a>
+</dt>
 <dd><p>(<code>proportion</code>)<br> confidence level of the interval.</p></dd>
 
 
-<dt id="arg-conf-type">conf_type<a class="anchor" aria-label="anchor" href="#arg-conf-type"></a></dt>
+<dt id="arg-conf-type">conf_type<a class="anchor" aria-label="anchor" href="#arg-conf-type"></a>
+</dt>
 <dd><p>(<code>string</code>)<br><code>normal</code> (default), <code>normal_log</code>, <code>exact</code>, or <code>byar</code>
 for confidence interval type.</p></dd>
 
 
-<dt id="arg-input-time-unit">input_time_unit<a class="anchor" aria-label="anchor" href="#arg-input-time-unit"></a></dt>
+<dt id="arg-input-time-unit">input_time_unit<a class="anchor" aria-label="anchor" href="#arg-input-time-unit"></a>
+</dt>
 <dd><p>(<code>string</code>)<br><code>day</code>, <code>week</code>, <code>month</code>, or <code>year</code> (default)
 indicating time unit for data input.</p></dd>
 
 
-<dt id="arg-num-pt-year">num_pt_year<a class="anchor" aria-label="anchor" href="#arg-num-pt-year"></a></dt>
+<dt id="arg-num-pt-year">num_pt_year<a class="anchor" aria-label="anchor" href="#arg-num-pt-year"></a>
+</dt>
 <dd><p>(<code>numeric(1)</code>)<br> number of patient-years to use when calculating adverse event rates.</p></dd>
 
-</dl></div>
+</dl>
+</div>
     <div class="section level2">
-    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
+    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a>
+</h2>
     <p>A list of components with the same names as the arguments.</p>
     </div>
     <div class="section level2">
-    <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"></a></h2>
+    <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"></a>
+</h2>
     <div class="dont-index"><p><a href="incidence_rate.html">incidence_rate</a></p></div>
     </div>
 
     <div class="section level2">
-    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
+    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="fu">control_incidence_rate</span><span class="op">(</span><span class="fl">0.9</span>, <span class="st">"exact"</span>, <span class="st">"month"</span>, <span class="fl">100</span><span class="op">)</span></span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> $conf_level</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0.9</span>
@@ -116,17 +190,19 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 </code></pre></div>
     </div>
   </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
-    </nav></aside></div>
+    </nav></aside>
+</div>
 
 
     <footer><div class="nest">
   <p>tern is a part of the <strong>NEST</strong> and <a href="https://pharmaverse.org/" class="external-link"><strong>pharmaverse</strong></a>.</p>
 </div>
-<script type="text/javascript" src="../analytics.js"></script></footer></div>
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+<script type="text/javascript" src="../analytics.js"></script></footer>
+</div>
 
 
 
 
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+</html>
diff --git a/main/reference/control_lineplot_vars.html b/main/reference/control_lineplot_vars.html
index e78a673ca5..3ecc008cf3 100644
--- a/main/reference/control_lineplot_vars.html
+++ b/main/reference/control_lineplot_vars.html
@@ -1,9 +1,32 @@
-<!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Control function for g_lineplot() — control_lineplot_vars • tern</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Control function for g_lineplot() — control_lineplot_vars"><meta name="description" content="
+<html lang="en">
+<head>
+<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+<meta charset="utf-8">
+<meta http-equiv="X-UA-Compatible" content="IE=edge">
+<meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<title>Control function for g_lineplot() — control_lineplot_vars • tern</title>
+<!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png">
+<link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png">
+<link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png">
+<link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png">
+<link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png">
+<link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png">
+<script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet">
+<script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet">
+<link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet">
+<script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Control function for g_lineplot() — control_lineplot_vars">
+<meta name="description" content="
 Default values for variables parameter in g_lineplot function.
-A variable's default value can be overwritten for any variable."><meta property="og:description" content="
+A variable's default value can be overwritten for any variable.">
+<meta property="og:description" content="
 Default values for variables parameter in g_lineplot function.
-A variable's default value can be overwritten for any variable."><meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png"><link rel="stylesheet" href="../consent.css"><script src="../consent.js" type="text/javascript" charset="utf-8"></script></head><body>
+A variable's default value can be overwritten for any variable.">
+<meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png">
+<link rel="stylesheet" href="../consent.css">
+<script src="../consent.js" type="text/javascript" charset="utf-8"></script>
+</head>
+<body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
 
 
@@ -19,33 +42,74 @@
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   <button class="nav-link dropdown-toggle" type="button" id="dropdown-articles" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Articles</button>
-  <ul class="dropdown-menu" aria-labelledby="dropdown-articles"><li><a class="dropdown-item" href="../articles/missing_values.html">Missing Values in Tern</a></li>
+  <ul class="dropdown-menu" aria-labelledby="dropdown-articles">
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+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
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+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a>
+</div>
+</li></div>
+</ul>
+<ul class="navbar-nav">
+<li class="nav-item"><form class="form-inline" role="search">
+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json">
+</form></li>
 <li class="nav-item"><a class="external-link nav-link" href="https://github.com/insightsengineering/tern" aria-label="GitHub"><span class="fa fa-github"></span></a></li>
-      </ul></div>
+      </ul>
+</div>
 
 
   </div>
 </nav><div class="container template-reference-topic">
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
-      <img src="../logo.png" class="logo" alt=""><h1>Control function for <code>g_lineplot()</code></h1>
+      <img src="../logo.png" class="logo" alt=""><h1>Control function for <code>g_lineplot()</code>
+</h1>
       <small class="dont-index">Source: <a href="https://github.com/insightsengineering/tern/blob/main/R/g_lineplot.R" class="external-link"><code>R/g_lineplot.R</code></a></small>
       <div class="d-none name"><code>control_lineplot_vars.Rd</code></div>
     </div>
@@ -57,7 +121,8 @@
     </div>
 
     <div class="section level2">
-    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
+    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">control_lineplot_vars</span><span class="op">(</span></span>
 <span>  x <span class="op">=</span> <span class="st">"AVISIT"</span>,</span>
 <span>  y <span class="op">=</span> <span class="st">"AVAL"</span>,</span>
@@ -70,44 +135,56 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
     </div>
 
     <div class="section level2">
-    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
+    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a>
+</h2>
 
 
-<dl><dt id="arg-x">x<a class="anchor" aria-label="anchor" href="#arg-x"></a></dt>
+<dl>
+<dt id="arg-x">x<a class="anchor" aria-label="anchor" href="#arg-x"></a>
+</dt>
 <dd><p>(<code>string</code>)<br> x-variable name.</p></dd>
 
 
-<dt id="arg-y">y<a class="anchor" aria-label="anchor" href="#arg-y"></a></dt>
+<dt id="arg-y">y<a class="anchor" aria-label="anchor" href="#arg-y"></a>
+</dt>
 <dd><p>(<code>string</code>)<br> y-variable name.</p></dd>
 
 
-<dt id="arg-group-var">group_var<a class="anchor" aria-label="anchor" href="#arg-group-var"></a></dt>
+<dt id="arg-group-var">group_var<a class="anchor" aria-label="anchor" href="#arg-group-var"></a>
+</dt>
 <dd><p>(<code>string</code> or <code>NA</code>)<br> group variable name.</p></dd>
 
 
-<dt id="arg-facet-var">facet_var<a class="anchor" aria-label="anchor" href="#arg-facet-var"></a></dt>
+<dt id="arg-facet-var">facet_var<a class="anchor" aria-label="anchor" href="#arg-facet-var"></a>
+</dt>
 <dd><p>(<code>string</code> or <code>NA</code>)<br> faceting variable name.</p></dd>
 
 
-<dt id="arg-paramcd">paramcd<a class="anchor" aria-label="anchor" href="#arg-paramcd"></a></dt>
+<dt id="arg-paramcd">paramcd<a class="anchor" aria-label="anchor" href="#arg-paramcd"></a>
+</dt>
 <dd><p>(<code>string</code> or <code>NA</code>)<br> parameter code variable name.</p></dd>
 
 
-<dt id="arg-y-unit">y_unit<a class="anchor" aria-label="anchor" href="#arg-y-unit"></a></dt>
+<dt id="arg-y-unit">y_unit<a class="anchor" aria-label="anchor" href="#arg-y-unit"></a>
+</dt>
 <dd><p>(<code>string</code> or <code>NA</code>)<br> y-axis unit variable name.</p></dd>
 
 
-<dt id="arg-subject-var">subject_var<a class="anchor" aria-label="anchor" href="#arg-subject-var"></a></dt>
+<dt id="arg-subject-var">subject_var<a class="anchor" aria-label="anchor" href="#arg-subject-var"></a>
+</dt>
 <dd><p>(<code>string</code> or <code>NA</code>)<br> subject variable name.</p></dd>
 
-</dl></div>
+</dl>
+</div>
     <div class="section level2">
-    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
+    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a>
+</h2>
     <p>A named character vector of variable names.</p>
     </div>
 
     <div class="section level2">
-    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
+    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="fu">control_lineplot_vars</span><span class="op">(</span><span class="op">)</span></span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>           x           y   group_var     paramcd      y_unit subject_var </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>    "AVISIT"      "AVAL"       "ARM"   "PARAMCD"     "AVALU"   "USUBJID" </span>
@@ -122,17 +199,19 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 </code></pre></div>
     </div>
   </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
-    </nav></aside></div>
+    </nav></aside>
+</div>
 
 
     <footer><div class="nest">
   <p>tern is a part of the <strong>NEST</strong> and <a href="https://pharmaverse.org/" class="external-link"><strong>pharmaverse</strong></a>.</p>
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-<script type="text/javascript" src="../analytics.js"></script></footer></div>
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+<script type="text/javascript" src="../analytics.js"></script></footer>
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diff --git a/main/reference/control_logistic.html b/main/reference/control_logistic.html
index 526008990f..e2412c073a 100644
--- a/main/reference/control_logistic.html
+++ b/main/reference/control_logistic.html
@@ -1,9 +1,32 @@
-<!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Control function for logistic regression model fitting — control_logistic • tern</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Control function for logistic regression model fitting — control_logistic"><meta name="description" content="
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+<meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<title>Control function for logistic regression model fitting — control_logistic • tern</title>
+<!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png">
+<link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png">
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+<script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet">
+<script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet">
+<link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet">
+<script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Control function for logistic regression model fitting — control_logistic">
+<meta name="description" content="
 This is an auxiliary function for controlling arguments for logistic regression models.
-conf_level refers to the confidence level used for the Odds Ratio CIs."><meta property="og:description" content="
+conf_level refers to the confidence level used for the Odds Ratio CIs.">
+<meta property="og:description" content="
 This is an auxiliary function for controlling arguments for logistic regression models.
-conf_level refers to the confidence level used for the Odds Ratio CIs."><meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png"><link rel="stylesheet" href="../consent.css"><script src="../consent.js" type="text/javascript" charset="utf-8"></script></head><body>
+conf_level refers to the confidence level used for the Odds Ratio CIs.">
+<meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png">
+<link rel="stylesheet" href="../consent.css">
+<script src="../consent.js" type="text/javascript" charset="utf-8"></script>
+</head>
+<body>
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@@ -19,26 +42,66 @@
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+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a>
+</div>
+</li></div>
+</ul>
+<ul class="navbar-nav">
+<li class="nav-item"><form class="form-inline" role="search">
+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json">
+</form></li>
 <li class="nav-item"><a class="external-link nav-link" href="https://github.com/insightsengineering/tern" aria-label="GitHub"><span class="fa fa-github"></span></a></li>
-      </ul></div>
+      </ul>
+</div>
 
 
   </div>
@@ -57,15 +120,19 @@
     </div>
 
     <div class="section level2">
-    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
+    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">control_logistic</span><span class="op">(</span>response_definition <span class="op">=</span> <span class="st">"response"</span>, conf_level <span class="op">=</span> <span class="fl">0.95</span><span class="op">)</span></span></code></pre></div>
     </div>
 
     <div class="section level2">
-    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
+    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a>
+</h2>
 
 
-<dl><dt id="arg-response-definition">response_definition<a class="anchor" aria-label="anchor" href="#arg-response-definition"></a></dt>
+<dl>
+<dt id="arg-response-definition">response_definition<a class="anchor" aria-label="anchor" href="#arg-response-definition"></a>
+</dt>
 <dd><p>(<code>string</code>)<br> the definition of what an event is in terms of <code>response</code>.
 This will be used when fitting the logistic regression model on the left hand side of the formula.
 Note that the evaluated expression should result in either a logical vector or a factor with 2
@@ -73,17 +140,21 @@ <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#argumen
 and not modified further.</p></dd>
 
 
-<dt id="arg-conf-level">conf_level<a class="anchor" aria-label="anchor" href="#arg-conf-level"></a></dt>
+<dt id="arg-conf-level">conf_level<a class="anchor" aria-label="anchor" href="#arg-conf-level"></a>
+</dt>
 <dd><p>(<code>proportion</code>)<br> confidence level of the interval.</p></dd>
 
-</dl></div>
+</dl>
+</div>
     <div class="section level2">
-    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
+    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a>
+</h2>
     <p>A list of components with the same names as the arguments.</p>
     </div>
 
     <div class="section level2">
-    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
+    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="co"># Standard options.</span></span></span>
 <span class="r-in"><span><span class="fu">control_logistic</span><span class="op">(</span><span class="op">)</span></span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> $response_definition</span>
@@ -114,17 +185,19 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 </code></pre></div>
     </div>
   </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
-    </nav></aside></div>
+    </nav></aside>
+</div>
 
 
     <footer><div class="nest">
   <p>tern is a part of the <strong>NEST</strong> and <a href="https://pharmaverse.org/" class="external-link"><strong>pharmaverse</strong></a>.</p>
 </div>
-<script type="text/javascript" src="../analytics.js"></script></footer></div>
-
+<script type="text/javascript" src="../analytics.js"></script></footer>
+</div>
 
 
 
 
-  </body></html>
 
+  </body>
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diff --git a/main/reference/control_riskdiff.html b/main/reference/control_riskdiff.html
index 4a3e8f74de..c6c5791904 100644
--- a/main/reference/control_riskdiff.html
+++ b/main/reference/control_riskdiff.html
@@ -1,9 +1,32 @@
-<!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Control function for risk difference column — control_riskdiff • tern</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Control function for risk difference column — control_riskdiff"><meta name="description" content="
+<html lang="en">
+<head>
+<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+<meta charset="utf-8">
+<meta http-equiv="X-UA-Compatible" content="IE=edge">
+<meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<title>Control function for risk difference column — control_riskdiff • tern</title>
+<!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png">
+<link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png">
+<link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png">
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+<link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png">
+<link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png">
+<script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet">
+<script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet">
+<link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet">
+<script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Control function for risk difference column — control_riskdiff">
+<meta name="description" content="
 Sets a list of parameters to use when generating a risk (proportion) difference column. Used as input to the
-riskdiff parameter of tabulate_rsp_subgroups() and tabulate_survival_subgroups()."><meta property="og:description" content="
+riskdiff parameter of tabulate_rsp_subgroups() and tabulate_survival_subgroups().">
+<meta property="og:description" content="
 Sets a list of parameters to use when generating a risk (proportion) difference column. Used as input to the
-riskdiff parameter of tabulate_rsp_subgroups() and tabulate_survival_subgroups()."><meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png"><link rel="stylesheet" href="../consent.css"><script src="../consent.js" type="text/javascript" charset="utf-8"></script></head><body>
+riskdiff parameter of tabulate_rsp_subgroups() and tabulate_survival_subgroups().">
+<meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png">
+<link rel="stylesheet" href="../consent.css">
+<script src="../consent.js" type="text/javascript" charset="utf-8"></script>
+</head>
+<body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
 
 
@@ -19,26 +42,66 @@
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+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a>
+</div>
+</li></div>
+</ul>
+<ul class="navbar-nav">
+<li class="nav-item"><form class="form-inline" role="search">
+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json">
+</form></li>
 <li class="nav-item"><a class="external-link nav-link" href="https://github.com/insightsengineering/tern" aria-label="GitHub"><span class="fa fa-github"></span></a></li>
-      </ul></div>
+      </ul>
+</div>
 
 
   </div>
@@ -57,7 +120,8 @@
     </div>
 
     <div class="section level2">
-    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
+    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">control_riskdiff</span><span class="op">(</span></span>
 <span>  arm_x <span class="op">=</span> <span class="cn">NULL</span>,</span>
 <span>  arm_y <span class="op">=</span> <span class="cn">NULL</span>,</span>
@@ -68,45 +132,56 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
     </div>
 
     <div class="section level2">
-    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
+    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a>
+</h2>
 
 
-<dl><dt id="arg-arm-x">arm_x<a class="anchor" aria-label="anchor" href="#arg-arm-x"></a></dt>
+<dl>
+<dt id="arg-arm-x">arm_x<a class="anchor" aria-label="anchor" href="#arg-arm-x"></a>
+</dt>
 <dd><p>(<code>string</code>)<br> name of reference arm to use in risk difference calculations.</p></dd>
 
 
-<dt id="arg-arm-y">arm_y<a class="anchor" aria-label="anchor" href="#arg-arm-y"></a></dt>
+<dt id="arg-arm-y">arm_y<a class="anchor" aria-label="anchor" href="#arg-arm-y"></a>
+</dt>
 <dd><p>(<code>character</code>)<br> names of one or more arms to compare to reference arm in risk difference
 calculations. A new column will be added for each value of <code>arm_y</code>.</p></dd>
 
 
-<dt id="arg-format">format<a class="anchor" aria-label="anchor" href="#arg-format"></a></dt>
+<dt id="arg-format">format<a class="anchor" aria-label="anchor" href="#arg-format"></a>
+</dt>
 <dd><p>(<code>string</code> or <code>function</code>)<br> the format label (string) or formatting function to apply to the risk
 difference statistic. See the <code>3d</code> string options in <code><a href="https://insightsengineering.github.io/formatters/latest-tag/reference/list_formats.html" class="external-link">formatters::list_valid_format_labels()</a></code> for possible format
 strings. Defaults to <code>"xx.x (xx.x - xx.x)"</code>.</p></dd>
 
 
-<dt id="arg-col-label">col_label<a class="anchor" aria-label="anchor" href="#arg-col-label"></a></dt>
+<dt id="arg-col-label">col_label<a class="anchor" aria-label="anchor" href="#arg-col-label"></a>
+</dt>
 <dd><p>(<code>character</code>)<br> labels to use when rendering the risk difference column within the table.
 If more than one comparison arm is specified in <code>arm_y</code>, default labels will specify which two arms are
 being compared (reference arm vs. comparison arm).</p></dd>
 
 
-<dt id="arg-pct">pct<a class="anchor" aria-label="anchor" href="#arg-pct"></a></dt>
+<dt id="arg-pct">pct<a class="anchor" aria-label="anchor" href="#arg-pct"></a>
+</dt>
 <dd><p>(<code>flag</code>)<br> whether output should be returned as percentages. Defaults to <code>TRUE</code>.</p></dd>
 
-</dl></div>
+</dl>
+</div>
     <div class="section level2">
-    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
+    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a>
+</h2>
     <p>A <code>list</code> of items with names corresponding to the arguments.</p>
     </div>
     <div class="section level2">
-    <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"></a></h2>
+    <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"></a>
+</h2>
     <div class="dont-index"><p><code><a href="add_riskdiff.html">add_riskdiff()</a></code>, <code><a href="response_subgroups.html">tabulate_rsp_subgroups()</a></code>, and <code><a href="survival_duration_subgroups.html">tabulate_survival_subgroups()</a></code>.</p></div>
     </div>
 
     <div class="section level2">
-    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
+    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="fu">control_riskdiff</span><span class="op">(</span><span class="op">)</span></span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> $arm_x</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> NULL</span>
@@ -143,17 +218,19 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 </code></pre></div>
     </div>
   </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
-    </nav></aside></div>
+    </nav></aside>
+</div>
 
 
     <footer><div class="nest">
   <p>tern is a part of the <strong>NEST</strong> and <a href="https://pharmaverse.org/" class="external-link"><strong>pharmaverse</strong></a>.</p>
 </div>
-<script type="text/javascript" src="../analytics.js"></script></footer></div>
-
+<script type="text/javascript" src="../analytics.js"></script></footer>
+</div>
 
 
 
 
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diff --git a/main/reference/control_step.html b/main/reference/control_step.html
index ff0498a187..423fd37be6 100644
--- a/main/reference/control_step.html
+++ b/main/reference/control_step.html
@@ -1,7 +1,30 @@
-<!DOCTYPE html>
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-This is an auxiliary function for controlling arguments for STEP calculations."><meta property="og:description" content="
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+<meta name="description" content="
+This is an auxiliary function for controlling arguments for STEP calculations.">
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+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
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+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a>
+</div>
+</li></div>
+</ul>
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+<li class="nav-item"><form class="form-inline" role="search">
+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json">
+</form></li>
 <li class="nav-item"><a class="external-link nav-link" href="https://github.com/insightsengineering/tern" aria-label="GitHub"><span class="fa fa-github"></span></a></li>
-      </ul></div>
+      </ul>
+</div>
 
 
   </div>
@@ -54,7 +117,8 @@
     </div>
 
     <div class="section level2">
-    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
+    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">control_step</span><span class="op">(</span></span>
 <span>  biomarker <span class="op">=</span> <span class="cn">NULL</span>,</span>
 <span>  use_percentile <span class="op">=</span> <span class="cn">TRUE</span>,</span>
@@ -65,22 +129,27 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
     </div>
 
     <div class="section level2">
-    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
+    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a>
+</h2>
 
 
-<dl><dt id="arg-biomarker">biomarker<a class="anchor" aria-label="anchor" href="#arg-biomarker"></a></dt>
+<dl>
+<dt id="arg-biomarker">biomarker<a class="anchor" aria-label="anchor" href="#arg-biomarker"></a>
+</dt>
 <dd><p>(<code>numeric</code> or <code>NULL</code>)<br> optional provision of the numeric biomarker variable, which
 could be used to infer <code>bandwidth</code>, see below.</p></dd>
 
 
-<dt id="arg-use-percentile">use_percentile<a class="anchor" aria-label="anchor" href="#arg-use-percentile"></a></dt>
+<dt id="arg-use-percentile">use_percentile<a class="anchor" aria-label="anchor" href="#arg-use-percentile"></a>
+</dt>
 <dd><p>(<code>flag</code>)<br> if <code>TRUE</code>, the running windows are created according to
 quantiles rather than actual values, i.e. the bandwidth refers to the percentage of data
 covered in each window. Suggest <code>TRUE</code> if the biomarker variable is not uniformly
 distributed.</p></dd>
 
 
-<dt id="arg-bandwidth">bandwidth<a class="anchor" aria-label="anchor" href="#arg-bandwidth"></a></dt>
+<dt id="arg-bandwidth">bandwidth<a class="anchor" aria-label="anchor" href="#arg-bandwidth"></a>
+</dt>
 <dd><p>(<code>numeric(1)</code> or <code>NULL</code>)<br> indicating the bandwidth of each window.
 Depending on the argument <code>use_percentile</code>, it can be either the length of actual-value
 windows on the real biomarker scale, or percentage windows.
@@ -90,25 +159,30 @@ <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#argumen
 variable for actual-value windows.</p></dd>
 
 
-<dt id="arg-degree">degree<a class="anchor" aria-label="anchor" href="#arg-degree"></a></dt>
+<dt id="arg-degree">degree<a class="anchor" aria-label="anchor" href="#arg-degree"></a>
+</dt>
 <dd><p>(<code>integer(1)</code>)<br> the degree of polynomial function of the biomarker as an interaction term
 with the treatment arm fitted at each window. If 0 (default), then the biomarker variable
 is not included in the model fitted in each biomarker window.</p></dd>
 
 
-<dt id="arg-num-points">num_points<a class="anchor" aria-label="anchor" href="#arg-num-points"></a></dt>
+<dt id="arg-num-points">num_points<a class="anchor" aria-label="anchor" href="#arg-num-points"></a>
+</dt>
 <dd><p>(<code>integer(1)</code>)<br> the number of points at which the hazard ratios are estimated. The
 smallest number is 2.</p></dd>
 
-</dl></div>
+</dl>
+</div>
     <div class="section level2">
-    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
+    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a>
+</h2>
     <p>A list of components with the same names as the arguments, except <code>biomarker</code> which is
 just used to calculate the <code>bandwidth</code> in case that actual biomarker windows are requested.</p>
     </div>
 
     <div class="section level2">
-    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
+    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="co"># Provide biomarker values and request actual values to be used,</span></span></span>
 <span class="r-in"><span><span class="co"># so that bandwidth is chosen from range.</span></span></span>
 <span class="r-in"><span><span class="fu">control_step</span><span class="op">(</span>biomarker <span class="op">=</span> <span class="fl">1</span><span class="op">:</span><span class="fl">10</span>, use_percentile <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span></span>
@@ -158,17 +232,19 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 </code></pre></div>
     </div>
   </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
-    </nav></aside></div>
+    </nav></aside>
+</div>
 
 
     <footer><div class="nest">
   <p>tern is a part of the <strong>NEST</strong> and <a href="https://pharmaverse.org/" class="external-link"><strong>pharmaverse</strong></a>.</p>
 </div>
-<script type="text/javascript" src="../analytics.js"></script></footer></div>
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+<script type="text/javascript" src="../analytics.js"></script></footer>
+</div>
 
 
 
 
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diff --git a/main/reference/control_surv_time.html b/main/reference/control_surv_time.html
index d9808695c5..a53f949dfc 100644
--- a/main/reference/control_surv_time.html
+++ b/main/reference/control_surv_time.html
@@ -1,9 +1,32 @@
-<!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Control function for survfit models for survival time — control_surv_time • tern</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Control function for survfit models for survival time — control_surv_time"><meta name="description" content="
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+<title>Control function for survfit models for survival time — control_surv_time • tern</title>
+<!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png">
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+<link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png">
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+<script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet">
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+<script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Control function for survfit models for survival time — control_surv_time">
+<meta name="description" content="
 This is an auxiliary function for controlling arguments for survfit model, typically used internally to specify
-details of survfit model for s_surv_time(). conf_level refers to survival time estimation."><meta property="og:description" content="
+details of survfit model for s_surv_time(). conf_level refers to survival time estimation.">
+<meta property="og:description" content="
 This is an auxiliary function for controlling arguments for survfit model, typically used internally to specify
-details of survfit model for s_surv_time(). conf_level refers to survival time estimation."><meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png"><link rel="stylesheet" href="../consent.css"><script src="../consent.js" type="text/javascript" charset="utf-8"></script></head><body>
+details of survfit model for s_surv_time(). conf_level refers to survival time estimation.">
+<meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png">
+<link rel="stylesheet" href="../consent.css">
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+</head>
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@@ -19,26 +42,66 @@
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+  <ul class="dropdown-menu" aria-labelledby="dropdown-articles">
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     <li><a class="dropdown-item" href="../articles/tern_functions_guide.html">Understanding `tern` functions</a></li>
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+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a>
+</div>
+</li></div>
+</ul>
+<ul class="navbar-nav">
+<li class="nav-item"><form class="form-inline" role="search">
+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json">
+</form></li>
 <li class="nav-item"><a class="external-link nav-link" href="https://github.com/insightsengineering/tern" aria-label="GitHub"><span class="fa fa-github"></span></a></li>
-      </ul></div>
+      </ul>
+</div>
 
 
   </div>
@@ -57,7 +120,8 @@
     </div>
 
     <div class="section level2">
-    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
+    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">control_surv_time</span><span class="op">(</span></span>
 <span>  conf_level <span class="op">=</span> <span class="fl">0.95</span>,</span>
 <span>  conf_type <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"plain"</span>, <span class="st">"log"</span>, <span class="st">"log-log"</span><span class="op">)</span>,</span>
@@ -66,39 +130,48 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
     </div>
 
     <div class="section level2">
-    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
+    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a>
+</h2>
 
 
-<dl><dt id="arg-conf-level">conf_level<a class="anchor" aria-label="anchor" href="#arg-conf-level"></a></dt>
+<dl>
+<dt id="arg-conf-level">conf_level<a class="anchor" aria-label="anchor" href="#arg-conf-level"></a>
+</dt>
 <dd><p>(<code>proportion</code>)<br> confidence level of the interval.</p></dd>
 
 
-<dt id="arg-conf-type">conf_type<a class="anchor" aria-label="anchor" href="#arg-conf-type"></a></dt>
+<dt id="arg-conf-type">conf_type<a class="anchor" aria-label="anchor" href="#arg-conf-type"></a>
+</dt>
 <dd><p>(<code>string</code>)<br> confidence interval type. Options are "plain" (default), "log", "log-log",
 see more in <code><a href="https://rdrr.io/pkg/survival/man/survfit.html" class="external-link">survival::survfit()</a></code>. Note option "none" is no longer supported.</p></dd>
 
 
-<dt id="arg-quantiles">quantiles<a class="anchor" aria-label="anchor" href="#arg-quantiles"></a></dt>
+<dt id="arg-quantiles">quantiles<a class="anchor" aria-label="anchor" href="#arg-quantiles"></a>
+</dt>
 <dd><p>(<code>numeric(2)</code>)<br> vector of length two specifying the quantiles of survival time.</p></dd>
 
-</dl></div>
+</dl>
+</div>
     <div class="section level2">
-    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
+    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a>
+</h2>
     <p>A list of components with the same names as the arguments.</p>
     </div>
 
   </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
-    </nav></aside></div>
+    </nav></aside>
+</div>
 
 
     <footer><div class="nest">
   <p>tern is a part of the <strong>NEST</strong> and <a href="https://pharmaverse.org/" class="external-link"><strong>pharmaverse</strong></a>.</p>
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+</div>
 
 
 
 
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diff --git a/main/reference/control_surv_timepoint.html b/main/reference/control_surv_timepoint.html
index bcc8142ee6..cec1a6dec2 100644
--- a/main/reference/control_surv_timepoint.html
+++ b/main/reference/control_surv_timepoint.html
@@ -1,9 +1,32 @@
-<!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Control function for survfit models for patients' survival rate at time points — control_surv_timepoint • tern</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Control function for survfit models for patients' survival rate at time points — control_surv_timepoint"><meta name="description" content="
+<html lang="en">
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+<meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<title>Control function for survfit models for patients' survival rate at time points — control_surv_timepoint • tern</title>
+<!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png">
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+<script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet">
+<script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet">
+<link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet">
+<script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Control function for survfit models for patients' survival rate at time points — control_surv_timepoint">
+<meta name="description" content="
 This is an auxiliary function for controlling arguments for survfit model, typically used internally to specify
-details of survfit model for s_surv_timepoint(). conf_level refers to patient risk estimation at a time point."><meta property="og:description" content="
+details of survfit model for s_surv_timepoint(). conf_level refers to patient risk estimation at a time point.">
+<meta property="og:description" content="
 This is an auxiliary function for controlling arguments for survfit model, typically used internally to specify
-details of survfit model for s_surv_timepoint(). conf_level refers to patient risk estimation at a time point."><meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png"><link rel="stylesheet" href="../consent.css"><script src="../consent.js" type="text/javascript" charset="utf-8"></script></head><body>
+details of survfit model for s_surv_timepoint(). conf_level refers to patient risk estimation at a time point.">
+<meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png">
+<link rel="stylesheet" href="../consent.css">
+<script src="../consent.js" type="text/javascript" charset="utf-8"></script>
+</head>
+<body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
 
 
@@ -19,26 +42,66 @@
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-      <ul class="navbar-nav me-auto"><li class="nav-item"><a class="nav-link" href="../articles/tern.html">Get started</a></li>
+      <ul class="navbar-nav me-auto">
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 <li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
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-  <ul class="dropdown-menu" aria-labelledby="dropdown-articles"><li><a class="dropdown-item" href="../articles/missing_values.html">Missing Values in Tern</a></li>
+  <ul class="dropdown-menu" aria-labelledby="dropdown-articles">
+<li><a class="dropdown-item" href="../articles/missing_values.html">Missing Values in Tern</a></li>
     <li><a class="dropdown-item" href="../articles/tables.html">Tabulation</a></li>
     <li><a class="dropdown-item" href="../articles/tern_formats.html">Formatting Functions</a></li>
     <li><a class="dropdown-item" href="../articles/tern_functions_guide.html">Understanding `tern` functions</a></li>
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+  </ul>
+</li>
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+  <ul class="dropdown-menu" aria-labelledby="dropdown-reports">
+<li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
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- <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json"></form></li>
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+    <div class="dropdown-menu" aria-labelledby="dropdown-versions">
+    <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
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+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.5">v0.9.5</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.4">v0.9.4</a>
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+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1-rc3">v0.9.1-rc3</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a>
+</div>
+</li></div>
+</ul>
+<ul class="navbar-nav">
+<li class="nav-item"><form class="form-inline" role="search">
+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json">
+</form></li>
 <li class="nav-item"><a class="external-link nav-link" href="https://github.com/insightsengineering/tern" aria-label="GitHub"><span class="fa fa-github"></span></a></li>
-      </ul></div>
+      </ul>
+</div>
 
 
   </div>
@@ -57,7 +120,8 @@
     </div>
 
     <div class="section level2">
-    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
+    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">control_surv_timepoint</span><span class="op">(</span></span>
 <span>  conf_level <span class="op">=</span> <span class="fl">0.95</span>,</span>
 <span>  conf_type <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"plain"</span>, <span class="st">"log"</span>, <span class="st">"log-log"</span><span class="op">)</span></span>
@@ -65,35 +129,43 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
     </div>
 
     <div class="section level2">
-    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
+    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a>
+</h2>
 
 
-<dl><dt id="arg-conf-level">conf_level<a class="anchor" aria-label="anchor" href="#arg-conf-level"></a></dt>
+<dl>
+<dt id="arg-conf-level">conf_level<a class="anchor" aria-label="anchor" href="#arg-conf-level"></a>
+</dt>
 <dd><p>(<code>proportion</code>)<br> confidence level of the interval.</p></dd>
 
 
-<dt id="arg-conf-type">conf_type<a class="anchor" aria-label="anchor" href="#arg-conf-type"></a></dt>
+<dt id="arg-conf-type">conf_type<a class="anchor" aria-label="anchor" href="#arg-conf-type"></a>
+</dt>
 <dd><p>(<code>string</code>)<br> confidence interval type. Options are "plain" (default), "log", "log-log",
 see more in <code><a href="https://rdrr.io/pkg/survival/man/survfit.html" class="external-link">survival::survfit()</a></code>. Note option "none" is no longer supported.</p></dd>
 
-</dl></div>
+</dl>
+</div>
     <div class="section level2">
-    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
+    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a>
+</h2>
     <p>A list of components with the same names as the arguments.</p>
     </div>
 
   </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
-    </nav></aside></div>
+    </nav></aside>
+</div>
 
 
     <footer><div class="nest">
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diff --git a/main/reference/count_cumulative.html b/main/reference/count_cumulative.html
index 2b73dc470d..59897b664f 100644
--- a/main/reference/count_cumulative.html
+++ b/main/reference/count_cumulative.html
@@ -1,19 +1,42 @@
-<!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Cumulative counts of numeric variable by thresholds — count_cumulative • tern</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Cumulative counts of numeric variable by thresholds — count_cumulative"><meta name="description" content="
+<html lang="en">
+<head>
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+<meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<title>Cumulative counts of numeric variable by thresholds — count_cumulative • tern</title>
+<!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png">
+<link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png">
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+<script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet">
+<link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet">
+<script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Cumulative counts of numeric variable by thresholds — count_cumulative">
+<meta name="description" content="
 The analyze function count_cumulative() creates a layout element to calculate cumulative counts of values in a
 numeric variable that are less than, less or equal to, greater than, or greater or equal to user-specified
 threshold values.
 This function analyzes numeric variable vars against the threshold values supplied to the thresholds
 argument as a numeric vector. Whether counts should include the threshold values, and whether to count
 values lower or higher than the threshold values can be set via the include_eq and lower_tail
-parameters, respectively."><meta property="og:description" content="
+parameters, respectively.">
+<meta property="og:description" content="
 The analyze function count_cumulative() creates a layout element to calculate cumulative counts of values in a
 numeric variable that are less than, less or equal to, greater than, or greater or equal to user-specified
 threshold values.
 This function analyzes numeric variable vars against the threshold values supplied to the thresholds
 argument as a numeric vector. Whether counts should include the threshold values, and whether to count
 values lower or higher than the threshold values can be set via the include_eq and lower_tail
-parameters, respectively."><meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png"><link rel="stylesheet" href="../consent.css"><script src="../consent.js" type="text/javascript" charset="utf-8"></script></head><body>
+parameters, respectively.">
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+</head>
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@@ -29,26 +52,66 @@
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+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a>
+</div>
+</li></div>
+</ul>
+<ul class="navbar-nav">
+<li class="nav-item"><form class="form-inline" role="search">
+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json">
+</form></li>
 <li class="nav-item"><a class="external-link nav-link" href="https://github.com/insightsengineering/tern" aria-label="GitHub"><span class="fa fa-github"></span></a></li>
-      </ul></div>
+      </ul>
+</div>
 
 
   </div>
@@ -72,7 +135,8 @@
     </div>
 
     <div class="section level2">
-    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
+    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">count_cumulative</span><span class="op">(</span></span>
 <span>  <span class="va">lyt</span>,</span>
 <span>  <span class="va">vars</span>,</span>
@@ -115,123 +179,163 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
     </div>
 
     <div class="section level2">
-    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
+    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a>
+</h2>
 
 
-<dl><dt id="arg-lyt">lyt<a class="anchor" aria-label="anchor" href="#arg-lyt"></a></dt>
+<dl>
+<dt id="arg-lyt">lyt<a class="anchor" aria-label="anchor" href="#arg-lyt"></a>
+</dt>
 <dd><p>(<code>PreDataTableLayouts</code>)<br> layout that analyses will be added to.</p></dd>
 
 
-<dt id="arg-vars">vars<a class="anchor" aria-label="anchor" href="#arg-vars"></a></dt>
+<dt id="arg-vars">vars<a class="anchor" aria-label="anchor" href="#arg-vars"></a>
+</dt>
 <dd><p>(<code>character</code>)<br> variable names for the primary analysis variable to be iterated over.</p></dd>
 
 
-<dt id="arg-thresholds">thresholds<a class="anchor" aria-label="anchor" href="#arg-thresholds"></a></dt>
+<dt id="arg-thresholds">thresholds<a class="anchor" aria-label="anchor" href="#arg-thresholds"></a>
+</dt>
 <dd><p>(<code>numeric</code>)<br> vector of cutoff values for the counts.</p></dd>
 
 
-<dt id="arg-lower-tail">lower_tail<a class="anchor" aria-label="anchor" href="#arg-lower-tail"></a></dt>
+<dt id="arg-lower-tail">lower_tail<a class="anchor" aria-label="anchor" href="#arg-lower-tail"></a>
+</dt>
 <dd><p>(<code>flag</code>)<br> whether to count lower tail, default is <code>TRUE</code>.</p></dd>
 
 
-<dt id="arg-include-eq">include_eq<a class="anchor" aria-label="anchor" href="#arg-include-eq"></a></dt>
+<dt id="arg-include-eq">include_eq<a class="anchor" aria-label="anchor" href="#arg-include-eq"></a>
+</dt>
 <dd><p>(<code>flag</code>)<br> whether to include value equal to the <code>threshold</code> in
 count, default is <code>TRUE</code>.</p></dd>
 
 
-<dt id="arg-var-labels">var_labels<a class="anchor" aria-label="anchor" href="#arg-var-labels"></a></dt>
+<dt id="arg-var-labels">var_labels<a class="anchor" aria-label="anchor" href="#arg-var-labels"></a>
+</dt>
 <dd><p>(<code>character</code>)<br> variable labels.</p></dd>
 
 
-<dt id="arg-show-labels">show_labels<a class="anchor" aria-label="anchor" href="#arg-show-labels"></a></dt>
+<dt id="arg-show-labels">show_labels<a class="anchor" aria-label="anchor" href="#arg-show-labels"></a>
+</dt>
 <dd><p>(<code>string</code>)<br> label visibility: one of "default", "visible" and "hidden".</p></dd>
 
 
-<dt id="arg-na-str">na_str<a class="anchor" aria-label="anchor" href="#arg-na-str"></a></dt>
+<dt id="arg-na-str">na_str<a class="anchor" aria-label="anchor" href="#arg-na-str"></a>
+</dt>
 <dd><p>(<code>string</code>)<br> string used to replace all <code>NA</code> or empty values in the output.</p></dd>
 
 
-<dt id="arg-nested">nested<a class="anchor" aria-label="anchor" href="#arg-nested"></a></dt>
+<dt id="arg-nested">nested<a class="anchor" aria-label="anchor" href="#arg-nested"></a>
+</dt>
 <dd><p>(<code>flag</code>)<br> whether this layout instruction should be applied within the existing layout structure _if
 possible (<code>TRUE</code>, the default) or as a new top-level element (<code>FALSE</code>). Ignored if it would nest a split.
 underneath analyses, which is not allowed.</p></dd>
 
 
-<dt id="arg--">...<a class="anchor" aria-label="anchor" href="#arg--"></a></dt>
+<dt id="arg--">...<a class="anchor" aria-label="anchor" href="#arg--"></a>
+</dt>
 <dd><p>additional arguments for the lower level functions.</p></dd>
 
 
-<dt id="arg-table-names">table_names<a class="anchor" aria-label="anchor" href="#arg-table-names"></a></dt>
+<dt id="arg-table-names">table_names<a class="anchor" aria-label="anchor" href="#arg-table-names"></a>
+</dt>
 <dd><p>(<code>character</code>)<br> this can be customized in the case that the same <code>vars</code> are analyzed multiple
 times, to avoid warnings from <code>rtables</code>.</p></dd>
 
 
-<dt id="arg--stats">.stats<a class="anchor" aria-label="anchor" href="#arg--stats"></a></dt>
-<dd><p>(<code>character</code>)<br> statistics to select for the table.</p>
-<p>Options are: <code>'count_fraction', 'count_fraction_fixed_dp'</code></p></dd>
+<dt id="arg--stats">.stats<a class="anchor" aria-label="anchor" href="#arg--stats"></a>
+</dt>
+<dd>
+<p>(<code>character</code>)<br> statistics to select for the table.</p>
+<p>Options are: <code>'count_fraction', 'count_fraction_fixed_dp'</code></p>
+</dd>
 
 
-<dt id="arg--formats">.formats<a class="anchor" aria-label="anchor" href="#arg--formats"></a></dt>
+<dt id="arg--formats">.formats<a class="anchor" aria-label="anchor" href="#arg--formats"></a>
+</dt>
 <dd><p>(named <code>character</code> or <code>list</code>)<br> formats for the statistics. See Details in <code>analyze_vars</code> for more
 information on the <code>"auto"</code> setting.</p></dd>
 
 
-<dt id="arg--labels">.labels<a class="anchor" aria-label="anchor" href="#arg--labels"></a></dt>
+<dt id="arg--labels">.labels<a class="anchor" aria-label="anchor" href="#arg--labels"></a>
+</dt>
 <dd><p>(named <code>character</code>)<br> labels for the statistics (without indent).</p></dd>
 
 
-<dt id="arg--indent-mods">.indent_mods<a class="anchor" aria-label="anchor" href="#arg--indent-mods"></a></dt>
+<dt id="arg--indent-mods">.indent_mods<a class="anchor" aria-label="anchor" href="#arg--indent-mods"></a>
+</dt>
 <dd><p>(named <code>integer</code>)<br> indent modifiers for the labels. Defaults to 0, which corresponds to the
 unmodified default behavior. Can be negative.</p></dd>
 
 
-<dt id="arg-x">x<a class="anchor" aria-label="anchor" href="#arg-x"></a></dt>
+<dt id="arg-x">x<a class="anchor" aria-label="anchor" href="#arg-x"></a>
+</dt>
 <dd><p>(<code>numeric</code>)<br> vector of numbers we want to analyze.</p></dd>
 
 
-<dt id="arg--n-col">.N_col<a class="anchor" aria-label="anchor" href="#arg--n-col"></a></dt>
+<dt id="arg--n-col">.N_col<a class="anchor" aria-label="anchor" href="#arg--n-col"></a>
+</dt>
 <dd><p>(<code>integer(1)</code>)<br> column-wise N (column count) for the full column being analyzed that is typically
 passed by <code>rtables</code>.</p></dd>
 
 
-<dt id="arg--n-row">.N_row<a class="anchor" aria-label="anchor" href="#arg--n-row"></a></dt>
+<dt id="arg--n-row">.N_row<a class="anchor" aria-label="anchor" href="#arg--n-row"></a>
+</dt>
 <dd><p>(<code>integer(1)</code>)<br> row-wise N (row group count) for the group of observations being analyzed
 (i.e. with no column-based subsetting) that is typically passed by <code>rtables</code>.</p></dd>
 
 
-<dt id="arg-denom">denom<a class="anchor" aria-label="anchor" href="#arg-denom"></a></dt>
-<dd><p>(<code>string</code>)<br> choice of denominator for proportion. Options are:</p><ul><li><p><code>n</code>: number of values in this row and column intersection.</p></li>
+<dt id="arg-denom">denom<a class="anchor" aria-label="anchor" href="#arg-denom"></a>
+</dt>
+<dd>
+<p>(<code>string</code>)<br> choice of denominator for proportion. Options are:</p>
+<ul>
+<li><p><code>n</code>: number of values in this row and column intersection.</p></li>
 <li><p><code>N_row</code>: total number of values in this row across columns.</p></li>
 <li><p><code>N_col</code>: total number of values in this column across rows.</p></li>
-</ul></dd>
+</ul>
+</dd>
 
-</dl></div>
+</dl>
+</div>
     <div class="section level2">
-    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
+    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a>
+</h2>
 
-<ul><li><p><code>count_cumulative()</code> returns a layout object suitable for passing to further layouting functions,
+<ul>
+<li><p><code>count_cumulative()</code> returns a layout object suitable for passing to further layouting functions,
 or to <code><a href="https://insightsengineering.github.io/rtables/latest-tag/reference/build_table.html" class="external-link">rtables::build_table()</a></code>. Adding this function to an <code>rtable</code> layout will add formatted rows containing
 the statistics from <code>s_count_cumulative()</code> to the table layout.</p></li>
-</ul><ul><li><p><code>s_count_cumulative()</code> returns a named list of <code>count_fraction</code>s: a list with each <code>thresholds</code> value as a
+</ul>
+<ul>
+<li><p><code>s_count_cumulative()</code> returns a named list of <code>count_fraction</code>s: a list with each <code>thresholds</code> value as a
 component, each component containing a vector for the count and fraction.</p></li>
-</ul><ul><li><p><code>a_count_cumulative()</code> returns the corresponding list with formatted <code><a href="https://insightsengineering.github.io/rtables/latest-tag/reference/CellValue.html" class="external-link">rtables::CellValue()</a></code>.</p></li>
-</ul></div>
+</ul>
+<ul>
+<li><p><code>a_count_cumulative()</code> returns the corresponding list with formatted <code><a href="https://insightsengineering.github.io/rtables/latest-tag/reference/CellValue.html" class="external-link">rtables::CellValue()</a></code>.</p></li>
+</ul>
+</div>
     <div class="section level2">
-    <h2 id="functions">Functions<a class="anchor" aria-label="anchor" href="#functions"></a></h2>
+    <h2 id="functions">Functions<a class="anchor" aria-label="anchor" href="#functions"></a>
+</h2>
 
-<ul><li><p><code>count_cumulative()</code>: Layout-creating function which can take statistics function arguments
+<ul>
+<li><p><code>count_cumulative()</code>: Layout-creating function which can take statistics function arguments
 and additional format arguments. This function is a wrapper for <code><a href="https://insightsengineering.github.io/rtables/latest-tag/reference/analyze.html" class="external-link">rtables::analyze()</a></code>.</p></li>
 <li><p><code>s_count_cumulative()</code>: Statistics function that produces a named list given a numeric vector of thresholds.</p></li>
 <li><p><code>a_count_cumulative()</code>: Formatted analysis function which is used as <code>afun</code>
 in <code>count_cumulative()</code>.</p></li>
-</ul></div>
+</ul>
+</div>
     <div class="section level2">
-    <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"></a></h2>
+    <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"></a>
+</h2>
     <div class="dont-index"><p>Relevant helper function <code><a href="h_count_cumulative.html">h_count_cumulative()</a></code>, and descriptive function <code><a href="d_count_cumulative.html">d_count_cumulative()</a></code>.</p></div>
     </div>
 
     <div class="section level2">
-    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
+    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="fu">basic_table</span><span class="op">(</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span></span>
 <span class="r-in"><span>  <span class="fu">split_cols_by</span><span class="op">(</span><span class="st">"ARM"</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span></span>
 <span class="r-in"><span>  <span class="fu">add_colcounts</span><span class="op">(</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span></span>
@@ -250,17 +354,19 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 </code></pre></div>
     </div>
   </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
-    </nav></aside></div>
+    </nav></aside>
+</div>
 
 
     <footer><div class="nest">
   <p>tern is a part of the <strong>NEST</strong> and <a href="https://pharmaverse.org/" class="external-link"><strong>pharmaverse</strong></a>.</p>
 </div>
-<script type="text/javascript" src="../analytics.js"></script></footer></div>
-
+<script type="text/javascript" src="../analytics.js"></script></footer>
+</div>
 
 
 
 
-  </body></html>
 
+  </body>
+</html>
diff --git a/main/reference/count_missed_doses.html b/main/reference/count_missed_doses.html
index f5b25f2225..79d8825410 100644
--- a/main/reference/count_missed_doses.html
+++ b/main/reference/count_missed_doses.html
@@ -1,15 +1,38 @@
-<!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Count number of patients with missed doses by thresholds — count_missed_doses • tern</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Count number of patients with missed doses by thresholds — count_missed_doses"><meta name="description" content="
+<html lang="en">
+<head>
+<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+<meta charset="utf-8">
+<meta http-equiv="X-UA-Compatible" content="IE=edge">
+<meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<title>Count number of patients with missed doses by thresholds — count_missed_doses • tern</title>
+<!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png">
+<link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png">
+<link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png">
+<link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png">
+<link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png">
+<link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png">
+<script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet">
+<script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet">
+<link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet">
+<script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Count number of patients with missed doses by thresholds — count_missed_doses">
+<meta name="description" content="
 The analyze function creates a layout element to calculate cumulative counts of patients with number of missed
 doses at least equal to user-specified threshold values.
 This function analyzes numeric variable vars, a variable with numbers of missed doses,
 against the threshold values supplied to the thresholds argument as a numeric vector. This function
-assumes that every row of the given data frame corresponds to a unique patient."><meta property="og:description" content="
+assumes that every row of the given data frame corresponds to a unique patient.">
+<meta property="og:description" content="
 The analyze function creates a layout element to calculate cumulative counts of patients with number of missed
 doses at least equal to user-specified threshold values.
 This function analyzes numeric variable vars, a variable with numbers of missed doses,
 against the threshold values supplied to the thresholds argument as a numeric vector. This function
-assumes that every row of the given data frame corresponds to a unique patient."><meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png"><link rel="stylesheet" href="../consent.css"><script src="../consent.js" type="text/javascript" charset="utf-8"></script></head><body>
+assumes that every row of the given data frame corresponds to a unique patient.">
+<meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png">
+<link rel="stylesheet" href="../consent.css">
+<script src="../consent.js" type="text/javascript" charset="utf-8"></script>
+</head>
+<body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
 
 
@@ -25,26 +48,66 @@
     </button>
 
     <div id="navbar" class="collapse navbar-collapse ms-3">
-      <ul class="navbar-nav me-auto"><li class="nav-item"><a class="nav-link" href="../articles/tern.html">Get started</a></li>
+      <ul class="navbar-nav me-auto">
+<li class="nav-item"><a class="nav-link" href="../articles/tern.html">Get started</a></li>
 <li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
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   <button class="nav-link dropdown-toggle" type="button" id="dropdown-articles" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Articles</button>
-  <ul class="dropdown-menu" aria-labelledby="dropdown-articles"><li><a class="dropdown-item" href="../articles/missing_values.html">Missing Values in Tern</a></li>
+  <ul class="dropdown-menu" aria-labelledby="dropdown-articles">
+<li><a class="dropdown-item" href="../articles/missing_values.html">Missing Values in Tern</a></li>
     <li><a class="dropdown-item" href="../articles/tables.html">Tabulation</a></li>
     <li><a class="dropdown-item" href="../articles/tern_formats.html">Formatting Functions</a></li>
     <li><a class="dropdown-item" href="../articles/tern_functions_guide.html">Understanding `tern` functions</a></li>
-  </ul></li>
+  </ul>
+</li>
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-  <ul class="dropdown-menu" aria-labelledby="dropdown-reports"><li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
+  <ul class="dropdown-menu" aria-labelledby="dropdown-reports">
+<li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
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- <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json"></form></li>
+  </ul>
+</li>
+      <div><li class="nav-item dropdown">
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+    <div class="dropdown-menu" aria-labelledby="dropdown-versions">
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+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/main">main</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.5">v0.9.5</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.4">v0.9.4</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.3">v0.9.3</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1-rc3">v0.9.1-rc3</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a>
+</div>
+</li></div>
+</ul>
+<ul class="navbar-nav">
+<li class="nav-item"><form class="form-inline" role="search">
+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json">
+</form></li>
 <li class="nav-item"><a class="external-link nav-link" href="https://github.com/insightsengineering/tern" aria-label="GitHub"><span class="fa fa-github"></span></a></li>
-      </ul></div>
+      </ul>
+</div>
 
 
   </div>
@@ -66,7 +129,8 @@
     </div>
 
     <div class="section level2">
-    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
+    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">count_missed_doses</span><span class="op">(</span></span>
 <span>  <span class="va">lyt</span>,</span>
 <span>  <span class="va">vars</span>,</span>
@@ -103,119 +167,161 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
     </div>
 
     <div class="section level2">
-    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
+    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a>
+</h2>
 
 
-<dl><dt id="arg-lyt">lyt<a class="anchor" aria-label="anchor" href="#arg-lyt"></a></dt>
+<dl>
+<dt id="arg-lyt">lyt<a class="anchor" aria-label="anchor" href="#arg-lyt"></a>
+</dt>
 <dd><p>(<code>PreDataTableLayouts</code>)<br> layout that analyses will be added to.</p></dd>
 
 
-<dt id="arg-vars">vars<a class="anchor" aria-label="anchor" href="#arg-vars"></a></dt>
+<dt id="arg-vars">vars<a class="anchor" aria-label="anchor" href="#arg-vars"></a>
+</dt>
 <dd><p>(<code>character</code>)<br> variable names for the primary analysis variable to be iterated over.</p></dd>
 
 
-<dt id="arg-thresholds">thresholds<a class="anchor" aria-label="anchor" href="#arg-thresholds"></a></dt>
+<dt id="arg-thresholds">thresholds<a class="anchor" aria-label="anchor" href="#arg-thresholds"></a>
+</dt>
 <dd><p>(<code>numeric</code>)<br> minimum number of missed doses the patients had.</p></dd>
 
 
-<dt id="arg-var-labels">var_labels<a class="anchor" aria-label="anchor" href="#arg-var-labels"></a></dt>
+<dt id="arg-var-labels">var_labels<a class="anchor" aria-label="anchor" href="#arg-var-labels"></a>
+</dt>
 <dd><p>(<code>character</code>)<br> variable labels.</p></dd>
 
 
-<dt id="arg-show-labels">show_labels<a class="anchor" aria-label="anchor" href="#arg-show-labels"></a></dt>
+<dt id="arg-show-labels">show_labels<a class="anchor" aria-label="anchor" href="#arg-show-labels"></a>
+</dt>
 <dd><p>(<code>string</code>)<br> label visibility: one of "default", "visible" and "hidden".</p></dd>
 
 
-<dt id="arg-na-str">na_str<a class="anchor" aria-label="anchor" href="#arg-na-str"></a></dt>
+<dt id="arg-na-str">na_str<a class="anchor" aria-label="anchor" href="#arg-na-str"></a>
+</dt>
 <dd><p>(<code>string</code>)<br> string used to replace all <code>NA</code> or empty values in the output.</p></dd>
 
 
-<dt id="arg-nested">nested<a class="anchor" aria-label="anchor" href="#arg-nested"></a></dt>
+<dt id="arg-nested">nested<a class="anchor" aria-label="anchor" href="#arg-nested"></a>
+</dt>
 <dd><p>(<code>flag</code>)<br> whether this layout instruction should be applied within the existing layout structure _if
 possible (<code>TRUE</code>, the default) or as a new top-level element (<code>FALSE</code>). Ignored if it would nest a split.
 underneath analyses, which is not allowed.</p></dd>
 
 
-<dt id="arg--">...<a class="anchor" aria-label="anchor" href="#arg--"></a></dt>
+<dt id="arg--">...<a class="anchor" aria-label="anchor" href="#arg--"></a>
+</dt>
 <dd><p>additional arguments for the lower level functions.</p></dd>
 
 
-<dt id="arg-table-names">table_names<a class="anchor" aria-label="anchor" href="#arg-table-names"></a></dt>
+<dt id="arg-table-names">table_names<a class="anchor" aria-label="anchor" href="#arg-table-names"></a>
+</dt>
 <dd><p>(<code>character</code>)<br> this can be customized in the case that the same <code>vars</code> are analyzed multiple
 times, to avoid warnings from <code>rtables</code>.</p></dd>
 
 
-<dt id="arg--stats">.stats<a class="anchor" aria-label="anchor" href="#arg--stats"></a></dt>
-<dd><p>(<code>character</code>)<br> statistics to select for the table.</p>
-<p>Options are: <code>'n', 'count_fraction', 'count_fraction_fixed_dp'</code></p></dd>
+<dt id="arg--stats">.stats<a class="anchor" aria-label="anchor" href="#arg--stats"></a>
+</dt>
+<dd>
+<p>(<code>character</code>)<br> statistics to select for the table.</p>
+<p>Options are: <code>'n', 'count_fraction', 'count_fraction_fixed_dp'</code></p>
+</dd>
 
 
-<dt id="arg--formats">.formats<a class="anchor" aria-label="anchor" href="#arg--formats"></a></dt>
+<dt id="arg--formats">.formats<a class="anchor" aria-label="anchor" href="#arg--formats"></a>
+</dt>
 <dd><p>(named <code>character</code> or <code>list</code>)<br> formats for the statistics. See Details in <code>analyze_vars</code> for more
 information on the <code>"auto"</code> setting.</p></dd>
 
 
-<dt id="arg--labels">.labels<a class="anchor" aria-label="anchor" href="#arg--labels"></a></dt>
+<dt id="arg--labels">.labels<a class="anchor" aria-label="anchor" href="#arg--labels"></a>
+</dt>
 <dd><p>(named <code>character</code>)<br> labels for the statistics (without indent).</p></dd>
 
 
-<dt id="arg--indent-mods">.indent_mods<a class="anchor" aria-label="anchor" href="#arg--indent-mods"></a></dt>
+<dt id="arg--indent-mods">.indent_mods<a class="anchor" aria-label="anchor" href="#arg--indent-mods"></a>
+</dt>
 <dd><p>(named <code>integer</code>)<br> indent modifiers for the labels. Defaults to 0, which corresponds to the
 unmodified default behavior. Can be negative.</p></dd>
 
 
-<dt id="arg-x">x<a class="anchor" aria-label="anchor" href="#arg-x"></a></dt>
+<dt id="arg-x">x<a class="anchor" aria-label="anchor" href="#arg-x"></a>
+</dt>
 <dd><p>(<code>numeric</code>)<br> vector of numbers we want to analyze.</p></dd>
 
 
-<dt id="arg--n-col">.N_col<a class="anchor" aria-label="anchor" href="#arg--n-col"></a></dt>
+<dt id="arg--n-col">.N_col<a class="anchor" aria-label="anchor" href="#arg--n-col"></a>
+</dt>
 <dd><p>(<code>integer(1)</code>)<br> column-wise N (column count) for the full column being analyzed that is typically
 passed by <code>rtables</code>.</p></dd>
 
 
-<dt id="arg--n-row">.N_row<a class="anchor" aria-label="anchor" href="#arg--n-row"></a></dt>
+<dt id="arg--n-row">.N_row<a class="anchor" aria-label="anchor" href="#arg--n-row"></a>
+</dt>
 <dd><p>(<code>integer(1)</code>)<br> row-wise N (row group count) for the group of observations being analyzed
 (i.e. with no column-based subsetting) that is typically passed by <code>rtables</code>.</p></dd>
 
 
-<dt id="arg-denom">denom<a class="anchor" aria-label="anchor" href="#arg-denom"></a></dt>
-<dd><p>(<code>string</code>)<br> choice of denominator for proportion. Options are:</p><ul><li><p><code>n</code>: number of values in this row and column intersection.</p></li>
+<dt id="arg-denom">denom<a class="anchor" aria-label="anchor" href="#arg-denom"></a>
+</dt>
+<dd>
+<p>(<code>string</code>)<br> choice of denominator for proportion. Options are:</p>
+<ul>
+<li><p><code>n</code>: number of values in this row and column intersection.</p></li>
 <li><p><code>N_row</code>: total number of values in this row across columns.</p></li>
 <li><p><code>N_col</code>: total number of values in this column across rows.</p></li>
-</ul></dd>
+</ul>
+</dd>
 
-</dl></div>
+</dl>
+</div>
     <div class="section level2">
-    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
+    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a>
+</h2>
 
-<ul><li><p><code>count_missed_doses()</code> returns a layout object suitable for passing to further layouting functions,
+<ul>
+<li><p><code>count_missed_doses()</code> returns a layout object suitable for passing to further layouting functions,
 or to <code><a href="https://insightsengineering.github.io/rtables/latest-tag/reference/build_table.html" class="external-link">rtables::build_table()</a></code>. Adding this function to an <code>rtable</code> layout will add formatted rows containing
 the statistics from <code>s_count_missed_doses()</code> to the table layout.</p></li>
-</ul><ul><li><p><code>s_count_nonmissing()</code> returns the statistic <code>n</code> which is the count of non-missing values in <code>x</code>.</p></li>
-</ul><ul><li><p><code>s_count_missed_doses()</code> returns the statistics <code>n</code> and <code>count_fraction</code> with one element for each threshold.</p></li>
-</ul><ul><li><p><code>a_count_missed_doses()</code> returns the corresponding list with formatted <code><a href="https://insightsengineering.github.io/rtables/latest-tag/reference/CellValue.html" class="external-link">rtables::CellValue()</a></code>.</p></li>
-</ul></div>
+</ul>
+<ul>
+<li><p><code>s_count_nonmissing()</code> returns the statistic <code>n</code> which is the count of non-missing values in <code>x</code>.</p></li>
+</ul>
+<ul>
+<li><p><code>s_count_missed_doses()</code> returns the statistics <code>n</code> and <code>count_fraction</code> with one element for each threshold.</p></li>
+</ul>
+<ul>
+<li><p><code>a_count_missed_doses()</code> returns the corresponding list with formatted <code><a href="https://insightsengineering.github.io/rtables/latest-tag/reference/CellValue.html" class="external-link">rtables::CellValue()</a></code>.</p></li>
+</ul>
+</div>
     <div class="section level2">
-    <h2 id="functions">Functions<a class="anchor" aria-label="anchor" href="#functions"></a></h2>
+    <h2 id="functions">Functions<a class="anchor" aria-label="anchor" href="#functions"></a>
+</h2>
 
-<ul><li><p><code>count_missed_doses()</code>: Layout-creating function which can take statistics function arguments
+<ul>
+<li><p><code>count_missed_doses()</code>: Layout-creating function which can take statistics function arguments
 and additional format arguments. This function is a wrapper for <code><a href="https://insightsengineering.github.io/rtables/latest-tag/reference/analyze.html" class="external-link">rtables::analyze()</a></code>.</p></li>
 <li><p><code>s_count_nonmissing()</code>: Statistics function to count non-missing values.</p></li>
 <li><p><code>s_count_missed_doses()</code>: Statistics function to count patients with missed doses.</p></li>
 <li><p><code>a_count_missed_doses()</code>: Formatted analysis function which is used as <code>afun</code>
 in <code>count_missed_doses()</code>.</p></li>
-</ul></div>
+</ul>
+</div>
     <div class="section level2">
-    <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"></a></h2>
+    <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"></a>
+</h2>
     <div class="dont-index">
-<ul><li><p>Relevant description function <code><a href="d_count_missed_doses.html">d_count_missed_doses()</a></code> which generates labels for <code>count_missed_doses()</code>.</p></li>
+<ul>
+<li><p>Relevant description function <code><a href="d_count_missed_doses.html">d_count_missed_doses()</a></code> which generates labels for <code>count_missed_doses()</code>.</p></li>
 <li><p>Similar analyze function <code><a href="count_cumulative.html">count_cumulative()</a></code> which more generally counts cumulative values and has more
 options for threshold handling, but uses different labels.</p></li>
-</ul></div>
+</ul>
+</div>
     </div>
 
     <div class="section level2">
-    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
+    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://dplyr.tidyverse.org" class="external-link">dplyr</a></span><span class="op">)</span></span></span>
 <span class="r-in"><span></span></span>
 <span class="r-in"><span><span class="va">anl</span> <span class="op">&lt;-</span> <span class="va">tern_ex_adsl</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span></span>
@@ -245,17 +351,19 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 </code></pre></div>
     </div>
   </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
-    </nav></aside></div>
+    </nav></aside>
+</div>
 
 
     <footer><div class="nest">
   <p>tern is a part of the <strong>NEST</strong> and <a href="https://pharmaverse.org/" class="external-link"><strong>pharmaverse</strong></a>.</p>
 </div>
-<script type="text/javascript" src="../analytics.js"></script></footer></div>
-
+<script type="text/javascript" src="../analytics.js"></script></footer>
+</div>
 
 
 
 
-  </body></html>
 
+  </body>
+</html>
diff --git a/main/reference/count_occurrences.html b/main/reference/count_occurrences.html
index bd0104fafe..3fd830c64e 100644
--- a/main/reference/count_occurrences.html
+++ b/main/reference/count_occurrences.html
@@ -1,5 +1,22 @@
-<!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Count occurrences — count_occurrences • tern</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Count occurrences — count_occurrences"><meta name="description" content="
+<html lang="en">
+<head>
+<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+<meta charset="utf-8">
+<meta http-equiv="X-UA-Compatible" content="IE=edge">
+<meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<title>Count occurrences — count_occurrences • tern</title>
+<!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png">
+<link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png">
+<link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png">
+<link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png">
+<link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png">
+<link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png">
+<script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet">
+<script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet">
+<link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet">
+<script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Count occurrences — count_occurrences">
+<meta name="description" content="
 The analyze function count_occurrences() creates a layout element to calculate occurrence counts for patients.
 This function analyzes the variable(s) supplied to vars and returns a table of occurrence counts for
 each unique value (or level) of the variable(s). This variable (or variables) must be
@@ -7,7 +24,8 @@
 If there are multiple occurrences of the same value recorded for a patient, the value is only counted once.
 The summarize function summarize_occurrences() performs the same function as count_occurrences() except it
 creates content rows, not data rows, to summarize the current table row/column context and operates on the level of
-the latest row split or the root of the table if no row splits have occurred."><meta property="og:description" content="
+the latest row split or the root of the table if no row splits have occurred.">
+<meta property="og:description" content="
 The analyze function count_occurrences() creates a layout element to calculate occurrence counts for patients.
 This function analyzes the variable(s) supplied to vars and returns a table of occurrence counts for
 each unique value (or level) of the variable(s). This variable (or variables) must be
@@ -15,7 +33,12 @@
 If there are multiple occurrences of the same value recorded for a patient, the value is only counted once.
 The summarize function summarize_occurrences() performs the same function as count_occurrences() except it
 creates content rows, not data rows, to summarize the current table row/column context and operates on the level of
-the latest row split or the root of the table if no row splits have occurred."><meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png"><link rel="stylesheet" href="../consent.css"><script src="../consent.js" type="text/javascript" charset="utf-8"></script></head><body>
+the latest row split or the root of the table if no row splits have occurred.">
+<meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png">
+<link rel="stylesheet" href="../consent.css">
+<script src="../consent.js" type="text/javascript" charset="utf-8"></script>
+</head>
+<body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
 
 
@@ -31,26 +54,66 @@
     </button>
 
     <div id="navbar" class="collapse navbar-collapse ms-3">
-      <ul class="navbar-nav me-auto"><li class="nav-item"><a class="nav-link" href="../articles/tern.html">Get started</a></li>
+      <ul class="navbar-nav me-auto">
+<li class="nav-item"><a class="nav-link" href="../articles/tern.html">Get started</a></li>
 <li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
 <li class="nav-item dropdown">
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-articles" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Articles</button>
-  <ul class="dropdown-menu" aria-labelledby="dropdown-articles"><li><a class="dropdown-item" href="../articles/missing_values.html">Missing Values in Tern</a></li>
+  <ul class="dropdown-menu" aria-labelledby="dropdown-articles">
+<li><a class="dropdown-item" href="../articles/missing_values.html">Missing Values in Tern</a></li>
     <li><a class="dropdown-item" href="../articles/tables.html">Tabulation</a></li>
     <li><a class="dropdown-item" href="../articles/tern_formats.html">Formatting Functions</a></li>
     <li><a class="dropdown-item" href="../articles/tern_functions_guide.html">Understanding `tern` functions</a></li>
-  </ul></li>
+  </ul>
+</li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
-  <ul class="dropdown-menu" aria-labelledby="dropdown-reports"><li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
+  <ul class="dropdown-menu" aria-labelledby="dropdown-reports">
+<li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
     <li><a class="dropdown-item" href="../unit-test-report/">Unit test report</a></li>
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-      </ul><ul class="navbar-nav"><li class="nav-item"><form class="form-inline" role="search">
- <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json"></form></li>
+  </ul>
+</li>
+      <div><li class="nav-item dropdown">
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+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/main">main</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.5">v0.9.5</a>
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+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.3">v0.9.3</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1-rc3">v0.9.1-rc3</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a>
+</div>
+</li></div>
+</ul>
+<ul class="navbar-nav">
+<li class="nav-item"><form class="form-inline" role="search">
+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json">
+</form></li>
 <li class="nav-item"><a class="external-link nav-link" href="https://github.com/insightsengineering/tern" aria-label="GitHub"><span class="fa fa-github"></span></a></li>
-      </ul></div>
+      </ul>
+</div>
 
 
   </div>
@@ -75,7 +138,8 @@
     </div>
 
     <div class="section level2">
-    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
+    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">count_occurrences</span><span class="op">(</span></span>
 <span>  <span class="va">lyt</span>,</span>
 <span>  <span class="va">vars</span>,</span>
@@ -138,133 +202,179 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
     </div>
 
     <div class="section level2">
-    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
+    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a>
+</h2>
 
 
-<dl><dt id="arg-lyt">lyt<a class="anchor" aria-label="anchor" href="#arg-lyt"></a></dt>
+<dl>
+<dt id="arg-lyt">lyt<a class="anchor" aria-label="anchor" href="#arg-lyt"></a>
+</dt>
 <dd><p>(<code>PreDataTableLayouts</code>)<br> layout that analyses will be added to.</p></dd>
 
 
-<dt id="arg-vars">vars<a class="anchor" aria-label="anchor" href="#arg-vars"></a></dt>
+<dt id="arg-vars">vars<a class="anchor" aria-label="anchor" href="#arg-vars"></a>
+</dt>
 <dd><p>(<code>character</code>)<br> variable names for the primary analysis variable to be iterated over.</p></dd>
 
 
-<dt id="arg-id">id<a class="anchor" aria-label="anchor" href="#arg-id"></a></dt>
+<dt id="arg-id">id<a class="anchor" aria-label="anchor" href="#arg-id"></a>
+</dt>
 <dd><p>(<code>string</code>)<br> subject variable name.</p></dd>
 
 
-<dt id="arg-drop">drop<a class="anchor" aria-label="anchor" href="#arg-drop"></a></dt>
+<dt id="arg-drop">drop<a class="anchor" aria-label="anchor" href="#arg-drop"></a>
+</dt>
 <dd><p>(<code>flag</code>)<br> whether non-appearing occurrence levels should be dropped from the resulting table.
 Note that in that case the remaining occurrence levels in the table are sorted alphabetically.</p></dd>
 
 
-<dt id="arg-var-labels">var_labels<a class="anchor" aria-label="anchor" href="#arg-var-labels"></a></dt>
+<dt id="arg-var-labels">var_labels<a class="anchor" aria-label="anchor" href="#arg-var-labels"></a>
+</dt>
 <dd><p>(<code>character</code>)<br> variable labels.</p></dd>
 
 
-<dt id="arg-show-labels">show_labels<a class="anchor" aria-label="anchor" href="#arg-show-labels"></a></dt>
+<dt id="arg-show-labels">show_labels<a class="anchor" aria-label="anchor" href="#arg-show-labels"></a>
+</dt>
 <dd><p>(<code>string</code>)<br> label visibility: one of "default", "visible" and "hidden".</p></dd>
 
 
-<dt id="arg-riskdiff">riskdiff<a class="anchor" aria-label="anchor" href="#arg-riskdiff"></a></dt>
+<dt id="arg-riskdiff">riskdiff<a class="anchor" aria-label="anchor" href="#arg-riskdiff"></a>
+</dt>
 <dd><p>(<code>flag</code>)<br> whether a risk difference column is present. When set to <code>TRUE</code>, <code><a href="add_riskdiff.html">add_riskdiff()</a></code> must be
 used as <code>split_fun</code> in the prior column split of the table layout, specifying which columns should be compared.
 See <code><a href="stat_propdiff_ci.html">stat_propdiff_ci()</a></code> for details on risk difference calculation.</p></dd>
 
 
-<dt id="arg-na-str">na_str<a class="anchor" aria-label="anchor" href="#arg-na-str"></a></dt>
+<dt id="arg-na-str">na_str<a class="anchor" aria-label="anchor" href="#arg-na-str"></a>
+</dt>
 <dd><p>(<code>string</code>)<br> string used to replace all <code>NA</code> or empty values in the output.</p></dd>
 
 
-<dt id="arg-nested">nested<a class="anchor" aria-label="anchor" href="#arg-nested"></a></dt>
+<dt id="arg-nested">nested<a class="anchor" aria-label="anchor" href="#arg-nested"></a>
+</dt>
 <dd><p>(<code>flag</code>)<br> whether this layout instruction should be applied within the existing layout structure _if
 possible (<code>TRUE</code>, the default) or as a new top-level element (<code>FALSE</code>). Ignored if it would nest a split.
 underneath analyses, which is not allowed.</p></dd>
 
 
-<dt id="arg--">...<a class="anchor" aria-label="anchor" href="#arg--"></a></dt>
+<dt id="arg--">...<a class="anchor" aria-label="anchor" href="#arg--"></a>
+</dt>
 <dd><p>additional arguments for the lower level functions.</p></dd>
 
 
-<dt id="arg-table-names">table_names<a class="anchor" aria-label="anchor" href="#arg-table-names"></a></dt>
+<dt id="arg-table-names">table_names<a class="anchor" aria-label="anchor" href="#arg-table-names"></a>
+</dt>
 <dd><p>(<code>character</code>)<br> this can be customized in the case that the same <code>vars</code> are analyzed multiple
 times, to avoid warnings from <code>rtables</code>.</p></dd>
 
 
-<dt id="arg--stats">.stats<a class="anchor" aria-label="anchor" href="#arg--stats"></a></dt>
-<dd><p>(<code>character</code>)<br> statistics to select for the table.</p>
-<p>Options are: <code>'count', 'count_fraction', 'count_fraction_fixed_dp', 'fraction'</code></p></dd>
+<dt id="arg--stats">.stats<a class="anchor" aria-label="anchor" href="#arg--stats"></a>
+</dt>
+<dd>
+<p>(<code>character</code>)<br> statistics to select for the table.</p>
+<p>Options are: <code>'count', 'count_fraction', 'count_fraction_fixed_dp', 'fraction'</code></p>
+</dd>
 
 
-<dt id="arg--formats">.formats<a class="anchor" aria-label="anchor" href="#arg--formats"></a></dt>
+<dt id="arg--formats">.formats<a class="anchor" aria-label="anchor" href="#arg--formats"></a>
+</dt>
 <dd><p>(named <code>character</code> or <code>list</code>)<br> formats for the statistics. See Details in <code>analyze_vars</code> for more
 information on the <code>"auto"</code> setting.</p></dd>
 
 
-<dt id="arg--labels">.labels<a class="anchor" aria-label="anchor" href="#arg--labels"></a></dt>
+<dt id="arg--labels">.labels<a class="anchor" aria-label="anchor" href="#arg--labels"></a>
+</dt>
 <dd><p>(named <code>character</code>)<br> labels for the statistics (without indent).</p></dd>
 
 
-<dt id="arg--indent-mods">.indent_mods<a class="anchor" aria-label="anchor" href="#arg--indent-mods"></a></dt>
+<dt id="arg--indent-mods">.indent_mods<a class="anchor" aria-label="anchor" href="#arg--indent-mods"></a>
+</dt>
 <dd><p>(named <code>integer</code>)<br> indent modifiers for the labels. Defaults to 0, which corresponds to the
 unmodified default behavior. Can be negative.</p></dd>
 
 
-<dt id="arg-df">df<a class="anchor" aria-label="anchor" href="#arg-df"></a></dt>
+<dt id="arg-df">df<a class="anchor" aria-label="anchor" href="#arg-df"></a>
+</dt>
 <dd><p>(<code>data.frame</code>)<br> data set containing all analysis variables.</p></dd>
 
 
-<dt id="arg-denom">denom<a class="anchor" aria-label="anchor" href="#arg-denom"></a></dt>
-<dd><p>(<code>string</code>)<br> choice of denominator for proportion. Options are:</p><ul><li><p><code>N_col</code>: total number of patients in this column across rows.</p></li>
+<dt id="arg-denom">denom<a class="anchor" aria-label="anchor" href="#arg-denom"></a>
+</dt>
+<dd>
+<p>(<code>string</code>)<br> choice of denominator for proportion. Options are:</p>
+<ul>
+<li><p><code>N_col</code>: total number of patients in this column across rows.</p></li>
 <li><p><code>n</code>: number of patients with any occurrences.</p></li>
 <li><p><code>N_row</code>: total number of patients in this row across columns.</p></li>
-</ul></dd>
+</ul>
+</dd>
 
 
-<dt id="arg--n-col">.N_col<a class="anchor" aria-label="anchor" href="#arg--n-col"></a></dt>
+<dt id="arg--n-col">.N_col<a class="anchor" aria-label="anchor" href="#arg--n-col"></a>
+</dt>
 <dd><p>(<code>integer(1)</code>)<br> column-wise N (column count) for the full column being analyzed that is typically
 passed by <code>rtables</code>.</p></dd>
 
 
-<dt id="arg--n-row">.N_row<a class="anchor" aria-label="anchor" href="#arg--n-row"></a></dt>
+<dt id="arg--n-row">.N_row<a class="anchor" aria-label="anchor" href="#arg--n-row"></a>
+</dt>
 <dd><p>(<code>integer(1)</code>)<br> row-wise N (row group count) for the group of observations being analyzed
 (i.e. with no column-based subsetting) that is typically passed by <code>rtables</code>.</p></dd>
 
 
-<dt id="arg--df-row">.df_row<a class="anchor" aria-label="anchor" href="#arg--df-row"></a></dt>
+<dt id="arg--df-row">.df_row<a class="anchor" aria-label="anchor" href="#arg--df-row"></a>
+</dt>
 <dd><p>(<code>data.frame</code>)<br> data frame across all of the columns for the given row split.</p></dd>
 
 
-<dt id="arg--var-var">.var, var<a class="anchor" aria-label="anchor" href="#arg--var-var"></a></dt>
+<dt id="arg--var-var">.var, var<a class="anchor" aria-label="anchor" href="#arg--var-var"></a>
+</dt>
 <dd><p>(<code>string</code>)<br> single variable name that is passed by <code>rtables</code> when requested
 by a statistics function.</p></dd>
 
 
-<dt id="arg-labelstr">labelstr<a class="anchor" aria-label="anchor" href="#arg-labelstr"></a></dt>
+<dt id="arg-labelstr">labelstr<a class="anchor" aria-label="anchor" href="#arg-labelstr"></a>
+</dt>
 <dd><p>(<code>string</code>)<br> label of the level of the parent split currently being summarized
 (must be present as second argument in Content Row Functions). See <code><a href="https://insightsengineering.github.io/rtables/latest-tag/reference/summarize_row_groups.html" class="external-link">rtables::summarize_row_groups()</a></code>
 for more information.</p></dd>
 
-</dl></div>
+</dl>
+</div>
     <div class="section level2">
-    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
+    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a>
+</h2>
 
-<ul><li><p><code>count_occurrences()</code> returns a layout object suitable for passing to further layouting functions,
+<ul>
+<li><p><code>count_occurrences()</code> returns a layout object suitable for passing to further layouting functions,
 or to <code><a href="https://insightsengineering.github.io/rtables/latest-tag/reference/build_table.html" class="external-link">rtables::build_table()</a></code>. Adding this function to an <code>rtable</code> layout will add formatted rows containing
 the statistics from <code>s_count_occurrences()</code> to the table layout.</p></li>
-</ul><ul><li><p><code>summarize_occurrences()</code> returns a layout object suitable for passing to further layouting functions,
+</ul>
+<ul>
+<li><p><code>summarize_occurrences()</code> returns a layout object suitable for passing to further layouting functions,
 or to <code><a href="https://insightsengineering.github.io/rtables/latest-tag/reference/build_table.html" class="external-link">rtables::build_table()</a></code>. Adding this function to an <code>rtable</code> layout will add formatted content rows
 containing the statistics from <code>s_count_occurrences()</code> to the table layout.</p></li>
-</ul><ul><li><p><code>s_count_occurrences()</code> returns a list with:</p><ul><li><p><code>count</code>: list of counts with one element per occurrence.</p></li>
+</ul>
+<ul>
+<li>
+<p><code>s_count_occurrences()</code> returns a list with:</p>
+<ul>
+<li><p><code>count</code>: list of counts with one element per occurrence.</p></li>
 <li><p><code>count_fraction</code>: list of counts and fractions with one element per occurrence.</p></li>
 <li><p><code>fraction</code>: list of numerators and denominators with one element per occurrence.</p></li>
-</ul></li>
-</ul><ul><li><p><code>a_count_occurrences()</code> returns the corresponding list with formatted <code><a href="https://insightsengineering.github.io/rtables/latest-tag/reference/CellValue.html" class="external-link">rtables::CellValue()</a></code>.</p></li>
-</ul></div>
+</ul>
+</li>
+</ul>
+<ul>
+<li><p><code>a_count_occurrences()</code> returns the corresponding list with formatted <code><a href="https://insightsengineering.github.io/rtables/latest-tag/reference/CellValue.html" class="external-link">rtables::CellValue()</a></code>.</p></li>
+</ul>
+</div>
     <div class="section level2">
-    <h2 id="functions">Functions<a class="anchor" aria-label="anchor" href="#functions"></a></h2>
+    <h2 id="functions">Functions<a class="anchor" aria-label="anchor" href="#functions"></a>
+</h2>
 
-<ul><li><p><code>count_occurrences()</code>: Layout-creating function which can take statistics function arguments
+<ul>
+<li><p><code>count_occurrences()</code>: Layout-creating function which can take statistics function arguments
 and additional format arguments. This function is a wrapper for <code><a href="https://insightsengineering.github.io/rtables/latest-tag/reference/analyze.html" class="external-link">rtables::analyze()</a></code>.</p></li>
 <li><p><code>summarize_occurrences()</code>: Layout-creating function which can take content function arguments
 and additional format arguments. This function is a wrapper for <code><a href="https://insightsengineering.github.io/rtables/latest-tag/reference/summarize_row_groups.html" class="external-link">rtables::summarize_row_groups()</a></code>.</p></li>
@@ -272,9 +382,11 @@ <h2 id="functions">Functions<a class="anchor" aria-label="anchor" href="#functio
 occurrence.</p></li>
 <li><p><code>a_count_occurrences()</code>: Formatted analysis function which is used as <code>afun</code>
 in <code>count_occurrences()</code>.</p></li>
-</ul></div>
+</ul>
+</div>
     <div class="section level2">
-    <h2 id="note">Note<a class="anchor" aria-label="anchor" href="#note"></a></h2>
+    <h2 id="note">Note<a class="anchor" aria-label="anchor" href="#note"></a>
+</h2>
     <p>By default, occurrences which don't appear in a given row split are dropped from the table and
 the occurrences in the table are sorted alphabetically per row split. Therefore, the corresponding layout
 needs to use <code>split_fun = drop_split_levels</code> in the <code>split_rows_by</code> calls. Use <code>drop = FALSE</code> if you would
@@ -282,7 +394,8 @@ <h2 id="note">Note<a class="anchor" aria-label="anchor" href="#note"></a></h2>
     </div>
 
     <div class="section level2">
-    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
+    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://dplyr.tidyverse.org" class="external-link">dplyr</a></span><span class="op">)</span></span></span>
 <span class="r-in"><span><span class="va">df</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a></span><span class="op">(</span></span></span>
 <span class="r-in"><span>  USUBJID <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/character.html" class="external-link">as.character</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span></span></span>
@@ -428,17 +541,19 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 </code></pre></div>
     </div>
   </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
-    </nav></aside></div>
+    </nav></aside>
+</div>
 
 
     <footer><div class="nest">
   <p>tern is a part of the <strong>NEST</strong> and <a href="https://pharmaverse.org/" class="external-link"><strong>pharmaverse</strong></a>.</p>
 </div>
-<script type="text/javascript" src="../analytics.js"></script></footer></div>
-
+<script type="text/javascript" src="../analytics.js"></script></footer>
+</div>
 
 
 
 
-  </body></html>
 
+  </body>
+</html>
diff --git a/main/reference/count_occurrences_by_grade.html b/main/reference/count_occurrences_by_grade.html
index 1e9c25f0f7..4b048291be 100644
--- a/main/reference/count_occurrences_by_grade.html
+++ b/main/reference/count_occurrences_by_grade.html
@@ -1,5 +1,22 @@
-<!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Count occurrences by grade — count_occurrences_by_grade • tern</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Count occurrences by grade — count_occurrences_by_grade"><meta name="description" content="
+<html lang="en">
+<head>
+<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+<meta charset="utf-8">
+<meta http-equiv="X-UA-Compatible" content="IE=edge">
+<meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<title>Count occurrences by grade — count_occurrences_by_grade • tern</title>
+<!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png">
+<link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png">
+<link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png">
+<link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png">
+<link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png">
+<link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png">
+<script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet">
+<script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet">
+<link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet">
+<script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Count occurrences by grade — count_occurrences_by_grade">
+<meta name="description" content="
 The analyze function count_occurrences_by_grade() creates a layout element to calculate occurrence counts by grade.
 This function analyzes primary analysis variable var which indicates toxicity grades. The id variable
 is used to indicate unique subject identifiers (defaults to USUBJID). The user can also supply a list of
@@ -9,7 +26,8 @@
 The summarize function summarize_occurrences_by_grade() performs the same function as
 count_occurrences_by_grade() except it creates content rows, not data rows, to summarize the current table
 row/column context and operates on the level of the latest row split or the root of the table if no row splits have
-occurred."><meta property="og:description" content="
+occurred.">
+<meta property="og:description" content="
 The analyze function count_occurrences_by_grade() creates a layout element to calculate occurrence counts by grade.
 This function analyzes primary analysis variable var which indicates toxicity grades. The id variable
 is used to indicate unique subject identifiers (defaults to USUBJID). The user can also supply a list of
@@ -19,7 +37,12 @@
 The summarize function summarize_occurrences_by_grade() performs the same function as
 count_occurrences_by_grade() except it creates content rows, not data rows, to summarize the current table
 row/column context and operates on the level of the latest row split or the root of the table if no row splits have
-occurred."><meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png"><link rel="stylesheet" href="../consent.css"><script src="../consent.js" type="text/javascript" charset="utf-8"></script></head><body>
+occurred.">
+<meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png">
+<link rel="stylesheet" href="../consent.css">
+<script src="../consent.js" type="text/javascript" charset="utf-8"></script>
+</head>
+<body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
 
 
@@ -35,26 +58,66 @@
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+<li class="nav-item"><a class="nav-link" href="../articles/tern.html">Get started</a></li>
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   <button class="nav-link dropdown-toggle" type="button" id="dropdown-articles" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Articles</button>
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+  <ul class="dropdown-menu" aria-labelledby="dropdown-articles">
+<li><a class="dropdown-item" href="../articles/missing_values.html">Missing Values in Tern</a></li>
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+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1-rc3">v0.9.1-rc3</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a>
+</div>
+</li></div>
+</ul>
+<ul class="navbar-nav">
+<li class="nav-item"><form class="form-inline" role="search">
+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json">
+</form></li>
 <li class="nav-item"><a class="external-link nav-link" href="https://github.com/insightsengineering/tern" aria-label="GitHub"><span class="fa fa-github"></span></a></li>
-      </ul></div>
+      </ul>
+</div>
 
 
   </div>
@@ -81,7 +144,8 @@
     </div>
 
     <div class="section level2">
-    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
+    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">count_occurrences_by_grade</span><span class="op">(</span></span>
 <span>  <span class="va">lyt</span>,</span>
 <span>  <span class="va">var</span>,</span>
@@ -152,138 +216,181 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
     </div>
 
     <div class="section level2">
-    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
+    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a>
+</h2>
 
 
-<dl><dt id="arg-lyt">lyt<a class="anchor" aria-label="anchor" href="#arg-lyt"></a></dt>
+<dl>
+<dt id="arg-lyt">lyt<a class="anchor" aria-label="anchor" href="#arg-lyt"></a>
+</dt>
 <dd><p>(<code>PreDataTableLayouts</code>)<br> layout that analyses will be added to.</p></dd>
 
 
-<dt id="arg-id">id<a class="anchor" aria-label="anchor" href="#arg-id"></a></dt>
+<dt id="arg-id">id<a class="anchor" aria-label="anchor" href="#arg-id"></a>
+</dt>
 <dd><p>(<code>string</code>)<br> subject variable name.</p></dd>
 
 
-<dt id="arg-grade-groups">grade_groups<a class="anchor" aria-label="anchor" href="#arg-grade-groups"></a></dt>
+<dt id="arg-grade-groups">grade_groups<a class="anchor" aria-label="anchor" href="#arg-grade-groups"></a>
+</dt>
 <dd><p>(named <code>list</code> of <code>character</code>)<br> list containing groupings of grades.</p></dd>
 
 
-<dt id="arg-remove-single">remove_single<a class="anchor" aria-label="anchor" href="#arg-remove-single"></a></dt>
+<dt id="arg-remove-single">remove_single<a class="anchor" aria-label="anchor" href="#arg-remove-single"></a>
+</dt>
 <dd><p>(<code>flag</code>)<br><code>TRUE</code> to not include the elements of one-element grade groups
 in the the output list; in this case only the grade groups names will be included in the output. If
 <code>only_grade_groups</code> is set to <code>TRUE</code> this argument is ignored.</p></dd>
 
 
-<dt id="arg-only-grade-groups">only_grade_groups<a class="anchor" aria-label="anchor" href="#arg-only-grade-groups"></a></dt>
+<dt id="arg-only-grade-groups">only_grade_groups<a class="anchor" aria-label="anchor" href="#arg-only-grade-groups"></a>
+</dt>
 <dd><p>(<code>flag</code>)<br> whether only the specified grade groups should be
 included, with individual grade rows removed (<code>TRUE</code>), or all grades and grade groups
 should be displayed (<code>FALSE</code>).</p></dd>
 
 
-<dt id="arg-var-labels">var_labels<a class="anchor" aria-label="anchor" href="#arg-var-labels"></a></dt>
+<dt id="arg-var-labels">var_labels<a class="anchor" aria-label="anchor" href="#arg-var-labels"></a>
+</dt>
 <dd><p>(<code>character</code>)<br> variable labels.</p></dd>
 
 
-<dt id="arg-show-labels">show_labels<a class="anchor" aria-label="anchor" href="#arg-show-labels"></a></dt>
+<dt id="arg-show-labels">show_labels<a class="anchor" aria-label="anchor" href="#arg-show-labels"></a>
+</dt>
 <dd><p>(<code>string</code>)<br> label visibility: one of "default", "visible" and "hidden".</p></dd>
 
 
-<dt id="arg-riskdiff">riskdiff<a class="anchor" aria-label="anchor" href="#arg-riskdiff"></a></dt>
+<dt id="arg-riskdiff">riskdiff<a class="anchor" aria-label="anchor" href="#arg-riskdiff"></a>
+</dt>
 <dd><p>(<code>flag</code>)<br> whether a risk difference column is present. When set to <code>TRUE</code>, <code><a href="add_riskdiff.html">add_riskdiff()</a></code> must be
 used as <code>split_fun</code> in the prior column split of the table layout, specifying which columns should be compared.
 See <code><a href="stat_propdiff_ci.html">stat_propdiff_ci()</a></code> for details on risk difference calculation.</p></dd>
 
 
-<dt id="arg-na-str">na_str<a class="anchor" aria-label="anchor" href="#arg-na-str"></a></dt>
+<dt id="arg-na-str">na_str<a class="anchor" aria-label="anchor" href="#arg-na-str"></a>
+</dt>
 <dd><p>(<code>string</code>)<br> string used to replace all <code>NA</code> or empty values in the output.</p></dd>
 
 
-<dt id="arg-nested">nested<a class="anchor" aria-label="anchor" href="#arg-nested"></a></dt>
+<dt id="arg-nested">nested<a class="anchor" aria-label="anchor" href="#arg-nested"></a>
+</dt>
 <dd><p>(<code>flag</code>)<br> whether this layout instruction should be applied within the existing layout structure _if
 possible (<code>TRUE</code>, the default) or as a new top-level element (<code>FALSE</code>). Ignored if it would nest a split.
 underneath analyses, which is not allowed.</p></dd>
 
 
-<dt id="arg--">...<a class="anchor" aria-label="anchor" href="#arg--"></a></dt>
+<dt id="arg--">...<a class="anchor" aria-label="anchor" href="#arg--"></a>
+</dt>
 <dd><p>additional arguments for the lower level functions.</p></dd>
 
 
-<dt id="arg-table-names">table_names<a class="anchor" aria-label="anchor" href="#arg-table-names"></a></dt>
+<dt id="arg-table-names">table_names<a class="anchor" aria-label="anchor" href="#arg-table-names"></a>
+</dt>
 <dd><p>(<code>character</code>)<br> this can be customized in the case that the same <code>vars</code> are analyzed multiple
 times, to avoid warnings from <code>rtables</code>.</p></dd>
 
 
-<dt id="arg--stats">.stats<a class="anchor" aria-label="anchor" href="#arg--stats"></a></dt>
-<dd><p>(<code>character</code>)<br> statistics to select for the table.</p>
-<p>Options are: <code>'count_fraction', 'count_fraction_fixed_dp'</code></p></dd>
+<dt id="arg--stats">.stats<a class="anchor" aria-label="anchor" href="#arg--stats"></a>
+</dt>
+<dd>
+<p>(<code>character</code>)<br> statistics to select for the table.</p>
+<p>Options are: <code>'count_fraction', 'count_fraction_fixed_dp'</code></p>
+</dd>
 
 
-<dt id="arg--formats">.formats<a class="anchor" aria-label="anchor" href="#arg--formats"></a></dt>
+<dt id="arg--formats">.formats<a class="anchor" aria-label="anchor" href="#arg--formats"></a>
+</dt>
 <dd><p>(named <code>character</code> or <code>list</code>)<br> formats for the statistics. See Details in <code>analyze_vars</code> for more
 information on the <code>"auto"</code> setting.</p></dd>
 
 
-<dt id="arg--indent-mods">.indent_mods<a class="anchor" aria-label="anchor" href="#arg--indent-mods"></a></dt>
+<dt id="arg--indent-mods">.indent_mods<a class="anchor" aria-label="anchor" href="#arg--indent-mods"></a>
+</dt>
 <dd><p>(named <code>integer</code>)<br> indent modifiers for the labels. Defaults to 0, which corresponds to the
 unmodified default behavior. Can be negative.</p></dd>
 
 
-<dt id="arg--labels">.labels<a class="anchor" aria-label="anchor" href="#arg--labels"></a></dt>
+<dt id="arg--labels">.labels<a class="anchor" aria-label="anchor" href="#arg--labels"></a>
+</dt>
 <dd><p>(named <code>character</code>)<br> labels for the statistics (without indent).</p></dd>
 
 
-<dt id="arg-df">df<a class="anchor" aria-label="anchor" href="#arg-df"></a></dt>
+<dt id="arg-df">df<a class="anchor" aria-label="anchor" href="#arg-df"></a>
+</dt>
 <dd><p>(<code>data.frame</code>)<br> data set containing all analysis variables.</p></dd>
 
 
-<dt id="arg--var-var">.var, var<a class="anchor" aria-label="anchor" href="#arg--var-var"></a></dt>
+<dt id="arg--var-var">.var, var<a class="anchor" aria-label="anchor" href="#arg--var-var"></a>
+</dt>
 <dd><p>(<code>string</code>)<br> single variable name that is passed by <code>rtables</code> when requested
 by a statistics function.</p></dd>
 
 
-<dt id="arg--n-row">.N_row<a class="anchor" aria-label="anchor" href="#arg--n-row"></a></dt>
+<dt id="arg--n-row">.N_row<a class="anchor" aria-label="anchor" href="#arg--n-row"></a>
+</dt>
 <dd><p>(<code>integer(1)</code>)<br> row-wise N (row group count) for the group of observations being analyzed
 (i.e. with no column-based subsetting) that is typically passed by <code>rtables</code>.</p></dd>
 
 
-<dt id="arg--n-col">.N_col<a class="anchor" aria-label="anchor" href="#arg--n-col"></a></dt>
+<dt id="arg--n-col">.N_col<a class="anchor" aria-label="anchor" href="#arg--n-col"></a>
+</dt>
 <dd><p>(<code>integer(1)</code>)<br> column-wise N (column count) for the full column being analyzed that is typically
 passed by <code>rtables</code>.</p></dd>
 
 
-<dt id="arg-denom">denom<a class="anchor" aria-label="anchor" href="#arg-denom"></a></dt>
-<dd><p>(<code>string</code>)<br> choice of denominator for proportion. Options are:</p><ul><li><p><code>N_col</code>: total number of patients in this column across rows.</p></li>
+<dt id="arg-denom">denom<a class="anchor" aria-label="anchor" href="#arg-denom"></a>
+</dt>
+<dd>
+<p>(<code>string</code>)<br> choice of denominator for proportion. Options are:</p>
+<ul>
+<li><p><code>N_col</code>: total number of patients in this column across rows.</p></li>
 <li><p><code>n</code>: number of patients with any occurrences.</p></li>
 <li><p><code>N_row</code>: total number of patients in this row across columns.</p></li>
-</ul></dd>
+</ul>
+</dd>
 
 
-<dt id="arg-labelstr">labelstr<a class="anchor" aria-label="anchor" href="#arg-labelstr"></a></dt>
+<dt id="arg-labelstr">labelstr<a class="anchor" aria-label="anchor" href="#arg-labelstr"></a>
+</dt>
 <dd><p>(<code>string</code>)<br> label of the level of the parent split currently being summarized
 (must be present as second argument in Content Row Functions). See <code><a href="https://insightsengineering.github.io/rtables/latest-tag/reference/summarize_row_groups.html" class="external-link">rtables::summarize_row_groups()</a></code>
 for more information.</p></dd>
 
 
-<dt id="arg--df-row">.df_row<a class="anchor" aria-label="anchor" href="#arg--df-row"></a></dt>
+<dt id="arg--df-row">.df_row<a class="anchor" aria-label="anchor" href="#arg--df-row"></a>
+</dt>
 <dd><p>(<code>data.frame</code>)<br> data frame across all of the columns for the given row split.</p></dd>
 
-</dl></div>
+</dl>
+</div>
     <div class="section level2">
-    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
+    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a>
+</h2>
 
-<ul><li><p><code>count_occurrences_by_grade()</code> returns a layout object suitable for passing to further layouting functions,
+<ul>
+<li><p><code>count_occurrences_by_grade()</code> returns a layout object suitable for passing to further layouting functions,
 or to <code><a href="https://insightsengineering.github.io/rtables/latest-tag/reference/build_table.html" class="external-link">rtables::build_table()</a></code>. Adding this function to an <code>rtable</code> layout will add formatted rows containing
 the statistics from <code>s_count_occurrences_by_grade()</code> to the table layout.</p></li>
-</ul><ul><li><p><code>summarize_occurrences_by_grade()</code> returns a layout object suitable for passing to further layouting functions,
+</ul>
+<ul>
+<li><p><code>summarize_occurrences_by_grade()</code> returns a layout object suitable for passing to further layouting functions,
 or to <code><a href="https://insightsengineering.github.io/rtables/latest-tag/reference/build_table.html" class="external-link">rtables::build_table()</a></code>. Adding this function to an <code>rtable</code> layout will add formatted content rows
 containing the statistics from <code>s_count_occurrences_by_grade()</code> to the table layout.</p></li>
-</ul><ul><li><p><code>s_count_occurrences_by_grade()</code> returns a list of counts and fractions with one element per grade level or
+</ul>
+<ul>
+<li><p><code>s_count_occurrences_by_grade()</code> returns a list of counts and fractions with one element per grade level or
 grade level grouping.</p></li>
-</ul><ul><li><p><code>a_count_occurrences_by_grade()</code> returns the corresponding list with formatted <code><a href="https://insightsengineering.github.io/rtables/latest-tag/reference/CellValue.html" class="external-link">rtables::CellValue()</a></code>.</p></li>
-</ul></div>
+</ul>
+<ul>
+<li><p><code>a_count_occurrences_by_grade()</code> returns the corresponding list with formatted <code><a href="https://insightsengineering.github.io/rtables/latest-tag/reference/CellValue.html" class="external-link">rtables::CellValue()</a></code>.</p></li>
+</ul>
+</div>
     <div class="section level2">
-    <h2 id="functions">Functions<a class="anchor" aria-label="anchor" href="#functions"></a></h2>
+    <h2 id="functions">Functions<a class="anchor" aria-label="anchor" href="#functions"></a>
+</h2>
 
-<ul><li><p><code>count_occurrences_by_grade()</code>: Layout-creating function which can take statistics function
+<ul>
+<li><p><code>count_occurrences_by_grade()</code>: Layout-creating function which can take statistics function
 arguments and additional format arguments. This function is a wrapper for <code><a href="https://insightsengineering.github.io/rtables/latest-tag/reference/analyze.html" class="external-link">rtables::analyze()</a></code>.</p></li>
 <li><p><code>summarize_occurrences_by_grade()</code>: Layout-creating function which can take content function arguments
 and additional format arguments. This function is a wrapper for <code><a href="https://insightsengineering.github.io/rtables/latest-tag/reference/summarize_row_groups.html" class="external-link">rtables::summarize_row_groups()</a></code>.</p></li>
@@ -291,14 +398,17 @@ <h2 id="functions">Functions<a class="anchor" aria-label="anchor" href="#functio
 number of patients by highest grade.</p></li>
 <li><p><code>a_count_occurrences_by_grade()</code>: Formatted analysis function which is used as <code>afun</code>
 in <code>count_occurrences_by_grade()</code>.</p></li>
-</ul></div>
+</ul>
+</div>
     <div class="section level2">
-    <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"></a></h2>
+    <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"></a>
+</h2>
     <div class="dont-index"><p>Relevant helper function <code><a href="h_append_grade_groups.html">h_append_grade_groups()</a></code>.</p></div>
     </div>
 
     <div class="section level2">
-    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
+    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://dplyr.tidyverse.org" class="external-link">dplyr</a></span><span class="op">)</span></span></span>
 <span class="r-in"><span></span></span>
 <span class="r-in"><span><span class="va">df</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a></span><span class="op">(</span></span></span>
@@ -461,17 +571,19 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 </code></pre></div>
     </div>
   </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
-    </nav></aside></div>
+    </nav></aside>
+</div>
 
 
     <footer><div class="nest">
   <p>tern is a part of the <strong>NEST</strong> and <a href="https://pharmaverse.org/" class="external-link"><strong>pharmaverse</strong></a>.</p>
 </div>
-<script type="text/javascript" src="../analytics.js"></script></footer></div>
-
+<script type="text/javascript" src="../analytics.js"></script></footer>
+</div>
 
 
 
 
-  </body></html>
 
+  </body>
+</html>
diff --git a/main/reference/count_patients_events_in_cols.html b/main/reference/count_patients_events_in_cols.html
index ae7443b17e..26cc826128 100644
--- a/main/reference/count_patients_events_in_cols.html
+++ b/main/reference/count_patients_events_in_cols.html
@@ -1,17 +1,40 @@
-<!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Count patient events in columns — count_patients_events_in_cols • tern</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Count patient events in columns — count_patients_events_in_cols"><meta name="description" content="
+<html lang="en">
+<head>
+<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+<meta charset="utf-8">
+<meta http-equiv="X-UA-Compatible" content="IE=edge">
+<meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<title>Count patient events in columns — count_patients_events_in_cols • tern</title>
+<!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png">
+<link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png">
+<link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png">
+<link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png">
+<link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png">
+<link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png">
+<script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet">
+<script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet">
+<link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet">
+<script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Count patient events in columns — count_patients_events_in_cols">
+<meta name="description" content="
 The summarize function summarize_patients_events_in_cols() creates a layout element to summarize patient
 event counts in columns.
 This function analyzes the elements (events) supplied via the filters_list parameter and returns a row
 with counts of number of patients for each event as well as the total numbers of patients and events.
 The id variable is used to indicate unique subject identifiers (defaults to USUBJID).
-If there are multiple occurrences of the same event recorded for a patient, the event is only counted once."><meta property="og:description" content="
+If there are multiple occurrences of the same event recorded for a patient, the event is only counted once.">
+<meta property="og:description" content="
 The summarize function summarize_patients_events_in_cols() creates a layout element to summarize patient
 event counts in columns.
 This function analyzes the elements (events) supplied via the filters_list parameter and returns a row
 with counts of number of patients for each event as well as the total numbers of patients and events.
 The id variable is used to indicate unique subject identifiers (defaults to USUBJID).
-If there are multiple occurrences of the same event recorded for a patient, the event is only counted once."><meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png"><link rel="stylesheet" href="../consent.css"><script src="../consent.js" type="text/javascript" charset="utf-8"></script></head><body>
+If there are multiple occurrences of the same event recorded for a patient, the event is only counted once.">
+<meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png">
+<link rel="stylesheet" href="../consent.css">
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+</head>
+<body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
 
 
@@ -27,26 +50,66 @@
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+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
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+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a>
+</div>
+</li></div>
+</ul>
+<ul class="navbar-nav">
+<li class="nav-item"><form class="form-inline" role="search">
+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json">
+</form></li>
 <li class="nav-item"><a class="external-link nav-link" href="https://github.com/insightsengineering/tern" aria-label="GitHub"><span class="fa fa-github"></span></a></li>
-      </ul></div>
+      </ul>
+</div>
 
 
   </div>
@@ -69,7 +132,8 @@
     </div>
 
     <div class="section level2">
-    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
+    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">summarize_patients_events_in_cols</span><span class="op">(</span></span>
 <span>  <span class="va">lyt</span>,</span>
 <span>  id <span class="op">=</span> <span class="st">"USUBJID"</span>,</span>
@@ -94,89 +158,119 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
     </div>
 
     <div class="section level2">
-    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
+    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a>
+</h2>
 
 
-<dl><dt id="arg-lyt">lyt<a class="anchor" aria-label="anchor" href="#arg-lyt"></a></dt>
+<dl>
+<dt id="arg-lyt">lyt<a class="anchor" aria-label="anchor" href="#arg-lyt"></a>
+</dt>
 <dd><p>(<code>PreDataTableLayouts</code>)<br> layout that analyses will be added to.</p></dd>
 
 
-<dt id="arg-id">id<a class="anchor" aria-label="anchor" href="#arg-id"></a></dt>
+<dt id="arg-id">id<a class="anchor" aria-label="anchor" href="#arg-id"></a>
+</dt>
 <dd><p>(<code>string</code>)<br> subject variable name.</p></dd>
 
 
-<dt id="arg-filters-list">filters_list<a class="anchor" aria-label="anchor" href="#arg-filters-list"></a></dt>
+<dt id="arg-filters-list">filters_list<a class="anchor" aria-label="anchor" href="#arg-filters-list"></a>
+</dt>
 <dd><p>(named <code>list</code> of <code>character</code>)<br> list where each element in this list describes one
 type of event describe by filters, in the same format as <code><a href="count_patients_with_event.html">s_count_patients_with_event()</a></code>.
 If it has a label, then this will be used for the column title.</p></dd>
 
 
-<dt id="arg-empty-stats">empty_stats<a class="anchor" aria-label="anchor" href="#arg-empty-stats"></a></dt>
+<dt id="arg-empty-stats">empty_stats<a class="anchor" aria-label="anchor" href="#arg-empty-stats"></a>
+</dt>
 <dd><p>(<code>character</code>)<br> optional names of the statistics that should be returned empty such
 that corresponding table cells will stay blank.</p></dd>
 
 
-<dt id="arg-na-str">na_str<a class="anchor" aria-label="anchor" href="#arg-na-str"></a></dt>
+<dt id="arg-na-str">na_str<a class="anchor" aria-label="anchor" href="#arg-na-str"></a>
+</dt>
 <dd><p>(<code>string</code>)<br> string used to replace all <code>NA</code> or empty values in the output.</p></dd>
 
 
-<dt id="arg--">...<a class="anchor" aria-label="anchor" href="#arg--"></a></dt>
+<dt id="arg--">...<a class="anchor" aria-label="anchor" href="#arg--"></a>
+</dt>
 <dd><p>additional arguments for the lower level functions.</p></dd>
 
 
-<dt id="arg--stats">.stats<a class="anchor" aria-label="anchor" href="#arg--stats"></a></dt>
-<dd><p>(<code>character</code>)<br> statistics to select for the table.</p>
+<dt id="arg--stats">.stats<a class="anchor" aria-label="anchor" href="#arg--stats"></a>
+</dt>
+<dd>
+<p>(<code>character</code>)<br> statistics to select for the table.</p>
 <p>In addition to any statistics added using <code>filters_list</code>, statistic options are:
-<code>'unique', 'all'</code></p></dd>
+<code>'unique', 'all'</code></p>
+</dd>
 
 
-<dt id="arg--labels">.labels<a class="anchor" aria-label="anchor" href="#arg--labels"></a></dt>
+<dt id="arg--labels">.labels<a class="anchor" aria-label="anchor" href="#arg--labels"></a>
+</dt>
 <dd><p>(named <code>character</code>)<br> labels for the statistics (without indent).</p></dd>
 
 
-<dt id="arg-col-split">col_split<a class="anchor" aria-label="anchor" href="#arg-col-split"></a></dt>
+<dt id="arg-col-split">col_split<a class="anchor" aria-label="anchor" href="#arg-col-split"></a>
+</dt>
 <dd><p>(<code>flag</code>)<br> whether the columns should be split.
 Set to <code>FALSE</code> when the required column split has been done already earlier in the layout pipe.</p></dd>
 
 
-<dt id="arg-df">df<a class="anchor" aria-label="anchor" href="#arg-df"></a></dt>
+<dt id="arg-df">df<a class="anchor" aria-label="anchor" href="#arg-df"></a>
+</dt>
 <dd><p>(<code>data.frame</code>)<br> data set containing all analysis variables.</p></dd>
 
 
-<dt id="arg-labelstr">labelstr<a class="anchor" aria-label="anchor" href="#arg-labelstr"></a></dt>
+<dt id="arg-labelstr">labelstr<a class="anchor" aria-label="anchor" href="#arg-labelstr"></a>
+</dt>
 <dd><p>(<code>string</code>)<br> label of the level of the parent split currently being summarized
 (must be present as second argument in Content Row Functions). See <code><a href="https://insightsengineering.github.io/rtables/latest-tag/reference/summarize_row_groups.html" class="external-link">rtables::summarize_row_groups()</a></code>
 for more information.</p></dd>
 
 
-<dt id="arg-custom-label">custom_label<a class="anchor" aria-label="anchor" href="#arg-custom-label"></a></dt>
+<dt id="arg-custom-label">custom_label<a class="anchor" aria-label="anchor" href="#arg-custom-label"></a>
+</dt>
 <dd><p>(<code>string</code> or <code>NULL</code>)<br> if provided and <code>labelstr</code> is empty then this will
 be used as label.</p></dd>
 
-</dl></div>
+</dl>
+</div>
     <div class="section level2">
-    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
+    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a>
+</h2>
 
-<ul><li><p><code>summarize_patients_events_in_cols()</code> returns a layout object suitable for passing to further layouting functions,
+<ul>
+<li><p><code>summarize_patients_events_in_cols()</code> returns a layout object suitable for passing to further layouting functions,
 or to <code><a href="https://insightsengineering.github.io/rtables/latest-tag/reference/build_table.html" class="external-link">rtables::build_table()</a></code>. Adding this function to an <code>rtable</code> layout will add formatted content rows
 containing the statistics from <code>s_count_patients_and_multiple_events()</code> to the table layout.</p></li>
-</ul><ul><li><p><code>s_count_patients_and_multiple_events()</code> returns a list with the statistics:</p><ul><li><p><code>unique</code>: number of unique patients in <code>df</code>.</p></li>
+</ul>
+<ul>
+<li>
+<p><code>s_count_patients_and_multiple_events()</code> returns a list with the statistics:</p>
+<ul>
+<li><p><code>unique</code>: number of unique patients in <code>df</code>.</p></li>
 <li><p><code>all</code>: number of rows in <code>df</code>.</p></li>
 <li><p>one element with the same name as in <code>filters_list</code>: number of rows in <code>df</code>,
 i.e. events, fulfilling the filter condition.</p></li>
-</ul></li>
-</ul></div>
+</ul>
+</li>
+</ul>
+</div>
     <div class="section level2">
-    <h2 id="functions">Functions<a class="anchor" aria-label="anchor" href="#functions"></a></h2>
+    <h2 id="functions">Functions<a class="anchor" aria-label="anchor" href="#functions"></a>
+</h2>
 
-<ul><li><p><code>summarize_patients_events_in_cols()</code>: Layout-creating function which can take statistics function
+<ul>
+<li><p><code>summarize_patients_events_in_cols()</code>: Layout-creating function which can take statistics function
 arguments and additional format arguments. This function is a wrapper for <code><a href="https://insightsengineering.github.io/rtables/latest-tag/reference/summarize_row_groups.html" class="external-link">rtables::summarize_row_groups()</a></code>.</p></li>
 <li><p><code>s_count_patients_and_multiple_events()</code>: Statistics function which counts numbers of patients and multiple
 events defined by filters. Used as analysis function <code>afun</code> in <code>summarize_patients_events_in_cols()</code>.</p></li>
-</ul></div>
+</ul>
+</div>
 
     <div class="section level2">
-    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
+    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">df</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a></span><span class="op">(</span></span></span>
 <span class="r-in"><span>  USUBJID <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/rep.html" class="external-link">rep</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"id1"</span>, <span class="st">"id2"</span>, <span class="st">"id3"</span>, <span class="st">"id4"</span><span class="op">)</span>, <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">2</span>, <span class="fl">3</span>, <span class="fl">1</span>, <span class="fl">1</span><span class="op">)</span><span class="op">)</span>,</span></span>
 <span class="r-in"><span>  ARM <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"A"</span>, <span class="st">"A"</span>, <span class="st">"B"</span>, <span class="st">"B"</span>, <span class="st">"B"</span>, <span class="st">"B"</span>, <span class="st">"A"</span><span class="op">)</span>,</span></span>
@@ -205,17 +299,19 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 </code></pre></div>
     </div>
   </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
-    </nav></aside></div>
+    </nav></aside>
+</div>
 
 
     <footer><div class="nest">
   <p>tern is a part of the <strong>NEST</strong> and <a href="https://pharmaverse.org/" class="external-link"><strong>pharmaverse</strong></a>.</p>
 </div>
-<script type="text/javascript" src="../analytics.js"></script></footer></div>
-
+<script type="text/javascript" src="../analytics.js"></script></footer>
+</div>
 
 
 
 
-  </body></html>
 
+  </body>
+</html>
diff --git a/main/reference/count_patients_with_event.html b/main/reference/count_patients_with_event.html
index c39ac53a9d..e3b7a8144f 100644
--- a/main/reference/count_patients_with_event.html
+++ b/main/reference/count_patients_with_event.html
@@ -1,17 +1,40 @@
-<!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Count the number of patients with a particular event — count_patients_with_event • tern</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Count the number of patients with a particular event — count_patients_with_event"><meta name="description" content="
+<html lang="en">
+<head>
+<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+<meta charset="utf-8">
+<meta http-equiv="X-UA-Compatible" content="IE=edge">
+<meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<title>Count the number of patients with a particular event — count_patients_with_event • tern</title>
+<!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png">
+<link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png">
+<link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png">
+<link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png">
+<link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png">
+<link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png">
+<script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
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+<script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet">
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+<script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Count the number of patients with a particular event — count_patients_with_event">
+<meta name="description" content="
 The analyze function count_patients_with_event() creates a layout element to calculate patient counts for a
 user-specified set of events.
 This function analyzes primary analysis variable vars which indicates unique subject identifiers. Events
 are defined by the user as a named vector via the filters argument, where each name corresponds to a
 variable and each value is the value(s) that that variable takes for the event.
-If there are multiple records with the same event recorded for a patient, only one occurrence is counted."><meta property="og:description" content="
+If there are multiple records with the same event recorded for a patient, only one occurrence is counted.">
+<meta property="og:description" content="
 The analyze function count_patients_with_event() creates a layout element to calculate patient counts for a
 user-specified set of events.
 This function analyzes primary analysis variable vars which indicates unique subject identifiers. Events
 are defined by the user as a named vector via the filters argument, where each name corresponds to a
 variable and each value is the value(s) that that variable takes for the event.
-If there are multiple records with the same event recorded for a patient, only one occurrence is counted."><meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png"><link rel="stylesheet" href="../consent.css"><script src="../consent.js" type="text/javascript" charset="utf-8"></script></head><body>
+If there are multiple records with the same event recorded for a patient, only one occurrence is counted.">
+<meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png">
+<link rel="stylesheet" href="../consent.css">
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+<body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
 
 
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+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a>
+</div>
+</li></div>
+</ul>
+<ul class="navbar-nav">
+<li class="nav-item"><form class="form-inline" role="search">
+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json">
+</form></li>
 <li class="nav-item"><a class="external-link nav-link" href="https://github.com/insightsengineering/tern" aria-label="GitHub"><span class="fa fa-github"></span></a></li>
-      </ul></div>
+      </ul>
+</div>
 
 
   </div>
@@ -69,7 +132,8 @@
     </div>
 
     <div class="section level2">
-    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
+    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">count_patients_with_event</span><span class="op">(</span></span>
 <span>  <span class="va">lyt</span>,</span>
 <span>  <span class="va">vars</span>,</span>
@@ -112,18 +176,23 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
     </div>
 
     <div class="section level2">
-    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
+    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a>
+</h2>
 
 
-<dl><dt id="arg-lyt">lyt<a class="anchor" aria-label="anchor" href="#arg-lyt"></a></dt>
+<dl>
+<dt id="arg-lyt">lyt<a class="anchor" aria-label="anchor" href="#arg-lyt"></a>
+</dt>
 <dd><p>(<code>PreDataTableLayouts</code>)<br> layout that analyses will be added to.</p></dd>
 
 
-<dt id="arg-vars">vars<a class="anchor" aria-label="anchor" href="#arg-vars"></a></dt>
+<dt id="arg-vars">vars<a class="anchor" aria-label="anchor" href="#arg-vars"></a>
+</dt>
 <dd><p>(<code>character</code>)<br> variable names for the primary analysis variable to be iterated over.</p></dd>
 
 
-<dt id="arg-filters">filters<a class="anchor" aria-label="anchor" href="#arg-filters"></a></dt>
+<dt id="arg-filters">filters<a class="anchor" aria-label="anchor" href="#arg-filters"></a>
+</dt>
 <dd><p>(<code>character</code>)<br> a character vector specifying the column names and flag variables
 to be used for counting the number of unique identifiers satisfying such conditions.
 Multiple column names and flags are accepted in this format
@@ -131,111 +200,146 @@ <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#argumen
 Note that only equality is being accepted as condition.</p></dd>
 
 
-<dt id="arg-riskdiff">riskdiff<a class="anchor" aria-label="anchor" href="#arg-riskdiff"></a></dt>
+<dt id="arg-riskdiff">riskdiff<a class="anchor" aria-label="anchor" href="#arg-riskdiff"></a>
+</dt>
 <dd><p>(<code>flag</code>)<br> whether a risk difference column is present. When set to <code>TRUE</code>, <code><a href="add_riskdiff.html">add_riskdiff()</a></code> must be
 used as <code>split_fun</code> in the prior column split of the table layout, specifying which columns should be compared.
 See <code><a href="stat_propdiff_ci.html">stat_propdiff_ci()</a></code> for details on risk difference calculation.</p></dd>
 
 
-<dt id="arg-na-str">na_str<a class="anchor" aria-label="anchor" href="#arg-na-str"></a></dt>
+<dt id="arg-na-str">na_str<a class="anchor" aria-label="anchor" href="#arg-na-str"></a>
+</dt>
 <dd><p>(<code>string</code>)<br> string used to replace all <code>NA</code> or empty values in the output.</p></dd>
 
 
-<dt id="arg-nested">nested<a class="anchor" aria-label="anchor" href="#arg-nested"></a></dt>
+<dt id="arg-nested">nested<a class="anchor" aria-label="anchor" href="#arg-nested"></a>
+</dt>
 <dd><p>(<code>flag</code>)<br> whether this layout instruction should be applied within the existing layout structure _if
 possible (<code>TRUE</code>, the default) or as a new top-level element (<code>FALSE</code>). Ignored if it would nest a split.
 underneath analyses, which is not allowed.</p></dd>
 
 
-<dt id="arg--">...<a class="anchor" aria-label="anchor" href="#arg--"></a></dt>
+<dt id="arg--">...<a class="anchor" aria-label="anchor" href="#arg--"></a>
+</dt>
 <dd><p>additional arguments for the lower level functions.</p></dd>
 
 
-<dt id="arg-table-names">table_names<a class="anchor" aria-label="anchor" href="#arg-table-names"></a></dt>
+<dt id="arg-table-names">table_names<a class="anchor" aria-label="anchor" href="#arg-table-names"></a>
+</dt>
 <dd><p>(<code>character</code>)<br> this can be customized in the case that the same <code>vars</code> are analyzed multiple
 times, to avoid warnings from <code>rtables</code>.</p></dd>
 
 
-<dt id="arg--stats">.stats<a class="anchor" aria-label="anchor" href="#arg--stats"></a></dt>
-<dd><p>(<code>character</code>)<br> statistics to select for the table.</p>
-<p>Options are: <code>'n', 'count', 'count_fraction', 'count_fraction_fixed_dp', 'n_blq'</code></p></dd>
+<dt id="arg--stats">.stats<a class="anchor" aria-label="anchor" href="#arg--stats"></a>
+</dt>
+<dd>
+<p>(<code>character</code>)<br> statistics to select for the table.</p>
+<p>Options are: <code>'n', 'count', 'count_fraction', 'count_fraction_fixed_dp', 'n_blq'</code></p>
+</dd>
 
 
-<dt id="arg--formats">.formats<a class="anchor" aria-label="anchor" href="#arg--formats"></a></dt>
+<dt id="arg--formats">.formats<a class="anchor" aria-label="anchor" href="#arg--formats"></a>
+</dt>
 <dd><p>(named <code>character</code> or <code>list</code>)<br> formats for the statistics. See Details in <code>analyze_vars</code> for more
 information on the <code>"auto"</code> setting.</p></dd>
 
 
-<dt id="arg--labels">.labels<a class="anchor" aria-label="anchor" href="#arg--labels"></a></dt>
+<dt id="arg--labels">.labels<a class="anchor" aria-label="anchor" href="#arg--labels"></a>
+</dt>
 <dd><p>(named <code>character</code>)<br> labels for the statistics (without indent).</p></dd>
 
 
-<dt id="arg--indent-mods">.indent_mods<a class="anchor" aria-label="anchor" href="#arg--indent-mods"></a></dt>
+<dt id="arg--indent-mods">.indent_mods<a class="anchor" aria-label="anchor" href="#arg--indent-mods"></a>
+</dt>
 <dd><p>(named <code>integer</code>)<br> indent modifiers for the labels. Defaults to 0, which corresponds to the
 unmodified default behavior. Can be negative.</p></dd>
 
 
-<dt id="arg-df">df<a class="anchor" aria-label="anchor" href="#arg-df"></a></dt>
+<dt id="arg-df">df<a class="anchor" aria-label="anchor" href="#arg-df"></a>
+</dt>
 <dd><p>(<code>data.frame</code>)<br> data set containing all analysis variables.</p></dd>
 
 
-<dt id="arg--var">.var<a class="anchor" aria-label="anchor" href="#arg--var"></a></dt>
+<dt id="arg--var">.var<a class="anchor" aria-label="anchor" href="#arg--var"></a>
+</dt>
 <dd><p>(<code>string</code>)<br> name of the column that contains the unique identifier.</p></dd>
 
 
-<dt id="arg--n-col">.N_col<a class="anchor" aria-label="anchor" href="#arg--n-col"></a></dt>
+<dt id="arg--n-col">.N_col<a class="anchor" aria-label="anchor" href="#arg--n-col"></a>
+</dt>
 <dd><p>(<code>integer(1)</code>)<br> column-wise N (column count) for the full column being analyzed that is typically
 passed by <code>rtables</code>.</p></dd>
 
 
-<dt id="arg--n-row">.N_row<a class="anchor" aria-label="anchor" href="#arg--n-row"></a></dt>
+<dt id="arg--n-row">.N_row<a class="anchor" aria-label="anchor" href="#arg--n-row"></a>
+</dt>
 <dd><p>(<code>integer(1)</code>)<br> row-wise N (row group count) for the group of observations being analyzed
 (i.e. with no column-based subsetting) that is typically passed by <code>rtables</code>.</p></dd>
 
 
-<dt id="arg-denom">denom<a class="anchor" aria-label="anchor" href="#arg-denom"></a></dt>
-<dd><p>(<code>string</code>)<br> choice of denominator for proportion. Options are:</p><ul><li><p><code>n</code>: number of values in this row and column intersection.</p></li>
+<dt id="arg-denom">denom<a class="anchor" aria-label="anchor" href="#arg-denom"></a>
+</dt>
+<dd>
+<p>(<code>string</code>)<br> choice of denominator for proportion. Options are:</p>
+<ul>
+<li><p><code>n</code>: number of values in this row and column intersection.</p></li>
 <li><p><code>N_row</code>: total number of values in this row across columns.</p></li>
 <li><p><code>N_col</code>: total number of values in this column across rows.</p></li>
-</ul></dd>
+</ul>
+</dd>
 
 
-<dt id="arg-labelstr">labelstr<a class="anchor" aria-label="anchor" href="#arg-labelstr"></a></dt>
+<dt id="arg-labelstr">labelstr<a class="anchor" aria-label="anchor" href="#arg-labelstr"></a>
+</dt>
 <dd><p>(<code>string</code>)<br> label of the level of the parent split currently being summarized
 (must be present as second argument in Content Row Functions). See <code><a href="https://insightsengineering.github.io/rtables/latest-tag/reference/summarize_row_groups.html" class="external-link">rtables::summarize_row_groups()</a></code>
 for more information.</p></dd>
 
 
-<dt id="arg--df-row">.df_row<a class="anchor" aria-label="anchor" href="#arg--df-row"></a></dt>
+<dt id="arg--df-row">.df_row<a class="anchor" aria-label="anchor" href="#arg--df-row"></a>
+</dt>
 <dd><p>(<code>data.frame</code>)<br> data frame across all of the columns for the given row split.</p></dd>
 
-</dl></div>
+</dl>
+</div>
     <div class="section level2">
-    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
+    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a>
+</h2>
 
-<ul><li><p><code>count_patients_with_event()</code> returns a layout object suitable for passing to further layouting functions,
+<ul>
+<li><p><code>count_patients_with_event()</code> returns a layout object suitable for passing to further layouting functions,
 or to <code><a href="https://insightsengineering.github.io/rtables/latest-tag/reference/build_table.html" class="external-link">rtables::build_table()</a></code>. Adding this function to an <code>rtable</code> layout will add formatted rows containing
 the statistics from <code>s_count_patients_with_event()</code> to the table layout.</p></li>
-</ul><ul><li><p><code>s_count_patients_with_event()</code> returns the count and fraction of unique identifiers with the defined event.</p></li>
-</ul><ul><li><p><code>a_count_patients_with_event()</code> returns the corresponding list with formatted <code><a href="https://insightsengineering.github.io/rtables/latest-tag/reference/CellValue.html" class="external-link">rtables::CellValue()</a></code>.</p></li>
-</ul></div>
+</ul>
+<ul>
+<li><p><code>s_count_patients_with_event()</code> returns the count and fraction of unique identifiers with the defined event.</p></li>
+</ul>
+<ul>
+<li><p><code>a_count_patients_with_event()</code> returns the corresponding list with formatted <code><a href="https://insightsengineering.github.io/rtables/latest-tag/reference/CellValue.html" class="external-link">rtables::CellValue()</a></code>.</p></li>
+</ul>
+</div>
     <div class="section level2">
-    <h2 id="functions">Functions<a class="anchor" aria-label="anchor" href="#functions"></a></h2>
+    <h2 id="functions">Functions<a class="anchor" aria-label="anchor" href="#functions"></a>
+</h2>
 
-<ul><li><p><code>count_patients_with_event()</code>: Layout-creating function which can take statistics function
+<ul>
+<li><p><code>count_patients_with_event()</code>: Layout-creating function which can take statistics function
 arguments and additional format arguments. This function is a wrapper for <code><a href="https://insightsengineering.github.io/rtables/latest-tag/reference/analyze.html" class="external-link">rtables::analyze()</a></code>.</p></li>
 <li><p><code>s_count_patients_with_event()</code>: Statistics function which counts the number of patients for which
 the defined event has occurred.</p></li>
 <li><p><code>a_count_patients_with_event()</code>: Formatted analysis function which is used as <code>afun</code>
 in <code>count_patients_with_event()</code>.</p></li>
-</ul></div>
+</ul>
+</div>
     <div class="section level2">
-    <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"></a></h2>
+    <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"></a>
+</h2>
     <div class="dont-index"><p><code><a href="count_patients_with_flags.html">count_patients_with_flags()</a></code></p></div>
     </div>
 
     <div class="section level2">
-    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
+    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">lyt</span> <span class="op">&lt;-</span> <span class="fu">basic_table</span><span class="op">(</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span></span>
 <span class="r-in"><span>  <span class="fu">split_cols_by</span><span class="op">(</span><span class="st">"ARM"</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span></span>
 <span class="r-in"><span>  <span class="fu">add_colcounts</span><span class="op">(</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span></span>
@@ -349,17 +453,19 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 </code></pre></div>
     </div>
   </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
-    </nav></aside></div>
+    </nav></aside>
+</div>
 
 
     <footer><div class="nest">
   <p>tern is a part of the <strong>NEST</strong> and <a href="https://pharmaverse.org/" class="external-link"><strong>pharmaverse</strong></a>.</p>
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-<script type="text/javascript" src="../analytics.js"></script></footer></div>
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+<script type="text/javascript" src="../analytics.js"></script></footer>
+</div>
 
 
 
 
-  </body></html>
 
+  </body>
+</html>
diff --git a/main/reference/count_patients_with_flags.html b/main/reference/count_patients_with_flags.html
index 23f99eca47..db459f1fcb 100644
--- a/main/reference/count_patients_with_flags.html
+++ b/main/reference/count_patients_with_flags.html
@@ -1,17 +1,40 @@
-<!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Count the number of patients with particular flags — count_patients_with_flags • tern</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Count the number of patients with particular flags — count_patients_with_flags"><meta name="description" content="
+<html lang="en">
+<head>
+<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+<meta charset="utf-8">
+<meta http-equiv="X-UA-Compatible" content="IE=edge">
+<meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<title>Count the number of patients with particular flags — count_patients_with_flags • tern</title>
+<!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png">
+<link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png">
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+<script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet">
+<script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet">
+<link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet">
+<script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Count the number of patients with particular flags — count_patients_with_flags">
+<meta name="description" content="
 The analyze function count_patients_with_flags() creates a layout element to calculate counts of patients for
 which user-specified flags are present.
 This function analyzes primary analysis variable var which indicates unique subject identifiers. Flags
 variables to analyze are specified by the user via the flag_variables argument, and must either take value
 TRUE (flag present) or FALSE (flag absent) for each record.
-If there are multiple records with the same flag present for a patient, only one occurrence is counted."><meta property="og:description" content="
+If there are multiple records with the same flag present for a patient, only one occurrence is counted.">
+<meta property="og:description" content="
 The analyze function count_patients_with_flags() creates a layout element to calculate counts of patients for
 which user-specified flags are present.
 This function analyzes primary analysis variable var which indicates unique subject identifiers. Flags
 variables to analyze are specified by the user via the flag_variables argument, and must either take value
 TRUE (flag present) or FALSE (flag absent) for each record.
-If there are multiple records with the same flag present for a patient, only one occurrence is counted."><meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png"><link rel="stylesheet" href="../consent.css"><script src="../consent.js" type="text/javascript" charset="utf-8"></script></head><body>
+If there are multiple records with the same flag present for a patient, only one occurrence is counted.">
+<meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png">
+<link rel="stylesheet" href="../consent.css">
+<script src="../consent.js" type="text/javascript" charset="utf-8"></script>
+</head>
+<body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
 
 
@@ -27,26 +50,66 @@
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+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
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+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
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+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a>
+</div>
+</li></div>
+</ul>
+<ul class="navbar-nav">
+<li class="nav-item"><form class="form-inline" role="search">
+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json">
+</form></li>
 <li class="nav-item"><a class="external-link nav-link" href="https://github.com/insightsengineering/tern" aria-label="GitHub"><span class="fa fa-github"></span></a></li>
-      </ul></div>
+      </ul>
+</div>
 
 
   </div>
@@ -69,7 +132,8 @@
     </div>
 
     <div class="section level2">
-    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
+    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">count_patients_with_flags</span><span class="op">(</span></span>
 <span>  <span class="va">lyt</span>,</span>
 <span>  <span class="va">var</span>,</span>
@@ -117,149 +181,193 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
     </div>
 
     <div class="section level2">
-    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
+    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a>
+</h2>
 
 
-<dl><dt id="arg-lyt">lyt<a class="anchor" aria-label="anchor" href="#arg-lyt"></a></dt>
+<dl>
+<dt id="arg-lyt">lyt<a class="anchor" aria-label="anchor" href="#arg-lyt"></a>
+</dt>
 <dd><p>(<code>PreDataTableLayouts</code>)<br> layout that analyses will be added to.</p></dd>
 
 
-<dt id="arg-var">var<a class="anchor" aria-label="anchor" href="#arg-var"></a></dt>
+<dt id="arg-var">var<a class="anchor" aria-label="anchor" href="#arg-var"></a>
+</dt>
 <dd><p>(<code>string</code>)<br> single variable name that is passed by <code>rtables</code> when requested
 by a statistics function.</p></dd>
 
 
-<dt id="arg-flag-variables">flag_variables<a class="anchor" aria-label="anchor" href="#arg-flag-variables"></a></dt>
+<dt id="arg-flag-variables">flag_variables<a class="anchor" aria-label="anchor" href="#arg-flag-variables"></a>
+</dt>
 <dd><p>(<code>character</code>)<br> a vector specifying the names of <code>logical</code> variables from analysis dataset
 used for counting the number of unique identifiers.</p></dd>
 
 
-<dt id="arg-flag-labels">flag_labels<a class="anchor" aria-label="anchor" href="#arg-flag-labels"></a></dt>
+<dt id="arg-flag-labels">flag_labels<a class="anchor" aria-label="anchor" href="#arg-flag-labels"></a>
+</dt>
 <dd><p>(<code>character</code>)<br> vector of labels to use for flag variables. If any labels are also specified via
 the <code>.labels</code> parameter, the <code>.labels</code> values will take precedence and replace these labels.</p></dd>
 
 
-<dt id="arg-var-labels">var_labels<a class="anchor" aria-label="anchor" href="#arg-var-labels"></a></dt>
+<dt id="arg-var-labels">var_labels<a class="anchor" aria-label="anchor" href="#arg-var-labels"></a>
+</dt>
 <dd><p>(<code>character</code>)<br> variable labels.</p></dd>
 
 
-<dt id="arg-show-labels">show_labels<a class="anchor" aria-label="anchor" href="#arg-show-labels"></a></dt>
+<dt id="arg-show-labels">show_labels<a class="anchor" aria-label="anchor" href="#arg-show-labels"></a>
+</dt>
 <dd><p>(<code>string</code>)<br> label visibility: one of "default", "visible" and "hidden".</p></dd>
 
 
-<dt id="arg-riskdiff">riskdiff<a class="anchor" aria-label="anchor" href="#arg-riskdiff"></a></dt>
+<dt id="arg-riskdiff">riskdiff<a class="anchor" aria-label="anchor" href="#arg-riskdiff"></a>
+</dt>
 <dd><p>(<code>flag</code>)<br> whether a risk difference column is present. When set to <code>TRUE</code>, <code><a href="add_riskdiff.html">add_riskdiff()</a></code> must be
 used as <code>split_fun</code> in the prior column split of the table layout, specifying which columns should be compared.
 See <code><a href="stat_propdiff_ci.html">stat_propdiff_ci()</a></code> for details on risk difference calculation.</p></dd>
 
 
-<dt id="arg-na-str">na_str<a class="anchor" aria-label="anchor" href="#arg-na-str"></a></dt>
+<dt id="arg-na-str">na_str<a class="anchor" aria-label="anchor" href="#arg-na-str"></a>
+</dt>
 <dd><p>(<code>string</code>)<br> string used to replace all <code>NA</code> or empty values in the output.</p></dd>
 
 
-<dt id="arg-nested">nested<a class="anchor" aria-label="anchor" href="#arg-nested"></a></dt>
+<dt id="arg-nested">nested<a class="anchor" aria-label="anchor" href="#arg-nested"></a>
+</dt>
 <dd><p>(<code>flag</code>)<br> whether this layout instruction should be applied within the existing layout structure _if
 possible (<code>TRUE</code>, the default) or as a new top-level element (<code>FALSE</code>). Ignored if it would nest a split.
 underneath analyses, which is not allowed.</p></dd>
 
 
-<dt id="arg--">...<a class="anchor" aria-label="anchor" href="#arg--"></a></dt>
+<dt id="arg--">...<a class="anchor" aria-label="anchor" href="#arg--"></a>
+</dt>
 <dd><p>additional arguments for the lower level functions.</p></dd>
 
 
-<dt id="arg-table-names">table_names<a class="anchor" aria-label="anchor" href="#arg-table-names"></a></dt>
+<dt id="arg-table-names">table_names<a class="anchor" aria-label="anchor" href="#arg-table-names"></a>
+</dt>
 <dd><p>(<code>character</code>)<br> this can be customized in the case that the same <code>vars</code> are analyzed multiple
 times, to avoid warnings from <code>rtables</code>.</p></dd>
 
 
-<dt id="arg--stats">.stats<a class="anchor" aria-label="anchor" href="#arg--stats"></a></dt>
-<dd><p>(<code>character</code>)<br> statistics to select for the table.</p>
-<p>Options are: <code>'n', 'count', 'count_fraction', 'count_fraction_fixed_dp', 'n_blq'</code></p></dd>
+<dt id="arg--stats">.stats<a class="anchor" aria-label="anchor" href="#arg--stats"></a>
+</dt>
+<dd>
+<p>(<code>character</code>)<br> statistics to select for the table.</p>
+<p>Options are: <code>'n', 'count', 'count_fraction', 'count_fraction_fixed_dp', 'n_blq'</code></p>
+</dd>
 
 
-<dt id="arg--formats">.formats<a class="anchor" aria-label="anchor" href="#arg--formats"></a></dt>
+<dt id="arg--formats">.formats<a class="anchor" aria-label="anchor" href="#arg--formats"></a>
+</dt>
 <dd><p>(named <code>character</code> or <code>list</code>)<br> formats for the statistics. See Details in <code>analyze_vars</code> for more
 information on the <code>"auto"</code> setting.</p></dd>
 
 
-<dt id="arg--indent-mods">.indent_mods<a class="anchor" aria-label="anchor" href="#arg--indent-mods"></a></dt>
+<dt id="arg--indent-mods">.indent_mods<a class="anchor" aria-label="anchor" href="#arg--indent-mods"></a>
+</dt>
 <dd><p>(named <code>integer</code>)<br> indent modifiers for the labels. Defaults to 0, which corresponds to the
 unmodified default behavior. Can be negative.</p></dd>
 
 
-<dt id="arg--labels">.labels<a class="anchor" aria-label="anchor" href="#arg--labels"></a></dt>
+<dt id="arg--labels">.labels<a class="anchor" aria-label="anchor" href="#arg--labels"></a>
+</dt>
 <dd><p>(named <code>character</code>)<br> labels for the statistics (without indent).</p></dd>
 
 
-<dt id="arg-df">df<a class="anchor" aria-label="anchor" href="#arg-df"></a></dt>
+<dt id="arg-df">df<a class="anchor" aria-label="anchor" href="#arg-df"></a>
+</dt>
 <dd><p>(<code>data.frame</code>)<br> data set containing all analysis variables.</p></dd>
 
 
-<dt id="arg--var">.var<a class="anchor" aria-label="anchor" href="#arg--var"></a></dt>
+<dt id="arg--var">.var<a class="anchor" aria-label="anchor" href="#arg--var"></a>
+</dt>
 <dd><p>(<code>string</code>)<br> name of the column that contains the unique identifier.</p></dd>
 
 
-<dt id="arg--n-col">.N_col<a class="anchor" aria-label="anchor" href="#arg--n-col"></a></dt>
+<dt id="arg--n-col">.N_col<a class="anchor" aria-label="anchor" href="#arg--n-col"></a>
+</dt>
 <dd><p>(<code>integer(1)</code>)<br> column-wise N (column count) for the full column being analyzed that is typically
 passed by <code>rtables</code>.</p></dd>
 
 
-<dt id="arg--n-row">.N_row<a class="anchor" aria-label="anchor" href="#arg--n-row"></a></dt>
+<dt id="arg--n-row">.N_row<a class="anchor" aria-label="anchor" href="#arg--n-row"></a>
+</dt>
 <dd><p>(<code>integer(1)</code>)<br> row-wise N (row group count) for the group of observations being analyzed
 (i.e. with no column-based subsetting) that is typically passed by <code>rtables</code>.</p></dd>
 
 
-<dt id="arg-denom">denom<a class="anchor" aria-label="anchor" href="#arg-denom"></a></dt>
-<dd><p>(<code>string</code>)<br> choice of denominator for proportion. Options are:</p><ul><li><p><code>n</code>: number of values in this row and column intersection.</p></li>
+<dt id="arg-denom">denom<a class="anchor" aria-label="anchor" href="#arg-denom"></a>
+</dt>
+<dd>
+<p>(<code>string</code>)<br> choice of denominator for proportion. Options are:</p>
+<ul>
+<li><p><code>n</code>: number of values in this row and column intersection.</p></li>
 <li><p><code>N_row</code>: total number of values in this row across columns.</p></li>
 <li><p><code>N_col</code>: total number of values in this column across rows.</p></li>
-</ul></dd>
+</ul>
+</dd>
 
 
-<dt id="arg-labelstr">labelstr<a class="anchor" aria-label="anchor" href="#arg-labelstr"></a></dt>
+<dt id="arg-labelstr">labelstr<a class="anchor" aria-label="anchor" href="#arg-labelstr"></a>
+</dt>
 <dd><p>(<code>string</code>)<br> label of the level of the parent split currently being summarized
 (must be present as second argument in Content Row Functions). See <code><a href="https://insightsengineering.github.io/rtables/latest-tag/reference/summarize_row_groups.html" class="external-link">rtables::summarize_row_groups()</a></code>
 for more information.</p></dd>
 
 
-<dt id="arg--df-row">.df_row<a class="anchor" aria-label="anchor" href="#arg--df-row"></a></dt>
+<dt id="arg--df-row">.df_row<a class="anchor" aria-label="anchor" href="#arg--df-row"></a>
+</dt>
 <dd><p>(<code>data.frame</code>)<br> data frame across all of the columns for the given row split.</p></dd>
 
-</dl></div>
+</dl>
+</div>
     <div class="section level2">
-    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
+    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a>
+</h2>
 
-<ul><li><p><code>count_patients_with_flags()</code> returns a layout object suitable for passing to further layouting functions,
+<ul>
+<li><p><code>count_patients_with_flags()</code> returns a layout object suitable for passing to further layouting functions,
 or to <code><a href="https://insightsengineering.github.io/rtables/latest-tag/reference/build_table.html" class="external-link">rtables::build_table()</a></code>. Adding this function to an <code>rtable</code> layout will add formatted rows containing
 the statistics from <code>s_count_patients_with_flags()</code> to the table layout.</p></li>
-</ul><ul><li><p><code>s_count_patients_with_flags()</code> returns the count and the fraction of unique identifiers with each particular
+</ul>
+<ul>
+<li><p><code>s_count_patients_with_flags()</code> returns the count and the fraction of unique identifiers with each particular
 flag as a list of statistics <code>n</code>, <code>count</code>, <code>count_fraction</code>, and <code>n_blq</code>, with one element per flag.</p></li>
-</ul><ul><li><p><code>a_count_patients_with_flags()</code> returns the corresponding list with formatted <code><a href="https://insightsengineering.github.io/rtables/latest-tag/reference/CellValue.html" class="external-link">rtables::CellValue()</a></code>.</p></li>
-</ul></div>
+</ul>
+<ul>
+<li><p><code>a_count_patients_with_flags()</code> returns the corresponding list with formatted <code><a href="https://insightsengineering.github.io/rtables/latest-tag/reference/CellValue.html" class="external-link">rtables::CellValue()</a></code>.</p></li>
+</ul>
+</div>
     <div class="section level2">
-    <h2 id="functions">Functions<a class="anchor" aria-label="anchor" href="#functions"></a></h2>
+    <h2 id="functions">Functions<a class="anchor" aria-label="anchor" href="#functions"></a>
+</h2>
 
-<ul><li><p><code>count_patients_with_flags()</code>: Layout-creating function which can take statistics function
+<ul>
+<li><p><code>count_patients_with_flags()</code>: Layout-creating function which can take statistics function
 arguments and additional format arguments. This function is a wrapper for <code><a href="https://insightsengineering.github.io/rtables/latest-tag/reference/analyze.html" class="external-link">rtables::analyze()</a></code>.</p></li>
 <li><p><code>s_count_patients_with_flags()</code>: Statistics function which counts the number of patients for which
 a particular flag variable is <code>TRUE</code>.</p></li>
 <li><p><code>a_count_patients_with_flags()</code>: Formatted analysis function which is used as <code>afun</code>
 in <code>count_patients_with_flags()</code>.</p></li>
-</ul></div>
+</ul>
+</div>
     <div class="section level2">
-    <h2 id="note">Note<a class="anchor" aria-label="anchor" href="#note"></a></h2>
+    <h2 id="note">Note<a class="anchor" aria-label="anchor" href="#note"></a>
+</h2>
     <p>If <code>flag_labels</code> is not specified, variables labels will be extracted from <code>df</code>. If variables are not
 labeled, variable names will be used instead. Alternatively, a named <code>vector</code> can be supplied to
 <code>flag_variables</code> such that within each name-value pair the name corresponds to the variable name and the value is
 the label to use for this variable.</p>
     </div>
     <div class="section level2">
-    <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"></a></h2>
+    <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"></a>
+</h2>
     <div class="dont-index"><p><a href="count_patients_with_event.html">count_patients_with_event</a></p></div>
     </div>
 
     <div class="section level2">
-    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
+    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="co"># Add labelled flag variables to analysis dataset.</span></span></span>
 <span class="r-in"><span><span class="va">adae</span> <span class="op">&lt;-</span> <span class="va">tern_ex_adae</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span></span>
 <span class="r-in"><span>  <span class="fu">dplyr</span><span class="fu">::</span><span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate.html" class="external-link">mutate</a></span><span class="op">(</span></span></span>
@@ -411,17 +519,19 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 </code></pre></div>
     </div>
   </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
-    </nav></aside></div>
+    </nav></aside>
+</div>
 
 
     <footer><div class="nest">
   <p>tern is a part of the <strong>NEST</strong> and <a href="https://pharmaverse.org/" class="external-link"><strong>pharmaverse</strong></a>.</p>
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-<script type="text/javascript" src="../analytics.js"></script></footer></div>
-
+<script type="text/javascript" src="../analytics.js"></script></footer>
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+  </body>
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diff --git a/main/reference/count_values.html b/main/reference/count_values.html
index cfa5eb8f0a..42fab70e17 100644
--- a/main/reference/count_values.html
+++ b/main/reference/count_values.html
@@ -1,15 +1,38 @@
-<!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Count specific values — count_values • tern</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Count specific values — count_values"><meta name="description" content="
+<html lang="en">
+<head>
+<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+<meta charset="utf-8">
+<meta http-equiv="X-UA-Compatible" content="IE=edge">
+<meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<title>Count specific values — count_values • tern</title>
+<!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png">
+<link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png">
+<link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png">
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+<link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png">
+<script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet">
+<script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet">
+<link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet">
+<script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Count specific values — count_values">
+<meta name="description" content="
 The analyze function count_values() creates a layout element to calculate counts of specific values within a
 variable of interest.
 This function analyzes one or more variables of interest supplied as a vector to vars. Values to
 count for variable(s) in vars can be given as a vector via the values argument. One row of
-counts will be generated for each variable."><meta property="og:description" content="
+counts will be generated for each variable.">
+<meta property="og:description" content="
 The analyze function count_values() creates a layout element to calculate counts of specific values within a
 variable of interest.
 This function analyzes one or more variables of interest supplied as a vector to vars. Values to
 count for variable(s) in vars can be given as a vector via the values argument. One row of
-counts will be generated for each variable."><meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png"><link rel="stylesheet" href="../consent.css"><script src="../consent.js" type="text/javascript" charset="utf-8"></script></head><body>
+counts will be generated for each variable.">
+<meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png">
+<link rel="stylesheet" href="../consent.css">
+<script src="../consent.js" type="text/javascript" charset="utf-8"></script>
+</head>
+<body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
 
 
@@ -25,26 +48,66 @@
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-  <ul class="dropdown-menu" aria-labelledby="dropdown-articles"><li><a class="dropdown-item" href="../articles/missing_values.html">Missing Values in Tern</a></li>
+  <ul class="dropdown-menu" aria-labelledby="dropdown-articles">
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+  </ul>
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+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
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+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a>
+</div>
+</li></div>
+</ul>
+<ul class="navbar-nav">
+<li class="nav-item"><form class="form-inline" role="search">
+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json">
+</form></li>
 <li class="nav-item"><a class="external-link nav-link" href="https://github.com/insightsengineering/tern" aria-label="GitHub"><span class="fa fa-github"></span></a></li>
-      </ul></div>
+      </ul>
+</div>
 
 
   </div>
@@ -66,7 +129,8 @@
     </div>
 
     <div class="section level2">
-    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
+    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">count_values</span><span class="op">(</span></span>
 <span>  <span class="va">lyt</span>,</span>
 <span>  <span class="va">vars</span>,</span>
@@ -110,97 +174,131 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
     </div>
 
     <div class="section level2">
-    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
+    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a>
+</h2>
 
 
-<dl><dt id="arg-lyt">lyt<a class="anchor" aria-label="anchor" href="#arg-lyt"></a></dt>
+<dl>
+<dt id="arg-lyt">lyt<a class="anchor" aria-label="anchor" href="#arg-lyt"></a>
+</dt>
 <dd><p>(<code>PreDataTableLayouts</code>)<br> layout that analyses will be added to.</p></dd>
 
 
-<dt id="arg-vars">vars<a class="anchor" aria-label="anchor" href="#arg-vars"></a></dt>
+<dt id="arg-vars">vars<a class="anchor" aria-label="anchor" href="#arg-vars"></a>
+</dt>
 <dd><p>(<code>character</code>)<br> variable names for the primary analysis variable to be iterated over.</p></dd>
 
 
-<dt id="arg-values">values<a class="anchor" aria-label="anchor" href="#arg-values"></a></dt>
+<dt id="arg-values">values<a class="anchor" aria-label="anchor" href="#arg-values"></a>
+</dt>
 <dd><p>(<code>character</code>)<br> specific values that should be counted.</p></dd>
 
 
-<dt id="arg-na-str">na_str<a class="anchor" aria-label="anchor" href="#arg-na-str"></a></dt>
+<dt id="arg-na-str">na_str<a class="anchor" aria-label="anchor" href="#arg-na-str"></a>
+</dt>
 <dd><p>(<code>string</code>)<br> string used to replace all <code>NA</code> or empty values in the output.</p></dd>
 
 
-<dt id="arg-nested">nested<a class="anchor" aria-label="anchor" href="#arg-nested"></a></dt>
+<dt id="arg-nested">nested<a class="anchor" aria-label="anchor" href="#arg-nested"></a>
+</dt>
 <dd><p>(<code>flag</code>)<br> whether this layout instruction should be applied within the existing layout structure _if
 possible (<code>TRUE</code>, the default) or as a new top-level element (<code>FALSE</code>). Ignored if it would nest a split.
 underneath analyses, which is not allowed.</p></dd>
 
 
-<dt id="arg--">...<a class="anchor" aria-label="anchor" href="#arg--"></a></dt>
+<dt id="arg--">...<a class="anchor" aria-label="anchor" href="#arg--"></a>
+</dt>
 <dd><p>additional arguments for the lower level functions.</p></dd>
 
 
-<dt id="arg-table-names">table_names<a class="anchor" aria-label="anchor" href="#arg-table-names"></a></dt>
+<dt id="arg-table-names">table_names<a class="anchor" aria-label="anchor" href="#arg-table-names"></a>
+</dt>
 <dd><p>(<code>character</code>)<br> this can be customized in the case that the same <code>vars</code> are analyzed multiple
 times, to avoid warnings from <code>rtables</code>.</p></dd>
 
 
-<dt id="arg--stats">.stats<a class="anchor" aria-label="anchor" href="#arg--stats"></a></dt>
-<dd><p>(<code>character</code>)<br> statistics to select for the table.</p>
-<p>Options are: <code>'n', 'count', 'count_fraction', 'count_fraction_fixed_dp', 'n_blq'</code></p></dd>
+<dt id="arg--stats">.stats<a class="anchor" aria-label="anchor" href="#arg--stats"></a>
+</dt>
+<dd>
+<p>(<code>character</code>)<br> statistics to select for the table.</p>
+<p>Options are: <code>'n', 'count', 'count_fraction', 'count_fraction_fixed_dp', 'n_blq'</code></p>
+</dd>
 
 
-<dt id="arg--formats">.formats<a class="anchor" aria-label="anchor" href="#arg--formats"></a></dt>
+<dt id="arg--formats">.formats<a class="anchor" aria-label="anchor" href="#arg--formats"></a>
+</dt>
 <dd><p>(named <code>character</code> or <code>list</code>)<br> formats for the statistics. See Details in <code>analyze_vars</code> for more
 information on the <code>"auto"</code> setting.</p></dd>
 
 
-<dt id="arg--labels">.labels<a class="anchor" aria-label="anchor" href="#arg--labels"></a></dt>
+<dt id="arg--labels">.labels<a class="anchor" aria-label="anchor" href="#arg--labels"></a>
+</dt>
 <dd><p>(named <code>character</code>)<br> labels for the statistics (without indent).</p></dd>
 
 
-<dt id="arg--indent-mods">.indent_mods<a class="anchor" aria-label="anchor" href="#arg--indent-mods"></a></dt>
+<dt id="arg--indent-mods">.indent_mods<a class="anchor" aria-label="anchor" href="#arg--indent-mods"></a>
+</dt>
 <dd><p>(named <code>integer</code>)<br> indent modifiers for the labels. Defaults to 0, which corresponds to the
 unmodified default behavior. Can be negative.</p></dd>
 
 
-<dt id="arg-x">x<a class="anchor" aria-label="anchor" href="#arg-x"></a></dt>
+<dt id="arg-x">x<a class="anchor" aria-label="anchor" href="#arg-x"></a>
+</dt>
 <dd><p>(<code>numeric</code>)<br> vector of numbers we want to analyze.</p></dd>
 
 
-<dt id="arg-na-rm">na.rm<a class="anchor" aria-label="anchor" href="#arg-na-rm"></a></dt>
+<dt id="arg-na-rm">na.rm<a class="anchor" aria-label="anchor" href="#arg-na-rm"></a>
+</dt>
 <dd><p>(<code>flag</code>)<br> whether <code>NA</code> values should be removed from <code>x</code> prior to analysis.</p></dd>
 
 
-<dt id="arg--n-col">.N_col<a class="anchor" aria-label="anchor" href="#arg--n-col"></a></dt>
+<dt id="arg--n-col">.N_col<a class="anchor" aria-label="anchor" href="#arg--n-col"></a>
+</dt>
 <dd><p>(<code>integer(1)</code>)<br> column-wise N (column count) for the full column being analyzed that is typically
 passed by <code>rtables</code>.</p></dd>
 
 
-<dt id="arg--n-row">.N_row<a class="anchor" aria-label="anchor" href="#arg--n-row"></a></dt>
+<dt id="arg--n-row">.N_row<a class="anchor" aria-label="anchor" href="#arg--n-row"></a>
+</dt>
 <dd><p>(<code>integer(1)</code>)<br> row-wise N (row group count) for the group of observations being analyzed
 (i.e. with no column-based subsetting) that is typically passed by <code>rtables</code>.</p></dd>
 
 
-<dt id="arg-denom">denom<a class="anchor" aria-label="anchor" href="#arg-denom"></a></dt>
-<dd><p>(<code>string</code>)<br> choice of denominator for proportion. Options are:</p><ul><li><p><code>n</code>: number of values in this row and column intersection.</p></li>
+<dt id="arg-denom">denom<a class="anchor" aria-label="anchor" href="#arg-denom"></a>
+</dt>
+<dd>
+<p>(<code>string</code>)<br> choice of denominator for proportion. Options are:</p>
+<ul>
+<li><p><code>n</code>: number of values in this row and column intersection.</p></li>
 <li><p><code>N_row</code>: total number of values in this row across columns.</p></li>
 <li><p><code>N_col</code>: total number of values in this column across rows.</p></li>
-</ul></dd>
+</ul>
+</dd>
 
-</dl></div>
+</dl>
+</div>
     <div class="section level2">
-    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
+    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a>
+</h2>
 
-<ul><li><p><code>count_values()</code> returns a layout object suitable for passing to further layouting functions,
+<ul>
+<li><p><code>count_values()</code> returns a layout object suitable for passing to further layouting functions,
 or to <code><a href="https://insightsengineering.github.io/rtables/latest-tag/reference/build_table.html" class="external-link">rtables::build_table()</a></code>. Adding this function to an <code>rtable</code> layout will add formatted rows containing
 the statistics from <code>s_count_values()</code> to the table layout.</p></li>
-</ul><ul><li><p><code>s_count_values()</code> returns output of <code><a href="analyze_variables.html">s_summary()</a></code> for specified values of a non-numeric variable.</p></li>
-</ul><ul><li><p><code>a_count_values()</code> returns the corresponding list with formatted <code><a href="https://insightsengineering.github.io/rtables/latest-tag/reference/CellValue.html" class="external-link">rtables::CellValue()</a></code>.</p></li>
-</ul></div>
+</ul>
+<ul>
+<li><p><code>s_count_values()</code> returns output of <code><a href="analyze_variables.html">s_summary()</a></code> for specified values of a non-numeric variable.</p></li>
+</ul>
+<ul>
+<li><p><code>a_count_values()</code> returns the corresponding list with formatted <code><a href="https://insightsengineering.github.io/rtables/latest-tag/reference/CellValue.html" class="external-link">rtables::CellValue()</a></code>.</p></li>
+</ul>
+</div>
     <div class="section level2">
-    <h2 id="functions">Functions<a class="anchor" aria-label="anchor" href="#functions"></a></h2>
+    <h2 id="functions">Functions<a class="anchor" aria-label="anchor" href="#functions"></a>
+</h2>
 
-<ul><li><p><code>count_values()</code>: Layout-creating function which can take statistics function arguments
+<ul>
+<li><p><code>count_values()</code>: Layout-creating function which can take statistics function arguments
 and additional format arguments. This function is a wrapper for <code><a href="https://insightsengineering.github.io/rtables/latest-tag/reference/analyze.html" class="external-link">rtables::analyze()</a></code>.</p></li>
 <li><p><code>s_count_values()</code>: S3 generic function to count values.</p></li>
 <li><p><code>s_count_values(character)</code>: Method for <code>character</code> class.</p></li>
@@ -209,18 +307,23 @@ <h2 id="functions">Functions<a class="anchor" aria-label="anchor" href="#functio
 <li><p><code>s_count_values(logical)</code>: Method for <code>logical</code> class.</p></li>
 <li><p><code>a_count_values()</code>: Formatted analysis function which is used as <code>afun</code>
 in <code>count_values()</code>.</p></li>
-</ul></div>
+</ul>
+</div>
     <div class="section level2">
-    <h2 id="note">Note<a class="anchor" aria-label="anchor" href="#note"></a></h2>
+    <h2 id="note">Note<a class="anchor" aria-label="anchor" href="#note"></a>
+</h2>
 
-<ul><li><p>For <code>factor</code> variables, <code>s_count_values</code> checks whether <code>values</code> are all included in the levels of <code>x</code>
+<ul>
+<li><p>For <code>factor</code> variables, <code>s_count_values</code> checks whether <code>values</code> are all included in the levels of <code>x</code>
 and fails otherwise.</p></li>
 <li><p>For <code>count_values()</code>, variable labels are shown when there is more than one element in <code>vars</code>,
 otherwise they are hidden.</p></li>
-</ul></div>
+</ul>
+</div>
 
     <div class="section level2">
-    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
+    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="co"># `count_values`</span></span></span>
 <span class="r-in"><span><span class="fu">basic_table</span><span class="op">(</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span></span>
 <span class="r-in"><span>  <span class="fu">count_values</span><span class="op">(</span><span class="st">"Species"</span>, values <span class="op">=</span> <span class="st">"setosa"</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span></span>
@@ -300,17 +403,19 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 </code></pre></div>
     </div>
   </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
-    </nav></aside></div>
+    </nav></aside>
+</div>
 
 
     <footer><div class="nest">
   <p>tern is a part of the <strong>NEST</strong> and <a href="https://pharmaverse.org/" class="external-link"><strong>pharmaverse</strong></a>.</p>
 </div>
-<script type="text/javascript" src="../analytics.js"></script></footer></div>
-
+<script type="text/javascript" src="../analytics.js"></script></footer>
+</div>
 
 
 
 
-  </body></html>
 
+  </body>
+</html>
diff --git a/main/reference/cox_regression.html b/main/reference/cox_regression.html
index c3cc25f574..f096457c4b 100644
--- a/main/reference/cox_regression.html
+++ b/main/reference/cox_regression.html
@@ -1,7 +1,30 @@
-<!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Cox proportional hazards regression — cox_regression • tern</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Cox proportional hazards regression — cox_regression"><meta name="description" content="
-Fits a Cox regression model and estimates hazard ratio to describe the effect size in a survival analysis."><meta property="og:description" content="
-Fits a Cox regression model and estimates hazard ratio to describe the effect size in a survival analysis."><meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png"><link rel="stylesheet" href="../consent.css"><script src="../consent.js" type="text/javascript" charset="utf-8"></script></head><body>
+<html lang="en">
+<head>
+<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+<meta charset="utf-8">
+<meta http-equiv="X-UA-Compatible" content="IE=edge">
+<meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<title>Cox proportional hazards regression — cox_regression • tern</title>
+<!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png">
+<link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png">
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+<link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png">
+<link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png">
+<script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet">
+<script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet">
+<link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet">
+<script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Cox proportional hazards regression — cox_regression">
+<meta name="description" content="
+Fits a Cox regression model and estimates hazard ratio to describe the effect size in a survival analysis.">
+<meta property="og:description" content="
+Fits a Cox regression model and estimates hazard ratio to describe the effect size in a survival analysis.">
+<meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png">
+<link rel="stylesheet" href="../consent.css">
+<script src="../consent.js" type="text/javascript" charset="utf-8"></script>
+</head>
+<body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
 
 
@@ -17,26 +40,66 @@
     </button>
 
     <div id="navbar" class="collapse navbar-collapse ms-3">
-      <ul class="navbar-nav me-auto"><li class="nav-item"><a class="nav-link" href="../articles/tern.html">Get started</a></li>
+      <ul class="navbar-nav me-auto">
+<li class="nav-item"><a class="nav-link" href="../articles/tern.html">Get started</a></li>
 <li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
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-  <ul class="dropdown-menu" aria-labelledby="dropdown-articles"><li><a class="dropdown-item" href="../articles/missing_values.html">Missing Values in Tern</a></li>
+  <ul class="dropdown-menu" aria-labelledby="dropdown-articles">
+<li><a class="dropdown-item" href="../articles/missing_values.html">Missing Values in Tern</a></li>
     <li><a class="dropdown-item" href="../articles/tables.html">Tabulation</a></li>
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     <li><a class="dropdown-item" href="../articles/tern_functions_guide.html">Understanding `tern` functions</a></li>
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+  </ul>
+</li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
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+  <ul class="dropdown-menu" aria-labelledby="dropdown-reports">
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+  </ul>
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+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
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+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
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+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a>
+</div>
+</li></div>
+</ul>
+<ul class="navbar-nav">
+<li class="nav-item"><form class="form-inline" role="search">
+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json">
+</form></li>
 <li class="nav-item"><a class="external-link nav-link" href="https://github.com/insightsengineering/tern" aria-label="GitHub"><span class="fa fa-github"></span></a></li>
-      </ul></div>
+      </ul>
+</div>
 
 
   </div>
@@ -54,7 +117,8 @@
     </div>
 
     <div class="section level2">
-    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
+    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">summarize_coxreg</span><span class="op">(</span></span>
 <span>  <span class="va">lyt</span>,</span>
 <span>  <span class="va">variables</span>,</span>
@@ -92,130 +156,166 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
     </div>
 
     <div class="section level2">
-    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
+    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a>
+</h2>
 
 
-<dl><dt id="arg-lyt">lyt<a class="anchor" aria-label="anchor" href="#arg-lyt"></a></dt>
+<dl>
+<dt id="arg-lyt">lyt<a class="anchor" aria-label="anchor" href="#arg-lyt"></a>
+</dt>
 <dd><p>(<code>PreDataTableLayouts</code>)<br> layout that analyses will be added to.</p></dd>
 
 
-<dt id="arg-variables">variables<a class="anchor" aria-label="anchor" href="#arg-variables"></a></dt>
+<dt id="arg-variables">variables<a class="anchor" aria-label="anchor" href="#arg-variables"></a>
+</dt>
 <dd><p>(named <code>list</code> of <code>string</code>)<br> list of additional analysis variables.</p></dd>
 
 
-<dt id="arg-control">control<a class="anchor" aria-label="anchor" href="#arg-control"></a></dt>
+<dt id="arg-control">control<a class="anchor" aria-label="anchor" href="#arg-control"></a>
+</dt>
 <dd><p>(<code>list</code>)<br> a list of parameters as returned by the helper function <code><a href="control_coxreg.html">control_coxreg()</a></code>.</p></dd>
 
 
-<dt id="arg-at">at<a class="anchor" aria-label="anchor" href="#arg-at"></a></dt>
+<dt id="arg-at">at<a class="anchor" aria-label="anchor" href="#arg-at"></a>
+</dt>
 <dd><p>(<code>list</code> of <code>numeric</code>)<br> when the candidate covariate is a <code>numeric</code>, use <code>at</code> to specify
 the value of the covariate at which the effect should be estimated.</p></dd>
 
 
-<dt id="arg-multivar">multivar<a class="anchor" aria-label="anchor" href="#arg-multivar"></a></dt>
+<dt id="arg-multivar">multivar<a class="anchor" aria-label="anchor" href="#arg-multivar"></a>
+</dt>
 <dd><p>(<code>flag</code>)<br> whether multivariate Cox regression should run (defaults to <code>FALSE</code>), otherwise
 univariate Cox regression will run.</p></dd>
 
 
-<dt id="arg-common-var">common_var<a class="anchor" aria-label="anchor" href="#arg-common-var"></a></dt>
+<dt id="arg-common-var">common_var<a class="anchor" aria-label="anchor" href="#arg-common-var"></a>
+</dt>
 <dd><p>(<code>string</code>)<br> the name of a factor variable in the dataset which takes the same value
 for all rows. This should be created during pre-processing if no such variable currently exists.</p></dd>
 
 
-<dt id="arg--stats">.stats<a class="anchor" aria-label="anchor" href="#arg--stats"></a></dt>
-<dd><p>(<code>character</code>)<br> the names of statistics to be reported among:</p><ul><li><p><code>n</code>: number of observations (univariate only)</p></li>
+<dt id="arg--stats">.stats<a class="anchor" aria-label="anchor" href="#arg--stats"></a>
+</dt>
+<dd>
+<p>(<code>character</code>)<br> the names of statistics to be reported among:</p>
+<ul>
+<li><p><code>n</code>: number of observations (univariate only)</p></li>
 <li><p><code>hr</code>: hazard ratio</p></li>
 <li><p><code>ci</code>: confidence interval</p></li>
 <li><p><code>pval</code>: p-value of the treatment effect</p></li>
 <li><p><code>pval_inter</code>: p-value of the interaction effect between the treatment and the covariate (univariate only)</p></li>
-</ul></dd>
+</ul>
+</dd>
 
 
-<dt id="arg--formats">.formats<a class="anchor" aria-label="anchor" href="#arg--formats"></a></dt>
+<dt id="arg--formats">.formats<a class="anchor" aria-label="anchor" href="#arg--formats"></a>
+</dt>
 <dd><p>(named <code>character</code> or <code>list</code>)<br> formats for the statistics. See Details in <code>analyze_vars</code> for more
 information on the <code>"auto"</code> setting.</p></dd>
 
 
-<dt id="arg-varlabels">varlabels<a class="anchor" aria-label="anchor" href="#arg-varlabels"></a></dt>
+<dt id="arg-varlabels">varlabels<a class="anchor" aria-label="anchor" href="#arg-varlabels"></a>
+</dt>
 <dd><p>(<code>list</code>)<br> a named list corresponds to the names of variables found in data, passed
 as a named list and corresponding to time, event, arm, strata, and covariates terms. If arm is missing
 from variables, then only Cox model(s) including the covariates will be fitted and the corresponding
 effect estimates will be tabulated later.</p></dd>
 
 
-<dt id="arg--indent-mods">.indent_mods<a class="anchor" aria-label="anchor" href="#arg--indent-mods"></a></dt>
+<dt id="arg--indent-mods">.indent_mods<a class="anchor" aria-label="anchor" href="#arg--indent-mods"></a>
+</dt>
 <dd><p>(named <code>integer</code>)<br> indent modifiers for the labels. Defaults to 0, which corresponds to the
 unmodified default behavior. Can be negative.</p></dd>
 
 
-<dt id="arg-na-str">na_str<a class="anchor" aria-label="anchor" href="#arg-na-str"></a></dt>
+<dt id="arg-na-str">na_str<a class="anchor" aria-label="anchor" href="#arg-na-str"></a>
+</dt>
 <dd><p>(<code>string</code>)<br> custom string to replace all <code>NA</code> values with. Defaults to <code>""</code>.</p></dd>
 
 
-<dt id="arg--section-div">.section_div<a class="anchor" aria-label="anchor" href="#arg--section-div"></a></dt>
+<dt id="arg--section-div">.section_div<a class="anchor" aria-label="anchor" href="#arg--section-div"></a>
+</dt>
 <dd><p>(<code>string</code> or <code>NA</code>)<br> string which should be repeated as a section divider between sections.
 Defaults to <code>NA</code> for no section divider. If a vector of two strings are given, the first will be used between
 treatment and covariate sections and the second between different covariates.</p></dd>
 
 
-<dt id="arg-model-df">model_df<a class="anchor" aria-label="anchor" href="#arg-model-df"></a></dt>
+<dt id="arg-model-df">model_df<a class="anchor" aria-label="anchor" href="#arg-model-df"></a>
+</dt>
 <dd><p>(<code>data.frame</code>)<br> contains the resulting model fit from a <a href="fit_coxreg.html">fit_coxreg</a>
 function with tidying applied via <code><a href="https://broom.tidymodels.org/reference/reexports.html" class="external-link">broom::tidy()</a></code>.</p></dd>
 
 
-<dt id="arg--which-vars">.which_vars<a class="anchor" aria-label="anchor" href="#arg--which-vars"></a></dt>
+<dt id="arg--which-vars">.which_vars<a class="anchor" aria-label="anchor" href="#arg--which-vars"></a>
+</dt>
 <dd><p>(<code>character</code>)<br> which rows should statistics be returned for from the given model.
 Defaults to <code>"all"</code>. Other options include <code>"var_main"</code> for main effects, <code>"inter"</code> for interaction effects,
 and <code>"multi_lvl"</code> for multivariate model covariate level rows. When <code>.which_vars</code> is <code>"all"</code>, specific
 variables can be selected by specifying <code>.var_nms</code>.</p></dd>
 
 
-<dt id="arg--var-nms">.var_nms<a class="anchor" aria-label="anchor" href="#arg--var-nms"></a></dt>
+<dt id="arg--var-nms">.var_nms<a class="anchor" aria-label="anchor" href="#arg--var-nms"></a>
+</dt>
 <dd><p>(<code>character</code>)<br> the <code>term</code> value of rows in <code>df</code> for which <code>.stats</code> should be returned. Typically
 this is the name of a variable. If using variable labels, <code>var</code> should be a vector of both the desired
 variable name and the variable label in that order to see all <code>.stats</code> related to that variable. When <code>.which_vars</code>
 is <code>"var_main"</code>, <code>.var_nms</code> should be only the variable name.</p></dd>
 
 
-<dt id="arg-df">df<a class="anchor" aria-label="anchor" href="#arg-df"></a></dt>
+<dt id="arg-df">df<a class="anchor" aria-label="anchor" href="#arg-df"></a>
+</dt>
 <dd><p>(<code>data.frame</code>)<br> data set containing all analysis variables.</p></dd>
 
 
-<dt id="arg-labelstr">labelstr<a class="anchor" aria-label="anchor" href="#arg-labelstr"></a></dt>
+<dt id="arg-labelstr">labelstr<a class="anchor" aria-label="anchor" href="#arg-labelstr"></a>
+</dt>
 <dd><p>(<code>string</code>)<br> label of the level of the parent split currently being summarized
 (must be present as second argument in Content Row Functions). See <code><a href="https://insightsengineering.github.io/rtables/latest-tag/reference/summarize_row_groups.html" class="external-link">rtables::summarize_row_groups()</a></code>
 for more information.</p></dd>
 
 
-<dt id="arg-eff">eff<a class="anchor" aria-label="anchor" href="#arg-eff"></a></dt>
+<dt id="arg-eff">eff<a class="anchor" aria-label="anchor" href="#arg-eff"></a>
+</dt>
 <dd><p>(<code>flag</code>)<br> whether treatment effect should be calculated. Defaults to <code>FALSE</code>.</p></dd>
 
 
-<dt id="arg-var-main">var_main<a class="anchor" aria-label="anchor" href="#arg-var-main"></a></dt>
+<dt id="arg-var-main">var_main<a class="anchor" aria-label="anchor" href="#arg-var-main"></a>
+</dt>
 <dd><p>(<code>flag</code>)<br> whether main effects should be calculated. Defaults to <code>FALSE</code>.</p></dd>
 
 
-<dt id="arg--spl-context">.spl_context<a class="anchor" aria-label="anchor" href="#arg--spl-context"></a></dt>
+<dt id="arg--spl-context">.spl_context<a class="anchor" aria-label="anchor" href="#arg--spl-context"></a>
+</dt>
 <dd><p>(<code>data.frame</code>)<br> gives information about ancestor split states
 that is passed by <code>rtables</code>.</p></dd>
 
 
-<dt id="arg-cache-env">cache_env<a class="anchor" aria-label="anchor" href="#arg-cache-env"></a></dt>
+<dt id="arg-cache-env">cache_env<a class="anchor" aria-label="anchor" href="#arg-cache-env"></a>
+</dt>
 <dd><p>(<code>environment</code>)<br> an environment object used to cache the regression model in order to
 avoid repeatedly fitting the same model for every row in the table. Defaults to <code>NULL</code> (no caching).</p></dd>
 
-</dl></div>
+</dl>
+</div>
     <div class="section level2">
-    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
+    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a>
+</h2>
 
-<ul><li><p><code>summarize_coxreg()</code> returns a layout object suitable for passing to further layouting functions,
+<ul>
+<li><p><code>summarize_coxreg()</code> returns a layout object suitable for passing to further layouting functions,
 or to <code><a href="https://insightsengineering.github.io/rtables/latest-tag/reference/build_table.html" class="external-link">rtables::build_table()</a></code>. Adding this function to an <code>rtable</code> layout will add a Cox regression table
 containing the chosen statistics to the table layout.</p></li>
-</ul><ul><li><p><code>s_coxreg()</code> returns the selected statistic for from the Cox regression model for the selected variable(s).</p></li>
-</ul><ul><li><p><code>a_coxreg()</code> returns formatted <code><a href="https://insightsengineering.github.io/rtables/latest-tag/reference/CellValue.html" class="external-link">rtables::CellValue()</a></code>.</p></li>
-</ul></div>
+</ul>
+<ul>
+<li><p><code>s_coxreg()</code> returns the selected statistic for from the Cox regression model for the selected variable(s).</p></li>
+</ul>
+<ul>
+<li><p><code>a_coxreg()</code> returns formatted <code><a href="https://insightsengineering.github.io/rtables/latest-tag/reference/CellValue.html" class="external-link">rtables::CellValue()</a></code>.</p></li>
+</ul>
+</div>
     <div class="section level2">
-    <h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a></h2>
+    <h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a>
+</h2>
     <p>Cox models are the most commonly used methods to estimate the magnitude of
 the effect in survival analysis. It assumes proportional hazards: the ratio
 of the hazards between groups (e.g., two arms) is constant over time.
@@ -224,27 +324,34 @@ <h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></
 analysis (NEST Team, 2020).</p>
     </div>
     <div class="section level2">
-    <h2 id="functions">Functions<a class="anchor" aria-label="anchor" href="#functions"></a></h2>
+    <h2 id="functions">Functions<a class="anchor" aria-label="anchor" href="#functions"></a>
+</h2>
 
-<ul><li><p><code>summarize_coxreg()</code>: Layout-creating function which creates a Cox regression summary table
+<ul>
+<li><p><code>summarize_coxreg()</code>: Layout-creating function which creates a Cox regression summary table
 layout. This function is a wrapper for several <code>rtables</code> layouting functions. This function
 is a wrapper for <code><a href="https://insightsengineering.github.io/rtables/latest-tag/reference/analyze_colvars.html" class="external-link">rtables::analyze_colvars()</a></code> and <code><a href="https://insightsengineering.github.io/rtables/latest-tag/reference/summarize_row_groups.html" class="external-link">rtables::summarize_row_groups()</a></code>.</p></li>
 <li><p><code>s_coxreg()</code>: Statistics function that transforms results tabulated
 from <code><a href="fit_coxreg.html">fit_coxreg_univar()</a></code> or <code><a href="fit_coxreg.html">fit_coxreg_multivar()</a></code> into a list.</p></li>
 <li><p><code>a_coxreg()</code>: Analysis function which is used as <code>afun</code> in <code><a href="https://insightsengineering.github.io/rtables/latest-tag/reference/analyze.html" class="external-link">rtables::analyze()</a></code>
 and <code>cfun</code> in <code><a href="https://insightsengineering.github.io/rtables/latest-tag/reference/summarize_row_groups.html" class="external-link">rtables::summarize_row_groups()</a></code> within <code>summarize_coxreg()</code>.</p></li>
-</ul></div>
+</ul>
+</div>
     <div class="section level2">
-    <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"></a></h2>
-    <div class="dont-index"><p><a href="fit_coxreg.html">fit_coxreg</a> for relevant fitting functions, <a href="h_cox_regression.html">h_cox_regression</a> for relevant
+    <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"></a>
+</h2>
+    <div class="dont-index">
+<p><a href="fit_coxreg.html">fit_coxreg</a> for relevant fitting functions, <a href="h_cox_regression.html">h_cox_regression</a> for relevant
 helper functions, and <a href="tidy_coxreg.html">tidy_coxreg</a> for custom tidy methods.</p>
 <p><code><a href="fit_coxreg.html">fit_coxreg_univar()</a></code> and <code><a href="fit_coxreg.html">fit_coxreg_multivar()</a></code> which also take the <code>variables</code>, <code>data</code>,
 <code>at</code> (univariate only), and <code>control</code> arguments but return unformatted univariate and multivariate
-Cox regression models, respectively.</p></div>
+Cox regression models, respectively.</p>
+</div>
     </div>
 
     <div class="section level2">
-    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
+    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://github.com/therneau/survival" class="external-link">survival</a></span><span class="op">)</span></span></span>
 <span class="r-in"><span></span></span>
 <span class="r-in"><span><span class="co"># Testing dataset [survival::bladder].</span></span></span>
@@ -493,17 +600,19 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 </code></pre></div>
     </div>
   </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
-    </nav></aside></div>
+    </nav></aside>
+</div>
 
 
     <footer><div class="nest">
   <p>tern is a part of the <strong>NEST</strong> and <a href="https://pharmaverse.org/" class="external-link"><strong>pharmaverse</strong></a>.</p>
 </div>
-<script type="text/javascript" src="../analytics.js"></script></footer></div>
-
+<script type="text/javascript" src="../analytics.js"></script></footer>
+</div>
 
 
 
 
-  </body></html>
 
+  </body>
+</html>
diff --git a/main/reference/cox_regression_inter.html b/main/reference/cox_regression_inter.html
index 408c3a0cee..af2ad1d5df 100644
--- a/main/reference/cox_regression_inter.html
+++ b/main/reference/cox_regression_inter.html
@@ -1,11 +1,34 @@
-<!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Cox regression helper function for interactions — cox_regression_inter • tern</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Cox regression helper function for interactions — cox_regression_inter"><meta name="description" content="
+<html lang="en">
+<head>
+<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+<meta charset="utf-8">
+<meta http-equiv="X-UA-Compatible" content="IE=edge">
+<meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<title>Cox regression helper function for interactions — cox_regression_inter • tern</title>
+<!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png">
+<link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png">
+<link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png">
+<link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png">
+<link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png">
+<link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png">
+<script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet">
+<script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet">
+<link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet">
+<script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Cox regression helper function for interactions — cox_regression_inter">
+<meta name="description" content="
 Test and estimate the effect of a treatment in interaction with a covariate.
 The effect is estimated as the HR of the tested treatment for a given level
-of the covariate, in comparison to the treatment control."><meta property="og:description" content="
+of the covariate, in comparison to the treatment control.">
+<meta property="og:description" content="
 Test and estimate the effect of a treatment in interaction with a covariate.
 The effect is estimated as the HR of the tested treatment for a given level
-of the covariate, in comparison to the treatment control."><meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png"><link rel="stylesheet" href="../consent.css"><script src="../consent.js" type="text/javascript" charset="utf-8"></script></head><body>
+of the covariate, in comparison to the treatment control.">
+<meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png">
+<link rel="stylesheet" href="../consent.css">
+<script src="../consent.js" type="text/javascript" charset="utf-8"></script>
+</head>
+<body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
 
 
@@ -21,26 +44,66 @@
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+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a>
+</div>
+</li></div>
+</ul>
+<ul class="navbar-nav">
+<li class="nav-item"><form class="form-inline" role="search">
+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json">
+</form></li>
 <li class="nav-item"><a class="external-link nav-link" href="https://github.com/insightsengineering/tern" aria-label="GitHub"><span class="fa fa-github"></span></a></li>
-      </ul></div>
+      </ul>
+</div>
 
 
   </div>
@@ -60,7 +123,8 @@
     </div>
 
     <div class="section level2">
-    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
+    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">h_coxreg_inter_effect</span><span class="op">(</span><span class="va">x</span>, <span class="va">effect</span>, <span class="va">covar</span>, <span class="va">mod</span>, <span class="va">label</span>, <span class="va">control</span>, <span class="va">...</span><span class="op">)</span></span>
 <span></span>
 <span><span class="co"># S3 method for class 'numeric'</span></span>
@@ -85,89 +149,121 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
     </div>
 
     <div class="section level2">
-    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
+    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a>
+</h2>
 
 
-<dl><dt id="arg-x">x<a class="anchor" aria-label="anchor" href="#arg-x"></a></dt>
+<dl>
+<dt id="arg-x">x<a class="anchor" aria-label="anchor" href="#arg-x"></a>
+</dt>
 <dd><p>(<code>numeric</code> or <code>factor</code>)<br> the values of the covariate to be tested.</p></dd>
 
 
-<dt id="arg-effect">effect<a class="anchor" aria-label="anchor" href="#arg-effect"></a></dt>
+<dt id="arg-effect">effect<a class="anchor" aria-label="anchor" href="#arg-effect"></a>
+</dt>
 <dd><p>(<code>string</code>)<br> the name of the effect to be tested and estimated.</p></dd>
 
 
-<dt id="arg-covar">covar<a class="anchor" aria-label="anchor" href="#arg-covar"></a></dt>
+<dt id="arg-covar">covar<a class="anchor" aria-label="anchor" href="#arg-covar"></a>
+</dt>
 <dd><p>(<code>string</code>)<br> the name of the covariate in the model.</p></dd>
 
 
-<dt id="arg-mod">mod<a class="anchor" aria-label="anchor" href="#arg-mod"></a></dt>
+<dt id="arg-mod">mod<a class="anchor" aria-label="anchor" href="#arg-mod"></a>
+</dt>
 <dd><p>(<code>coxph</code>)<br> a fitted Cox regression model (see <code><a href="https://rdrr.io/pkg/survival/man/coxph.html" class="external-link">survival::coxph()</a></code>).</p></dd>
 
 
-<dt id="arg-label">label<a class="anchor" aria-label="anchor" href="#arg-label"></a></dt>
+<dt id="arg-label">label<a class="anchor" aria-label="anchor" href="#arg-label"></a>
+</dt>
 <dd><p>(<code>string</code>)<br> the label to be returned as <code>term_label</code>.</p></dd>
 
 
-<dt id="arg-control">control<a class="anchor" aria-label="anchor" href="#arg-control"></a></dt>
+<dt id="arg-control">control<a class="anchor" aria-label="anchor" href="#arg-control"></a>
+</dt>
 <dd><p>(<code>list</code>)<br> a list of controls as returned by <code><a href="control_coxreg.html">control_coxreg()</a></code>.</p></dd>
 
 
-<dt id="arg--">...<a class="anchor" aria-label="anchor" href="#arg--"></a></dt>
+<dt id="arg--">...<a class="anchor" aria-label="anchor" href="#arg--"></a>
+</dt>
 <dd><p>see methods.</p></dd>
 
 
-<dt id="arg-at">at<a class="anchor" aria-label="anchor" href="#arg-at"></a></dt>
+<dt id="arg-at">at<a class="anchor" aria-label="anchor" href="#arg-at"></a>
+</dt>
 <dd><p>(<code>list</code>)<br> a list with items named after the covariate, every
 item is a vector of levels at which the interaction should be estimated.</p></dd>
 
 
-<dt id="arg-data">data<a class="anchor" aria-label="anchor" href="#arg-data"></a></dt>
+<dt id="arg-data">data<a class="anchor" aria-label="anchor" href="#arg-data"></a>
+</dt>
 <dd><p>(<code>data.frame</code>)<br> the data frame on which the model was fit.</p></dd>
 
 
-<dt id="arg-variable-given">variable, given<a class="anchor" aria-label="anchor" href="#arg-variable-given"></a></dt>
+<dt id="arg-variable-given">variable, given<a class="anchor" aria-label="anchor" href="#arg-variable-given"></a>
+</dt>
 <dd><p>(<code>string</code>)<br> the name of variables in interaction. We seek the estimation
 of the levels of <code>variable</code> given the levels of <code>given</code>.</p></dd>
 
 
-<dt id="arg-lvl-var-lvl-given">lvl_var, lvl_given<a class="anchor" aria-label="anchor" href="#arg-lvl-var-lvl-given"></a></dt>
+<dt id="arg-lvl-var-lvl-given">lvl_var, lvl_given<a class="anchor" aria-label="anchor" href="#arg-lvl-var-lvl-given"></a>
+</dt>
 <dd><p>(<code>character</code>)<br> corresponding levels as given by <code><a href="https://rdrr.io/r/base/levels.html" class="external-link">levels()</a></code>.</p></dd>
 
 
-<dt id="arg-conf-level">conf_level<a class="anchor" aria-label="anchor" href="#arg-conf-level"></a></dt>
+<dt id="arg-conf-level">conf_level<a class="anchor" aria-label="anchor" href="#arg-conf-level"></a>
+</dt>
 <dd><p>(<code>proportion</code>)<br> confidence level of the interval.</p></dd>
 
-</dl></div>
+</dl>
+</div>
     <div class="section level2">
-    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
+    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a>
+</h2>
 
-<ul><li><p><code>h_coxreg_inter_effect()</code> returns a <code>data.frame</code> of covariate interaction effects consisting of the following
+<ul>
+<li><p><code>h_coxreg_inter_effect()</code> returns a <code>data.frame</code> of covariate interaction effects consisting of the following
 variables: <code>effect</code>, <code>term</code>, <code>term_label</code>, <code>level</code>, <code>n</code>, <code>hr</code>, <code>lcl</code>, <code>ucl</code>, <code>pval</code>, and <code>pval_inter</code>.</p></li>
-</ul><ul><li><p><code>h_coxreg_extract_interaction()</code> returns the result of an interaction test and the estimated values. If
+</ul>
+<ul>
+<li><p><code>h_coxreg_extract_interaction()</code> returns the result of an interaction test and the estimated values. If
 no interaction, <code><a href="h_cox_regression.html">h_coxreg_univar_extract()</a></code> is applied instead.</p></li>
-</ul><ul><li><p><code>h_coxreg_inter_estimations()</code> returns a list of matrices (one per level of variable) with rows corresponding
-to the combinations of <code>variable</code> and <code>given</code>, with columns:</p><ul><li><p><code>coef_hat</code>: Estimation of the coefficient.</p></li>
+</ul>
+<ul>
+<li>
+<p><code>h_coxreg_inter_estimations()</code> returns a list of matrices (one per level of variable) with rows corresponding
+to the combinations of <code>variable</code> and <code>given</code>, with columns:</p>
+<ul>
+<li><p><code>coef_hat</code>: Estimation of the coefficient.</p></li>
 <li><p><code>coef_se</code>: Standard error of the estimation.</p></li>
 <li><p><code>hr</code>: Hazard ratio.</p></li>
 <li><p><code>lcl, ucl</code>: Lower/upper confidence limit of the hazard ratio.</p></li>
-</ul></li>
-</ul></div>
+</ul>
+</li>
+</ul>
+</div>
     <div class="section level2">
-    <h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a></h2>
+    <h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a>
+</h2>
     <p>Given the cox regression investigating the effect of Arm (A, B, C; reference A)
 and Sex (F, M; reference Female) and the model being abbreviated: y ~ Arm + Sex + Arm:Sex.
-The cox regression estimates the coefficients along with a variance-covariance matrix for:</p><ul><li><p>b1 (arm b), b2 (arm c)</p></li>
+The cox regression estimates the coefficients along with a variance-covariance matrix for:</p>
+<ul>
+<li><p>b1 (arm b), b2 (arm c)</p></li>
 <li><p>b3 (sex m)</p></li>
 <li><p>b4 (arm b: sex m), b5 (arm c: sex m)</p></li>
-</ul><p>The estimation of the Hazard Ratio for arm C/sex M is given in reference
+</ul>
+<p>The estimation of the Hazard Ratio for arm C/sex M is given in reference
 to arm A/Sex M by exp(b2 + b3 + b5)/ exp(b3) = exp(b2 + b5).
 The interaction coefficient is deduced by b2 + b5 while the standard error
 is obtained as $sqrt(Var b2 + Var b5 + 2 * covariance (b2,b5))$.</p>
     </div>
     <div class="section level2">
-    <h2 id="functions">Functions<a class="anchor" aria-label="anchor" href="#functions"></a></h2>
+    <h2 id="functions">Functions<a class="anchor" aria-label="anchor" href="#functions"></a>
+</h2>
 
-<ul><li><p><code>h_coxreg_inter_effect()</code>: S3 generic helper function to determine interaction effect.</p></li>
+<ul>
+<li><p><code>h_coxreg_inter_effect()</code>: S3 generic helper function to determine interaction effect.</p></li>
 <li><p><code>h_coxreg_inter_effect(numeric)</code>: Method for <code>numeric</code> class. Estimates the interaction with a <code>numeric</code> covariate.</p></li>
 <li><p><code>h_coxreg_inter_effect(factor)</code>: Method for <code>factor</code> class. Estimate the interaction with a <code>factor</code> covariate.</p></li>
 <li><p><code>h_coxreg_inter_effect(character)</code>: Method for <code>character</code> class. Estimate the interaction with a <code>character</code> covariate.
@@ -175,17 +271,22 @@ <h2 id="functions">Functions<a class="anchor" aria-label="anchor" href="#functio
 <li><p><code>h_coxreg_extract_interaction()</code>: A higher level function to get
 the results of the interaction test and the estimated values.</p></li>
 <li><p><code>h_coxreg_inter_estimations()</code>: Hazard ratio estimation in interactions.</p></li>
-</ul></div>
+</ul>
+</div>
     <div class="section level2">
-    <h2 id="note">Note<a class="anchor" aria-label="anchor" href="#note"></a></h2>
+    <h2 id="note">Note<a class="anchor" aria-label="anchor" href="#note"></a>
+</h2>
 
-<ul><li><p>Automatic conversion of character to factor does not guarantee results can be generated correctly. It is
+<ul>
+<li><p>Automatic conversion of character to factor does not guarantee results can be generated correctly. It is
 therefore better to always pre-process the dataset such that factors are manually created from character
 variables before passing the dataset to <code><a href="https://insightsengineering.github.io/rtables/latest-tag/reference/build_table.html" class="external-link">rtables::build_table()</a></code>.</p></li>
-</ul></div>
+</ul>
+</div>
 
     <div class="section level2">
-    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
+    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://github.com/therneau/survival" class="external-link">survival</a></span><span class="op">)</span></span></span>
 <span class="r-in"><span></span></span>
 <span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/Random.html" class="external-link">set.seed</a></span><span class="op">(</span><span class="fl">1</span>, kind <span class="op">=</span> <span class="st">"Mersenne-Twister"</span><span class="op">)</span></span></span>
@@ -256,17 +357,19 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 </code></pre></div>
     </div>
   </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
-    </nav></aside></div>
+    </nav></aside>
+</div>
 
 
     <footer><div class="nest">
   <p>tern is a part of the <strong>NEST</strong> and <a href="https://pharmaverse.org/" class="external-link"><strong>pharmaverse</strong></a>.</p>
 </div>
-<script type="text/javascript" src="../analytics.js"></script></footer></div>
-
+<script type="text/javascript" src="../analytics.js"></script></footer>
+</div>
 
 
 
 
-  </body></html>
 
+  </body>
+</html>
diff --git a/main/reference/cut_quantile_bins.html b/main/reference/cut_quantile_bins.html
index ef28254848..bb57795376 100644
--- a/main/reference/cut_quantile_bins.html
+++ b/main/reference/cut_quantile_bins.html
@@ -1,7 +1,30 @@
-<!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Cut numeric vector into empirical quantile bins — cut_quantile_bins • tern</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Cut numeric vector into empirical quantile bins — cut_quantile_bins"><meta name="description" content="
-This cuts a numeric vector into sample quantile bins."><meta property="og:description" content="
-This cuts a numeric vector into sample quantile bins."><meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png"><link rel="stylesheet" href="../consent.css"><script src="../consent.js" type="text/javascript" charset="utf-8"></script></head><body>
+<html lang="en">
+<head>
+<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+<meta charset="utf-8">
+<meta http-equiv="X-UA-Compatible" content="IE=edge">
+<meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<title>Cut numeric vector into empirical quantile bins — cut_quantile_bins • tern</title>
+<!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png">
+<link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png">
+<link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png">
+<link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png">
+<link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png">
+<link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png">
+<script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet">
+<script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet">
+<link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet">
+<script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Cut numeric vector into empirical quantile bins — cut_quantile_bins">
+<meta name="description" content="
+This cuts a numeric vector into sample quantile bins.">
+<meta property="og:description" content="
+This cuts a numeric vector into sample quantile bins.">
+<meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png">
+<link rel="stylesheet" href="../consent.css">
+<script src="../consent.js" type="text/javascript" charset="utf-8"></script>
+</head>
+<body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
 
 
@@ -17,26 +40,66 @@
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-      <ul class="navbar-nav me-auto"><li class="nav-item"><a class="nav-link" href="../articles/tern.html">Get started</a></li>
+      <ul class="navbar-nav me-auto">
+<li class="nav-item"><a class="nav-link" href="../articles/tern.html">Get started</a></li>
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   <button class="nav-link dropdown-toggle" type="button" id="dropdown-articles" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Articles</button>
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+  <ul class="dropdown-menu" aria-labelledby="dropdown-articles">
+<li><a class="dropdown-item" href="../articles/missing_values.html">Missing Values in Tern</a></li>
     <li><a class="dropdown-item" href="../articles/tables.html">Tabulation</a></li>
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     <li><a class="dropdown-item" href="../articles/tern_functions_guide.html">Understanding `tern` functions</a></li>
-  </ul></li>
+  </ul>
+</li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
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   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
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- <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json"></form></li>
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+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1-rc3">v0.9.1-rc3</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a>
+</div>
+</li></div>
+</ul>
+<ul class="navbar-nav">
+<li class="nav-item"><form class="form-inline" role="search">
+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json">
+</form></li>
 <li class="nav-item"><a class="external-link nav-link" href="https://github.com/insightsengineering/tern" aria-label="GitHub"><span class="fa fa-github"></span></a></li>
-      </ul></div>
+      </ul>
+</div>
 
 
   </div>
@@ -54,7 +117,8 @@
     </div>
 
     <div class="section level2">
-    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
+    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">cut_quantile_bins</span><span class="op">(</span></span>
 <span>  <span class="va">x</span>,</span>
 <span>  probs <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">0.25</span>, <span class="fl">0.5</span>, <span class="fl">0.75</span><span class="op">)</span>,</span>
@@ -65,47 +129,58 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
     </div>
 
     <div class="section level2">
-    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
+    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a>
+</h2>
 
 
-<dl><dt id="arg-x">x<a class="anchor" aria-label="anchor" href="#arg-x"></a></dt>
+<dl>
+<dt id="arg-x">x<a class="anchor" aria-label="anchor" href="#arg-x"></a>
+</dt>
 <dd><p>(<code>numeric</code>)<br> the continuous variable values which should be cut into
 quantile bins. This may contain <code>NA</code> values, which are then
 not used for the quantile calculations, but included in the return vector.</p></dd>
 
 
-<dt id="arg-probs">probs<a class="anchor" aria-label="anchor" href="#arg-probs"></a></dt>
+<dt id="arg-probs">probs<a class="anchor" aria-label="anchor" href="#arg-probs"></a>
+</dt>
 <dd><p>(<code>numeric</code>)<br> the probabilities identifying the quantiles.
 This is a sorted vector of unique <code>proportion</code> values, i.e. between 0 and 1, where
 the boundaries 0 and 1 must not be included.</p></dd>
 
 
-<dt id="arg-labels">labels<a class="anchor" aria-label="anchor" href="#arg-labels"></a></dt>
+<dt id="arg-labels">labels<a class="anchor" aria-label="anchor" href="#arg-labels"></a>
+</dt>
 <dd><p>(<code>character</code>)<br> the unique labels for the quantile bins. When there are <code>n</code>
 probabilities in <code>probs</code>, then this must be <code>n + 1</code> long.</p></dd>
 
 
-<dt id="arg-type">type<a class="anchor" aria-label="anchor" href="#arg-type"></a></dt>
+<dt id="arg-type">type<a class="anchor" aria-label="anchor" href="#arg-type"></a>
+</dt>
 <dd><p>(<code>integer(1)</code>)<br> type of quantiles to use, see <code><a href="https://rdrr.io/r/stats/quantile.html" class="external-link">stats::quantile()</a></code> for details.</p></dd>
 
 
-<dt id="arg-ordered">ordered<a class="anchor" aria-label="anchor" href="#arg-ordered"></a></dt>
+<dt id="arg-ordered">ordered<a class="anchor" aria-label="anchor" href="#arg-ordered"></a>
+</dt>
 <dd><p>(<code>flag</code>)<br> should the result be an ordered factor.</p></dd>
 
-</dl></div>
+</dl>
+</div>
     <div class="section level2">
-    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
+    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a>
+</h2>
     <p>A <code>factor</code> variable with appropriately-labeled bins as levels.</p>
     </div>
     <div class="section level2">
-    <h2 id="note">Note<a class="anchor" aria-label="anchor" href="#note"></a></h2>
+    <h2 id="note">Note<a class="anchor" aria-label="anchor" href="#note"></a>
+</h2>
     <p>Intervals are closed on the right side. That is, the first bin is the interval
 <code>[-Inf, q1]</code> where <code>q1</code> is the first quantile, the second bin is then <code>(q1, q2]</code>, etc.,
 and the last bin is <code>(qn, +Inf]</code> where <code>qn</code> is the last quantile.</p>
     </div>
 
     <div class="section level2">
-    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
+    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="co"># Default is to cut into quartile bins.</span></span></span>
 <span class="r-in"><span><span class="fu">cut_quantile_bins</span><span class="op">(</span><span class="va">cars</span><span class="op">$</span><span class="va">speed</span><span class="op">)</span></span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>  [1] [0%,25%]   [0%,25%]   [0%,25%]   [0%,25%]   [0%,25%]   [0%,25%]  </span>
@@ -176,17 +251,19 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 </code></pre></div>
     </div>
   </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
-    </nav></aside></div>
+    </nav></aside>
+</div>
 
 
     <footer><div class="nest">
   <p>tern is a part of the <strong>NEST</strong> and <a href="https://pharmaverse.org/" class="external-link"><strong>pharmaverse</strong></a>.</p>
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diff --git a/main/reference/d_count_abnormal_by_baseline.html b/main/reference/d_count_abnormal_by_baseline.html
index 5c26aecf62..d104c6455e 100644
--- a/main/reference/d_count_abnormal_by_baseline.html
+++ b/main/reference/d_count_abnormal_by_baseline.html
@@ -1,7 +1,30 @@
-<!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Description function for s_count_abnormal_by_baseline() — d_count_abnormal_by_baseline • tern</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Description function for s_count_abnormal_by_baseline() — d_count_abnormal_by_baseline"><meta name="description" content="
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+<script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet">
+<script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet">
+<link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet">
+<script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Description function for s_count_abnormal_by_baseline() — d_count_abnormal_by_baseline">
+<meta name="description" content="
+Description function that produces the labels for s_count_abnormal_by_baseline().">
+<meta property="og:description" content="
+Description function that produces the labels for s_count_abnormal_by_baseline().">
+<meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png">
+<link rel="stylesheet" href="../consent.css">
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+</head>
+<body>
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+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
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+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
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+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a>
+</div>
+</li></div>
+</ul>
+<ul class="navbar-nav">
+<li class="nav-item"><form class="form-inline" role="search">
+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json">
+</form></li>
 <li class="nav-item"><a class="external-link nav-link" href="https://github.com/insightsengineering/tern" aria-label="GitHub"><span class="fa fa-github"></span></a></li>
-      </ul></div>
+      </ul>
+</div>
 
 
   </div>
 </nav><div class="container template-reference-topic">
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
-      <img src="../logo.png" class="logo" alt=""><h1>Description function for <code>s_count_abnormal_by_baseline()</code></h1>
+      <img src="../logo.png" class="logo" alt=""><h1>Description function for <code>s_count_abnormal_by_baseline()</code>
+</h1>
       <small class="dont-index">Source: <a href="https://github.com/insightsengineering/tern/blob/main/R/abnormal_by_baseline.R" class="external-link"><code>R/abnormal_by_baseline.R</code></a></small>
       <div class="d-none name"><code>d_count_abnormal_by_baseline.Rd</code></div>
     </div>
@@ -54,25 +118,32 @@
     </div>
 
     <div class="section level2">
-    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
+    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">d_count_abnormal_by_baseline</span><span class="op">(</span><span class="va">abnormal</span><span class="op">)</span></span></code></pre></div>
     </div>
 
     <div class="section level2">
-    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
+    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a>
+</h2>
 
 
-<dl><dt id="arg-abnormal">abnormal<a class="anchor" aria-label="anchor" href="#arg-abnormal"></a></dt>
+<dl>
+<dt id="arg-abnormal">abnormal<a class="anchor" aria-label="anchor" href="#arg-abnormal"></a>
+</dt>
 <dd><p>(<code>character</code>)<br> values identifying the abnormal range level(s) in <code>.var</code>.</p></dd>
 
-</dl></div>
+</dl>
+</div>
     <div class="section level2">
-    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
+    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a>
+</h2>
     <p>Abnormal category labels for <code><a href="abnormal_by_baseline.html">s_count_abnormal_by_baseline()</a></code>.</p>
     </div>
 
     <div class="section level2">
-    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
+    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="fu">d_count_abnormal_by_baseline</span><span class="op">(</span><span class="st">"LOW"</span><span class="op">)</span></span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> $not_abnormal</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> [1] "Not low"</span>
@@ -87,17 +158,19 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 </code></pre></div>
     </div>
   </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
-    </nav></aside></div>
+    </nav></aside>
+</div>
 
 
     <footer><div class="nest">
   <p>tern is a part of the <strong>NEST</strong> and <a href="https://pharmaverse.org/" class="external-link"><strong>pharmaverse</strong></a>.</p>
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-<script type="text/javascript" src="../analytics.js"></script></footer></div>
-
+<script type="text/javascript" src="../analytics.js"></script></footer>
+</div>
 
 
 
 
-  </body></html>
 
+  </body>
+</html>
diff --git a/main/reference/d_count_cumulative.html b/main/reference/d_count_cumulative.html
index 49757c9187..b53787b3d0 100644
--- a/main/reference/d_count_cumulative.html
+++ b/main/reference/d_count_cumulative.html
@@ -1,7 +1,30 @@
-<!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Description of cumulative count — d_count_cumulative • tern</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Description of cumulative count — d_count_cumulative"><meta name="description" content="
-This is a helper function that describes the analysis in s_count_cumulative()."><meta property="og:description" content="
-This is a helper function that describes the analysis in s_count_cumulative()."><meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png"><link rel="stylesheet" href="../consent.css"><script src="../consent.js" type="text/javascript" charset="utf-8"></script></head><body>
+<html lang="en">
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+<meta charset="utf-8">
+<meta http-equiv="X-UA-Compatible" content="IE=edge">
+<meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<title>Description of cumulative count — d_count_cumulative • tern</title>
+<!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png">
+<link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png">
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+<script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet">
+<script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet">
+<link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet">
+<script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Description of cumulative count — d_count_cumulative">
+<meta name="description" content="
+This is a helper function that describes the analysis in s_count_cumulative().">
+<meta property="og:description" content="
+This is a helper function that describes the analysis in s_count_cumulative().">
+<meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png">
+<link rel="stylesheet" href="../consent.css">
+<script src="../consent.js" type="text/javascript" charset="utf-8"></script>
+</head>
+<body>
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@@ -17,26 +40,66 @@
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+  <ul class="dropdown-menu" aria-labelledby="dropdown-articles">
+<li><a class="dropdown-item" href="../articles/missing_values.html">Missing Values in Tern</a></li>
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     <li><a class="dropdown-item" href="../articles/tern_functions_guide.html">Understanding `tern` functions</a></li>
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+  </ul>
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+  <ul class="dropdown-menu" aria-labelledby="dropdown-reports">
+<li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
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- <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json"></form></li>
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+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
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+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a>
+</div>
+</li></div>
+</ul>
+<ul class="navbar-nav">
+<li class="nav-item"><form class="form-inline" role="search">
+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json">
+</form></li>
 <li class="nav-item"><a class="external-link nav-link" href="https://github.com/insightsengineering/tern" aria-label="GitHub"><span class="fa fa-github"></span></a></li>
-      </ul></div>
+      </ul>
+</div>
 
 
   </div>
@@ -54,44 +117,54 @@
     </div>
 
     <div class="section level2">
-    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
+    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">d_count_cumulative</span><span class="op">(</span><span class="va">threshold</span>, lower_tail <span class="op">=</span> <span class="cn">TRUE</span>, include_eq <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></code></pre></div>
     </div>
 
     <div class="section level2">
-    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
+    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a>
+</h2>
 
 
-<dl><dt id="arg-threshold">threshold<a class="anchor" aria-label="anchor" href="#arg-threshold"></a></dt>
+<dl>
+<dt id="arg-threshold">threshold<a class="anchor" aria-label="anchor" href="#arg-threshold"></a>
+</dt>
 <dd><p>(<code>numeric(1)</code>)<br> a cutoff value as threshold to count values of <code>x</code>.</p></dd>
 
 
-<dt id="arg-lower-tail">lower_tail<a class="anchor" aria-label="anchor" href="#arg-lower-tail"></a></dt>
+<dt id="arg-lower-tail">lower_tail<a class="anchor" aria-label="anchor" href="#arg-lower-tail"></a>
+</dt>
 <dd><p>(<code>flag</code>)<br> whether to count lower tail, default is <code>TRUE</code>.</p></dd>
 
 
-<dt id="arg-include-eq">include_eq<a class="anchor" aria-label="anchor" href="#arg-include-eq"></a></dt>
+<dt id="arg-include-eq">include_eq<a class="anchor" aria-label="anchor" href="#arg-include-eq"></a>
+</dt>
 <dd><p>(<code>flag</code>)<br> whether to include value equal to the <code>threshold</code> in
 count, default is <code>TRUE</code>.</p></dd>
 
-</dl></div>
+</dl>
+</div>
     <div class="section level2">
-    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
+    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a>
+</h2>
     <p>Labels for <code><a href="count_cumulative.html">s_count_cumulative()</a></code>.</p>
     </div>
 
   </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
-    </nav></aside></div>
+    </nav></aside>
+</div>
 
 
     <footer><div class="nest">
   <p>tern is a part of the <strong>NEST</strong> and <a href="https://pharmaverse.org/" class="external-link"><strong>pharmaverse</strong></a>.</p>
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+  </body>
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diff --git a/main/reference/d_count_missed_doses.html b/main/reference/d_count_missed_doses.html
index 1d13438c6d..25b02ab6f1 100644
--- a/main/reference/d_count_missed_doses.html
+++ b/main/reference/d_count_missed_doses.html
@@ -1,5 +1,28 @@
-<!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Description function that calculates labels for s_count_missed_doses() — d_count_missed_doses • tern</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Description function that calculates labels for s_count_missed_doses() — d_count_missed_doses"><meta name="description" content=""><meta property="og:description" content=""><meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png"><link rel="stylesheet" href="../consent.css"><script src="../consent.js" type="text/javascript" charset="utf-8"></script></head><body>
+<html lang="en">
+<head>
+<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+<meta charset="utf-8">
+<meta http-equiv="X-UA-Compatible" content="IE=edge">
+<meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<title>Description function that calculates labels for s_count_missed_doses() — d_count_missed_doses • tern</title>
+<!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png">
+<link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png">
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+<script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Description function that calculates labels for s_count_missed_doses() — d_count_missed_doses">
+<meta name="description" content="">
+<meta property="og:description" content="">
+<meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png">
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+</head>
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@@ -15,33 +38,74 @@
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+  <ul class="dropdown-menu" aria-labelledby="dropdown-articles">
+<li><a class="dropdown-item" href="../articles/missing_values.html">Missing Values in Tern</a></li>
     <li><a class="dropdown-item" href="../articles/tables.html">Tabulation</a></li>
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+  </ul>
+</li>
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   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
-  <ul class="dropdown-menu" aria-labelledby="dropdown-reports"><li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
+  <ul class="dropdown-menu" aria-labelledby="dropdown-reports">
+<li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
     <li><a class="dropdown-item" href="../unit-test-report/">Unit test report</a></li>
     <li><a class="dropdown-item" href="../unit-test-report-non-cran/">Non-CRAN unit test report</a></li>
-  </ul></li>
-      </ul><ul class="navbar-nav"><li class="nav-item"><form class="form-inline" role="search">
- <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json"></form></li>
+  </ul>
+</li>
+      <div><li class="nav-item dropdown">
+    <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-versions">Versions</a>
+    <div class="dropdown-menu" aria-labelledby="dropdown-versions">
+    <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/main">main</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.5">v0.9.5</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.4">v0.9.4</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.3">v0.9.3</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1-rc3">v0.9.1-rc3</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a>
+</div>
+</li></div>
+</ul>
+<ul class="navbar-nav">
+<li class="nav-item"><form class="form-inline" role="search">
+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json">
+</form></li>
 <li class="nav-item"><a class="external-link nav-link" href="https://github.com/insightsengineering/tern" aria-label="GitHub"><span class="fa fa-github"></span></a></li>
-      </ul></div>
+      </ul>
+</div>
 
 
   </div>
 </nav><div class="container template-reference-topic">
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
-      <img src="../logo.png" class="logo" alt=""><h1>Description function that calculates labels for <code>s_count_missed_doses()</code></h1>
+      <img src="../logo.png" class="logo" alt=""><h1>Description function that calculates labels for <code>s_count_missed_doses()</code>
+</h1>
       <small class="dont-index">Source: <a href="https://github.com/insightsengineering/tern/blob/main/R/count_missed_doses.R" class="external-link"><code>R/count_missed_doses.R</code></a></small>
       <div class="d-none name"><code>d_count_missed_doses.Rd</code></div>
     </div>
@@ -51,39 +115,48 @@
     </div>
 
     <div class="section level2">
-    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
+    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">d_count_missed_doses</span><span class="op">(</span><span class="va">thresholds</span><span class="op">)</span></span></code></pre></div>
     </div>
 
     <div class="section level2">
-    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
+    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a>
+</h2>
 
 
-<dl><dt id="arg-thresholds">thresholds<a class="anchor" aria-label="anchor" href="#arg-thresholds"></a></dt>
+<dl>
+<dt id="arg-thresholds">thresholds<a class="anchor" aria-label="anchor" href="#arg-thresholds"></a>
+</dt>
 <dd><p>(<code>numeric</code>)<br> minimum number of missed doses the patients had.</p></dd>
 
-</dl></div>
+</dl>
+</div>
     <div class="section level2">
-    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
+    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a>
+</h2>
     <p><code>d_count_missed_doses()</code> returns a named <code>character</code> vector with the labels.</p>
     </div>
     <div class="section level2">
-    <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"></a></h2>
+    <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"></a>
+</h2>
     <div class="dont-index"><p><code><a href="count_missed_doses.html">s_count_missed_doses()</a></code></p></div>
     </div>
 
   </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
-    </nav></aside></div>
+    </nav></aside>
+</div>
 
 
     <footer><div class="nest">
   <p>tern is a part of the <strong>NEST</strong> and <a href="https://pharmaverse.org/" class="external-link"><strong>pharmaverse</strong></a>.</p>
 </div>
-<script type="text/javascript" src="../analytics.js"></script></footer></div>
-
+<script type="text/javascript" src="../analytics.js"></script></footer>
+</div>
 
 
 
 
-  </body></html>
 
+  </body>
+</html>
diff --git a/main/reference/d_onco_rsp_label.html b/main/reference/d_onco_rsp_label.html
index 5ddf1b1c5f..8c21576e14 100644
--- a/main/reference/d_onco_rsp_label.html
+++ b/main/reference/d_onco_rsp_label.html
@@ -1,7 +1,30 @@
-<!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Description of standard oncology response — d_onco_rsp_label • tern</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Description of standard oncology response — d_onco_rsp_label"><meta name="description" content="
-Describe the oncology response in a standard way."><meta property="og:description" content="
-Describe the oncology response in a standard way."><meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png"><link rel="stylesheet" href="../consent.css"><script src="../consent.js" type="text/javascript" charset="utf-8"></script></head><body>
+<html lang="en">
+<head>
+<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+<meta charset="utf-8">
+<meta http-equiv="X-UA-Compatible" content="IE=edge">
+<meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<title>Description of standard oncology response — d_onco_rsp_label • tern</title>
+<!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png">
+<link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png">
+<link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png">
+<link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png">
+<link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png">
+<link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png">
+<script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet">
+<script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet">
+<link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet">
+<script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Description of standard oncology response — d_onco_rsp_label">
+<meta name="description" content="
+Describe the oncology response in a standard way.">
+<meta property="og:description" content="
+Describe the oncology response in a standard way.">
+<meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png">
+<link rel="stylesheet" href="../consent.css">
+<script src="../consent.js" type="text/javascript" charset="utf-8"></script>
+</head>
+<body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
 
 
@@ -17,26 +40,66 @@
     </button>
 
     <div id="navbar" class="collapse navbar-collapse ms-3">
-      <ul class="navbar-nav me-auto"><li class="nav-item"><a class="nav-link" href="../articles/tern.html">Get started</a></li>
+      <ul class="navbar-nav me-auto">
+<li class="nav-item"><a class="nav-link" href="../articles/tern.html">Get started</a></li>
 <li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
 <li class="nav-item dropdown">
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-articles" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Articles</button>
-  <ul class="dropdown-menu" aria-labelledby="dropdown-articles"><li><a class="dropdown-item" href="../articles/missing_values.html">Missing Values in Tern</a></li>
+  <ul class="dropdown-menu" aria-labelledby="dropdown-articles">
+<li><a class="dropdown-item" href="../articles/missing_values.html">Missing Values in Tern</a></li>
     <li><a class="dropdown-item" href="../articles/tables.html">Tabulation</a></li>
     <li><a class="dropdown-item" href="../articles/tern_formats.html">Formatting Functions</a></li>
     <li><a class="dropdown-item" href="../articles/tern_functions_guide.html">Understanding `tern` functions</a></li>
-  </ul></li>
+  </ul>
+</li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
-  <ul class="dropdown-menu" aria-labelledby="dropdown-reports"><li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
+  <ul class="dropdown-menu" aria-labelledby="dropdown-reports">
+<li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
     <li><a class="dropdown-item" href="../unit-test-report/">Unit test report</a></li>
     <li><a class="dropdown-item" href="../unit-test-report-non-cran/">Non-CRAN unit test report</a></li>
-  </ul></li>
-      </ul><ul class="navbar-nav"><li class="nav-item"><form class="form-inline" role="search">
- <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json"></form></li>
+  </ul>
+</li>
+      <div><li class="nav-item dropdown">
+    <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-versions">Versions</a>
+    <div class="dropdown-menu" aria-labelledby="dropdown-versions">
+    <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/main">main</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.5">v0.9.5</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.4">v0.9.4</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.3">v0.9.3</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1-rc3">v0.9.1-rc3</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a>
+</div>
+</li></div>
+</ul>
+<ul class="navbar-nav">
+<li class="nav-item"><form class="form-inline" role="search">
+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json">
+</form></li>
 <li class="nav-item"><a class="external-link nav-link" href="https://github.com/insightsengineering/tern" aria-label="GitHub"><span class="fa fa-github"></span></a></li>
-      </ul></div>
+      </ul>
+</div>
 
 
   </div>
@@ -54,29 +117,37 @@
     </div>
 
     <div class="section level2">
-    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
+    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">d_onco_rsp_label</span><span class="op">(</span><span class="va">x</span><span class="op">)</span></span></code></pre></div>
     </div>
 
     <div class="section level2">
-    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
+    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a>
+</h2>
 
 
-<dl><dt id="arg-x">x<a class="anchor" aria-label="anchor" href="#arg-x"></a></dt>
+<dl>
+<dt id="arg-x">x<a class="anchor" aria-label="anchor" href="#arg-x"></a>
+</dt>
 <dd><p>(<code>character</code>)<br> the standard oncology codes to be described.</p></dd>
 
-</dl></div>
+</dl>
+</div>
     <div class="section level2">
-    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
+    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a>
+</h2>
     <p>Response labels.</p>
     </div>
     <div class="section level2">
-    <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"></a></h2>
+    <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"></a>
+</h2>
     <div class="dont-index"><p><code><a href="estimate_multinomial_rsp.html">estimate_multinomial_rsp()</a></code></p></div>
     </div>
 
     <div class="section level2">
-    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
+    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="fu">d_onco_rsp_label</span><span class="op">(</span></span></span>
 <span class="r-in"><span>  <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"CR"</span>, <span class="st">"PR"</span>, <span class="st">"SD"</span>, <span class="st">"NON CR/PD"</span>, <span class="st">"PD"</span>, <span class="st">"NE"</span>, <span class="st">"Missing"</span>, <span class="st">"&lt;Missing&gt;"</span>, <span class="st">"NE/Missing"</span><span class="op">)</span></span></span>
 <span class="r-in"><span><span class="op">)</span></span></span>
@@ -106,17 +177,19 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 </code></pre></div>
     </div>
   </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
-    </nav></aside></div>
+    </nav></aside>
+</div>
 
 
     <footer><div class="nest">
   <p>tern is a part of the <strong>NEST</strong> and <a href="https://pharmaverse.org/" class="external-link"><strong>pharmaverse</strong></a>.</p>
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-<script type="text/javascript" src="../analytics.js"></script></footer></div>
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+<script type="text/javascript" src="../analytics.js"></script></footer>
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diff --git a/main/reference/d_pkparam.html b/main/reference/d_pkparam.html
index 47f7f9aed0..744fb6a657 100644
--- a/main/reference/d_pkparam.html
+++ b/main/reference/d_pkparam.html
@@ -1,5 +1,28 @@
-<!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Generate PK reference dataset — d_pkparam • tern</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Generate PK reference dataset — d_pkparam"><meta name="description" content=""><meta property="og:description" content=""><meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png"><link rel="stylesheet" href="../consent.css"><script src="../consent.js" type="text/javascript" charset="utf-8"></script></head><body>
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+<meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
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+<!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png">
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+<script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Generate PK reference dataset — d_pkparam">
+<meta name="description" content="">
+<meta property="og:description" content="">
+<meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png">
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+</head>
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@@ -15,26 +38,66 @@
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+  <ul class="dropdown-menu" aria-labelledby="dropdown-articles">
+<li><a class="dropdown-item" href="../articles/missing_values.html">Missing Values in Tern</a></li>
     <li><a class="dropdown-item" href="../articles/tables.html">Tabulation</a></li>
     <li><a class="dropdown-item" href="../articles/tern_formats.html">Formatting Functions</a></li>
     <li><a class="dropdown-item" href="../articles/tern_functions_guide.html">Understanding `tern` functions</a></li>
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+  </ul>
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+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a>
+</div>
+</li></div>
+</ul>
+<ul class="navbar-nav">
+<li class="nav-item"><form class="form-inline" role="search">
+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json">
+</form></li>
 <li class="nav-item"><a class="external-link nav-link" href="https://github.com/insightsengineering/tern" aria-label="GitHub"><span class="fa fa-github"></span></a></li>
-      </ul></div>
+      </ul>
+</div>
 
 
   </div>
@@ -51,33 +114,38 @@
     </div>
 
     <div class="section level2">
-    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
+    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">d_pkparam</span><span class="op">(</span><span class="op">)</span></span></code></pre></div>
     </div>
 
     <div class="section level2">
-    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
+    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a>
+</h2>
     <p>A <code>data.frame</code> of PK parameters.</p>
     </div>
 
     <div class="section level2">
-    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
+    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">pk_reference_dataset</span> <span class="op">&lt;-</span> <span class="fu">d_pkparam</span><span class="op">(</span><span class="op">)</span></span></span>
 <span class="r-in"><span></span></span>
 </code></pre></div>
     </div>
   </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
-    </nav></aside></div>
+    </nav></aside>
+</div>
 
 
     <footer><div class="nest">
   <p>tern is a part of the <strong>NEST</strong> and <a href="https://pharmaverse.org/" class="external-link"><strong>pharmaverse</strong></a>.</p>
 </div>
-<script type="text/javascript" src="../analytics.js"></script></footer></div>
-
+<script type="text/javascript" src="../analytics.js"></script></footer>
+</div>
 
 
 
 
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+  </body>
+</html>
diff --git a/main/reference/d_proportion.html b/main/reference/d_proportion.html
index 0c714cface..3e0afe5535 100644
--- a/main/reference/d_proportion.html
+++ b/main/reference/d_proportion.html
@@ -1,7 +1,30 @@
-<!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Description of the proportion summary — d_proportion • tern</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Description of the proportion summary — d_proportion"><meta name="description" content="
-This is a helper function that describes the analysis in s_proportion()."><meta property="og:description" content="
-This is a helper function that describes the analysis in s_proportion()."><meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png"><link rel="stylesheet" href="../consent.css"><script src="../consent.js" type="text/javascript" charset="utf-8"></script></head><body>
+<html lang="en">
+<head>
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+<meta charset="utf-8">
+<meta http-equiv="X-UA-Compatible" content="IE=edge">
+<meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<title>Description of the proportion summary — d_proportion • tern</title>
+<!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png">
+<link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png">
+<link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png">
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+<script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet">
+<script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet">
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+<script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Description of the proportion summary — d_proportion">
+<meta name="description" content="
+This is a helper function that describes the analysis in s_proportion().">
+<meta property="og:description" content="
+This is a helper function that describes the analysis in s_proportion().">
+<meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png">
+<link rel="stylesheet" href="../consent.css">
+<script src="../consent.js" type="text/javascript" charset="utf-8"></script>
+</head>
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+</div>
 
 
   </div>
@@ -54,45 +117,55 @@
     </div>
 
     <div class="section level2">
-    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
+    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">d_proportion</span><span class="op">(</span><span class="va">conf_level</span>, <span class="va">method</span>, long <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span></code></pre></div>
     </div>
 
     <div class="section level2">
-    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
+    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a>
+</h2>
 
 
-<dl><dt id="arg-conf-level">conf_level<a class="anchor" aria-label="anchor" href="#arg-conf-level"></a></dt>
+<dl>
+<dt id="arg-conf-level">conf_level<a class="anchor" aria-label="anchor" href="#arg-conf-level"></a>
+</dt>
 <dd><p>(<code>proportion</code>)<br> confidence level of the interval.</p></dd>
 
 
-<dt id="arg-method">method<a class="anchor" aria-label="anchor" href="#arg-method"></a></dt>
+<dt id="arg-method">method<a class="anchor" aria-label="anchor" href="#arg-method"></a>
+</dt>
 <dd><p>(<code>string</code>)<br> the method used to construct the confidence interval
 for proportion of successful outcomes; one of <code>waldcc</code>, <code>wald</code>, <code>clopper-pearson</code>,
 <code>wilson</code>, <code>wilsonc</code>, <code>strat_wilson</code>, <code>strat_wilsonc</code>, <code>agresti-coull</code> or <code>jeffreys</code>.</p></dd>
 
 
-<dt id="arg-long">long<a class="anchor" aria-label="anchor" href="#arg-long"></a></dt>
+<dt id="arg-long">long<a class="anchor" aria-label="anchor" href="#arg-long"></a>
+</dt>
 <dd><p>(<code>flag</code>)<br> whether a long or a short (default) description is required.</p></dd>
 
-</dl></div>
+</dl>
+</div>
     <div class="section level2">
-    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
+    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a>
+</h2>
     <p>String describing the analysis.</p>
     </div>
 
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diff --git a/main/reference/d_proportion_diff.html b/main/reference/d_proportion_diff.html
index c662af0984..d4fe9533f1 100644
--- a/main/reference/d_proportion_diff.html
+++ b/main/reference/d_proportion_diff.html
@@ -1,9 +1,32 @@
-<!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Description of method used for proportion comparison — d_proportion_diff • tern</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Description of method used for proportion comparison — d_proportion_diff"><meta name="description" content="
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+<title>Description of method used for proportion comparison — d_proportion_diff • tern</title>
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+<meta name="description" content="
 This is an auxiliary function that describes the analysis in
-s_proportion_diff()."><meta property="og:description" content="
+s_proportion_diff().">
+<meta property="og:description" content="
 This is an auxiliary function that describes the analysis in
-s_proportion_diff()."><meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png"><link rel="stylesheet" href="../consent.css"><script src="../consent.js" type="text/javascript" charset="utf-8"></script></head><body>
+s_proportion_diff().">
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@@ -57,47 +120,58 @@
     </div>
 
     <div class="section level2">
-    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
+    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">d_proportion_diff</span><span class="op">(</span><span class="va">conf_level</span>, <span class="va">method</span>, long <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span></code></pre></div>
     </div>
 
     <div class="section level2">
-    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
+    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a>
+</h2>
 
 
-<dl><dt id="arg-conf-level">conf_level<a class="anchor" aria-label="anchor" href="#arg-conf-level"></a></dt>
+<dl>
+<dt id="arg-conf-level">conf_level<a class="anchor" aria-label="anchor" href="#arg-conf-level"></a>
+</dt>
 <dd><p>(<code>proportion</code>)<br> confidence level of the interval.</p></dd>
 
 
-<dt id="arg-method">method<a class="anchor" aria-label="anchor" href="#arg-method"></a></dt>
+<dt id="arg-method">method<a class="anchor" aria-label="anchor" href="#arg-method"></a>
+</dt>
 <dd><p>(<code>string</code>)<br> the method used for the confidence interval estimation.</p></dd>
 
 
-<dt id="arg-long">long<a class="anchor" aria-label="anchor" href="#arg-long"></a></dt>
+<dt id="arg-long">long<a class="anchor" aria-label="anchor" href="#arg-long"></a>
+</dt>
 <dd><p>(<code>flag</code>)<br> whether a long (<code>TRUE</code>) or a short (<code>FALSE</code>, default) description is required.</p></dd>
 
-</dl></div>
+</dl>
+</div>
     <div class="section level2">
-    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
+    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a>
+</h2>
     <p>A <code>string</code> describing the analysis.</p>
     </div>
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-    <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"></a></h2>
+    <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"></a>
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     <div class="dont-index"><p><a href="prop_diff.html">prop_diff</a></p></div>
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diff --git a/main/reference/d_rsp_subgroups_colvars.html b/main/reference/d_rsp_subgroups_colvars.html
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@@ -1,7 +1,30 @@
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-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Labels for column variables in binary response by subgroup table — d_rsp_subgroups_colvars • tern</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Labels for column variables in binary response by subgroup table — d_rsp_subgroups_colvars"><meta name="description" content="
-Internal function to check variables included in tabulate_rsp_subgroups() and create column labels."><meta property="og:description" content="
-Internal function to check variables included in tabulate_rsp_subgroups() and create column labels."><meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png"><link rel="stylesheet" href="../consent.css"><script src="../consent.js" type="text/javascript" charset="utf-8"></script></head><body>
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+<title>Labels for column variables in binary response by subgroup table — d_rsp_subgroups_colvars • tern</title>
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+<script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
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+<script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Labels for column variables in binary response by subgroup table — d_rsp_subgroups_colvars">
+<meta name="description" content="
+Internal function to check variables included in tabulate_rsp_subgroups() and create column labels.">
+<meta property="og:description" content="
+Internal function to check variables included in tabulate_rsp_subgroups() and create column labels.">
+<meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png">
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@@ -17,26 +40,66 @@
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+<li><a class="dropdown-item" href="../articles/missing_values.html">Missing Values in Tern</a></li>
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+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a>
+</div>
+</li></div>
+</ul>
+<ul class="navbar-nav">
+<li class="nav-item"><form class="form-inline" role="search">
+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json">
+</form></li>
 <li class="nav-item"><a class="external-link nav-link" href="https://github.com/insightsengineering/tern" aria-label="GitHub"><span class="fa fa-github"></span></a></li>
-      </ul></div>
+      </ul>
+</div>
 
 
   </div>
@@ -54,44 +117,54 @@
     </div>
 
     <div class="section level2">
-    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
+    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">d_rsp_subgroups_colvars</span><span class="op">(</span><span class="va">vars</span>, conf_level <span class="op">=</span> <span class="cn">NULL</span>, method <span class="op">=</span> <span class="cn">NULL</span><span class="op">)</span></span></code></pre></div>
     </div>
 
     <div class="section level2">
-    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
+    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a>
+</h2>
 
 
-<dl><dt id="arg-vars">vars<a class="anchor" aria-label="anchor" href="#arg-vars"></a></dt>
+<dl>
+<dt id="arg-vars">vars<a class="anchor" aria-label="anchor" href="#arg-vars"></a>
+</dt>
 <dd><p>(<code>character</code>)<br> variable names for the primary analysis variable to be iterated over.</p></dd>
 
 
-<dt id="arg-conf-level">conf_level<a class="anchor" aria-label="anchor" href="#arg-conf-level"></a></dt>
+<dt id="arg-conf-level">conf_level<a class="anchor" aria-label="anchor" href="#arg-conf-level"></a>
+</dt>
 <dd><p>(<code>proportion</code>)<br> confidence level of the interval.</p></dd>
 
 
-<dt id="arg-method">method<a class="anchor" aria-label="anchor" href="#arg-method"></a></dt>
+<dt id="arg-method">method<a class="anchor" aria-label="anchor" href="#arg-method"></a>
+</dt>
 <dd><p>(<code>string</code> or <code>NULL</code>)<br> specifies the test used to calculate the p-value for the difference between
 two proportions. For options, see <code><a href="prop_diff_test.html">test_proportion_diff()</a></code>. Default is <code>NULL</code> so no test is performed.</p></dd>
 
-</dl></div>
+</dl>
+</div>
     <div class="section level2">
-    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
+    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a>
+</h2>
     <p>A <code>list</code> of variables to tabulate and their labels.</p>
     </div>
 
   </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
-    </nav></aside></div>
+    </nav></aside>
+</div>
 
 
     <footer><div class="nest">
   <p>tern is a part of the <strong>NEST</strong> and <a href="https://pharmaverse.org/" class="external-link"><strong>pharmaverse</strong></a>.</p>
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-<script type="text/javascript" src="../analytics.js"></script></footer></div>
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+<script type="text/javascript" src="../analytics.js"></script></footer>
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diff --git a/main/reference/d_survival_subgroups_colvars.html b/main/reference/d_survival_subgroups_colvars.html
index 8d878c0804..52571bc846 100644
--- a/main/reference/d_survival_subgroups_colvars.html
+++ b/main/reference/d_survival_subgroups_colvars.html
@@ -1,7 +1,30 @@
-<!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Labels for column variables in survival duration by subgroup table — d_survival_subgroups_colvars • tern</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Labels for column variables in survival duration by subgroup table — d_survival_subgroups_colvars"><meta name="description" content="
-Internal function to check variables included in tabulate_survival_subgroups() and create column labels."><meta property="og:description" content="
-Internal function to check variables included in tabulate_survival_subgroups() and create column labels."><meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png"><link rel="stylesheet" href="../consent.css"><script src="../consent.js" type="text/javascript" charset="utf-8"></script></head><body>
+<html lang="en">
+<head>
+<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
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+<title>Labels for column variables in survival duration by subgroup table — d_survival_subgroups_colvars • tern</title>
+<!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png">
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+<link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png">
+<link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png">
+<link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png">
+<script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet">
+<script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet">
+<link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet">
+<script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Labels for column variables in survival duration by subgroup table — d_survival_subgroups_colvars">
+<meta name="description" content="
+Internal function to check variables included in tabulate_survival_subgroups() and create column labels.">
+<meta property="og:description" content="
+Internal function to check variables included in tabulate_survival_subgroups() and create column labels.">
+<meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png">
+<link rel="stylesheet" href="../consent.css">
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@@ -17,26 +40,66 @@
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+  <ul class="dropdown-menu" aria-labelledby="dropdown-articles">
+<li><a class="dropdown-item" href="../articles/missing_values.html">Missing Values in Tern</a></li>
     <li><a class="dropdown-item" href="../articles/tables.html">Tabulation</a></li>
     <li><a class="dropdown-item" href="../articles/tern_formats.html">Formatting Functions</a></li>
     <li><a class="dropdown-item" href="../articles/tern_functions_guide.html">Understanding `tern` functions</a></li>
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+</li>
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+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
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+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a>
+</div>
+</li></div>
+</ul>
+<ul class="navbar-nav">
+<li class="nav-item"><form class="form-inline" role="search">
+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json">
+</form></li>
 <li class="nav-item"><a class="external-link nav-link" href="https://github.com/insightsengineering/tern" aria-label="GitHub"><span class="fa fa-github"></span></a></li>
-      </ul></div>
+      </ul>
+</div>
 
 
   </div>
@@ -54,16 +117,23 @@
     </div>
 
     <div class="section level2">
-    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
+    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">d_survival_subgroups_colvars</span><span class="op">(</span><span class="va">vars</span>, <span class="va">conf_level</span>, <span class="va">method</span>, time_unit <span class="op">=</span> <span class="cn">NULL</span><span class="op">)</span></span></code></pre></div>
     </div>
 
     <div class="section level2">
-    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
+    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a>
+</h2>
 
 
-<dl><dt id="arg-vars">vars<a class="anchor" aria-label="anchor" href="#arg-vars"></a></dt>
-<dd><p>(<code>character</code>)<br> the names of statistics to be reported among:</p><ul><li><p><code>n_tot_events</code>: Total number of events per group.</p></li>
+<dl>
+<dt id="arg-vars">vars<a class="anchor" aria-label="anchor" href="#arg-vars"></a>
+</dt>
+<dd>
+<p>(<code>character</code>)<br> the names of statistics to be reported among:</p>
+<ul>
+<li><p><code>n_tot_events</code>: Total number of events per group.</p></li>
 <li><p><code>n_events</code>: Number of events per group.</p></li>
 <li><p><code>n_tot</code>: Total number of observations per group.</p></li>
 <li><p><code>n</code>: Number of observations per group.</p></li>
@@ -73,42 +143,51 @@ <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#argumen
 <li><p><code>pval</code>: p-value of the effect.
 Note, one of the statistics <code>n_tot</code> and <code>n_tot_events</code>, as well as both <code>hr</code> and <code>ci</code>
 are required.</p></li>
-</ul></dd>
+</ul>
+</dd>
 
 
-<dt id="arg-conf-level">conf_level<a class="anchor" aria-label="anchor" href="#arg-conf-level"></a></dt>
+<dt id="arg-conf-level">conf_level<a class="anchor" aria-label="anchor" href="#arg-conf-level"></a>
+</dt>
 <dd><p>(<code>proportion</code>)<br> confidence level of the interval.</p></dd>
 
 
-<dt id="arg-method">method<a class="anchor" aria-label="anchor" href="#arg-method"></a></dt>
+<dt id="arg-method">method<a class="anchor" aria-label="anchor" href="#arg-method"></a>
+</dt>
 <dd><p>(<code>string</code>)<br> p-value method for testing hazard ratio = 1.</p></dd>
 
 
-<dt id="arg-time-unit">time_unit<a class="anchor" aria-label="anchor" href="#arg-time-unit"></a></dt>
+<dt id="arg-time-unit">time_unit<a class="anchor" aria-label="anchor" href="#arg-time-unit"></a>
+</dt>
 <dd><p>(<code>string</code>)<br> label with unit of median survival time. Default <code>NULL</code> skips displaying unit.</p></dd>
 
-</dl></div>
+</dl>
+</div>
     <div class="section level2">
-    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
+    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a>
+</h2>
     <p>A <code>list</code> of variables and their labels to tabulate.</p>
     </div>
     <div class="section level2">
-    <h2 id="note">Note<a class="anchor" aria-label="anchor" href="#note"></a></h2>
+    <h2 id="note">Note<a class="anchor" aria-label="anchor" href="#note"></a>
+</h2>
     <p>At least one of <code>n_tot</code> and <code>n_tot_events</code> must be provided in <code>vars</code>.</p>
     </div>
 
   </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
-    </nav></aside></div>
+    </nav></aside>
+</div>
 
 
     <footer><div class="nest">
   <p>tern is a part of the <strong>NEST</strong> and <a href="https://pharmaverse.org/" class="external-link"><strong>pharmaverse</strong></a>.</p>
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-<script type="text/javascript" src="../analytics.js"></script></footer></div>
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diff --git a/main/reference/d_test_proportion_diff.html b/main/reference/d_test_proportion_diff.html
index 79c67de022..ea86d98cd7 100644
--- a/main/reference/d_test_proportion_diff.html
+++ b/main/reference/d_test_proportion_diff.html
@@ -1,7 +1,30 @@
-<!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Description of the difference test between two proportions — d_test_proportion_diff • tern</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Description of the difference test between two proportions — d_test_proportion_diff"><meta name="description" content="
-This is an auxiliary function that describes the analysis in s_test_proportion_diff."><meta property="og:description" content="
-This is an auxiliary function that describes the analysis in s_test_proportion_diff."><meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png"><link rel="stylesheet" href="../consent.css"><script src="../consent.js" type="text/javascript" charset="utf-8"></script></head><body>
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+<script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Description of the difference test between two proportions — d_test_proportion_diff">
+<meta name="description" content="
+This is an auxiliary function that describes the analysis in s_test_proportion_diff.">
+<meta property="og:description" content="
+This is an auxiliary function that describes the analysis in s_test_proportion_diff.">
+<meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png">
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+<body>
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+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
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+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
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+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a>
+</div>
+</li></div>
+</ul>
+<ul class="navbar-nav">
+<li class="nav-item"><form class="form-inline" role="search">
+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json">
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-      </ul></div>
+      </ul>
+</div>
 
 
   </div>
@@ -54,36 +117,44 @@
     </div>
 
     <div class="section level2">
-    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
+    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">d_test_proportion_diff</span><span class="op">(</span><span class="va">method</span><span class="op">)</span></span></code></pre></div>
     </div>
 
     <div class="section level2">
-    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
+    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a>
+</h2>
 
 
-<dl><dt id="arg-method">method<a class="anchor" aria-label="anchor" href="#arg-method"></a></dt>
+<dl>
+<dt id="arg-method">method<a class="anchor" aria-label="anchor" href="#arg-method"></a>
+</dt>
 <dd><p>(<code>string</code>)<br> one of <code>chisq</code>, <code>cmh</code>, <code>fisher</code>, or <code>schouten</code>; specifies the test used
 to calculate the p-value.</p></dd>
 
-</dl></div>
+</dl>
+</div>
     <div class="section level2">
-    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
+    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a>
+</h2>
     <p>A <code>string</code> describing the test from which the p-value is derived.</p>
     </div>
 
   </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
-    </nav></aside></div>
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diff --git a/main/reference/day2month.html b/main/reference/day2month.html
index ce62fff44d..a98215a6cf 100644
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+++ b/main/reference/day2month.html
@@ -1,5 +1,28 @@
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@@ -15,26 +38,66 @@
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+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
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+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
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+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a>
+</div>
+</li></div>
+</ul>
+<ul class="navbar-nav">
+<li class="nav-item"><form class="form-inline" role="search">
+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json">
+</form></li>
 <li class="nav-item"><a class="external-link nav-link" href="https://github.com/insightsengineering/tern" aria-label="GitHub"><span class="fa fa-github"></span></a></li>
-      </ul></div>
+      </ul>
+</div>
 
 
   </div>
@@ -51,25 +114,32 @@
     </div>
 
     <div class="section level2">
-    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
+    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">day2month</span><span class="op">(</span><span class="va">x</span><span class="op">)</span></span></code></pre></div>
     </div>
 
     <div class="section level2">
-    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
+    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a>
+</h2>
 
 
-<dl><dt id="arg-x">x<a class="anchor" aria-label="anchor" href="#arg-x"></a></dt>
+<dl>
+<dt id="arg-x">x<a class="anchor" aria-label="anchor" href="#arg-x"></a>
+</dt>
 <dd><p>(<code>numeric(1)</code>)<br> time in days.</p></dd>
 
-</dl></div>
+</dl>
+</div>
     <div class="section level2">
-    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
+    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a>
+</h2>
     <p>A <code>numeric</code> vector with the time in months.</p>
     </div>
 
     <div class="section level2">
-    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
+    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">x</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">403</span>, <span class="fl">248</span>, <span class="fl">30</span>, <span class="fl">86</span><span class="op">)</span></span></span>
 <span class="r-in"><span><span class="fu">day2month</span><span class="op">(</span><span class="va">x</span><span class="op">)</span></span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> [1] 13.2402464  8.1478439  0.9856263  2.8254620</span>
@@ -77,17 +147,19 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 </code></pre></div>
     </div>
   </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
-    </nav></aside></div>
+    </nav></aside>
+</div>
 
 
     <footer><div class="nest">
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diff --git a/main/reference/decorate_grob.html b/main/reference/decorate_grob.html
index 7fe8f37492..e38e844a7c 100644
--- a/main/reference/decorate_grob.html
+++ b/main/reference/decorate_grob.html
@@ -1,9 +1,32 @@
-<!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Add titles, footnotes, page Number, and a bounding box to a grid grob — decorate_grob • tern</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Add titles, footnotes, page Number, and a bounding box to a grid grob — decorate_grob"><meta name="description" content="
+<html lang="en">
+<head>
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+<meta http-equiv="X-UA-Compatible" content="IE=edge">
+<meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<title>Add titles, footnotes, page Number, and a bounding box to a grid grob — decorate_grob • tern</title>
+<!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png">
+<link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png">
+<link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png">
+<link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png">
+<link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png">
+<link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png">
+<script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet">
+<script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet">
+<link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet">
+<script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Add titles, footnotes, page Number, and a bounding box to a grid grob — decorate_grob">
+<meta name="description" content="
 This function is useful to label grid grobs (also ggplot2, and lattice plots)
-with title, footnote, and page numbers."><meta property="og:description" content="
+with title, footnote, and page numbers.">
+<meta property="og:description" content="
 This function is useful to label grid grobs (also ggplot2, and lattice plots)
-with title, footnote, and page numbers."><meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png"><link rel="stylesheet" href="../consent.css"><script src="../consent.js" type="text/javascript" charset="utf-8"></script></head><body>
+with title, footnote, and page numbers.">
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@@ -19,26 +42,66 @@
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     <li><a class="dropdown-item" href="../articles/tables.html">Tabulation</a></li>
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+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.5">v0.9.5</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.4">v0.9.4</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.3">v0.9.3</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1-rc3">v0.9.1-rc3</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a>
+</div>
+</li></div>
+</ul>
+<ul class="navbar-nav">
+<li class="nav-item"><form class="form-inline" role="search">
+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json">
+</form></li>
 <li class="nav-item"><a class="external-link nav-link" href="https://github.com/insightsengineering/tern" aria-label="GitHub"><span class="fa fa-github"></span></a></li>
-      </ul></div>
+      </ul>
+</div>
 
 
   </div>
@@ -57,7 +120,8 @@
     </div>
 
     <div class="section level2">
-    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
+    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">decorate_grob</span><span class="op">(</span></span>
 <span>  <span class="va">grob</span>,</span>
 <span>  <span class="va">titles</span>,</span>
@@ -78,92 +142,113 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
     </div>
 
     <div class="section level2">
-    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
+    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a>
+</h2>
 
 
-<dl><dt id="arg-grob">grob<a class="anchor" aria-label="anchor" href="#arg-grob"></a></dt>
+<dl>
+<dt id="arg-grob">grob<a class="anchor" aria-label="anchor" href="#arg-grob"></a>
+</dt>
 <dd><p>(<code>grob</code>)<br> a grid grob object, optionally <code>NULL</code> if only a <code>grob</code> with the decoration should be shown.</p></dd>
 
 
-<dt id="arg-titles">titles<a class="anchor" aria-label="anchor" href="#arg-titles"></a></dt>
+<dt id="arg-titles">titles<a class="anchor" aria-label="anchor" href="#arg-titles"></a>
+</dt>
 <dd><p>(<code>character</code>)<br> titles given as a vector of strings that are each separated by a newline and wrapped
 according to the page width.</p></dd>
 
 
-<dt id="arg-footnotes">footnotes<a class="anchor" aria-label="anchor" href="#arg-footnotes"></a></dt>
+<dt id="arg-footnotes">footnotes<a class="anchor" aria-label="anchor" href="#arg-footnotes"></a>
+</dt>
 <dd><p>(<code>character</code>)<br> footnotes. Uses the same formatting rules as <code>titles</code>.</p></dd>
 
 
-<dt id="arg-page">page<a class="anchor" aria-label="anchor" href="#arg-page"></a></dt>
+<dt id="arg-page">page<a class="anchor" aria-label="anchor" href="#arg-page"></a>
+</dt>
 <dd><p>(<code>string</code> or <code>NULL</code>)<br> page numeration. If <code>NULL</code> then no page number is displayed.</p></dd>
 
 
-<dt id="arg-width-titles">width_titles<a class="anchor" aria-label="anchor" href="#arg-width-titles"></a></dt>
+<dt id="arg-width-titles">width_titles<a class="anchor" aria-label="anchor" href="#arg-width-titles"></a>
+</dt>
 <dd><p>(<code><a href="https://rdrr.io/r/grid/unit.html" class="external-link">grid::unit</a></code>)<br> width of titles. Usually defined as all the available space
 <code>grid::unit(1, "npc")</code>, it is affected by the parameter <code>outer_margins</code>. Right margins (<code>outer_margins[4]</code>)
 need to be subtracted to the allowed width.</p></dd>
 
 
-<dt id="arg-width-footnotes">width_footnotes<a class="anchor" aria-label="anchor" href="#arg-width-footnotes"></a></dt>
+<dt id="arg-width-footnotes">width_footnotes<a class="anchor" aria-label="anchor" href="#arg-width-footnotes"></a>
+</dt>
 <dd><p>(<code><a href="https://rdrr.io/r/grid/unit.html" class="external-link">grid::unit</a></code>)<br> width of footnotes. Same default and margin correction as <code>width_titles</code>.</p></dd>
 
 
-<dt id="arg-border">border<a class="anchor" aria-label="anchor" href="#arg-border"></a></dt>
+<dt id="arg-border">border<a class="anchor" aria-label="anchor" href="#arg-border"></a>
+</dt>
 <dd><p>(<code>flag</code>)<br> whether a border should be drawn around the plot or not.</p></dd>
 
 
-<dt id="arg-padding">padding<a class="anchor" aria-label="anchor" href="#arg-padding"></a></dt>
+<dt id="arg-padding">padding<a class="anchor" aria-label="anchor" href="#arg-padding"></a>
+</dt>
 <dd><p>(<code><a href="https://rdrr.io/r/grid/unit.html" class="external-link">grid::unit</a></code>)<br> padding. A unit object of length 4. Innermost margin between the plot (<code>grob</code>)
 and, possibly, the border of the plot. Usually expressed in 4 identical values (usually <code>"lines"</code>). It defaults
 to <code>grid::unit(rep(1, 4), "lines")</code>.</p></dd>
 
 
-<dt id="arg-margins">margins<a class="anchor" aria-label="anchor" href="#arg-margins"></a></dt>
+<dt id="arg-margins">margins<a class="anchor" aria-label="anchor" href="#arg-margins"></a>
+</dt>
 <dd><p>(<code><a href="https://rdrr.io/r/grid/unit.html" class="external-link">grid::unit</a></code>)<br> margins. A unit object of length 4. Margins between the plot and the other
 elements in the list (e.g. titles, plot, and footers). This is usually expressed in 4 <code>"lines"</code>, where the
 lateral ones are 0s, while top and bottom are 1s. It defaults to <code>grid::unit(c(1, 0, 1, 0), "lines")</code>.</p></dd>
 
 
-<dt id="arg-outer-margins">outer_margins<a class="anchor" aria-label="anchor" href="#arg-outer-margins"></a></dt>
+<dt id="arg-outer-margins">outer_margins<a class="anchor" aria-label="anchor" href="#arg-outer-margins"></a>
+</dt>
 <dd><p>(<code><a href="https://rdrr.io/r/grid/unit.html" class="external-link">grid::unit</a></code>)<br> outer margins. A unit object of length 4. It defines the general margin of
 the plot, considering also decorations like titles, footnotes, and page numbers. It defaults to
 <code>grid::unit(c(2, 1.5, 3, 1.5), "cm")</code>.</p></dd>
 
 
-<dt id="arg-gp-titles">gp_titles<a class="anchor" aria-label="anchor" href="#arg-gp-titles"></a></dt>
+<dt id="arg-gp-titles">gp_titles<a class="anchor" aria-label="anchor" href="#arg-gp-titles"></a>
+</dt>
 <dd><p>(<code>gpar</code>)<br> a <code>gpar</code> object. Mainly used to set different <code>"fontsize"</code>.</p></dd>
 
 
-<dt id="arg-gp-footnotes">gp_footnotes<a class="anchor" aria-label="anchor" href="#arg-gp-footnotes"></a></dt>
+<dt id="arg-gp-footnotes">gp_footnotes<a class="anchor" aria-label="anchor" href="#arg-gp-footnotes"></a>
+</dt>
 <dd><p>(<code>gpar</code>)<br> a <code>gpar</code> object. Mainly used to set different <code>"fontsize"</code>.</p></dd>
 
 
-<dt id="arg-name">name<a class="anchor" aria-label="anchor" href="#arg-name"></a></dt>
+<dt id="arg-name">name<a class="anchor" aria-label="anchor" href="#arg-name"></a>
+</dt>
 <dd><p>a character identifier for the grob.  Used to find the
     grob on the display list and/or as a child of another grob.</p></dd>
 
 
-<dt id="arg-gp">gp<a class="anchor" aria-label="anchor" href="#arg-gp"></a></dt>
+<dt id="arg-gp">gp<a class="anchor" aria-label="anchor" href="#arg-gp"></a>
+</dt>
 <dd><p>A <code>"gpar"</code> object, typically the output
     from a call to the function <code><a href="https://rdrr.io/r/grid/gpar.html" class="external-link">gpar</a></code>.  This is basically
     a list of graphical parameter settings.</p></dd>
 
 
-<dt id="arg-vp">vp<a class="anchor" aria-label="anchor" href="#arg-vp"></a></dt>
+<dt id="arg-vp">vp<a class="anchor" aria-label="anchor" href="#arg-vp"></a>
+</dt>
 <dd><p>a <code><a href="https://rdrr.io/r/grid/viewport.html" class="external-link">viewport</a></code> object (or <code>NULL</code>).</p></dd>
 
-</dl></div>
+</dl>
+</div>
     <div class="section level2">
-    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
+    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a>
+</h2>
     <p>A grid grob (<code>gTree</code>).</p>
     </div>
     <div class="section level2">
-    <h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a></h2>
+    <h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a>
+</h2>
     <p>The titles and footnotes will be ragged, i.e. each title will be wrapped individually.</p>
     </div>
 
     <div class="section level2">
-    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
+    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va">grid</span><span class="op">)</span></span></span>
 <span class="r-in"><span></span></span>
 <span class="r-in"><span><span class="va">titles</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span></span></span>
@@ -283,17 +368,19 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 </code></pre></div>
     </div>
   </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
-    </nav></aside></div>
+    </nav></aside>
+</div>
 
 
     <footer><div class="nest">
   <p>tern is a part of the <strong>NEST</strong> and <a href="https://pharmaverse.org/" class="external-link"><strong>pharmaverse</strong></a>.</p>
 </div>
-<script type="text/javascript" src="../analytics.js"></script></footer></div>
-
+<script type="text/javascript" src="../analytics.js"></script></footer>
+</div>
 
 
 
 
-  </body></html>
 
+  </body>
+</html>
diff --git a/main/reference/decorate_grob_factory.html b/main/reference/decorate_grob_factory.html
index 363cc4daf4..0ed967e44e 100644
--- a/main/reference/decorate_grob_factory.html
+++ b/main/reference/decorate_grob_factory.html
@@ -1,5 +1,28 @@
-<!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Update page number — decorate_grob_factory • tern</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Update page number — decorate_grob_factory"><meta name="description" content="Automatically updates page number."><meta property="og:description" content="Automatically updates page number."><meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png"><link rel="stylesheet" href="../consent.css"><script src="../consent.js" type="text/javascript" charset="utf-8"></script></head><body>
+<html lang="en">
+<head>
+<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+<meta charset="utf-8">
+<meta http-equiv="X-UA-Compatible" content="IE=edge">
+<meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<title>Update page number — decorate_grob_factory • tern</title>
+<!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png">
+<link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png">
+<link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png">
+<link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png">
+<link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png">
+<link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png">
+<script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet">
+<script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet">
+<link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet">
+<script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Update page number — decorate_grob_factory">
+<meta name="description" content="Automatically updates page number.">
+<meta property="og:description" content="Automatically updates page number.">
+<meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png">
+<link rel="stylesheet" href="../consent.css">
+<script src="../consent.js" type="text/javascript" charset="utf-8"></script>
+</head>
+<body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
 
 
@@ -15,26 +38,66 @@
     </button>
 
     <div id="navbar" class="collapse navbar-collapse ms-3">
-      <ul class="navbar-nav me-auto"><li class="nav-item"><a class="nav-link" href="../articles/tern.html">Get started</a></li>
+      <ul class="navbar-nav me-auto">
+<li class="nav-item"><a class="nav-link" href="../articles/tern.html">Get started</a></li>
 <li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
 <li class="nav-item dropdown">
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-articles" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Articles</button>
-  <ul class="dropdown-menu" aria-labelledby="dropdown-articles"><li><a class="dropdown-item" href="../articles/missing_values.html">Missing Values in Tern</a></li>
+  <ul class="dropdown-menu" aria-labelledby="dropdown-articles">
+<li><a class="dropdown-item" href="../articles/missing_values.html">Missing Values in Tern</a></li>
     <li><a class="dropdown-item" href="../articles/tables.html">Tabulation</a></li>
     <li><a class="dropdown-item" href="../articles/tern_formats.html">Formatting Functions</a></li>
     <li><a class="dropdown-item" href="../articles/tern_functions_guide.html">Understanding `tern` functions</a></li>
-  </ul></li>
+  </ul>
+</li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
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   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
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+  <ul class="dropdown-menu" aria-labelledby="dropdown-reports">
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- <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json"></form></li>
+  </ul>
+</li>
+      <div><li class="nav-item dropdown">
+    <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-versions">Versions</a>
+    <div class="dropdown-menu" aria-labelledby="dropdown-versions">
+    <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
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+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
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+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
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+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a>
+</div>
+</li></div>
+</ul>
+<ul class="navbar-nav">
+<li class="nav-item"><form class="form-inline" role="search">
+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json">
+</form></li>
 <li class="nav-item"><a class="external-link nav-link" href="https://github.com/insightsengineering/tern" aria-label="GitHub"><span class="fa fa-github"></span></a></li>
-      </ul></div>
+      </ul>
+</div>
 
 
   </div>
@@ -51,39 +114,48 @@
     </div>
 
     <div class="section level2">
-    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
+    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">decorate_grob_factory</span><span class="op">(</span><span class="va">npages</span>, <span class="va">...</span><span class="op">)</span></span></code></pre></div>
     </div>
 
     <div class="section level2">
-    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
+    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a>
+</h2>
 
 
-<dl><dt id="arg-npages">npages<a class="anchor" aria-label="anchor" href="#arg-npages"></a></dt>
+<dl>
+<dt id="arg-npages">npages<a class="anchor" aria-label="anchor" href="#arg-npages"></a>
+</dt>
 <dd><p>(<code>numeric(1)</code>)<br> total number of pages.</p></dd>
 
 
-<dt id="arg--">...<a class="anchor" aria-label="anchor" href="#arg--"></a></dt>
+<dt id="arg--">...<a class="anchor" aria-label="anchor" href="#arg--"></a>
+</dt>
 <dd><p>arguments passed on to <code><a href="decorate_grob.html">decorate_grob()</a></code>.</p></dd>
 
-</dl></div>
+</dl>
+</div>
     <div class="section level2">
-    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
+    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a>
+</h2>
     <p>Closure that increments the page number.</p>
     </div>
 
   </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
-    </nav></aside></div>
+    </nav></aside>
+</div>
 
 
     <footer><div class="nest">
   <p>tern is a part of the <strong>NEST</strong> and <a href="https://pharmaverse.org/" class="external-link"><strong>pharmaverse</strong></a>.</p>
 </div>
-<script type="text/javascript" src="../analytics.js"></script></footer></div>
-
+<script type="text/javascript" src="../analytics.js"></script></footer>
+</div>
 
 
 
 
-  </body></html>
 
+  </body>
+</html>
diff --git a/main/reference/decorate_grob_set.html b/main/reference/decorate_grob_set.html
index f9cd6f1591..5a82f81cf2 100644
--- a/main/reference/decorate_grob_set.html
+++ b/main/reference/decorate_grob_set.html
@@ -1,7 +1,30 @@
-<!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Decorate set of grobs and add page numbering — decorate_grob_set • tern</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Decorate set of grobs and add page numbering — decorate_grob_set"><meta name="description" content="
-Note that this uses the decorate_grob_factory() function."><meta property="og:description" content="
-Note that this uses the decorate_grob_factory() function."><meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png"><link rel="stylesheet" href="../consent.css"><script src="../consent.js" type="text/javascript" charset="utf-8"></script></head><body>
+<html lang="en">
+<head>
+<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+<meta charset="utf-8">
+<meta http-equiv="X-UA-Compatible" content="IE=edge">
+<meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<title>Decorate set of grobs and add page numbering — decorate_grob_set • tern</title>
+<!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png">
+<link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png">
+<link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png">
+<link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png">
+<link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png">
+<link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png">
+<script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet">
+<script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet">
+<link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet">
+<script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Decorate set of grobs and add page numbering — decorate_grob_set">
+<meta name="description" content="
+Note that this uses the decorate_grob_factory() function.">
+<meta property="og:description" content="
+Note that this uses the decorate_grob_factory() function.">
+<meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png">
+<link rel="stylesheet" href="../consent.css">
+<script src="../consent.js" type="text/javascript" charset="utf-8"></script>
+</head>
+<body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
 
 
@@ -17,26 +40,66 @@
     </button>
 
     <div id="navbar" class="collapse navbar-collapse ms-3">
-      <ul class="navbar-nav me-auto"><li class="nav-item"><a class="nav-link" href="../articles/tern.html">Get started</a></li>
+      <ul class="navbar-nav me-auto">
+<li class="nav-item"><a class="nav-link" href="../articles/tern.html">Get started</a></li>
 <li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
 <li class="nav-item dropdown">
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-articles" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Articles</button>
-  <ul class="dropdown-menu" aria-labelledby="dropdown-articles"><li><a class="dropdown-item" href="../articles/missing_values.html">Missing Values in Tern</a></li>
+  <ul class="dropdown-menu" aria-labelledby="dropdown-articles">
+<li><a class="dropdown-item" href="../articles/missing_values.html">Missing Values in Tern</a></li>
     <li><a class="dropdown-item" href="../articles/tables.html">Tabulation</a></li>
     <li><a class="dropdown-item" href="../articles/tern_formats.html">Formatting Functions</a></li>
     <li><a class="dropdown-item" href="../articles/tern_functions_guide.html">Understanding `tern` functions</a></li>
-  </ul></li>
+  </ul>
+</li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
-  <ul class="dropdown-menu" aria-labelledby="dropdown-reports"><li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
+  <ul class="dropdown-menu" aria-labelledby="dropdown-reports">
+<li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
     <li><a class="dropdown-item" href="../unit-test-report/">Unit test report</a></li>
     <li><a class="dropdown-item" href="../unit-test-report-non-cran/">Non-CRAN unit test report</a></li>
-  </ul></li>
-      </ul><ul class="navbar-nav"><li class="nav-item"><form class="form-inline" role="search">
- <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json"></form></li>
+  </ul>
+</li>
+      <div><li class="nav-item dropdown">
+    <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-versions">Versions</a>
+    <div class="dropdown-menu" aria-labelledby="dropdown-versions">
+    <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/main">main</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.5">v0.9.5</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.4">v0.9.4</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.3">v0.9.3</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1-rc3">v0.9.1-rc3</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a>
+</div>
+</li></div>
+</ul>
+<ul class="navbar-nav">
+<li class="nav-item"><form class="form-inline" role="search">
+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json">
+</form></li>
 <li class="nav-item"><a class="external-link nav-link" href="https://github.com/insightsengineering/tern" aria-label="GitHub"><span class="fa fa-github"></span></a></li>
-      </ul></div>
+      </ul>
+</div>
 
 
   </div>
@@ -54,29 +117,37 @@
     </div>
 
     <div class="section level2">
-    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
+    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">decorate_grob_set</span><span class="op">(</span><span class="va">grobs</span>, <span class="va">...</span><span class="op">)</span></span></code></pre></div>
     </div>
 
     <div class="section level2">
-    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
+    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a>
+</h2>
 
 
-<dl><dt id="arg-grobs">grobs<a class="anchor" aria-label="anchor" href="#arg-grobs"></a></dt>
+<dl>
+<dt id="arg-grobs">grobs<a class="anchor" aria-label="anchor" href="#arg-grobs"></a>
+</dt>
 <dd><p>(<code>list</code> of <code>grob</code>)<br> a list of grid grobs.</p></dd>
 
 
-<dt id="arg--">...<a class="anchor" aria-label="anchor" href="#arg--"></a></dt>
+<dt id="arg--">...<a class="anchor" aria-label="anchor" href="#arg--"></a>
+</dt>
 <dd><p>arguments passed on to <code><a href="decorate_grob.html">decorate_grob()</a></code>.</p></dd>
 
-</dl></div>
+</dl>
+</div>
     <div class="section level2">
-    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
+    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a>
+</h2>
     <p>A decorated grob.</p>
     </div>
 
     <div class="section level2">
-    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
+    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://ggplot2.tidyverse.org" class="external-link">ggplot2</a></span><span class="op">)</span></span></span>
 <span class="r-in"><span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va">grid</span><span class="op">)</span></span></span>
 <span class="r-in"><span><span class="va">g</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/with.html" class="external-link">with</a></span><span class="op">(</span>data <span class="op">=</span> <span class="va">iris</span>, <span class="op">{</span></span></span>
@@ -121,17 +192,19 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 </code></pre></div>
     </div>
   </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
-    </nav></aside></div>
+    </nav></aside>
+</div>
 
 
     <footer><div class="nest">
   <p>tern is a part of the <strong>NEST</strong> and <a href="https://pharmaverse.org/" class="external-link"><strong>pharmaverse</strong></a>.</p>
 </div>
-<script type="text/javascript" src="../analytics.js"></script></footer></div>
-
+<script type="text/javascript" src="../analytics.js"></script></footer>
+</div>
 
 
 
 
-  </body></html>
 
+  </body>
+</html>
diff --git a/main/reference/default_na_str.html b/main/reference/default_na_str.html
index 708d4b7b0c..e6758428f6 100644
--- a/main/reference/default_na_str.html
+++ b/main/reference/default_na_str.html
@@ -1,15 +1,38 @@
-<!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Default string replacement for NA values — default_na_str • tern</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Default string replacement for NA values — default_na_str"><meta name="description" content="
+<html lang="en">
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+<title>Default string replacement for NA values — default_na_str • tern</title>
+<!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png">
+<link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png">
+<link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png">
+<link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png">
+<link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png">
+<link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png">
+<script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet">
+<script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet">
+<link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet">
+<script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Default string replacement for NA values — default_na_str">
+<meta name="description" content="
 The default string used to represent NA values. This value is used as the default
 value for the na_str argument throughout the tern package, and printed in place
 of NA values in output tables. If not specified for each tern function by the user
 via the na_str argument, or in the R environment options via set_default_na_str(),
-then NA is used."><meta property="og:description" content="
+then NA is used.">
+<meta property="og:description" content="
 The default string used to represent NA values. This value is used as the default
 value for the na_str argument throughout the tern package, and printed in place
 of NA values in output tables. If not specified for each tern function by the user
 via the na_str argument, or in the R environment options via set_default_na_str(),
-then NA is used."><meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png"><link rel="stylesheet" href="../consent.css"><script src="../consent.js" type="text/javascript" charset="utf-8"></script></head><body>
+then NA is used.">
+<meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png">
+<link rel="stylesheet" href="../consent.css">
+<script src="../consent.js" type="text/javascript" charset="utf-8"></script>
+</head>
+<body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
 
 
@@ -25,26 +48,66 @@
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+  </ul>
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   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
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+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.5">v0.9.5</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.4">v0.9.4</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.3">v0.9.3</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1-rc3">v0.9.1-rc3</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a>
+</div>
+</li></div>
+</ul>
+<ul class="navbar-nav">
+<li class="nav-item"><form class="form-inline" role="search">
+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json">
+</form></li>
 <li class="nav-item"><a class="external-link nav-link" href="https://github.com/insightsengineering/tern" aria-label="GitHub"><span class="fa fa-github"></span></a></li>
-      </ul></div>
+      </ul>
+</div>
 
 
   </div>
@@ -66,39 +129,53 @@
     </div>
 
     <div class="section level2">
-    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
+    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">default_na_str</span><span class="op">(</span><span class="op">)</span></span>
 <span></span>
 <span><span class="fu">set_default_na_str</span><span class="op">(</span><span class="va">na_str</span><span class="op">)</span></span></code></pre></div>
     </div>
 
     <div class="section level2">
-    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
+    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a>
+</h2>
 
 
-<dl><dt id="arg-na-str">na_str<a class="anchor" aria-label="anchor" href="#arg-na-str"></a></dt>
+<dl>
+<dt id="arg-na-str">na_str<a class="anchor" aria-label="anchor" href="#arg-na-str"></a>
+</dt>
 <dd><p>(<code>string</code>)<br> single string value to set in the R environment options as
 the default value to replace <code>NA</code>s. Use <code>getOption("tern_default_na_str")</code> to check the
 current value set in the R environment (defaults to <code>NULL</code> if not set).</p></dd>
 
-</dl></div>
+</dl>
+</div>
     <div class="section level2">
-    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
+    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a>
+</h2>
 
-<ul><li><p><code>default_na_str</code> returns the current value if an R environment option has been set
+<ul>
+<li><p><code>default_na_str</code> returns the current value if an R environment option has been set
 for <code>"tern_default_na_str"</code>, or <code>NA_character_</code> otherwise.</p></li>
-</ul><ul><li><p><code>set_default_na_str</code> has no return value.</p></li>
-</ul></div>
+</ul>
+<ul>
+<li><p><code>set_default_na_str</code> has no return value.</p></li>
+</ul>
+</div>
     <div class="section level2">
-    <h2 id="functions">Functions<a class="anchor" aria-label="anchor" href="#functions"></a></h2>
+    <h2 id="functions">Functions<a class="anchor" aria-label="anchor" href="#functions"></a>
+</h2>
 
-<ul><li><p><code>default_na_str()</code>: Accessor for default <code>NA</code> value replacement string.</p></li>
+<ul>
+<li><p><code>default_na_str()</code>: Accessor for default <code>NA</code> value replacement string.</p></li>
 <li><p><code>set_default_na_str()</code>: Setter for default <code>NA</code> value replacement string. Sets the
 option <code>"tern_default_na_str"</code> within the R environment.</p></li>
-</ul></div>
+</ul>
+</div>
 
     <div class="section level2">
-    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
+    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="co"># Default settings</span></span></span>
 <span class="r-in"><span><span class="fu">default_na_str</span><span class="op">(</span><span class="op">)</span></span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> [1] NA</span>
@@ -117,17 +194,19 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 </code></pre></div>
     </div>
   </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
-    </nav></aside></div>
+    </nav></aside>
+</div>
 
 
     <footer><div class="nest">
   <p>tern is a part of the <strong>NEST</strong> and <a href="https://pharmaverse.org/" class="external-link"><strong>pharmaverse</strong></a>.</p>
 </div>
-<script type="text/javascript" src="../analytics.js"></script></footer></div>
-
+<script type="text/javascript" src="../analytics.js"></script></footer>
+</div>
 
 
 
 
-  </body></html>
 
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diff --git a/main/reference/default_stats_formats_labels.html b/main/reference/default_stats_formats_labels.html
index be01c1e44d..631651c5fc 100644
--- a/main/reference/default_stats_formats_labels.html
+++ b/main/reference/default_stats_formats_labels.html
@@ -1,13 +1,36 @@
-<!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Get default statistical methods and their associated formats, labels, and indent modifiers — default_stats_formats_labels • tern</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Get default statistical methods and their associated formats, labels, and indent modifiers — default_stats_formats_labels"><meta name="description" content="
+<html lang="en">
+<head>
+<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+<meta charset="utf-8">
+<meta http-equiv="X-UA-Compatible" content="IE=edge">
+<meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<title>Get default statistical methods and their associated formats, labels, and indent modifiers — default_stats_formats_labels • tern</title>
+<!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png">
+<link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png">
+<link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png">
+<link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png">
+<link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png">
+<link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png">
+<script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet">
+<script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet">
+<link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet">
+<script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Get default statistical methods and their associated formats, labels, and indent modifiers — default_stats_formats_labels">
+<meta name="description" content="
 Utility functions to get valid statistic methods for different method groups
 (.stats) and their associated formats (.formats), labels (.labels), and indent modifiers
 (.indent_mods). This utility is used across tern, but some of its working principles can be
-seen in analyze_vars(). See notes to understand why this is experimental."><meta property="og:description" content="
+seen in analyze_vars(). See notes to understand why this is experimental.">
+<meta property="og:description" content="
 Utility functions to get valid statistic methods for different method groups
 (.stats) and their associated formats (.formats), labels (.labels), and indent modifiers
 (.indent_mods). This utility is used across tern, but some of its working principles can be
-seen in analyze_vars(). See notes to understand why this is experimental."><meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png"><link rel="stylesheet" href="../consent.css"><script src="../consent.js" type="text/javascript" charset="utf-8"></script></head><body>
+seen in analyze_vars(). See notes to understand why this is experimental.">
+<meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png">
+<link rel="stylesheet" href="../consent.css">
+<script src="../consent.js" type="text/javascript" charset="utf-8"></script>
+</head>
+<body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
 
 
@@ -23,26 +46,66 @@
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-      <ul class="navbar-nav me-auto"><li class="nav-item"><a class="nav-link" href="../articles/tern.html">Get started</a></li>
+      <ul class="navbar-nav me-auto">
+<li class="nav-item"><a class="nav-link" href="../articles/tern.html">Get started</a></li>
 <li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
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-  <ul class="dropdown-menu" aria-labelledby="dropdown-articles"><li><a class="dropdown-item" href="../articles/missing_values.html">Missing Values in Tern</a></li>
+  <ul class="dropdown-menu" aria-labelledby="dropdown-articles">
+<li><a class="dropdown-item" href="../articles/missing_values.html">Missing Values in Tern</a></li>
     <li><a class="dropdown-item" href="../articles/tables.html">Tabulation</a></li>
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-  </ul></li>
+  </ul>
+</li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
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+  <ul class="dropdown-menu" aria-labelledby="dropdown-reports">
+<li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
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-      </ul><ul class="navbar-nav"><li class="nav-item"><form class="form-inline" role="search">
- <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json"></form></li>
+  </ul>
+</li>
+      <div><li class="nav-item dropdown">
+    <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-versions">Versions</a>
+    <div class="dropdown-menu" aria-labelledby="dropdown-versions">
+    <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/main">main</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.5">v0.9.5</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.4">v0.9.4</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.3">v0.9.3</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1-rc3">v0.9.1-rc3</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a>
+</div>
+</li></div>
+</ul>
+<ul class="navbar-nav">
+<li class="nav-item"><form class="form-inline" role="search">
+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json">
+</form></li>
 <li class="nav-item"><a class="external-link nav-link" href="https://github.com/insightsengineering/tern" aria-label="GitHub"><span class="fa fa-github"></span></a></li>
-      </ul></div>
+      </ul>
+</div>
 
 
   </div>
@@ -63,7 +126,8 @@
     </div>
 
     <div class="section level2">
-    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
+    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">get_stats</span><span class="op">(</span></span>
 <span>  method_groups <span class="op">=</span> <span class="st">"analyze_vars_numeric"</span>,</span>
 <span>  stats_in <span class="op">=</span> <span class="cn">NULL</span>,</span>
@@ -88,48 +152,64 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
     </div>
 
     <div class="section level2">
-    <h2 id="format">Format<a class="anchor" aria-label="anchor" href="#format"></a></h2>
+    <h2 id="format">Format<a class="anchor" aria-label="anchor" href="#format"></a>
+</h2>
 
-<ul><li><p><code>tern_default_stats</code> is a named list of available statistics, with each element
+<ul>
+<li><p><code>tern_default_stats</code> is a named list of available statistics, with each element
 named for their corresponding statistical method group.</p></li>
-</ul><ul><li><p><code>tern_default_formats</code> is a named vector of available default formats, with each element
+</ul>
+<ul>
+<li><p><code>tern_default_formats</code> is a named vector of available default formats, with each element
 named for their corresponding statistic.</p></li>
-</ul><ul><li><p><code>tern_default_labels</code> is a named <code>character</code> vector of available default labels, with each element
+</ul>
+<ul>
+<li><p><code>tern_default_labels</code> is a named <code>character</code> vector of available default labels, with each element
 named for their corresponding statistic.</p></li>
-</ul></div>
+</ul>
+</div>
     <div class="section level2">
-    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
+    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a>
+</h2>
 
 
-<dl><dt id="arg-method-groups">method_groups<a class="anchor" aria-label="anchor" href="#arg-method-groups"></a></dt>
+<dl>
+<dt id="arg-method-groups">method_groups<a class="anchor" aria-label="anchor" href="#arg-method-groups"></a>
+</dt>
 <dd><p>(<code>character</code>)<br> indicates the statistical method group (<code>tern</code> analyze function)
 to retrieve default statistics for. A character vector can be used to specify more than one statistical
 method group.</p></dd>
 
 
-<dt id="arg-stats-in">stats_in<a class="anchor" aria-label="anchor" href="#arg-stats-in"></a></dt>
+<dt id="arg-stats-in">stats_in<a class="anchor" aria-label="anchor" href="#arg-stats-in"></a>
+</dt>
 <dd><p>(<code>character</code>)<br> statistics to retrieve for the selected method group.</p></dd>
 
 
-<dt id="arg-add-pval">add_pval<a class="anchor" aria-label="anchor" href="#arg-add-pval"></a></dt>
+<dt id="arg-add-pval">add_pval<a class="anchor" aria-label="anchor" href="#arg-add-pval"></a>
+</dt>
 <dd><p>(<code>flag</code>)<br> should <code>"pval"</code> (or <code>"pval_counts"</code> if <code>method_groups</code> contains
 <code>"analyze_vars_counts"</code>) be added to the statistical methods?</p></dd>
 
 
-<dt id="arg-stats">stats<a class="anchor" aria-label="anchor" href="#arg-stats"></a></dt>
+<dt id="arg-stats">stats<a class="anchor" aria-label="anchor" href="#arg-stats"></a>
+</dt>
 <dd><p>(<code>character</code>)<br> statistical methods to get defaults for.</p></dd>
 
 
-<dt id="arg-formats-in">formats_in<a class="anchor" aria-label="anchor" href="#arg-formats-in"></a></dt>
+<dt id="arg-formats-in">formats_in<a class="anchor" aria-label="anchor" href="#arg-formats-in"></a>
+</dt>
 <dd><p>(named <code>vector</code>)<br> inserted formats to replace defaults. It can be a
 character vector from <code><a href="https://insightsengineering.github.io/formatters/latest-tag/reference/list_formats.html" class="external-link">formatters::list_valid_format_labels()</a></code> or a custom format function.</p></dd>
 
 
-<dt id="arg-labels-in">labels_in<a class="anchor" aria-label="anchor" href="#arg-labels-in"></a></dt>
+<dt id="arg-labels-in">labels_in<a class="anchor" aria-label="anchor" href="#arg-labels-in"></a>
+</dt>
 <dd><p>(named <code>character</code>)<br> inserted labels to replace defaults.</p></dd>
 
 
-<dt id="arg-row-nms">row_nms<a class="anchor" aria-label="anchor" href="#arg-row-nms"></a></dt>
+<dt id="arg-row-nms">row_nms<a class="anchor" aria-label="anchor" href="#arg-row-nms"></a>
+</dt>
 <dd><p>(<code>character</code>)<br> row names. Levels of a <code>factor</code> or <code>character</code> variable, each
 of which the statistics in <code>.stats</code> will be calculated for. If this parameter is set, these
 variable levels will be used as the defaults, and the names of the given custom values should
@@ -137,42 +217,62 @@ <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#argumen
 variable names if rows correspond to different variables instead of levels. Defaults to <code>NULL</code>.</p></dd>
 
 
-<dt id="arg-indents-in">indents_in<a class="anchor" aria-label="anchor" href="#arg-indents-in"></a></dt>
+<dt id="arg-indents-in">indents_in<a class="anchor" aria-label="anchor" href="#arg-indents-in"></a>
+</dt>
 <dd><p>(named <code>vector</code>)<br> inserted indent modifiers to replace defaults (default is <code>0L</code>).</p></dd>
 
 
-<dt id="arg-type">type<a class="anchor" aria-label="anchor" href="#arg-type"></a></dt>
+<dt id="arg-type">type<a class="anchor" aria-label="anchor" href="#arg-type"></a>
+</dt>
 <dd><p>(<code>string</code>)<br><code>"numeric"</code> or <code>"counts"</code>.</p></dd>
 
 
-<dt id="arg-include-pval">include_pval<a class="anchor" aria-label="anchor" href="#arg-include-pval"></a></dt>
+<dt id="arg-include-pval">include_pval<a class="anchor" aria-label="anchor" href="#arg-include-pval"></a>
+</dt>
 <dd><p>(<code>flag</code>)<br> same as the <code>add_pval</code> argument in <code>get_stats()</code>.</p></dd>
 
-</dl></div>
+</dl>
+</div>
     <div class="section level2">
-    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
-
-<ul><li><p><code>get_stats()</code> returns a <code>character</code> vector of statistical methods.</p></li>
-</ul><ul><li><p><code>get_formats_from_stats()</code> returns a named vector of formats (if present in either
+    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a>
+</h2>
+
+<ul>
+<li><p><code>get_stats()</code> returns a <code>character</code> vector of statistical methods.</p></li>
+</ul>
+<ul>
+<li><p><code>get_formats_from_stats()</code> returns a named vector of formats (if present in either
 <code>tern_default_formats</code> or <code>formats_in</code>, otherwise <code>NULL</code>). Values can be taken from
 <code><a href="https://insightsengineering.github.io/formatters/latest-tag/reference/list_formats.html" class="external-link">formatters::list_valid_format_labels()</a></code> or a custom function (e.g. <a href="formatting_functions.html">formatting_functions</a>).</p></li>
-</ul><ul><li><p><code>get_labels_from_stats()</code> returns a named <code>character</code> vector of labels (if present in either
+</ul>
+<ul>
+<li><p><code>get_labels_from_stats()</code> returns a named <code>character</code> vector of labels (if present in either
 <code>tern_default_labels</code> or <code>labels_in</code>, otherwise <code>NULL</code>).</p></li>
-</ul><ul><li><p><code>get_indents_from_stats()</code> returns a single indent modifier value to apply to all rows
+</ul>
+<ul>
+<li><p><code>get_indents_from_stats()</code> returns a single indent modifier value to apply to all rows
 or a named numeric vector of indent modifiers (if present, otherwise <code>NULL</code>).</p></li>
-</ul><ul><li><p><code>summary_formats()</code> returns a named <code>vector</code> of default statistic formats for the given data type.</p></li>
-</ul><ul><li><p><code>summary_labels</code> returns a named <code>vector</code> of default statistic labels for the given data type.</p></li>
-</ul></div>
+</ul>
+<ul>
+<li><p><code>summary_formats()</code> returns a named <code>vector</code> of default statistic formats for the given data type.</p></li>
+</ul>
+<ul>
+<li><p><code>summary_labels</code> returns a named <code>vector</code> of default statistic labels for the given data type.</p></li>
+</ul>
+</div>
     <div class="section level2">
-    <h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a></h2>
+    <h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a>
+</h2>
     <p>Current choices for <code>type</code> are <code>counts</code> and <code>numeric</code> for <code><a href="analyze_variables.html">analyze_vars()</a></code> and affect <code>get_stats()</code>.</p>
 <p><code>summary_*</code> quick get functions for labels or formats uses <code>get_stats</code> and <code>get_labels_from_stats</code> or
 <code>get_formats_from_stats</code> respectively to retrieve relevant information.</p>
     </div>
     <div class="section level2">
-    <h2 id="functions">Functions<a class="anchor" aria-label="anchor" href="#functions"></a></h2>
+    <h2 id="functions">Functions<a class="anchor" aria-label="anchor" href="#functions"></a>
+</h2>
 
-<ul><li><p><code>get_stats()</code>: Get statistics available for a given method
+<ul>
+<li><p><code>get_stats()</code>: Get statistics available for a given method
 group (analyze function). To check available defaults see <code>tern::tern_default_stats</code> list.</p></li>
 <li><p><code>get_formats_from_stats()</code>: Get formats corresponding to a list of statistics.
 To check available defaults see <code>tern::tern_default_formats</code> list.</p></li>
@@ -190,21 +290,25 @@ <h2 id="functions">Functions<a class="anchor" aria-label="anchor" href="#functio
 <li><p><code>summary_labels()</code>: <a href="https://lifecycle.r-lib.org/articles/stages.html#stable" class="external-link"><img src="figures/lifecycle-stable.svg" alt="[Stable]"></a>
 Quick function to retrieve default labels for summary statistics.
 Returns labels of descriptive statistics which are understood by <code>rtables</code>. Similar to <code>summary_formats</code>.</p></li>
-</ul></div>
+</ul>
+</div>
     <div class="section level2">
-    <h2 id="note">Note<a class="anchor" aria-label="anchor" href="#note"></a></h2>
+    <h2 id="note">Note<a class="anchor" aria-label="anchor" href="#note"></a>
+</h2>
     <p>These defaults are experimental because we use the names of functions to retrieve the default
 statistics. This should be generalized in groups of methods according to more reasonable groupings.</p>
 <p>Formats in <code>tern</code> and <code>rtables</code> can be functions that take in the table cell value and
 return a string. This is well documented in <code><a href="https://insightsengineering.github.io/rtables/latest-tag/articles/custom_appearance.html" class="external-link">vignette("custom_appearance", package = "rtables")</a></code>.</p>
     </div>
     <div class="section level2">
-    <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"></a></h2>
+    <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"></a>
+</h2>
     <div class="dont-index"><p><a href="formatting_functions.html">formatting_functions</a></p></div>
     </div>
 
     <div class="section level2">
-    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
+    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="co"># analyze_vars is numeric</span></span></span>
 <span class="r-in"><span><span class="va">num_stats</span> <span class="op">&lt;-</span> <span class="fu">get_stats</span><span class="op">(</span><span class="st">"analyze_vars_numeric"</span><span class="op">)</span> <span class="co"># also the default</span></span></span>
 <span class="r-in"><span></span></span>
@@ -874,17 +978,19 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 </code></pre></div>
     </div>
   </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
-    </nav></aside></div>
+    </nav></aside>
+</div>
 
 
     <footer><div class="nest">
   <p>tern is a part of the <strong>NEST</strong> and <a href="https://pharmaverse.org/" class="external-link"><strong>pharmaverse</strong></a>.</p>
 </div>
-<script type="text/javascript" src="../analytics.js"></script></footer></div>
-
+<script type="text/javascript" src="../analytics.js"></script></footer>
+</div>
 
 
 
 
-  </body></html>
 
+  </body>
+</html>
diff --git a/main/reference/desctools_binom.html b/main/reference/desctools_binom.html
index ebb10f3f90..5db90d9856 100644
--- a/main/reference/desctools_binom.html
+++ b/main/reference/desctools_binom.html
@@ -1,7 +1,30 @@
-<!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Confidence intervals for a difference of binomials — desctools_binom • tern</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Confidence intervals for a difference of binomials — desctools_binom"><meta name="description" content="
-Several confidence intervals for the difference between proportions."><meta property="og:description" content="
-Several confidence intervals for the difference between proportions."><meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png"><link rel="stylesheet" href="../consent.css"><script src="../consent.js" type="text/javascript" charset="utf-8"></script></head><body>
+<html lang="en">
+<head>
+<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+<meta charset="utf-8">
+<meta http-equiv="X-UA-Compatible" content="IE=edge">
+<meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<title>Confidence intervals for a difference of binomials — desctools_binom • tern</title>
+<!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png">
+<link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png">
+<link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png">
+<link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png">
+<link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png">
+<link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png">
+<script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet">
+<script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet">
+<link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet">
+<script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Confidence intervals for a difference of binomials — desctools_binom">
+<meta name="description" content="
+Several confidence intervals for the difference between proportions.">
+<meta property="og:description" content="
+Several confidence intervals for the difference between proportions.">
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+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
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+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
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+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a>
+</div>
+</li></div>
+</ul>
+<ul class="navbar-nav">
+<li class="nav-item"><form class="form-inline" role="search">
+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json">
+</form></li>
 <li class="nav-item"><a class="external-link nav-link" href="https://github.com/insightsengineering/tern" aria-label="GitHub"><span class="fa fa-github"></span></a></li>
-      </ul></div>
+      </ul>
+</div>
 
 
   </div>
@@ -54,7 +117,8 @@
     </div>
 
     <div class="section level2">
-    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
+    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">desctools_binom</span><span class="op">(</span></span>
 <span>  <span class="va">x1</span>,</span>
 <span>  <span class="va">n1</span>,</span>
@@ -80,60 +144,80 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
     </div>
 
     <div class="section level2">
-    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
+    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a>
+</h2>
 
 
-<dl><dt id="arg-conf-level">conf.level<a class="anchor" aria-label="anchor" href="#arg-conf-level"></a></dt>
+<dl>
+<dt id="arg-conf-level">conf.level<a class="anchor" aria-label="anchor" href="#arg-conf-level"></a>
+</dt>
 <dd><p>(<code>proportion</code>)<br> confidence level, defaults to 0.95.</p></dd>
 
 
-<dt id="arg-sides">sides<a class="anchor" aria-label="anchor" href="#arg-sides"></a></dt>
+<dt id="arg-sides">sides<a class="anchor" aria-label="anchor" href="#arg-sides"></a>
+</dt>
 <dd><p>(<code>string</code>)<br> side of the confidence interval to compute. Must be one of <code>"two-sided"</code> (default),
 <code>"left"</code>, or <code>"right"</code>.</p></dd>
 
 
-<dt id="arg-method">method<a class="anchor" aria-label="anchor" href="#arg-method"></a></dt>
+<dt id="arg-method">method<a class="anchor" aria-label="anchor" href="#arg-method"></a>
+</dt>
 <dd><p>(<code>string</code>)<br> method to use. Can be one out of: <code>"wald"</code>, <code>"wilson"</code>, <code>"wilsoncc"</code>,
 <code>"agresti-coull"</code>, <code>"jeffreys"</code>, <code>"modified wilson"</code>, <code>"modified jeffreys"</code>, <code>"clopper-pearson"</code>, <code>"arcsine"</code>,
 <code>"logit"</code>, <code>"witting"</code>, <code>"pratt"</code>, <code>"midp"</code>, <code>"lik"</code>, and <code>"blaker"</code>.</p></dd>
 
 
-<dt id="arg-x">x<a class="anchor" aria-label="anchor" href="#arg-x"></a></dt>
+<dt id="arg-x">x<a class="anchor" aria-label="anchor" href="#arg-x"></a>
+</dt>
 <dd><p>(<code>integer(1)</code>)<br> number of successes.</p></dd>
 
 
-<dt id="arg-n">n<a class="anchor" aria-label="anchor" href="#arg-n"></a></dt>
+<dt id="arg-n">n<a class="anchor" aria-label="anchor" href="#arg-n"></a>
+</dt>
 <dd><p>(<code>integer(1)</code>)<br> number of trials.</p></dd>
 
-</dl></div>
+</dl>
+</div>
     <div class="section level2">
-    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
-    <p>A <code>matrix</code> of 3 values:</p><ul><li><p><code>est</code>: estimate of proportion difference.</p></li>
+    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a>
+</h2>
+    <p>A <code>matrix</code> of 3 values:</p>
+<ul>
+<li><p><code>est</code>: estimate of proportion difference.</p></li>
 <li><p><code>lwr.ci</code>: estimate of lower end of the confidence interval.</p></li>
 <li><p><code>upr.ci</code>: estimate of upper end of the confidence interval.</p></li>
-</ul><p>A <code>matrix</code> with 3 columns containing:</p><ul><li><p><code>est</code>: estimate of proportion difference.</p></li>
+</ul>
+<p>A <code>matrix</code> with 3 columns containing:</p>
+<ul>
+<li><p><code>est</code>: estimate of proportion difference.</p></li>
 <li><p><code>lwr.ci</code>: lower end of the confidence interval.</p></li>
 <li><p><code>upr.ci</code>: upper end of the confidence interval.</p></li>
-</ul></div>
+</ul>
+</div>
     <div class="section level2">
-    <h2 id="functions">Functions<a class="anchor" aria-label="anchor" href="#functions"></a></h2>
+    <h2 id="functions">Functions<a class="anchor" aria-label="anchor" href="#functions"></a>
+</h2>
 
-<ul><li><p><code>desctools_binom()</code>: Several confidence intervals for the difference between proportions.</p></li>
+<ul>
+<li><p><code>desctools_binom()</code>: Several confidence intervals for the difference between proportions.</p></li>
 <li><p><code>desctools_binomci()</code>: Compute confidence intervals for binomial proportions.</p></li>
-</ul></div>
+</ul>
+</div>
 
   </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
-    </nav></aside></div>
+    </nav></aside>
+</div>
 
 
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index 0c1b935f49..c09a7ab1d9 100644
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+++ b/main/reference/df2gg.html
@@ -1,9 +1,32 @@
-<!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Convert data.frame object to ggplot object — df2gg • tern</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Convert data.frame object to ggplot object — df2gg"><meta name="description" content="
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+<meta name="description" content="
 Given a data.frame object, performs basic conversion to a ggplot2::ggplot() object built using
-functions from the ggplot2 package."><meta property="og:description" content="
+functions from the ggplot2 package.">
+<meta property="og:description" content="
 Given a data.frame object, performs basic conversion to a ggplot2::ggplot() object built using
-functions from the ggplot2 package."><meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png"><link rel="stylesheet" href="../consent.css"><script src="../consent.js" type="text/javascript" charset="utf-8"></script></head><body>
+functions from the ggplot2 package.">
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+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a>
+</div>
+</li></div>
+</ul>
+<ul class="navbar-nav">
+<li class="nav-item"><form class="form-inline" role="search">
+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json">
+</form></li>
 <li class="nav-item"><a class="external-link nav-link" href="https://github.com/insightsengineering/tern" aria-label="GitHub"><span class="fa fa-github"></span></a></li>
-      </ul></div>
+      </ul>
+</div>
 
 
   </div>
@@ -57,7 +120,8 @@
     </div>
 
     <div class="section level2">
-    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
+    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">df2gg</span><span class="op">(</span></span>
 <span>  <span class="va">df</span>,</span>
 <span>  colwidths <span class="op">=</span> <span class="cn">NULL</span>,</span>
@@ -70,48 +134,60 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
     </div>
 
     <div class="section level2">
-    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
+    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a>
+</h2>
 
 
-<dl><dt id="arg-df">df<a class="anchor" aria-label="anchor" href="#arg-df"></a></dt>
+<dl>
+<dt id="arg-df">df<a class="anchor" aria-label="anchor" href="#arg-df"></a>
+</dt>
 <dd><p>(<code>data.frame</code>)<br> a data frame.</p></dd>
 
 
-<dt id="arg-colwidths">colwidths<a class="anchor" aria-label="anchor" href="#arg-colwidths"></a></dt>
+<dt id="arg-colwidths">colwidths<a class="anchor" aria-label="anchor" href="#arg-colwidths"></a>
+</dt>
 <dd><p>(<code>numeric</code> or <code>NULL</code>)<br> a vector of column widths. Each element's position in
 <code>colwidths</code> corresponds to the column of <code>df</code> in the same position. If <code>NULL</code>, column widths
 are calculated according to maximum number of characters per column.</p></dd>
 
 
-<dt id="arg-font-size">font_size<a class="anchor" aria-label="anchor" href="#arg-font-size"></a></dt>
+<dt id="arg-font-size">font_size<a class="anchor" aria-label="anchor" href="#arg-font-size"></a>
+</dt>
 <dd><p>(<code>numeric(1)</code>)<br> font size.</p></dd>
 
 
-<dt id="arg-col-labels">col_labels<a class="anchor" aria-label="anchor" href="#arg-col-labels"></a></dt>
+<dt id="arg-col-labels">col_labels<a class="anchor" aria-label="anchor" href="#arg-col-labels"></a>
+</dt>
 <dd><p>(<code>flag</code>)<br> whether the column names (labels) of <code>df</code> should be used as the first row
 of the output table.</p></dd>
 
 
-<dt id="arg-col-lab-fontface">col_lab_fontface<a class="anchor" aria-label="anchor" href="#arg-col-lab-fontface"></a></dt>
+<dt id="arg-col-lab-fontface">col_lab_fontface<a class="anchor" aria-label="anchor" href="#arg-col-lab-fontface"></a>
+</dt>
 <dd><p>(<code>string</code>)<br> font face to apply to the first row (of column labels
 if <code>col_labels = TRUE</code>). Defaults to <code>"bold"</code>.</p></dd>
 
 
-<dt id="arg-hline">hline<a class="anchor" aria-label="anchor" href="#arg-hline"></a></dt>
+<dt id="arg-hline">hline<a class="anchor" aria-label="anchor" href="#arg-hline"></a>
+</dt>
 <dd><p>(<code>flag</code>)<br> whether a horizontal line should be printed below the first row of the table.</p></dd>
 
 
-<dt id="arg-bg-fill">bg_fill<a class="anchor" aria-label="anchor" href="#arg-bg-fill"></a></dt>
+<dt id="arg-bg-fill">bg_fill<a class="anchor" aria-label="anchor" href="#arg-bg-fill"></a>
+</dt>
 <dd><p>(<code>string</code>)<br> table background fill color.</p></dd>
 
-</dl></div>
+</dl>
+</div>
     <div class="section level2">
-    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
+    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a>
+</h2>
     <p>A <code>ggplot</code> object.</p>
     </div>
 
     <div class="section level2">
-    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
+    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="cn">FALSE</span><span class="op">)</span> <span class="op">{</span> <span class="co"># \dontrun{</span></span></span>
 <span class="r-in"><span><span class="fu">df2gg</span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/utils/head.html" class="external-link">head</a></span><span class="op">(</span><span class="va">iris</span>, <span class="fl">5</span><span class="op">)</span><span class="op">)</span></span></span>
 <span class="r-in"><span></span></span>
@@ -120,17 +196,19 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 </code></pre></div>
     </div>
   </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
-    </nav></aside></div>
+    </nav></aside>
+</div>
 
 
     <footer><div class="nest">
   <p>tern is a part of the <strong>NEST</strong> and <a href="https://pharmaverse.org/" class="external-link"><strong>pharmaverse</strong></a>.</p>
 </div>
-<script type="text/javascript" src="../analytics.js"></script></footer></div>
-
+<script type="text/javascript" src="../analytics.js"></script></footer>
+</div>
 
 
 
 
-  </body></html>
 
+  </body>
+</html>
diff --git a/main/reference/df_explicit_na.html b/main/reference/df_explicit_na.html
index 748f43c206..bf3fb05454 100644
--- a/main/reference/df_explicit_na.html
+++ b/main/reference/df_explicit_na.html
@@ -1,9 +1,32 @@
-<!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Encode categorical missing values in a data frame — df_explicit_na • tern</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Encode categorical missing values in a data frame — df_explicit_na"><meta name="description" content="
+<html lang="en">
+<head>
+<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+<meta charset="utf-8">
+<meta http-equiv="X-UA-Compatible" content="IE=edge">
+<meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<title>Encode categorical missing values in a data frame — df_explicit_na • tern</title>
+<!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png">
+<link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png">
+<link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png">
+<link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png">
+<link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png">
+<link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png">
+<script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet">
+<script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet">
+<link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet">
+<script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Encode categorical missing values in a data frame — df_explicit_na">
+<meta name="description" content="
 This is a helper function to encode missing entries across groups of categorical
-variables in a data frame."><meta property="og:description" content="
+variables in a data frame.">
+<meta property="og:description" content="
 This is a helper function to encode missing entries across groups of categorical
-variables in a data frame."><meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png"><link rel="stylesheet" href="../consent.css"><script src="../consent.js" type="text/javascript" charset="utf-8"></script></head><body>
+variables in a data frame.">
+<meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png">
+<link rel="stylesheet" href="../consent.css">
+<script src="../consent.js" type="text/javascript" charset="utf-8"></script>
+</head>
+<body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
 
 
@@ -19,26 +42,66 @@
     </button>
 
     <div id="navbar" class="collapse navbar-collapse ms-3">
-      <ul class="navbar-nav me-auto"><li class="nav-item"><a class="nav-link" href="../articles/tern.html">Get started</a></li>
+      <ul class="navbar-nav me-auto">
+<li class="nav-item"><a class="nav-link" href="../articles/tern.html">Get started</a></li>
 <li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
 <li class="nav-item dropdown">
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-articles" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Articles</button>
-  <ul class="dropdown-menu" aria-labelledby="dropdown-articles"><li><a class="dropdown-item" href="../articles/missing_values.html">Missing Values in Tern</a></li>
+  <ul class="dropdown-menu" aria-labelledby="dropdown-articles">
+<li><a class="dropdown-item" href="../articles/missing_values.html">Missing Values in Tern</a></li>
     <li><a class="dropdown-item" href="../articles/tables.html">Tabulation</a></li>
     <li><a class="dropdown-item" href="../articles/tern_formats.html">Formatting Functions</a></li>
     <li><a class="dropdown-item" href="../articles/tern_functions_guide.html">Understanding `tern` functions</a></li>
-  </ul></li>
+  </ul>
+</li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
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+  <ul class="dropdown-menu" aria-labelledby="dropdown-reports">
+<li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
     <li><a class="dropdown-item" href="../unit-test-report/">Unit test report</a></li>
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-      </ul><ul class="navbar-nav"><li class="nav-item"><form class="form-inline" role="search">
- <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json"></form></li>
+  </ul>
+</li>
+      <div><li class="nav-item dropdown">
+    <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-versions">Versions</a>
+    <div class="dropdown-menu" aria-labelledby="dropdown-versions">
+    <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/main">main</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.5">v0.9.5</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.4">v0.9.4</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.3">v0.9.3</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1-rc3">v0.9.1-rc3</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a>
+</div>
+</li></div>
+</ul>
+<ul class="navbar-nav">
+<li class="nav-item"><form class="form-inline" role="search">
+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json">
+</form></li>
 <li class="nav-item"><a class="external-link nav-link" href="https://github.com/insightsengineering/tern" aria-label="GitHub"><span class="fa fa-github"></span></a></li>
-      </ul></div>
+      </ul>
+</div>
 
 
   </div>
@@ -57,7 +120,8 @@
     </div>
 
     <div class="section level2">
-    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
+    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">df_explicit_na</span><span class="op">(</span></span>
 <span>  <span class="va">data</span>,</span>
 <span>  omit_columns <span class="op">=</span> <span class="cn">NULL</span>,</span>
@@ -68,39 +132,49 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
     </div>
 
     <div class="section level2">
-    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
+    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a>
+</h2>
 
 
-<dl><dt id="arg-data">data<a class="anchor" aria-label="anchor" href="#arg-data"></a></dt>
+<dl>
+<dt id="arg-data">data<a class="anchor" aria-label="anchor" href="#arg-data"></a>
+</dt>
 <dd><p>(<code>data.frame</code>)<br> data set.</p></dd>
 
 
-<dt id="arg-omit-columns">omit_columns<a class="anchor" aria-label="anchor" href="#arg-omit-columns"></a></dt>
+<dt id="arg-omit-columns">omit_columns<a class="anchor" aria-label="anchor" href="#arg-omit-columns"></a>
+</dt>
 <dd><p>(<code>character</code>)<br> names of variables from <code>data</code> that should
 not be modified by this function.</p></dd>
 
 
-<dt id="arg-char-as-factor">char_as_factor<a class="anchor" aria-label="anchor" href="#arg-char-as-factor"></a></dt>
+<dt id="arg-char-as-factor">char_as_factor<a class="anchor" aria-label="anchor" href="#arg-char-as-factor"></a>
+</dt>
 <dd><p>(<code>flag</code>)<br> whether to convert character variables
 in <code>data</code> to factors.</p></dd>
 
 
-<dt id="arg-logical-as-factor">logical_as_factor<a class="anchor" aria-label="anchor" href="#arg-logical-as-factor"></a></dt>
+<dt id="arg-logical-as-factor">logical_as_factor<a class="anchor" aria-label="anchor" href="#arg-logical-as-factor"></a>
+</dt>
 <dd><p>(<code>flag</code>)<br> whether to convert logical variables
 in <code>data</code> to factors.</p></dd>
 
 
-<dt id="arg-na-level">na_level<a class="anchor" aria-label="anchor" href="#arg-na-level"></a></dt>
+<dt id="arg-na-level">na_level<a class="anchor" aria-label="anchor" href="#arg-na-level"></a>
+</dt>
 <dd><p>(<code>string</code>)<br> string used to replace all <code>NA</code> or empty
 values inside non-<code>omit_columns</code> columns.</p></dd>
 
-</dl></div>
+</dl>
+</div>
     <div class="section level2">
-    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
+    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a>
+</h2>
     <p>A <code>data.frame</code> with the chosen modifications applied.</p>
     </div>
     <div class="section level2">
-    <h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a></h2>
+    <h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a>
+</h2>
     <p>Missing entries are those with <code>NA</code> or empty strings and will
 be replaced with a specified value. If factor variables include missing
 values, the missing value will be inserted as the last level.
@@ -109,12 +183,14 @@ <h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></
 be set as the last level.</p>
     </div>
     <div class="section level2">
-    <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"></a></h2>
+    <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"></a>
+</h2>
     <div class="dont-index"><p><code><a href="sas_na.html">sas_na()</a></code> and <code><a href="explicit_na.html">explicit_na()</a></code> for other missing data helper functions.</p></div>
     </div>
 
     <div class="section level2">
-    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
+    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">my_data</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a></span><span class="op">(</span></span></span>
 <span class="r-in"><span>  u <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="cn">TRUE</span>, <span class="cn">FALSE</span>, <span class="cn">NA</span>, <span class="cn">TRUE</span><span class="op">)</span>,</span></span>
 <span class="r-in"><span>  v <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/factor.html" class="external-link">factor</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"A"</span>, <span class="cn">NA</span>, <span class="cn">NA</span>, <span class="cn">NA</span><span class="op">)</span>, levels <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"Z"</span>, <span class="st">"A"</span><span class="op">)</span><span class="op">)</span>,</span></span>
@@ -172,17 +248,19 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 </code></pre></div>
     </div>
   </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
-    </nav></aside></div>
+    </nav></aside>
+</div>
 
 
     <footer><div class="nest">
   <p>tern is a part of the <strong>NEST</strong> and <a href="https://pharmaverse.org/" class="external-link"><strong>pharmaverse</strong></a>.</p>
 </div>
-<script type="text/javascript" src="../analytics.js"></script></footer></div>
-
+<script type="text/javascript" src="../analytics.js"></script></footer>
+</div>
 
 
 
 
-  </body></html>
 
+  </body>
+</html>
diff --git a/main/reference/dot-is_equal_float.html b/main/reference/dot-is_equal_float.html
index 2ee2b28a6a..060e7788a5 100644
--- a/main/reference/dot-is_equal_float.html
+++ b/main/reference/dot-is_equal_float.html
@@ -1,5 +1,28 @@
-<!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Utility function to check if a float value is equal to another float value — .is_equal_float • tern</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Utility function to check if a float value is equal to another float value — .is_equal_float"><meta name="description" content="Uses .Machine$double.eps as the tolerance for the comparison."><meta property="og:description" content="Uses .Machine$double.eps as the tolerance for the comparison."><meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png"><link rel="stylesheet" href="../consent.css"><script src="../consent.js" type="text/javascript" charset="utf-8"></script></head><body>
+<html lang="en">
+<head>
+<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+<meta charset="utf-8">
+<meta http-equiv="X-UA-Compatible" content="IE=edge">
+<meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<title>Utility function to check if a float value is equal to another float value — .is_equal_float • tern</title>
+<!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png">
+<link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png">
+<link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png">
+<link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png">
+<link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png">
+<link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png">
+<script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet">
+<script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet">
+<link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet">
+<script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Utility function to check if a float value is equal to another float value — .is_equal_float">
+<meta name="description" content="Uses .Machine$double.eps as the tolerance for the comparison.">
+<meta property="og:description" content="Uses .Machine$double.eps as the tolerance for the comparison.">
+<meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png">
+<link rel="stylesheet" href="../consent.css">
+<script src="../consent.js" type="text/javascript" charset="utf-8"></script>
+</head>
+<body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
 
 
@@ -15,26 +38,66 @@
     </button>
 
     <div id="navbar" class="collapse navbar-collapse ms-3">
-      <ul class="navbar-nav me-auto"><li class="nav-item"><a class="nav-link" href="../articles/tern.html">Get started</a></li>
+      <ul class="navbar-nav me-auto">
+<li class="nav-item"><a class="nav-link" href="../articles/tern.html">Get started</a></li>
 <li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
 <li class="nav-item dropdown">
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-articles" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Articles</button>
-  <ul class="dropdown-menu" aria-labelledby="dropdown-articles"><li><a class="dropdown-item" href="../articles/missing_values.html">Missing Values in Tern</a></li>
+  <ul class="dropdown-menu" aria-labelledby="dropdown-articles">
+<li><a class="dropdown-item" href="../articles/missing_values.html">Missing Values in Tern</a></li>
     <li><a class="dropdown-item" href="../articles/tables.html">Tabulation</a></li>
     <li><a class="dropdown-item" href="../articles/tern_formats.html">Formatting Functions</a></li>
     <li><a class="dropdown-item" href="../articles/tern_functions_guide.html">Understanding `tern` functions</a></li>
-  </ul></li>
+  </ul>
+</li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
-  <ul class="dropdown-menu" aria-labelledby="dropdown-reports"><li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
+  <ul class="dropdown-menu" aria-labelledby="dropdown-reports">
+<li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
     <li><a class="dropdown-item" href="../unit-test-report/">Unit test report</a></li>
     <li><a class="dropdown-item" href="../unit-test-report-non-cran/">Non-CRAN unit test report</a></li>
-  </ul></li>
-      </ul><ul class="navbar-nav"><li class="nav-item"><form class="form-inline" role="search">
- <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json"></form></li>
+  </ul>
+</li>
+      <div><li class="nav-item dropdown">
+    <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-versions">Versions</a>
+    <div class="dropdown-menu" aria-labelledby="dropdown-versions">
+    <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/main">main</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.5">v0.9.5</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.4">v0.9.4</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.3">v0.9.3</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1-rc3">v0.9.1-rc3</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a>
+</div>
+</li></div>
+</ul>
+<ul class="navbar-nav">
+<li class="nav-item"><form class="form-inline" role="search">
+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json">
+</form></li>
 <li class="nav-item"><a class="external-link nav-link" href="https://github.com/insightsengineering/tern" aria-label="GitHub"><span class="fa fa-github"></span></a></li>
-      </ul></div>
+      </ul>
+</div>
 
 
   </div>
@@ -51,39 +114,48 @@
     </div>
 
     <div class="section level2">
-    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
+    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">.is_equal_float</span><span class="op">(</span><span class="va">x</span>, <span class="va">y</span><span class="op">)</span></span></code></pre></div>
     </div>
 
     <div class="section level2">
-    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
+    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a>
+</h2>
 
 
-<dl><dt id="arg-x">x<a class="anchor" aria-label="anchor" href="#arg-x"></a></dt>
+<dl>
+<dt id="arg-x">x<a class="anchor" aria-label="anchor" href="#arg-x"></a>
+</dt>
 <dd><p>(<code>numeric(1)</code>)<br> a float number.</p></dd>
 
 
-<dt id="arg-y">y<a class="anchor" aria-label="anchor" href="#arg-y"></a></dt>
+<dt id="arg-y">y<a class="anchor" aria-label="anchor" href="#arg-y"></a>
+</dt>
 <dd><p>(<code>numeric(1)</code>)<br> a float number.</p></dd>
 
-</dl></div>
+</dl>
+</div>
     <div class="section level2">
-    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
+    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a>
+</h2>
     <p><code>TRUE</code> if identical, otherwise <code>FALSE</code>.</p>
     </div>
 
   </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
-    </nav></aside></div>
+    </nav></aside>
+</div>
 
 
     <footer><div class="nest">
   <p>tern is a part of the <strong>NEST</strong> and <a href="https://pharmaverse.org/" class="external-link"><strong>pharmaverse</strong></a>.</p>
 </div>
-<script type="text/javascript" src="../analytics.js"></script></footer></div>
-
+<script type="text/javascript" src="../analytics.js"></script></footer>
+</div>
 
 
 
 
-  </body></html>
 
+  </body>
+</html>
diff --git a/main/reference/draw_grob.html b/main/reference/draw_grob.html
index 8cc50bc934..68b9359b9a 100644
--- a/main/reference/draw_grob.html
+++ b/main/reference/draw_grob.html
@@ -1,7 +1,30 @@
-<!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Draw grob — draw_grob • tern</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Draw grob — draw_grob"><meta name="description" content="
-Draw grob on device page."><meta property="og:description" content="
-Draw grob on device page."><meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png"><link rel="stylesheet" href="../consent.css"><script src="../consent.js" type="text/javascript" charset="utf-8"></script></head><body>
+<html lang="en">
+<head>
+<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+<meta charset="utf-8">
+<meta http-equiv="X-UA-Compatible" content="IE=edge">
+<meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<title>Draw grob — draw_grob • tern</title>
+<!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png">
+<link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png">
+<link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png">
+<link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png">
+<link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png">
+<link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png">
+<script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet">
+<script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet">
+<link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet">
+<script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Draw grob — draw_grob">
+<meta name="description" content="
+Draw grob on device page.">
+<meta property="og:description" content="
+Draw grob on device page.">
+<meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png">
+<link rel="stylesheet" href="../consent.css">
+<script src="../consent.js" type="text/javascript" charset="utf-8"></script>
+</head>
+<body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
 
 
@@ -17,33 +40,74 @@
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-      <ul class="navbar-nav me-auto"><li class="nav-item"><a class="nav-link" href="../articles/tern.html">Get started</a></li>
+      <ul class="navbar-nav me-auto">
+<li class="nav-item"><a class="nav-link" href="../articles/tern.html">Get started</a></li>
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   <button class="nav-link dropdown-toggle" type="button" id="dropdown-articles" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Articles</button>
-  <ul class="dropdown-menu" aria-labelledby="dropdown-articles"><li><a class="dropdown-item" href="../articles/missing_values.html">Missing Values in Tern</a></li>
+  <ul class="dropdown-menu" aria-labelledby="dropdown-articles">
+<li><a class="dropdown-item" href="../articles/missing_values.html">Missing Values in Tern</a></li>
     <li><a class="dropdown-item" href="../articles/tables.html">Tabulation</a></li>
     <li><a class="dropdown-item" href="../articles/tern_formats.html">Formatting Functions</a></li>
     <li><a class="dropdown-item" href="../articles/tern_functions_guide.html">Understanding `tern` functions</a></li>
-  </ul></li>
+  </ul>
+</li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
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   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
-  <ul class="dropdown-menu" aria-labelledby="dropdown-reports"><li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
+  <ul class="dropdown-menu" aria-labelledby="dropdown-reports">
+<li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
     <li><a class="dropdown-item" href="../unit-test-report/">Unit test report</a></li>
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-      </ul><ul class="navbar-nav"><li class="nav-item"><form class="form-inline" role="search">
- <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json"></form></li>
+  </ul>
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+      <div><li class="nav-item dropdown">
+    <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-versions">Versions</a>
+    <div class="dropdown-menu" aria-labelledby="dropdown-versions">
+    <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/main">main</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.5">v0.9.5</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.4">v0.9.4</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.3">v0.9.3</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1-rc3">v0.9.1-rc3</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a>
+</div>
+</li></div>
+</ul>
+<ul class="navbar-nav">
+<li class="nav-item"><form class="form-inline" role="search">
+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json">
+</form></li>
 <li class="nav-item"><a class="external-link nav-link" href="https://github.com/insightsengineering/tern" aria-label="GitHub"><span class="fa fa-github"></span></a></li>
-      </ul></div>
+      </ul>
+</div>
 
 
   </div>
 </nav><div class="container template-reference-topic">
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
-      <img src="../logo.png" class="logo" alt=""><h1>Draw <code>grob</code></h1>
+      <img src="../logo.png" class="logo" alt=""><h1>Draw <code>grob</code>
+</h1>
       <small class="dont-index">Source: <a href="https://github.com/insightsengineering/tern/blob/main/R/utils_grid.R" class="external-link"><code>R/utils_grid.R</code></a></small>
       <div class="d-none name"><code>draw_grob.Rd</code></div>
     </div>
@@ -54,33 +118,42 @@
     </div>
 
     <div class="section level2">
-    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
+    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">draw_grob</span><span class="op">(</span><span class="va">grob</span>, newpage <span class="op">=</span> <span class="cn">TRUE</span>, vp <span class="op">=</span> <span class="cn">NULL</span><span class="op">)</span></span></code></pre></div>
     </div>
 
     <div class="section level2">
-    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
+    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a>
+</h2>
 
 
-<dl><dt id="arg-grob">grob<a class="anchor" aria-label="anchor" href="#arg-grob"></a></dt>
+<dl>
+<dt id="arg-grob">grob<a class="anchor" aria-label="anchor" href="#arg-grob"></a>
+</dt>
 <dd><p>(<code>grob</code>)<br> grid object.</p></dd>
 
 
-<dt id="arg-newpage">newpage<a class="anchor" aria-label="anchor" href="#arg-newpage"></a></dt>
+<dt id="arg-newpage">newpage<a class="anchor" aria-label="anchor" href="#arg-newpage"></a>
+</dt>
 <dd><p>(<code>flag</code>)<br> draw on a new page.</p></dd>
 
 
-<dt id="arg-vp">vp<a class="anchor" aria-label="anchor" href="#arg-vp"></a></dt>
+<dt id="arg-vp">vp<a class="anchor" aria-label="anchor" href="#arg-vp"></a>
+</dt>
 <dd><p>(<code>viewport</code> or <code>NULL</code>)<br> a <code><a href="https://rdrr.io/r/grid/viewport.html" class="external-link">viewport()</a></code> object (or <code>NULL</code>).</p></dd>
 
-</dl></div>
+</dl>
+</div>
     <div class="section level2">
-    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
+    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a>
+</h2>
     <p>A <code>grob</code>.</p>
     </div>
 
     <div class="section level2">
-    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
+    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://dplyr.tidyverse.org" class="external-link">dplyr</a></span><span class="op">)</span></span></span>
 <span class="r-in"><span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va">grid</span><span class="op">)</span></span></span>
 <span class="r-in"><span></span></span>
@@ -105,17 +178,19 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 </code></pre></div>
     </div>
   </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
-    </nav></aside></div>
+    </nav></aside>
+</div>
 
 
     <footer><div class="nest">
   <p>tern is a part of the <strong>NEST</strong> and <a href="https://pharmaverse.org/" class="external-link"><strong>pharmaverse</strong></a>.</p>
 </div>
-<script type="text/javascript" src="../analytics.js"></script></footer></div>
-
+<script type="text/javascript" src="../analytics.js"></script></footer>
+</div>
 
 
 
 
-  </body></html>
 
+  </body>
+</html>
diff --git a/main/reference/empty_vector_if_na.html b/main/reference/empty_vector_if_na.html
index 5c58a3cdba..277863f5e5 100644
--- a/main/reference/empty_vector_if_na.html
+++ b/main/reference/empty_vector_if_na.html
@@ -1,5 +1,28 @@
-<!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Return an empty numeric if all elements are NA. — empty_vector_if_na • tern</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Return an empty numeric if all elements are NA. — empty_vector_if_na"><meta name="description" content="Return an empty numeric if all elements are NA."><meta property="og:description" content="Return an empty numeric if all elements are NA."><meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png"><link rel="stylesheet" href="../consent.css"><script src="../consent.js" type="text/javascript" charset="utf-8"></script></head><body>
+<html lang="en">
+<head>
+<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+<meta charset="utf-8">
+<meta http-equiv="X-UA-Compatible" content="IE=edge">
+<meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<title>Return an empty numeric if all elements are NA. — empty_vector_if_na • tern</title>
+<!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png">
+<link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png">
+<link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png">
+<link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png">
+<link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png">
+<link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png">
+<script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet">
+<script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet">
+<link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet">
+<script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Return an empty numeric if all elements are NA. — empty_vector_if_na">
+<meta name="description" content="Return an empty numeric if all elements are NA.">
+<meta property="og:description" content="Return an empty numeric if all elements are NA.">
+<meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png">
+<link rel="stylesheet" href="../consent.css">
+<script src="../consent.js" type="text/javascript" charset="utf-8"></script>
+</head>
+<body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
 
 
@@ -15,26 +38,66 @@
     </button>
 
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-      <ul class="navbar-nav me-auto"><li class="nav-item"><a class="nav-link" href="../articles/tern.html">Get started</a></li>
+      <ul class="navbar-nav me-auto">
+<li class="nav-item"><a class="nav-link" href="../articles/tern.html">Get started</a></li>
 <li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
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   <button class="nav-link dropdown-toggle" type="button" id="dropdown-articles" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Articles</button>
-  <ul class="dropdown-menu" aria-labelledby="dropdown-articles"><li><a class="dropdown-item" href="../articles/missing_values.html">Missing Values in Tern</a></li>
+  <ul class="dropdown-menu" aria-labelledby="dropdown-articles">
+<li><a class="dropdown-item" href="../articles/missing_values.html">Missing Values in Tern</a></li>
     <li><a class="dropdown-item" href="../articles/tables.html">Tabulation</a></li>
     <li><a class="dropdown-item" href="../articles/tern_formats.html">Formatting Functions</a></li>
     <li><a class="dropdown-item" href="../articles/tern_functions_guide.html">Understanding `tern` functions</a></li>
-  </ul></li>
+  </ul>
+</li>
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+  <ul class="dropdown-menu" aria-labelledby="dropdown-reports">
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- <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json"></form></li>
+  </ul>
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+      <div><li class="nav-item dropdown">
+    <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-versions">Versions</a>
+    <div class="dropdown-menu" aria-labelledby="dropdown-versions">
+    <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/main">main</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.5">v0.9.5</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.4">v0.9.4</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.3">v0.9.3</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1-rc3">v0.9.1-rc3</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a>
+</div>
+</li></div>
+</ul>
+<ul class="navbar-nav">
+<li class="nav-item"><form class="form-inline" role="search">
+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json">
+</form></li>
 <li class="nav-item"><a class="external-link nav-link" href="https://github.com/insightsengineering/tern" aria-label="GitHub"><span class="fa fa-github"></span></a></li>
-      </ul></div>
+      </ul>
+</div>
 
 
   </div>
@@ -51,41 +114,50 @@
     </div>
 
     <div class="section level2">
-    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
+    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">empty_vector_if_na</span><span class="op">(</span><span class="va">x</span><span class="op">)</span></span></code></pre></div>
     </div>
 
     <div class="section level2">
-    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
+    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a>
+</h2>
 
 
-<dl><dt id="arg-x">x<a class="anchor" aria-label="anchor" href="#arg-x"></a></dt>
+<dl>
+<dt id="arg-x">x<a class="anchor" aria-label="anchor" href="#arg-x"></a>
+</dt>
 <dd><p>(<code>numeric</code>)<br> vector.</p></dd>
 
-</dl></div>
+</dl>
+</div>
     <div class="section level2">
-    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
+    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a>
+</h2>
     <p>An empty <code>numeric</code> if all elements of <code>x</code> are <code>NA</code>, otherwise <code>x</code>.</p>
     </div>
 
     <div class="section level2">
-    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
+    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">x</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="cn">NA</span>, <span class="cn">NA</span>, <span class="cn">NA</span><span class="op">)</span></span></span>
 <span class="r-in"><span><span class="co"># Internal function - empty_vector_if_na</span></span></span>
 </code></pre></div>
     </div>
   </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
-    </nav></aside></div>
+    </nav></aside>
+</div>
 
 
     <footer><div class="nest">
   <p>tern is a part of the <strong>NEST</strong> and <a href="https://pharmaverse.org/" class="external-link"><strong>pharmaverse</strong></a>.</p>
 </div>
-<script type="text/javascript" src="../analytics.js"></script></footer></div>
-
+<script type="text/javascript" src="../analytics.js"></script></footer>
+</div>
 
 
 
 
-  </body></html>
 
+  </body>
+</html>
diff --git a/main/reference/estimate_coef.html b/main/reference/estimate_coef.html
index 14f1677410..5958437e14 100644
--- a/main/reference/estimate_coef.html
+++ b/main/reference/estimate_coef.html
@@ -1,7 +1,30 @@
-<!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Hazard ratio estimation in interactions — estimate_coef • tern</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Hazard ratio estimation in interactions — estimate_coef"><meta name="description" content="This function estimates the hazard ratios between arms when an interaction variable is given with
-specific values."><meta property="og:description" content="This function estimates the hazard ratios between arms when an interaction variable is given with
-specific values."><meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png"><link rel="stylesheet" href="../consent.css"><script src="../consent.js" type="text/javascript" charset="utf-8"></script></head><body>
+<html lang="en">
+<head>
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+<meta charset="utf-8">
+<meta http-equiv="X-UA-Compatible" content="IE=edge">
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+<title>Hazard ratio estimation in interactions — estimate_coef • tern</title>
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+<link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png">
+<script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet">
+<script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet">
+<link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet">
+<script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Hazard ratio estimation in interactions — estimate_coef">
+<meta name="description" content="This function estimates the hazard ratios between arms when an interaction variable is given with
+specific values.">
+<meta property="og:description" content="This function estimates the hazard ratios between arms when an interaction variable is given with
+specific values.">
+<meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png">
+<link rel="stylesheet" href="../consent.css">
+<script src="../consent.js" type="text/javascript" charset="utf-8"></script>
+</head>
+<body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
 
 
@@ -17,26 +40,66 @@
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 <li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
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+  <ul class="dropdown-menu" aria-labelledby="dropdown-articles">
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+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
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+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
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+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1-rc3">v0.9.1-rc3</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
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+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a>
+</div>
+</li></div>
+</ul>
+<ul class="navbar-nav">
+<li class="nav-item"><form class="form-inline" role="search">
+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json">
+</form></li>
 <li class="nav-item"><a class="external-link nav-link" href="https://github.com/insightsengineering/tern" aria-label="GitHub"><span class="fa fa-github"></span></a></li>
-      </ul></div>
+      </ul>
+</div>
 
 
   </div>
@@ -54,7 +117,8 @@
     </div>
 
     <div class="section level2">
-    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
+    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">estimate_coef</span><span class="op">(</span></span>
 <span>  <span class="va">variable</span>,</span>
 <span>  <span class="va">given</span>,</span>
@@ -68,61 +132,80 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
     </div>
 
     <div class="section level2">
-    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
+    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a>
+</h2>
 
 
-<dl><dt id="arg-variable-given">variable, given<a class="anchor" aria-label="anchor" href="#arg-variable-given"></a></dt>
+<dl>
+<dt id="arg-variable-given">variable, given<a class="anchor" aria-label="anchor" href="#arg-variable-given"></a>
+</dt>
 <dd><p>(<code>character(2)</code>)<br> names of the two variables in the interaction. We seek the estimation of
 the levels of <code>variable</code> given the levels of <code>given</code>.</p></dd>
 
 
-<dt id="arg-lvl-var-lvl-given">lvl_var, lvl_given<a class="anchor" aria-label="anchor" href="#arg-lvl-var-lvl-given"></a></dt>
+<dt id="arg-lvl-var-lvl-given">lvl_var, lvl_given<a class="anchor" aria-label="anchor" href="#arg-lvl-var-lvl-given"></a>
+</dt>
 <dd><p>(<code>character</code>)<br> corresponding levels given by <code><a href="https://rdrr.io/r/base/levels.html" class="external-link">levels()</a></code>.</p></dd>
 
 
-<dt id="arg-coef">coef<a class="anchor" aria-label="anchor" href="#arg-coef"></a></dt>
+<dt id="arg-coef">coef<a class="anchor" aria-label="anchor" href="#arg-coef"></a>
+</dt>
 <dd><p>(<code>numeric</code>)<br> vector of estimated coefficients.</p></dd>
 
 
-<dt id="arg-mmat">mmat<a class="anchor" aria-label="anchor" href="#arg-mmat"></a></dt>
+<dt id="arg-mmat">mmat<a class="anchor" aria-label="anchor" href="#arg-mmat"></a>
+</dt>
 <dd><p>(named <code>numeric</code>) a vector filled with <code>0</code>s used as a template to obtain the design matrix.</p></dd>
 
 
-<dt id="arg-vcov">vcov<a class="anchor" aria-label="anchor" href="#arg-vcov"></a></dt>
+<dt id="arg-vcov">vcov<a class="anchor" aria-label="anchor" href="#arg-vcov"></a>
+</dt>
 <dd><p>(<code>matrix</code>)<br> variance-covariance matrix of underlying model.</p></dd>
 
 
-<dt id="arg-conf-level">conf_level<a class="anchor" aria-label="anchor" href="#arg-conf-level"></a></dt>
+<dt id="arg-conf-level">conf_level<a class="anchor" aria-label="anchor" href="#arg-conf-level"></a>
+</dt>
 <dd><p>(<code>proportion</code>)<br> confidence level of estimate intervals.</p></dd>
 
-</dl></div>
+</dl>
+</div>
     <div class="section level2">
-    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
+    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a>
+</h2>
     <p>A list of matrices (one per level of variable) with rows corresponding to the combinations of
-<code>variable</code> and <code>given</code>, with columns:</p><ul><li><p><code>coef_hat</code>: Estimation of the coefficient.</p></li>
+<code>variable</code> and <code>given</code>, with columns:</p>
+<ul>
+<li><p><code>coef_hat</code>: Estimation of the coefficient.</p></li>
 <li><p><code>coef_se</code>: Standard error of the estimation.</p></li>
 <li><p><code>hr</code>: Hazard ratio.</p></li>
 <li><p><code>lcl, ucl</code>: Lower/upper confidence limit of the hazard ratio.</p></li>
-</ul></div>
+</ul>
+</div>
     <div class="section level2">
-    <h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a></h2>
+    <h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a>
+</h2>
     <p>Given the cox regression investigating the effect of Arm (A, B, C; reference A)
 and Sex (F, M; reference Female). The model is abbreviated: y ~ Arm + Sex + Arm x Sex.
-The cox regression estimates the coefficients along with a variance-covariance matrix for:</p><ul><li><p>b1 (arm b), b2 (arm c)</p></li>
+The cox regression estimates the coefficients along with a variance-covariance matrix for:</p>
+<ul>
+<li><p>b1 (arm b), b2 (arm c)</p></li>
 <li><p>b3 (sex m)</p></li>
 <li><p>b4 (arm b: sex m), b5 (arm c: sex m)</p></li>
-</ul><p>Given that I want an estimation of the Hazard Ratio for arm C/sex M, the estimation
+</ul>
+<p>Given that I want an estimation of the Hazard Ratio for arm C/sex M, the estimation
 will be given in reference to arm A/Sex M by exp(b2 + b3 + b5)/ exp(b3) = exp(b2 + b5),
 therefore the interaction coefficient is given by b2 + b5 while the standard error is obtained
 as $1.96 * sqrt(Var b2 + Var b5 + 2 * covariance (b2,b5))$ for a confidence level of 0.95.</p>
     </div>
     <div class="section level2">
-    <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"></a></h2>
+    <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"></a>
+</h2>
     <div class="dont-index"><p><code><a href="s_cox_multivariate.html">s_cox_multivariate()</a></code>.</p></div>
     </div>
 
     <div class="section level2">
-    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
+    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://dplyr.tidyverse.org" class="external-link">dplyr</a></span><span class="op">)</span></span></span>
 <span class="r-in"><span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://github.com/therneau/survival" class="external-link">survival</a></span><span class="op">)</span></span></span>
 <span class="r-in"><span></span></span>
@@ -144,17 +227,19 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 </code></pre></div>
     </div>
   </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
-    </nav></aside></div>
+    </nav></aside>
+</div>
 
 
     <footer><div class="nest">
   <p>tern is a part of the <strong>NEST</strong> and <a href="https://pharmaverse.org/" class="external-link"><strong>pharmaverse</strong></a>.</p>
 </div>
-<script type="text/javascript" src="../analytics.js"></script></footer></div>
-
+<script type="text/javascript" src="../analytics.js"></script></footer>
+</div>
 
 
 
 
-  </body></html>
 
+  </body>
+</html>
diff --git a/main/reference/estimate_multinomial_rsp.html b/main/reference/estimate_multinomial_rsp.html
index c630fd4108..7fa27fbe05 100644
--- a/main/reference/estimate_multinomial_rsp.html
+++ b/main/reference/estimate_multinomial_rsp.html
@@ -1,11 +1,34 @@
-<!DOCTYPE html>
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+<title>Estimate proportions of each level of a variable — estimate_multinomial_rsp • tern</title>
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+<meta name="description" content="
 The analyze &amp;amp; summarize function estimate_multinomial_response() creates a layout element to estimate the
 proportion and proportion confidence interval for each level of a factor variable. The primary analysis variable,
-var, should be a factor variable, the values of which will be used as labels within the output table."><meta property="og:description" content="
+var, should be a factor variable, the values of which will be used as labels within the output table.">
+<meta property="og:description" content="
 The analyze &amp;amp; summarize function estimate_multinomial_response() creates a layout element to estimate the
 proportion and proportion confidence interval for each level of a factor variable. The primary analysis variable,
-var, should be a factor variable, the values of which will be used as labels within the output table."><meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png"><link rel="stylesheet" href="../consent.css"><script src="../consent.js" type="text/javascript" charset="utf-8"></script></head><body>
+var, should be a factor variable, the values of which will be used as labels within the output table.">
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   </div>
@@ -60,7 +123,8 @@
     </div>
 
     <div class="section level2">
-    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
+    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">estimate_multinomial_response</span><span class="op">(</span></span>
 <span>  <span class="va">lyt</span>,</span>
 <span>  <span class="va">var</span>,</span>
@@ -81,96 +145,126 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
     </div>
 
     <div class="section level2">
-    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
+    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a>
+</h2>
 
 
-<dl><dt id="arg-lyt">lyt<a class="anchor" aria-label="anchor" href="#arg-lyt"></a></dt>
+<dl>
+<dt id="arg-lyt">lyt<a class="anchor" aria-label="anchor" href="#arg-lyt"></a>
+</dt>
 <dd><p>(<code>PreDataTableLayouts</code>)<br> layout that analyses will be added to.</p></dd>
 
 
-<dt id="arg-var">var<a class="anchor" aria-label="anchor" href="#arg-var"></a></dt>
+<dt id="arg-var">var<a class="anchor" aria-label="anchor" href="#arg-var"></a>
+</dt>
 <dd><p>(<code>string</code>)<br> single variable name that is passed by <code>rtables</code> when requested
 by a statistics function.</p></dd>
 
 
-<dt id="arg-na-str">na_str<a class="anchor" aria-label="anchor" href="#arg-na-str"></a></dt>
+<dt id="arg-na-str">na_str<a class="anchor" aria-label="anchor" href="#arg-na-str"></a>
+</dt>
 <dd><p>(<code>string</code>)<br> string used to replace all <code>NA</code> or empty values in the output.</p></dd>
 
 
-<dt id="arg-nested">nested<a class="anchor" aria-label="anchor" href="#arg-nested"></a></dt>
+<dt id="arg-nested">nested<a class="anchor" aria-label="anchor" href="#arg-nested"></a>
+</dt>
 <dd><p>(<code>flag</code>)<br> whether this layout instruction should be applied within the existing layout structure _if
 possible (<code>TRUE</code>, the default) or as a new top-level element (<code>FALSE</code>). Ignored if it would nest a split.
 underneath analyses, which is not allowed.</p></dd>
 
 
-<dt id="arg--">...<a class="anchor" aria-label="anchor" href="#arg--"></a></dt>
+<dt id="arg--">...<a class="anchor" aria-label="anchor" href="#arg--"></a>
+</dt>
 <dd><p>additional arguments for the lower level functions.</p></dd>
 
 
-<dt id="arg-show-labels">show_labels<a class="anchor" aria-label="anchor" href="#arg-show-labels"></a></dt>
+<dt id="arg-show-labels">show_labels<a class="anchor" aria-label="anchor" href="#arg-show-labels"></a>
+</dt>
 <dd><p>(<code>string</code>)<br> label visibility: one of "default", "visible" and "hidden".</p></dd>
 
 
-<dt id="arg-table-names">table_names<a class="anchor" aria-label="anchor" href="#arg-table-names"></a></dt>
+<dt id="arg-table-names">table_names<a class="anchor" aria-label="anchor" href="#arg-table-names"></a>
+</dt>
 <dd><p>(<code>character</code>)<br> this can be customized in the case that the same <code>vars</code> are analyzed multiple
 times, to avoid warnings from <code>rtables</code>.</p></dd>
 
 
-<dt id="arg--stats">.stats<a class="anchor" aria-label="anchor" href="#arg--stats"></a></dt>
-<dd><p>(<code>character</code>)<br> statistics to select for the table.</p>
-<p>Options are: <code>'n_prop', 'prop_ci'</code></p></dd>
+<dt id="arg--stats">.stats<a class="anchor" aria-label="anchor" href="#arg--stats"></a>
+</dt>
+<dd>
+<p>(<code>character</code>)<br> statistics to select for the table.</p>
+<p>Options are: <code>'n_prop', 'prop_ci'</code></p>
+</dd>
 
 
-<dt id="arg--formats">.formats<a class="anchor" aria-label="anchor" href="#arg--formats"></a></dt>
+<dt id="arg--formats">.formats<a class="anchor" aria-label="anchor" href="#arg--formats"></a>
+</dt>
 <dd><p>(named <code>character</code> or <code>list</code>)<br> formats for the statistics. See Details in <code>analyze_vars</code> for more
 information on the <code>"auto"</code> setting.</p></dd>
 
 
-<dt id="arg--labels">.labels<a class="anchor" aria-label="anchor" href="#arg--labels"></a></dt>
+<dt id="arg--labels">.labels<a class="anchor" aria-label="anchor" href="#arg--labels"></a>
+</dt>
 <dd><p>(named <code>character</code>)<br> labels for the statistics (without indent).</p></dd>
 
 
-<dt id="arg--indent-mods">.indent_mods<a class="anchor" aria-label="anchor" href="#arg--indent-mods"></a></dt>
+<dt id="arg--indent-mods">.indent_mods<a class="anchor" aria-label="anchor" href="#arg--indent-mods"></a>
+</dt>
 <dd><p>(named <code>integer</code>)<br> indent modifiers for the labels. Defaults to 0, which corresponds to the
 unmodified default behavior. Can be negative.</p></dd>
 
 
-<dt id="arg-x">x<a class="anchor" aria-label="anchor" href="#arg-x"></a></dt>
+<dt id="arg-x">x<a class="anchor" aria-label="anchor" href="#arg-x"></a>
+</dt>
 <dd><p>(<code>numeric</code>)<br> vector of numbers we want to analyze.</p></dd>
 
 
-<dt id="arg--n-col">.N_col<a class="anchor" aria-label="anchor" href="#arg--n-col"></a></dt>
+<dt id="arg--n-col">.N_col<a class="anchor" aria-label="anchor" href="#arg--n-col"></a>
+</dt>
 <dd><p>(<code>integer(1)</code>)<br> column-wise N (column count) for the full column being analyzed that is typically
 passed by <code>rtables</code>.</p></dd>
 
-</dl></div>
+</dl>
+</div>
     <div class="section level2">
-    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
+    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a>
+</h2>
 
-<ul><li><p><code>estimate_multinomial_response()</code> returns a layout object suitable for passing to further layouting functions,
+<ul>
+<li><p><code>estimate_multinomial_response()</code> returns a layout object suitable for passing to further layouting functions,
 or to <code><a href="https://insightsengineering.github.io/rtables/latest-tag/reference/build_table.html" class="external-link">rtables::build_table()</a></code>. Adding this function to an <code>rtable</code> layout will add formatted rows containing
 the statistics from <code>s_length_proportion()</code> to the table layout.</p></li>
-</ul><ul><li><p><code>s_length_proportion()</code> returns statistics from <code><a href="estimate_proportion.html">s_proportion()</a></code>.</p></li>
-</ul><ul><li><p><code>a_length_proportion()</code> returns the corresponding list with formatted <code><a href="https://insightsengineering.github.io/rtables/latest-tag/reference/CellValue.html" class="external-link">rtables::CellValue()</a></code>.</p></li>
-</ul></div>
+</ul>
+<ul>
+<li><p><code>s_length_proportion()</code> returns statistics from <code><a href="estimate_proportion.html">s_proportion()</a></code>.</p></li>
+</ul>
+<ul>
+<li><p><code>a_length_proportion()</code> returns the corresponding list with formatted <code><a href="https://insightsengineering.github.io/rtables/latest-tag/reference/CellValue.html" class="external-link">rtables::CellValue()</a></code>.</p></li>
+</ul>
+</div>
     <div class="section level2">
-    <h2 id="functions">Functions<a class="anchor" aria-label="anchor" href="#functions"></a></h2>
+    <h2 id="functions">Functions<a class="anchor" aria-label="anchor" href="#functions"></a>
+</h2>
 
-<ul><li><p><code>estimate_multinomial_response()</code>: Layout-creating function which can take statistics function arguments
+<ul>
+<li><p><code>estimate_multinomial_response()</code>: Layout-creating function which can take statistics function arguments
 and additional format arguments. This function is a wrapper for <code><a href="https://insightsengineering.github.io/rtables/latest-tag/reference/analyze.html" class="external-link">rtables::analyze()</a></code> and
 <code><a href="https://insightsengineering.github.io/rtables/latest-tag/reference/summarize_row_groups.html" class="external-link">rtables::summarize_row_groups()</a></code>.</p></li>
 <li><p><code>s_length_proportion()</code>: Statistics function which feeds the length of <code>x</code> as number
 of successes, and <code>.N_col</code> as total number of successes and failures into <code><a href="estimate_proportion.html">s_proportion()</a></code>.</p></li>
 <li><p><code>a_length_proportion()</code>: Formatted analysis function which is used as <code>afun</code>
 in <code>estimate_multinomial_response()</code>.</p></li>
-</ul></div>
+</ul>
+</div>
     <div class="section level2">
-    <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"></a></h2>
+    <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"></a>
+</h2>
     <div class="dont-index"><p>Relevant description function <code><a href="d_onco_rsp_label.html">d_onco_rsp_label()</a></code>.</p></div>
     </div>
 
     <div class="section level2">
-    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
+    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://dplyr.tidyverse.org" class="external-link">dplyr</a></span><span class="op">)</span></span></span>
 <span class="r-in"><span></span></span>
 <span class="r-in"><span><span class="co"># Use of the layout creating function.</span></span></span>
@@ -238,17 +332,19 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 </code></pre></div>
     </div>
   </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
-    </nav></aside></div>
+    </nav></aside>
+</div>
 
 
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   <p>tern is a part of the <strong>NEST</strong> and <a href="https://pharmaverse.org/" class="external-link"><strong>pharmaverse</strong></a>.</p>
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-<script type="text/javascript" src="../analytics.js"></script></footer></div>
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+<script type="text/javascript" src="../analytics.js"></script></footer>
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diff --git a/main/reference/estimate_proportion.html b/main/reference/estimate_proportion.html
index b8b611f2da..a85a814d1f 100644
--- a/main/reference/estimate_proportion.html
+++ b/main/reference/estimate_proportion.html
@@ -1,15 +1,38 @@
-<!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Proportion estimation — estimate_proportion • tern</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Proportion estimation — estimate_proportion"><meta name="description" content="
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+<title>Proportion estimation — estimate_proportion • tern</title>
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+<meta name="description" content="
 The analyze function estimate_proportion() creates a layout element to estimate the proportion of responders
 within a studied population. The primary analysis variable, vars, indicates whether a response has occurred for
 each record. See the method parameter for options of methods to use when constructing the confidence interval of
 the proportion. Additionally, a stratification variable can be supplied via the strata element of the variables
-argument."><meta property="og:description" content="
+argument.">
+<meta property="og:description" content="
 The analyze function estimate_proportion() creates a layout element to estimate the proportion of responders
 within a studied population. The primary analysis variable, vars, indicates whether a response has occurred for
 each record. See the method parameter for options of methods to use when constructing the confidence interval of
 the proportion. Additionally, a stratification variable can be supplied via the strata element of the variables
-argument."><meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png"><link rel="stylesheet" href="../consent.css"><script src="../consent.js" type="text/javascript" charset="utf-8"></script></head><body>
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   </div>
@@ -66,7 +129,8 @@
     </div>
 
     <div class="section level2">
-    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
+    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">estimate_proportion</span><span class="op">(</span></span>
 <span>  <span class="va">lyt</span>,</span>
 <span>  <span class="va">vars</span>,</span>
@@ -114,89 +178,111 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
     </div>
 
     <div class="section level2">
-    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
+    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a>
+</h2>
 
 
-<dl><dt id="arg-lyt">lyt<a class="anchor" aria-label="anchor" href="#arg-lyt"></a></dt>
+<dl>
+<dt id="arg-lyt">lyt<a class="anchor" aria-label="anchor" href="#arg-lyt"></a>
+</dt>
 <dd><p>(<code>PreDataTableLayouts</code>)<br> layout that analyses will be added to.</p></dd>
 
 
-<dt id="arg-vars">vars<a class="anchor" aria-label="anchor" href="#arg-vars"></a></dt>
+<dt id="arg-vars">vars<a class="anchor" aria-label="anchor" href="#arg-vars"></a>
+</dt>
 <dd><p>(<code>character</code>)<br> variable names for the primary analysis variable to be iterated over.</p></dd>
 
 
-<dt id="arg-conf-level">conf_level<a class="anchor" aria-label="anchor" href="#arg-conf-level"></a></dt>
+<dt id="arg-conf-level">conf_level<a class="anchor" aria-label="anchor" href="#arg-conf-level"></a>
+</dt>
 <dd><p>(<code>proportion</code>)<br> confidence level of the interval.</p></dd>
 
 
-<dt id="arg-method">method<a class="anchor" aria-label="anchor" href="#arg-method"></a></dt>
+<dt id="arg-method">method<a class="anchor" aria-label="anchor" href="#arg-method"></a>
+</dt>
 <dd><p>(<code>string</code>)<br> the method used to construct the confidence interval
 for proportion of successful outcomes; one of <code>waldcc</code>, <code>wald</code>, <code>clopper-pearson</code>,
 <code>wilson</code>, <code>wilsonc</code>, <code>strat_wilson</code>, <code>strat_wilsonc</code>, <code>agresti-coull</code> or <code>jeffreys</code>.</p></dd>
 
 
-<dt id="arg-weights">weights<a class="anchor" aria-label="anchor" href="#arg-weights"></a></dt>
+<dt id="arg-weights">weights<a class="anchor" aria-label="anchor" href="#arg-weights"></a>
+</dt>
 <dd><p>(<code>numeric</code> or <code>NULL</code>)<br> weights for each level of the strata. If <code>NULL</code>, they are
 estimated using the iterative algorithm proposed in Yan2010-jt;textualtern that
 minimizes the weighted squared length of the confidence interval.</p></dd>
 
 
-<dt id="arg-max-iterations">max_iterations<a class="anchor" aria-label="anchor" href="#arg-max-iterations"></a></dt>
+<dt id="arg-max-iterations">max_iterations<a class="anchor" aria-label="anchor" href="#arg-max-iterations"></a>
+</dt>
 <dd><p>(<code>count</code>)<br> maximum number of iterations for the iterative procedure used
 to find estimates of optimal weights.</p></dd>
 
 
-<dt id="arg-variables">variables<a class="anchor" aria-label="anchor" href="#arg-variables"></a></dt>
+<dt id="arg-variables">variables<a class="anchor" aria-label="anchor" href="#arg-variables"></a>
+</dt>
 <dd><p>(named <code>list</code> of <code>string</code>)<br> list of additional analysis variables.</p></dd>
 
 
-<dt id="arg-long">long<a class="anchor" aria-label="anchor" href="#arg-long"></a></dt>
+<dt id="arg-long">long<a class="anchor" aria-label="anchor" href="#arg-long"></a>
+</dt>
 <dd><p>(<code>flag</code>)<br> whether a long description is required.</p></dd>
 
 
-<dt id="arg-na-str">na_str<a class="anchor" aria-label="anchor" href="#arg-na-str"></a></dt>
+<dt id="arg-na-str">na_str<a class="anchor" aria-label="anchor" href="#arg-na-str"></a>
+</dt>
 <dd><p>(<code>string</code>)<br> string used to replace all <code>NA</code> or empty values in the output.</p></dd>
 
 
-<dt id="arg-nested">nested<a class="anchor" aria-label="anchor" href="#arg-nested"></a></dt>
+<dt id="arg-nested">nested<a class="anchor" aria-label="anchor" href="#arg-nested"></a>
+</dt>
 <dd><p>(<code>flag</code>)<br> whether this layout instruction should be applied within the existing layout structure _if
 possible (<code>TRUE</code>, the default) or as a new top-level element (<code>FALSE</code>). Ignored if it would nest a split.
 underneath analyses, which is not allowed.</p></dd>
 
 
-<dt id="arg--">...<a class="anchor" aria-label="anchor" href="#arg--"></a></dt>
+<dt id="arg--">...<a class="anchor" aria-label="anchor" href="#arg--"></a>
+</dt>
 <dd><p>additional arguments for the lower level functions.</p></dd>
 
 
-<dt id="arg-show-labels">show_labels<a class="anchor" aria-label="anchor" href="#arg-show-labels"></a></dt>
+<dt id="arg-show-labels">show_labels<a class="anchor" aria-label="anchor" href="#arg-show-labels"></a>
+</dt>
 <dd><p>(<code>string</code>)<br> label visibility: one of "default", "visible" and "hidden".</p></dd>
 
 
-<dt id="arg-table-names">table_names<a class="anchor" aria-label="anchor" href="#arg-table-names"></a></dt>
+<dt id="arg-table-names">table_names<a class="anchor" aria-label="anchor" href="#arg-table-names"></a>
+</dt>
 <dd><p>(<code>character</code>)<br> this can be customized in the case that the same <code>vars</code> are analyzed multiple
 times, to avoid warnings from <code>rtables</code>.</p></dd>
 
 
-<dt id="arg--stats">.stats<a class="anchor" aria-label="anchor" href="#arg--stats"></a></dt>
-<dd><p>(<code>character</code>)<br> statistics to select for the table.</p>
-<p>Options are: <code>'n_prop', 'prop_ci'</code></p></dd>
+<dt id="arg--stats">.stats<a class="anchor" aria-label="anchor" href="#arg--stats"></a>
+</dt>
+<dd>
+<p>(<code>character</code>)<br> statistics to select for the table.</p>
+<p>Options are: <code>'n_prop', 'prop_ci'</code></p>
+</dd>
 
 
-<dt id="arg--formats">.formats<a class="anchor" aria-label="anchor" href="#arg--formats"></a></dt>
+<dt id="arg--formats">.formats<a class="anchor" aria-label="anchor" href="#arg--formats"></a>
+</dt>
 <dd><p>(named <code>character</code> or <code>list</code>)<br> formats for the statistics. See Details in <code>analyze_vars</code> for more
 information on the <code>"auto"</code> setting.</p></dd>
 
 
-<dt id="arg--labels">.labels<a class="anchor" aria-label="anchor" href="#arg--labels"></a></dt>
+<dt id="arg--labels">.labels<a class="anchor" aria-label="anchor" href="#arg--labels"></a>
+</dt>
 <dd><p>(named <code>character</code>)<br> labels for the statistics (without indent).</p></dd>
 
 
-<dt id="arg--indent-mods">.indent_mods<a class="anchor" aria-label="anchor" href="#arg--indent-mods"></a></dt>
+<dt id="arg--indent-mods">.indent_mods<a class="anchor" aria-label="anchor" href="#arg--indent-mods"></a>
+</dt>
 <dd><p>(named <code>integer</code>)<br> indent modifiers for the labels. Defaults to 0, which corresponds to the
 unmodified default behavior. Can be negative.</p></dd>
 
 
-<dt id="arg-df">df<a class="anchor" aria-label="anchor" href="#arg-df"></a></dt>
+<dt id="arg-df">df<a class="anchor" aria-label="anchor" href="#arg-df"></a>
+</dt>
 <dd><p>(<code>logical</code> or <code>data.frame</code>)<br> if only a logical vector is used,
 it indicates whether each subject is a responder or not. <code>TRUE</code> represents
 a successful outcome. If a <code>data.frame</code> is provided, also the <code>strata</code> variable
@@ -205,38 +291,52 @@ <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#argumen
 variable name in <code>.var</code>.</p></dd>
 
 
-<dt id="arg--var">.var<a class="anchor" aria-label="anchor" href="#arg--var"></a></dt>
+<dt id="arg--var">.var<a class="anchor" aria-label="anchor" href="#arg--var"></a>
+</dt>
 <dd><p>(<code>string</code>)<br> single variable name that is passed by <code>rtables</code> when requested
 by a statistics function.</p></dd>
 
-</dl></div>
+</dl>
+</div>
     <div class="section level2">
-    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
+    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a>
+</h2>
 
-<ul><li><p><code>estimate_proportion()</code> returns a layout object suitable for passing to further layouting functions,
+<ul>
+<li><p><code>estimate_proportion()</code> returns a layout object suitable for passing to further layouting functions,
 or to <code><a href="https://insightsengineering.github.io/rtables/latest-tag/reference/build_table.html" class="external-link">rtables::build_table()</a></code>. Adding this function to an <code>rtable</code> layout will add formatted rows containing
 the statistics from <code>s_proportion()</code> to the table layout.</p></li>
-</ul><ul><li><p><code>s_proportion()</code> returns statistics <code>n_prop</code> (<code>n</code> and proportion) and <code>prop_ci</code> (proportion CI) for a
+</ul>
+<ul>
+<li><p><code>s_proportion()</code> returns statistics <code>n_prop</code> (<code>n</code> and proportion) and <code>prop_ci</code> (proportion CI) for a
 given variable.</p></li>
-</ul><ul><li><p><code>a_proportion()</code> returns the corresponding list with formatted <code><a href="https://insightsengineering.github.io/rtables/latest-tag/reference/CellValue.html" class="external-link">rtables::CellValue()</a></code>.</p></li>
-</ul></div>
+</ul>
+<ul>
+<li><p><code>a_proportion()</code> returns the corresponding list with formatted <code><a href="https://insightsengineering.github.io/rtables/latest-tag/reference/CellValue.html" class="external-link">rtables::CellValue()</a></code>.</p></li>
+</ul>
+</div>
     <div class="section level2">
-    <h2 id="functions">Functions<a class="anchor" aria-label="anchor" href="#functions"></a></h2>
+    <h2 id="functions">Functions<a class="anchor" aria-label="anchor" href="#functions"></a>
+</h2>
 
-<ul><li><p><code>estimate_proportion()</code>: Layout-creating function which can take statistics function arguments
+<ul>
+<li><p><code>estimate_proportion()</code>: Layout-creating function which can take statistics function arguments
 and additional format arguments. This function is a wrapper for <code><a href="https://insightsengineering.github.io/rtables/latest-tag/reference/analyze.html" class="external-link">rtables::analyze()</a></code>.</p></li>
 <li><p><code>s_proportion()</code>: Statistics function estimating a
 proportion along with its confidence interval.</p></li>
 <li><p><code>a_proportion()</code>: Formatted analysis function which is used as <code>afun</code>
 in <code>estimate_proportion()</code>.</p></li>
-</ul></div>
+</ul>
+</div>
     <div class="section level2">
-    <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"></a></h2>
+    <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"></a>
+</h2>
     <div class="dont-index"><p><a href="h_proportions.html">h_proportions</a></p></div>
     </div>
 
     <div class="section level2">
-    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
+    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">dta_test</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a></span><span class="op">(</span></span></span>
 <span class="r-in"><span>  USUBJID <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/paste.html" class="external-link">paste0</a></span><span class="op">(</span><span class="st">"S"</span>, <span class="fl">1</span><span class="op">:</span><span class="fl">12</span><span class="op">)</span>,</span></span>
 <span class="r-in"><span>  ARM     <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/rep.html" class="external-link">rep</a></span><span class="op">(</span><span class="va">LETTERS</span><span class="op">[</span><span class="fl">1</span><span class="op">:</span><span class="fl">3</span><span class="op">]</span>, each <span class="op">=</span> <span class="fl">4</span><span class="op">)</span>,</span></span>
@@ -298,17 +398,19 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 </code></pre></div>
     </div>
   </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
-    </nav></aside></div>
+    </nav></aside>
+</div>
 
 
     <footer><div class="nest">
   <p>tern is a part of the <strong>NEST</strong> and <a href="https://pharmaverse.org/" class="external-link"><strong>pharmaverse</strong></a>.</p>
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-<script type="text/javascript" src="../analytics.js"></script></footer></div>
-
+<script type="text/javascript" src="../analytics.js"></script></footer>
+</div>
 
 
 
 
-  </body></html>
 
+  </body>
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diff --git a/main/reference/ex_data.html b/main/reference/ex_data.html
index 12c318c2a6..0b86b5bc09 100644
--- a/main/reference/ex_data.html
+++ b/main/reference/ex_data.html
@@ -1,5 +1,28 @@
-<!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Simulated CDISC data for examples — ex_data • tern</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Simulated CDISC data for examples — ex_data"><meta name="description" content="Simulated CDISC data for examples"><meta property="og:description" content="Simulated CDISC data for examples"><meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png"><link rel="stylesheet" href="../consent.css"><script src="../consent.js" type="text/javascript" charset="utf-8"></script></head><body>
+<html lang="en">
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+<meta http-equiv="X-UA-Compatible" content="IE=edge">
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+<title>Simulated CDISC data for examples — ex_data • tern</title>
+<!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png">
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+<script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
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+<script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet">
+<link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet">
+<script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Simulated CDISC data for examples — ex_data">
+<meta name="description" content="Simulated CDISC data for examples">
+<meta property="og:description" content="Simulated CDISC data for examples">
+<meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png">
+<link rel="stylesheet" href="../consent.css">
+<script src="../consent.js" type="text/javascript" charset="utf-8"></script>
+</head>
+<body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
 
 
@@ -15,26 +38,66 @@
     </button>
 
     <div id="navbar" class="collapse navbar-collapse ms-3">
-      <ul class="navbar-nav me-auto"><li class="nav-item"><a class="nav-link" href="../articles/tern.html">Get started</a></li>
+      <ul class="navbar-nav me-auto">
+<li class="nav-item"><a class="nav-link" href="../articles/tern.html">Get started</a></li>
 <li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
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   <button class="nav-link dropdown-toggle" type="button" id="dropdown-articles" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Articles</button>
-  <ul class="dropdown-menu" aria-labelledby="dropdown-articles"><li><a class="dropdown-item" href="../articles/missing_values.html">Missing Values in Tern</a></li>
+  <ul class="dropdown-menu" aria-labelledby="dropdown-articles">
+<li><a class="dropdown-item" href="../articles/missing_values.html">Missing Values in Tern</a></li>
     <li><a class="dropdown-item" href="../articles/tables.html">Tabulation</a></li>
     <li><a class="dropdown-item" href="../articles/tern_formats.html">Formatting Functions</a></li>
     <li><a class="dropdown-item" href="../articles/tern_functions_guide.html">Understanding `tern` functions</a></li>
-  </ul></li>
+  </ul>
+</li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
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+  <ul class="dropdown-menu" aria-labelledby="dropdown-reports">
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- <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json"></form></li>
+  </ul>
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+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/main">main</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
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+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.3">v0.9.3</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1-rc3">v0.9.1-rc3</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a>
+</div>
+</li></div>
+</ul>
+<ul class="navbar-nav">
+<li class="nav-item"><form class="form-inline" role="search">
+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json">
+</form></li>
 <li class="nav-item"><a class="external-link nav-link" href="https://github.com/insightsengineering/tern" aria-label="GitHub"><span class="fa fa-github"></span></a></li>
-      </ul></div>
+      </ul>
+</div>
 
 
   </div>
@@ -51,7 +114,8 @@
     </div>
 
     <div class="section level2">
-    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
+    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="va">tern_ex_adsl</span></span>
 <span></span>
 <span><span class="va">tern_ex_adae</span></span>
@@ -66,7 +130,8 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
     </div>
 
     <div class="section level2">
-    <h2 id="format">Format<a class="anchor" aria-label="anchor" href="#format"></a></h2>
+    <h2 id="format">Format<a class="anchor" aria-label="anchor" href="#format"></a>
+</h2>
     <p><code>rds</code> (<code>data.frame</code>)</p>
 <p>An object of class <code>tbl_df</code> (inherits from <code>tbl</code>, <code>data.frame</code>) with 200 rows and 21 columns.</p>
 <p>An object of class <code>tbl_df</code> (inherits from <code>tbl</code>, <code>data.frame</code>) with 541 rows and 42 columns.</p>
@@ -76,28 +141,33 @@ <h2 id="format">Format<a class="anchor" aria-label="anchor" href="#format"></a><
 <p>An object of class <code>tbl_df</code> (inherits from <code>tbl</code>, <code>data.frame</code>) with 1000 rows and 28 columns.</p>
     </div>
     <div class="section level2">
-    <h2 id="functions">Functions<a class="anchor" aria-label="anchor" href="#functions"></a></h2>
+    <h2 id="functions">Functions<a class="anchor" aria-label="anchor" href="#functions"></a>
+</h2>
 
-<ul><li><p><code>tern_ex_adsl</code>: ADSL data</p></li>
+<ul>
+<li><p><code>tern_ex_adsl</code>: ADSL data</p></li>
 <li><p><code>tern_ex_adae</code>: ADAE data</p></li>
 <li><p><code>tern_ex_adlb</code>: ADLB data</p></li>
 <li><p><code>tern_ex_adpp</code>: ADPP data</p></li>
 <li><p><code>tern_ex_adrs</code>: ADRS data</p></li>
 <li><p><code>tern_ex_adtte</code>: ADTTE data</p></li>
-</ul></div>
+</ul>
+</div>
 
   </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
-    </nav></aside></div>
+    </nav></aside>
+</div>
 
 
     <footer><div class="nest">
   <p>tern is a part of the <strong>NEST</strong> and <a href="https://pharmaverse.org/" class="external-link"><strong>pharmaverse</strong></a>.</p>
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-<script type="text/javascript" src="../analytics.js"></script></footer></div>
-
+<script type="text/javascript" src="../analytics.js"></script></footer>
+</div>
 
 
 
 
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+  </body>
+</html>
diff --git a/main/reference/explicit_na.html b/main/reference/explicit_na.html
index 8de58589b2..326e4e03be 100644
--- a/main/reference/explicit_na.html
+++ b/main/reference/explicit_na.html
@@ -1,7 +1,30 @@
-<!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Missing data — explicit_na • tern</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Missing data — explicit_na"><meta name="description" content="
-Substitute missing data with a string or factor level."><meta property="og:description" content="
-Substitute missing data with a string or factor level."><meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png"><link rel="stylesheet" href="../consent.css"><script src="../consent.js" type="text/javascript" charset="utf-8"></script></head><body>
+<html lang="en">
+<head>
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+<meta http-equiv="X-UA-Compatible" content="IE=edge">
+<meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<title>Missing data — explicit_na • tern</title>
+<!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png">
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+<script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet">
+<script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet">
+<link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet">
+<script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Missing data — explicit_na">
+<meta name="description" content="
+Substitute missing data with a string or factor level.">
+<meta property="og:description" content="
+Substitute missing data with a string or factor level.">
+<meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png">
+<link rel="stylesheet" href="../consent.css">
+<script src="../consent.js" type="text/javascript" charset="utf-8"></script>
+</head>
+<body>
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@@ -17,26 +40,66 @@
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   <button class="nav-link dropdown-toggle" type="button" id="dropdown-articles" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Articles</button>
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+  <ul class="dropdown-menu" aria-labelledby="dropdown-articles">
+<li><a class="dropdown-item" href="../articles/missing_values.html">Missing Values in Tern</a></li>
     <li><a class="dropdown-item" href="../articles/tables.html">Tabulation</a></li>
     <li><a class="dropdown-item" href="../articles/tern_formats.html">Formatting Functions</a></li>
     <li><a class="dropdown-item" href="../articles/tern_functions_guide.html">Understanding `tern` functions</a></li>
-  </ul></li>
+  </ul>
+</li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
-  <ul class="dropdown-menu" aria-labelledby="dropdown-reports"><li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
+  <ul class="dropdown-menu" aria-labelledby="dropdown-reports">
+<li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
     <li><a class="dropdown-item" href="../unit-test-report/">Unit test report</a></li>
     <li><a class="dropdown-item" href="../unit-test-report-non-cran/">Non-CRAN unit test report</a></li>
-  </ul></li>
-      </ul><ul class="navbar-nav"><li class="nav-item"><form class="form-inline" role="search">
- <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json"></form></li>
+  </ul>
+</li>
+      <div><li class="nav-item dropdown">
+    <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-versions">Versions</a>
+    <div class="dropdown-menu" aria-labelledby="dropdown-versions">
+    <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/main">main</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.5">v0.9.5</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.4">v0.9.4</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.3">v0.9.3</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1-rc3">v0.9.1-rc3</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a>
+</div>
+</li></div>
+</ul>
+<ul class="navbar-nav">
+<li class="nav-item"><form class="form-inline" role="search">
+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json">
+</form></li>
 <li class="nav-item"><a class="external-link nav-link" href="https://github.com/insightsengineering/tern" aria-label="GitHub"><span class="fa fa-github"></span></a></li>
-      </ul></div>
+      </ul>
+</div>
 
 
   </div>
@@ -54,29 +117,37 @@
     </div>
 
     <div class="section level2">
-    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
+    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">explicit_na</span><span class="op">(</span><span class="va">x</span>, label <span class="op">=</span> <span class="st">"&lt;Missing&gt;"</span><span class="op">)</span></span></code></pre></div>
     </div>
 
     <div class="section level2">
-    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
+    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a>
+</h2>
 
 
-<dl><dt id="arg-x">x<a class="anchor" aria-label="anchor" href="#arg-x"></a></dt>
+<dl>
+<dt id="arg-x">x<a class="anchor" aria-label="anchor" href="#arg-x"></a>
+</dt>
 <dd><p>(<code>factor</code> or <code>character</code>)<br> values for which any missing values should be substituted.</p></dd>
 
 
-<dt id="arg-label">label<a class="anchor" aria-label="anchor" href="#arg-label"></a></dt>
+<dt id="arg-label">label<a class="anchor" aria-label="anchor" href="#arg-label"></a>
+</dt>
 <dd><p>(<code>string</code>)<br> string that missing data should be replaced with.</p></dd>
 
-</dl></div>
+</dl>
+</div>
     <div class="section level2">
-    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
+    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a>
+</h2>
     <p><code>x</code> with any <code>NA</code> values substituted by <code>label</code>.</p>
     </div>
 
     <div class="section level2">
-    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
+    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="fu">explicit_na</span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="cn">NA</span>, <span class="st">"a"</span>, <span class="st">"b"</span><span class="op">)</span><span class="op">)</span></span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> [1] "&lt;Missing&gt;" "a"         "b"        </span>
 <span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/NA.html" class="external-link">is.na</a></span><span class="op">(</span><span class="fu">explicit_na</span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="cn">NA</span>, <span class="st">"a"</span>, <span class="st">"b"</span><span class="op">)</span><span class="op">)</span><span class="op">)</span></span></span>
@@ -94,17 +165,19 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 </code></pre></div>
     </div>
   </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
-    </nav></aside></div>
+    </nav></aside>
+</div>
 
 
     <footer><div class="nest">
   <p>tern is a part of the <strong>NEST</strong> and <a href="https://pharmaverse.org/" class="external-link"><strong>pharmaverse</strong></a>.</p>
 </div>
-<script type="text/javascript" src="../analytics.js"></script></footer></div>
-
+<script type="text/javascript" src="../analytics.js"></script></footer>
+</div>
 
 
 
 
-  </body></html>
 
+  </body>
+</html>
diff --git a/main/reference/extract_by_name.html b/main/reference/extract_by_name.html
index 68f08091a8..86e431d686 100644
--- a/main/reference/extract_by_name.html
+++ b/main/reference/extract_by_name.html
@@ -1,7 +1,30 @@
-<!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Extract elements by name — extract_by_name • tern</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Extract elements by name — extract_by_name"><meta name="description" content="This utility function extracts elements from a vector x by names.
-Differences to the standard [ function are:"><meta property="og:description" content="This utility function extracts elements from a vector x by names.
-Differences to the standard [ function are:"><meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png"><link rel="stylesheet" href="../consent.css"><script src="../consent.js" type="text/javascript" charset="utf-8"></script></head><body>
+<html lang="en">
+<head>
+<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+<meta charset="utf-8">
+<meta http-equiv="X-UA-Compatible" content="IE=edge">
+<meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<title>Extract elements by name — extract_by_name • tern</title>
+<!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png">
+<link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png">
+<link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png">
+<link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png">
+<link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png">
+<link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png">
+<script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet">
+<script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet">
+<link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet">
+<script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Extract elements by name — extract_by_name">
+<meta name="description" content="This utility function extracts elements from a vector x by names.
+Differences to the standard [ function are:">
+<meta property="og:description" content="This utility function extracts elements from a vector x by names.
+Differences to the standard [ function are:">
+<meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png">
+<link rel="stylesheet" href="../consent.css">
+<script src="../consent.js" type="text/javascript" charset="utf-8"></script>
+</head>
+<body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
 
 
@@ -17,26 +40,66 @@
     </button>
 
     <div id="navbar" class="collapse navbar-collapse ms-3">
-      <ul class="navbar-nav me-auto"><li class="nav-item"><a class="nav-link" href="../articles/tern.html">Get started</a></li>
+      <ul class="navbar-nav me-auto">
+<li class="nav-item"><a class="nav-link" href="../articles/tern.html">Get started</a></li>
 <li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
 <li class="nav-item dropdown">
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-articles" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Articles</button>
-  <ul class="dropdown-menu" aria-labelledby="dropdown-articles"><li><a class="dropdown-item" href="../articles/missing_values.html">Missing Values in Tern</a></li>
+  <ul class="dropdown-menu" aria-labelledby="dropdown-articles">
+<li><a class="dropdown-item" href="../articles/missing_values.html">Missing Values in Tern</a></li>
     <li><a class="dropdown-item" href="../articles/tables.html">Tabulation</a></li>
     <li><a class="dropdown-item" href="../articles/tern_formats.html">Formatting Functions</a></li>
     <li><a class="dropdown-item" href="../articles/tern_functions_guide.html">Understanding `tern` functions</a></li>
-  </ul></li>
+  </ul>
+</li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
-  <ul class="dropdown-menu" aria-labelledby="dropdown-reports"><li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
+  <ul class="dropdown-menu" aria-labelledby="dropdown-reports">
+<li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
     <li><a class="dropdown-item" href="../unit-test-report/">Unit test report</a></li>
     <li><a class="dropdown-item" href="../unit-test-report-non-cran/">Non-CRAN unit test report</a></li>
-  </ul></li>
-      </ul><ul class="navbar-nav"><li class="nav-item"><form class="form-inline" role="search">
- <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json"></form></li>
+  </ul>
+</li>
+      <div><li class="nav-item dropdown">
+    <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-versions">Versions</a>
+    <div class="dropdown-menu" aria-labelledby="dropdown-versions">
+    <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/main">main</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.5">v0.9.5</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.4">v0.9.4</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.3">v0.9.3</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1-rc3">v0.9.1-rc3</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a>
+</div>
+</li></div>
+</ul>
+<ul class="navbar-nav">
+<li class="nav-item"><form class="form-inline" role="search">
+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json">
+</form></li>
 <li class="nav-item"><a class="external-link nav-link" href="https://github.com/insightsengineering/tern" aria-label="GitHub"><span class="fa fa-github"></span></a></li>
-      </ul></div>
+      </ul>
+</div>
 
 
   </div>
@@ -54,46 +117,58 @@
     </div>
 
     <div class="section level2">
-    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
+    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">extract_by_name</span><span class="op">(</span><span class="va">x</span>, <span class="va">names</span><span class="op">)</span></span></code></pre></div>
     </div>
 
     <div class="section level2">
-    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
+    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a>
+</h2>
 
 
-<dl><dt id="arg-x">x<a class="anchor" aria-label="anchor" href="#arg-x"></a></dt>
+<dl>
+<dt id="arg-x">x<a class="anchor" aria-label="anchor" href="#arg-x"></a>
+</dt>
 <dd><p>(named <code>vector</code>)<br> where to extract named elements from.</p></dd>
 
 
-<dt id="arg-names">names<a class="anchor" aria-label="anchor" href="#arg-names"></a></dt>
+<dt id="arg-names">names<a class="anchor" aria-label="anchor" href="#arg-names"></a>
+</dt>
 <dd><p>(<code>character</code>)<br> vector of names to extract.</p></dd>
 
-</dl></div>
+</dl>
+</div>
     <div class="section level2">
-    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
+    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a>
+</h2>
     <p><code>NULL</code> if <code>x</code> is <code>NULL</code>, otherwise the extracted elements from <code>x</code>.</p>
     </div>
     <div class="section level2">
-    <h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a></h2>
+    <h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a>
+</h2>
 
-<ul><li><p>If <code>x</code> is <code>NULL</code>, then still always <code>NULL</code> is returned (same as in base function).</p></li>
+<ul>
+<li><p>If <code>x</code> is <code>NULL</code>, then still always <code>NULL</code> is returned (same as in base function).</p></li>
 <li><p>If <code>x</code> is not <code>NULL</code>, then the intersection of its names is made with <code>names</code> and those
 elements are returned. That is, <code>names</code> which don't appear in <code>x</code> are not returned as <code>NA</code>s.</p></li>
-</ul></div>
+</ul>
+</div>
 
   </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
-    </nav></aside></div>
+    </nav></aside>
+</div>
 
 
     <footer><div class="nest">
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diff --git a/main/reference/extract_rsp_biomarkers.html b/main/reference/extract_rsp_biomarkers.html
index 93a4e63a94..1d0526d664 100644
--- a/main/reference/extract_rsp_biomarkers.html
+++ b/main/reference/extract_rsp_biomarkers.html
@@ -1,19 +1,42 @@
-<!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Prepare response data estimates for multiple biomarkers in a single data frame — extract_rsp_biomarkers • tern</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Prepare response data estimates for multiple biomarkers in a single data frame — extract_rsp_biomarkers"><meta name="description" content="
+<html lang="en">
+<head>
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+<meta http-equiv="X-UA-Compatible" content="IE=edge">
+<meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<title>Prepare response data estimates for multiple biomarkers in a single data frame — extract_rsp_biomarkers • tern</title>
+<!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png">
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+<link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet">
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+<link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet">
+<script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Prepare response data estimates for multiple biomarkers in a single data frame — extract_rsp_biomarkers">
+<meta name="description" content="
 Prepares estimates for number of responses, patients and overall response rate,
 as well as odds ratio estimates, confidence intervals and p-values,
 for multiple biomarkers across population subgroups in a single data frame.
 variables corresponds to the names of variables found in data, passed as a
 named list and requires elements rsp and biomarkers (vector of continuous
 biomarker variables) and optionally covariates, subgroups and strata.
-groups_lists optionally specifies groupings for subgroups variables."><meta property="og:description" content="
+groups_lists optionally specifies groupings for subgroups variables.">
+<meta property="og:description" content="
 Prepares estimates for number of responses, patients and overall response rate,
 as well as odds ratio estimates, confidence intervals and p-values,
 for multiple biomarkers across population subgroups in a single data frame.
 variables corresponds to the names of variables found in data, passed as a
 named list and requires elements rsp and biomarkers (vector of continuous
 biomarker variables) and optionally covariates, subgroups and strata.
-groups_lists optionally specifies groupings for subgroups variables."><meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png"><link rel="stylesheet" href="../consent.css"><script src="../consent.js" type="text/javascript" charset="utf-8"></script></head><body>
+groups_lists optionally specifies groupings for subgroups variables.">
+<meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png">
+<link rel="stylesheet" href="../consent.css">
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@@ -29,26 +52,66 @@
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+</div>
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 <li class="nav-item"><a class="external-link nav-link" href="https://github.com/insightsengineering/tern" aria-label="GitHub"><span class="fa fa-github"></span></a></li>
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+      </ul>
+</div>
 
 
   </div>
@@ -72,7 +135,8 @@
     </div>
 
     <div class="section level2">
-    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
+    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">extract_rsp_biomarkers</span><span class="op">(</span></span>
 <span>  <span class="va">variables</span>,</span>
 <span>  <span class="va">data</span>,</span>
@@ -83,51 +147,63 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
     </div>
 
     <div class="section level2">
-    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
+    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a>
+</h2>
 
 
-<dl><dt id="arg-variables">variables<a class="anchor" aria-label="anchor" href="#arg-variables"></a></dt>
+<dl>
+<dt id="arg-variables">variables<a class="anchor" aria-label="anchor" href="#arg-variables"></a>
+</dt>
 <dd><p>(named <code>list</code> of <code>string</code>)<br> list of additional analysis variables.</p></dd>
 
 
-<dt id="arg-data">data<a class="anchor" aria-label="anchor" href="#arg-data"></a></dt>
+<dt id="arg-data">data<a class="anchor" aria-label="anchor" href="#arg-data"></a>
+</dt>
 <dd><p>(<code>data.frame</code>)<br> the dataset containing the variables to summarize.</p></dd>
 
 
-<dt id="arg-groups-lists">groups_lists<a class="anchor" aria-label="anchor" href="#arg-groups-lists"></a></dt>
+<dt id="arg-groups-lists">groups_lists<a class="anchor" aria-label="anchor" href="#arg-groups-lists"></a>
+</dt>
 <dd><p>(named <code>list</code> of <code>list</code>)<br> optionally contains for each <code>subgroups</code> variable a
 list, which specifies the new group levels via the names and the
 levels that belong to it in the character vectors that are elements of the list.</p></dd>
 
 
-<dt id="arg-control">control<a class="anchor" aria-label="anchor" href="#arg-control"></a></dt>
+<dt id="arg-control">control<a class="anchor" aria-label="anchor" href="#arg-control"></a>
+</dt>
 <dd><p>(named <code>list</code>)<br> controls for the response definition and the
 confidence level produced by <code><a href="control_logistic.html">control_logistic()</a></code>.</p></dd>
 
 
-<dt id="arg-label-all">label_all<a class="anchor" aria-label="anchor" href="#arg-label-all"></a></dt>
+<dt id="arg-label-all">label_all<a class="anchor" aria-label="anchor" href="#arg-label-all"></a>
+</dt>
 <dd><p>(<code>string</code>)<br> label for the total population analysis.</p></dd>
 
-</dl></div>
+</dl>
+</div>
     <div class="section level2">
-    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
+    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a>
+</h2>
     <p>A <code>data.frame</code> with columns <code>biomarker</code>, <code>biomarker_label</code>, <code>n_tot</code>, <code>n_rsp</code>,
 <code>prop</code>, <code>or</code>, <code>lcl</code>, <code>ucl</code>, <code>conf_level</code>, <code>pval</code>, <code>pval_label</code>, <code>subgroup</code>, <code>var</code>,
 <code>var_label</code>, and <code>row_type</code>.</p>
     </div>
     <div class="section level2">
-    <h2 id="note">Note<a class="anchor" aria-label="anchor" href="#note"></a></h2>
+    <h2 id="note">Note<a class="anchor" aria-label="anchor" href="#note"></a>
+</h2>
     <p>You can also specify a continuous variable in <code>rsp</code> and then use the
 <code>response_definition</code> control to convert that internally to a logical
 variable reflecting binary response.</p>
     </div>
     <div class="section level2">
-    <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"></a></h2>
+    <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"></a>
+</h2>
     <div class="dont-index"><p><code><a href="h_response_biomarkers_subgroups.html">h_logistic_mult_cont_df()</a></code> which is used internally.</p></div>
     </div>
 
     <div class="section level2">
-    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
+    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://dplyr.tidyverse.org" class="external-link">dplyr</a></span><span class="op">)</span></span></span>
 <span class="r-in"><span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://forcats.tidyverse.org/" class="external-link">forcats</a></span><span class="op">)</span></span></span>
 <span class="r-in"><span></span></span>
@@ -235,17 +311,19 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 </code></pre></div>
     </div>
   </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
-    </nav></aside></div>
+    </nav></aside>
+</div>
 
 
     <footer><div class="nest">
   <p>tern is a part of the <strong>NEST</strong> and <a href="https://pharmaverse.org/" class="external-link"><strong>pharmaverse</strong></a>.</p>
 </div>
-<script type="text/javascript" src="../analytics.js"></script></footer></div>
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+</div>
 
 
 
 
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diff --git a/main/reference/extract_rsp_subgroups.html b/main/reference/extract_rsp_subgroups.html
index 427fd96697..60df440202 100644
--- a/main/reference/extract_rsp_subgroups.html
+++ b/main/reference/extract_rsp_subgroups.html
@@ -1,15 +1,38 @@
-<!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Prepare response data for population subgroups in data frames — extract_rsp_subgroups • tern</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Prepare response data for population subgroups in data frames — extract_rsp_subgroups"><meta name="description" content="
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+<title>Prepare response data for population subgroups in data frames — extract_rsp_subgroups • tern</title>
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+<meta name="description" content="
 Prepares response rates and odds ratios for population subgroups in data frames. Simple wrapper
 for h_odds_ratio_subgroups_df() and h_proportion_subgroups_df(). Result is a list of two
 data.frames: prop and or. variables corresponds to the names of variables found in data,
 passed as a named list and requires elements rsp, arm and optionally subgroups and strata.
-groups_lists optionally specifies groupings for subgroups variables."><meta property="og:description" content="
+groups_lists optionally specifies groupings for subgroups variables.">
+<meta property="og:description" content="
 Prepares response rates and odds ratios for population subgroups in data frames. Simple wrapper
 for h_odds_ratio_subgroups_df() and h_proportion_subgroups_df(). Result is a list of two
 data.frames: prop and or. variables corresponds to the names of variables found in data,
 passed as a named list and requires elements rsp, arm and optionally subgroups and strata.
-groups_lists optionally specifies groupings for subgroups variables."><meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png"><link rel="stylesheet" href="../consent.css"><script src="../consent.js" type="text/javascript" charset="utf-8"></script></head><body>
+groups_lists optionally specifies groupings for subgroups variables.">
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+</div>
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+      </ul>
+</div>
 
 
   </div>
@@ -66,7 +129,8 @@
     </div>
 
     <div class="section level2">
-    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
+    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">extract_rsp_subgroups</span><span class="op">(</span></span>
 <span>  <span class="va">variables</span>,</span>
 <span>  <span class="va">data</span>,</span>
@@ -78,60 +142,76 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
     </div>
 
     <div class="section level2">
-    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
+    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a>
+</h2>
 
 
-<dl><dt id="arg-variables">variables<a class="anchor" aria-label="anchor" href="#arg-variables"></a></dt>
+<dl>
+<dt id="arg-variables">variables<a class="anchor" aria-label="anchor" href="#arg-variables"></a>
+</dt>
 <dd><p>(named <code>list</code> of <code>string</code>)<br> list of additional analysis variables.</p></dd>
 
 
-<dt id="arg-data">data<a class="anchor" aria-label="anchor" href="#arg-data"></a></dt>
+<dt id="arg-data">data<a class="anchor" aria-label="anchor" href="#arg-data"></a>
+</dt>
 <dd><p>(<code>data.frame</code>)<br> the dataset containing the variables to summarize.</p></dd>
 
 
-<dt id="arg-groups-lists">groups_lists<a class="anchor" aria-label="anchor" href="#arg-groups-lists"></a></dt>
+<dt id="arg-groups-lists">groups_lists<a class="anchor" aria-label="anchor" href="#arg-groups-lists"></a>
+</dt>
 <dd><p>(named <code>list</code> of <code>list</code>)<br> optionally contains for each <code>subgroups</code> variable a
 list, which specifies the new group levels via the names and the
 levels that belong to it in the character vectors that are elements of the list.</p></dd>
 
 
-<dt id="arg-conf-level">conf_level<a class="anchor" aria-label="anchor" href="#arg-conf-level"></a></dt>
+<dt id="arg-conf-level">conf_level<a class="anchor" aria-label="anchor" href="#arg-conf-level"></a>
+</dt>
 <dd><p>(<code>proportion</code>)<br> confidence level of the interval.</p></dd>
 
 
-<dt id="arg-method">method<a class="anchor" aria-label="anchor" href="#arg-method"></a></dt>
+<dt id="arg-method">method<a class="anchor" aria-label="anchor" href="#arg-method"></a>
+</dt>
 <dd><p>(<code>string</code> or <code>NULL</code>)<br> specifies the test used to calculate the p-value for the difference between
 two proportions. For options, see <code><a href="prop_diff_test.html">test_proportion_diff()</a></code>. Default is <code>NULL</code> so no test is performed.</p></dd>
 
 
-<dt id="arg-label-all">label_all<a class="anchor" aria-label="anchor" href="#arg-label-all"></a></dt>
+<dt id="arg-label-all">label_all<a class="anchor" aria-label="anchor" href="#arg-label-all"></a>
+</dt>
 <dd><p>(<code>string</code>)<br> label for the total population analysis.</p></dd>
 
-</dl></div>
+</dl>
+</div>
     <div class="section level2">
-    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
-    <p>A named list of two elements:</p><ul><li><p><code>prop</code>: A <code>data.frame</code> containing columns <code>arm</code>, <code>n</code>, <code>n_rsp</code>, <code>prop</code>, <code>subgroup</code>, <code>var</code>,
+    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a>
+</h2>
+    <p>A named list of two elements:</p>
+<ul>
+<li><p><code>prop</code>: A <code>data.frame</code> containing columns <code>arm</code>, <code>n</code>, <code>n_rsp</code>, <code>prop</code>, <code>subgroup</code>, <code>var</code>,
 <code>var_label</code>, and <code>row_type</code>.</p></li>
 <li><p><code>or</code>: A <code>data.frame</code> containing columns <code>arm</code>, <code>n_tot</code>, <code>or</code>, <code>lcl</code>, <code>ucl</code>, <code>conf_level</code>,
 <code>subgroup</code>, <code>var</code>, <code>var_label</code>, and <code>row_type</code>.</p></li>
-</ul></div>
+</ul>
+</div>
     <div class="section level2">
-    <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"></a></h2>
+    <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"></a>
+</h2>
     <div class="dont-index"><p><a href="response_subgroups.html">response_subgroups</a></p></div>
     </div>
 
   </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
-    </nav></aside></div>
+    </nav></aside>
+</div>
 
 
     <footer><div class="nest">
   <p>tern is a part of the <strong>NEST</strong> and <a href="https://pharmaverse.org/" class="external-link"><strong>pharmaverse</strong></a>.</p>
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diff --git a/main/reference/extract_survival_biomarkers.html b/main/reference/extract_survival_biomarkers.html
index 94441a5f24..8065c16b0b 100644
--- a/main/reference/extract_survival_biomarkers.html
+++ b/main/reference/extract_survival_biomarkers.html
@@ -1,15 +1,38 @@
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-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Prepare survival data estimates for multiple biomarkers in a single data frame — extract_survival_biomarkers • tern</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Prepare survival data estimates for multiple biomarkers in a single data frame — extract_survival_biomarkers"><meta name="description" content="
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+<script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Prepare survival data estimates for multiple biomarkers in a single data frame — extract_survival_biomarkers">
+<meta name="description" content="
 Prepares estimates for number of events, patients and median survival times, as well as hazard ratio estimates,
 confidence intervals and p-values, for multiple biomarkers across population subgroups in a single data frame.
 variables corresponds to the names of variables found in data, passed as a named list and requires elements
 tte, is_event, biomarkers (vector of continuous biomarker variables), and optionally subgroups and strata.
-groups_lists optionally specifies groupings for subgroups variables."><meta property="og:description" content="
+groups_lists optionally specifies groupings for subgroups variables.">
+<meta property="og:description" content="
 Prepares estimates for number of events, patients and median survival times, as well as hazard ratio estimates,
 confidence intervals and p-values, for multiple biomarkers across population subgroups in a single data frame.
 variables corresponds to the names of variables found in data, passed as a named list and requires elements
 tte, is_event, biomarkers (vector of continuous biomarker variables), and optionally subgroups and strata.
-groups_lists optionally specifies groupings for subgroups variables."><meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png"><link rel="stylesheet" href="../consent.css"><script src="../consent.js" type="text/javascript" charset="utf-8"></script></head><body>
+groups_lists optionally specifies groupings for subgroups variables.">
+<meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png">
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 <li class="nav-item"><a class="external-link nav-link" href="https://github.com/insightsengineering/tern" aria-label="GitHub"><span class="fa fa-github"></span></a></li>
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   </div>
@@ -66,7 +129,8 @@
     </div>
 
     <div class="section level2">
-    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
+    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">extract_survival_biomarkers</span><span class="op">(</span></span>
 <span>  <span class="va">variables</span>,</span>
 <span>  <span class="va">data</span>,</span>
@@ -77,54 +141,66 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
     </div>
 
     <div class="section level2">
-    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
+    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a>
+</h2>
 
 
-<dl><dt id="arg-variables">variables<a class="anchor" aria-label="anchor" href="#arg-variables"></a></dt>
+<dl>
+<dt id="arg-variables">variables<a class="anchor" aria-label="anchor" href="#arg-variables"></a>
+</dt>
 <dd><p>(named <code>list</code> of <code>string</code>)<br> list of additional analysis variables.</p></dd>
 
 
-<dt id="arg-data">data<a class="anchor" aria-label="anchor" href="#arg-data"></a></dt>
+<dt id="arg-data">data<a class="anchor" aria-label="anchor" href="#arg-data"></a>
+</dt>
 <dd><p>(<code>data.frame</code>)<br> the dataset containing the variables to summarize.</p></dd>
 
 
-<dt id="arg-groups-lists">groups_lists<a class="anchor" aria-label="anchor" href="#arg-groups-lists"></a></dt>
+<dt id="arg-groups-lists">groups_lists<a class="anchor" aria-label="anchor" href="#arg-groups-lists"></a>
+</dt>
 <dd><p>(named <code>list</code> of <code>list</code>)<br> optionally contains for each <code>subgroups</code> variable a
 list, which specifies the new group levels via the names and the
 levels that belong to it in the character vectors that are elements of the list.</p></dd>
 
 
-<dt id="arg-control">control<a class="anchor" aria-label="anchor" href="#arg-control"></a></dt>
+<dt id="arg-control">control<a class="anchor" aria-label="anchor" href="#arg-control"></a>
+</dt>
 <dd><p>(<code>list</code>)<br> a list of parameters as returned by the helper function <code><a href="control_coxreg.html">control_coxreg()</a></code>.</p></dd>
 
 
-<dt id="arg-label-all">label_all<a class="anchor" aria-label="anchor" href="#arg-label-all"></a></dt>
+<dt id="arg-label-all">label_all<a class="anchor" aria-label="anchor" href="#arg-label-all"></a>
+</dt>
 <dd><p>(<code>string</code>)<br> label for the total population analysis.</p></dd>
 
-</dl></div>
+</dl>
+</div>
     <div class="section level2">
-    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
+    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a>
+</h2>
     <p>A <code>data.frame</code> with columns <code>biomarker</code>, <code>biomarker_label</code>, <code>n_tot</code>, <code>n_tot_events</code>,
 <code>median</code>, <code>hr</code>, <code>lcl</code>, <code>ucl</code>, <code>conf_level</code>, <code>pval</code>, <code>pval_label</code>, <code>subgroup</code>, <code>var</code>,
 <code>var_label</code>, and <code>row_type</code>.</p>
     </div>
     <div class="section level2">
-    <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"></a></h2>
+    <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"></a>
+</h2>
     <div class="dont-index"><p><code><a href="h_survival_biomarkers_subgroups.html">h_coxreg_mult_cont_df()</a></code> which is used internally, <code><a href="survival_biomarkers_subgroups.html">tabulate_survival_biomarkers()</a></code>.</p></div>
     </div>
 
   </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
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+    </nav></aside>
+</div>
 
 
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   <p>tern is a part of the <strong>NEST</strong> and <a href="https://pharmaverse.org/" class="external-link"><strong>pharmaverse</strong></a>.</p>
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diff --git a/main/reference/extract_survival_subgroups.html b/main/reference/extract_survival_subgroups.html
index 54b8949e5c..60c9de96c9 100644
--- a/main/reference/extract_survival_subgroups.html
+++ b/main/reference/extract_survival_subgroups.html
@@ -1,15 +1,38 @@
-<!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Prepare survival data for population subgroups in data frames — extract_survival_subgroups • tern</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Prepare survival data for population subgroups in data frames — extract_survival_subgroups"><meta name="description" content="
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+<title>Prepare survival data for population subgroups in data frames — extract_survival_subgroups • tern</title>
+<!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png">
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+<script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Prepare survival data for population subgroups in data frames — extract_survival_subgroups">
+<meta name="description" content="
 Prepares estimates of median survival times and treatment hazard ratios for population subgroups in
 data frames. Simple wrapper for h_survtime_subgroups_df() and h_coxph_subgroups_df(). Result is a list
 of two data.frames: survtime and hr. variables corresponds to the names of variables found in data,
 passed as a named list and requires elements tte, is_event, arm and optionally subgroups and strata.
-groups_lists optionally specifies groupings for subgroups variables."><meta property="og:description" content="
+groups_lists optionally specifies groupings for subgroups variables.">
+<meta property="og:description" content="
 Prepares estimates of median survival times and treatment hazard ratios for population subgroups in
 data frames. Simple wrapper for h_survtime_subgroups_df() and h_coxph_subgroups_df(). Result is a list
 of two data.frames: survtime and hr. variables corresponds to the names of variables found in data,
 passed as a named list and requires elements tte, is_event, arm and optionally subgroups and strata.
-groups_lists optionally specifies groupings for subgroups variables."><meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png"><link rel="stylesheet" href="../consent.css"><script src="../consent.js" type="text/javascript" charset="utf-8"></script></head><body>
+groups_lists optionally specifies groupings for subgroups variables.">
+<meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png">
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@@ -66,7 +129,8 @@
     </div>
 
     <div class="section level2">
-    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
+    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">extract_survival_subgroups</span><span class="op">(</span></span>
 <span>  <span class="va">variables</span>,</span>
 <span>  <span class="va">data</span>,</span>
@@ -77,62 +141,81 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
     </div>
 
     <div class="section level2">
-    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
+    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a>
+</h2>
 
 
-<dl><dt id="arg-variables">variables<a class="anchor" aria-label="anchor" href="#arg-variables"></a></dt>
+<dl>
+<dt id="arg-variables">variables<a class="anchor" aria-label="anchor" href="#arg-variables"></a>
+</dt>
 <dd><p>(named <code>list</code> of <code>string</code>)<br> list of additional analysis variables.</p></dd>
 
 
-<dt id="arg-data">data<a class="anchor" aria-label="anchor" href="#arg-data"></a></dt>
+<dt id="arg-data">data<a class="anchor" aria-label="anchor" href="#arg-data"></a>
+</dt>
 <dd><p>(<code>data.frame</code>)<br> the dataset containing the variables to summarize.</p></dd>
 
 
-<dt id="arg-groups-lists">groups_lists<a class="anchor" aria-label="anchor" href="#arg-groups-lists"></a></dt>
+<dt id="arg-groups-lists">groups_lists<a class="anchor" aria-label="anchor" href="#arg-groups-lists"></a>
+</dt>
 <dd><p>(named <code>list</code> of <code>list</code>)<br> optionally contains for each <code>subgroups</code> variable a
 list, which specifies the new group levels via the names and the
 levels that belong to it in the character vectors that are elements of the list.</p></dd>
 
 
-<dt id="arg-control">control<a class="anchor" aria-label="anchor" href="#arg-control"></a></dt>
-<dd><p>(<code>list</code>)<br> parameters for comparison details, specified by using the helper function
-<code><a href="control_coxph.html">control_coxph()</a></code>. Some possible parameter options are:</p><ul><li><p><code>pval_method</code> (<code>string</code>)<br> p-value method for testing the null hypothesis that hazard ratio = 1. Default
+<dt id="arg-control">control<a class="anchor" aria-label="anchor" href="#arg-control"></a>
+</dt>
+<dd>
+<p>(<code>list</code>)<br> parameters for comparison details, specified by using the helper function
+<code><a href="control_coxph.html">control_coxph()</a></code>. Some possible parameter options are:</p>
+<ul>
+<li><p><code>pval_method</code> (<code>string</code>)<br> p-value method for testing the null hypothesis that hazard ratio = 1. Default
 method is <code>"log-rank"</code> which comes from <code><a href="https://rdrr.io/pkg/survival/man/survdiff.html" class="external-link">survival::survdiff()</a></code>, can also be set to <code>"wald"</code> or <code>"likelihood"</code>
 (from <code><a href="https://rdrr.io/pkg/survival/man/coxph.html" class="external-link">survival::coxph()</a></code>).</p></li>
 <li><p><code>ties</code> (<code>string</code>)<br> specifying the method for tie handling. Default is <code>"efron"</code>,
 can also be set to <code>"breslow"</code> or <code>"exact"</code>. See more in <code><a href="https://rdrr.io/pkg/survival/man/coxph.html" class="external-link">survival::coxph()</a></code>.</p></li>
 <li><p><code>conf_level</code> (<code>proportion</code>)<br> confidence level of the interval for HR.</p></li>
-</ul></dd>
+</ul>
+</dd>
 
 
-<dt id="arg-label-all">label_all<a class="anchor" aria-label="anchor" href="#arg-label-all"></a></dt>
+<dt id="arg-label-all">label_all<a class="anchor" aria-label="anchor" href="#arg-label-all"></a>
+</dt>
 <dd><p>(<code>string</code>)<br> label for the total population analysis.</p></dd>
 
-</dl></div>
+</dl>
+</div>
     <div class="section level2">
-    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
-    <p>A named <code>list</code> of two elements:</p><ul><li><p><code>survtime</code>: A <code>data.frame</code> containing columns <code>arm</code>, <code>n</code>, <code>n_events</code>, <code>median</code>, <code>subgroup</code>, <code>var</code>,
+    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a>
+</h2>
+    <p>A named <code>list</code> of two elements:</p>
+<ul>
+<li><p><code>survtime</code>: A <code>data.frame</code> containing columns <code>arm</code>, <code>n</code>, <code>n_events</code>, <code>median</code>, <code>subgroup</code>, <code>var</code>,
 <code>var_label</code>, and <code>row_type</code>.</p></li>
 <li><p><code>hr</code>: A <code>data.frame</code> containing columns <code>arm</code>, <code>n_tot</code>, <code>n_tot_events</code>, <code>hr</code>, <code>lcl</code>, <code>ucl</code>, <code>conf_level</code>,
 <code>pval</code>, <code>pval_label</code>, <code>subgroup</code>, <code>var</code>, <code>var_label</code>, and <code>row_type</code>.</p></li>
-</ul></div>
+</ul>
+</div>
     <div class="section level2">
-    <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"></a></h2>
+    <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"></a>
+</h2>
     <div class="dont-index"><p><a href="survival_duration_subgroups.html">survival_duration_subgroups</a></p></div>
     </div>
 
   </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
-    </nav></aside></div>
+    </nav></aside>
+</div>
 
 
     <footer><div class="nest">
   <p>tern is a part of the <strong>NEST</strong> and <a href="https://pharmaverse.org/" class="external-link"><strong>pharmaverse</strong></a>.</p>
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diff --git a/main/reference/extreme_format.html b/main/reference/extreme_format.html
index de6a87e394..b5e05d06bb 100644
--- a/main/reference/extreme_format.html
+++ b/main/reference/extreme_format.html
@@ -1,7 +1,30 @@
-<!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Format extreme values — extreme_format • tern</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Format extreme values — extreme_format"><meta name="description" content="
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+<script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet">
+<script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet">
+<link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet">
+<script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Format extreme values — extreme_format">
+<meta name="description" content="
+rtables formatting functions that handle extreme values.">
+<meta property="og:description" content="
+rtables formatting functions that handle extreme values.">
+<meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png">
+<link rel="stylesheet" href="../consent.css">
+<script src="../consent.js" type="text/javascript" charset="utf-8"></script>
+</head>
+<body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
 
 
@@ -17,26 +40,66 @@
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+  <ul class="dropdown-menu" aria-labelledby="dropdown-articles">
+<li><a class="dropdown-item" href="../articles/missing_values.html">Missing Values in Tern</a></li>
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+  </ul>
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+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
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+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
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+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a>
+</div>
+</li></div>
+</ul>
+<ul class="navbar-nav">
+<li class="nav-item"><form class="form-inline" role="search">
+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json">
+</form></li>
 <li class="nav-item"><a class="external-link nav-link" href="https://github.com/insightsengineering/tern" aria-label="GitHub"><span class="fa fa-github"></span></a></li>
-      </ul></div>
+      </ul>
+</div>
 
 
   </div>
@@ -54,49 +117,65 @@
     </div>
 
     <div class="section level2">
-    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
+    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">h_get_format_threshold</span><span class="op">(</span>digits <span class="op">=</span> <span class="fl">2L</span><span class="op">)</span></span>
 <span></span>
 <span><span class="fu">h_format_threshold</span><span class="op">(</span><span class="va">x</span>, digits <span class="op">=</span> <span class="fl">2L</span><span class="op">)</span></span></code></pre></div>
     </div>
 
     <div class="section level2">
-    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
+    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a>
+</h2>
 
 
-<dl><dt id="arg-digits">digits<a class="anchor" aria-label="anchor" href="#arg-digits"></a></dt>
+<dl>
+<dt id="arg-digits">digits<a class="anchor" aria-label="anchor" href="#arg-digits"></a>
+</dt>
 <dd><p>(<code>integer(1)</code>)<br> number of decimal places to display.</p></dd>
 
 
-<dt id="arg-x">x<a class="anchor" aria-label="anchor" href="#arg-x"></a></dt>
+<dt id="arg-x">x<a class="anchor" aria-label="anchor" href="#arg-x"></a>
+</dt>
 <dd><p>(<code>numeric(1)</code>)<br> value to format.</p></dd>
 
-</dl></div>
+</dl>
+</div>
     <div class="section level2">
-    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
+    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a>
+</h2>
 
-<ul><li><p><code>h_get_format_threshold()</code> returns a <code>list</code> of 2 elements: <code>threshold</code>, with <code>low</code> and <code>high</code> thresholds,
+<ul>
+<li><p><code>h_get_format_threshold()</code> returns a <code>list</code> of 2 elements: <code>threshold</code>, with <code>low</code> and <code>high</code> thresholds,
 and <code>format_string</code>, with thresholds formatted as strings.</p></li>
-</ul><ul><li><p><code>h_format_threshold()</code> returns the given value, or if the value is not within the digit threshold the relation
+</ul>
+<ul>
+<li><p><code>h_format_threshold()</code> returns the given value, or if the value is not within the digit threshold the relation
 of the given value to the digit threshold, as a formatted string.</p></li>
-</ul></div>
+</ul>
+</div>
     <div class="section level2">
-    <h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a></h2>
+    <h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a>
+</h2>
     <p>For each input, apply a format to the specified number of <code>digits</code>. If the value is
 below a threshold, it returns "&lt;0.01" e.g. if the number of <code>digits</code> is 2. If the value is
 above a threshold, it returns "&gt;999.99" e.g. if the number of <code>digits</code> is 2.
 If it is zero, then returns "0.00".</p>
     </div>
     <div class="section level2">
-    <h2 id="functions">Functions<a class="anchor" aria-label="anchor" href="#functions"></a></h2>
+    <h2 id="functions">Functions<a class="anchor" aria-label="anchor" href="#functions"></a>
+</h2>
 
-<ul><li><p><code>h_get_format_threshold()</code>: Internal helper function to calculate the threshold and create formatted strings
+<ul>
+<li><p><code>h_get_format_threshold()</code>: Internal helper function to calculate the threshold and create formatted strings
 used in Formatting Functions. Returns a list with elements <code>threshold</code> and <code>format_string</code>.</p></li>
 <li><p><code>h_format_threshold()</code>: Internal helper function to apply a threshold format to a value.
 Creates a formatted string to be used in Formatting Functions.</p></li>
-</ul></div>
+</ul>
+</div>
     <div class="section level2">
-    <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"></a></h2>
+    <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"></a>
+</h2>
     <div class="dont-index"><p>Other formatting functions:
 <code><a href="format_auto.html">format_auto</a>()</code>,
 <code><a href="format_count_fraction.html">format_count_fraction</a>()</code>,
@@ -113,7 +192,8 @@ <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"
     </div>
 
     <div class="section level2">
-    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
+    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="fu">h_get_format_threshold</span><span class="op">(</span><span class="fl">2L</span><span class="op">)</span></span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> $threshold</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>    low   high </span>
@@ -132,17 +212,19 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 </code></pre></div>
     </div>
   </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
-    </nav></aside></div>
+    </nav></aside>
+</div>
 
 
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   <p>tern is a part of the <strong>NEST</strong> and <a href="https://pharmaverse.org/" class="external-link"><strong>pharmaverse</strong></a>.</p>
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index 1c06f94fae..14f1477d01 100644
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   </div>
@@ -51,35 +114,43 @@
     </div>
 
     <div class="section level2">
-    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
+    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">f_conf_level</span><span class="op">(</span><span class="va">conf_level</span><span class="op">)</span></span></code></pre></div>
     </div>
 
     <div class="section level2">
-    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
+    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a>
+</h2>
 
 
-<dl><dt id="arg-conf-level">conf_level<a class="anchor" aria-label="anchor" href="#arg-conf-level"></a></dt>
+<dl>
+<dt id="arg-conf-level">conf_level<a class="anchor" aria-label="anchor" href="#arg-conf-level"></a>
+</dt>
 <dd><p>(<code>proportion</code>)<br> confidence level of the interval.</p></dd>
 
-</dl></div>
+</dl>
+</div>
     <div class="section level2">
-    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
+    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a>
+</h2>
     <p>A <code>string</code>.</p>
     </div>
 
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+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a>
+</div>
+</li></div>
+</ul>
+<ul class="navbar-nav">
+<li class="nav-item"><form class="form-inline" role="search">
+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json">
+</form></li>
 <li class="nav-item"><a class="external-link nav-link" href="https://github.com/insightsengineering/tern" aria-label="GitHub"><span class="fa fa-github"></span></a></li>
-      </ul></div>
+      </ul>
+</div>
 
 
   </div>
@@ -51,35 +114,43 @@
     </div>
 
     <div class="section level2">
-    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
+    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">f_pval</span><span class="op">(</span><span class="va">test_mean</span><span class="op">)</span></span></code></pre></div>
     </div>
 
     <div class="section level2">
-    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
+    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a>
+</h2>
 
 
-<dl><dt id="arg-test-mean">test_mean<a class="anchor" aria-label="anchor" href="#arg-test-mean"></a></dt>
+<dl>
+<dt id="arg-test-mean">test_mean<a class="anchor" aria-label="anchor" href="#arg-test-mean"></a>
+</dt>
 <dd><p>(<code>numeric(1)</code>)<br> mean value to test under the null hypothesis.</p></dd>
 
-</dl></div>
+</dl>
+</div>
     <div class="section level2">
-    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
+    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a>
+</h2>
     <p>A <code>string</code>.</p>
     </div>
 
   </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
-    </nav></aside></div>
+    </nav></aside>
+</div>
 
 
     <footer><div class="nest">
   <p>tern is a part of the <strong>NEST</strong> and <a href="https://pharmaverse.org/" class="external-link"><strong>pharmaverse</strong></a>.</p>
 </div>
-<script type="text/javascript" src="../analytics.js"></script></footer></div>
-
+<script type="text/javascript" src="../analytics.js"></script></footer>
+</div>
 
 
 
 
-  </body></html>
 
+  </body>
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diff --git a/main/reference/fct_collapse_only.html b/main/reference/fct_collapse_only.html
index b723a792a1..3abddeec90 100644
--- a/main/reference/fct_collapse_only.html
+++ b/main/reference/fct_collapse_only.html
@@ -1,11 +1,34 @@
-<!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Collapse factor levels and keep only those new group levels — fct_collapse_only • tern</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Collapse factor levels and keep only those new group levels — fct_collapse_only"><meta name="description" content="
+<html lang="en">
+<head>
+<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+<meta charset="utf-8">
+<meta http-equiv="X-UA-Compatible" content="IE=edge">
+<meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<title>Collapse factor levels and keep only those new group levels — fct_collapse_only • tern</title>
+<!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png">
+<link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png">
+<link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png">
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+<script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet">
+<script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet">
+<link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet">
+<script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Collapse factor levels and keep only those new group levels — fct_collapse_only">
+<meta name="description" content="
 This collapses levels and only keeps those new group levels, in the order provided.
 The returned factor has levels in the order given, with the possible missing level last (this will
-only be included if there are missing values)."><meta property="og:description" content="
+only be included if there are missing values).">
+<meta property="og:description" content="
 This collapses levels and only keeps those new group levels, in the order provided.
 The returned factor has levels in the order given, with the possible missing level last (this will
-only be included if there are missing values)."><meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png"><link rel="stylesheet" href="../consent.css"><script src="../consent.js" type="text/javascript" charset="utf-8"></script></head><body>
+only be included if there are missing values).">
+<meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png">
+<link rel="stylesheet" href="../consent.css">
+<script src="../consent.js" type="text/javascript" charset="utf-8"></script>
+</head>
+<body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
 
 
@@ -21,26 +44,66 @@
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     <div id="navbar" class="collapse navbar-collapse ms-3">
-      <ul class="navbar-nav me-auto"><li class="nav-item"><a class="nav-link" href="../articles/tern.html">Get started</a></li>
+      <ul class="navbar-nav me-auto">
+<li class="nav-item"><a class="nav-link" href="../articles/tern.html">Get started</a></li>
 <li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
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   <button class="nav-link dropdown-toggle" type="button" id="dropdown-articles" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Articles</button>
-  <ul class="dropdown-menu" aria-labelledby="dropdown-articles"><li><a class="dropdown-item" href="../articles/missing_values.html">Missing Values in Tern</a></li>
+  <ul class="dropdown-menu" aria-labelledby="dropdown-articles">
+<li><a class="dropdown-item" href="../articles/missing_values.html">Missing Values in Tern</a></li>
     <li><a class="dropdown-item" href="../articles/tables.html">Tabulation</a></li>
     <li><a class="dropdown-item" href="../articles/tern_formats.html">Formatting Functions</a></li>
     <li><a class="dropdown-item" href="../articles/tern_functions_guide.html">Understanding `tern` functions</a></li>
-  </ul></li>
+  </ul>
+</li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
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+  <ul class="dropdown-menu" aria-labelledby="dropdown-reports">
+<li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
     <li><a class="dropdown-item" href="../unit-test-report/">Unit test report</a></li>
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- <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json"></form></li>
+  </ul>
+</li>
+      <div><li class="nav-item dropdown">
+    <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-versions">Versions</a>
+    <div class="dropdown-menu" aria-labelledby="dropdown-versions">
+    <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
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+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.5">v0.9.5</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.4">v0.9.4</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.3">v0.9.3</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1-rc3">v0.9.1-rc3</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a>
+</div>
+</li></div>
+</ul>
+<ul class="navbar-nav">
+<li class="nav-item"><form class="form-inline" role="search">
+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json">
+</form></li>
 <li class="nav-item"><a class="external-link nav-link" href="https://github.com/insightsengineering/tern" aria-label="GitHub"><span class="fa fa-github"></span></a></li>
-      </ul></div>
+      </ul>
+</div>
 
 
   </div>
@@ -60,45 +123,56 @@
     </div>
 
     <div class="section level2">
-    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
+    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">fct_collapse_only</span><span class="op">(</span><span class="va">.f</span>, <span class="va">...</span>, .na_level <span class="op">=</span> <span class="st">"&lt;Missing&gt;"</span><span class="op">)</span></span></code></pre></div>
     </div>
 
     <div class="section level2">
-    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
+    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a>
+</h2>
 
 
-<dl><dt id="arg--f">.f<a class="anchor" aria-label="anchor" href="#arg--f"></a></dt>
+<dl>
+<dt id="arg--f">.f<a class="anchor" aria-label="anchor" href="#arg--f"></a>
+</dt>
 <dd><p>(<code>factor</code> or <code>character</code>)<br> original vector.</p></dd>
 
 
-<dt id="arg--">...<a class="anchor" aria-label="anchor" href="#arg--"></a></dt>
+<dt id="arg--">...<a class="anchor" aria-label="anchor" href="#arg--"></a>
+</dt>
 <dd><p>(named <code>character</code>)<br> levels in each vector provided will be collapsed into
 the new level given by the respective name.</p></dd>
 
 
-<dt id="arg--na-level">.na_level<a class="anchor" aria-label="anchor" href="#arg--na-level"></a></dt>
+<dt id="arg--na-level">.na_level<a class="anchor" aria-label="anchor" href="#arg--na-level"></a>
+</dt>
 <dd><p>(<code>string</code>)<br> which level to use for other levels, which should be missing in the
 new factor. Note that this level must not be contained in the new levels specified in <code>...</code>.</p></dd>
 
-</dl></div>
+</dl>
+</div>
     <div class="section level2">
-    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
+    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a>
+</h2>
     <p>A modified <code>factor</code> with collapsed levels. Values and levels which are not included
 in the given <code>character</code> vector input will be set to the missing level <code>.na_level</code>.</p>
     </div>
     <div class="section level2">
-    <h2 id="note">Note<a class="anchor" aria-label="anchor" href="#note"></a></h2>
+    <h2 id="note">Note<a class="anchor" aria-label="anchor" href="#note"></a>
+</h2>
     <p>Any existing <code>NA</code>s in the input vector will not be replaced by the missing level. If needed,
 <code><a href="explicit_na.html">explicit_na()</a></code> can be called separately on the result.</p>
     </div>
     <div class="section level2">
-    <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"></a></h2>
+    <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"></a>
+</h2>
     <div class="dont-index"><p><code><a href="https://forcats.tidyverse.org/reference/fct_collapse.html" class="external-link">forcats::fct_collapse()</a></code>, <code><a href="https://forcats.tidyverse.org/reference/fct_relevel.html" class="external-link">forcats::fct_relevel()</a></code> which are used internally.</p></div>
     </div>
 
     <div class="section level2">
-    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
+    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="fu">fct_collapse_only</span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/factor.html" class="external-link">factor</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"a"</span>, <span class="st">"b"</span>, <span class="st">"c"</span>, <span class="st">"d"</span><span class="op">)</span><span class="op">)</span>, TRT <span class="op">=</span> <span class="st">"b"</span>, CTRL <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"c"</span>, <span class="st">"d"</span><span class="op">)</span><span class="op">)</span></span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> [1] &lt;Missing&gt; TRT       CTRL      CTRL     </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> Levels: TRT CTRL &lt;Missing&gt;</span>
@@ -106,17 +180,19 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 </code></pre></div>
     </div>
   </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
-    </nav></aside></div>
+    </nav></aside>
+</div>
 
 
     <footer><div class="nest">
   <p>tern is a part of the <strong>NEST</strong> and <a href="https://pharmaverse.org/" class="external-link"><strong>pharmaverse</strong></a>.</p>
 </div>
-<script type="text/javascript" src="../analytics.js"></script></footer></div>
-
+<script type="text/javascript" src="../analytics.js"></script></footer>
+</div>
 
 
 
 
-  </body></html>
 
+  </body>
+</html>
diff --git a/main/reference/fct_discard.html b/main/reference/fct_discard.html
index a773b158ba..6838139edc 100644
--- a/main/reference/fct_discard.html
+++ b/main/reference/fct_discard.html
@@ -1,7 +1,30 @@
-<!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Discard specified levels of a factor — fct_discard • tern</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Discard specified levels of a factor — fct_discard"><meta name="description" content="
-This discards the observations as well as the levels specified from a factor."><meta property="og:description" content="
-This discards the observations as well as the levels specified from a factor."><meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png"><link rel="stylesheet" href="../consent.css"><script src="../consent.js" type="text/javascript" charset="utf-8"></script></head><body>
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+<title>Discard specified levels of a factor — fct_discard • tern</title>
+<!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png">
+<link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png">
+<link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png">
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+<link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png">
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+<script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet">
+<script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet">
+<link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet">
+<script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Discard specified levels of a factor — fct_discard">
+<meta name="description" content="
+This discards the observations as well as the levels specified from a factor.">
+<meta property="og:description" content="
+This discards the observations as well as the levels specified from a factor.">
+<meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png">
+<link rel="stylesheet" href="../consent.css">
+<script src="../consent.js" type="text/javascript" charset="utf-8"></script>
+</head>
+<body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
 
 
@@ -17,26 +40,66 @@
     </button>
 
     <div id="navbar" class="collapse navbar-collapse ms-3">
-      <ul class="navbar-nav me-auto"><li class="nav-item"><a class="nav-link" href="../articles/tern.html">Get started</a></li>
+      <ul class="navbar-nav me-auto">
+<li class="nav-item"><a class="nav-link" href="../articles/tern.html">Get started</a></li>
 <li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
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   <button class="nav-link dropdown-toggle" type="button" id="dropdown-articles" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Articles</button>
-  <ul class="dropdown-menu" aria-labelledby="dropdown-articles"><li><a class="dropdown-item" href="../articles/missing_values.html">Missing Values in Tern</a></li>
+  <ul class="dropdown-menu" aria-labelledby="dropdown-articles">
+<li><a class="dropdown-item" href="../articles/missing_values.html">Missing Values in Tern</a></li>
     <li><a class="dropdown-item" href="../articles/tables.html">Tabulation</a></li>
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+  </ul>
+</li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
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+  <ul class="dropdown-menu" aria-labelledby="dropdown-reports">
+<li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
     <li><a class="dropdown-item" href="../unit-test-report/">Unit test report</a></li>
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- <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json"></form></li>
+  </ul>
+</li>
+      <div><li class="nav-item dropdown">
+    <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-versions">Versions</a>
+    <div class="dropdown-menu" aria-labelledby="dropdown-versions">
+    <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
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+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
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+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.3">v0.9.3</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
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+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
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+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a>
+</div>
+</li></div>
+</ul>
+<ul class="navbar-nav">
+<li class="nav-item"><form class="form-inline" role="search">
+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json">
+</form></li>
 <li class="nav-item"><a class="external-link nav-link" href="https://github.com/insightsengineering/tern" aria-label="GitHub"><span class="fa fa-github"></span></a></li>
-      </ul></div>
+      </ul>
+</div>
 
 
   </div>
@@ -54,29 +117,37 @@
     </div>
 
     <div class="section level2">
-    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
+    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">fct_discard</span><span class="op">(</span><span class="va">x</span>, <span class="va">discard</span><span class="op">)</span></span></code></pre></div>
     </div>
 
     <div class="section level2">
-    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
+    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a>
+</h2>
 
 
-<dl><dt id="arg-x">x<a class="anchor" aria-label="anchor" href="#arg-x"></a></dt>
+<dl>
+<dt id="arg-x">x<a class="anchor" aria-label="anchor" href="#arg-x"></a>
+</dt>
 <dd><p>(<code>factor</code>)<br> the original factor.</p></dd>
 
 
-<dt id="arg-discard">discard<a class="anchor" aria-label="anchor" href="#arg-discard"></a></dt>
+<dt id="arg-discard">discard<a class="anchor" aria-label="anchor" href="#arg-discard"></a>
+</dt>
 <dd><p>(<code>character</code>)<br> levels to discard.</p></dd>
 
-</dl></div>
+</dl>
+</div>
     <div class="section level2">
-    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
+    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a>
+</h2>
     <p>A modified <code>factor</code> with observations as well as levels from <code>discard</code> dropped.</p>
     </div>
 
     <div class="section level2">
-    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
+    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="fu">fct_discard</span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/factor.html" class="external-link">factor</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"a"</span>, <span class="st">"b"</span>, <span class="st">"c"</span><span class="op">)</span><span class="op">)</span>, <span class="st">"c"</span><span class="op">)</span></span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> [1] a b</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> Levels: a b</span>
@@ -84,17 +155,19 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 </code></pre></div>
     </div>
   </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
-    </nav></aside></div>
+    </nav></aside>
+</div>
 
 
     <footer><div class="nest">
   <p>tern is a part of the <strong>NEST</strong> and <a href="https://pharmaverse.org/" class="external-link"><strong>pharmaverse</strong></a>.</p>
 </div>
-<script type="text/javascript" src="../analytics.js"></script></footer></div>
-
+<script type="text/javascript" src="../analytics.js"></script></footer>
+</div>
 
 
 
 
-  </body></html>
 
+  </body>
+</html>
diff --git a/main/reference/fct_explicit_na_if.html b/main/reference/fct_explicit_na_if.html
index 3475c8acf2..8c0b4dd346 100644
--- a/main/reference/fct_explicit_na_if.html
+++ b/main/reference/fct_explicit_na_if.html
@@ -1,9 +1,32 @@
-<!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Insertion of explicit missing values in a factor — fct_explicit_na_if • tern</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Insertion of explicit missing values in a factor — fct_explicit_na_if"><meta name="description" content="
+<html lang="en">
+<head>
+<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+<meta charset="utf-8">
+<meta http-equiv="X-UA-Compatible" content="IE=edge">
+<meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<title>Insertion of explicit missing values in a factor — fct_explicit_na_if • tern</title>
+<!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png">
+<link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png">
+<link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png">
+<link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png">
+<link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png">
+<link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png">
+<script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet">
+<script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet">
+<link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet">
+<script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Insertion of explicit missing values in a factor — fct_explicit_na_if">
+<meta name="description" content="
 This inserts explicit missing values in a factor based on a condition. Additionally,
-existing NA values will be explicitly converted to given na_level."><meta property="og:description" content="
+existing NA values will be explicitly converted to given na_level.">
+<meta property="og:description" content="
 This inserts explicit missing values in a factor based on a condition. Additionally,
-existing NA values will be explicitly converted to given na_level."><meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png"><link rel="stylesheet" href="../consent.css"><script src="../consent.js" type="text/javascript" charset="utf-8"></script></head><body>
+existing NA values will be explicitly converted to given na_level.">
+<meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png">
+<link rel="stylesheet" href="../consent.css">
+<script src="../consent.js" type="text/javascript" charset="utf-8"></script>
+</head>
+<body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
 
 
@@ -19,26 +42,66 @@
     </button>
 
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-      <ul class="navbar-nav me-auto"><li class="nav-item"><a class="nav-link" href="../articles/tern.html">Get started</a></li>
+      <ul class="navbar-nav me-auto">
+<li class="nav-item"><a class="nav-link" href="../articles/tern.html">Get started</a></li>
 <li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
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   <button class="nav-link dropdown-toggle" type="button" id="dropdown-articles" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Articles</button>
-  <ul class="dropdown-menu" aria-labelledby="dropdown-articles"><li><a class="dropdown-item" href="../articles/missing_values.html">Missing Values in Tern</a></li>
+  <ul class="dropdown-menu" aria-labelledby="dropdown-articles">
+<li><a class="dropdown-item" href="../articles/missing_values.html">Missing Values in Tern</a></li>
     <li><a class="dropdown-item" href="../articles/tables.html">Tabulation</a></li>
     <li><a class="dropdown-item" href="../articles/tern_formats.html">Formatting Functions</a></li>
     <li><a class="dropdown-item" href="../articles/tern_functions_guide.html">Understanding `tern` functions</a></li>
-  </ul></li>
+  </ul>
+</li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
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+  <ul class="dropdown-menu" aria-labelledby="dropdown-reports">
+<li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
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- <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json"></form></li>
+  </ul>
+</li>
+      <div><li class="nav-item dropdown">
+    <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-versions">Versions</a>
+    <div class="dropdown-menu" aria-labelledby="dropdown-versions">
+    <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
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+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.5">v0.9.5</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.4">v0.9.4</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.3">v0.9.3</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1-rc3">v0.9.1-rc3</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a>
+</div>
+</li></div>
+</ul>
+<ul class="navbar-nav">
+<li class="nav-item"><form class="form-inline" role="search">
+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json">
+</form></li>
 <li class="nav-item"><a class="external-link nav-link" href="https://github.com/insightsengineering/tern" aria-label="GitHub"><span class="fa fa-github"></span></a></li>
-      </ul></div>
+      </ul>
+</div>
 
 
   </div>
@@ -57,37 +120,47 @@
     </div>
 
     <div class="section level2">
-    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
+    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">fct_explicit_na_if</span><span class="op">(</span><span class="va">x</span>, <span class="va">condition</span>, na_level <span class="op">=</span> <span class="st">"&lt;Missing&gt;"</span><span class="op">)</span></span></code></pre></div>
     </div>
 
     <div class="section level2">
-    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
+    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a>
+</h2>
 
 
-<dl><dt id="arg-x">x<a class="anchor" aria-label="anchor" href="#arg-x"></a></dt>
+<dl>
+<dt id="arg-x">x<a class="anchor" aria-label="anchor" href="#arg-x"></a>
+</dt>
 <dd><p>(<code>factor</code>)<br> the original factor.</p></dd>
 
 
-<dt id="arg-condition">condition<a class="anchor" aria-label="anchor" href="#arg-condition"></a></dt>
+<dt id="arg-condition">condition<a class="anchor" aria-label="anchor" href="#arg-condition"></a>
+</dt>
 <dd><p>(<code>logical</code>)<br> positions at which to insert missing values.</p></dd>
 
 
-<dt id="arg-na-level">na_level<a class="anchor" aria-label="anchor" href="#arg-na-level"></a></dt>
+<dt id="arg-na-level">na_level<a class="anchor" aria-label="anchor" href="#arg-na-level"></a>
+</dt>
 <dd><p>(<code>string</code>)<br> which level to use for missing values.</p></dd>
 
-</dl></div>
+</dl>
+</div>
     <div class="section level2">
-    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
+    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a>
+</h2>
     <p>A modified <code>factor</code> with inserted and existing <code>NA</code> converted to <code>na_level</code>.</p>
     </div>
     <div class="section level2">
-    <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"></a></h2>
+    <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"></a>
+</h2>
     <div class="dont-index"><p><code><a href="https://forcats.tidyverse.org/reference/fct_na_value_to_level.html" class="external-link">forcats::fct_na_value_to_level()</a></code> which is used internally.</p></div>
     </div>
 
     <div class="section level2">
-    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
+    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="fu">fct_explicit_na_if</span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/factor.html" class="external-link">factor</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"a"</span>, <span class="st">"b"</span>, <span class="cn">NA</span><span class="op">)</span><span class="op">)</span>, <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="cn">TRUE</span>, <span class="cn">FALSE</span>, <span class="cn">FALSE</span><span class="op">)</span><span class="op">)</span></span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> [1] &lt;Missing&gt; b         &lt;Missing&gt;</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> Levels: a b &lt;Missing&gt;</span>
@@ -95,17 +168,19 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 </code></pre></div>
     </div>
   </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
-    </nav></aside></div>
+    </nav></aside>
+</div>
 
 
     <footer><div class="nest">
   <p>tern is a part of the <strong>NEST</strong> and <a href="https://pharmaverse.org/" class="external-link"><strong>pharmaverse</strong></a>.</p>
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-<script type="text/javascript" src="../analytics.js"></script></footer></div>
-
+<script type="text/javascript" src="../analytics.js"></script></footer>
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diff --git a/main/reference/fit_coxreg.html b/main/reference/fit_coxreg.html
index 32e6594050..8f30aae816 100644
--- a/main/reference/fit_coxreg.html
+++ b/main/reference/fit_coxreg.html
@@ -1,7 +1,30 @@
-<!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Fitting functions for Cox proportional hazards regression — fit_coxreg • tern</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Fitting functions for Cox proportional hazards regression — fit_coxreg"><meta name="description" content="
-Fitting functions for univariate and multivariate Cox regression models."><meta property="og:description" content="
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+<link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet">
+<script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet">
+<link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet">
+<script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Fitting functions for Cox proportional hazards regression — fit_coxreg">
+<meta name="description" content="
+Fitting functions for univariate and multivariate Cox regression models.">
+<meta property="og:description" content="
+Fitting functions for univariate and multivariate Cox regression models.">
+<meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png">
+<link rel="stylesheet" href="../consent.css">
+<script src="../consent.js" type="text/javascript" charset="utf-8"></script>
+</head>
+<body>
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@@ -17,26 +40,66 @@
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+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
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+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a>
+</div>
+</li></div>
+</ul>
+<ul class="navbar-nav">
+<li class="nav-item"><form class="form-inline" role="search">
+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json">
+</form></li>
 <li class="nav-item"><a class="external-link nav-link" href="https://github.com/insightsengineering/tern" aria-label="GitHub"><span class="fa fa-github"></span></a></li>
-      </ul></div>
+      </ul>
+</div>
 
 
   </div>
@@ -54,70 +117,97 @@
     </div>
 
     <div class="section level2">
-    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
+    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">fit_coxreg_univar</span><span class="op">(</span><span class="va">variables</span>, <span class="va">data</span>, at <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span><span class="op">)</span>, control <span class="op">=</span> <span class="fu"><a href="control_coxreg.html">control_coxreg</a></span><span class="op">(</span><span class="op">)</span><span class="op">)</span></span>
 <span></span>
 <span><span class="fu">fit_coxreg_multivar</span><span class="op">(</span><span class="va">variables</span>, <span class="va">data</span>, control <span class="op">=</span> <span class="fu"><a href="control_coxreg.html">control_coxreg</a></span><span class="op">(</span><span class="op">)</span><span class="op">)</span></span></code></pre></div>
     </div>
 
     <div class="section level2">
-    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
+    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a>
+</h2>
 
 
-<dl><dt id="arg-variables">variables<a class="anchor" aria-label="anchor" href="#arg-variables"></a></dt>
+<dl>
+<dt id="arg-variables">variables<a class="anchor" aria-label="anchor" href="#arg-variables"></a>
+</dt>
 <dd><p>(named <code>list</code>)<br> the names of the variables found in <code>data</code>, passed as a named list and
 corresponding to the <code>time</code>, <code>event</code>, <code>arm</code>, <code>strata</code>, and <code>covariates</code> terms. If <code>arm</code> is missing from
 <code>variables</code>, then only Cox model(s) including the <code>covariates</code> will be fitted and the corresponding effect
 estimates will be tabulated later.</p></dd>
 
 
-<dt id="arg-data">data<a class="anchor" aria-label="anchor" href="#arg-data"></a></dt>
+<dt id="arg-data">data<a class="anchor" aria-label="anchor" href="#arg-data"></a>
+</dt>
 <dd><p>(<code>data.frame</code>)<br> the dataset containing the variables to fit the models.</p></dd>
 
 
-<dt id="arg-at">at<a class="anchor" aria-label="anchor" href="#arg-at"></a></dt>
+<dt id="arg-at">at<a class="anchor" aria-label="anchor" href="#arg-at"></a>
+</dt>
 <dd><p>(<code>list</code> of <code>numeric</code>)<br> when the candidate covariate is a <code>numeric</code>, use <code>at</code> to specify
 the value of the covariate at which the effect should be estimated.</p></dd>
 
 
-<dt id="arg-control">control<a class="anchor" aria-label="anchor" href="#arg-control"></a></dt>
+<dt id="arg-control">control<a class="anchor" aria-label="anchor" href="#arg-control"></a>
+</dt>
 <dd><p>(<code>list</code>)<br> a list of parameters as returned by the helper function <code><a href="control_coxreg.html">control_coxreg()</a></code>.</p></dd>
 
-</dl></div>
+</dl>
+</div>
     <div class="section level2">
-    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
+    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a>
+</h2>
 
-<ul><li><p><code>fit_coxreg_univar()</code> returns a <code>coxreg.univar</code> class object which is a named <code>list</code>
-with 5 elements:</p><ul><li><p><code>mod</code>: Cox regression models fitted by <code><a href="https://rdrr.io/pkg/survival/man/coxph.html" class="external-link">survival::coxph()</a></code>.</p></li>
+<ul>
+<li>
+<p><code>fit_coxreg_univar()</code> returns a <code>coxreg.univar</code> class object which is a named <code>list</code>
+with 5 elements:</p>
+<ul>
+<li><p><code>mod</code>: Cox regression models fitted by <code><a href="https://rdrr.io/pkg/survival/man/coxph.html" class="external-link">survival::coxph()</a></code>.</p></li>
 <li><p><code>data</code>: The original data frame input.</p></li>
 <li><p><code>control</code>: The original control input.</p></li>
 <li><p><code>vars</code>: The variables used in the model.</p></li>
 <li><p><code>at</code>: Value of the covariate at which the effect should be estimated.</p></li>
-</ul></li>
-</ul><ul><li><p><code>fit_coxreg_multivar()</code> returns a <code>coxreg.multivar</code> class object which is a named list
-with 4 elements:</p><ul><li><p><code>mod</code>: Cox regression model fitted by <code><a href="https://rdrr.io/pkg/survival/man/coxph.html" class="external-link">survival::coxph()</a></code>.</p></li>
+</ul>
+</li>
+</ul>
+<ul>
+<li>
+<p><code>fit_coxreg_multivar()</code> returns a <code>coxreg.multivar</code> class object which is a named list
+with 4 elements:</p>
+<ul>
+<li><p><code>mod</code>: Cox regression model fitted by <code><a href="https://rdrr.io/pkg/survival/man/coxph.html" class="external-link">survival::coxph()</a></code>.</p></li>
 <li><p><code>data</code>: The original data frame input.</p></li>
 <li><p><code>control</code>: The original control input.</p></li>
 <li><p><code>vars</code>: The variables used in the model.</p></li>
-</ul></li>
-</ul></div>
+</ul>
+</li>
+</ul>
+</div>
     <div class="section level2">
-    <h2 id="functions">Functions<a class="anchor" aria-label="anchor" href="#functions"></a></h2>
+    <h2 id="functions">Functions<a class="anchor" aria-label="anchor" href="#functions"></a>
+</h2>
 
-<ul><li><p><code>fit_coxreg_univar()</code>: Fit a series of univariate Cox regression models given the inputs.</p></li>
+<ul>
+<li><p><code>fit_coxreg_univar()</code>: Fit a series of univariate Cox regression models given the inputs.</p></li>
 <li><p><code>fit_coxreg_multivar()</code>: Fit a multivariate Cox regression model.</p></li>
-</ul></div>
+</ul>
+</div>
     <div class="section level2">
-    <h2 id="note">Note<a class="anchor" aria-label="anchor" href="#note"></a></h2>
+    <h2 id="note">Note<a class="anchor" aria-label="anchor" href="#note"></a>
+</h2>
     <p>When using <code>fit_coxreg_univar</code> there should be two study arms.</p>
     </div>
     <div class="section level2">
-    <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"></a></h2>
+    <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"></a>
+</h2>
     <div class="dont-index"><p><a href="h_cox_regression.html">h_cox_regression</a> for relevant helper functions, <a href="cox_regression.html">cox_regression</a>.</p></div>
     </div>
 
     <div class="section level2">
-    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
+    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://github.com/therneau/survival" class="external-link">survival</a></span><span class="op">)</span></span></span>
 <span class="r-in"><span></span></span>
 <span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/Random.html" class="external-link">set.seed</a></span><span class="op">(</span><span class="fl">1</span>, kind <span class="op">=</span> <span class="st">"Mersenne-Twister"</span><span class="op">)</span></span></span>
@@ -212,17 +302,19 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 </code></pre></div>
     </div>
   </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
-    </nav></aside></div>
+    </nav></aside>
+</div>
 
 
     <footer><div class="nest">
   <p>tern is a part of the <strong>NEST</strong> and <a href="https://pharmaverse.org/" class="external-link"><strong>pharmaverse</strong></a>.</p>
 </div>
-<script type="text/javascript" src="../analytics.js"></script></footer></div>
-
+<script type="text/javascript" src="../analytics.js"></script></footer>
+</div>
 
 
 
 
-  </body></html>
 
+  </body>
+</html>
diff --git a/main/reference/fit_logistic.html b/main/reference/fit_logistic.html
index 08a2a754bf..2f32b1d562 100644
--- a/main/reference/fit_logistic.html
+++ b/main/reference/fit_logistic.html
@@ -1,7 +1,30 @@
-<!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Fit for logistic regression — fit_logistic • tern</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Fit for logistic regression — fit_logistic"><meta name="description" content="
-Fit a (conditional) logistic regression model."><meta property="og:description" content="
-Fit a (conditional) logistic regression model."><meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png"><link rel="stylesheet" href="../consent.css"><script src="../consent.js" type="text/javascript" charset="utf-8"></script></head><body>
+<html lang="en">
+<head>
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+<meta charset="utf-8">
+<meta http-equiv="X-UA-Compatible" content="IE=edge">
+<meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
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+<!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png">
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+<link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png">
+<script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet">
+<script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet">
+<link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet">
+<script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Fit for logistic regression — fit_logistic">
+<meta name="description" content="
+Fit a (conditional) logistic regression model.">
+<meta property="og:description" content="
+Fit a (conditional) logistic regression model.">
+<meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png">
+<link rel="stylesheet" href="../consent.css">
+<script src="../consent.js" type="text/javascript" charset="utf-8"></script>
+</head>
+<body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
 
 
@@ -17,26 +40,66 @@
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     <div id="navbar" class="collapse navbar-collapse ms-3">
-      <ul class="navbar-nav me-auto"><li class="nav-item"><a class="nav-link" href="../articles/tern.html">Get started</a></li>
+      <ul class="navbar-nav me-auto">
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 <li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
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-  <ul class="dropdown-menu" aria-labelledby="dropdown-articles"><li><a class="dropdown-item" href="../articles/missing_values.html">Missing Values in Tern</a></li>
+  <ul class="dropdown-menu" aria-labelledby="dropdown-articles">
+<li><a class="dropdown-item" href="../articles/missing_values.html">Missing Values in Tern</a></li>
     <li><a class="dropdown-item" href="../articles/tables.html">Tabulation</a></li>
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     <li><a class="dropdown-item" href="../articles/tern_functions_guide.html">Understanding `tern` functions</a></li>
-  </ul></li>
+  </ul>
+</li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
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   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
-  <ul class="dropdown-menu" aria-labelledby="dropdown-reports"><li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
+  <ul class="dropdown-menu" aria-labelledby="dropdown-reports">
+<li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
     <li><a class="dropdown-item" href="../unit-test-report/">Unit test report</a></li>
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- <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json"></form></li>
+  </ul>
+</li>
+      <div><li class="nav-item dropdown">
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+    <div class="dropdown-menu" aria-labelledby="dropdown-versions">
+    <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
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+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
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+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1-rc3">v0.9.1-rc3</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a>
+</div>
+</li></div>
+</ul>
+<ul class="navbar-nav">
+<li class="nav-item"><form class="form-inline" role="search">
+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json">
+</form></li>
 <li class="nav-item"><a class="external-link nav-link" href="https://github.com/insightsengineering/tern" aria-label="GitHub"><span class="fa fa-github"></span></a></li>
-      </ul></div>
+      </ul>
+</div>
 
 
   </div>
@@ -54,7 +117,8 @@
     </div>
 
     <div class="section level2">
-    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
+    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">fit_logistic</span><span class="op">(</span></span>
 <span>  <span class="va">data</span>,</span>
 <span>  variables <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span>response <span class="op">=</span> <span class="st">"Response"</span>, arm <span class="op">=</span> <span class="st">"ARMCD"</span>, covariates <span class="op">=</span> <span class="cn">NULL</span>, interaction <span class="op">=</span></span>
@@ -64,41 +128,53 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
     </div>
 
     <div class="section level2">
-    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
+    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a>
+</h2>
 
 
-<dl><dt id="arg-data">data<a class="anchor" aria-label="anchor" href="#arg-data"></a></dt>
+<dl>
+<dt id="arg-data">data<a class="anchor" aria-label="anchor" href="#arg-data"></a>
+</dt>
 <dd><p>(<code>data.frame</code>)<br> the data frame on which the model was fit.</p></dd>
 
 
-<dt id="arg-variables">variables<a class="anchor" aria-label="anchor" href="#arg-variables"></a></dt>
+<dt id="arg-variables">variables<a class="anchor" aria-label="anchor" href="#arg-variables"></a>
+</dt>
 <dd><p>(named <code>list</code> of <code>string</code>)<br> list of additional analysis variables.</p></dd>
 
 
-<dt id="arg-response-definition">response_definition<a class="anchor" aria-label="anchor" href="#arg-response-definition"></a></dt>
+<dt id="arg-response-definition">response_definition<a class="anchor" aria-label="anchor" href="#arg-response-definition"></a>
+</dt>
 <dd><p>(<code>string</code>)<br> the definition of what an event is in terms of <code>response</code>.
 This will be used when fitting the (conditional) logistic regression model on the left hand
 side of the formula.</p></dd>
 
-</dl></div>
+</dl>
+</div>
     <div class="section level2">
-    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
+    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a>
+</h2>
     <p>A fitted logistic regression model.</p>
     </div>
     <div class="section level2">
-    <h2 id="model-specification">Model Specification<a class="anchor" aria-label="anchor" href="#model-specification"></a></h2>
+    <h2 id="model-specification">Model Specification<a class="anchor" aria-label="anchor" href="#model-specification"></a>
+</h2>
 
 
 
-<p>The <code>variables</code> list needs to include the following elements:</p><ul><li><p><code>arm</code>: Treatment arm variable name.</p></li>
+<p>The <code>variables</code> list needs to include the following elements:</p>
+<ul>
+<li><p><code>arm</code>: Treatment arm variable name.</p></li>
 <li><p><code>response</code>: The response arm variable name. Usually this is a 0/1 variable.</p></li>
 <li><p><code>covariates</code>: This is either <code>NULL</code> (no covariates) or a character vector of covariate variable names.</p></li>
 <li><p><code>interaction</code>: This is either <code>NULL</code> (no interaction) or a string of a single covariate variable name already
 included in <code>covariates</code>. Then the interaction with the treatment arm is included in the model.</p></li>
-</ul></div>
+</ul>
+</div>
 
     <div class="section level2">
-    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
+    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://dplyr.tidyverse.org" class="external-link">dplyr</a></span><span class="op">)</span></span></span>
 <span class="r-in"><span></span></span>
 <span class="r-in"><span><span class="va">adrs_f</span> <span class="op">&lt;-</span> <span class="va">tern_ex_adrs</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span></span>
@@ -133,17 +209,19 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 </code></pre></div>
     </div>
   </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
-    </nav></aside></div>
+    </nav></aside>
+</div>
 
 
     <footer><div class="nest">
   <p>tern is a part of the <strong>NEST</strong> and <a href="https://pharmaverse.org/" class="external-link"><strong>pharmaverse</strong></a>.</p>
 </div>
-<script type="text/javascript" src="../analytics.js"></script></footer></div>
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diff --git a/main/reference/fit_rsp_step.html b/main/reference/fit_rsp_step.html
index d74f0ac030..669943625d 100644
--- a/main/reference/fit_rsp_step.html
+++ b/main/reference/fit_rsp_step.html
@@ -1,19 +1,42 @@
-<!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Subgroup treatment effect pattern (STEP) fit for binary (response) outcome — fit_rsp_step • tern</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Subgroup treatment effect pattern (STEP) fit for binary (response) outcome — fit_rsp_step"><meta name="description" content="
+<html lang="en">
+<head>
+<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+<meta charset="utf-8">
+<meta http-equiv="X-UA-Compatible" content="IE=edge">
+<meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<title>Subgroup treatment effect pattern (STEP) fit for binary (response) outcome — fit_rsp_step • tern</title>
+<!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png">
+<link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png">
+<link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png">
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+<script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet">
+<script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet">
+<link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet">
+<script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Subgroup treatment effect pattern (STEP) fit for binary (response) outcome — fit_rsp_step">
+<meta name="description" content="
 This fits the Subgroup Treatment Effect Pattern logistic regression models for a binary
 (response) outcome. The treatment arm variable must have exactly 2 levels,
 where the first one is taken as reference and the estimated odds ratios are
 for the comparison of the second level vs. the first one.
 The (conditional) logistic regression model which is fit is:
 response ~ arm * poly(biomarker, degree) + covariates + strata(strata)
-where degree is specified by control_step()."><meta property="og:description" content="
+where degree is specified by control_step().">
+<meta property="og:description" content="
 This fits the Subgroup Treatment Effect Pattern logistic regression models for a binary
 (response) outcome. The treatment arm variable must have exactly 2 levels,
 where the first one is taken as reference and the estimated odds ratios are
 for the comparison of the second level vs. the first one.
 The (conditional) logistic regression model which is fit is:
 response ~ arm * poly(biomarker, degree) + covariates + strata(strata)
-where degree is specified by control_step()."><meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png"><link rel="stylesheet" href="../consent.css"><script src="../consent.js" type="text/javascript" charset="utf-8"></script></head><body>
+where degree is specified by control_step().">
+<meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png">
+<link rel="stylesheet" href="../consent.css">
+<script src="../consent.js" type="text/javascript" charset="utf-8"></script>
+</head>
+<body>
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@@ -29,26 +52,66 @@
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+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a>
+</div>
+</li></div>
+</ul>
+<ul class="navbar-nav">
+<li class="nav-item"><form class="form-inline" role="search">
+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json">
+</form></li>
 <li class="nav-item"><a class="external-link nav-link" href="https://github.com/insightsengineering/tern" aria-label="GitHub"><span class="fa fa-github"></span></a></li>
-      </ul></div>
+      </ul>
+</div>
 
 
   </div>
@@ -72,47 +135,58 @@
     </div>
 
     <div class="section level2">
-    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
+    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">fit_rsp_step</span><span class="op">(</span><span class="va">variables</span>, <span class="va">data</span>, control <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fu"><a href="control_step.html">control_step</a></span><span class="op">(</span><span class="op">)</span>, <span class="fu"><a href="control_logistic.html">control_logistic</a></span><span class="op">(</span><span class="op">)</span><span class="op">)</span><span class="op">)</span></span></code></pre></div>
     </div>
 
     <div class="section level2">
-    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
+    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a>
+</h2>
 
 
-<dl><dt id="arg-variables">variables<a class="anchor" aria-label="anchor" href="#arg-variables"></a></dt>
+<dl>
+<dt id="arg-variables">variables<a class="anchor" aria-label="anchor" href="#arg-variables"></a>
+</dt>
 <dd><p>(named <code>list</code> of <code>character</code>)<br> list of analysis variables:
 needs <code>response</code>, <code>arm</code>, <code>biomarker</code>, and optional <code>covariates</code> and <code>strata</code>.</p></dd>
 
 
-<dt id="arg-data">data<a class="anchor" aria-label="anchor" href="#arg-data"></a></dt>
+<dt id="arg-data">data<a class="anchor" aria-label="anchor" href="#arg-data"></a>
+</dt>
 <dd><p>(<code>data.frame</code>)<br> the dataset containing the variables to summarize.</p></dd>
 
 
-<dt id="arg-control">control<a class="anchor" aria-label="anchor" href="#arg-control"></a></dt>
+<dt id="arg-control">control<a class="anchor" aria-label="anchor" href="#arg-control"></a>
+</dt>
 <dd><p>(named <code>list</code>)<br> combined control list from <code><a href="control_step.html">control_step()</a></code>
 and <code><a href="control_logistic.html">control_logistic()</a></code>.</p></dd>
 
-</dl></div>
+</dl>
+</div>
     <div class="section level2">
-    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
+    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a>
+</h2>
     <p>A matrix of class <code>step</code>. The first part of the columns describe the
 subgroup intervals used for the biomarker variable, including where the
 center of the intervals are and their bounds. The second part of the
 columns contain the estimates for the treatment arm comparison.</p>
     </div>
     <div class="section level2">
-    <h2 id="note">Note<a class="anchor" aria-label="anchor" href="#note"></a></h2>
+    <h2 id="note">Note<a class="anchor" aria-label="anchor" href="#note"></a>
+</h2>
     <p>For the default degree 0 the <code>biomarker</code> variable is not included in the model.</p>
     </div>
     <div class="section level2">
-    <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"></a></h2>
+    <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"></a>
+</h2>
     <div class="dont-index"><p><code><a href="control_step.html">control_step()</a></code> and <code><a href="control_logistic.html">control_logistic()</a></code> for the available
 customization options.</p></div>
     </div>
 
     <div class="section level2">
-    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
+    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="co"># Testing dataset with just two treatment arms.</span></span></span>
 <span class="r-in"><span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://github.com/therneau/survival" class="external-link">survival</a></span><span class="op">)</span></span></span>
 <span class="r-in"><span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://dplyr.tidyverse.org" class="external-link">dplyr</a></span><span class="op">)</span></span></span>
@@ -194,17 +268,19 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 </code></pre></div>
     </div>
   </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
-    </nav></aside></div>
+    </nav></aside>
+</div>
 
 
     <footer><div class="nest">
   <p>tern is a part of the <strong>NEST</strong> and <a href="https://pharmaverse.org/" class="external-link"><strong>pharmaverse</strong></a>.</p>
 </div>
-<script type="text/javascript" src="../analytics.js"></script></footer></div>
-
+<script type="text/javascript" src="../analytics.js"></script></footer>
+</div>
 
 
 
 
-  </body></html>
 
+  </body>
+</html>
diff --git a/main/reference/fit_survival_step.html b/main/reference/fit_survival_step.html
index 2d87d0a405..0ca22c8a68 100644
--- a/main/reference/fit_survival_step.html
+++ b/main/reference/fit_survival_step.html
@@ -1,17 +1,40 @@
-<!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Subgroup treatment effect pattern (STEP) fit for survival outcome — fit_survival_step • tern</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Subgroup treatment effect pattern (STEP) fit for survival outcome — fit_survival_step"><meta name="description" content="
+<html lang="en">
+<head>
+<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+<meta charset="utf-8">
+<meta http-equiv="X-UA-Compatible" content="IE=edge">
+<meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<title>Subgroup treatment effect pattern (STEP) fit for survival outcome — fit_survival_step • tern</title>
+<!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png">
+<link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png">
+<link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png">
+<link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png">
+<link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png">
+<link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png">
+<script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet">
+<script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet">
+<link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet">
+<script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Subgroup treatment effect pattern (STEP) fit for survival outcome — fit_survival_step">
+<meta name="description" content="
 This fits the subgroup treatment effect pattern (STEP) models for a survival outcome. The treatment arm
 variable must have exactly 2 levels, where the first one is taken as reference and the estimated
 hazard ratios are for the comparison of the second level vs. the first one.
 The model which is fit is:
 Surv(time, event) ~ arm * poly(biomarker, degree) + covariates + strata(strata)
-where degree is specified by control_step()."><meta property="og:description" content="
+where degree is specified by control_step().">
+<meta property="og:description" content="
 This fits the subgroup treatment effect pattern (STEP) models for a survival outcome. The treatment arm
 variable must have exactly 2 levels, where the first one is taken as reference and the estimated
 hazard ratios are for the comparison of the second level vs. the first one.
 The model which is fit is:
 Surv(time, event) ~ arm * poly(biomarker, degree) + covariates + strata(strata)
-where degree is specified by control_step()."><meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png"><link rel="stylesheet" href="../consent.css"><script src="../consent.js" type="text/javascript" charset="utf-8"></script></head><body>
+where degree is specified by control_step().">
+<meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png">
+<link rel="stylesheet" href="../consent.css">
+<script src="../consent.js" type="text/javascript" charset="utf-8"></script>
+</head>
+<body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
 
 
@@ -27,26 +50,66 @@
     </button>
 
     <div id="navbar" class="collapse navbar-collapse ms-3">
-      <ul class="navbar-nav me-auto"><li class="nav-item"><a class="nav-link" href="../articles/tern.html">Get started</a></li>
+      <ul class="navbar-nav me-auto">
+<li class="nav-item"><a class="nav-link" href="../articles/tern.html">Get started</a></li>
 <li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
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   <button class="nav-link dropdown-toggle" type="button" id="dropdown-articles" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Articles</button>
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+  <ul class="dropdown-menu" aria-labelledby="dropdown-articles">
+<li><a class="dropdown-item" href="../articles/missing_values.html">Missing Values in Tern</a></li>
     <li><a class="dropdown-item" href="../articles/tables.html">Tabulation</a></li>
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     <li><a class="dropdown-item" href="../articles/tern_functions_guide.html">Understanding `tern` functions</a></li>
-  </ul></li>
+  </ul>
+</li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
-  <ul class="dropdown-menu" aria-labelledby="dropdown-reports"><li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
+  <ul class="dropdown-menu" aria-labelledby="dropdown-reports">
+<li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
     <li><a class="dropdown-item" href="../unit-test-report/">Unit test report</a></li>
     <li><a class="dropdown-item" href="../unit-test-report-non-cran/">Non-CRAN unit test report</a></li>
-  </ul></li>
-      </ul><ul class="navbar-nav"><li class="nav-item"><form class="form-inline" role="search">
- <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json"></form></li>
+  </ul>
+</li>
+      <div><li class="nav-item dropdown">
+    <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-versions">Versions</a>
+    <div class="dropdown-menu" aria-labelledby="dropdown-versions">
+    <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/main">main</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.5">v0.9.5</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.4">v0.9.4</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.3">v0.9.3</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1-rc3">v0.9.1-rc3</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a>
+</div>
+</li></div>
+</ul>
+<ul class="navbar-nav">
+<li class="nav-item"><form class="form-inline" role="search">
+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json">
+</form></li>
 <li class="nav-item"><a class="external-link nav-link" href="https://github.com/insightsengineering/tern" aria-label="GitHub"><span class="fa fa-github"></span></a></li>
-      </ul></div>
+      </ul>
+</div>
 
 
   </div>
@@ -69,7 +132,8 @@
     </div>
 
     <div class="section level2">
-    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
+    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">fit_survival_step</span><span class="op">(</span></span>
 <span>  <span class="va">variables</span>,</span>
 <span>  <span class="va">data</span>,</span>
@@ -78,39 +142,49 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
     </div>
 
     <div class="section level2">
-    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
+    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a>
+</h2>
 
 
-<dl><dt id="arg-variables">variables<a class="anchor" aria-label="anchor" href="#arg-variables"></a></dt>
+<dl>
+<dt id="arg-variables">variables<a class="anchor" aria-label="anchor" href="#arg-variables"></a>
+</dt>
 <dd><p>(named <code>list</code> of <code>character</code>)<br> list of analysis variables: needs <code>time</code>, <code>event</code>,
 <code>arm</code>, <code>biomarker</code>, and optional <code>covariates</code> and <code>strata</code>.</p></dd>
 
 
-<dt id="arg-data">data<a class="anchor" aria-label="anchor" href="#arg-data"></a></dt>
+<dt id="arg-data">data<a class="anchor" aria-label="anchor" href="#arg-data"></a>
+</dt>
 <dd><p>(<code>data.frame</code>)<br> the dataset containing the variables to summarize.</p></dd>
 
 
-<dt id="arg-control">control<a class="anchor" aria-label="anchor" href="#arg-control"></a></dt>
+<dt id="arg-control">control<a class="anchor" aria-label="anchor" href="#arg-control"></a>
+</dt>
 <dd><p>(named <code>list</code>)<br> combined control list from <code><a href="control_step.html">control_step()</a></code> and <code><a href="control_coxph.html">control_coxph()</a></code>.</p></dd>
 
-</dl></div>
+</dl>
+</div>
     <div class="section level2">
-    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
+    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a>
+</h2>
     <p>A matrix of class <code>step</code>. The first part of the columns describe the subgroup intervals used
 for the biomarker variable, including where the center of the intervals are and their bounds. The
 second part of the columns contain the estimates for the treatment arm comparison.</p>
     </div>
     <div class="section level2">
-    <h2 id="note">Note<a class="anchor" aria-label="anchor" href="#note"></a></h2>
+    <h2 id="note">Note<a class="anchor" aria-label="anchor" href="#note"></a>
+</h2>
     <p>For the default degree 0 the <code>biomarker</code> variable is not included in the model.</p>
     </div>
     <div class="section level2">
-    <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"></a></h2>
+    <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"></a>
+</h2>
     <div class="dont-index"><p><code><a href="control_step.html">control_step()</a></code> and <code><a href="control_coxph.html">control_coxph()</a></code> for the available customization options.</p></div>
     </div>
 
     <div class="section level2">
-    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
+    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="co"># Testing dataset with just two treatment arms.</span></span></span>
 <span class="r-in"><span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://dplyr.tidyverse.org" class="external-link">dplyr</a></span><span class="op">)</span></span></span>
 <span class="r-in"><span></span></span>
@@ -183,17 +257,19 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 </code></pre></div>
     </div>
   </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
-    </nav></aside></div>
+    </nav></aside>
+</div>
 
 
     <footer><div class="nest">
   <p>tern is a part of the <strong>NEST</strong> and <a href="https://pharmaverse.org/" class="external-link"><strong>pharmaverse</strong></a>.</p>
 </div>
-<script type="text/javascript" src="../analytics.js"></script></footer></div>
-
+<script type="text/javascript" src="../analytics.js"></script></footer>
+</div>
 
 
 
 
-  </body></html>
 
+  </body>
+</html>
diff --git a/main/reference/forest_viewport.html b/main/reference/forest_viewport.html
index e54e82a142..da2d18643b 100644
--- a/main/reference/forest_viewport.html
+++ b/main/reference/forest_viewport.html
@@ -1,5 +1,28 @@
-<!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Create a viewport tree for the forest plot — forest_viewport • tern</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Create a viewport tree for the forest plot — forest_viewport"><meta name="description" content=""><meta property="og:description" content=""><meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png"><link rel="stylesheet" href="../consent.css"><script src="../consent.js" type="text/javascript" charset="utf-8"></script></head><body>
+<html lang="en">
+<head>
+<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+<meta charset="utf-8">
+<meta http-equiv="X-UA-Compatible" content="IE=edge">
+<meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<title>Create a viewport tree for the forest plot — forest_viewport • tern</title>
+<!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png">
+<link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png">
+<link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png">
+<link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png">
+<link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png">
+<link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png">
+<script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet">
+<script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet">
+<link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet">
+<script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Create a viewport tree for the forest plot — forest_viewport">
+<meta name="description" content="">
+<meta property="og:description" content="">
+<meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png">
+<link rel="stylesheet" href="../consent.css">
+<script src="../consent.js" type="text/javascript" charset="utf-8"></script>
+</head>
+<body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
 
 
@@ -15,26 +38,66 @@
     </button>
 
     <div id="navbar" class="collapse navbar-collapse ms-3">
-      <ul class="navbar-nav me-auto"><li class="nav-item"><a class="nav-link" href="../articles/tern.html">Get started</a></li>
+      <ul class="navbar-nav me-auto">
+<li class="nav-item"><a class="nav-link" href="../articles/tern.html">Get started</a></li>
 <li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
 <li class="nav-item dropdown">
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-articles" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Articles</button>
-  <ul class="dropdown-menu" aria-labelledby="dropdown-articles"><li><a class="dropdown-item" href="../articles/missing_values.html">Missing Values in Tern</a></li>
+  <ul class="dropdown-menu" aria-labelledby="dropdown-articles">
+<li><a class="dropdown-item" href="../articles/missing_values.html">Missing Values in Tern</a></li>
     <li><a class="dropdown-item" href="../articles/tables.html">Tabulation</a></li>
     <li><a class="dropdown-item" href="../articles/tern_formats.html">Formatting Functions</a></li>
     <li><a class="dropdown-item" href="../articles/tern_functions_guide.html">Understanding `tern` functions</a></li>
-  </ul></li>
+  </ul>
+</li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
-  <ul class="dropdown-menu" aria-labelledby="dropdown-reports"><li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
+  <ul class="dropdown-menu" aria-labelledby="dropdown-reports">
+<li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
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-  </ul></li>
-      </ul><ul class="navbar-nav"><li class="nav-item"><form class="form-inline" role="search">
- <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json"></form></li>
+  </ul>
+</li>
+      <div><li class="nav-item dropdown">
+    <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-versions">Versions</a>
+    <div class="dropdown-menu" aria-labelledby="dropdown-versions">
+    <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/main">main</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.5">v0.9.5</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.4">v0.9.4</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.3">v0.9.3</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1-rc3">v0.9.1-rc3</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a>
+</div>
+</li></div>
+</ul>
+<ul class="navbar-nav">
+<li class="nav-item"><form class="form-inline" role="search">
+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json">
+</form></li>
 <li class="nav-item"><a class="external-link nav-link" href="https://github.com/insightsengineering/tern" aria-label="GitHub"><span class="fa fa-github"></span></a></li>
-      </ul></div>
+      </ul>
+</div>
 
 
   </div>
@@ -51,7 +114,8 @@
     </div>
 
     <div class="section level2">
-    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
+    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">forest_viewport</span><span class="op">(</span></span>
 <span>  <span class="va">tbl</span>,</span>
 <span>  width_row_names <span class="op">=</span> <span class="cn">NULL</span>,</span>
@@ -64,44 +128,56 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
     </div>
 
     <div class="section level2">
-    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
+    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a>
+</h2>
 
 
-<dl><dt id="arg-tbl">tbl<a class="anchor" aria-label="anchor" href="#arg-tbl"></a></dt>
+<dl>
+<dt id="arg-tbl">tbl<a class="anchor" aria-label="anchor" href="#arg-tbl"></a>
+</dt>
 <dd><p>(<code>VTableTree</code>)<br><code>rtables</code> table object.</p></dd>
 
 
-<dt id="arg-width-row-names">width_row_names<a class="anchor" aria-label="anchor" href="#arg-width-row-names"></a></dt>
+<dt id="arg-width-row-names">width_row_names<a class="anchor" aria-label="anchor" href="#arg-width-row-names"></a>
+</dt>
 <dd><p>(<code><a href="https://rdrr.io/r/grid/unit.html" class="external-link">grid::unit</a></code>)<br> width of row names.</p></dd>
 
 
-<dt id="arg-width-columns">width_columns<a class="anchor" aria-label="anchor" href="#arg-width-columns"></a></dt>
+<dt id="arg-width-columns">width_columns<a class="anchor" aria-label="anchor" href="#arg-width-columns"></a>
+</dt>
 <dd><p>(<code><a href="https://rdrr.io/r/grid/unit.html" class="external-link">grid::unit</a></code>)<br> width of column spans.</p></dd>
 
 
-<dt id="arg-width-forest">width_forest<a class="anchor" aria-label="anchor" href="#arg-width-forest"></a></dt>
+<dt id="arg-width-forest">width_forest<a class="anchor" aria-label="anchor" href="#arg-width-forest"></a>
+</dt>
 <dd><p>(<code><a href="https://rdrr.io/r/grid/unit.html" class="external-link">grid::unit</a></code>)<br> width of the forest plot.</p></dd>
 
 
-<dt id="arg-gap-column">gap_column<a class="anchor" aria-label="anchor" href="#arg-gap-column"></a></dt>
+<dt id="arg-gap-column">gap_column<a class="anchor" aria-label="anchor" href="#arg-gap-column"></a>
+</dt>
 <dd><p>(<code><a href="https://rdrr.io/r/grid/unit.html" class="external-link">grid::unit</a></code>)<br> gap width between the columns.</p></dd>
 
 
-<dt id="arg-gap-header">gap_header<a class="anchor" aria-label="anchor" href="#arg-gap-header"></a></dt>
+<dt id="arg-gap-header">gap_header<a class="anchor" aria-label="anchor" href="#arg-gap-header"></a>
+</dt>
 <dd><p>(<code><a href="https://rdrr.io/r/grid/unit.html" class="external-link">grid::unit</a></code>)<br> gap width between the header.</p></dd>
 
 
-<dt id="arg-mat-form">mat_form<a class="anchor" aria-label="anchor" href="#arg-mat-form"></a></dt>
+<dt id="arg-mat-form">mat_form<a class="anchor" aria-label="anchor" href="#arg-mat-form"></a>
+</dt>
 <dd><p>(<code>MatrixPrintForm</code>)<br> matrix print form of the table.</p></dd>
 
-</dl></div>
+</dl>
+</div>
     <div class="section level2">
-    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
+    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a>
+</h2>
     <p>A viewport tree.</p>
     </div>
 
     <div class="section level2">
-    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
+    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va">grid</span><span class="op">)</span></span></span>
 <span class="r-in"><span></span></span>
 <span class="r-in"><span><span class="va">tbl</span> <span class="op">&lt;-</span> <span class="fu">rtable</span><span class="op">(</span></span></span>
@@ -134,17 +210,19 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 </code></pre></div>
     </div>
   </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
-    </nav></aside></div>
+    </nav></aside>
+</div>
 
 
     <footer><div class="nest">
   <p>tern is a part of the <strong>NEST</strong> and <a href="https://pharmaverse.org/" class="external-link"><strong>pharmaverse</strong></a>.</p>
 </div>
-<script type="text/javascript" src="../analytics.js"></script></footer></div>
-
+<script type="text/javascript" src="../analytics.js"></script></footer>
+</div>
 
 
 
 
-  </body></html>
 
+  </body>
+</html>
diff --git a/main/reference/format_auto.html b/main/reference/format_auto.html
index d3e266d97e..de43cabdaa 100644
--- a/main/reference/format_auto.html
+++ b/main/reference/format_auto.html
@@ -1,15 +1,38 @@
-<!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Format automatically using data significant digits — format_auto • tern</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Format automatically using data significant digits — format_auto"><meta name="description" content='
+<html lang="en">
+<head>
+<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+<meta charset="utf-8">
+<meta http-equiv="X-UA-Compatible" content="IE=edge">
+<meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<title>Format automatically using data significant digits — format_auto • tern</title>
+<!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png">
+<link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png">
+<link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png">
+<link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png">
+<link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png">
+<link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png">
+<script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet">
+<script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet">
+<link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet">
+<script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Format automatically using data significant digits — format_auto">
+<meta name="description" content='
 Formatting function for the majority of default methods used in analyze_vars().
 For non-derived values, the significant digits of data is used (e.g. range), while derived
 values have one more digits (measure of location and dispersion like mean, standard deviation).
 This function can be called internally with "auto" like, for example,
-.formats = c("mean" = "auto"). See details to see how this works with the inner function.'><meta property="og:description" content='
+.formats = c("mean" = "auto"). See details to see how this works with the inner function.'>
+<meta property="og:description" content='
 Formatting function for the majority of default methods used in analyze_vars().
 For non-derived values, the significant digits of data is used (e.g. range), while derived
 values have one more digits (measure of location and dispersion like mean, standard deviation).
 This function can be called internally with "auto" like, for example,
-.formats = c("mean" = "auto"). See details to see how this works with the inner function.'><meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png"><link rel="stylesheet" href="../consent.css"><script src="../consent.js" type="text/javascript" charset="utf-8"></script></head><body>
+.formats = c("mean" = "auto"). See details to see how this works with the inner function.'>
+<meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png">
+<link rel="stylesheet" href="../consent.css">
+<script src="../consent.js" type="text/javascript" charset="utf-8"></script>
+</head>
+<body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
 
 
@@ -25,26 +48,66 @@
     </button>
 
     <div id="navbar" class="collapse navbar-collapse ms-3">
-      <ul class="navbar-nav me-auto"><li class="nav-item"><a class="nav-link" href="../articles/tern.html">Get started</a></li>
+      <ul class="navbar-nav me-auto">
+<li class="nav-item"><a class="nav-link" href="../articles/tern.html">Get started</a></li>
 <li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
 <li class="nav-item dropdown">
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-articles" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Articles</button>
-  <ul class="dropdown-menu" aria-labelledby="dropdown-articles"><li><a class="dropdown-item" href="../articles/missing_values.html">Missing Values in Tern</a></li>
+  <ul class="dropdown-menu" aria-labelledby="dropdown-articles">
+<li><a class="dropdown-item" href="../articles/missing_values.html">Missing Values in Tern</a></li>
     <li><a class="dropdown-item" href="../articles/tables.html">Tabulation</a></li>
     <li><a class="dropdown-item" href="../articles/tern_formats.html">Formatting Functions</a></li>
     <li><a class="dropdown-item" href="../articles/tern_functions_guide.html">Understanding `tern` functions</a></li>
-  </ul></li>
+  </ul>
+</li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
-  <ul class="dropdown-menu" aria-labelledby="dropdown-reports"><li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
+  <ul class="dropdown-menu" aria-labelledby="dropdown-reports">
+<li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
     <li><a class="dropdown-item" href="../unit-test-report/">Unit test report</a></li>
     <li><a class="dropdown-item" href="../unit-test-report-non-cran/">Non-CRAN unit test report</a></li>
-  </ul></li>
-      </ul><ul class="navbar-nav"><li class="nav-item"><form class="form-inline" role="search">
- <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json"></form></li>
+  </ul>
+</li>
+      <div><li class="nav-item dropdown">
+    <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-versions">Versions</a>
+    <div class="dropdown-menu" aria-labelledby="dropdown-versions">
+    <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/main">main</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.5">v0.9.5</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.4">v0.9.4</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.3">v0.9.3</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1-rc3">v0.9.1-rc3</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a>
+</div>
+</li></div>
+</ul>
+<ul class="navbar-nav">
+<li class="nav-item"><form class="form-inline" role="search">
+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json">
+</form></li>
 <li class="nav-item"><a class="external-link nav-link" href="https://github.com/insightsengineering/tern" aria-label="GitHub"><span class="fa fa-github"></span></a></li>
-      </ul></div>
+      </ul>
+</div>
 
 
   </div>
@@ -66,37 +129,46 @@
     </div>
 
     <div class="section level2">
-    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
+    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">format_auto</span><span class="op">(</span><span class="va">dt_var</span>, <span class="va">x_stat</span><span class="op">)</span></span></code></pre></div>
     </div>
 
     <div class="section level2">
-    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
+    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a>
+</h2>
 
 
-<dl><dt id="arg-dt-var">dt_var<a class="anchor" aria-label="anchor" href="#arg-dt-var"></a></dt>
+<dl>
+<dt id="arg-dt-var">dt_var<a class="anchor" aria-label="anchor" href="#arg-dt-var"></a>
+</dt>
 <dd><p>(<code>numeric</code>)<br> variable data the statistics were calculated from. Used only to
 find significant digits. In <a href="analyze_variables.html">analyze_vars</a> this comes from <code>.df_row</code> (see
 <a href="https://insightsengineering.github.io/rtables/latest-tag/reference/additional_fun_params.html" class="external-link">rtables::additional_fun_params</a>), and it is the row data after the above row splits. No
 column split is considered.</p></dd>
 
 
-<dt id="arg-x-stat">x_stat<a class="anchor" aria-label="anchor" href="#arg-x-stat"></a></dt>
+<dt id="arg-x-stat">x_stat<a class="anchor" aria-label="anchor" href="#arg-x-stat"></a>
+</dt>
 <dd><p>(<code>string</code>)<br> string indicating the current statistical method used.</p></dd>
 
-</dl></div>
+</dl>
+</div>
     <div class="section level2">
-    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
+    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a>
+</h2>
     <p>A string that <code>rtables</code> prints in a table cell.</p>
     </div>
     <div class="section level2">
-    <h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a></h2>
+    <h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a>
+</h2>
     <p>The internal function is needed to work with <code>rtables</code> default structure for
 format functions, i.e. <code>function(x, ...)</code>, where is x are results from statistical evaluation.
 It can be more than one element (e.g. for <code>.stats = "mean_sd"</code>).</p>
     </div>
     <div class="section level2">
-    <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"></a></h2>
+    <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"></a>
+</h2>
     <div class="dont-index"><p>Other formatting functions:
 <code><a href="extreme_format.html">extreme_format</a></code>,
 <code><a href="format_count_fraction.html">format_count_fraction</a>()</code>,
@@ -113,7 +185,8 @@ <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"
     </div>
 
     <div class="section level2">
-    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
+    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">x_todo</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">0.001</span>, <span class="fl">0.2</span>, <span class="fl">0.0011000</span>, <span class="fl">3</span>, <span class="fl">4</span><span class="op">)</span></span></span>
 <span class="r-in"><span><span class="va">res</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/mean.html" class="external-link">mean</a></span><span class="op">(</span><span class="va">x_todo</span><span class="op">[</span><span class="fl">1</span><span class="op">:</span><span class="fl">3</span><span class="op">]</span><span class="op">)</span>, <span class="fu"><a href="https://rdrr.io/r/stats/sd.html" class="external-link">sd</a></span><span class="op">(</span><span class="va">x_todo</span><span class="op">[</span><span class="fl">1</span><span class="op">:</span><span class="fl">3</span><span class="op">]</span><span class="op">)</span><span class="op">)</span></span></span>
 <span class="r-in"><span></span></span>
@@ -129,17 +202,19 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 </code></pre></div>
     </div>
   </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
-    </nav></aside></div>
+    </nav></aside>
+</div>
 
 
     <footer><div class="nest">
   <p>tern is a part of the <strong>NEST</strong> and <a href="https://pharmaverse.org/" class="external-link"><strong>pharmaverse</strong></a>.</p>
 </div>
-<script type="text/javascript" src="../analytics.js"></script></footer></div>
-
+<script type="text/javascript" src="../analytics.js"></script></footer>
+</div>
 
 
 
 
-  </body></html>
 
+  </body>
+</html>
diff --git a/main/reference/format_count_fraction.html b/main/reference/format_count_fraction.html
index f092018388..2f33ee8582 100644
--- a/main/reference/format_count_fraction.html
+++ b/main/reference/format_count_fraction.html
@@ -1,7 +1,30 @@
-<!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Format count and fraction — format_count_fraction • tern</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Format count and fraction — format_count_fraction"><meta name="description" content="
-Formats a count together with fraction with special consideration when count is 0."><meta property="og:description" content="
-Formats a count together with fraction with special consideration when count is 0."><meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png"><link rel="stylesheet" href="../consent.css"><script src="../consent.js" type="text/javascript" charset="utf-8"></script></head><body>
+<html lang="en">
+<head>
+<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+<meta charset="utf-8">
+<meta http-equiv="X-UA-Compatible" content="IE=edge">
+<meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<title>Format count and fraction — format_count_fraction • tern</title>
+<!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png">
+<link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png">
+<link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png">
+<link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png">
+<link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png">
+<link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png">
+<script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet">
+<script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet">
+<link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet">
+<script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Format count and fraction — format_count_fraction">
+<meta name="description" content="
+Formats a count together with fraction with special consideration when count is 0.">
+<meta property="og:description" content="
+Formats a count together with fraction with special consideration when count is 0.">
+<meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png">
+<link rel="stylesheet" href="../consent.css">
+<script src="../consent.js" type="text/javascript" charset="utf-8"></script>
+</head>
+<body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
 
 
@@ -17,26 +40,66 @@
     </button>
 
     <div id="navbar" class="collapse navbar-collapse ms-3">
-      <ul class="navbar-nav me-auto"><li class="nav-item"><a class="nav-link" href="../articles/tern.html">Get started</a></li>
+      <ul class="navbar-nav me-auto">
+<li class="nav-item"><a class="nav-link" href="../articles/tern.html">Get started</a></li>
 <li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
 <li class="nav-item dropdown">
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-articles" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Articles</button>
-  <ul class="dropdown-menu" aria-labelledby="dropdown-articles"><li><a class="dropdown-item" href="../articles/missing_values.html">Missing Values in Tern</a></li>
+  <ul class="dropdown-menu" aria-labelledby="dropdown-articles">
+<li><a class="dropdown-item" href="../articles/missing_values.html">Missing Values in Tern</a></li>
     <li><a class="dropdown-item" href="../articles/tables.html">Tabulation</a></li>
     <li><a class="dropdown-item" href="../articles/tern_formats.html">Formatting Functions</a></li>
     <li><a class="dropdown-item" href="../articles/tern_functions_guide.html">Understanding `tern` functions</a></li>
-  </ul></li>
+  </ul>
+</li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
-  <ul class="dropdown-menu" aria-labelledby="dropdown-reports"><li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
+  <ul class="dropdown-menu" aria-labelledby="dropdown-reports">
+<li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
     <li><a class="dropdown-item" href="../unit-test-report/">Unit test report</a></li>
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-  </ul></li>
-      </ul><ul class="navbar-nav"><li class="nav-item"><form class="form-inline" role="search">
- <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json"></form></li>
+  </ul>
+</li>
+      <div><li class="nav-item dropdown">
+    <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-versions">Versions</a>
+    <div class="dropdown-menu" aria-labelledby="dropdown-versions">
+    <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/main">main</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.5">v0.9.5</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.4">v0.9.4</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.3">v0.9.3</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1-rc3">v0.9.1-rc3</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a>
+</div>
+</li></div>
+</ul>
+<ul class="navbar-nav">
+<li class="nav-item"><form class="form-inline" role="search">
+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json">
+</form></li>
 <li class="nav-item"><a class="external-link nav-link" href="https://github.com/insightsengineering/tern" aria-label="GitHub"><span class="fa fa-github"></span></a></li>
-      </ul></div>
+      </ul>
+</div>
 
 
   </div>
@@ -54,28 +117,36 @@
     </div>
 
     <div class="section level2">
-    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
+    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">format_count_fraction</span><span class="op">(</span><span class="va">x</span>, <span class="va">...</span><span class="op">)</span></span></code></pre></div>
     </div>
 
     <div class="section level2">
-    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
+    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a>
+</h2>
 
 
-<dl><dt id="arg-x">x<a class="anchor" aria-label="anchor" href="#arg-x"></a></dt>
+<dl>
+<dt id="arg-x">x<a class="anchor" aria-label="anchor" href="#arg-x"></a>
+</dt>
 <dd><p>(<code>numeric(2)</code>)<br> vector of length 2 with count and fraction, respectively.</p></dd>
 
 
-<dt id="arg--">...<a class="anchor" aria-label="anchor" href="#arg--"></a></dt>
+<dt id="arg--">...<a class="anchor" aria-label="anchor" href="#arg--"></a>
+</dt>
 <dd><p>not used. Required for <code>rtables</code> interface.</p></dd>
 
-</dl></div>
+</dl>
+</div>
     <div class="section level2">
-    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
+    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a>
+</h2>
     <p>A string in the format <code>count (fraction %)</code>. If <code>count</code> is 0, the format is <code>0</code>.</p>
     </div>
     <div class="section level2">
-    <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"></a></h2>
+    <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"></a>
+</h2>
     <div class="dont-index"><p>Other formatting functions:
 <code><a href="extreme_format.html">extreme_format</a></code>,
 <code><a href="format_auto.html">format_auto</a>()</code>,
@@ -92,7 +163,8 @@ <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"
     </div>
 
     <div class="section level2">
-    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
+    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="fu">format_count_fraction</span><span class="op">(</span>x <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">2</span>, <span class="fl">0.6667</span><span class="op">)</span><span class="op">)</span></span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> [1] "2 (66.7%)"</span>
 <span class="r-in"><span><span class="fu">format_count_fraction</span><span class="op">(</span>x <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">0</span>, <span class="fl">0</span><span class="op">)</span><span class="op">)</span></span></span>
@@ -101,17 +173,19 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 </code></pre></div>
     </div>
   </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
-    </nav></aside></div>
+    </nav></aside>
+</div>
 
 
     <footer><div class="nest">
   <p>tern is a part of the <strong>NEST</strong> and <a href="https://pharmaverse.org/" class="external-link"><strong>pharmaverse</strong></a>.</p>
 </div>
-<script type="text/javascript" src="../analytics.js"></script></footer></div>
-
+<script type="text/javascript" src="../analytics.js"></script></footer>
+</div>
 
 
 
 
-  </body></html>
 
+  </body>
+</html>
diff --git a/main/reference/format_count_fraction_fixed_dp.html b/main/reference/format_count_fraction_fixed_dp.html
index be833ab812..9f678d929a 100644
--- a/main/reference/format_count_fraction_fixed_dp.html
+++ b/main/reference/format_count_fraction_fixed_dp.html
@@ -1,7 +1,30 @@
-<!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Format count and percentage with fixed single decimal place — format_count_fraction_fixed_dp • tern</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Format count and percentage with fixed single decimal place — format_count_fraction_fixed_dp"><meta name="description" content="
-Formats a count together with fraction with special consideration when count is 0."><meta property="og:description" content="
-Formats a count together with fraction with special consideration when count is 0."><meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png"><link rel="stylesheet" href="../consent.css"><script src="../consent.js" type="text/javascript" charset="utf-8"></script></head><body>
+<html lang="en">
+<head>
+<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+<meta charset="utf-8">
+<meta http-equiv="X-UA-Compatible" content="IE=edge">
+<meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<title>Format count and percentage with fixed single decimal place — format_count_fraction_fixed_dp • tern</title>
+<!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png">
+<link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png">
+<link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png">
+<link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png">
+<link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png">
+<link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png">
+<script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet">
+<script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet">
+<link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet">
+<script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Format count and percentage with fixed single decimal place — format_count_fraction_fixed_dp">
+<meta name="description" content="
+Formats a count together with fraction with special consideration when count is 0.">
+<meta property="og:description" content="
+Formats a count together with fraction with special consideration when count is 0.">
+<meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png">
+<link rel="stylesheet" href="../consent.css">
+<script src="../consent.js" type="text/javascript" charset="utf-8"></script>
+</head>
+<body>
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@@ -17,26 +40,66 @@
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     <div id="navbar" class="collapse navbar-collapse ms-3">
-      <ul class="navbar-nav me-auto"><li class="nav-item"><a class="nav-link" href="../articles/tern.html">Get started</a></li>
+      <ul class="navbar-nav me-auto">
+<li class="nav-item"><a class="nav-link" href="../articles/tern.html">Get started</a></li>
 <li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
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-  <ul class="dropdown-menu" aria-labelledby="dropdown-articles"><li><a class="dropdown-item" href="../articles/missing_values.html">Missing Values in Tern</a></li>
+  <ul class="dropdown-menu" aria-labelledby="dropdown-articles">
+<li><a class="dropdown-item" href="../articles/missing_values.html">Missing Values in Tern</a></li>
     <li><a class="dropdown-item" href="../articles/tables.html">Tabulation</a></li>
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     <li><a class="dropdown-item" href="../articles/tern_functions_guide.html">Understanding `tern` functions</a></li>
-  </ul></li>
+  </ul>
+</li>
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   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
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+  <ul class="dropdown-menu" aria-labelledby="dropdown-reports">
+<li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
     <li><a class="dropdown-item" href="../unit-test-report/">Unit test report</a></li>
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-      </ul><ul class="navbar-nav"><li class="nav-item"><form class="form-inline" role="search">
- <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json"></form></li>
+  </ul>
+</li>
+      <div><li class="nav-item dropdown">
+    <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-versions">Versions</a>
+    <div class="dropdown-menu" aria-labelledby="dropdown-versions">
+    <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/main">main</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.5">v0.9.5</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.4">v0.9.4</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.3">v0.9.3</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1-rc3">v0.9.1-rc3</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a>
+</div>
+</li></div>
+</ul>
+<ul class="navbar-nav">
+<li class="nav-item"><form class="form-inline" role="search">
+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json">
+</form></li>
 <li class="nav-item"><a class="external-link nav-link" href="https://github.com/insightsengineering/tern" aria-label="GitHub"><span class="fa fa-github"></span></a></li>
-      </ul></div>
+      </ul>
+</div>
 
 
   </div>
@@ -54,28 +117,36 @@
     </div>
 
     <div class="section level2">
-    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
+    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">format_count_fraction_fixed_dp</span><span class="op">(</span><span class="va">x</span>, <span class="va">...</span><span class="op">)</span></span></code></pre></div>
     </div>
 
     <div class="section level2">
-    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
+    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a>
+</h2>
 
 
-<dl><dt id="arg-x">x<a class="anchor" aria-label="anchor" href="#arg-x"></a></dt>
+<dl>
+<dt id="arg-x">x<a class="anchor" aria-label="anchor" href="#arg-x"></a>
+</dt>
 <dd><p>(<code>numeric(2)</code>)<br> vector of length 2 with count and fraction, respectively.</p></dd>
 
 
-<dt id="arg--">...<a class="anchor" aria-label="anchor" href="#arg--"></a></dt>
+<dt id="arg--">...<a class="anchor" aria-label="anchor" href="#arg--"></a>
+</dt>
 <dd><p>not used. Required for <code>rtables</code> interface.</p></dd>
 
-</dl></div>
+</dl>
+</div>
     <div class="section level2">
-    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
+    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a>
+</h2>
     <p>A string in the format <code>count (fraction %)</code>. If <code>count</code> is 0, the format is <code>0</code>.</p>
     </div>
     <div class="section level2">
-    <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"></a></h2>
+    <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"></a>
+</h2>
     <div class="dont-index"><p>Other formatting functions:
 <code><a href="extreme_format.html">extreme_format</a></code>,
 <code><a href="format_auto.html">format_auto</a>()</code>,
@@ -92,7 +163,8 @@ <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"
     </div>
 
     <div class="section level2">
-    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
+    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="fu">format_count_fraction_fixed_dp</span><span class="op">(</span>x <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">2</span>, <span class="fl">0.6667</span><span class="op">)</span><span class="op">)</span></span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> [1] "2 (66.7%)"</span>
 <span class="r-in"><span><span class="fu">format_count_fraction_fixed_dp</span><span class="op">(</span>x <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">2</span>, <span class="fl">0.5</span><span class="op">)</span><span class="op">)</span></span></span>
@@ -103,17 +175,19 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 </code></pre></div>
     </div>
   </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
-    </nav></aside></div>
+    </nav></aside>
+</div>
 
 
     <footer><div class="nest">
   <p>tern is a part of the <strong>NEST</strong> and <a href="https://pharmaverse.org/" class="external-link"><strong>pharmaverse</strong></a>.</p>
 </div>
-<script type="text/javascript" src="../analytics.js"></script></footer></div>
-
+<script type="text/javascript" src="../analytics.js"></script></footer>
+</div>
 
 
 
 
-  </body></html>
 
+  </body>
+</html>
diff --git a/main/reference/format_count_fraction_lt10.html b/main/reference/format_count_fraction_lt10.html
index 1621901cf2..7006a6cd17 100644
--- a/main/reference/format_count_fraction_lt10.html
+++ b/main/reference/format_count_fraction_lt10.html
@@ -1,7 +1,30 @@
-<!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Format count and fraction with special case for count &lt; 10 — format_count_fraction_lt10 • tern</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Format count and fraction with special case for count &lt; 10 — format_count_fraction_lt10"><meta name="description" content="
-Formats a count together with fraction with special consideration when count is less than 10."><meta property="og:description" content="
-Formats a count together with fraction with special consideration when count is less than 10."><meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png"><link rel="stylesheet" href="../consent.css"><script src="../consent.js" type="text/javascript" charset="utf-8"></script></head><body>
+<html lang="en">
+<head>
+<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+<meta charset="utf-8">
+<meta http-equiv="X-UA-Compatible" content="IE=edge">
+<meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<title>Format count and fraction with special case for count &lt; 10 — format_count_fraction_lt10 • tern</title>
+<!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png">
+<link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png">
+<link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png">
+<link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png">
+<link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png">
+<link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png">
+<script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet">
+<script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet">
+<link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet">
+<script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Format count and fraction with special case for count &lt; 10 — format_count_fraction_lt10">
+<meta name="description" content="
+Formats a count together with fraction with special consideration when count is less than 10.">
+<meta property="og:description" content="
+Formats a count together with fraction with special consideration when count is less than 10.">
+<meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png">
+<link rel="stylesheet" href="../consent.css">
+<script src="../consent.js" type="text/javascript" charset="utf-8"></script>
+</head>
+<body>
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@@ -17,26 +40,66 @@
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+      <ul class="navbar-nav me-auto">
+<li class="nav-item"><a class="nav-link" href="../articles/tern.html">Get started</a></li>
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-  <ul class="dropdown-menu" aria-labelledby="dropdown-articles"><li><a class="dropdown-item" href="../articles/missing_values.html">Missing Values in Tern</a></li>
+  <ul class="dropdown-menu" aria-labelledby="dropdown-articles">
+<li><a class="dropdown-item" href="../articles/missing_values.html">Missing Values in Tern</a></li>
     <li><a class="dropdown-item" href="../articles/tables.html">Tabulation</a></li>
     <li><a class="dropdown-item" href="../articles/tern_formats.html">Formatting Functions</a></li>
     <li><a class="dropdown-item" href="../articles/tern_functions_guide.html">Understanding `tern` functions</a></li>
-  </ul></li>
+  </ul>
+</li>
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+  <ul class="dropdown-menu" aria-labelledby="dropdown-reports">
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+  </ul>
+</li>
+      <div><li class="nav-item dropdown">
+    <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-versions">Versions</a>
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+    <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
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+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
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+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.3">v0.9.3</a>
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+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1-rc3">v0.9.1-rc3</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a>
+</div>
+</li></div>
+</ul>
+<ul class="navbar-nav">
+<li class="nav-item"><form class="form-inline" role="search">
+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json">
+</form></li>
 <li class="nav-item"><a class="external-link nav-link" href="https://github.com/insightsengineering/tern" aria-label="GitHub"><span class="fa fa-github"></span></a></li>
-      </ul></div>
+      </ul>
+</div>
 
 
   </div>
@@ -54,28 +117,36 @@
     </div>
 
     <div class="section level2">
-    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
+    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">format_count_fraction_lt10</span><span class="op">(</span><span class="va">x</span>, <span class="va">...</span><span class="op">)</span></span></code></pre></div>
     </div>
 
     <div class="section level2">
-    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
+    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a>
+</h2>
 
 
-<dl><dt id="arg-x">x<a class="anchor" aria-label="anchor" href="#arg-x"></a></dt>
+<dl>
+<dt id="arg-x">x<a class="anchor" aria-label="anchor" href="#arg-x"></a>
+</dt>
 <dd><p>(<code>numeric(2)</code>)<br> vector of length 2 with count and fraction, respectively.</p></dd>
 
 
-<dt id="arg--">...<a class="anchor" aria-label="anchor" href="#arg--"></a></dt>
+<dt id="arg--">...<a class="anchor" aria-label="anchor" href="#arg--"></a>
+</dt>
 <dd><p>not used. Required for <code>rtables</code> interface.</p></dd>
 
-</dl></div>
+</dl>
+</div>
     <div class="section level2">
-    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
+    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a>
+</h2>
     <p>A string in the format <code>count (fraction %)</code>. If <code>count</code> is less than 10, only <code>count</code> is printed.</p>
     </div>
     <div class="section level2">
-    <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"></a></h2>
+    <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"></a>
+</h2>
     <div class="dont-index"><p>Other formatting functions:
 <code><a href="extreme_format.html">extreme_format</a></code>,
 <code><a href="format_auto.html">format_auto</a>()</code>,
@@ -92,7 +163,8 @@ <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"
     </div>
 
     <div class="section level2">
-    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
+    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="fu">format_count_fraction_lt10</span><span class="op">(</span>x <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">275</span>, <span class="fl">0.9673</span><span class="op">)</span><span class="op">)</span></span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> [1] "275 (96.7%)"</span>
 <span class="r-in"><span><span class="fu">format_count_fraction_lt10</span><span class="op">(</span>x <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">2</span>, <span class="fl">0.6667</span><span class="op">)</span><span class="op">)</span></span></span>
@@ -103,17 +175,19 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 </code></pre></div>
     </div>
   </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
-    </nav></aside></div>
+    </nav></aside>
+</div>
 
 
     <footer><div class="nest">
   <p>tern is a part of the <strong>NEST</strong> and <a href="https://pharmaverse.org/" class="external-link"><strong>pharmaverse</strong></a>.</p>
 </div>
-<script type="text/javascript" src="../analytics.js"></script></footer></div>
-
+<script type="text/javascript" src="../analytics.js"></script></footer>
+</div>
 
 
 
 
-  </body></html>
 
+  </body>
+</html>
diff --git a/main/reference/format_extreme_values.html b/main/reference/format_extreme_values.html
index 8e459ef708..57a115984f 100644
--- a/main/reference/format_extreme_values.html
+++ b/main/reference/format_extreme_values.html
@@ -1,7 +1,30 @@
-<!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Format a single extreme value — format_extreme_values • tern</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Format a single extreme value — format_extreme_values"><meta name="description" content="
-Create a formatting function for a single extreme value."><meta property="og:description" content="
-Create a formatting function for a single extreme value."><meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png"><link rel="stylesheet" href="../consent.css"><script src="../consent.js" type="text/javascript" charset="utf-8"></script></head><body>
+<html lang="en">
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+<meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<title>Format a single extreme value — format_extreme_values • tern</title>
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+<link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png">
+<link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png">
+<script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet">
+<script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet">
+<link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet">
+<script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Format a single extreme value — format_extreme_values">
+<meta name="description" content="
+Create a formatting function for a single extreme value.">
+<meta property="og:description" content="
+Create a formatting function for a single extreme value.">
+<meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png">
+<link rel="stylesheet" href="../consent.css">
+<script src="../consent.js" type="text/javascript" charset="utf-8"></script>
+</head>
+<body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
 
 
@@ -17,26 +40,66 @@
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     <div id="navbar" class="collapse navbar-collapse ms-3">
-      <ul class="navbar-nav me-auto"><li class="nav-item"><a class="nav-link" href="../articles/tern.html">Get started</a></li>
+      <ul class="navbar-nav me-auto">
+<li class="nav-item"><a class="nav-link" href="../articles/tern.html">Get started</a></li>
 <li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
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   <button class="nav-link dropdown-toggle" type="button" id="dropdown-articles" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Articles</button>
-  <ul class="dropdown-menu" aria-labelledby="dropdown-articles"><li><a class="dropdown-item" href="../articles/missing_values.html">Missing Values in Tern</a></li>
+  <ul class="dropdown-menu" aria-labelledby="dropdown-articles">
+<li><a class="dropdown-item" href="../articles/missing_values.html">Missing Values in Tern</a></li>
     <li><a class="dropdown-item" href="../articles/tables.html">Tabulation</a></li>
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     <li><a class="dropdown-item" href="../articles/tern_functions_guide.html">Understanding `tern` functions</a></li>
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+  </ul>
+</li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
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+  </ul>
+</li>
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+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.5">v0.9.5</a>
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+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1-rc3">v0.9.1-rc3</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a>
+</div>
+</li></div>
+</ul>
+<ul class="navbar-nav">
+<li class="nav-item"><form class="form-inline" role="search">
+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json">
+</form></li>
 <li class="nav-item"><a class="external-link nav-link" href="https://github.com/insightsengineering/tern" aria-label="GitHub"><span class="fa fa-github"></span></a></li>
-      </ul></div>
+      </ul>
+</div>
 
 
   </div>
@@ -54,24 +117,31 @@
     </div>
 
     <div class="section level2">
-    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
+    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">format_extreme_values</span><span class="op">(</span>digits <span class="op">=</span> <span class="fl">2L</span><span class="op">)</span></span></code></pre></div>
     </div>
 
     <div class="section level2">
-    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
+    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a>
+</h2>
 
 
-<dl><dt id="arg-digits">digits<a class="anchor" aria-label="anchor" href="#arg-digits"></a></dt>
+<dl>
+<dt id="arg-digits">digits<a class="anchor" aria-label="anchor" href="#arg-digits"></a>
+</dt>
 <dd><p>(<code>integer(1)</code>)<br> number of decimal places to display.</p></dd>
 
-</dl></div>
+</dl>
+</div>
     <div class="section level2">
-    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
+    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a>
+</h2>
     <p>An <code>rtables</code> formatting function that uses threshold <code>digits</code> to return a formatted extreme value.</p>
     </div>
     <div class="section level2">
-    <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"></a></h2>
+    <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"></a>
+</h2>
     <div class="dont-index"><p>Other formatting functions:
 <code><a href="extreme_format.html">extreme_format</a></code>,
 <code><a href="format_auto.html">format_auto</a>()</code>,
@@ -88,7 +158,8 @@ <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"
     </div>
 
     <div class="section level2">
-    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
+    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">format_fun</span> <span class="op">&lt;-</span> <span class="fu">format_extreme_values</span><span class="op">(</span><span class="fl">2L</span><span class="op">)</span></span></span>
 <span class="r-in"><span><span class="fu">format_fun</span><span class="op">(</span>x <span class="op">=</span> <span class="fl">0.127</span><span class="op">)</span></span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> [1] "0.13"</span>
@@ -102,17 +173,19 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 </code></pre></div>
     </div>
   </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
-    </nav></aside></div>
+    </nav></aside>
+</div>
 
 
     <footer><div class="nest">
   <p>tern is a part of the <strong>NEST</strong> and <a href="https://pharmaverse.org/" class="external-link"><strong>pharmaverse</strong></a>.</p>
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-<script type="text/javascript" src="../analytics.js"></script></footer></div>
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diff --git a/main/reference/format_extreme_values_ci.html b/main/reference/format_extreme_values_ci.html
index eed01c43a3..2e9d0cab06 100644
--- a/main/reference/format_extreme_values_ci.html
+++ b/main/reference/format_extreme_values_ci.html
@@ -1,9 +1,32 @@
-<!DOCTYPE html>
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+<meta name="description" content='
 Formatting Function for extreme values part of a confidence interval. Values
-are formatted as e.g. "(xx.xx, xx.xx)" if the number of digits is 2.'><meta property="og:description" content='
+are formatted as e.g. "(xx.xx, xx.xx)" if the number of digits is 2.'>
+<meta property="og:description" content='
 Formatting Function for extreme values part of a confidence interval. Values
-are formatted as e.g. "(xx.xx, xx.xx)" if the number of digits is 2.'><meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png"><link rel="stylesheet" href="../consent.css"><script src="../consent.js" type="text/javascript" charset="utf-8"></script></head><body>
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@@ -19,26 +42,66 @@
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+</div>
 
 
   </div>
@@ -57,25 +120,32 @@
     </div>
 
     <div class="section level2">
-    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
+    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">format_extreme_values_ci</span><span class="op">(</span>digits <span class="op">=</span> <span class="fl">2L</span><span class="op">)</span></span></code></pre></div>
     </div>
 
     <div class="section level2">
-    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
+    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a>
+</h2>
 
 
-<dl><dt id="arg-digits">digits<a class="anchor" aria-label="anchor" href="#arg-digits"></a></dt>
+<dl>
+<dt id="arg-digits">digits<a class="anchor" aria-label="anchor" href="#arg-digits"></a>
+</dt>
 <dd><p>(<code>integer(1)</code>)<br> number of decimal places to display.</p></dd>
 
-</dl></div>
+</dl>
+</div>
     <div class="section level2">
-    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
+    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a>
+</h2>
     <p>An <code>rtables</code> formatting function that uses threshold <code>digits</code> to return a formatted extreme
 values confidence interval.</p>
     </div>
     <div class="section level2">
-    <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"></a></h2>
+    <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"></a>
+</h2>
     <div class="dont-index"><p>Other formatting functions:
 <code><a href="extreme_format.html">extreme_format</a></code>,
 <code><a href="format_auto.html">format_auto</a>()</code>,
@@ -92,7 +162,8 @@ <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"
     </div>
 
     <div class="section level2">
-    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
+    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">format_fun</span> <span class="op">&lt;-</span> <span class="fu">format_extreme_values_ci</span><span class="op">(</span><span class="fl">2L</span><span class="op">)</span></span></span>
 <span class="r-in"><span><span class="fu">format_fun</span><span class="op">(</span>x <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">0.127</span>, <span class="cn">Inf</span><span class="op">)</span><span class="op">)</span></span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> [1] "(0.13, &gt;999.99)"</span>
@@ -102,17 +173,19 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 </code></pre></div>
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diff --git a/main/reference/format_fraction.html b/main/reference/format_fraction.html
index 078cc8e075..73cfb1ce83 100644
--- a/main/reference/format_fraction.html
+++ b/main/reference/format_fraction.html
@@ -1,7 +1,30 @@
-<!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Format fraction and percentage — format_fraction • tern</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Format fraction and percentage — format_fraction"><meta name="description" content="
-Formats a fraction together with ratio in percent."><meta property="og:description" content="
-Formats a fraction together with ratio in percent."><meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png"><link rel="stylesheet" href="../consent.css"><script src="../consent.js" type="text/javascript" charset="utf-8"></script></head><body>
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+<title>Format fraction and percentage — format_fraction • tern</title>
+<!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png">
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+<meta name="description" content="
+Formats a fraction together with ratio in percent.">
+<meta property="og:description" content="
+Formats a fraction together with ratio in percent.">
+<meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png">
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@@ -17,26 +40,66 @@
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-  </ul></li>
-      </ul><ul class="navbar-nav"><li class="nav-item"><form class="form-inline" role="search">
- <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json"></form></li>
+  </ul>
+</li>
+      <div><li class="nav-item dropdown">
+    <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-versions">Versions</a>
+    <div class="dropdown-menu" aria-labelledby="dropdown-versions">
+    <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/main">main</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.5">v0.9.5</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.4">v0.9.4</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.3">v0.9.3</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1-rc3">v0.9.1-rc3</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a>
+</div>
+</li></div>
+</ul>
+<ul class="navbar-nav">
+<li class="nav-item"><form class="form-inline" role="search">
+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json">
+</form></li>
 <li class="nav-item"><a class="external-link nav-link" href="https://github.com/insightsengineering/tern" aria-label="GitHub"><span class="fa fa-github"></span></a></li>
-      </ul></div>
+      </ul>
+</div>
 
 
   </div>
@@ -54,28 +117,36 @@
     </div>
 
     <div class="section level2">
-    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
+    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">format_fraction</span><span class="op">(</span><span class="va">x</span>, <span class="va">...</span><span class="op">)</span></span></code></pre></div>
     </div>
 
     <div class="section level2">
-    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
+    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a>
+</h2>
 
 
-<dl><dt id="arg-x">x<a class="anchor" aria-label="anchor" href="#arg-x"></a></dt>
+<dl>
+<dt id="arg-x">x<a class="anchor" aria-label="anchor" href="#arg-x"></a>
+</dt>
 <dd><p>(named <code>integer</code>)<br> vector with elements <code>num</code> and <code>denom</code>.</p></dd>
 
 
-<dt id="arg--">...<a class="anchor" aria-label="anchor" href="#arg--"></a></dt>
+<dt id="arg--">...<a class="anchor" aria-label="anchor" href="#arg--"></a>
+</dt>
 <dd><p>not used. Required for <code>rtables</code> interface.</p></dd>
 
-</dl></div>
+</dl>
+</div>
     <div class="section level2">
-    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
+    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a>
+</h2>
     <p>A string in the format <code>num / denom (ratio %)</code>. If <code>num</code> is 0, the format is <code>num / denom</code>.</p>
     </div>
     <div class="section level2">
-    <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"></a></h2>
+    <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"></a>
+</h2>
     <div class="dont-index"><p>Other formatting functions:
 <code><a href="extreme_format.html">extreme_format</a></code>,
 <code><a href="format_auto.html">format_auto</a>()</code>,
@@ -92,7 +163,8 @@ <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"
     </div>
 
     <div class="section level2">
-    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
+    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="fu">format_fraction</span><span class="op">(</span>x <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>num <span class="op">=</span> <span class="fl">2L</span>, denom <span class="op">=</span> <span class="fl">3L</span><span class="op">)</span><span class="op">)</span></span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> [1] "2/3 (66.7%)"</span>
 <span class="r-in"><span><span class="fu">format_fraction</span><span class="op">(</span>x <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>num <span class="op">=</span> <span class="fl">0L</span>, denom <span class="op">=</span> <span class="fl">3L</span><span class="op">)</span><span class="op">)</span></span></span>
@@ -101,17 +173,19 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 </code></pre></div>
     </div>
   </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
-    </nav></aside></div>
+    </nav></aside>
+</div>
 
 
     <footer><div class="nest">
   <p>tern is a part of the <strong>NEST</strong> and <a href="https://pharmaverse.org/" class="external-link"><strong>pharmaverse</strong></a>.</p>
 </div>
-<script type="text/javascript" src="../analytics.js"></script></footer></div>
-
+<script type="text/javascript" src="../analytics.js"></script></footer>
+</div>
 
 
 
 
-  </body></html>
 
+  </body>
+</html>
diff --git a/main/reference/format_fraction_fixed_dp.html b/main/reference/format_fraction_fixed_dp.html
index 2c9143dd0b..5a641051bb 100644
--- a/main/reference/format_fraction_fixed_dp.html
+++ b/main/reference/format_fraction_fixed_dp.html
@@ -1,9 +1,32 @@
-<!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Format fraction and percentage with fixed single decimal place — format_fraction_fixed_dp • tern</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Format fraction and percentage with fixed single decimal place — format_fraction_fixed_dp"><meta name="description" content="
+<html lang="en">
+<head>
+<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+<meta charset="utf-8">
+<meta http-equiv="X-UA-Compatible" content="IE=edge">
+<meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<title>Format fraction and percentage with fixed single decimal place — format_fraction_fixed_dp • tern</title>
+<!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png">
+<link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png">
+<link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png">
+<link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png">
+<link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png">
+<link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png">
+<script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet">
+<script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet">
+<link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet">
+<script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Format fraction and percentage with fixed single decimal place — format_fraction_fixed_dp">
+<meta name="description" content="
 Formats a fraction together with ratio in percent with fixed single decimal place.
-Includes trailing zero in case of whole number percentages to always keep one decimal place."><meta property="og:description" content="
+Includes trailing zero in case of whole number percentages to always keep one decimal place.">
+<meta property="og:description" content="
 Formats a fraction together with ratio in percent with fixed single decimal place.
-Includes trailing zero in case of whole number percentages to always keep one decimal place."><meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png"><link rel="stylesheet" href="../consent.css"><script src="../consent.js" type="text/javascript" charset="utf-8"></script></head><body>
+Includes trailing zero in case of whole number percentages to always keep one decimal place.">
+<meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png">
+<link rel="stylesheet" href="../consent.css">
+<script src="../consent.js" type="text/javascript" charset="utf-8"></script>
+</head>
+<body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
 
 
@@ -19,26 +42,66 @@
     </button>
 
     <div id="navbar" class="collapse navbar-collapse ms-3">
-      <ul class="navbar-nav me-auto"><li class="nav-item"><a class="nav-link" href="../articles/tern.html">Get started</a></li>
+      <ul class="navbar-nav me-auto">
+<li class="nav-item"><a class="nav-link" href="../articles/tern.html">Get started</a></li>
 <li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
 <li class="nav-item dropdown">
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-articles" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Articles</button>
-  <ul class="dropdown-menu" aria-labelledby="dropdown-articles"><li><a class="dropdown-item" href="../articles/missing_values.html">Missing Values in Tern</a></li>
+  <ul class="dropdown-menu" aria-labelledby="dropdown-articles">
+<li><a class="dropdown-item" href="../articles/missing_values.html">Missing Values in Tern</a></li>
     <li><a class="dropdown-item" href="../articles/tables.html">Tabulation</a></li>
     <li><a class="dropdown-item" href="../articles/tern_formats.html">Formatting Functions</a></li>
     <li><a class="dropdown-item" href="../articles/tern_functions_guide.html">Understanding `tern` functions</a></li>
-  </ul></li>
+  </ul>
+</li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
-  <ul class="dropdown-menu" aria-labelledby="dropdown-reports"><li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
+  <ul class="dropdown-menu" aria-labelledby="dropdown-reports">
+<li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
     <li><a class="dropdown-item" href="../unit-test-report/">Unit test report</a></li>
     <li><a class="dropdown-item" href="../unit-test-report-non-cran/">Non-CRAN unit test report</a></li>
-  </ul></li>
-      </ul><ul class="navbar-nav"><li class="nav-item"><form class="form-inline" role="search">
- <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json"></form></li>
+  </ul>
+</li>
+      <div><li class="nav-item dropdown">
+    <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-versions">Versions</a>
+    <div class="dropdown-menu" aria-labelledby="dropdown-versions">
+    <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/main">main</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.5">v0.9.5</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.4">v0.9.4</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.3">v0.9.3</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1-rc3">v0.9.1-rc3</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a>
+</div>
+</li></div>
+</ul>
+<ul class="navbar-nav">
+<li class="nav-item"><form class="form-inline" role="search">
+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json">
+</form></li>
 <li class="nav-item"><a class="external-link nav-link" href="https://github.com/insightsengineering/tern" aria-label="GitHub"><span class="fa fa-github"></span></a></li>
-      </ul></div>
+      </ul>
+</div>
 
 
   </div>
@@ -57,28 +120,36 @@
     </div>
 
     <div class="section level2">
-    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
+    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">format_fraction_fixed_dp</span><span class="op">(</span><span class="va">x</span>, <span class="va">...</span><span class="op">)</span></span></code></pre></div>
     </div>
 
     <div class="section level2">
-    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
+    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a>
+</h2>
 
 
-<dl><dt id="arg-x">x<a class="anchor" aria-label="anchor" href="#arg-x"></a></dt>
+<dl>
+<dt id="arg-x">x<a class="anchor" aria-label="anchor" href="#arg-x"></a>
+</dt>
 <dd><p>(named <code>integer</code>)<br> vector with elements <code>num</code> and <code>denom</code>.</p></dd>
 
 
-<dt id="arg--">...<a class="anchor" aria-label="anchor" href="#arg--"></a></dt>
+<dt id="arg--">...<a class="anchor" aria-label="anchor" href="#arg--"></a>
+</dt>
 <dd><p>not used. Required for <code>rtables</code> interface.</p></dd>
 
-</dl></div>
+</dl>
+</div>
     <div class="section level2">
-    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
+    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a>
+</h2>
     <p>A string in the format <code>num / denom (ratio %)</code>. If <code>num</code> is 0, the format is <code>num / denom</code>.</p>
     </div>
     <div class="section level2">
-    <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"></a></h2>
+    <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"></a>
+</h2>
     <div class="dont-index"><p>Other formatting functions:
 <code><a href="extreme_format.html">extreme_format</a></code>,
 <code><a href="format_auto.html">format_auto</a>()</code>,
@@ -95,7 +166,8 @@ <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"
     </div>
 
     <div class="section level2">
-    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
+    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="fu">format_fraction_fixed_dp</span><span class="op">(</span>x <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>num <span class="op">=</span> <span class="fl">1L</span>, denom <span class="op">=</span> <span class="fl">2L</span><span class="op">)</span><span class="op">)</span></span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> [1] "1/2 (50.0%)"</span>
 <span class="r-in"><span><span class="fu">format_fraction_fixed_dp</span><span class="op">(</span>x <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>num <span class="op">=</span> <span class="fl">1L</span>, denom <span class="op">=</span> <span class="fl">4L</span><span class="op">)</span><span class="op">)</span></span></span>
@@ -106,17 +178,19 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 </code></pre></div>
     </div>
   </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
-    </nav></aside></div>
+    </nav></aside>
+</div>
 
 
     <footer><div class="nest">
   <p>tern is a part of the <strong>NEST</strong> and <a href="https://pharmaverse.org/" class="external-link"><strong>pharmaverse</strong></a>.</p>
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-<script type="text/javascript" src="../analytics.js"></script></footer></div>
-
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diff --git a/main/reference/format_fraction_threshold.html b/main/reference/format_fraction_threshold.html
index 79fb23fd17..f3c763fa5d 100644
--- a/main/reference/format_fraction_threshold.html
+++ b/main/reference/format_fraction_threshold.html
@@ -1,9 +1,32 @@
-<!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Format fraction with lower threshold — format_fraction_threshold • tern</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Format fraction with lower threshold — format_fraction_threshold"><meta name="description" content="
+<html lang="en">
+<head>
+<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+<meta charset="utf-8">
+<meta http-equiv="X-UA-Compatible" content="IE=edge">
+<meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<title>Format fraction with lower threshold — format_fraction_threshold • tern</title>
+<!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png">
+<link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png">
+<link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png">
+<link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png">
+<link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png">
+<link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png">
+<script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet">
+<script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet">
+<link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet">
+<script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Format fraction with lower threshold — format_fraction_threshold">
+<meta name="description" content="
 Formats a fraction when the second element of the input x is the fraction. It applies
-a lower threshold, below which it is just stated that the fraction is smaller than that."><meta property="og:description" content="
+a lower threshold, below which it is just stated that the fraction is smaller than that.">
+<meta property="og:description" content="
 Formats a fraction when the second element of the input x is the fraction. It applies
-a lower threshold, below which it is just stated that the fraction is smaller than that."><meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png"><link rel="stylesheet" href="../consent.css"><script src="../consent.js" type="text/javascript" charset="utf-8"></script></head><body>
+a lower threshold, below which it is just stated that the fraction is smaller than that.">
+<meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png">
+<link rel="stylesheet" href="../consent.css">
+<script src="../consent.js" type="text/javascript" charset="utf-8"></script>
+</head>
+<body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
 
 
@@ -19,26 +42,66 @@
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+  <ul class="dropdown-menu" aria-labelledby="dropdown-articles">
+<li><a class="dropdown-item" href="../articles/missing_values.html">Missing Values in Tern</a></li>
     <li><a class="dropdown-item" href="../articles/tables.html">Tabulation</a></li>
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     <li><a class="dropdown-item" href="../articles/tern_functions_guide.html">Understanding `tern` functions</a></li>
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+  </ul>
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+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
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+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a>
+</div>
+</li></div>
+</ul>
+<ul class="navbar-nav">
+<li class="nav-item"><form class="form-inline" role="search">
+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json">
+</form></li>
 <li class="nav-item"><a class="external-link nav-link" href="https://github.com/insightsengineering/tern" aria-label="GitHub"><span class="fa fa-github"></span></a></li>
-      </ul></div>
+      </ul>
+</div>
 
 
   </div>
@@ -57,27 +120,34 @@
     </div>
 
     <div class="section level2">
-    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
+    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">format_fraction_threshold</span><span class="op">(</span><span class="va">threshold</span><span class="op">)</span></span></code></pre></div>
     </div>
 
     <div class="section level2">
-    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
+    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a>
+</h2>
 
 
-<dl><dt id="arg-threshold">threshold<a class="anchor" aria-label="anchor" href="#arg-threshold"></a></dt>
+<dl>
+<dt id="arg-threshold">threshold<a class="anchor" aria-label="anchor" href="#arg-threshold"></a>
+</dt>
 <dd><p>(<code>proportion</code>)<br> lower threshold.</p></dd>
 
-</dl></div>
+</dl>
+</div>
     <div class="section level2">
-    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
+    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a>
+</h2>
     <p>An <code>rtables</code> formatting function that takes numeric input <code>x</code> where the second
 element is the fraction that is formatted. If the fraction is above or equal to the threshold,
 then it is displayed in percentage. If it is positive but below the threshold, it returns,
 e.g. "&lt;1" if the threshold is <code>0.01</code>. If it is zero, then just "0" is returned.</p>
     </div>
     <div class="section level2">
-    <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"></a></h2>
+    <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"></a>
+</h2>
     <div class="dont-index"><p>Other formatting functions:
 <code><a href="extreme_format.html">extreme_format</a></code>,
 <code><a href="format_auto.html">format_auto</a>()</code>,
@@ -94,7 +164,8 @@ <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"
     </div>
 
     <div class="section level2">
-    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
+    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">format_fun</span> <span class="op">&lt;-</span> <span class="fu">format_fraction_threshold</span><span class="op">(</span><span class="fl">0.05</span><span class="op">)</span></span></span>
 <span class="r-in"><span><span class="fu">format_fun</span><span class="op">(</span>x <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">20</span>, <span class="fl">0.1</span><span class="op">)</span><span class="op">)</span></span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> [1] 10</span>
@@ -106,17 +177,19 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 </code></pre></div>
     </div>
   </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
-    </nav></aside></div>
+    </nav></aside>
+</div>
 
 
     <footer><div class="nest">
   <p>tern is a part of the <strong>NEST</strong> and <a href="https://pharmaverse.org/" class="external-link"><strong>pharmaverse</strong></a>.</p>
 </div>
-<script type="text/javascript" src="../analytics.js"></script></footer></div>
-
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+</div>
 
 
 
 
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diff --git a/main/reference/format_sigfig.html b/main/reference/format_sigfig.html
index fb3e969182..a21a472fce 100644
--- a/main/reference/format_sigfig.html
+++ b/main/reference/format_sigfig.html
@@ -1,5 +1,28 @@
-<!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Format numeric values by significant figures — format_sigfig • tern</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Format numeric values by significant figures — format_sigfig"><meta name="description" content="Format numeric values to print with a specified number of significant figures."><meta property="og:description" content="Format numeric values to print with a specified number of significant figures."><meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png"><link rel="stylesheet" href="../consent.css"><script src="../consent.js" type="text/javascript" charset="utf-8"></script></head><body>
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+<title>Format numeric values by significant figures — format_sigfig • tern</title>
+<!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png">
+<link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png">
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+<link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png">
+<script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet">
+<script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet">
+<link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet">
+<script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Format numeric values by significant figures — format_sigfig">
+<meta name="description" content="Format numeric values to print with a specified number of significant figures.">
+<meta property="og:description" content="Format numeric values to print with a specified number of significant figures.">
+<meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png">
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+</head>
+<body>
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@@ -15,26 +38,66 @@
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-      <ul class="navbar-nav me-auto"><li class="nav-item"><a class="nav-link" href="../articles/tern.html">Get started</a></li>
+      <ul class="navbar-nav me-auto">
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+  <ul class="dropdown-menu" aria-labelledby="dropdown-articles">
+<li><a class="dropdown-item" href="../articles/missing_values.html">Missing Values in Tern</a></li>
     <li><a class="dropdown-item" href="../articles/tables.html">Tabulation</a></li>
     <li><a class="dropdown-item" href="../articles/tern_formats.html">Formatting Functions</a></li>
     <li><a class="dropdown-item" href="../articles/tern_functions_guide.html">Understanding `tern` functions</a></li>
-  </ul></li>
+  </ul>
+</li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
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   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
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+  <ul class="dropdown-menu" aria-labelledby="dropdown-reports">
+<li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
     <li><a class="dropdown-item" href="../unit-test-report/">Unit test report</a></li>
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- <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json"></form></li>
+  </ul>
+</li>
+      <div><li class="nav-item dropdown">
+    <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-versions">Versions</a>
+    <div class="dropdown-menu" aria-labelledby="dropdown-versions">
+    <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/main">main</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.5">v0.9.5</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.4">v0.9.4</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.3">v0.9.3</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1-rc3">v0.9.1-rc3</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a>
+</div>
+</li></div>
+</ul>
+<ul class="navbar-nav">
+<li class="nav-item"><form class="form-inline" role="search">
+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json">
+</form></li>
 <li class="nav-item"><a class="external-link nav-link" href="https://github.com/insightsengineering/tern" aria-label="GitHub"><span class="fa fa-github"></span></a></li>
-      </ul></div>
+      </ul>
+</div>
 
 
   </div>
@@ -51,37 +114,46 @@
     </div>
 
     <div class="section level2">
-    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
+    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">format_sigfig</span><span class="op">(</span><span class="va">sigfig</span>, format <span class="op">=</span> <span class="st">"xx"</span>, num_fmt <span class="op">=</span> <span class="st">"fg"</span><span class="op">)</span></span></code></pre></div>
     </div>
 
     <div class="section level2">
-    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
+    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a>
+</h2>
 
 
-<dl><dt id="arg-sigfig">sigfig<a class="anchor" aria-label="anchor" href="#arg-sigfig"></a></dt>
+<dl>
+<dt id="arg-sigfig">sigfig<a class="anchor" aria-label="anchor" href="#arg-sigfig"></a>
+</dt>
 <dd><p>(<code>integer(1)</code>)<br> number of significant figures to display.</p></dd>
 
 
-<dt id="arg-format">format<a class="anchor" aria-label="anchor" href="#arg-format"></a></dt>
+<dt id="arg-format">format<a class="anchor" aria-label="anchor" href="#arg-format"></a>
+</dt>
 <dd><p>(<code>string</code>)<br> the format label (string) to apply when printing the value. Decimal
 places in string are ignored in favor of formatting by significant figures. Formats options are:
 <code>"xx"</code>, <code>"xx / xx"</code>, <code>"(xx, xx)"</code>, <code>"xx - xx"</code>, and <code>"xx (xx)"</code>.</p></dd>
 
 
-<dt id="arg-num-fmt">num_fmt<a class="anchor" aria-label="anchor" href="#arg-num-fmt"></a></dt>
+<dt id="arg-num-fmt">num_fmt<a class="anchor" aria-label="anchor" href="#arg-num-fmt"></a>
+</dt>
 <dd><p>(<code>string</code>)<br> numeric format modifiers to apply to the value. Defaults to <code>"fg"</code> for
 standard significant figures formatting - fixed (non-scientific notation) format (<code>"f"</code>)
 and <code>sigfig</code> equal to number of significant figures instead of decimal places (<code>"g"</code>). See the
 <code><a href="https://rdrr.io/r/base/formatc.html" class="external-link">formatC()</a></code> <code>format</code> argument for more options.</p></dd>
 
-</dl></div>
+</dl>
+</div>
     <div class="section level2">
-    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
+    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a>
+</h2>
     <p>An <code>rtables</code> formatting function.</p>
     </div>
     <div class="section level2">
-    <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"></a></h2>
+    <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"></a>
+</h2>
     <div class="dont-index"><p>Other formatting functions:
 <code><a href="extreme_format.html">extreme_format</a></code>,
 <code><a href="format_auto.html">format_auto</a>()</code>,
@@ -98,7 +170,8 @@ <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"
     </div>
 
     <div class="section level2">
-    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
+    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">fmt_3sf</span> <span class="op">&lt;-</span> <span class="fu">format_sigfig</span><span class="op">(</span><span class="fl">3</span><span class="op">)</span></span></span>
 <span class="r-in"><span><span class="fu">fmt_3sf</span><span class="op">(</span><span class="fl">1.658</span><span class="op">)</span></span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> [1] "1.66"</span>
@@ -114,17 +187,19 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 </code></pre></div>
     </div>
   </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
-    </nav></aside></div>
+    </nav></aside>
+</div>
 
 
     <footer><div class="nest">
   <p>tern is a part of the <strong>NEST</strong> and <a href="https://pharmaverse.org/" class="external-link"><strong>pharmaverse</strong></a>.</p>
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-<script type="text/javascript" src="../analytics.js"></script></footer></div>
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+<script type="text/javascript" src="../analytics.js"></script></footer>
+</div>
 
 
 
 
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+  </body>
+</html>
diff --git a/main/reference/format_xx.html b/main/reference/format_xx.html
index e450075362..93d5eeb243 100644
--- a/main/reference/format_xx.html
+++ b/main/reference/format_xx.html
@@ -1,7 +1,30 @@
-<!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Format XX as a formatting function — format_xx • tern</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Format XX as a formatting function — format_xx"><meta name="description" content="Translate a string where x and dots are interpreted as number place
-holders, and others as formatting elements."><meta property="og:description" content="Translate a string where x and dots are interpreted as number place
-holders, and others as formatting elements."><meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png"><link rel="stylesheet" href="../consent.css"><script src="../consent.js" type="text/javascript" charset="utf-8"></script></head><body>
+<html lang="en">
+<head>
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+<meta charset="utf-8">
+<meta http-equiv="X-UA-Compatible" content="IE=edge">
+<meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<title>Format XX as a formatting function — format_xx • tern</title>
+<!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png">
+<link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png">
+<link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png">
+<link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png">
+<link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png">
+<link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png">
+<script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet">
+<script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet">
+<link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet">
+<script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Format XX as a formatting function — format_xx">
+<meta name="description" content="Translate a string where x and dots are interpreted as number place
+holders, and others as formatting elements.">
+<meta property="og:description" content="Translate a string where x and dots are interpreted as number place
+holders, and others as formatting elements.">
+<meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png">
+<link rel="stylesheet" href="../consent.css">
+<script src="../consent.js" type="text/javascript" charset="utf-8"></script>
+</head>
+<body>
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@@ -17,26 +40,66 @@
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+  <ul class="dropdown-menu" aria-labelledby="dropdown-articles">
+<li><a class="dropdown-item" href="../articles/missing_values.html">Missing Values in Tern</a></li>
     <li><a class="dropdown-item" href="../articles/tables.html">Tabulation</a></li>
     <li><a class="dropdown-item" href="../articles/tern_formats.html">Formatting Functions</a></li>
     <li><a class="dropdown-item" href="../articles/tern_functions_guide.html">Understanding `tern` functions</a></li>
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+  </ul>
+</li>
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+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
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+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1-rc3">v0.9.1-rc3</a>
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+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a>
+</div>
+</li></div>
+</ul>
+<ul class="navbar-nav">
+<li class="nav-item"><form class="form-inline" role="search">
+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json">
+</form></li>
 <li class="nav-item"><a class="external-link nav-link" href="https://github.com/insightsengineering/tern" aria-label="GitHub"><span class="fa fa-github"></span></a></li>
-      </ul></div>
+      </ul>
+</div>
 
 
   </div>
@@ -54,24 +117,31 @@
     </div>
 
     <div class="section level2">
-    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
+    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">format_xx</span><span class="op">(</span><span class="va">str</span><span class="op">)</span></span></code></pre></div>
     </div>
 
     <div class="section level2">
-    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
+    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a>
+</h2>
 
 
-<dl><dt id="arg-str">str<a class="anchor" aria-label="anchor" href="#arg-str"></a></dt>
+<dl>
+<dt id="arg-str">str<a class="anchor" aria-label="anchor" href="#arg-str"></a>
+</dt>
 <dd><p>(<code>string</code>)<br> template.</p></dd>
 
-</dl></div>
+</dl>
+</div>
     <div class="section level2">
-    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
+    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a>
+</h2>
     <p>An <code>rtables</code> formatting function.</p>
     </div>
     <div class="section level2">
-    <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"></a></h2>
+    <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"></a>
+</h2>
     <div class="dont-index"><p>Other formatting functions:
 <code><a href="extreme_format.html">extreme_format</a></code>,
 <code><a href="format_auto.html">format_auto</a>()</code>,
@@ -88,7 +158,8 @@ <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"
     </div>
 
     <div class="section level2">
-    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
+    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">test</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">1.658</span>, <span class="fl">0.5761</span><span class="op">)</span>, <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">1e1</span>, <span class="fl">785.6</span><span class="op">)</span><span class="op">)</span></span></span>
 <span class="r-in"><span></span></span>
 <span class="r-in"><span><span class="va">z</span> <span class="op">&lt;-</span> <span class="fu">format_xx</span><span class="op">(</span><span class="st">"xx (xx.x)"</span><span class="op">)</span></span></span>
@@ -106,17 +177,19 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 </code></pre></div>
     </div>
   </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
-    </nav></aside></div>
+    </nav></aside>
+</div>
 
 
     <footer><div class="nest">
   <p>tern is a part of the <strong>NEST</strong> and <a href="https://pharmaverse.org/" class="external-link"><strong>pharmaverse</strong></a>.</p>
 </div>
-<script type="text/javascript" src="../analytics.js"></script></footer></div>
-
+<script type="text/javascript" src="../analytics.js"></script></footer>
+</div>
 
 
 
 
-  </body></html>
 
+  </body>
+</html>
diff --git a/main/reference/formatting_functions.html b/main/reference/formatting_functions.html
index 9612cdcb65..518b294489 100644
--- a/main/reference/formatting_functions.html
+++ b/main/reference/formatting_functions.html
@@ -1,5 +1,28 @@
-<!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Formatting functions — formatting_functions • tern</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Formatting functions — formatting_functions"><meta name="description" content="See below for the list of formatting functions created in tern to work with rtables."><meta property="og:description" content="See below for the list of formatting functions created in tern to work with rtables."><meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png"><link rel="stylesheet" href="../consent.css"><script src="../consent.js" type="text/javascript" charset="utf-8"></script></head><body>
+<html lang="en">
+<head>
+<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+<meta charset="utf-8">
+<meta http-equiv="X-UA-Compatible" content="IE=edge">
+<meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<title>Formatting functions — formatting_functions • tern</title>
+<!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png">
+<link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png">
+<link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png">
+<link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png">
+<link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png">
+<link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png">
+<script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet">
+<script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet">
+<link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet">
+<script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Formatting functions — formatting_functions">
+<meta name="description" content="See below for the list of formatting functions created in tern to work with rtables.">
+<meta property="og:description" content="See below for the list of formatting functions created in tern to work with rtables.">
+<meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png">
+<link rel="stylesheet" href="../consent.css">
+<script src="../consent.js" type="text/javascript" charset="utf-8"></script>
+</head>
+<body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
 
 
@@ -15,26 +38,66 @@
     </button>
 
     <div id="navbar" class="collapse navbar-collapse ms-3">
-      <ul class="navbar-nav me-auto"><li class="nav-item"><a class="nav-link" href="../articles/tern.html">Get started</a></li>
+      <ul class="navbar-nav me-auto">
+<li class="nav-item"><a class="nav-link" href="../articles/tern.html">Get started</a></li>
 <li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
 <li class="nav-item dropdown">
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-articles" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Articles</button>
-  <ul class="dropdown-menu" aria-labelledby="dropdown-articles"><li><a class="dropdown-item" href="../articles/missing_values.html">Missing Values in Tern</a></li>
+  <ul class="dropdown-menu" aria-labelledby="dropdown-articles">
+<li><a class="dropdown-item" href="../articles/missing_values.html">Missing Values in Tern</a></li>
     <li><a class="dropdown-item" href="../articles/tables.html">Tabulation</a></li>
     <li><a class="dropdown-item" href="../articles/tern_formats.html">Formatting Functions</a></li>
     <li><a class="dropdown-item" href="../articles/tern_functions_guide.html">Understanding `tern` functions</a></li>
-  </ul></li>
+  </ul>
+</li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
-  <ul class="dropdown-menu" aria-labelledby="dropdown-reports"><li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
+  <ul class="dropdown-menu" aria-labelledby="dropdown-reports">
+<li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
     <li><a class="dropdown-item" href="../unit-test-report/">Unit test report</a></li>
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- <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json"></form></li>
+  </ul>
+</li>
+      <div><li class="nav-item dropdown">
+    <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-versions">Versions</a>
+    <div class="dropdown-menu" aria-labelledby="dropdown-versions">
+    <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/main">main</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.5">v0.9.5</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.4">v0.9.4</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.3">v0.9.3</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1-rc3">v0.9.1-rc3</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a>
+</div>
+</li></div>
+</ul>
+<ul class="navbar-nav">
+<li class="nav-item"><form class="form-inline" role="search">
+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json">
+</form></li>
 <li class="nav-item"><a class="external-link nav-link" href="https://github.com/insightsengineering/tern" aria-label="GitHub"><span class="fa fa-github"></span></a></li>
-      </ul></div>
+      </ul>
+</div>
 
 
   </div>
@@ -52,12 +115,14 @@
 
 
     <div class="section level2">
-    <h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a></h2>
+    <h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a>
+</h2>
     <p>Other available formats can be listed via <code><a href="https://insightsengineering.github.io/formatters/latest-tag/reference/list_formats.html" class="external-link">formatters::list_valid_format_labels()</a></code>. Additional
 custom formats can be created via the <code><a href="https://insightsengineering.github.io/formatters/latest-tag/reference/sprintf_format.html" class="external-link">formatters::sprintf_format()</a></code> function.</p>
     </div>
     <div class="section level2">
-    <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"></a></h2>
+    <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"></a>
+</h2>
     <div class="dont-index"><p>Other formatting functions:
 <code><a href="extreme_format.html">extreme_format</a></code>,
 <code><a href="format_auto.html">format_auto</a>()</code>,
@@ -74,17 +139,19 @@ <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"
     </div>
 
   </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
-    </nav></aside></div>
+    </nav></aside>
+</div>
 
 
     <footer><div class="nest">
   <p>tern is a part of the <strong>NEST</strong> and <a href="https://pharmaverse.org/" class="external-link"><strong>pharmaverse</strong></a>.</p>
 </div>
-<script type="text/javascript" src="../analytics.js"></script></footer></div>
-
+<script type="text/javascript" src="../analytics.js"></script></footer>
+</div>
 
 
 
 
-  </body></html>
 
+  </body>
+</html>
diff --git a/main/reference/g_bland_altman.html b/main/reference/g_bland_altman.html
index 1915c38e88..20ec99e9f8 100644
--- a/main/reference/g_bland_altman.html
+++ b/main/reference/g_bland_altman.html
@@ -1,7 +1,30 @@
-<!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Bland-Altman plot — g_bland_altman • tern</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Bland-Altman plot — g_bland_altman"><meta name="description" content="
-Graphing function that produces a Bland-Altman plot."><meta property="og:description" content="
-Graphing function that produces a Bland-Altman plot."><meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png"><link rel="stylesheet" href="../consent.css"><script src="../consent.js" type="text/javascript" charset="utf-8"></script></head><body>
+<html lang="en">
+<head>
+<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+<meta charset="utf-8">
+<meta http-equiv="X-UA-Compatible" content="IE=edge">
+<meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<title>Bland-Altman plot — g_bland_altman • tern</title>
+<!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png">
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+<link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet">
+<script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Bland-Altman plot — g_bland_altman">
+<meta name="description" content="
+Graphing function that produces a Bland-Altman plot.">
+<meta property="og:description" content="
+Graphing function that produces a Bland-Altman plot.">
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@@ -17,26 +40,66 @@
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+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
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+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a>
+</div>
+</li></div>
+</ul>
+<ul class="navbar-nav">
+<li class="nav-item"><form class="form-inline" role="search">
+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json">
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 <li class="nav-item"><a class="external-link nav-link" href="https://github.com/insightsengineering/tern" aria-label="GitHub"><span class="fa fa-github"></span></a></li>
-      </ul></div>
+      </ul>
+</div>
 
 
   </div>
@@ -54,33 +117,42 @@
     </div>
 
     <div class="section level2">
-    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
+    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">g_bland_altman</span><span class="op">(</span><span class="va">x</span>, <span class="va">y</span>, conf_level <span class="op">=</span> <span class="fl">0.95</span><span class="op">)</span></span></code></pre></div>
     </div>
 
     <div class="section level2">
-    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
+    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a>
+</h2>
 
 
-<dl><dt id="arg-x">x<a class="anchor" aria-label="anchor" href="#arg-x"></a></dt>
+<dl>
+<dt id="arg-x">x<a class="anchor" aria-label="anchor" href="#arg-x"></a>
+</dt>
 <dd><p>(<code>numeric</code>)<br> vector of numbers we want to analyze.</p></dd>
 
 
-<dt id="arg-y">y<a class="anchor" aria-label="anchor" href="#arg-y"></a></dt>
+<dt id="arg-y">y<a class="anchor" aria-label="anchor" href="#arg-y"></a>
+</dt>
 <dd><p>(<code>numeric</code>)<br> vector of numbers we want to analyze, to be compared with <code>x</code>.</p></dd>
 
 
-<dt id="arg-conf-level">conf_level<a class="anchor" aria-label="anchor" href="#arg-conf-level"></a></dt>
+<dt id="arg-conf-level">conf_level<a class="anchor" aria-label="anchor" href="#arg-conf-level"></a>
+</dt>
 <dd><p>(<code>proportion</code>)<br> confidence level of the interval.</p></dd>
 
-</dl></div>
+</dl>
+</div>
     <div class="section level2">
-    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
+    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a>
+</h2>
     <p>A <code>ggplot</code> Bland-Altman plot.</p>
     </div>
 
     <div class="section level2">
-    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
+    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">x</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/seq.html" class="external-link">seq</a></span><span class="op">(</span><span class="fl">1</span>, <span class="fl">60</span>, <span class="fl">5</span><span class="op">)</span></span></span>
 <span class="r-in"><span><span class="va">y</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/seq.html" class="external-link">seq</a></span><span class="op">(</span><span class="fl">5</span>, <span class="fl">50</span>, <span class="fl">4</span><span class="op">)</span></span></span>
 <span class="r-in"><span></span></span>
@@ -90,17 +162,19 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 </code></pre></div>
     </div>
   </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
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index 9182cd5da3..69844f6ace 100644
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+++ b/main/reference/g_forest.html
@@ -1,5 +1,28 @@
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@@ -15,33 +38,74 @@
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+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a>
+</div>
+</li></div>
+</ul>
+<ul class="navbar-nav">
+<li class="nav-item"><form class="form-inline" role="search">
+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json">
+</form></li>
 <li class="nav-item"><a class="external-link nav-link" href="https://github.com/insightsengineering/tern" aria-label="GitHub"><span class="fa fa-github"></span></a></li>
-      </ul></div>
+      </ul>
+</div>
 
 
   </div>
 </nav><div class="container template-reference-topic">
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
-      <img src="../logo.png" class="logo" alt=""><h1>Create a forest plot from an <code>rtable</code></h1>
+      <img src="../logo.png" class="logo" alt=""><h1>Create a forest plot from an <code>rtable</code>
+</h1>
       <small class="dont-index">Source: <a href="https://github.com/insightsengineering/tern/blob/main/R/g_forest.R" class="external-link"><code>R/g_forest.R</code></a></small>
       <div class="d-none name"><code>g_forest.Rd</code></div>
     </div>
@@ -51,7 +115,8 @@
     </div>
 
     <div class="section level2">
-    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
+    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">g_forest</span><span class="op">(</span></span>
 <span>  <span class="va">tbl</span>,</span>
 <span>  col_x <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/attr.html" class="external-link">attr</a></span><span class="op">(</span><span class="va">tbl</span>, <span class="st">"col_x"</span><span class="op">)</span>,</span>
@@ -78,127 +143,154 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
     </div>
 
     <div class="section level2">
-    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
+    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a>
+</h2>
 
 
-<dl><dt id="arg-tbl">tbl<a class="anchor" aria-label="anchor" href="#arg-tbl"></a></dt>
+<dl>
+<dt id="arg-tbl">tbl<a class="anchor" aria-label="anchor" href="#arg-tbl"></a>
+</dt>
 <dd><p>(<code>VTableTree</code>)<br><code>rtables</code> table with at least one column with a single value and one column with 2
 values.</p></dd>
 
 
-<dt id="arg-col-x">col_x<a class="anchor" aria-label="anchor" href="#arg-col-x"></a></dt>
+<dt id="arg-col-x">col_x<a class="anchor" aria-label="anchor" href="#arg-col-x"></a>
+</dt>
 <dd><p>(<code>integer(1)</code> or <code>NULL</code>)<br> column index with estimator. By default tries to get this from
 <code>tbl</code> attribute <code>col_x</code>, otherwise needs to be manually specified. If <code>NULL</code>, points will be excluded
 from forest plot.</p></dd>
 
 
-<dt id="arg-col-ci">col_ci<a class="anchor" aria-label="anchor" href="#arg-col-ci"></a></dt>
+<dt id="arg-col-ci">col_ci<a class="anchor" aria-label="anchor" href="#arg-col-ci"></a>
+</dt>
 <dd><p>(<code>integer(1)</code> or <code>NULL</code>)<br> column index with confidence intervals. By default tries to get this from
 <code>tbl</code> attribute <code>col_ci</code>, otherwise needs to be manually specified. If <code>NULL</code>, lines will be excluded
 from forest plot.</p></dd>
 
 
-<dt id="arg-vline">vline<a class="anchor" aria-label="anchor" href="#arg-vline"></a></dt>
+<dt id="arg-vline">vline<a class="anchor" aria-label="anchor" href="#arg-vline"></a>
+</dt>
 <dd><p>(<code>numeric(1)</code> or <code>NULL</code>)<br> x coordinate for vertical line, if <code>NULL</code> then the line is omitted.</p></dd>
 
 
-<dt id="arg-forest-header">forest_header<a class="anchor" aria-label="anchor" href="#arg-forest-header"></a></dt>
+<dt id="arg-forest-header">forest_header<a class="anchor" aria-label="anchor" href="#arg-forest-header"></a>
+</dt>
 <dd><p>(<code>character(2)</code>)<br> text displayed to the left and right of <code>vline</code>, respectively.
 If <code>vline = NULL</code> then <code>forest_header</code> is not printed. By default tries to get this from <code>tbl</code> attribute
 <code>forest_header</code>. If <code>NULL</code>, defaults will be extracted from the table if possible, and set to
 <code>"Comparison\nBetter"</code> and <code>"Treatment\nBetter"</code> if not.</p></dd>
 
 
-<dt id="arg-xlim">xlim<a class="anchor" aria-label="anchor" href="#arg-xlim"></a></dt>
+<dt id="arg-xlim">xlim<a class="anchor" aria-label="anchor" href="#arg-xlim"></a>
+</dt>
 <dd><p>(<code>numeric(2)</code>)<br> limits for x axis.</p></dd>
 
 
-<dt id="arg-logx">logx<a class="anchor" aria-label="anchor" href="#arg-logx"></a></dt>
+<dt id="arg-logx">logx<a class="anchor" aria-label="anchor" href="#arg-logx"></a>
+</dt>
 <dd><p>(<code>flag</code>)<br> show the x-values on logarithm scale.</p></dd>
 
 
-<dt id="arg-x-at">x_at<a class="anchor" aria-label="anchor" href="#arg-x-at"></a></dt>
+<dt id="arg-x-at">x_at<a class="anchor" aria-label="anchor" href="#arg-x-at"></a>
+</dt>
 <dd><p>(<code>numeric</code>)<br> x-tick locations, if <code>NULL</code>, <code>x_at</code> is set to <code>vline</code> and both <code>xlim</code> values.</p></dd>
 
 
-<dt id="arg-width-row-names">width_row_names<a class="anchor" aria-label="anchor" href="#arg-width-row-names"></a></dt>
+<dt id="arg-width-row-names">width_row_names<a class="anchor" aria-label="anchor" href="#arg-width-row-names"></a>
+</dt>
 <dd><p><a href="https://lifecycle.r-lib.org/articles/stages.html#deprecated" class="external-link"><img src="figures/lifecycle-deprecated.svg" alt="[Deprecated]"></a> Please use the <code>lbl_col_padding</code> argument instead.</p></dd>
 
 
-<dt id="arg-width-columns">width_columns<a class="anchor" aria-label="anchor" href="#arg-width-columns"></a></dt>
+<dt id="arg-width-columns">width_columns<a class="anchor" aria-label="anchor" href="#arg-width-columns"></a>
+</dt>
 <dd><p>(<code>numeric</code>)<br> a vector of column widths. Each element's position in
 <code>colwidths</code> corresponds to the column of <code>tbl</code> in the same position. If <code>NULL</code>, column widths are calculated
 according to maximum number of characters per column.</p></dd>
 
 
-<dt id="arg-width-forest">width_forest<a class="anchor" aria-label="anchor" href="#arg-width-forest"></a></dt>
+<dt id="arg-width-forest">width_forest<a class="anchor" aria-label="anchor" href="#arg-width-forest"></a>
+</dt>
 <dd><p><a href="https://lifecycle.r-lib.org/articles/stages.html#deprecated" class="external-link"><img src="figures/lifecycle-deprecated.svg" alt="[Deprecated]"></a> Please use the <code>rel_width_forest</code> argument instead.</p></dd>
 
 
-<dt id="arg-lbl-col-padding">lbl_col_padding<a class="anchor" aria-label="anchor" href="#arg-lbl-col-padding"></a></dt>
+<dt id="arg-lbl-col-padding">lbl_col_padding<a class="anchor" aria-label="anchor" href="#arg-lbl-col-padding"></a>
+</dt>
 <dd><p>(<code>numeric</code>)<br> additional padding to use when calculating spacing between
 the first (label) column and the second column of <code>tbl</code>. If <code>colwidths</code> is specified,
 the width of the first column becomes <code>colwidths[1] + lbl_col_padding</code>. Defaults to 0.</p></dd>
 
 
-<dt id="arg-rel-width-forest">rel_width_forest<a class="anchor" aria-label="anchor" href="#arg-rel-width-forest"></a></dt>
+<dt id="arg-rel-width-forest">rel_width_forest<a class="anchor" aria-label="anchor" href="#arg-rel-width-forest"></a>
+</dt>
 <dd><p>(<code>proportion</code>)<br> proportion of total width to allocate to the forest plot. Relative
 width of table is then <code>1 - rel_width_forest</code>. If <code>as_list = TRUE</code>, this parameter is ignored.</p></dd>
 
 
-<dt id="arg-font-size">font_size<a class="anchor" aria-label="anchor" href="#arg-font-size"></a></dt>
+<dt id="arg-font-size">font_size<a class="anchor" aria-label="anchor" href="#arg-font-size"></a>
+</dt>
 <dd><p>(<code>numeric(1)</code>)<br> font size.</p></dd>
 
 
-<dt id="arg-col-symbol-size">col_symbol_size<a class="anchor" aria-label="anchor" href="#arg-col-symbol-size"></a></dt>
+<dt id="arg-col-symbol-size">col_symbol_size<a class="anchor" aria-label="anchor" href="#arg-col-symbol-size"></a>
+</dt>
 <dd><p>(<code>numeric</code> or <code>NULL</code>)<br> column index from <code>tbl</code> containing data to be used
 to determine relative size for estimator plot symbol. Typically, the symbol size is proportional
 to the sample size used to calculate the estimator. If <code>NULL</code>, the same symbol size is used for all subgroups.
 By default tries to get this from <code>tbl</code> attribute <code>col_symbol_size</code>, otherwise needs to be manually specified.</p></dd>
 
 
-<dt id="arg-col">col<a class="anchor" aria-label="anchor" href="#arg-col"></a></dt>
+<dt id="arg-col">col<a class="anchor" aria-label="anchor" href="#arg-col"></a>
+</dt>
 <dd><p>(<code>character</code>)<br> color(s).</p></dd>
 
 
-<dt id="arg-ggtheme">ggtheme<a class="anchor" aria-label="anchor" href="#arg-ggtheme"></a></dt>
+<dt id="arg-ggtheme">ggtheme<a class="anchor" aria-label="anchor" href="#arg-ggtheme"></a>
+</dt>
 <dd><p>(<code>theme</code>)<br> a graphical theme as provided by <code>ggplot2</code> to control styling of the plot.</p></dd>
 
 
-<dt id="arg-as-list">as_list<a class="anchor" aria-label="anchor" href="#arg-as-list"></a></dt>
+<dt id="arg-as-list">as_list<a class="anchor" aria-label="anchor" href="#arg-as-list"></a>
+</dt>
 <dd><p>(<code>flag</code>)<br> whether the two <code>ggplot</code> objects should be returned as a list. If <code>TRUE</code>, a named list
 with two elements, <code>table</code> and <code>plot</code>, will be returned. If <code>FALSE</code> (default) the table and forest plot are
 printed side-by-side via <code><a href="https://wilkelab.org/cowplot/reference/plot_grid.html" class="external-link">cowplot::plot_grid()</a></code>.</p></dd>
 
 
-<dt id="arg-gp">gp<a class="anchor" aria-label="anchor" href="#arg-gp"></a></dt>
+<dt id="arg-gp">gp<a class="anchor" aria-label="anchor" href="#arg-gp"></a>
+</dt>
 <dd><p><a href="https://lifecycle.r-lib.org/articles/stages.html#deprecated" class="external-link"><img src="figures/lifecycle-deprecated.svg" alt="[Deprecated]"></a> <code>g_forest</code> is now generated as a <code>ggplot</code> object. This argument
 is no longer used.</p></dd>
 
 
-<dt id="arg-draw">draw<a class="anchor" aria-label="anchor" href="#arg-draw"></a></dt>
+<dt id="arg-draw">draw<a class="anchor" aria-label="anchor" href="#arg-draw"></a>
+</dt>
 <dd><p><a href="https://lifecycle.r-lib.org/articles/stages.html#deprecated" class="external-link"><img src="figures/lifecycle-deprecated.svg" alt="[Deprecated]"></a> <code>g_forest</code> is now generated as a <code>ggplot</code> object. This argument
 is no longer used.</p></dd>
 
 
-<dt id="arg-newpage">newpage<a class="anchor" aria-label="anchor" href="#arg-newpage"></a></dt>
+<dt id="arg-newpage">newpage<a class="anchor" aria-label="anchor" href="#arg-newpage"></a>
+</dt>
 <dd><p><a href="https://lifecycle.r-lib.org/articles/stages.html#deprecated" class="external-link"><img src="figures/lifecycle-deprecated.svg" alt="[Deprecated]"></a> <code>g_forest</code> is now generated as a <code>ggplot</code> object. This argument
 is no longer used.</p></dd>
 
-</dl></div>
+</dl>
+</div>
     <div class="section level2">
-    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
+    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a>
+</h2>
     <p><code>ggplot</code> forest plot and table.</p>
     </div>
     <div class="section level2">
-    <h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a></h2>
+    <h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a>
+</h2>
     <p>Given a <code><a href="https://insightsengineering.github.io/rtables/latest-tag/reference/rtable.html" class="external-link">rtables::rtable()</a></code> object with at least one column with a single value and one column with 2
 values, converts table to a <code><a href="https://ggplot2.tidyverse.org/reference/ggplot.html" class="external-link">ggplot2::ggplot()</a></code> object and generates an accompanying forest plot. The
 table and forest plot are printed side-by-side.</p>
     </div>
 
     <div class="section level2">
-    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
+    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://dplyr.tidyverse.org" class="external-link">dplyr</a></span><span class="op">)</span></span></span>
 <span class="r-in"><span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://forcats.tidyverse.org/" class="external-link">forcats</a></span><span class="op">)</span></span></span>
 <span class="r-in"><span></span></span>
@@ -312,17 +404,19 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 </code></pre></div>
     </div>
   </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
-    </nav></aside></div>
+    </nav></aside>
+</div>
 
 
     <footer><div class="nest">
   <p>tern is a part of the <strong>NEST</strong> and <a href="https://pharmaverse.org/" class="external-link"><strong>pharmaverse</strong></a>.</p>
 </div>
-<script type="text/javascript" src="../analytics.js"></script></footer></div>
-
+<script type="text/javascript" src="../analytics.js"></script></footer>
+</div>
 
 
 
 
-  </body></html>
 
+  </body>
+</html>
diff --git a/main/reference/g_ipp.html b/main/reference/g_ipp.html
index 98e33162c7..437a70dd9b 100644
--- a/main/reference/g_ipp.html
+++ b/main/reference/g_ipp.html
@@ -1,9 +1,32 @@
-<!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Individual patient plots — g_ipp • tern</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Individual patient plots — g_ipp"><meta name="description" content="
+<html lang="en">
+<head>
+<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+<meta charset="utf-8">
+<meta http-equiv="X-UA-Compatible" content="IE=edge">
+<meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<title>Individual patient plots — g_ipp • tern</title>
+<!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png">
+<link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png">
+<link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png">
+<link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png">
+<link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png">
+<link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png">
+<script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet">
+<script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet">
+<link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet">
+<script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Individual patient plots — g_ipp">
+<meta name="description" content="
 Line plot(s) displaying trend in patients' parameter values over time is rendered.
-Patients' individual baseline values can be added to the plot(s) as reference."><meta property="og:description" content="
+Patients' individual baseline values can be added to the plot(s) as reference.">
+<meta property="og:description" content="
 Line plot(s) displaying trend in patients' parameter values over time is rendered.
-Patients' individual baseline values can be added to the plot(s) as reference."><meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png"><link rel="stylesheet" href="../consent.css"><script src="../consent.js" type="text/javascript" charset="utf-8"></script></head><body>
+Patients' individual baseline values can be added to the plot(s) as reference.">
+<meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png">
+<link rel="stylesheet" href="../consent.css">
+<script src="../consent.js" type="text/javascript" charset="utf-8"></script>
+</head>
+<body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
 
 
@@ -19,26 +42,66 @@
     </button>
 
     <div id="navbar" class="collapse navbar-collapse ms-3">
-      <ul class="navbar-nav me-auto"><li class="nav-item"><a class="nav-link" href="../articles/tern.html">Get started</a></li>
+      <ul class="navbar-nav me-auto">
+<li class="nav-item"><a class="nav-link" href="../articles/tern.html">Get started</a></li>
 <li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
 <li class="nav-item dropdown">
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-articles" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Articles</button>
-  <ul class="dropdown-menu" aria-labelledby="dropdown-articles"><li><a class="dropdown-item" href="../articles/missing_values.html">Missing Values in Tern</a></li>
+  <ul class="dropdown-menu" aria-labelledby="dropdown-articles">
+<li><a class="dropdown-item" href="../articles/missing_values.html">Missing Values in Tern</a></li>
     <li><a class="dropdown-item" href="../articles/tables.html">Tabulation</a></li>
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     <li><a class="dropdown-item" href="../articles/tern_functions_guide.html">Understanding `tern` functions</a></li>
-  </ul></li>
+  </ul>
+</li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
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   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
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+  <ul class="dropdown-menu" aria-labelledby="dropdown-reports">
+<li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
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-  </ul></li>
-      </ul><ul class="navbar-nav"><li class="nav-item"><form class="form-inline" role="search">
- <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json"></form></li>
+  </ul>
+</li>
+      <div><li class="nav-item dropdown">
+    <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-versions">Versions</a>
+    <div class="dropdown-menu" aria-labelledby="dropdown-versions">
+    <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/main">main</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.5">v0.9.5</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.4">v0.9.4</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.3">v0.9.3</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1-rc3">v0.9.1-rc3</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a>
+</div>
+</li></div>
+</ul>
+<ul class="navbar-nav">
+<li class="nav-item"><form class="form-inline" role="search">
+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json">
+</form></li>
 <li class="nav-item"><a class="external-link nav-link" href="https://github.com/insightsengineering/tern" aria-label="GitHub"><span class="fa fa-github"></span></a></li>
-      </ul></div>
+      </ul>
+</div>
 
 
   </div>
@@ -57,7 +120,8 @@
     </div>
 
     <div class="section level2">
-    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
+    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">g_ipp</span><span class="op">(</span></span>
 <span>  <span class="va">df</span>,</span>
 <span>  <span class="va">xvar</span>,</span>
@@ -78,92 +142,116 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
     </div>
 
     <div class="section level2">
-    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
+    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a>
+</h2>
 
 
-<dl><dt id="arg-df">df<a class="anchor" aria-label="anchor" href="#arg-df"></a></dt>
+<dl>
+<dt id="arg-df">df<a class="anchor" aria-label="anchor" href="#arg-df"></a>
+</dt>
 <dd><p>(<code>data.frame</code>)<br> data set containing all analysis variables.</p></dd>
 
 
-<dt id="arg-xvar">xvar<a class="anchor" aria-label="anchor" href="#arg-xvar"></a></dt>
+<dt id="arg-xvar">xvar<a class="anchor" aria-label="anchor" href="#arg-xvar"></a>
+</dt>
 <dd><p>(<code>string</code>)<br> time point variable to be plotted on x-axis.</p></dd>
 
 
-<dt id="arg-yvar">yvar<a class="anchor" aria-label="anchor" href="#arg-yvar"></a></dt>
+<dt id="arg-yvar">yvar<a class="anchor" aria-label="anchor" href="#arg-yvar"></a>
+</dt>
 <dd><p>(<code>string</code>)<br> continuous analysis variable to be plotted on y-axis.</p></dd>
 
 
-<dt id="arg-xlab">xlab<a class="anchor" aria-label="anchor" href="#arg-xlab"></a></dt>
+<dt id="arg-xlab">xlab<a class="anchor" aria-label="anchor" href="#arg-xlab"></a>
+</dt>
 <dd><p>(<code>string</code>)<br> plot label for x-axis.</p></dd>
 
 
-<dt id="arg-ylab">ylab<a class="anchor" aria-label="anchor" href="#arg-ylab"></a></dt>
+<dt id="arg-ylab">ylab<a class="anchor" aria-label="anchor" href="#arg-ylab"></a>
+</dt>
 <dd><p>(<code>string</code>)<br> plot label for y-axis.</p></dd>
 
 
-<dt id="arg-id-var">id_var<a class="anchor" aria-label="anchor" href="#arg-id-var"></a></dt>
+<dt id="arg-id-var">id_var<a class="anchor" aria-label="anchor" href="#arg-id-var"></a>
+</dt>
 <dd><p>(<code>string</code>)<br> variable used as patient identifier.</p></dd>
 
 
-<dt id="arg-title">title<a class="anchor" aria-label="anchor" href="#arg-title"></a></dt>
+<dt id="arg-title">title<a class="anchor" aria-label="anchor" href="#arg-title"></a>
+</dt>
 <dd><p>(<code>string</code>)<br> title for plot.</p></dd>
 
 
-<dt id="arg-subtitle">subtitle<a class="anchor" aria-label="anchor" href="#arg-subtitle"></a></dt>
+<dt id="arg-subtitle">subtitle<a class="anchor" aria-label="anchor" href="#arg-subtitle"></a>
+</dt>
 <dd><p>(<code>string</code>)<br> subtitle for plot.</p></dd>
 
 
-<dt id="arg-caption">caption<a class="anchor" aria-label="anchor" href="#arg-caption"></a></dt>
+<dt id="arg-caption">caption<a class="anchor" aria-label="anchor" href="#arg-caption"></a>
+</dt>
 <dd><p>(<code>string</code>)<br> optional caption below the plot.</p></dd>
 
 
-<dt id="arg-add-baseline-hline">add_baseline_hline<a class="anchor" aria-label="anchor" href="#arg-add-baseline-hline"></a></dt>
+<dt id="arg-add-baseline-hline">add_baseline_hline<a class="anchor" aria-label="anchor" href="#arg-add-baseline-hline"></a>
+</dt>
 <dd><p>(<code>flag</code>)<br> adds horizontal line at baseline y-value on
 plot when <code>TRUE</code>.</p></dd>
 
 
-<dt id="arg-yvar-baseline">yvar_baseline<a class="anchor" aria-label="anchor" href="#arg-yvar-baseline"></a></dt>
+<dt id="arg-yvar-baseline">yvar_baseline<a class="anchor" aria-label="anchor" href="#arg-yvar-baseline"></a>
+</dt>
 <dd><p>(<code>string</code>)<br> variable with baseline values only.
 Ignored when <code>add_baseline_hline</code> is <code>FALSE</code>.</p></dd>
 
 
-<dt id="arg-ggtheme">ggtheme<a class="anchor" aria-label="anchor" href="#arg-ggtheme"></a></dt>
+<dt id="arg-ggtheme">ggtheme<a class="anchor" aria-label="anchor" href="#arg-ggtheme"></a>
+</dt>
 <dd><p>(<code>theme</code>)<br> optional graphical theme function as provided
 by <code>ggplot2</code> to control outlook of plot. Use <code><a href="https://ggplot2.tidyverse.org/reference/theme.html" class="external-link">ggplot2::theme()</a></code> to tweak the display.</p></dd>
 
 
-<dt id="arg-plotting-choices">plotting_choices<a class="anchor" aria-label="anchor" href="#arg-plotting-choices"></a></dt>
+<dt id="arg-plotting-choices">plotting_choices<a class="anchor" aria-label="anchor" href="#arg-plotting-choices"></a>
+</dt>
 <dd><p>(<code>string</code>)<br> specifies options for displaying
 plots. Must be one of <code>"all_in_one"</code>, <code>"split_by_max_obs"</code>, or <code>"separate_by_obs"</code>.</p></dd>
 
 
-<dt id="arg-max-obs-per-plot">max_obs_per_plot<a class="anchor" aria-label="anchor" href="#arg-max-obs-per-plot"></a></dt>
+<dt id="arg-max-obs-per-plot">max_obs_per_plot<a class="anchor" aria-label="anchor" href="#arg-max-obs-per-plot"></a>
+</dt>
 <dd><p>(<code>integer(1)</code>)<br> number of observations to be plotted on one
 plot. Ignored if <code>plotting_choices</code> is not <code>"separate_by_obs"</code>.</p></dd>
 
 
-<dt id="arg-col">col<a class="anchor" aria-label="anchor" href="#arg-col"></a></dt>
+<dt id="arg-col">col<a class="anchor" aria-label="anchor" href="#arg-col"></a>
+</dt>
 <dd><p>(<code>character</code>)<br> line colors.</p></dd>
 
-</dl></div>
+</dl>
+</div>
     <div class="section level2">
-    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
+    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a>
+</h2>
     <p>A <code>ggplot</code> object or a list of <code>ggplot</code> objects.</p>
     </div>
     <div class="section level2">
-    <h2 id="functions">Functions<a class="anchor" aria-label="anchor" href="#functions"></a></h2>
+    <h2 id="functions">Functions<a class="anchor" aria-label="anchor" href="#functions"></a>
+</h2>
 
-<ul><li><p><code>g_ipp()</code>: Plotting function for individual patient plots which, depending on user
+<ul>
+<li><p><code>g_ipp()</code>: Plotting function for individual patient plots which, depending on user
 preference, renders a single graphic or compiles a list of graphics that show trends in individual's parameter
 values over time.</p></li>
-</ul></div>
+</ul>
+</div>
     <div class="section level2">
-    <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"></a></h2>
+    <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"></a>
+</h2>
     <div class="dont-index"><p>Relevant helper function <code><a href="h_g_ipp.html">h_g_ipp()</a></code>.</p></div>
     </div>
 
     <div class="section level2">
-    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
+    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://dplyr.tidyverse.org" class="external-link">dplyr</a></span><span class="op">)</span></span></span>
 <span class="r-in"><span></span></span>
 <span class="r-in"><span><span class="co"># Select a small sample of data to plot.</span></span></span>
@@ -193,17 +281,19 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 </code></pre></div>
     </div>
   </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
-    </nav></aside></div>
+    </nav></aside>
+</div>
 
 
     <footer><div class="nest">
   <p>tern is a part of the <strong>NEST</strong> and <a href="https://pharmaverse.org/" class="external-link"><strong>pharmaverse</strong></a>.</p>
 </div>
-<script type="text/javascript" src="../analytics.js"></script></footer></div>
-
+<script type="text/javascript" src="../analytics.js"></script></footer>
+</div>
 
 
 
 
-  </body></html>
 
+  </body>
+</html>
diff --git a/main/reference/g_km.html b/main/reference/g_km.html
index 3b7fead995..7156043dee 100644
--- a/main/reference/g_km.html
+++ b/main/reference/g_km.html
@@ -1,11 +1,34 @@
-<!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Kaplan-Meier plot — g_km • tern</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Kaplan-Meier plot — g_km"><meta name="description" content="
+<html lang="en">
+<head>
+<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+<meta charset="utf-8">
+<meta http-equiv="X-UA-Compatible" content="IE=edge">
+<meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<title>Kaplan-Meier plot — g_km • tern</title>
+<!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png">
+<link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png">
+<link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png">
+<link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png">
+<link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png">
+<link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png">
+<script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet">
+<script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet">
+<link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet">
+<script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Kaplan-Meier plot — g_km">
+<meta name="description" content="
 From a survival model, a graphic is rendered along with tabulated annotation
 including the number of patient at risk at given time and the median survival
-per group."><meta property="og:description" content="
+per group.">
+<meta property="og:description" content="
 From a survival model, a graphic is rendered along with tabulated annotation
 including the number of patient at risk at given time and the median survival
-per group."><meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png"><link rel="stylesheet" href="../consent.css"><script src="../consent.js" type="text/javascript" charset="utf-8"></script></head><body>
+per group.">
+<meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png">
+<link rel="stylesheet" href="../consent.css">
+<script src="../consent.js" type="text/javascript" charset="utf-8"></script>
+</head>
+<body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
 
 
@@ -21,26 +44,66 @@
     </button>
 
     <div id="navbar" class="collapse navbar-collapse ms-3">
-      <ul class="navbar-nav me-auto"><li class="nav-item"><a class="nav-link" href="../articles/tern.html">Get started</a></li>
+      <ul class="navbar-nav me-auto">
+<li class="nav-item"><a class="nav-link" href="../articles/tern.html">Get started</a></li>
 <li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
 <li class="nav-item dropdown">
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-articles" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Articles</button>
-  <ul class="dropdown-menu" aria-labelledby="dropdown-articles"><li><a class="dropdown-item" href="../articles/missing_values.html">Missing Values in Tern</a></li>
+  <ul class="dropdown-menu" aria-labelledby="dropdown-articles">
+<li><a class="dropdown-item" href="../articles/missing_values.html">Missing Values in Tern</a></li>
     <li><a class="dropdown-item" href="../articles/tables.html">Tabulation</a></li>
     <li><a class="dropdown-item" href="../articles/tern_formats.html">Formatting Functions</a></li>
     <li><a class="dropdown-item" href="../articles/tern_functions_guide.html">Understanding `tern` functions</a></li>
-  </ul></li>
+  </ul>
+</li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
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   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
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+  <ul class="dropdown-menu" aria-labelledby="dropdown-reports">
+<li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
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- <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json"></form></li>
+  </ul>
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+    <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-versions">Versions</a>
+    <div class="dropdown-menu" aria-labelledby="dropdown-versions">
+    <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
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+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
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+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.4">v0.9.4</a>
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+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
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+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1-rc3">v0.9.1-rc3</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a>
+</div>
+</li></div>
+</ul>
+<ul class="navbar-nav">
+<li class="nav-item"><form class="form-inline" role="search">
+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json">
+</form></li>
 <li class="nav-item"><a class="external-link nav-link" href="https://github.com/insightsengineering/tern" aria-label="GitHub"><span class="fa fa-github"></span></a></li>
-      </ul></div>
+      </ul>
+</div>
 
 
   </div>
@@ -60,7 +123,8 @@
     </div>
 
     <div class="section level2">
-    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
+    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">g_km</span><span class="op">(</span></span>
 <span>  <span class="va">df</span>,</span>
 <span>  <span class="va">variables</span>,</span>
@@ -108,226 +172,285 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
     </div>
 
     <div class="section level2">
-    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
+    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a>
+</h2>
 
 
-<dl><dt id="arg-df">df<a class="anchor" aria-label="anchor" href="#arg-df"></a></dt>
+<dl>
+<dt id="arg-df">df<a class="anchor" aria-label="anchor" href="#arg-df"></a>
+</dt>
 <dd><p>(<code>data.frame</code>)<br> data set containing all analysis variables.</p></dd>
 
 
-<dt id="arg-variables">variables<a class="anchor" aria-label="anchor" href="#arg-variables"></a></dt>
-<dd><p>(named <code>list</code>)<br> variable names. Details are:</p><ul><li><p><code>tte</code> (<code>numeric</code>)<br> variable indicating time-to-event duration values.</p></li>
+<dt id="arg-variables">variables<a class="anchor" aria-label="anchor" href="#arg-variables"></a>
+</dt>
+<dd>
+<p>(named <code>list</code>)<br> variable names. Details are:</p>
+<ul>
+<li><p><code>tte</code> (<code>numeric</code>)<br> variable indicating time-to-event duration values.</p></li>
 <li><p><code>is_event</code> (<code>logical</code>)<br> event variable. <code>TRUE</code> if event, <code>FALSE</code> if time to event is censored.</p></li>
 <li><p><code>arm</code> (<code>factor</code>)<br> the treatment group variable.</p></li>
 <li><p><code>strata</code> (<code>character</code> or <code>NULL</code>)<br> variable names indicating stratification factors.</p></li>
-</ul></dd>
+</ul>
+</dd>
 
 
-<dt id="arg-control-surv">control_surv<a class="anchor" aria-label="anchor" href="#arg-control-surv"></a></dt>
-<dd><p>(<code>list</code>)<br> parameters for comparison details, specified by using
-the helper function <code><a href="control_surv_timepoint.html">control_surv_timepoint()</a></code>. Some possible parameter options are:</p><ul><li><p><code>conf_level</code> (<code>proportion</code>)<br> confidence level of the interval for survival rate.</p></li>
+<dt id="arg-control-surv">control_surv<a class="anchor" aria-label="anchor" href="#arg-control-surv"></a>
+</dt>
+<dd>
+<p>(<code>list</code>)<br> parameters for comparison details, specified by using
+the helper function <code><a href="control_surv_timepoint.html">control_surv_timepoint()</a></code>. Some possible parameter options are:</p>
+<ul>
+<li><p><code>conf_level</code> (<code>proportion</code>)<br> confidence level of the interval for survival rate.</p></li>
 <li><p><code>conf_type</code> (<code>string</code>)<br><code>"plain"</code> (default), <code>"log"</code>, <code>"log-log"</code> for confidence interval type,
 see more in <code><a href="https://rdrr.io/pkg/survival/man/survfit.html" class="external-link">survival::survfit()</a></code>. Note that the option "none" is no longer supported.</p></li>
-</ul></dd>
+</ul>
+</dd>
 
 
-<dt id="arg-col">col<a class="anchor" aria-label="anchor" href="#arg-col"></a></dt>
+<dt id="arg-col">col<a class="anchor" aria-label="anchor" href="#arg-col"></a>
+</dt>
 <dd><p>(<code>character</code>)<br> lines colors. Length of a vector should be equal
 to number of strata from <code><a href="https://rdrr.io/pkg/survival/man/survfit.html" class="external-link">survival::survfit()</a></code>.</p></dd>
 
 
-<dt id="arg-lty">lty<a class="anchor" aria-label="anchor" href="#arg-lty"></a></dt>
+<dt id="arg-lty">lty<a class="anchor" aria-label="anchor" href="#arg-lty"></a>
+</dt>
 <dd><p>(<code>numeric</code>)<br> line type. If a vector is given, its length should be equal to the number of strata from
 <code><a href="https://rdrr.io/pkg/survival/man/survfit.html" class="external-link">survival::survfit()</a></code>.</p></dd>
 
 
-<dt id="arg-lwd">lwd<a class="anchor" aria-label="anchor" href="#arg-lwd"></a></dt>
+<dt id="arg-lwd">lwd<a class="anchor" aria-label="anchor" href="#arg-lwd"></a>
+</dt>
 <dd><p>(<code>numeric</code>)<br> line width. If a vector is given, its length should be equal to the number of strata from
 <code><a href="https://rdrr.io/pkg/survival/man/survfit.html" class="external-link">survival::survfit()</a></code>.</p></dd>
 
 
-<dt id="arg-censor-show">censor_show<a class="anchor" aria-label="anchor" href="#arg-censor-show"></a></dt>
+<dt id="arg-censor-show">censor_show<a class="anchor" aria-label="anchor" href="#arg-censor-show"></a>
+</dt>
 <dd><p>(<code>flag</code>)<br> whether to show censored observations.</p></dd>
 
 
-<dt id="arg-pch">pch<a class="anchor" aria-label="anchor" href="#arg-pch"></a></dt>
+<dt id="arg-pch">pch<a class="anchor" aria-label="anchor" href="#arg-pch"></a>
+</dt>
 <dd><p>(<code>string</code>)<br> name of symbol or character to use as point symbol to indicate censored cases.</p></dd>
 
 
-<dt id="arg-size">size<a class="anchor" aria-label="anchor" href="#arg-size"></a></dt>
+<dt id="arg-size">size<a class="anchor" aria-label="anchor" href="#arg-size"></a>
+</dt>
 <dd><p>(<code>numeric(1)</code>)<br> size of censored point symbols.</p></dd>
 
 
-<dt id="arg-max-time">max_time<a class="anchor" aria-label="anchor" href="#arg-max-time"></a></dt>
+<dt id="arg-max-time">max_time<a class="anchor" aria-label="anchor" href="#arg-max-time"></a>
+</dt>
 <dd><p>(<code>numeric(1)</code>)<br> maximum value to show on x-axis. Only data values less than or up to
 this threshold value will be plotted (defaults to <code>NULL</code>).</p></dd>
 
 
-<dt id="arg-xticks">xticks<a class="anchor" aria-label="anchor" href="#arg-xticks"></a></dt>
+<dt id="arg-xticks">xticks<a class="anchor" aria-label="anchor" href="#arg-xticks"></a>
+</dt>
 <dd><p>(<code>numeric</code> or <code>NULL</code>)<br> numeric vector of tick positions or a single number with spacing
 between ticks on the x-axis. If <code>NULL</code> (default), <code><a href="https://rdrr.io/pkg/labeling/man/extended.html" class="external-link">labeling::extended()</a></code> is used to determine
 optimal tick positions on the x-axis.</p></dd>
 
 
-<dt id="arg-xlab">xlab<a class="anchor" aria-label="anchor" href="#arg-xlab"></a></dt>
+<dt id="arg-xlab">xlab<a class="anchor" aria-label="anchor" href="#arg-xlab"></a>
+</dt>
 <dd><p>(<code>string</code>)<br> x-axis label.</p></dd>
 
 
-<dt id="arg-yval">yval<a class="anchor" aria-label="anchor" href="#arg-yval"></a></dt>
+<dt id="arg-yval">yval<a class="anchor" aria-label="anchor" href="#arg-yval"></a>
+</dt>
 <dd><p>(<code>string</code>)<br> type of plot, to be plotted on the y-axis. Options are <code>Survival</code> (default) and <code>Failure</code>
 probability.</p></dd>
 
 
-<dt id="arg-ylab">ylab<a class="anchor" aria-label="anchor" href="#arg-ylab"></a></dt>
+<dt id="arg-ylab">ylab<a class="anchor" aria-label="anchor" href="#arg-ylab"></a>
+</dt>
 <dd><p>(<code>string</code>)<br> y-axis label.</p></dd>
 
 
-<dt id="arg-ylim">ylim<a class="anchor" aria-label="anchor" href="#arg-ylim"></a></dt>
+<dt id="arg-ylim">ylim<a class="anchor" aria-label="anchor" href="#arg-ylim"></a>
+</dt>
 <dd><p>(<code>numeric(2)</code>)<br> vector containing lower and upper limits for the y-axis, respectively.
 If <code>NULL</code> (default), the default scale range is used.</p></dd>
 
 
-<dt id="arg-title">title<a class="anchor" aria-label="anchor" href="#arg-title"></a></dt>
+<dt id="arg-title">title<a class="anchor" aria-label="anchor" href="#arg-title"></a>
+</dt>
 <dd><p>(<code>string</code>)<br> plot title.</p></dd>
 
 
-<dt id="arg-footnotes">footnotes<a class="anchor" aria-label="anchor" href="#arg-footnotes"></a></dt>
+<dt id="arg-footnotes">footnotes<a class="anchor" aria-label="anchor" href="#arg-footnotes"></a>
+</dt>
 <dd><p>(<code>string</code>)<br> plot footnotes.</p></dd>
 
 
-<dt id="arg-font-size">font_size<a class="anchor" aria-label="anchor" href="#arg-font-size"></a></dt>
+<dt id="arg-font-size">font_size<a class="anchor" aria-label="anchor" href="#arg-font-size"></a>
+</dt>
 <dd><p>(<code>numeric(1)</code>)<br> font size to use for all text.</p></dd>
 
 
-<dt id="arg-ci-ribbon">ci_ribbon<a class="anchor" aria-label="anchor" href="#arg-ci-ribbon"></a></dt>
+<dt id="arg-ci-ribbon">ci_ribbon<a class="anchor" aria-label="anchor" href="#arg-ci-ribbon"></a>
+</dt>
 <dd><p>(<code>flag</code>)<br> whether the confidence interval should be drawn around the Kaplan-Meier curve.</p></dd>
 
 
-<dt id="arg-annot-at-risk">annot_at_risk<a class="anchor" aria-label="anchor" href="#arg-annot-at-risk"></a></dt>
+<dt id="arg-annot-at-risk">annot_at_risk<a class="anchor" aria-label="anchor" href="#arg-annot-at-risk"></a>
+</dt>
 <dd><p>(<code>flag</code>)<br> compute and add the annotation table reporting the number of patient at risk
 matching the main grid of the Kaplan-Meier curve.</p></dd>
 
 
-<dt id="arg-annot-at-risk-title">annot_at_risk_title<a class="anchor" aria-label="anchor" href="#arg-annot-at-risk-title"></a></dt>
+<dt id="arg-annot-at-risk-title">annot_at_risk_title<a class="anchor" aria-label="anchor" href="#arg-annot-at-risk-title"></a>
+</dt>
 <dd><p>(<code>flag</code>)<br> whether the "Patients at Risk" title should be added above the <code>annot_at_risk</code>
 table. Has no effect if <code>annot_at_risk</code> is <code>FALSE</code>. Defaults to <code>TRUE</code>.</p></dd>
 
 
-<dt id="arg-annot-surv-med">annot_surv_med<a class="anchor" aria-label="anchor" href="#arg-annot-surv-med"></a></dt>
+<dt id="arg-annot-surv-med">annot_surv_med<a class="anchor" aria-label="anchor" href="#arg-annot-surv-med"></a>
+</dt>
 <dd><p>(<code>flag</code>)<br> compute and add the annotation table on the Kaplan-Meier curve estimating the
 median survival time per group.</p></dd>
 
 
-<dt id="arg-annot-coxph">annot_coxph<a class="anchor" aria-label="anchor" href="#arg-annot-coxph"></a></dt>
+<dt id="arg-annot-coxph">annot_coxph<a class="anchor" aria-label="anchor" href="#arg-annot-coxph"></a>
+</dt>
 <dd><p>(<code>flag</code>)<br> whether to add the annotation table from a <code><a href="https://rdrr.io/pkg/survival/man/coxph.html" class="external-link">survival::coxph()</a></code> model.</p></dd>
 
 
-<dt id="arg-annot-stats">annot_stats<a class="anchor" aria-label="anchor" href="#arg-annot-stats"></a></dt>
+<dt id="arg-annot-stats">annot_stats<a class="anchor" aria-label="anchor" href="#arg-annot-stats"></a>
+</dt>
 <dd><p>(<code>string</code> or <code>NULL</code>)<br> statistics annotations to add to the plot. Options are
 <code>median</code> (median survival follow-up time) and <code>min</code> (minimum survival follow-up time).</p></dd>
 
 
-<dt id="arg-annot-stats-vlines">annot_stats_vlines<a class="anchor" aria-label="anchor" href="#arg-annot-stats-vlines"></a></dt>
+<dt id="arg-annot-stats-vlines">annot_stats_vlines<a class="anchor" aria-label="anchor" href="#arg-annot-stats-vlines"></a>
+</dt>
 <dd><p>(<code>flag</code>)<br> add vertical lines corresponding to each of the statistics
 specified by <code>annot_stats</code>. If <code>annot_stats</code> is <code>NULL</code> no lines will be added.</p></dd>
 
 
-<dt id="arg-control-coxph-pw">control_coxph_pw<a class="anchor" aria-label="anchor" href="#arg-control-coxph-pw"></a></dt>
-<dd><p>(<code>list</code>)<br> parameters for comparison details, specified using the helper function
-<code><a href="control_coxph.html">control_coxph()</a></code>. Some possible parameter options are:</p><ul><li><p><code>pval_method</code> (<code>string</code>)<br> p-value method for testing hazard ratio = 1.
+<dt id="arg-control-coxph-pw">control_coxph_pw<a class="anchor" aria-label="anchor" href="#arg-control-coxph-pw"></a>
+</dt>
+<dd>
+<p>(<code>list</code>)<br> parameters for comparison details, specified using the helper function
+<code><a href="control_coxph.html">control_coxph()</a></code>. Some possible parameter options are:</p>
+<ul>
+<li><p><code>pval_method</code> (<code>string</code>)<br> p-value method for testing hazard ratio = 1.
 Default method is <code>"log-rank"</code>, can also be set to <code>"wald"</code> or <code>"likelihood"</code>.</p></li>
 <li><p><code>ties</code> (<code>string</code>)<br> method for tie handling. Default is <code>"efron"</code>,
 can also be set to <code>"breslow"</code> or <code>"exact"</code>. See more in <code><a href="https://rdrr.io/pkg/survival/man/coxph.html" class="external-link">survival::coxph()</a></code></p></li>
 <li><p><code>conf_level</code> (<code>proportion</code>)<br> confidence level of the interval for HR.</p></li>
-</ul></dd>
+</ul>
+</dd>
 
 
-<dt id="arg-ref-group-coxph">ref_group_coxph<a class="anchor" aria-label="anchor" href="#arg-ref-group-coxph"></a></dt>
+<dt id="arg-ref-group-coxph">ref_group_coxph<a class="anchor" aria-label="anchor" href="#arg-ref-group-coxph"></a>
+</dt>
 <dd><p>(<code>string</code> or <code>NULL</code>)<br> level of arm variable to use as reference group in calculations for
 <code>annot_coxph</code> table. If <code>NULL</code> (default), uses the first level of the arm variable.</p></dd>
 
 
-<dt id="arg-control-annot-surv-med">control_annot_surv_med<a class="anchor" aria-label="anchor" href="#arg-control-annot-surv-med"></a></dt>
+<dt id="arg-control-annot-surv-med">control_annot_surv_med<a class="anchor" aria-label="anchor" href="#arg-control-annot-surv-med"></a>
+</dt>
 <dd><p>(<code>list</code>)<br> parameters to control the position and size of the annotation table added
 to the plot when <code>annot_surv_med = TRUE</code>, specified using the <code><a href="control_annot.html">control_surv_med_annot()</a></code> function. Parameter
 options are: <code>x</code>, <code>y</code>, <code>w</code>, <code>h</code>, and <code>fill</code>. See <code><a href="control_annot.html">control_surv_med_annot()</a></code> for details.</p></dd>
 
 
-<dt id="arg-control-annot-coxph">control_annot_coxph<a class="anchor" aria-label="anchor" href="#arg-control-annot-coxph"></a></dt>
+<dt id="arg-control-annot-coxph">control_annot_coxph<a class="anchor" aria-label="anchor" href="#arg-control-annot-coxph"></a>
+</dt>
 <dd><p>(<code>list</code>)<br> parameters to control the position and size of the annotation table added
 to the plot when <code>annot_coxph = TRUE</code>, specified using the <code><a href="control_annot.html">control_coxph_annot()</a></code> function. Parameter
 options are: <code>x</code>, <code>y</code>, <code>w</code>, <code>h</code>, <code>fill</code>, and <code>ref_lbls</code>. See <code><a href="control_annot.html">control_coxph_annot()</a></code> for details.</p></dd>
 
 
-<dt id="arg-legend-pos">legend_pos<a class="anchor" aria-label="anchor" href="#arg-legend-pos"></a></dt>
+<dt id="arg-legend-pos">legend_pos<a class="anchor" aria-label="anchor" href="#arg-legend-pos"></a>
+</dt>
 <dd><p>(<code>numeric(2)</code> or <code>NULL</code>)<br> vector containing x- and y-coordinates, respectively, for the legend
 position relative to the KM plot area. If <code>NULL</code> (default), the legend is positioned in the bottom right corner of
 the plot, or the middle right of the plot if needed to prevent overlapping.</p></dd>
 
 
-<dt id="arg-rel-height-plot">rel_height_plot<a class="anchor" aria-label="anchor" href="#arg-rel-height-plot"></a></dt>
+<dt id="arg-rel-height-plot">rel_height_plot<a class="anchor" aria-label="anchor" href="#arg-rel-height-plot"></a>
+</dt>
 <dd><p>(<code>proportion</code>)<br> proportion of total figure height to allocate to the Kaplan-Meier plot.
 Relative height of patients at risk table is then <code>1 - rel_height_plot</code>. If <code>annot_at_risk = FALSE</code> or
 <code>as_list = TRUE</code>, this parameter is ignored.</p></dd>
 
 
-<dt id="arg-ggtheme">ggtheme<a class="anchor" aria-label="anchor" href="#arg-ggtheme"></a></dt>
+<dt id="arg-ggtheme">ggtheme<a class="anchor" aria-label="anchor" href="#arg-ggtheme"></a>
+</dt>
 <dd><p>(<code>theme</code>)<br> a graphical theme as provided by <code>ggplot2</code> to format the Kaplan-Meier plot.</p></dd>
 
 
-<dt id="arg-as-list">as_list<a class="anchor" aria-label="anchor" href="#arg-as-list"></a></dt>
+<dt id="arg-as-list">as_list<a class="anchor" aria-label="anchor" href="#arg-as-list"></a>
+</dt>
 <dd><p>(<code>flag</code>)<br> whether the two <code>ggplot</code> objects should be returned as a list when <code>annot_at_risk = TRUE</code>.
 If <code>TRUE</code>, a named list with two elements, <code>plot</code> and <code>table</code>, will be returned. If <code>FALSE</code> (default) the patients
 at risk table is printed below the plot via <code><a href="https://wilkelab.org/cowplot/reference/plot_grid.html" class="external-link">cowplot::plot_grid()</a></code>.</p></dd>
 
 
-<dt id="arg-draw">draw<a class="anchor" aria-label="anchor" href="#arg-draw"></a></dt>
+<dt id="arg-draw">draw<a class="anchor" aria-label="anchor" href="#arg-draw"></a>
+</dt>
 <dd><p><a href="https://lifecycle.r-lib.org/articles/stages.html#deprecated" class="external-link"><img src="figures/lifecycle-deprecated.svg" alt="[Deprecated]"></a> This function no longer generates <code>grob</code> objects.</p></dd>
 
 
-<dt id="arg-newpage">newpage<a class="anchor" aria-label="anchor" href="#arg-newpage"></a></dt>
+<dt id="arg-newpage">newpage<a class="anchor" aria-label="anchor" href="#arg-newpage"></a>
+</dt>
 <dd><p><a href="https://lifecycle.r-lib.org/articles/stages.html#deprecated" class="external-link"><img src="figures/lifecycle-deprecated.svg" alt="[Deprecated]"></a> This function no longer generates <code>grob</code> objects.</p></dd>
 
 
-<dt id="arg-gp">gp<a class="anchor" aria-label="anchor" href="#arg-gp"></a></dt>
+<dt id="arg-gp">gp<a class="anchor" aria-label="anchor" href="#arg-gp"></a>
+</dt>
 <dd><p><a href="https://lifecycle.r-lib.org/articles/stages.html#deprecated" class="external-link"><img src="figures/lifecycle-deprecated.svg" alt="[Deprecated]"></a> This function no longer generates <code>grob</code> objects.</p></dd>
 
 
-<dt id="arg-vp">vp<a class="anchor" aria-label="anchor" href="#arg-vp"></a></dt>
+<dt id="arg-vp">vp<a class="anchor" aria-label="anchor" href="#arg-vp"></a>
+</dt>
 <dd><p><a href="https://lifecycle.r-lib.org/articles/stages.html#deprecated" class="external-link"><img src="figures/lifecycle-deprecated.svg" alt="[Deprecated]"></a> This function no longer generates <code>grob</code> objects.</p></dd>
 
 
-<dt id="arg-name">name<a class="anchor" aria-label="anchor" href="#arg-name"></a></dt>
+<dt id="arg-name">name<a class="anchor" aria-label="anchor" href="#arg-name"></a>
+</dt>
 <dd><p><a href="https://lifecycle.r-lib.org/articles/stages.html#deprecated" class="external-link"><img src="figures/lifecycle-deprecated.svg" alt="[Deprecated]"></a> This function no longer generates <code>grob</code> objects.</p></dd>
 
 
-<dt id="arg-annot-coxph-ref-lbls">annot_coxph_ref_lbls<a class="anchor" aria-label="anchor" href="#arg-annot-coxph-ref-lbls"></a></dt>
+<dt id="arg-annot-coxph-ref-lbls">annot_coxph_ref_lbls<a class="anchor" aria-label="anchor" href="#arg-annot-coxph-ref-lbls"></a>
+</dt>
 <dd><p><a href="https://lifecycle.r-lib.org/articles/stages.html#deprecated" class="external-link"><img src="figures/lifecycle-deprecated.svg" alt="[Deprecated]"></a> Please use the <code>ref_lbls</code> element of
 <code>control_annot_coxph</code> instead.</p></dd>
 
 
-<dt id="arg-position-coxph">position_coxph<a class="anchor" aria-label="anchor" href="#arg-position-coxph"></a></dt>
+<dt id="arg-position-coxph">position_coxph<a class="anchor" aria-label="anchor" href="#arg-position-coxph"></a>
+</dt>
 <dd><p><a href="https://lifecycle.r-lib.org/articles/stages.html#deprecated" class="external-link"><img src="figures/lifecycle-deprecated.svg" alt="[Deprecated]"></a>  Please use the <code>x</code> and <code>y</code> elements of
 <code>control_annot_coxph</code> instead.</p></dd>
 
 
-<dt id="arg-position-surv-med">position_surv_med<a class="anchor" aria-label="anchor" href="#arg-position-surv-med"></a></dt>
+<dt id="arg-position-surv-med">position_surv_med<a class="anchor" aria-label="anchor" href="#arg-position-surv-med"></a>
+</dt>
 <dd><p><a href="https://lifecycle.r-lib.org/articles/stages.html#deprecated" class="external-link"><img src="figures/lifecycle-deprecated.svg" alt="[Deprecated]"></a> Please use the <code>x</code> and <code>y</code> elements of
 <code>control_annot_surv_med</code> instead.</p></dd>
 
 
-<dt id="arg-width-annots">width_annots<a class="anchor" aria-label="anchor" href="#arg-width-annots"></a></dt>
+<dt id="arg-width-annots">width_annots<a class="anchor" aria-label="anchor" href="#arg-width-annots"></a>
+</dt>
 <dd><p><a href="https://lifecycle.r-lib.org/articles/stages.html#deprecated" class="external-link"><img src="figures/lifecycle-deprecated.svg" alt="[Deprecated]"></a> Please use the <code>w</code> element of <code>control_annot_surv_med</code>
 (for <code>surv_med</code>) and <code>control_annot_coxph</code> (for <code>coxph</code>)."</p></dd>
 
-</dl></div>
+</dl>
+</div>
     <div class="section level2">
-    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
+    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a>
+</h2>
     <p>A <code>ggplot</code> Kaplan-Meier plot and (optionally) summary table.</p>
     </div>
 
     <div class="section level2">
-    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
+    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://dplyr.tidyverse.org" class="external-link">dplyr</a></span><span class="op">)</span></span></span>
 <span class="r-in"><span></span></span>
 <span class="r-in"><span><span class="va">df</span> <span class="op">&lt;-</span> <span class="va">tern_ex_adtte</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span></span>
@@ -375,17 +498,19 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 </code></pre></div>
     </div>
   </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
-    </nav></aside></div>
+    </nav></aside>
+</div>
 
 
     <footer><div class="nest">
   <p>tern is a part of the <strong>NEST</strong> and <a href="https://pharmaverse.org/" class="external-link"><strong>pharmaverse</strong></a>.</p>
 </div>
-<script type="text/javascript" src="../analytics.js"></script></footer></div>
-
+<script type="text/javascript" src="../analytics.js"></script></footer>
+</div>
 
 
 
 
-  </body></html>
 
+  </body>
+</html>
diff --git a/main/reference/g_lineplot.html b/main/reference/g_lineplot.html
index 9d92d1283f..1acc6c4339 100644
--- a/main/reference/g_lineplot.html
+++ b/main/reference/g_lineplot.html
@@ -1,7 +1,30 @@
-<!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Line plot with optional table — g_lineplot • tern</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Line plot with optional table — g_lineplot"><meta name="description" content="
-Line plot with optional table."><meta property="og:description" content="
-Line plot with optional table."><meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png"><link rel="stylesheet" href="../consent.css"><script src="../consent.js" type="text/javascript" charset="utf-8"></script></head><body>
+<html lang="en">
+<head>
+<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+<meta charset="utf-8">
+<meta http-equiv="X-UA-Compatible" content="IE=edge">
+<meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<title>Line plot with optional table — g_lineplot • tern</title>
+<!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png">
+<link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png">
+<link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png">
+<link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png">
+<link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png">
+<link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png">
+<script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet">
+<script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet">
+<link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet">
+<script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Line plot with optional table — g_lineplot">
+<meta name="description" content="
+Line plot with optional table.">
+<meta property="og:description" content="
+Line plot with optional table.">
+<meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png">
+<link rel="stylesheet" href="../consent.css">
+<script src="../consent.js" type="text/javascript" charset="utf-8"></script>
+</head>
+<body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
 
 
@@ -17,26 +40,66 @@
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-      <ul class="navbar-nav me-auto"><li class="nav-item"><a class="nav-link" href="../articles/tern.html">Get started</a></li>
+      <ul class="navbar-nav me-auto">
+<li class="nav-item"><a class="nav-link" href="../articles/tern.html">Get started</a></li>
 <li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
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   <button class="nav-link dropdown-toggle" type="button" id="dropdown-articles" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Articles</button>
-  <ul class="dropdown-menu" aria-labelledby="dropdown-articles"><li><a class="dropdown-item" href="../articles/missing_values.html">Missing Values in Tern</a></li>
+  <ul class="dropdown-menu" aria-labelledby="dropdown-articles">
+<li><a class="dropdown-item" href="../articles/missing_values.html">Missing Values in Tern</a></li>
     <li><a class="dropdown-item" href="../articles/tables.html">Tabulation</a></li>
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     <li><a class="dropdown-item" href="../articles/tern_functions_guide.html">Understanding `tern` functions</a></li>
-  </ul></li>
+  </ul>
+</li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
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-  <ul class="dropdown-menu" aria-labelledby="dropdown-reports"><li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
+  <ul class="dropdown-menu" aria-labelledby="dropdown-reports">
+<li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
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- <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json"></form></li>
+  </ul>
+</li>
+      <div><li class="nav-item dropdown">
+    <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-versions">Versions</a>
+    <div class="dropdown-menu" aria-labelledby="dropdown-versions">
+    <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
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+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.5">v0.9.5</a>
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+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
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+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a>
+</div>
+</li></div>
+</ul>
+<ul class="navbar-nav">
+<li class="nav-item"><form class="form-inline" role="search">
+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json">
+</form></li>
 <li class="nav-item"><a class="external-link nav-link" href="https://github.com/insightsengineering/tern" aria-label="GitHub"><span class="fa fa-github"></span></a></li>
-      </ul></div>
+      </ul>
+</div>
 
 
   </div>
@@ -54,7 +117,8 @@
     </div>
 
     <div class="section level2">
-    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
+    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">g_lineplot</span><span class="op">(</span></span>
 <span>  <span class="va">df</span>,</span>
 <span>  alt_counts_df <span class="op">=</span> <span class="cn">NULL</span>,</span>
@@ -96,20 +160,28 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
     </div>
 
     <div class="section level2">
-    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
+    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a>
+</h2>
 
 
-<dl><dt id="arg-df">df<a class="anchor" aria-label="anchor" href="#arg-df"></a></dt>
+<dl>
+<dt id="arg-df">df<a class="anchor" aria-label="anchor" href="#arg-df"></a>
+</dt>
 <dd><p>(<code>data.frame</code>)<br> data set containing all analysis variables.</p></dd>
 
 
-<dt id="arg-alt-counts-df">alt_counts_df<a class="anchor" aria-label="anchor" href="#arg-alt-counts-df"></a></dt>
+<dt id="arg-alt-counts-df">alt_counts_df<a class="anchor" aria-label="anchor" href="#arg-alt-counts-df"></a>
+</dt>
 <dd><p>(<code>data.frame</code> or <code>NULL</code>)<br> data set that will be used (only)
 to counts objects in groups for stratification.</p></dd>
 
 
-<dt id="arg-variables">variables<a class="anchor" aria-label="anchor" href="#arg-variables"></a></dt>
-<dd><p>(named <code>character</code>) vector of variable names in <code>df</code> which should include:</p><ul><li><p><code>x</code> (<code>string</code>)<br> name of x-axis variable.</p></li>
+<dt id="arg-variables">variables<a class="anchor" aria-label="anchor" href="#arg-variables"></a>
+</dt>
+<dd>
+<p>(named <code>character</code>) vector of variable names in <code>df</code> which should include:</p>
+<ul>
+<li><p><code>x</code> (<code>string</code>)<br> name of x-axis variable.</p></li>
 <li><p><code>y</code> (<code>string</code>)<br> name of y-axis variable.</p></li>
 <li><p><code>group_var</code> (<code>string</code> or <code>NULL</code>)<br> name of grouping variable (or strata), i.e. treatment arm.
 Can be <code>NA</code> to indicate lack of groups.</p></li>
@@ -121,176 +193,213 @@ <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#argumen
 Can be <code>NA</code> if y unit is not to be added to the y-axis label or subtitle.</p></li>
 <li><p><code>facet_var</code> (<code>string</code> or <code>NA</code>)<br> name of the secondary grouping variable used for plot faceting, i.e. treatment
 arm. Can be <code>NA</code> to indicate lack of groups.</p></li>
-</ul></dd>
+</ul>
+</dd>
 
 
-<dt id="arg-mid">mid<a class="anchor" aria-label="anchor" href="#arg-mid"></a></dt>
+<dt id="arg-mid">mid<a class="anchor" aria-label="anchor" href="#arg-mid"></a>
+</dt>
 <dd><p>(<code>character</code> or <code>NULL</code>)<br> names of the statistics that will be plotted as midpoints.
 All the statistics indicated in <code>mid</code> variable must be present in the object returned by <code>sfun</code>,
 and be of a <code>double</code> or <code>numeric</code> type vector of length one.</p></dd>
 
 
-<dt id="arg-interval">interval<a class="anchor" aria-label="anchor" href="#arg-interval"></a></dt>
+<dt id="arg-interval">interval<a class="anchor" aria-label="anchor" href="#arg-interval"></a>
+</dt>
 <dd><p>(<code>character</code> or <code>NULL</code>)<br> names of the statistics that will be plotted as intervals.
 All the statistics indicated in <code>interval</code> variable must be present in the object returned by <code>sfun</code>,
 and be of a <code>double</code> or <code>numeric</code> type vector of length two. Set <code>interval = NULL</code> if intervals should not be
 added to the plot.</p></dd>
 
 
-<dt id="arg-whiskers">whiskers<a class="anchor" aria-label="anchor" href="#arg-whiskers"></a></dt>
+<dt id="arg-whiskers">whiskers<a class="anchor" aria-label="anchor" href="#arg-whiskers"></a>
+</dt>
 <dd><p>(<code>character</code>)<br> names of the interval whiskers that will be plotted. Names must match names
 of the list element <code>interval</code> that will be returned by <code>sfun</code> (e.g. <code>mean_ci_lwr</code> element of
 <code>sfun(x)[["mean_ci"]]</code>). It is possible to specify one whisker only, or to suppress all whiskers by setting
 <code>interval = NULL</code>.</p></dd>
 
 
-<dt id="arg-table">table<a class="anchor" aria-label="anchor" href="#arg-table"></a></dt>
+<dt id="arg-table">table<a class="anchor" aria-label="anchor" href="#arg-table"></a>
+</dt>
 <dd><p>(<code>character</code> or <code>NULL</code>)<br> names of the statistics that will be displayed in the table below the plot.
 All the statistics indicated in <code>table</code> variable must be present in the object returned by <code>sfun</code>.</p></dd>
 
 
-<dt id="arg-sfun">sfun<a class="anchor" aria-label="anchor" href="#arg-sfun"></a></dt>
+<dt id="arg-sfun">sfun<a class="anchor" aria-label="anchor" href="#arg-sfun"></a>
+</dt>
 <dd><p>(<code>function</code>)<br> the function to compute the values of required statistics. It must return a named <code>list</code>
 with atomic vectors. The names of the <code>list</code> elements refer to the names of the statistics and are used by <code>mid</code>,
 <code>interval</code>, <code>table</code>. It must be able to accept as input a vector with data for which statistics are computed.</p></dd>
 
 
-<dt id="arg--">...<a class="anchor" aria-label="anchor" href="#arg--"></a></dt>
+<dt id="arg--">...<a class="anchor" aria-label="anchor" href="#arg--"></a>
+</dt>
 <dd><p>optional arguments to <code>sfun</code>.</p></dd>
 
 
-<dt id="arg-mid-type">mid_type<a class="anchor" aria-label="anchor" href="#arg-mid-type"></a></dt>
+<dt id="arg-mid-type">mid_type<a class="anchor" aria-label="anchor" href="#arg-mid-type"></a>
+</dt>
 <dd><p>(<code>string</code>)<br> controls the type of the <code>mid</code> plot, it can be point (<code>"p"</code>), line (<code>"l"</code>),
 or point and line (<code>"pl"</code>).</p></dd>
 
 
-<dt id="arg-mid-point-size">mid_point_size<a class="anchor" aria-label="anchor" href="#arg-mid-point-size"></a></dt>
+<dt id="arg-mid-point-size">mid_point_size<a class="anchor" aria-label="anchor" href="#arg-mid-point-size"></a>
+</dt>
 <dd><p>(<code>numeric(1)</code>)<br> font size of the <code>mid</code> plot points.</p></dd>
 
 
-<dt id="arg-position">position<a class="anchor" aria-label="anchor" href="#arg-position"></a></dt>
+<dt id="arg-position">position<a class="anchor" aria-label="anchor" href="#arg-position"></a>
+</dt>
 <dd><p>(<code>character</code> or <code>call</code>)<br> geom element position adjustment, either as a string, or the result of
 a call to a position adjustment function.</p></dd>
 
 
-<dt id="arg-legend-title">legend_title<a class="anchor" aria-label="anchor" href="#arg-legend-title"></a></dt>
+<dt id="arg-legend-title">legend_title<a class="anchor" aria-label="anchor" href="#arg-legend-title"></a>
+</dt>
 <dd><p>(<code>string</code>)<br> legend title.</p></dd>
 
 
-<dt id="arg-legend-position">legend_position<a class="anchor" aria-label="anchor" href="#arg-legend-position"></a></dt>
+<dt id="arg-legend-position">legend_position<a class="anchor" aria-label="anchor" href="#arg-legend-position"></a>
+</dt>
 <dd><p>(<code>string</code>)<br> the position of the plot legend (<code>"none"</code>, <code>"left"</code>, <code>"right"</code>, <code>"bottom"</code>,
 <code>"top"</code>, or a two-element numeric vector).</p></dd>
 
 
-<dt id="arg-ggtheme">ggtheme<a class="anchor" aria-label="anchor" href="#arg-ggtheme"></a></dt>
+<dt id="arg-ggtheme">ggtheme<a class="anchor" aria-label="anchor" href="#arg-ggtheme"></a>
+</dt>
 <dd><p>(<code>theme</code>)<br> a graphical theme as provided by <code>ggplot2</code> to control styling of the plot.</p></dd>
 
 
-<dt id="arg-xticks">xticks<a class="anchor" aria-label="anchor" href="#arg-xticks"></a></dt>
+<dt id="arg-xticks">xticks<a class="anchor" aria-label="anchor" href="#arg-xticks"></a>
+</dt>
 <dd><p>(<code>numeric</code> or <code>NULL</code>)<br> numeric vector of tick positions or a single number with spacing
 between ticks on the x-axis, for use when <code>variables$x</code> is numeric. If <code>NULL</code> (default), <code><a href="https://rdrr.io/pkg/labeling/man/extended.html" class="external-link">labeling::extended()</a></code> is
 used to determine optimal tick positions on the x-axis. If <code>variables$x</code> is not numeric, this argument is ignored.</p></dd>
 
 
-<dt id="arg-xlim">xlim<a class="anchor" aria-label="anchor" href="#arg-xlim"></a></dt>
+<dt id="arg-xlim">xlim<a class="anchor" aria-label="anchor" href="#arg-xlim"></a>
+</dt>
 <dd><p>(<code>numeric(2)</code>)<br> vector containing lower and upper limits for the x-axis, respectively.
 If <code>NULL</code> (default), the default scale range is used.</p></dd>
 
 
-<dt id="arg-ylim">ylim<a class="anchor" aria-label="anchor" href="#arg-ylim"></a></dt>
+<dt id="arg-ylim">ylim<a class="anchor" aria-label="anchor" href="#arg-ylim"></a>
+</dt>
 <dd><p>(<code>numeric(2)</code>)<br> vector containing lower and upper limits for the y-axis, respectively.
 If <code>NULL</code> (default), the default scale range is used.</p></dd>
 
 
-<dt id="arg-x-lab">x_lab<a class="anchor" aria-label="anchor" href="#arg-x-lab"></a></dt>
+<dt id="arg-x-lab">x_lab<a class="anchor" aria-label="anchor" href="#arg-x-lab"></a>
+</dt>
 <dd><p>(<code>string</code> or <code>NULL</code>)<br> x-axis label. If <code>NULL</code> then no label will be added.</p></dd>
 
 
-<dt id="arg-y-lab">y_lab<a class="anchor" aria-label="anchor" href="#arg-y-lab"></a></dt>
+<dt id="arg-y-lab">y_lab<a class="anchor" aria-label="anchor" href="#arg-y-lab"></a>
+</dt>
 <dd><p>(<code>string</code> or <code>NULL</code>)<br> y-axis label. If <code>NULL</code> then no label will be added.</p></dd>
 
 
-<dt id="arg-y-lab-add-paramcd">y_lab_add_paramcd<a class="anchor" aria-label="anchor" href="#arg-y-lab-add-paramcd"></a></dt>
+<dt id="arg-y-lab-add-paramcd">y_lab_add_paramcd<a class="anchor" aria-label="anchor" href="#arg-y-lab-add-paramcd"></a>
+</dt>
 <dd><p>(<code>flag</code>)<br> whether <code>paramcd</code>, i.e. <code>unique(df[[variables["paramcd"]]])</code> should be added
 to the y-axis label (<code>y_lab</code>).</p></dd>
 
 
-<dt id="arg-y-lab-add-unit">y_lab_add_unit<a class="anchor" aria-label="anchor" href="#arg-y-lab-add-unit"></a></dt>
+<dt id="arg-y-lab-add-unit">y_lab_add_unit<a class="anchor" aria-label="anchor" href="#arg-y-lab-add-unit"></a>
+</dt>
 <dd><p>(<code>flag</code>)<br> whether y-axis unit, i.e. <code>unique(df[[variables["y_unit"]]])</code> should be added
 to the y-axis label (<code>y_lab</code>).</p></dd>
 
 
-<dt id="arg-title">title<a class="anchor" aria-label="anchor" href="#arg-title"></a></dt>
+<dt id="arg-title">title<a class="anchor" aria-label="anchor" href="#arg-title"></a>
+</dt>
 <dd><p>(<code>string</code>)<br> plot title.</p></dd>
 
 
-<dt id="arg-subtitle">subtitle<a class="anchor" aria-label="anchor" href="#arg-subtitle"></a></dt>
+<dt id="arg-subtitle">subtitle<a class="anchor" aria-label="anchor" href="#arg-subtitle"></a>
+</dt>
 <dd><p>(<code>string</code>)<br> plot subtitle.</p></dd>
 
 
-<dt id="arg-subtitle-add-paramcd">subtitle_add_paramcd<a class="anchor" aria-label="anchor" href="#arg-subtitle-add-paramcd"></a></dt>
+<dt id="arg-subtitle-add-paramcd">subtitle_add_paramcd<a class="anchor" aria-label="anchor" href="#arg-subtitle-add-paramcd"></a>
+</dt>
 <dd><p>(<code>flag</code>)<br> whether <code>paramcd</code>, i.e. <code>unique(df[[variables["paramcd"]]])</code> should be
 added to the plot's subtitle (<code>subtitle</code>).</p></dd>
 
 
-<dt id="arg-subtitle-add-unit">subtitle_add_unit<a class="anchor" aria-label="anchor" href="#arg-subtitle-add-unit"></a></dt>
+<dt id="arg-subtitle-add-unit">subtitle_add_unit<a class="anchor" aria-label="anchor" href="#arg-subtitle-add-unit"></a>
+</dt>
 <dd><p>(<code>flag</code>)<br> whether the y-axis unit, i.e. <code>unique(df[[variables["y_unit"]]])</code> should be
 added to the plot's subtitle (<code>subtitle</code>).</p></dd>
 
 
-<dt id="arg-caption">caption<a class="anchor" aria-label="anchor" href="#arg-caption"></a></dt>
+<dt id="arg-caption">caption<a class="anchor" aria-label="anchor" href="#arg-caption"></a>
+</dt>
 <dd><p>(<code>string</code>)<br> optional caption below the plot.</p></dd>
 
 
-<dt id="arg-table-format">table_format<a class="anchor" aria-label="anchor" href="#arg-table-format"></a></dt>
+<dt id="arg-table-format">table_format<a class="anchor" aria-label="anchor" href="#arg-table-format"></a>
+</dt>
 <dd><p>(named <code>character</code> or <code>NULL</code>)<br> format patterns for descriptive statistics used in the
 (optional) table appended to the plot. It is passed directly to the <code>h_format_row</code> function through the <code>format</code>
 parameter. Names of <code>table_format</code> must match the names of statistics returned by <code>sfun</code> function.</p></dd>
 
 
-<dt id="arg-table-labels">table_labels<a class="anchor" aria-label="anchor" href="#arg-table-labels"></a></dt>
+<dt id="arg-table-labels">table_labels<a class="anchor" aria-label="anchor" href="#arg-table-labels"></a>
+</dt>
 <dd><p>(named <code>character</code> or <code>NULL</code>)<br> labels for descriptive statistics used in the (optional) table
 appended to the plot. Names of <code>table_labels</code> must match the names of statistics returned by <code>sfun</code> function.</p></dd>
 
 
-<dt id="arg-table-font-size">table_font_size<a class="anchor" aria-label="anchor" href="#arg-table-font-size"></a></dt>
+<dt id="arg-table-font-size">table_font_size<a class="anchor" aria-label="anchor" href="#arg-table-font-size"></a>
+</dt>
 <dd><p>(<code>numeric(1)</code>)<br> font size of the text in the table.</p></dd>
 
 
-<dt id="arg-errorbar-width">errorbar_width<a class="anchor" aria-label="anchor" href="#arg-errorbar-width"></a></dt>
+<dt id="arg-errorbar-width">errorbar_width<a class="anchor" aria-label="anchor" href="#arg-errorbar-width"></a>
+</dt>
 <dd><p>(<code>numeric(1)</code>)<br> width of the error bars.</p></dd>
 
 
-<dt id="arg-newpage">newpage<a class="anchor" aria-label="anchor" href="#arg-newpage"></a></dt>
+<dt id="arg-newpage">newpage<a class="anchor" aria-label="anchor" href="#arg-newpage"></a>
+</dt>
 <dd><p><a href="https://lifecycle.r-lib.org/articles/stages.html#deprecated" class="external-link"><img src="figures/lifecycle-deprecated.svg" alt="[Deprecated]"></a> not used.</p></dd>
 
 
-<dt id="arg-col">col<a class="anchor" aria-label="anchor" href="#arg-col"></a></dt>
+<dt id="arg-col">col<a class="anchor" aria-label="anchor" href="#arg-col"></a>
+</dt>
 <dd><p>(<code>character</code>)<br> color(s). See <code><a href="https://ggplot2.tidyverse.org/reference/aes_colour_fill_alpha.html" class="external-link">?ggplot2::aes_colour_fill_alpha</a></code> for example values.</p></dd>
 
 
-<dt id="arg-linetype">linetype<a class="anchor" aria-label="anchor" href="#arg-linetype"></a></dt>
+<dt id="arg-linetype">linetype<a class="anchor" aria-label="anchor" href="#arg-linetype"></a>
+</dt>
 <dd><p>(<code>character</code>)<br> line type(s). See <code><a href="https://ggplot2.tidyverse.org/reference/aes_linetype_size_shape.html" class="external-link">?ggplot2::aes_linetype_size_shape</a></code> for example values.</p></dd>
 
 
-<dt id="arg-rel-height-plot">rel_height_plot<a class="anchor" aria-label="anchor" href="#arg-rel-height-plot"></a></dt>
+<dt id="arg-rel-height-plot">rel_height_plot<a class="anchor" aria-label="anchor" href="#arg-rel-height-plot"></a>
+</dt>
 <dd><p>(<code>proportion</code>)<br> proportion of total figure height to allocate to the line plot.
 Relative height of annotation table is then <code>1 - rel_height_plot</code>. If <code>table = NULL</code>, this parameter is ignored.</p></dd>
 
 
-<dt id="arg-as-list">as_list<a class="anchor" aria-label="anchor" href="#arg-as-list"></a></dt>
+<dt id="arg-as-list">as_list<a class="anchor" aria-label="anchor" href="#arg-as-list"></a>
+</dt>
 <dd><p>(<code>flag</code>)<br> whether the two <code>ggplot</code> objects should be returned as a list when <code>table</code> is not <code>NULL</code>.
 If <code>TRUE</code>, a named list with two elements, <code>plot</code> and <code>table</code>, will be returned. If <code>FALSE</code> (default) the
 annotation table is printed below the plot via <code><a href="https://wilkelab.org/cowplot/reference/plot_grid.html" class="external-link">cowplot::plot_grid()</a></code>.</p></dd>
 
-</dl></div>
+</dl>
+</div>
     <div class="section level2">
-    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
+    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a>
+</h2>
     <p>A <code>ggplot</code> line plot (and statistics table if applicable).</p>
     </div>
 
     <div class="section level2">
-    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
+    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span></span></span>
 <span class="r-in"><span><span class="va">adsl</span> <span class="op">&lt;-</span> <span class="va">tern_ex_adsl</span></span></span>
 <span class="r-in"><span><span class="va">adlb</span> <span class="op">&lt;-</span> <span class="va">tern_ex_adlb</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> <span class="fu">dplyr</span><span class="fu">::</span><span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter</a></span><span class="op">(</span><span class="va">ANL01FL</span> <span class="op">==</span> <span class="st">"Y"</span>, <span class="va">PARAMCD</span> <span class="op">==</span> <span class="st">"ALT"</span>, <span class="va">AVISIT</span> <span class="op">!=</span> <span class="st">"SCREENING"</span><span class="op">)</span></span></span>
@@ -354,17 +463,19 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 </code></pre></div>
     </div>
   </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
-    </nav></aside></div>
+    </nav></aside>
+</div>
 
 
     <footer><div class="nest">
   <p>tern is a part of the <strong>NEST</strong> and <a href="https://pharmaverse.org/" class="external-link"><strong>pharmaverse</strong></a>.</p>
 </div>
-<script type="text/javascript" src="../analytics.js"></script></footer></div>
-
+<script type="text/javascript" src="../analytics.js"></script></footer>
+</div>
 
 
 
 
-  </body></html>
 
+  </body>
+</html>
diff --git a/main/reference/g_step.html b/main/reference/g_step.html
index 7b0397743c..f0d4c136bd 100644
--- a/main/reference/g_step.html
+++ b/main/reference/g_step.html
@@ -1,9 +1,32 @@
-<!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Create a STEP graph — g_step • tern</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Create a STEP graph — g_step"><meta name="description" content="
+<html lang="en">
+<head>
+<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+<meta charset="utf-8">
+<meta http-equiv="X-UA-Compatible" content="IE=edge">
+<meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<title>Create a STEP graph — g_step • tern</title>
+<!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png">
+<link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png">
+<link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png">
+<link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png">
+<link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png">
+<link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png">
+<script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet">
+<script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet">
+<link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet">
+<script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Create a STEP graph — g_step">
+<meta name="description" content="
 Based on the STEP results, creates a ggplot graph showing the estimated HR or OR
-along the continuous biomarker value subgroups."><meta property="og:description" content="
+along the continuous biomarker value subgroups.">
+<meta property="og:description" content="
 Based on the STEP results, creates a ggplot graph showing the estimated HR or OR
-along the continuous biomarker value subgroups."><meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png"><link rel="stylesheet" href="../consent.css"><script src="../consent.js" type="text/javascript" charset="utf-8"></script></head><body>
+along the continuous biomarker value subgroups.">
+<meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png">
+<link rel="stylesheet" href="../consent.css">
+<script src="../consent.js" type="text/javascript" charset="utf-8"></script>
+</head>
+<body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
 
 
@@ -19,26 +42,66 @@
     </button>
 
     <div id="navbar" class="collapse navbar-collapse ms-3">
-      <ul class="navbar-nav me-auto"><li class="nav-item"><a class="nav-link" href="../articles/tern.html">Get started</a></li>
+      <ul class="navbar-nav me-auto">
+<li class="nav-item"><a class="nav-link" href="../articles/tern.html">Get started</a></li>
 <li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
 <li class="nav-item dropdown">
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-articles" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Articles</button>
-  <ul class="dropdown-menu" aria-labelledby="dropdown-articles"><li><a class="dropdown-item" href="../articles/missing_values.html">Missing Values in Tern</a></li>
+  <ul class="dropdown-menu" aria-labelledby="dropdown-articles">
+<li><a class="dropdown-item" href="../articles/missing_values.html">Missing Values in Tern</a></li>
     <li><a class="dropdown-item" href="../articles/tables.html">Tabulation</a></li>
     <li><a class="dropdown-item" href="../articles/tern_formats.html">Formatting Functions</a></li>
     <li><a class="dropdown-item" href="../articles/tern_functions_guide.html">Understanding `tern` functions</a></li>
-  </ul></li>
+  </ul>
+</li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
-  <ul class="dropdown-menu" aria-labelledby="dropdown-reports"><li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
+  <ul class="dropdown-menu" aria-labelledby="dropdown-reports">
+<li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
     <li><a class="dropdown-item" href="../unit-test-report/">Unit test report</a></li>
     <li><a class="dropdown-item" href="../unit-test-report-non-cran/">Non-CRAN unit test report</a></li>
-  </ul></li>
-      </ul><ul class="navbar-nav"><li class="nav-item"><form class="form-inline" role="search">
- <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json"></form></li>
+  </ul>
+</li>
+      <div><li class="nav-item dropdown">
+    <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-versions">Versions</a>
+    <div class="dropdown-menu" aria-labelledby="dropdown-versions">
+    <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/main">main</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.5">v0.9.5</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.4">v0.9.4</a>
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+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1-rc3">v0.9.1-rc3</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a>
+</div>
+</li></div>
+</ul>
+<ul class="navbar-nav">
+<li class="nav-item"><form class="form-inline" role="search">
+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json">
+</form></li>
 <li class="nav-item"><a class="external-link nav-link" href="https://github.com/insightsengineering/tern" aria-label="GitHub"><span class="fa fa-github"></span></a></li>
-      </ul></div>
+      </ul>
+</div>
 
 
   </div>
@@ -57,7 +120,8 @@
     </div>
 
     <div class="section level2">
-    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
+    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">g_step</span><span class="op">(</span></span>
 <span>  <span class="va">df</span>,</span>
 <span>  use_percentile <span class="op">=</span> <span class="st">"Percentile Center"</span> <span class="op"><a href="https://rdrr.io/r/base/match.html" class="external-link">%in%</a></span> <span class="fu"><a href="https://rdrr.io/r/base/names.html" class="external-link">names</a></span><span class="op">(</span><span class="va">df</span><span class="op">)</span>,</span>
@@ -68,42 +132,53 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
     </div>
 
     <div class="section level2">
-    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
+    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a>
+</h2>
 
 
-<dl><dt id="arg-df">df<a class="anchor" aria-label="anchor" href="#arg-df"></a></dt>
+<dl>
+<dt id="arg-df">df<a class="anchor" aria-label="anchor" href="#arg-df"></a>
+</dt>
 <dd><p>(<code>tibble</code>)<br> result of <code><a href="tidy.step.html">tidy.step()</a></code>.</p></dd>
 
 
-<dt id="arg-use-percentile">use_percentile<a class="anchor" aria-label="anchor" href="#arg-use-percentile"></a></dt>
+<dt id="arg-use-percentile">use_percentile<a class="anchor" aria-label="anchor" href="#arg-use-percentile"></a>
+</dt>
 <dd><p>(<code>flag</code>)<br> whether to use percentiles for the x axis or actual
 biomarker values.</p></dd>
 
 
-<dt id="arg-est">est<a class="anchor" aria-label="anchor" href="#arg-est"></a></dt>
+<dt id="arg-est">est<a class="anchor" aria-label="anchor" href="#arg-est"></a>
+</dt>
 <dd><p>(named <code>list</code>)<br><code>col</code> and <code>lty</code> settings for estimate line.</p></dd>
 
 
-<dt id="arg-ci-ribbon">ci_ribbon<a class="anchor" aria-label="anchor" href="#arg-ci-ribbon"></a></dt>
+<dt id="arg-ci-ribbon">ci_ribbon<a class="anchor" aria-label="anchor" href="#arg-ci-ribbon"></a>
+</dt>
 <dd><p>(named <code>list</code> or <code>NULL</code>)<br><code>fill</code> and <code>alpha</code> settings for the confidence interval
 ribbon area, or <code>NULL</code> to not plot a CI ribbon.</p></dd>
 
 
-<dt id="arg-col">col<a class="anchor" aria-label="anchor" href="#arg-col"></a></dt>
+<dt id="arg-col">col<a class="anchor" aria-label="anchor" href="#arg-col"></a>
+</dt>
 <dd><p>(<code>character</code>)<br> color(s).</p></dd>
 
-</dl></div>
+</dl>
+</div>
     <div class="section level2">
-    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
+    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a>
+</h2>
     <p>A <code>ggplot</code> STEP graph.</p>
     </div>
     <div class="section level2">
-    <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"></a></h2>
+    <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"></a>
+</h2>
     <div class="dont-index"><p>Custom tidy method <code><a href="tidy.step.html">tidy.step()</a></code>.</p></div>
     </div>
 
     <div class="section level2">
-    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
+    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://github.com/therneau/survival" class="external-link">survival</a></span><span class="op">)</span></span></span>
 <span class="r-in"><span><span class="va">lung</span><span class="op">$</span><span class="va">sex</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/factor.html" class="external-link">factor</a></span><span class="op">(</span><span class="va">lung</span><span class="op">$</span><span class="va">sex</span><span class="op">)</span></span></span>
 <span class="r-in"><span></span></span>
@@ -170,17 +245,19 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 </code></pre></div>
     </div>
   </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
-    </nav></aside></div>
+    </nav></aside>
+</div>
 
 
     <footer><div class="nest">
   <p>tern is a part of the <strong>NEST</strong> and <a href="https://pharmaverse.org/" class="external-link"><strong>pharmaverse</strong></a>.</p>
 </div>
-<script type="text/javascript" src="../analytics.js"></script></footer></div>
-
+<script type="text/javascript" src="../analytics.js"></script></footer>
+</div>
 
 
 
 
-  </body></html>
 
+  </body>
+</html>
diff --git a/main/reference/g_waterfall.html b/main/reference/g_waterfall.html
index 59d7eed100..ad1e0594f1 100644
--- a/main/reference/g_waterfall.html
+++ b/main/reference/g_waterfall.html
@@ -1,7 +1,30 @@
-<!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Horizontal waterfall plot — g_waterfall • tern</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Horizontal waterfall plot — g_waterfall"><meta name="description" content="
-This basic waterfall plot visualizes a quantity height ordered by value with some markup."><meta property="og:description" content="
-This basic waterfall plot visualizes a quantity height ordered by value with some markup."><meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png"><link rel="stylesheet" href="../consent.css"><script src="../consent.js" type="text/javascript" charset="utf-8"></script></head><body>
+<html lang="en">
+<head>
+<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+<meta charset="utf-8">
+<meta http-equiv="X-UA-Compatible" content="IE=edge">
+<meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<title>Horizontal waterfall plot — g_waterfall • tern</title>
+<!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png">
+<link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png">
+<link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png">
+<link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png">
+<link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png">
+<link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png">
+<script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet">
+<script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet">
+<link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet">
+<script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Horizontal waterfall plot — g_waterfall">
+<meta name="description" content="
+This basic waterfall plot visualizes a quantity height ordered by value with some markup.">
+<meta property="og:description" content="
+This basic waterfall plot visualizes a quantity height ordered by value with some markup.">
+<meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png">
+<link rel="stylesheet" href="../consent.css">
+<script src="../consent.js" type="text/javascript" charset="utf-8"></script>
+</head>
+<body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
 
 
@@ -17,26 +40,66 @@
     </button>
 
     <div id="navbar" class="collapse navbar-collapse ms-3">
-      <ul class="navbar-nav me-auto"><li class="nav-item"><a class="nav-link" href="../articles/tern.html">Get started</a></li>
+      <ul class="navbar-nav me-auto">
+<li class="nav-item"><a class="nav-link" href="../articles/tern.html">Get started</a></li>
 <li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
 <li class="nav-item dropdown">
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-articles" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Articles</button>
-  <ul class="dropdown-menu" aria-labelledby="dropdown-articles"><li><a class="dropdown-item" href="../articles/missing_values.html">Missing Values in Tern</a></li>
+  <ul class="dropdown-menu" aria-labelledby="dropdown-articles">
+<li><a class="dropdown-item" href="../articles/missing_values.html">Missing Values in Tern</a></li>
     <li><a class="dropdown-item" href="../articles/tables.html">Tabulation</a></li>
     <li><a class="dropdown-item" href="../articles/tern_formats.html">Formatting Functions</a></li>
     <li><a class="dropdown-item" href="../articles/tern_functions_guide.html">Understanding `tern` functions</a></li>
-  </ul></li>
+  </ul>
+</li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
-  <ul class="dropdown-menu" aria-labelledby="dropdown-reports"><li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
+  <ul class="dropdown-menu" aria-labelledby="dropdown-reports">
+<li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
     <li><a class="dropdown-item" href="../unit-test-report/">Unit test report</a></li>
     <li><a class="dropdown-item" href="../unit-test-report-non-cran/">Non-CRAN unit test report</a></li>
-  </ul></li>
-      </ul><ul class="navbar-nav"><li class="nav-item"><form class="form-inline" role="search">
- <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json"></form></li>
+  </ul>
+</li>
+      <div><li class="nav-item dropdown">
+    <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-versions">Versions</a>
+    <div class="dropdown-menu" aria-labelledby="dropdown-versions">
+    <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/main">main</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.5">v0.9.5</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.4">v0.9.4</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.3">v0.9.3</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1-rc3">v0.9.1-rc3</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a>
+</div>
+</li></div>
+</ul>
+<ul class="navbar-nav">
+<li class="nav-item"><form class="form-inline" role="search">
+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json">
+</form></li>
 <li class="nav-item"><a class="external-link nav-link" href="https://github.com/insightsengineering/tern" aria-label="GitHub"><span class="fa fa-github"></span></a></li>
-      </ul></div>
+      </ul>
+</div>
 
 
   </div>
@@ -54,7 +117,8 @@
     </div>
 
     <div class="section level2">
-    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
+    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">g_waterfall</span><span class="op">(</span></span>
 <span>  <span class="va">height</span>,</span>
 <span>  <span class="va">id</span>,</span>
@@ -68,48 +132,61 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
     </div>
 
     <div class="section level2">
-    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
+    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a>
+</h2>
 
 
-<dl><dt id="arg-height">height<a class="anchor" aria-label="anchor" href="#arg-height"></a></dt>
+<dl>
+<dt id="arg-height">height<a class="anchor" aria-label="anchor" href="#arg-height"></a>
+</dt>
 <dd><p>(<code>numeric</code>)<br> vector containing values to be plotted as the waterfall bars.</p></dd>
 
 
-<dt id="arg-id">id<a class="anchor" aria-label="anchor" href="#arg-id"></a></dt>
+<dt id="arg-id">id<a class="anchor" aria-label="anchor" href="#arg-id"></a>
+</dt>
 <dd><p>(<code>character</code>)<br> vector containing identifiers to use as the x-axis label for the waterfall bars.</p></dd>
 
 
-<dt id="arg-col-var">col_var<a class="anchor" aria-label="anchor" href="#arg-col-var"></a></dt>
+<dt id="arg-col-var">col_var<a class="anchor" aria-label="anchor" href="#arg-col-var"></a>
+</dt>
 <dd><p>(<code>factor</code>, <code>character</code>, or <code>NULL</code>)<br> categorical variable for bar coloring. <code>NULL</code> by default.</p></dd>
 
 
-<dt id="arg-col">col<a class="anchor" aria-label="anchor" href="#arg-col"></a></dt>
+<dt id="arg-col">col<a class="anchor" aria-label="anchor" href="#arg-col"></a>
+</dt>
 <dd><p>(<code>character</code>)<br> color(s).</p></dd>
 
 
-<dt id="arg-xlab">xlab<a class="anchor" aria-label="anchor" href="#arg-xlab"></a></dt>
+<dt id="arg-xlab">xlab<a class="anchor" aria-label="anchor" href="#arg-xlab"></a>
+</dt>
 <dd><p>(<code>string</code>)<br> x label. Default is <code>"ID"</code>.</p></dd>
 
 
-<dt id="arg-ylab">ylab<a class="anchor" aria-label="anchor" href="#arg-ylab"></a></dt>
+<dt id="arg-ylab">ylab<a class="anchor" aria-label="anchor" href="#arg-ylab"></a>
+</dt>
 <dd><p>(<code>string</code>)<br> y label. Default is <code>"Value"</code>.</p></dd>
 
 
-<dt id="arg-col-legend-title">col_legend_title<a class="anchor" aria-label="anchor" href="#arg-col-legend-title"></a></dt>
+<dt id="arg-col-legend-title">col_legend_title<a class="anchor" aria-label="anchor" href="#arg-col-legend-title"></a>
+</dt>
 <dd><p>(<code>string</code>)<br> text to be displayed as legend title.</p></dd>
 
 
-<dt id="arg-title">title<a class="anchor" aria-label="anchor" href="#arg-title"></a></dt>
+<dt id="arg-title">title<a class="anchor" aria-label="anchor" href="#arg-title"></a>
+</dt>
 <dd><p>(<code>string</code>)<br> text to be displayed as plot title.</p></dd>
 
-</dl></div>
+</dl>
+</div>
     <div class="section level2">
-    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
+    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a>
+</h2>
     <p>A <code>ggplot</code> waterfall plot.</p>
     </div>
 
     <div class="section level2">
-    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
+    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://dplyr.tidyverse.org" class="external-link">dplyr</a></span><span class="op">)</span></span></span>
 <span class="r-in"><span></span></span>
 <span class="r-in"><span><span class="fu">g_waterfall</span><span class="op">(</span>height <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">3</span>, <span class="fl">5</span>, <span class="op">-</span><span class="fl">1</span><span class="op">)</span>, id <span class="op">=</span> <span class="va">letters</span><span class="op">[</span><span class="fl">1</span><span class="op">:</span><span class="fl">3</span><span class="op">]</span><span class="op">)</span></span></span>
@@ -172,17 +249,19 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 </code></pre></div>
     </div>
   </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
-    </nav></aside></div>
+    </nav></aside>
+</div>
 
 
     <footer><div class="nest">
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diff --git a/main/reference/get_covariates.html b/main/reference/get_covariates.html
index 22e44093f8..326843866e 100644
--- a/main/reference/get_covariates.html
+++ b/main/reference/get_covariates.html
@@ -1,5 +1,28 @@
-<!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Utility function to return a named list of covariate names — get_covariates • tern</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Utility function to return a named list of covariate names — get_covariates"><meta name="description" content="Utility function to return a named list of covariate names"><meta property="og:description" content="Utility function to return a named list of covariate names"><meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png"><link rel="stylesheet" href="../consent.css"><script src="../consent.js" type="text/javascript" charset="utf-8"></script></head><body>
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+<script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Utility function to return a named list of covariate names — get_covariates">
+<meta name="description" content="Utility function to return a named list of covariate names">
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@@ -15,26 +38,66 @@
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+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a>
+</div>
+</li></div>
+</ul>
+<ul class="navbar-nav">
+<li class="nav-item"><form class="form-inline" role="search">
+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json">
+</form></li>
 <li class="nav-item"><a class="external-link nav-link" href="https://github.com/insightsengineering/tern" aria-label="GitHub"><span class="fa fa-github"></span></a></li>
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+      </ul>
+</div>
 
 
   </div>
@@ -51,36 +114,44 @@
     </div>
 
     <div class="section level2">
-    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
+    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">get_covariates</span><span class="op">(</span><span class="va">covariates</span><span class="op">)</span></span></code></pre></div>
     </div>
 
     <div class="section level2">
-    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
+    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a>
+</h2>
 
 
-<dl><dt id="arg-covariates">covariates<a class="anchor" aria-label="anchor" href="#arg-covariates"></a></dt>
+<dl>
+<dt id="arg-covariates">covariates<a class="anchor" aria-label="anchor" href="#arg-covariates"></a>
+</dt>
 <dd><p>(<code>character</code>)<br> a vector that can contain single variable names (such as
 <code>"X1"</code>), and/or interaction terms indicated by <code>"X1 * X2"</code>.</p></dd>
 
-</dl></div>
+</dl>
+</div>
     <div class="section level2">
-    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
+    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a>
+</h2>
     <p>A named <code>list</code> of <code>character</code> vector.</p>
     </div>
 
   </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
-    </nav></aside></div>
+    </nav></aside>
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diff --git a/main/reference/get_smooths.html b/main/reference/get_smooths.html
index 3755482258..ceb012fea0 100644
--- a/main/reference/get_smooths.html
+++ b/main/reference/get_smooths.html
@@ -1,7 +1,30 @@
-<!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Smooth function with optional grouping — get_smooths • tern</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Smooth function with optional grouping — get_smooths"><meta name="description" content="
-This produces loess smoothed estimates of y with Student confidence intervals."><meta property="og:description" content="
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+<meta name="description" content="
+This produces loess smoothed estimates of y with Student confidence intervals.">
+<meta property="og:description" content="
+This produces loess smoothed estimates of y with Student confidence intervals.">
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+<li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
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- <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json"></form></li>
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+    <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
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+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
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+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
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+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
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+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a>
+</div>
+</li></div>
+</ul>
+<ul class="navbar-nav">
+<li class="nav-item"><form class="form-inline" role="search">
+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json">
+</form></li>
 <li class="nav-item"><a class="external-link nav-link" href="https://github.com/insightsengineering/tern" aria-label="GitHub"><span class="fa fa-github"></span></a></li>
-      </ul></div>
+      </ul>
+</div>
 
 
   </div>
@@ -54,52 +117,64 @@
     </div>
 
     <div class="section level2">
-    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
+    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">get_smooths</span><span class="op">(</span><span class="va">df</span>, <span class="va">x</span>, <span class="va">y</span>, groups <span class="op">=</span> <span class="cn">NULL</span>, level <span class="op">=</span> <span class="fl">0.95</span><span class="op">)</span></span></code></pre></div>
     </div>
 
     <div class="section level2">
-    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
+    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a>
+</h2>
 
 
-<dl><dt id="arg-df">df<a class="anchor" aria-label="anchor" href="#arg-df"></a></dt>
+<dl>
+<dt id="arg-df">df<a class="anchor" aria-label="anchor" href="#arg-df"></a>
+</dt>
 <dd><p>(<code>data.frame</code>)<br> data set containing all analysis variables.</p></dd>
 
 
-<dt id="arg-x">x<a class="anchor" aria-label="anchor" href="#arg-x"></a></dt>
+<dt id="arg-x">x<a class="anchor" aria-label="anchor" href="#arg-x"></a>
+</dt>
 <dd><p>(<code>string</code>)<br> x column name.</p></dd>
 
 
-<dt id="arg-y">y<a class="anchor" aria-label="anchor" href="#arg-y"></a></dt>
+<dt id="arg-y">y<a class="anchor" aria-label="anchor" href="#arg-y"></a>
+</dt>
 <dd><p>(<code>string</code>)<br> y column name.</p></dd>
 
 
-<dt id="arg-groups">groups<a class="anchor" aria-label="anchor" href="#arg-groups"></a></dt>
+<dt id="arg-groups">groups<a class="anchor" aria-label="anchor" href="#arg-groups"></a>
+</dt>
 <dd><p>(<code>character</code> or <code>NULL</code>)<br> vector with optional grouping variables names.</p></dd>
 
 
-<dt id="arg-level">level<a class="anchor" aria-label="anchor" href="#arg-level"></a></dt>
+<dt id="arg-level">level<a class="anchor" aria-label="anchor" href="#arg-level"></a>
+</dt>
 <dd><p>(<code>proportion</code>)<br> level of confidence interval to use (0.95 by default).</p></dd>
 
-</dl></div>
+</dl>
+</div>
     <div class="section level2">
-    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
+    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a>
+</h2>
     <p>A <code>data.frame</code> with original <code>x</code>, smoothed <code>y</code>, <code>ylow</code>, and <code>yhigh</code>, and
 optional <code>groups</code> variables formatted as <code>factor</code> type.</p>
     </div>
 
   </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
-    </nav></aside></div>
+    </nav></aside>
+</div>
 
 
     <footer><div class="nest">
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diff --git a/main/reference/groups_list_to_df.html b/main/reference/groups_list_to_df.html
index ec1dbe0826..3dae1cc9b3 100644
--- a/main/reference/groups_list_to_df.html
+++ b/main/reference/groups_list_to_df.html
@@ -1,5 +1,28 @@
-<!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Convert list of groups to a data frame — groups_list_to_df • tern</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Convert list of groups to a data frame — groups_list_to_df"><meta name="description" content="This converts a list of group levels into a data frame format which is expected by rtables::add_combo_levels()."><meta property="og:description" content="This converts a list of group levels into a data frame format which is expected by rtables::add_combo_levels()."><meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png"><link rel="stylesheet" href="../consent.css"><script src="../consent.js" type="text/javascript" charset="utf-8"></script></head><body>
+<html lang="en">
+<head>
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+<title>Convert list of groups to a data frame — groups_list_to_df • tern</title>
+<!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png">
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+<link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet">
+<script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet">
+<link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet">
+<script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Convert list of groups to a data frame — groups_list_to_df">
+<meta name="description" content="This converts a list of group levels into a data frame format which is expected by rtables::add_combo_levels().">
+<meta property="og:description" content="This converts a list of group levels into a data frame format which is expected by rtables::add_combo_levels().">
+<meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png">
+<link rel="stylesheet" href="../consent.css">
+<script src="../consent.js" type="text/javascript" charset="utf-8"></script>
+</head>
+<body>
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@@ -15,26 +38,66 @@
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+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a>
+</div>
+</li></div>
+</ul>
+<ul class="navbar-nav">
+<li class="nav-item"><form class="form-inline" role="search">
+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json">
+</form></li>
 <li class="nav-item"><a class="external-link nav-link" href="https://github.com/insightsengineering/tern" aria-label="GitHub"><span class="fa fa-github"></span></a></li>
-      </ul></div>
+      </ul>
+</div>
 
 
   </div>
@@ -51,26 +114,33 @@
     </div>
 
     <div class="section level2">
-    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
+    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">groups_list_to_df</span><span class="op">(</span><span class="va">groups_list</span><span class="op">)</span></span></code></pre></div>
     </div>
 
     <div class="section level2">
-    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
+    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a>
+</h2>
 
 
-<dl><dt id="arg-groups-list">groups_list<a class="anchor" aria-label="anchor" href="#arg-groups-list"></a></dt>
+<dl>
+<dt id="arg-groups-list">groups_list<a class="anchor" aria-label="anchor" href="#arg-groups-list"></a>
+</dt>
 <dd><p>(named <code>list</code> of <code>character</code>)<br> specifies the new group levels via the names and the
 levels that belong to it in the character vectors that are elements of the list.</p></dd>
 
-</dl></div>
+</dl>
+</div>
     <div class="section level2">
-    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
+    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a>
+</h2>
     <p>A <code>tibble</code> in the required format.</p>
     </div>
 
     <div class="section level2">
-    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
+    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">grade_groups</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span></span></span>
 <span class="r-in"><span>  <span class="st">"Any Grade (%)"</span> <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"1"</span>, <span class="st">"2"</span>, <span class="st">"3"</span>, <span class="st">"4"</span>, <span class="st">"5"</span><span class="op">)</span>,</span></span>
 <span class="r-in"><span>  <span class="st">"Grade 3-4 (%)"</span> <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"3"</span>, <span class="st">"4"</span><span class="op">)</span>,</span></span>
@@ -87,17 +157,19 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 </code></pre></div>
     </div>
   </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
-    </nav></aside></div>
+    </nav></aside>
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index aad9612f30..5fd3ef3203 100644
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+<meta name="description" content='
 Helper function to prepare an ADLB data frame to be used as input in
 count_abnormal_by_worst_grade(). The following pre-processing steps are applied:
 adlb is filtered on variable avisit to only include post-baseline visits.
@@ -17,7 +34,8 @@
 
 Unused factor levels are dropped from adlb via droplevels().
 
-'><meta property="og:description" content='
+'>
+<meta property="og:description" content='
 Helper function to prepare an ADLB data frame to be used as input in
 count_abnormal_by_worst_grade(). The following pre-processing steps are applied:
 adlb is filtered on variable avisit to only include post-baseline visits.
@@ -35,7 +53,12 @@
 
 Unused factor levels are dropped from adlb via droplevels().
 
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-      <img src="../logo.png" class="logo" alt=""><h1>Helper function to prepare ADLB for <code>count_abnormal_by_worst_grade()</code></h1>
+      <img src="../logo.png" class="logo" alt=""><h1>Helper function to prepare ADLB for <code>count_abnormal_by_worst_grade()</code>
+</h1>
       <small class="dont-index">Source: <a href="https://github.com/insightsengineering/tern/blob/main/R/abnormal_by_worst_grade.R" class="external-link"><code>R/abnormal_by_worst_grade.R</code></a></small>
       <div class="d-none name"><code>h_adlb_abnormal_by_worst_grade.Rd</code></div>
     </div>
@@ -85,20 +149,28 @@
     <div class="ref-description section level2">
     <p><a href="https://lifecycle.r-lib.org/articles/stages.html#stable" class="external-link"><img src="figures/lifecycle-stable.svg" alt="[Stable]"></a></p>
 <p>Helper function to prepare an ADLB data frame to be used as input in
-<code><a href="abnormal_by_worst_grade.html">count_abnormal_by_worst_grade()</a></code>. The following pre-processing steps are applied:</p><ol><li><p><code>adlb</code> is filtered on variable <code>avisit</code> to only include post-baseline visits.</p></li>
+<code><a href="abnormal_by_worst_grade.html">count_abnormal_by_worst_grade()</a></code>. The following pre-processing steps are applied:</p>
+<ol>
+<li><p><code>adlb</code> is filtered on variable <code>avisit</code> to only include post-baseline visits.</p></li>
 <li><p><code>adlb</code> is filtered on variables <code>worst_flag_low</code> and <code>worst_flag_high</code> so that only
 worst grades (in either direction) are included.</p></li>
 <li><p>From the standard lab grade variable <code>atoxgr</code>, the following two variables are derived
 and added to <code>adlb</code>:</p></li>
-</ol><ul><li><p>A grade direction variable (e.g. <code>GRADE_DIR</code>). The variable takes value <code>"HIGH"</code> when
+</ol>
+<ul>
+<li><p>A grade direction variable (e.g. <code>GRADE_DIR</code>). The variable takes value <code>"HIGH"</code> when
 <code>atoxgr &gt; 0</code>, <code>"LOW"</code> when <code>atoxgr &lt; 0</code>, and <code>"ZERO"</code> otherwise.</p></li>
 <li><p>A toxicity grade variable (e.g. <code>GRADE_ANL</code>) where all negative values from <code>atoxgr</code> are
 replaced by their absolute values.</p></li>
-</ul><ol><li><p>Unused factor levels are dropped from <code>adlb</code> via <code><a href="https://rdrr.io/r/base/droplevels.html" class="external-link">droplevels()</a></code>.</p></li>
-</ol></div>
+</ul>
+<ol>
+<li><p>Unused factor levels are dropped from <code>adlb</code> via <code><a href="https://rdrr.io/r/base/droplevels.html" class="external-link">droplevels()</a></code>.</p></li>
+</ol>
+</div>
 
     <div class="section level2">
-    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
+    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">h_adlb_abnormal_by_worst_grade</span><span class="op">(</span></span>
 <span>  <span class="va">adlb</span>,</span>
 <span>  atoxgr <span class="op">=</span> <span class="st">"ATOXGR"</span>,</span>
@@ -109,44 +181,55 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
     </div>
 
     <div class="section level2">
-    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
+    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a>
+</h2>
 
 
-<dl><dt id="arg-adlb">adlb<a class="anchor" aria-label="anchor" href="#arg-adlb"></a></dt>
+<dl>
+<dt id="arg-adlb">adlb<a class="anchor" aria-label="anchor" href="#arg-adlb"></a>
+</dt>
 <dd><p>(<code>data.frame</code>)<br> ADLB data frame.</p></dd>
 
 
-<dt id="arg-atoxgr">atoxgr<a class="anchor" aria-label="anchor" href="#arg-atoxgr"></a></dt>
+<dt id="arg-atoxgr">atoxgr<a class="anchor" aria-label="anchor" href="#arg-atoxgr"></a>
+</dt>
 <dd><p>(<code>string</code>)<br> name of the analysis toxicity grade variable. This must be a <code>factor</code>
 variable.</p></dd>
 
 
-<dt id="arg-avisit">avisit<a class="anchor" aria-label="anchor" href="#arg-avisit"></a></dt>
+<dt id="arg-avisit">avisit<a class="anchor" aria-label="anchor" href="#arg-avisit"></a>
+</dt>
 <dd><p>(<code>string</code>)<br> name of the analysis visit variable.</p></dd>
 
 
-<dt id="arg-worst-flag-low">worst_flag_low<a class="anchor" aria-label="anchor" href="#arg-worst-flag-low"></a></dt>
+<dt id="arg-worst-flag-low">worst_flag_low<a class="anchor" aria-label="anchor" href="#arg-worst-flag-low"></a>
+</dt>
 <dd><p>(<code>string</code>)<br> name of the worst low lab grade flag variable. This variable is
 set to <code>"Y"</code> when indicating records of worst low lab grades.</p></dd>
 
 
-<dt id="arg-worst-flag-high">worst_flag_high<a class="anchor" aria-label="anchor" href="#arg-worst-flag-high"></a></dt>
+<dt id="arg-worst-flag-high">worst_flag_high<a class="anchor" aria-label="anchor" href="#arg-worst-flag-high"></a>
+</dt>
 <dd><p>(<code>string</code>)<br> name of the worst high lab grade flag variable. This variable is
 set to <code>"Y"</code> when indicating records of worst high lab grades.</p></dd>
 
-</dl></div>
+</dl>
+</div>
     <div class="section level2">
-    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
+    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a>
+</h2>
     <p><code>h_adlb_abnormal_by_worst_grade()</code> returns the <code>adlb</code> data frame with two new
 variables: <code>GRADE_DIR</code> and <code>GRADE_ANL</code>.</p>
     </div>
     <div class="section level2">
-    <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"></a></h2>
+    <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"></a>
+</h2>
     <div class="dont-index"><p><a href="abnormal_by_worst_grade.html">abnormal_by_worst_grade</a></p></div>
     </div>
 
     <div class="section level2">
-    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
+    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="fu">h_adlb_abnormal_by_worst_grade</span><span class="op">(</span><span class="va">tern_ex_adlb</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span></span>
 <span class="r-in"><span>  <span class="fu">dplyr</span><span class="fu">::</span><span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html" class="external-link">select</a></span><span class="op">(</span><span class="va">ATOXGR</span>, <span class="va">GRADE_DIR</span>, <span class="va">GRADE_ANL</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span></span>
 <span class="r-in"><span>  <span class="fu"><a href="https://rdrr.io/r/utils/head.html" class="external-link">head</a></span><span class="op">(</span><span class="fl">10</span><span class="op">)</span></span></span>
@@ -167,17 +250,19 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 </code></pre></div>
     </div>
   </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
-    </nav></aside></div>
+    </nav></aside>
+</div>
 
 
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index bd2070b92b..4b9f01bcee 100644
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+++ b/main/reference/h_adlb_worsen.html
@@ -1,7 +1,30 @@
-<!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Helper function to prepare ADLB with worst labs — h_adlb_worsen • tern</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Helper function to prepare ADLB with worst labs — h_adlb_worsen"><meta name="description" content="
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+<meta name="description" content="
+Helper function to prepare a df for generate the patient count shift table.">
+<meta property="og:description" content="
+Helper function to prepare a df for generate the patient count shift table.">
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   </div>
@@ -54,7 +117,8 @@
     </div>
 
     <div class="section level2">
-    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
+    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">h_adlb_worsen</span><span class="op">(</span></span>
 <span>  <span class="va">adlb</span>,</span>
 <span>  worst_flag_low <span class="op">=</span> <span class="cn">NULL</span>,</span>
@@ -64,33 +128,45 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
     </div>
 
     <div class="section level2">
-    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
+    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a>
+</h2>
 
 
-<dl><dt id="arg-adlb">adlb<a class="anchor" aria-label="anchor" href="#arg-adlb"></a></dt>
+<dl>
+<dt id="arg-adlb">adlb<a class="anchor" aria-label="anchor" href="#arg-adlb"></a>
+</dt>
 <dd><p>(<code>data.frame</code>)<br> ADLB data frame.</p></dd>
 
 
-<dt id="arg-worst-flag-low">worst_flag_low<a class="anchor" aria-label="anchor" href="#arg-worst-flag-low"></a></dt>
+<dt id="arg-worst-flag-low">worst_flag_low<a class="anchor" aria-label="anchor" href="#arg-worst-flag-low"></a>
+</dt>
 <dd><p>(named <code>vector</code>)<br> worst low post-baseline lab grade flag variable. See how this is
 implemented in the following examples.</p></dd>
 
 
-<dt id="arg-worst-flag-high">worst_flag_high<a class="anchor" aria-label="anchor" href="#arg-worst-flag-high"></a></dt>
+<dt id="arg-worst-flag-high">worst_flag_high<a class="anchor" aria-label="anchor" href="#arg-worst-flag-high"></a>
+</dt>
 <dd><p>(named <code>vector</code>)<br> worst high post-baseline lab grade flag variable. See how this is
 implemented in the following examples.</p></dd>
 
 
-<dt id="arg-direction-var">direction_var<a class="anchor" aria-label="anchor" href="#arg-direction-var"></a></dt>
-<dd><p>(<code>string</code>)<br> name of the direction variable specifying the direction of the shift table of
-interest. Only lab records flagged by <code>L</code>, <code>H</code> or <code>B</code> are included in the shift table.</p><ul><li><p><code>L</code>: low direction only</p></li>
+<dt id="arg-direction-var">direction_var<a class="anchor" aria-label="anchor" href="#arg-direction-var"></a>
+</dt>
+<dd>
+<p>(<code>string</code>)<br> name of the direction variable specifying the direction of the shift table of
+interest. Only lab records flagged by <code>L</code>, <code>H</code> or <code>B</code> are included in the shift table.</p>
+<ul>
+<li><p><code>L</code>: low direction only</p></li>
 <li><p><code>H</code>: high direction only</p></li>
 <li><p><code>B</code>: both low and high directions</p></li>
-</ul></dd>
+</ul>
+</dd>
 
-</dl></div>
+</dl>
+</div>
     <div class="section level2">
-    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
+    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a>
+</h2>
     <p><code>h_adlb_worsen()</code> returns the <code>adlb</code> <code>data.frame</code> containing only the
 worst labs specified according to <code>worst_flag_low</code> or <code>worst_flag_high</code> for the
 direction specified according to <code>direction_var</code>. For instance, for a lab that is
@@ -100,12 +176,14 @@ <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2
 for the high direction.</p>
     </div>
     <div class="section level2">
-    <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"></a></h2>
+    <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"></a>
+</h2>
     <div class="dont-index"><p><a href="abnormal_by_worst_grade_worsen.html">abnormal_by_worst_grade_worsen</a></p></div>
     </div>
 
     <div class="section level2">
-    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
+    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://dplyr.tidyverse.org" class="external-link">dplyr</a></span><span class="op">)</span></span></span>
 <span class="r-in"><span></span></span>
 <span class="r-in"><span><span class="co"># The direction variable, GRADDR, is based on metadata</span></span></span>
@@ -129,17 +207,19 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 </code></pre></div>
     </div>
   </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
-    </nav></aside></div>
+    </nav></aside>
+</div>
 
 
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   <p>tern is a part of the <strong>NEST</strong> and <a href="https://pharmaverse.org/" class="external-link"><strong>pharmaverse</strong></a>.</p>
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diff --git a/main/reference/h_adsl_adlb_merge_using_worst_flag.html b/main/reference/h_adsl_adlb_merge_using_worst_flag.html
index 3cbb8cc8e4..e16b9b4586 100644
--- a/main/reference/h_adsl_adlb_merge_using_worst_flag.html
+++ b/main/reference/h_adsl_adlb_merge_using_worst_flag.html
@@ -1,11 +1,34 @@
-<!DOCTYPE html>
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+<html lang="en">
+<head>
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+<meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<title>Helper function for deriving analysis datasets for select laboratory tables — h_adsl_adlb_merge_using_worst_flag • tern</title>
+<!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png">
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+<link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png">
+<link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png">
+<script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet">
+<script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet">
+<link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet">
+<script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Helper function for deriving analysis datasets for select laboratory tables — h_adsl_adlb_merge_using_worst_flag">
+<meta name="description" content="
 Helper function that merges ADSL and ADLB datasets so that missing lab test records are inserted in the
 output dataset. Remember that na_level must match the needed pre-processing
-done with df_explicit_na() to have the desired output."><meta property="og:description" content="
+done with df_explicit_na() to have the desired output.">
+<meta property="og:description" content="
 Helper function that merges ADSL and ADLB datasets so that missing lab test records are inserted in the
 output dataset. Remember that na_level must match the needed pre-processing
-done with df_explicit_na() to have the desired output."><meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png"><link rel="stylesheet" href="../consent.css"><script src="../consent.js" type="text/javascript" charset="utf-8"></script></head><body>
+done with df_explicit_na() to have the desired output.">
+<meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png">
+<link rel="stylesheet" href="../consent.css">
+<script src="../consent.js" type="text/javascript" charset="utf-8"></script>
+</head>
+<body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
 
 
@@ -21,26 +44,66 @@
     </button>
 
     <div id="navbar" class="collapse navbar-collapse ms-3">
-      <ul class="navbar-nav me-auto"><li class="nav-item"><a class="nav-link" href="../articles/tern.html">Get started</a></li>
+      <ul class="navbar-nav me-auto">
+<li class="nav-item"><a class="nav-link" href="../articles/tern.html">Get started</a></li>
 <li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
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+  <ul class="dropdown-menu" aria-labelledby="dropdown-articles">
+<li><a class="dropdown-item" href="../articles/missing_values.html">Missing Values in Tern</a></li>
     <li><a class="dropdown-item" href="../articles/tables.html">Tabulation</a></li>
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     <li><a class="dropdown-item" href="../articles/tern_functions_guide.html">Understanding `tern` functions</a></li>
-  </ul></li>
+  </ul>
+</li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
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   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
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+  <ul class="dropdown-menu" aria-labelledby="dropdown-reports">
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- <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json"></form></li>
+  </ul>
+</li>
+      <div><li class="nav-item dropdown">
+    <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-versions">Versions</a>
+    <div class="dropdown-menu" aria-labelledby="dropdown-versions">
+    <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/main">main</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.5">v0.9.5</a>
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+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.3">v0.9.3</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1-rc3">v0.9.1-rc3</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a>
+</div>
+</li></div>
+</ul>
+<ul class="navbar-nav">
+<li class="nav-item"><form class="form-inline" role="search">
+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json">
+</form></li>
 <li class="nav-item"><a class="external-link nav-link" href="https://github.com/insightsengineering/tern" aria-label="GitHub"><span class="fa fa-github"></span></a></li>
-      </ul></div>
+      </ul>
+</div>
 
 
   </div>
@@ -60,7 +123,8 @@
     </div>
 
     <div class="section level2">
-    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
+    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">h_adsl_adlb_merge_using_worst_flag</span><span class="op">(</span></span>
 <span>  <span class="va">adsl</span>,</span>
 <span>  <span class="va">adlb</span>,</span>
@@ -71,48 +135,62 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
     </div>
 
     <div class="section level2">
-    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
+    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a>
+</h2>
 
 
-<dl><dt id="arg-adsl">adsl<a class="anchor" aria-label="anchor" href="#arg-adsl"></a></dt>
+<dl>
+<dt id="arg-adsl">adsl<a class="anchor" aria-label="anchor" href="#arg-adsl"></a>
+</dt>
 <dd><p>(<code>data.frame</code>)<br> ADSL data frame.</p></dd>
 
 
-<dt id="arg-adlb">adlb<a class="anchor" aria-label="anchor" href="#arg-adlb"></a></dt>
+<dt id="arg-adlb">adlb<a class="anchor" aria-label="anchor" href="#arg-adlb"></a>
+</dt>
 <dd><p>(<code>data.frame</code>)<br> ADLB data frame.</p></dd>
 
 
-<dt id="arg-worst-flag">worst_flag<a class="anchor" aria-label="anchor" href="#arg-worst-flag"></a></dt>
+<dt id="arg-worst-flag">worst_flag<a class="anchor" aria-label="anchor" href="#arg-worst-flag"></a>
+</dt>
 <dd><p>(named <code>character</code>)<br> worst post-baseline lab flag variable. See how this is implemented in the
 following examples.</p></dd>
 
 
-<dt id="arg-by-visit">by_visit<a class="anchor" aria-label="anchor" href="#arg-by-visit"></a></dt>
+<dt id="arg-by-visit">by_visit<a class="anchor" aria-label="anchor" href="#arg-by-visit"></a>
+</dt>
 <dd><p>(<code>flag</code>)<br> defaults to <code>FALSE</code> to generate worst grade per patient.
 If worst grade per patient per visit is specified for <code>worst_flag</code>, then
 <code>by_visit</code> should be <code>TRUE</code> to generate worst grade patient per visit.</p></dd>
 
 
-<dt id="arg-no-fillin-visits">no_fillin_visits<a class="anchor" aria-label="anchor" href="#arg-no-fillin-visits"></a></dt>
+<dt id="arg-no-fillin-visits">no_fillin_visits<a class="anchor" aria-label="anchor" href="#arg-no-fillin-visits"></a>
+</dt>
 <dd><p>(named <code>character</code>)<br> visits that are not considered for post-baseline worst toxicity
 grade. Defaults to <code>c("SCREENING", "BASELINE")</code>.</p></dd>
 
-</dl></div>
+</dl>
+</div>
     <div class="section level2">
-    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
+    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a>
+</h2>
     <p><code>df</code> containing variables shared between <code>adlb</code> and <code>adsl</code> along with variables <code>PARAM</code>, <code>PARAMCD</code>,
 <code>ATOXGR</code>, and <code>BTOXGR</code> relevant for analysis. Optionally, <code>AVISIT</code> are <code>AVISITN</code> are included when
 <code>by_visit = TRUE</code> and <code>no_fillin_visits = c("SCREENING", "BASELINE")</code>.</p>
     </div>
     <div class="section level2">
-    <h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a></h2>
-    <p>In the result data missing records will be created for the following situations:</p><ul><li><p>Patients who are present in <code>adsl</code> but have no lab data in <code>adlb</code> (both baseline and post-baseline).</p></li>
+    <h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a>
+</h2>
+    <p>In the result data missing records will be created for the following situations:</p>
+<ul>
+<li><p>Patients who are present in <code>adsl</code> but have no lab data in <code>adlb</code> (both baseline and post-baseline).</p></li>
 <li><p>Patients who do not have any post-baseline lab values.</p></li>
 <li><p>Patients without any post-baseline values flagged as the worst.</p></li>
-</ul></div>
+</ul>
+</div>
 
     <div class="section level2">
-    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
+    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="co"># `h_adsl_adlb_merge_using_worst_flag`</span></span></span>
 <span class="r-in"><span><span class="va">adlb_out</span> <span class="op">&lt;-</span> <span class="fu">h_adsl_adlb_merge_using_worst_flag</span><span class="op">(</span></span></span>
 <span class="r-in"><span>  <span class="va">tern_ex_adsl</span>,</span></span>
@@ -131,17 +209,19 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 </code></pre></div>
     </div>
   </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
-    </nav></aside></div>
+    </nav></aside>
+</div>
 
 
     <footer><div class="nest">
   <p>tern is a part of the <strong>NEST</strong> and <a href="https://pharmaverse.org/" class="external-link"><strong>pharmaverse</strong></a>.</p>
 </div>
-<script type="text/javascript" src="../analytics.js"></script></footer></div>
-
+<script type="text/javascript" src="../analytics.js"></script></footer>
+</div>
 
 
 
 
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diff --git a/main/reference/h_ancova.html b/main/reference/h_ancova.html
index 5689fafa90..997e5fdce8 100644
--- a/main/reference/h_ancova.html
+++ b/main/reference/h_ancova.html
@@ -1,5 +1,28 @@
-<!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Helper function to return results of a linear model — h_ancova • tern</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Helper function to return results of a linear model — h_ancova"><meta name="description" content=""><meta property="og:description" content=""><meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png"><link rel="stylesheet" href="../consent.css"><script src="../consent.js" type="text/javascript" charset="utf-8"></script></head><body>
+<html lang="en">
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+<meta http-equiv="X-UA-Compatible" content="IE=edge">
+<meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<title>Helper function to return results of a linear model — h_ancova • tern</title>
+<!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png">
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+<link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png">
+<script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet">
+<script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet">
+<link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet">
+<script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Helper function to return results of a linear model — h_ancova">
+<meta name="description" content="">
+<meta property="og:description" content="">
+<meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png">
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+<script src="../consent.js" type="text/javascript" charset="utf-8"></script>
+</head>
+<body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
 
 
@@ -15,26 +38,66 @@
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-      <ul class="navbar-nav me-auto"><li class="nav-item"><a class="nav-link" href="../articles/tern.html">Get started</a></li>
+      <ul class="navbar-nav me-auto">
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+  </ul>
+</li>
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+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a>
+</div>
+</li></div>
+</ul>
+<ul class="navbar-nav">
+<li class="nav-item"><form class="form-inline" role="search">
+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json">
+</form></li>
 <li class="nav-item"><a class="external-link nav-link" href="https://github.com/insightsengineering/tern" aria-label="GitHub"><span class="fa fa-github"></span></a></li>
-      </ul></div>
+      </ul>
+</div>
 
 
   </div>
@@ -51,43 +114,57 @@
     </div>
 
     <div class="section level2">
-    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
+    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">h_ancova</span><span class="op">(</span><span class="va">.var</span>, <span class="va">.df_row</span>, <span class="va">variables</span>, interaction_item <span class="op">=</span> <span class="cn">NULL</span><span class="op">)</span></span></code></pre></div>
     </div>
 
     <div class="section level2">
-    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
+    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a>
+</h2>
 
 
-<dl><dt id="arg--var">.var<a class="anchor" aria-label="anchor" href="#arg--var"></a></dt>
+<dl>
+<dt id="arg--var">.var<a class="anchor" aria-label="anchor" href="#arg--var"></a>
+</dt>
 <dd><p>(<code>string</code>)<br> single variable name that is passed by <code>rtables</code> when requested
 by a statistics function.</p></dd>
 
 
-<dt id="arg--df-row">.df_row<a class="anchor" aria-label="anchor" href="#arg--df-row"></a></dt>
+<dt id="arg--df-row">.df_row<a class="anchor" aria-label="anchor" href="#arg--df-row"></a>
+</dt>
 <dd><p>(<code>data.frame</code>)<br> data set that includes all the variables that are called in <code>.var</code> and <code>variables</code>.</p></dd>
 
 
-<dt id="arg-variables">variables<a class="anchor" aria-label="anchor" href="#arg-variables"></a></dt>
-<dd><p>(named <code>list</code> of <code>string</code>)<br> list of additional analysis variables, with expected elements:</p><ul><li><p><code>arm</code> (<code>string</code>)<br> group variable, for which the covariate adjusted means of multiple groups will be
+<dt id="arg-variables">variables<a class="anchor" aria-label="anchor" href="#arg-variables"></a>
+</dt>
+<dd>
+<p>(named <code>list</code> of <code>string</code>)<br> list of additional analysis variables, with expected elements:</p>
+<ul>
+<li><p><code>arm</code> (<code>string</code>)<br> group variable, for which the covariate adjusted means of multiple groups will be
 summarized. Specifically, the first level of <code>arm</code> variable is taken as the reference group.</p></li>
 <li><p><code>covariates</code> (<code>character</code>)<br> a vector that can contain single variable names (such as <code>"X1"</code>), and/or
 interaction terms indicated by <code>"X1 * X2"</code>.</p></li>
-</ul></dd>
+</ul>
+</dd>
 
 
-<dt id="arg-interaction-item">interaction_item<a class="anchor" aria-label="anchor" href="#arg-interaction-item"></a></dt>
+<dt id="arg-interaction-item">interaction_item<a class="anchor" aria-label="anchor" href="#arg-interaction-item"></a>
+</dt>
 <dd><p>(<code>string</code> or <code>NULL</code>)<br> name of the variable that should have interactions
 with arm. if the interaction is not needed, the default option is <code>NULL</code>.</p></dd>
 
-</dl></div>
+</dl>
+</div>
     <div class="section level2">
-    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
+    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a>
+</h2>
     <p>The summary of a linear model.</p>
     </div>
 
     <div class="section level2">
-    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
+    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="fu">h_ancova</span><span class="op">(</span></span></span>
 <span class="r-in"><span>  .var <span class="op">=</span> <span class="st">"Sepal.Length"</span>,</span></span>
 <span class="r-in"><span>  .df_row <span class="op">=</span> <span class="va">iris</span>,</span></span>
@@ -103,17 +180,19 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 </code></pre></div>
     </div>
   </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
-    </nav></aside></div>
+    </nav></aside>
+</div>
 
 
     <footer><div class="nest">
   <p>tern is a part of the <strong>NEST</strong> and <a href="https://pharmaverse.org/" class="external-link"><strong>pharmaverse</strong></a>.</p>
 </div>
-<script type="text/javascript" src="../analytics.js"></script></footer></div>
-
+<script type="text/javascript" src="../analytics.js"></script></footer>
+</div>
 
 
 
 
-  </body></html>
 
+  </body>
+</html>
diff --git a/main/reference/h_append_grade_groups.html b/main/reference/h_append_grade_groups.html
index ad221194f7..5888174884 100644
--- a/main/reference/h_append_grade_groups.html
+++ b/main/reference/h_append_grade_groups.html
@@ -1,13 +1,36 @@
-<!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Helper function for s_count_occurrences_by_grade() — h_append_grade_groups • tern</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Helper function for s_count_occurrences_by_grade() — h_append_grade_groups"><meta name="description" content="
+<html lang="en">
+<head>
+<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+<meta charset="utf-8">
+<meta http-equiv="X-UA-Compatible" content="IE=edge">
+<meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<title>Helper function for s_count_occurrences_by_grade() — h_append_grade_groups • tern</title>
+<!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png">
+<link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png">
+<link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png">
+<link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png">
+<link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png">
+<link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png">
+<script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet">
+<script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet">
+<link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet">
+<script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Helper function for s_count_occurrences_by_grade() — h_append_grade_groups">
+<meta name="description" content="
 Helper function for s_count_occurrences_by_grade() to insert grade groupings into list with
 individual grade frequencies. The order of the final result follows the order of grade_groups.
 The elements under any-grade group (if any), i.e. the grade group equal to refs will be moved to
-the end. Grade groups names must be unique."><meta property="og:description" content="
+the end. Grade groups names must be unique.">
+<meta property="og:description" content="
 Helper function for s_count_occurrences_by_grade() to insert grade groupings into list with
 individual grade frequencies. The order of the final result follows the order of grade_groups.
 The elements under any-grade group (if any), i.e. the grade group equal to refs will be moved to
-the end. Grade groups names must be unique."><meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png"><link rel="stylesheet" href="../consent.css"><script src="../consent.js" type="text/javascript" charset="utf-8"></script></head><body>
+the end. Grade groups names must be unique.">
+<meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png">
+<link rel="stylesheet" href="../consent.css">
+<script src="../consent.js" type="text/javascript" charset="utf-8"></script>
+</head>
+<body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
 
 
@@ -23,33 +46,74 @@
     </button>
 
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-      <ul class="navbar-nav me-auto"><li class="nav-item"><a class="nav-link" href="../articles/tern.html">Get started</a></li>
+      <ul class="navbar-nav me-auto">
+<li class="nav-item"><a class="nav-link" href="../articles/tern.html">Get started</a></li>
 <li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
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   <button class="nav-link dropdown-toggle" type="button" id="dropdown-articles" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Articles</button>
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+  <ul class="dropdown-menu" aria-labelledby="dropdown-articles">
+<li><a class="dropdown-item" href="../articles/missing_values.html">Missing Values in Tern</a></li>
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+  </ul>
+</li>
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- <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json"></form></li>
+  </ul>
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+      <div><li class="nav-item dropdown">
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+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
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+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.3">v0.9.3</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1-rc3">v0.9.1-rc3</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a>
+</div>
+</li></div>
+</ul>
+<ul class="navbar-nav">
+<li class="nav-item"><form class="form-inline" role="search">
+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json">
+</form></li>
 <li class="nav-item"><a class="external-link nav-link" href="https://github.com/insightsengineering/tern" aria-label="GitHub"><span class="fa fa-github"></span></a></li>
-      </ul></div>
+      </ul>
+</div>
 
 
   </div>
 </nav><div class="container template-reference-topic">
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
-      <img src="../logo.png" class="logo" alt=""><h1>Helper function for <code>s_count_occurrences_by_grade()</code></h1>
+      <img src="../logo.png" class="logo" alt=""><h1>Helper function for <code>s_count_occurrences_by_grade()</code>
+</h1>
       <small class="dont-index">Source: <a href="https://github.com/insightsengineering/tern/blob/main/R/count_occurrences_by_grade.R" class="external-link"><code>R/count_occurrences_by_grade.R</code></a></small>
       <div class="d-none name"><code>h_append_grade_groups.Rd</code></div>
     </div>
@@ -63,7 +127,8 @@
     </div>
 
     <div class="section level2">
-    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
+    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">h_append_grade_groups</span><span class="op">(</span></span>
 <span>  <span class="va">grade_groups</span>,</span>
 <span>  <span class="va">refs</span>,</span>
@@ -73,37 +138,46 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
     </div>
 
     <div class="section level2">
-    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
+    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a>
+</h2>
 
 
-<dl><dt id="arg-grade-groups">grade_groups<a class="anchor" aria-label="anchor" href="#arg-grade-groups"></a></dt>
+<dl>
+<dt id="arg-grade-groups">grade_groups<a class="anchor" aria-label="anchor" href="#arg-grade-groups"></a>
+</dt>
 <dd><p>(named <code>list</code> of <code>character</code>)<br> list containing groupings of grades.</p></dd>
 
 
-<dt id="arg-refs">refs<a class="anchor" aria-label="anchor" href="#arg-refs"></a></dt>
+<dt id="arg-refs">refs<a class="anchor" aria-label="anchor" href="#arg-refs"></a>
+</dt>
 <dd><p>(named <code>list</code> of <code>numeric</code>)<br> named list where each name corresponds to a reference grade level
 and each entry represents a count.</p></dd>
 
 
-<dt id="arg-remove-single">remove_single<a class="anchor" aria-label="anchor" href="#arg-remove-single"></a></dt>
+<dt id="arg-remove-single">remove_single<a class="anchor" aria-label="anchor" href="#arg-remove-single"></a>
+</dt>
 <dd><p>(<code>flag</code>)<br><code>TRUE</code> to not include the elements of one-element grade groups
 in the the output list; in this case only the grade groups names will be included in the output. If
 <code>only_grade_groups</code> is set to <code>TRUE</code> this argument is ignored.</p></dd>
 
 
-<dt id="arg-only-grade-groups">only_grade_groups<a class="anchor" aria-label="anchor" href="#arg-only-grade-groups"></a></dt>
+<dt id="arg-only-grade-groups">only_grade_groups<a class="anchor" aria-label="anchor" href="#arg-only-grade-groups"></a>
+</dt>
 <dd><p>(<code>flag</code>)<br> whether only the specified grade groups should be
 included, with individual grade rows removed (<code>TRUE</code>), or all grades and grade groups
 should be displayed (<code>FALSE</code>).</p></dd>
 
-</dl></div>
+</dl>
+</div>
     <div class="section level2">
-    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
+    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a>
+</h2>
     <p>Formatted list of grade groupings.</p>
     </div>
 
     <div class="section level2">
-    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
+    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="fu">h_append_grade_groups</span><span class="op">(</span></span></span>
 <span class="r-in"><span>  <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span></span></span>
 <span class="r-in"><span>    <span class="st">"Any Grade"</span> <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/character.html" class="external-link">as.character</a></span><span class="op">(</span><span class="fl">1</span><span class="op">:</span><span class="fl">5</span><span class="op">)</span>,</span></span>
@@ -197,17 +271,19 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 </code></pre></div>
     </div>
   </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
-    </nav></aside></div>
+    </nav></aside>
+</div>
 
 
     <footer><div class="nest">
   <p>tern is a part of the <strong>NEST</strong> and <a href="https://pharmaverse.org/" class="external-link"><strong>pharmaverse</strong></a>.</p>
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-<script type="text/javascript" src="../analytics.js"></script></footer></div>
-
+<script type="text/javascript" src="../analytics.js"></script></footer>
+</div>
 
 
 
 
-  </body></html>
 
+  </body>
+</html>
diff --git a/main/reference/h_col_indices.html b/main/reference/h_col_indices.html
index 644c63f0a1..a76f4185c1 100644
--- a/main/reference/h_col_indices.html
+++ b/main/reference/h_col_indices.html
@@ -1,9 +1,32 @@
-<!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Obtain column indices — h_col_indices • tern</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Obtain column indices — h_col_indices"><meta name="description" content="
+<html lang="en">
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+<meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
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+<!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png">
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+<script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet">
+<script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet">
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+<script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Obtain column indices — h_col_indices">
+<meta name="description" content="
 Helper function to extract column indices from a VTableTree for a given
-vector of column names."><meta property="og:description" content="
+vector of column names.">
+<meta property="og:description" content="
 Helper function to extract column indices from a VTableTree for a given
-vector of column names."><meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png"><link rel="stylesheet" href="../consent.css"><script src="../consent.js" type="text/javascript" charset="utf-8"></script></head><body>
+vector of column names.">
+<meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png">
+<link rel="stylesheet" href="../consent.css">
+<script src="../consent.js" type="text/javascript" charset="utf-8"></script>
+</head>
+<body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
 
 
@@ -19,26 +42,66 @@
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+      <ul class="navbar-nav me-auto">
+<li class="nav-item"><a class="nav-link" href="../articles/tern.html">Get started</a></li>
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-  <ul class="dropdown-menu" aria-labelledby="dropdown-articles"><li><a class="dropdown-item" href="../articles/missing_values.html">Missing Values in Tern</a></li>
+  <ul class="dropdown-menu" aria-labelledby="dropdown-articles">
+<li><a class="dropdown-item" href="../articles/missing_values.html">Missing Values in Tern</a></li>
     <li><a class="dropdown-item" href="../articles/tables.html">Tabulation</a></li>
     <li><a class="dropdown-item" href="../articles/tern_formats.html">Formatting Functions</a></li>
     <li><a class="dropdown-item" href="../articles/tern_functions_guide.html">Understanding `tern` functions</a></li>
-  </ul></li>
+  </ul>
+</li>
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-  <ul class="dropdown-menu" aria-labelledby="dropdown-reports"><li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
+  <ul class="dropdown-menu" aria-labelledby="dropdown-reports">
+<li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
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+  </ul>
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+    <div class="dropdown-menu" aria-labelledby="dropdown-versions">
+    <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
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+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
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+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.3">v0.9.3</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
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+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a>
+</div>
+</li></div>
+</ul>
+<ul class="navbar-nav">
+<li class="nav-item"><form class="form-inline" role="search">
+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json">
+</form></li>
 <li class="nav-item"><a class="external-link nav-link" href="https://github.com/insightsengineering/tern" aria-label="GitHub"><span class="fa fa-github"></span></a></li>
-      </ul></div>
+      </ul>
+</div>
 
 
   </div>
@@ -57,39 +120,48 @@
     </div>
 
     <div class="section level2">
-    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
+    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">h_col_indices</span><span class="op">(</span><span class="va">table_tree</span>, <span class="va">col_names</span><span class="op">)</span></span></code></pre></div>
     </div>
 
     <div class="section level2">
-    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
+    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a>
+</h2>
 
 
-<dl><dt id="arg-table-tree">table_tree<a class="anchor" aria-label="anchor" href="#arg-table-tree"></a></dt>
+<dl>
+<dt id="arg-table-tree">table_tree<a class="anchor" aria-label="anchor" href="#arg-table-tree"></a>
+</dt>
 <dd><p>(<code>VTableTree</code>)<br><code>rtables</code> table object to extract the indices from.</p></dd>
 
 
-<dt id="arg-col-names">col_names<a class="anchor" aria-label="anchor" href="#arg-col-names"></a></dt>
+<dt id="arg-col-names">col_names<a class="anchor" aria-label="anchor" href="#arg-col-names"></a>
+</dt>
 <dd><p>(<code>character</code>)<br> vector of column names.</p></dd>
 
-</dl></div>
+</dl>
+</div>
     <div class="section level2">
-    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
+    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a>
+</h2>
     <p>A vector of column indices.</p>
     </div>
 
   </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
-    </nav></aside></div>
+    </nav></aside>
+</div>
 
 
     <footer><div class="nest">
   <p>tern is a part of the <strong>NEST</strong> and <a href="https://pharmaverse.org/" class="external-link"><strong>pharmaverse</strong></a>.</p>
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+</html>
diff --git a/main/reference/h_count_cumulative.html b/main/reference/h_count_cumulative.html
index de124e6f6c..c692622404 100644
--- a/main/reference/h_count_cumulative.html
+++ b/main/reference/h_count_cumulative.html
@@ -1,7 +1,30 @@
-<!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Helper function for s_count_cumulative() — h_count_cumulative • tern</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Helper function for s_count_cumulative() — h_count_cumulative"><meta name="description" content="
-Helper function to calculate count and fraction of x values in the lower or upper tail given a threshold."><meta property="og:description" content="
-Helper function to calculate count and fraction of x values in the lower or upper tail given a threshold."><meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png"><link rel="stylesheet" href="../consent.css"><script src="../consent.js" type="text/javascript" charset="utf-8"></script></head><body>
+<html lang="en">
+<head>
+<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
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+<meta http-equiv="X-UA-Compatible" content="IE=edge">
+<meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<title>Helper function for s_count_cumulative() — h_count_cumulative • tern</title>
+<!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png">
+<link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png">
+<link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png">
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+<link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png">
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+<script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet">
+<script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet">
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+<script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Helper function for s_count_cumulative() — h_count_cumulative">
+<meta name="description" content="
+Helper function to calculate count and fraction of x values in the lower or upper tail given a threshold.">
+<meta property="og:description" content="
+Helper function to calculate count and fraction of x values in the lower or upper tail given a threshold.">
+<meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png">
+<link rel="stylesheet" href="../consent.css">
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+</head>
+<body>
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@@ -17,33 +40,74 @@
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     <li><a class="dropdown-item" href="../articles/tables.html">Tabulation</a></li>
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-  <ul class="dropdown-menu" aria-labelledby="dropdown-reports"><li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
+  <ul class="dropdown-menu" aria-labelledby="dropdown-reports">
+<li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
     <li><a class="dropdown-item" href="../unit-test-report/">Unit test report</a></li>
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- <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json"></form></li>
+  </ul>
+</li>
+      <div><li class="nav-item dropdown">
+    <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-versions">Versions</a>
+    <div class="dropdown-menu" aria-labelledby="dropdown-versions">
+    <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
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+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.5">v0.9.5</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.4">v0.9.4</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.3">v0.9.3</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1-rc3">v0.9.1-rc3</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a>
+</div>
+</li></div>
+</ul>
+<ul class="navbar-nav">
+<li class="nav-item"><form class="form-inline" role="search">
+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json">
+</form></li>
 <li class="nav-item"><a class="external-link nav-link" href="https://github.com/insightsengineering/tern" aria-label="GitHub"><span class="fa fa-github"></span></a></li>
-      </ul></div>
+      </ul>
+</div>
 
 
   </div>
 </nav><div class="container template-reference-topic">
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
-      <img src="../logo.png" class="logo" alt=""><h1>Helper function for <code>s_count_cumulative()</code></h1>
+      <img src="../logo.png" class="logo" alt=""><h1>Helper function for <code>s_count_cumulative()</code>
+</h1>
       <small class="dont-index">Source: <a href="https://github.com/insightsengineering/tern/blob/main/R/count_cumulative.R" class="external-link"><code>R/count_cumulative.R</code></a></small>
       <div class="d-none name"><code>h_count_cumulative.Rd</code></div>
     </div>
@@ -54,7 +118,8 @@
     </div>
 
     <div class="section level2">
-    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
+    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">h_count_cumulative</span><span class="op">(</span></span>
 <span>  <span class="va">x</span>,</span>
 <span>  <span class="va">threshold</span>,</span>
@@ -66,48 +131,63 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
     </div>
 
     <div class="section level2">
-    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
+    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a>
+</h2>
 
 
-<dl><dt id="arg-x">x<a class="anchor" aria-label="anchor" href="#arg-x"></a></dt>
+<dl>
+<dt id="arg-x">x<a class="anchor" aria-label="anchor" href="#arg-x"></a>
+</dt>
 <dd><p>(<code>numeric</code>)<br> vector of numbers we want to analyze.</p></dd>
 
 
-<dt id="arg-threshold">threshold<a class="anchor" aria-label="anchor" href="#arg-threshold"></a></dt>
+<dt id="arg-threshold">threshold<a class="anchor" aria-label="anchor" href="#arg-threshold"></a>
+</dt>
 <dd><p>(<code>numeric(1)</code>)<br> a cutoff value as threshold to count values of <code>x</code>.</p></dd>
 
 
-<dt id="arg-lower-tail">lower_tail<a class="anchor" aria-label="anchor" href="#arg-lower-tail"></a></dt>
+<dt id="arg-lower-tail">lower_tail<a class="anchor" aria-label="anchor" href="#arg-lower-tail"></a>
+</dt>
 <dd><p>(<code>flag</code>)<br> whether to count lower tail, default is <code>TRUE</code>.</p></dd>
 
 
-<dt id="arg-include-eq">include_eq<a class="anchor" aria-label="anchor" href="#arg-include-eq"></a></dt>
+<dt id="arg-include-eq">include_eq<a class="anchor" aria-label="anchor" href="#arg-include-eq"></a>
+</dt>
 <dd><p>(<code>flag</code>)<br> whether to include value equal to the <code>threshold</code> in
 count, default is <code>TRUE</code>.</p></dd>
 
 
-<dt id="arg-na-rm">na.rm<a class="anchor" aria-label="anchor" href="#arg-na-rm"></a></dt>
+<dt id="arg-na-rm">na.rm<a class="anchor" aria-label="anchor" href="#arg-na-rm"></a>
+</dt>
 <dd><p>(<code>flag</code>)<br> whether <code>NA</code> values should be removed from <code>x</code> prior to analysis.</p></dd>
 
 
-<dt id="arg--n-col">.N_col<a class="anchor" aria-label="anchor" href="#arg--n-col"></a></dt>
+<dt id="arg--n-col">.N_col<a class="anchor" aria-label="anchor" href="#arg--n-col"></a>
+</dt>
 <dd><p>(<code>integer(1)</code>)<br> column-wise N (column count) for the full column being analyzed that is typically
 passed by <code>rtables</code>.</p></dd>
 
-</dl></div>
+</dl>
+</div>
     <div class="section level2">
-    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
-    <p>A named vector with items:</p><ul><li><p><code>count</code>: the count of values less than, less or equal to, greater than, or greater or equal to a threshold
+    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a>
+</h2>
+    <p>A named vector with items:</p>
+<ul>
+<li><p><code>count</code>: the count of values less than, less or equal to, greater than, or greater or equal to a threshold
 of user specification.</p></li>
 <li><p><code>fraction</code>: the fraction of the count.</p></li>
-</ul></div>
+</ul>
+</div>
     <div class="section level2">
-    <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"></a></h2>
+    <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"></a>
+</h2>
     <div class="dont-index"><p><a href="count_cumulative.html">count_cumulative</a></p></div>
     </div>
 
     <div class="section level2">
-    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
+    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/Random.html" class="external-link">set.seed</a></span><span class="op">(</span><span class="fl">1</span>, kind <span class="op">=</span> <span class="st">"Mersenne-Twister"</span><span class="op">)</span></span></span>
 <span class="r-in"><span><span class="va">x</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/sample.html" class="external-link">sample</a></span><span class="op">(</span><span class="fl">1</span><span class="op">:</span><span class="fl">10</span>, <span class="fl">10</span><span class="op">)</span>, <span class="cn">NA</span><span class="op">)</span></span></span>
 <span class="r-in"><span><span class="va">.N_col</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/length.html" class="external-link">length</a></span><span class="op">(</span><span class="va">x</span><span class="op">)</span></span></span>
@@ -128,17 +208,19 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 </code></pre></div>
     </div>
   </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
-    </nav></aside></div>
+    </nav></aside>
+</div>
 
 
     <footer><div class="nest">
   <p>tern is a part of the <strong>NEST</strong> and <a href="https://pharmaverse.org/" class="external-link"><strong>pharmaverse</strong></a>.</p>
 </div>
-<script type="text/javascript" src="../analytics.js"></script></footer></div>
-
+<script type="text/javascript" src="../analytics.js"></script></footer>
+</div>
 
 
 
 
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diff --git a/main/reference/h_cox_regression.html b/main/reference/h_cox_regression.html
index a7ed72fad3..3f00e94d43 100644
--- a/main/reference/h_cox_regression.html
+++ b/main/reference/h_cox_regression.html
@@ -1,7 +1,30 @@
-<!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Helper functions for Cox proportional hazards regression — h_cox_regression • tern</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Helper functions for Cox proportional hazards regression — h_cox_regression"><meta name="description" content="
-Helper functions used in fit_coxreg_univar() and fit_coxreg_multivar()."><meta property="og:description" content="
-Helper functions used in fit_coxreg_univar() and fit_coxreg_multivar()."><meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png"><link rel="stylesheet" href="../consent.css"><script src="../consent.js" type="text/javascript" charset="utf-8"></script></head><body>
+<html lang="en">
+<head>
+<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+<meta charset="utf-8">
+<meta http-equiv="X-UA-Compatible" content="IE=edge">
+<meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<title>Helper functions for Cox proportional hazards regression — h_cox_regression • tern</title>
+<!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png">
+<link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png">
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+<link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png">
+<link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png">
+<link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png">
+<script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet">
+<script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet">
+<link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet">
+<script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Helper functions for Cox proportional hazards regression — h_cox_regression">
+<meta name="description" content="
+Helper functions used in fit_coxreg_univar() and fit_coxreg_multivar().">
+<meta property="og:description" content="
+Helper functions used in fit_coxreg_univar() and fit_coxreg_multivar().">
+<meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png">
+<link rel="stylesheet" href="../consent.css">
+<script src="../consent.js" type="text/javascript" charset="utf-8"></script>
+</head>
+<body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
 
 
@@ -17,26 +40,66 @@
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+      <ul class="navbar-nav me-auto">
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+  <ul class="dropdown-menu" aria-labelledby="dropdown-articles">
+<li><a class="dropdown-item" href="../articles/missing_values.html">Missing Values in Tern</a></li>
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     <li><a class="dropdown-item" href="../articles/tern_functions_guide.html">Understanding `tern` functions</a></li>
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+  </ul>
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+  <ul class="dropdown-menu" aria-labelledby="dropdown-reports">
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+    <div class="dropdown-menu" aria-labelledby="dropdown-versions">
+    <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
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+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
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+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.3">v0.9.3</a>
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+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
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+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a>
+</div>
+</li></div>
+</ul>
+<ul class="navbar-nav">
+<li class="nav-item"><form class="form-inline" role="search">
+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json">
+</form></li>
 <li class="nav-item"><a class="external-link nav-link" href="https://github.com/insightsengineering/tern" aria-label="GitHub"><span class="fa fa-github"></span></a></li>
-      </ul></div>
+      </ul>
+</div>
 
 
   </div>
@@ -54,7 +117,8 @@
     </div>
 
     <div class="section level2">
-    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
+    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">h_coxreg_univar_formulas</span><span class="op">(</span><span class="va">variables</span>, interaction <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span>
 <span></span>
 <span><span class="fu">h_coxreg_multivar_formula</span><span class="op">(</span><span class="va">variables</span><span class="op">)</span></span>
@@ -65,58 +129,80 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
     </div>
 
     <div class="section level2">
-    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
+    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a>
+</h2>
 
 
-<dl><dt id="arg-variables">variables<a class="anchor" aria-label="anchor" href="#arg-variables"></a></dt>
+<dl>
+<dt id="arg-variables">variables<a class="anchor" aria-label="anchor" href="#arg-variables"></a>
+</dt>
 <dd><p>(named <code>list</code> of <code>string</code>)<br> list of additional analysis variables.</p></dd>
 
 
-<dt id="arg-interaction">interaction<a class="anchor" aria-label="anchor" href="#arg-interaction"></a></dt>
+<dt id="arg-interaction">interaction<a class="anchor" aria-label="anchor" href="#arg-interaction"></a>
+</dt>
 <dd><p>(<code>flag</code>)<br> if <code>TRUE</code>, the model includes the interaction between the studied
 treatment and candidate covariate. Note that for univariate models without treatment arm, and
 multivariate models, no interaction can be used so that this needs to be <code>FALSE</code>.</p></dd>
 
 
-<dt id="arg-effect">effect<a class="anchor" aria-label="anchor" href="#arg-effect"></a></dt>
+<dt id="arg-effect">effect<a class="anchor" aria-label="anchor" href="#arg-effect"></a>
+</dt>
 <dd><p>(<code>string</code>)<br> the treatment variable.</p></dd>
 
 
-<dt id="arg-covar">covar<a class="anchor" aria-label="anchor" href="#arg-covar"></a></dt>
+<dt id="arg-covar">covar<a class="anchor" aria-label="anchor" href="#arg-covar"></a>
+</dt>
 <dd><p>(<code>string</code>)<br> the name of the covariate in the model.</p></dd>
 
 
-<dt id="arg-data">data<a class="anchor" aria-label="anchor" href="#arg-data"></a></dt>
+<dt id="arg-data">data<a class="anchor" aria-label="anchor" href="#arg-data"></a>
+</dt>
 <dd><p>(<code>data.frame</code>)<br> the dataset containing the variables to summarize.</p></dd>
 
 
-<dt id="arg-mod">mod<a class="anchor" aria-label="anchor" href="#arg-mod"></a></dt>
+<dt id="arg-mod">mod<a class="anchor" aria-label="anchor" href="#arg-mod"></a>
+</dt>
 <dd><p>(<code>coxph</code>)<br> Cox regression model fitted by <code><a href="https://rdrr.io/pkg/survival/man/coxph.html" class="external-link">survival::coxph()</a></code>.</p></dd>
 
 
-<dt id="arg-control">control<a class="anchor" aria-label="anchor" href="#arg-control"></a></dt>
+<dt id="arg-control">control<a class="anchor" aria-label="anchor" href="#arg-control"></a>
+</dt>
 <dd><p>(<code>list</code>)<br> a list of controls as returned by <code><a href="control_coxreg.html">control_coxreg()</a></code>.</p></dd>
 
 
-<dt id="arg-var">var<a class="anchor" aria-label="anchor" href="#arg-var"></a></dt>
+<dt id="arg-var">var<a class="anchor" aria-label="anchor" href="#arg-var"></a>
+</dt>
 <dd><p>(<code>string</code>)<br> single variable name that is passed by <code>rtables</code> when requested
 by a statistics function.</p></dd>
 
-</dl></div>
+</dl>
+</div>
     <div class="section level2">
-    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
-
-<ul><li><p><code>h_coxreg_univar_formulas()</code> returns a <code>character</code> vector coercible into formulas (e.g <code><a href="https://rdrr.io/r/stats/formula.html" class="external-link">stats::as.formula()</a></code>).</p></li>
-</ul><ul><li><p><code>h_coxreg_multivar_formula()</code> returns a <code>string</code> coercible into a formula (e.g <code><a href="https://rdrr.io/r/stats/formula.html" class="external-link">stats::as.formula()</a></code>).</p></li>
-</ul><ul><li><p><code>h_coxreg_univar_extract()</code> returns a <code>data.frame</code> with variables <code>effect</code>, <code>term</code>, <code>term_label</code>, <code>level</code>,
+    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a>
+</h2>
+
+<ul>
+<li><p><code>h_coxreg_univar_formulas()</code> returns a <code>character</code> vector coercible into formulas (e.g <code><a href="https://rdrr.io/r/stats/formula.html" class="external-link">stats::as.formula()</a></code>).</p></li>
+</ul>
+<ul>
+<li><p><code>h_coxreg_multivar_formula()</code> returns a <code>string</code> coercible into a formula (e.g <code><a href="https://rdrr.io/r/stats/formula.html" class="external-link">stats::as.formula()</a></code>).</p></li>
+</ul>
+<ul>
+<li><p><code>h_coxreg_univar_extract()</code> returns a <code>data.frame</code> with variables <code>effect</code>, <code>term</code>, <code>term_label</code>, <code>level</code>,
 <code>n</code>, <code>hr</code>, <code>lcl</code>, <code>ucl</code>, and <code>pval</code>.</p></li>
-</ul><ul><li><p><code>h_coxreg_multivar_extract()</code> returns a <code>data.frame</code> with variables <code>pval</code>, <code>hr</code>, <code>lcl</code>, <code>ucl</code>, <code>level</code>,
+</ul>
+<ul>
+<li><p><code>h_coxreg_multivar_extract()</code> returns a <code>data.frame</code> with variables <code>pval</code>, <code>hr</code>, <code>lcl</code>, <code>ucl</code>, <code>level</code>,
 <code>n</code>, <code>term</code>, and <code>term_label</code>.</p></li>
-</ul></div>
+</ul>
+</div>
     <div class="section level2">
-    <h2 id="functions">Functions<a class="anchor" aria-label="anchor" href="#functions"></a></h2>
+    <h2 id="functions">Functions<a class="anchor" aria-label="anchor" href="#functions"></a>
+</h2>
 
-<ul><li><p><code>h_coxreg_univar_formulas()</code>: Helper for Cox regression formula. Creates a list of formulas. It is used
+<ul>
+<li><p><code>h_coxreg_univar_formulas()</code>: Helper for Cox regression formula. Creates a list of formulas. It is used
 internally by <code><a href="fit_coxreg.html">fit_coxreg_univar()</a></code> for the comparison of univariate Cox regression models.</p></li>
 <li><p><code>h_coxreg_multivar_formula()</code>: Helper for multivariate Cox regression formula. Creates a formulas
 string. It is used internally by <code><a href="fit_coxreg.html">fit_coxreg_multivar()</a></code> for the comparison of multivariate Cox
@@ -125,14 +211,17 @@ <h2 id="functions">Functions<a class="anchor" aria-label="anchor" href="#functio
 a univariate Cox regression model.</p></li>
 <li><p><code>h_coxreg_multivar_extract()</code>: Tabulation of multivariate Cox regressions. Utility function to help
 tabulate the result of a multivariate Cox regression model for a treatment/covariate variable.</p></li>
-</ul></div>
+</ul>
+</div>
     <div class="section level2">
-    <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"></a></h2>
+    <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"></a>
+</h2>
     <div class="dont-index"><p><a href="cox_regression.html">cox_regression</a></p></div>
     </div>
 
     <div class="section level2">
-    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
+    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="co"># `h_coxreg_univar_formulas`</span></span></span>
 <span class="r-in"><span></span></span>
 <span class="r-in"><span><span class="co">## Simple formulas.</span></span></span>
@@ -243,17 +332,19 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 </code></pre></div>
     </div>
   </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
-    </nav></aside></div>
+    </nav></aside>
+</div>
 
 
     <footer><div class="nest">
   <p>tern is a part of the <strong>NEST</strong> and <a href="https://pharmaverse.org/" class="external-link"><strong>pharmaverse</strong></a>.</p>
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-<script type="text/javascript" src="../analytics.js"></script></footer></div>
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+<script type="text/javascript" src="../analytics.js"></script></footer>
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diff --git a/main/reference/h_data_plot.html b/main/reference/h_data_plot.html
index 8cf46df921..a1969b7af8 100644
--- a/main/reference/h_data_plot.html
+++ b/main/reference/h_data_plot.html
@@ -1,5 +1,22 @@
-<!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Helper function to tidy survival fit data — h_data_plot • tern</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Helper function to tidy survival fit data — h_data_plot"><meta name="description" content="
+<html lang="en">
+<head>
+<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
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+<meta http-equiv="X-UA-Compatible" content="IE=edge">
+<meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<title>Helper function to tidy survival fit data — h_data_plot • tern</title>
+<!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png">
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+<script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet">
+<script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet">
+<link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet">
+<script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Helper function to tidy survival fit data — h_data_plot">
+<meta name="description" content="
 Convert the survival fit data into a data frame designed for plotting
 within g_km.
 This starts from the broom::tidy() result, and then:
@@ -9,7 +26,8 @@
 Adds a censor column.
 Filters the rows before max_time.
 
-"><meta property="og:description" content="
+">
+<meta property="og:description" content="
 Convert the survival fit data into a data frame designed for plotting
 within g_km.
 This starts from the broom::tidy() result, and then:
@@ -19,7 +37,12 @@
 Adds a censor column.
 Filters the rows before max_time.
 
-"><meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png"><link rel="stylesheet" href="../consent.css"><script src="../consent.js" type="text/javascript" charset="utf-8"></script></head><body>
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+      </ul>
+</div>
 
 
   </div>
@@ -70,43 +133,55 @@
     <p><a href="https://lifecycle.r-lib.org/articles/stages.html#stable" class="external-link"><img src="figures/lifecycle-stable.svg" alt="[Stable]"></a></p>
 <p>Convert the survival fit data into a data frame designed for plotting
 within <code>g_km</code>.</p>
-<p>This starts from the <code><a href="https://broom.tidymodels.org/reference/reexports.html" class="external-link">broom::tidy()</a></code> result, and then:</p><ul><li><p>Post-processes the <code>strata</code> column into a factor.</p></li>
+<p>This starts from the <code><a href="https://broom.tidymodels.org/reference/reexports.html" class="external-link">broom::tidy()</a></code> result, and then:</p>
+<ul>
+<li><p>Post-processes the <code>strata</code> column into a factor.</p></li>
 <li><p>Extends each stratum by an additional first row with time 0 and probability 1 so that
 downstream plot lines start at those coordinates.</p></li>
 <li><p>Adds a <code>censor</code> column.</p></li>
 <li><p>Filters the rows before <code>max_time</code>.</p></li>
-</ul></div>
+</ul>
+</div>
 
     <div class="section level2">
-    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
+    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">h_data_plot</span><span class="op">(</span><span class="va">fit_km</span>, armval <span class="op">=</span> <span class="st">"All"</span>, max_time <span class="op">=</span> <span class="cn">NULL</span><span class="op">)</span></span></code></pre></div>
     </div>
 
     <div class="section level2">
-    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
+    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a>
+</h2>
 
 
-<dl><dt id="arg-fit-km">fit_km<a class="anchor" aria-label="anchor" href="#arg-fit-km"></a></dt>
+<dl>
+<dt id="arg-fit-km">fit_km<a class="anchor" aria-label="anchor" href="#arg-fit-km"></a>
+</dt>
 <dd><p>(<code>survfit</code>)<br> result of <code><a href="https://rdrr.io/pkg/survival/man/survfit.html" class="external-link">survival::survfit()</a></code>.</p></dd>
 
 
-<dt id="arg-armval">armval<a class="anchor" aria-label="anchor" href="#arg-armval"></a></dt>
+<dt id="arg-armval">armval<a class="anchor" aria-label="anchor" href="#arg-armval"></a>
+</dt>
 <dd><p>(<code>string</code>)<br> used as strata name when treatment arm variable only has one level. Default is <code>"All"</code>.</p></dd>
 
 
-<dt id="arg-max-time">max_time<a class="anchor" aria-label="anchor" href="#arg-max-time"></a></dt>
+<dt id="arg-max-time">max_time<a class="anchor" aria-label="anchor" href="#arg-max-time"></a>
+</dt>
 <dd><p>(<code>numeric(1)</code>)<br> maximum value to show on x-axis. Only data values less than or up to
 this threshold value will be plotted (defaults to <code>NULL</code>).</p></dd>
 
-</dl></div>
+</dl>
+</div>
     <div class="section level2">
-    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
+    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a>
+</h2>
     <p>A <code>tibble</code> with columns <code>time</code>, <code>n.risk</code>, <code>n.event</code>, <code>n.censor</code>, <code>estimate</code>, <code>std.error</code>, <code>conf.high</code>,
 <code>conf.low</code>, <code>strata</code>, and <code>censor</code>.</p>
     </div>
 
     <div class="section level2">
-    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
+    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://dplyr.tidyverse.org" class="external-link">dplyr</a></span><span class="op">)</span></span></span>
 <span class="r-in"><span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://github.com/therneau/survival" class="external-link">survival</a></span><span class="op">)</span></span></span>
 <span class="r-in"><span></span></span>
@@ -155,17 +230,19 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 </code></pre></div>
     </div>
   </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
-    </nav></aside></div>
+    </nav></aside>
+</div>
 
 
     <footer><div class="nest">
   <p>tern is a part of the <strong>NEST</strong> and <a href="https://pharmaverse.org/" class="external-link"><strong>pharmaverse</strong></a>.</p>
 </div>
-<script type="text/javascript" src="../analytics.js"></script></footer></div>
-
+<script type="text/javascript" src="../analytics.js"></script></footer>
+</div>
 
 
 
 
-  </body></html>
 
+  </body>
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diff --git a/main/reference/h_decompose_gg.html b/main/reference/h_decompose_gg.html
index e43e2d56e6..c0e006660c 100644
--- a/main/reference/h_decompose_gg.html
+++ b/main/reference/h_decompose_gg.html
@@ -1,7 +1,30 @@
-<!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>ggplot decomposition — h_decompose_gg • tern</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="ggplot decomposition — h_decompose_gg"><meta name="description" content="
-The elements composing the ggplot are extracted and organized in a list."><meta property="og:description" content="
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+<script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
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+<script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet">
+<link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet">
+<script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="ggplot decomposition — h_decompose_gg">
+<meta name="description" content="
+The elements composing the ggplot are extracted and organized in a list.">
+<meta property="og:description" content="
+The elements composing the ggplot are extracted and organized in a list.">
+<meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png">
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+<script src="../consent.js" type="text/javascript" charset="utf-8"></script>
+</head>
+<body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
 
 
@@ -17,33 +40,74 @@
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+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a>
+</div>
+</li></div>
+</ul>
+<ul class="navbar-nav">
+<li class="nav-item"><form class="form-inline" role="search">
+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json">
+</form></li>
 <li class="nav-item"><a class="external-link nav-link" href="https://github.com/insightsengineering/tern" aria-label="GitHub"><span class="fa fa-github"></span></a></li>
-      </ul></div>
+      </ul>
+</div>
 
 
   </div>
 </nav><div class="container template-reference-topic">
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
-      <img src="../logo.png" class="logo" alt=""><h1><code>ggplot</code> decomposition</h1>
+      <img src="../logo.png" class="logo" alt=""><h1>
+<code>ggplot</code> decomposition</h1>
       <small class="dont-index">Source: <a href="https://github.com/insightsengineering/tern/blob/main/R/h_km.R" class="external-link"><code>R/h_km.R</code></a></small>
       <div class="d-none name"><code>h_decompose_gg.Rd</code></div>
     </div>
@@ -54,30 +118,40 @@
     </div>
 
     <div class="section level2">
-    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
+    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">h_decompose_gg</span><span class="op">(</span><span class="va">gg</span><span class="op">)</span></span></code></pre></div>
     </div>
 
     <div class="section level2">
-    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
+    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a>
+</h2>
 
 
-<dl><dt id="arg-gg">gg<a class="anchor" aria-label="anchor" href="#arg-gg"></a></dt>
+<dl>
+<dt id="arg-gg">gg<a class="anchor" aria-label="anchor" href="#arg-gg"></a>
+</dt>
 <dd><p>(<code>ggplot</code>)<br> a graphic to decompose.</p></dd>
 
-</dl></div>
+</dl>
+</div>
     <div class="section level2">
-    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
-    <p>A named <code>list</code> with elements:</p><ul><li><p><code>panel</code>: The panel.</p></li>
+    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a>
+</h2>
+    <p>A named <code>list</code> with elements:</p>
+<ul>
+<li><p><code>panel</code>: The panel.</p></li>
 <li><p><code>yaxis</code>: The y-axis.</p></li>
 <li><p><code>xaxis</code>: The x-axis.</p></li>
 <li><p><code>xlab</code>: The x-axis label.</p></li>
 <li><p><code>ylab</code>: The y-axis label.</p></li>
 <li><p><code>guide</code>: The legend.</p></li>
-</ul></div>
+</ul>
+</div>
 
     <div class="section level2">
-    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
+    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="co"># \donttest{</span></span></span>
 <span class="r-in"><span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://dplyr.tidyverse.org" class="external-link">dplyr</a></span><span class="op">)</span></span></span>
 <span class="r-in"><span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://github.com/therneau/survival" class="external-link">survival</a></span><span class="op">)</span></span></span>
@@ -118,17 +192,19 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 </code></pre></div>
     </div>
   </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
-    </nav></aside></div>
+    </nav></aside>
+</div>
 
 
     <footer><div class="nest">
   <p>tern is a part of the <strong>NEST</strong> and <a href="https://pharmaverse.org/" class="external-link"><strong>pharmaverse</strong></a>.</p>
 </div>
-<script type="text/javascript" src="../analytics.js"></script></footer></div>
-
+<script type="text/javascript" src="../analytics.js"></script></footer>
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+</html>
diff --git a/main/reference/h_format_row.html b/main/reference/h_format_row.html
index 9b2740dd80..9e339b76ab 100644
--- a/main/reference/h_format_row.html
+++ b/main/reference/h_format_row.html
@@ -1,5 +1,28 @@
-<!DOCTYPE html>
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@@ -15,26 +38,66 @@
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+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
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+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a>
+</div>
+</li></div>
+</ul>
+<ul class="navbar-nav">
+<li class="nav-item"><form class="form-inline" role="search">
+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json">
+</form></li>
 <li class="nav-item"><a class="external-link nav-link" href="https://github.com/insightsengineering/tern" aria-label="GitHub"><span class="fa fa-github"></span></a></li>
-      </ul></div>
+      </ul>
+</div>
 
 
   </div>
@@ -51,40 +114,49 @@
     </div>
 
     <div class="section level2">
-    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
+    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">h_format_row</span><span class="op">(</span><span class="va">x</span>, <span class="va">format</span>, labels <span class="op">=</span> <span class="cn">NULL</span><span class="op">)</span></span></code></pre></div>
     </div>
 
     <div class="section level2">
-    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
+    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a>
+</h2>
 
 
-<dl><dt id="arg-x">x<a class="anchor" aria-label="anchor" href="#arg-x"></a></dt>
+<dl>
+<dt id="arg-x">x<a class="anchor" aria-label="anchor" href="#arg-x"></a>
+</dt>
 <dd><p>(named <code>list</code>)<br> list of numerical values to be formatted and optionally labeled.
 Elements of <code>x</code> must be <code>numeric</code> vectors.</p></dd>
 
 
-<dt id="arg-format">format<a class="anchor" aria-label="anchor" href="#arg-format"></a></dt>
+<dt id="arg-format">format<a class="anchor" aria-label="anchor" href="#arg-format"></a>
+</dt>
 <dd><p>(named <code>character</code> or <code>NULL</code>)<br> format patterns for <code>x</code>. Names of the <code>format</code> must
 match the names of <code>x</code>. This parameter is passed directly to the <code><a href="https://insightsengineering.github.io/rtables/latest-tag/reference/format_rcell.html" class="external-link">rtables::format_rcell</a></code>
 function through the <code>format</code> parameter.</p></dd>
 
 
-<dt id="arg-labels">labels<a class="anchor" aria-label="anchor" href="#arg-labels"></a></dt>
+<dt id="arg-labels">labels<a class="anchor" aria-label="anchor" href="#arg-labels"></a>
+</dt>
 <dd><p>(named <code>character</code> or <code>NULL</code>)<br> optional labels for <code>x</code>. Names of the <code>labels</code> must
 match the names of <code>x</code>. When a label is not specified for an element of <code>x</code>,
 then this function tries to use <code>label</code> or <code>names</code> (in this order) attribute of that element
 (depending on which one exists and it is not <code>NULL</code> or <code>NA</code> or <code>NaN</code>). If none of these attributes
 are attached to a given element of <code>x</code>, then the label is automatically generated.</p></dd>
 
-</dl></div>
+</dl>
+</div>
     <div class="section level2">
-    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
+    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a>
+</h2>
     <p>A single row <code>data.frame</code> object.</p>
     </div>
 
     <div class="section level2">
-    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
+    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">mean_ci</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">48</span>, <span class="fl">51</span><span class="op">)</span></span></span>
 <span class="r-in"><span><span class="va">x</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span>mean <span class="op">=</span> <span class="fl">50</span>, mean_ci <span class="op">=</span> <span class="va">mean_ci</span><span class="op">)</span></span></span>
 <span class="r-in"><span><span class="va">format</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>mean <span class="op">=</span> <span class="st">"xx.x"</span>, mean_ci <span class="op">=</span> <span class="st">"(xx.xx, xx.xx)"</span><span class="op">)</span></span></span>
@@ -102,17 +174,19 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 </code></pre></div>
     </div>
   </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
-    </nav></aside></div>
+    </nav></aside>
+</div>
 
 
     <footer><div class="nest">
   <p>tern is a part of the <strong>NEST</strong> and <a href="https://pharmaverse.org/" class="external-link"><strong>pharmaverse</strong></a>.</p>
 </div>
-<script type="text/javascript" src="../analytics.js"></script></footer></div>
-
+<script type="text/javascript" src="../analytics.js"></script></footer>
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diff --git a/main/reference/h_g_ipp.html b/main/reference/h_g_ipp.html
index b03e0a212a..e3949ccf1d 100644
--- a/main/reference/h_g_ipp.html
+++ b/main/reference/h_g_ipp.html
@@ -1,7 +1,30 @@
-<!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Helper function to create simple line plot over time — h_g_ipp • tern</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Helper function to create simple line plot over time — h_g_ipp"><meta name="description" content="
-Function that generates a simple line plot displaying parameter trends over time."><meta property="og:description" content="
-Function that generates a simple line plot displaying parameter trends over time."><meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png"><link rel="stylesheet" href="../consent.css"><script src="../consent.js" type="text/javascript" charset="utf-8"></script></head><body>
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+<meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<title>Helper function to create simple line plot over time — h_g_ipp • tern</title>
+<!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png">
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+<script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet">
+<script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet">
+<link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet">
+<script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Helper function to create simple line plot over time — h_g_ipp">
+<meta name="description" content="
+Function that generates a simple line plot displaying parameter trends over time.">
+<meta property="og:description" content="
+Function that generates a simple line plot displaying parameter trends over time.">
+<meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png">
+<link rel="stylesheet" href="../consent.css">
+<script src="../consent.js" type="text/javascript" charset="utf-8"></script>
+</head>
+<body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
 
 
@@ -17,26 +40,66 @@
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   <button class="nav-link dropdown-toggle" type="button" id="dropdown-articles" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Articles</button>
-  <ul class="dropdown-menu" aria-labelledby="dropdown-articles"><li><a class="dropdown-item" href="../articles/missing_values.html">Missing Values in Tern</a></li>
+  <ul class="dropdown-menu" aria-labelledby="dropdown-articles">
+<li><a class="dropdown-item" href="../articles/missing_values.html">Missing Values in Tern</a></li>
     <li><a class="dropdown-item" href="../articles/tables.html">Tabulation</a></li>
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     <li><a class="dropdown-item" href="../articles/tern_functions_guide.html">Understanding `tern` functions</a></li>
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+</li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
-  <ul class="dropdown-menu" aria-labelledby="dropdown-reports"><li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
+  <ul class="dropdown-menu" aria-labelledby="dropdown-reports">
+<li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
     <li><a class="dropdown-item" href="../unit-test-report/">Unit test report</a></li>
     <li><a class="dropdown-item" href="../unit-test-report-non-cran/">Non-CRAN unit test report</a></li>
-  </ul></li>
-      </ul><ul class="navbar-nav"><li class="nav-item"><form class="form-inline" role="search">
- <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json"></form></li>
+  </ul>
+</li>
+      <div><li class="nav-item dropdown">
+    <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-versions">Versions</a>
+    <div class="dropdown-menu" aria-labelledby="dropdown-versions">
+    <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/main">main</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.5">v0.9.5</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.4">v0.9.4</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.3">v0.9.3</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1-rc3">v0.9.1-rc3</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a>
+</div>
+</li></div>
+</ul>
+<ul class="navbar-nav">
+<li class="nav-item"><form class="form-inline" role="search">
+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json">
+</form></li>
 <li class="nav-item"><a class="external-link nav-link" href="https://github.com/insightsengineering/tern" aria-label="GitHub"><span class="fa fa-github"></span></a></li>
-      </ul></div>
+      </ul>
+</div>
 
 
   </div>
@@ -54,7 +117,8 @@
     </div>
 
     <div class="section level2">
-    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
+    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">h_g_ipp</span><span class="op">(</span></span>
 <span>  <span class="va">df</span>,</span>
 <span>  <span class="va">xvar</span>,</span>
@@ -73,75 +137,94 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
     </div>
 
     <div class="section level2">
-    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
+    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a>
+</h2>
 
 
-<dl><dt id="arg-df">df<a class="anchor" aria-label="anchor" href="#arg-df"></a></dt>
+<dl>
+<dt id="arg-df">df<a class="anchor" aria-label="anchor" href="#arg-df"></a>
+</dt>
 <dd><p>(<code>data.frame</code>)<br> data set containing all analysis variables.</p></dd>
 
 
-<dt id="arg-xvar">xvar<a class="anchor" aria-label="anchor" href="#arg-xvar"></a></dt>
+<dt id="arg-xvar">xvar<a class="anchor" aria-label="anchor" href="#arg-xvar"></a>
+</dt>
 <dd><p>(<code>string</code>)<br> time point variable to be plotted on x-axis.</p></dd>
 
 
-<dt id="arg-yvar">yvar<a class="anchor" aria-label="anchor" href="#arg-yvar"></a></dt>
+<dt id="arg-yvar">yvar<a class="anchor" aria-label="anchor" href="#arg-yvar"></a>
+</dt>
 <dd><p>(<code>string</code>)<br> continuous analysis variable to be plotted on y-axis.</p></dd>
 
 
-<dt id="arg-xlab">xlab<a class="anchor" aria-label="anchor" href="#arg-xlab"></a></dt>
+<dt id="arg-xlab">xlab<a class="anchor" aria-label="anchor" href="#arg-xlab"></a>
+</dt>
 <dd><p>(<code>string</code>)<br> plot label for x-axis.</p></dd>
 
 
-<dt id="arg-ylab">ylab<a class="anchor" aria-label="anchor" href="#arg-ylab"></a></dt>
+<dt id="arg-ylab">ylab<a class="anchor" aria-label="anchor" href="#arg-ylab"></a>
+</dt>
 <dd><p>(<code>string</code>)<br> plot label for y-axis.</p></dd>
 
 
-<dt id="arg-id-var">id_var<a class="anchor" aria-label="anchor" href="#arg-id-var"></a></dt>
+<dt id="arg-id-var">id_var<a class="anchor" aria-label="anchor" href="#arg-id-var"></a>
+</dt>
 <dd><p>(<code>string</code>)<br> variable used as patient identifier.</p></dd>
 
 
-<dt id="arg-title">title<a class="anchor" aria-label="anchor" href="#arg-title"></a></dt>
+<dt id="arg-title">title<a class="anchor" aria-label="anchor" href="#arg-title"></a>
+</dt>
 <dd><p>(<code>string</code>)<br> title for plot.</p></dd>
 
 
-<dt id="arg-subtitle">subtitle<a class="anchor" aria-label="anchor" href="#arg-subtitle"></a></dt>
+<dt id="arg-subtitle">subtitle<a class="anchor" aria-label="anchor" href="#arg-subtitle"></a>
+</dt>
 <dd><p>(<code>string</code>)<br> subtitle for plot.</p></dd>
 
 
-<dt id="arg-caption">caption<a class="anchor" aria-label="anchor" href="#arg-caption"></a></dt>
+<dt id="arg-caption">caption<a class="anchor" aria-label="anchor" href="#arg-caption"></a>
+</dt>
 <dd><p>(<code>string</code>)<br> optional caption below the plot.</p></dd>
 
 
-<dt id="arg-add-baseline-hline">add_baseline_hline<a class="anchor" aria-label="anchor" href="#arg-add-baseline-hline"></a></dt>
+<dt id="arg-add-baseline-hline">add_baseline_hline<a class="anchor" aria-label="anchor" href="#arg-add-baseline-hline"></a>
+</dt>
 <dd><p>(<code>flag</code>)<br> adds horizontal line at baseline y-value on
 plot when <code>TRUE</code>.</p></dd>
 
 
-<dt id="arg-yvar-baseline">yvar_baseline<a class="anchor" aria-label="anchor" href="#arg-yvar-baseline"></a></dt>
+<dt id="arg-yvar-baseline">yvar_baseline<a class="anchor" aria-label="anchor" href="#arg-yvar-baseline"></a>
+</dt>
 <dd><p>(<code>string</code>)<br> variable with baseline values only.
 Ignored when <code>add_baseline_hline</code> is <code>FALSE</code>.</p></dd>
 
 
-<dt id="arg-ggtheme">ggtheme<a class="anchor" aria-label="anchor" href="#arg-ggtheme"></a></dt>
+<dt id="arg-ggtheme">ggtheme<a class="anchor" aria-label="anchor" href="#arg-ggtheme"></a>
+</dt>
 <dd><p>(<code>theme</code>)<br> optional graphical theme function as provided
 by <code>ggplot2</code> to control outlook of plot. Use <code><a href="https://ggplot2.tidyverse.org/reference/theme.html" class="external-link">ggplot2::theme()</a></code> to tweak the display.</p></dd>
 
 
-<dt id="arg-col">col<a class="anchor" aria-label="anchor" href="#arg-col"></a></dt>
+<dt id="arg-col">col<a class="anchor" aria-label="anchor" href="#arg-col"></a>
+</dt>
 <dd><p>(<code>character</code>)<br> line colors.</p></dd>
 
-</dl></div>
+</dl>
+</div>
     <div class="section level2">
-    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
+    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a>
+</h2>
     <p>A <code>ggplot</code> line plot.</p>
     </div>
     <div class="section level2">
-    <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"></a></h2>
+    <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"></a>
+</h2>
     <div class="dont-index"><p><code><a href="g_ipp.html">g_ipp()</a></code> which uses this function.</p></div>
     </div>
 
     <div class="section level2">
-    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
+    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://dplyr.tidyverse.org" class="external-link">dplyr</a></span><span class="op">)</span></span></span>
 <span class="r-in"><span></span></span>
 <span class="r-in"><span><span class="co"># Select a small sample of data to plot.</span></span></span>
@@ -164,17 +247,19 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 </code></pre></div>
     </div>
   </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
-    </nav></aside></div>
+    </nav></aside>
+</div>
 
 
     <footer><div class="nest">
   <p>tern is a part of the <strong>NEST</strong> and <a href="https://pharmaverse.org/" class="external-link"><strong>pharmaverse</strong></a>.</p>
 </div>
-<script type="text/javascript" src="../analytics.js"></script></footer></div>
-
+<script type="text/javascript" src="../analytics.js"></script></footer>
+</div>
 
 
 
 
-  </body></html>
 
+  </body>
+</html>
diff --git a/main/reference/h_ggkm.html b/main/reference/h_ggkm.html
index 2128b7a8b8..fe0c34fc39 100644
--- a/main/reference/h_ggkm.html
+++ b/main/reference/h_ggkm.html
@@ -1,7 +1,30 @@
-<!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Helper function to create a KM plot — h_ggkm • tern</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Helper function to create a KM plot — h_ggkm"><meta name="description" content="
-Draw the Kaplan-Meier plot using ggplot2."><meta property="og:description" content="
-Draw the Kaplan-Meier plot using ggplot2."><meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png"><link rel="stylesheet" href="../consent.css"><script src="../consent.js" type="text/javascript" charset="utf-8"></script></head><body>
+<html lang="en">
+<head>
+<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+<meta charset="utf-8">
+<meta http-equiv="X-UA-Compatible" content="IE=edge">
+<meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<title>Helper function to create a KM plot — h_ggkm • tern</title>
+<!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png">
+<link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png">
+<link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png">
+<link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png">
+<link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png">
+<link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png">
+<script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet">
+<script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet">
+<link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet">
+<script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Helper function to create a KM plot — h_ggkm">
+<meta name="description" content="
+Draw the Kaplan-Meier plot using ggplot2.">
+<meta property="og:description" content="
+Draw the Kaplan-Meier plot using ggplot2.">
+<meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png">
+<link rel="stylesheet" href="../consent.css">
+<script src="../consent.js" type="text/javascript" charset="utf-8"></script>
+</head>
+<body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
 
 
@@ -17,26 +40,66 @@
     </button>
 
     <div id="navbar" class="collapse navbar-collapse ms-3">
-      <ul class="navbar-nav me-auto"><li class="nav-item"><a class="nav-link" href="../articles/tern.html">Get started</a></li>
+      <ul class="navbar-nav me-auto">
+<li class="nav-item"><a class="nav-link" href="../articles/tern.html">Get started</a></li>
 <li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
 <li class="nav-item dropdown">
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-articles" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Articles</button>
-  <ul class="dropdown-menu" aria-labelledby="dropdown-articles"><li><a class="dropdown-item" href="../articles/missing_values.html">Missing Values in Tern</a></li>
+  <ul class="dropdown-menu" aria-labelledby="dropdown-articles">
+<li><a class="dropdown-item" href="../articles/missing_values.html">Missing Values in Tern</a></li>
     <li><a class="dropdown-item" href="../articles/tables.html">Tabulation</a></li>
     <li><a class="dropdown-item" href="../articles/tern_formats.html">Formatting Functions</a></li>
     <li><a class="dropdown-item" href="../articles/tern_functions_guide.html">Understanding `tern` functions</a></li>
-  </ul></li>
+  </ul>
+</li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
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   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
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+  <ul class="dropdown-menu" aria-labelledby="dropdown-reports">
+<li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
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     <li><a class="dropdown-item" href="../unit-test-report-non-cran/">Non-CRAN unit test report</a></li>
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-      </ul><ul class="navbar-nav"><li class="nav-item"><form class="form-inline" role="search">
- <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json"></form></li>
+  </ul>
+</li>
+      <div><li class="nav-item dropdown">
+    <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-versions">Versions</a>
+    <div class="dropdown-menu" aria-labelledby="dropdown-versions">
+    <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/main">main</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.5">v0.9.5</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.4">v0.9.4</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.3">v0.9.3</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1-rc3">v0.9.1-rc3</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
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+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a>
+</div>
+</li></div>
+</ul>
+<ul class="navbar-nav">
+<li class="nav-item"><form class="form-inline" role="search">
+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json">
+</form></li>
 <li class="nav-item"><a class="external-link nav-link" href="https://github.com/insightsengineering/tern" aria-label="GitHub"><span class="fa fa-github"></span></a></li>
-      </ul></div>
+      </ul>
+</div>
 
 
   </div>
@@ -54,7 +117,8 @@
     </div>
 
     <div class="section level2">
-    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
+    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">h_ggkm</span><span class="op">(</span></span>
 <span>  <span class="va">data</span>,</span>
 <span>  xticks <span class="op">=</span> <span class="cn">NULL</span>,</span>
@@ -77,92 +141,114 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
     </div>
 
     <div class="section level2">
-    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
+    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a>
+</h2>
 
 
-<dl><dt id="arg-data">data<a class="anchor" aria-label="anchor" href="#arg-data"></a></dt>
+<dl>
+<dt id="arg-data">data<a class="anchor" aria-label="anchor" href="#arg-data"></a>
+</dt>
 <dd><p>(<code>data.frame</code>)<br> survival data as pre-processed by <code>h_data_plot</code>.</p></dd>
 
 
-<dt id="arg-xticks">xticks<a class="anchor" aria-label="anchor" href="#arg-xticks"></a></dt>
+<dt id="arg-xticks">xticks<a class="anchor" aria-label="anchor" href="#arg-xticks"></a>
+</dt>
 <dd><p>(<code>numeric</code> or <code>NULL</code>)<br> numeric vector of tick positions or a single number with spacing
 between ticks on the x-axis. If <code>NULL</code> (default), <code><a href="https://rdrr.io/pkg/labeling/man/extended.html" class="external-link">labeling::extended()</a></code> is used to determine
 optimal tick positions on the x-axis.</p></dd>
 
 
-<dt id="arg-yval">yval<a class="anchor" aria-label="anchor" href="#arg-yval"></a></dt>
+<dt id="arg-yval">yval<a class="anchor" aria-label="anchor" href="#arg-yval"></a>
+</dt>
 <dd><p>(<code>string</code>)<br> type of plot, to be plotted on the y-axis. Options are <code>Survival</code> (default) and <code>Failure</code>
 probability.</p></dd>
 
 
-<dt id="arg-censor-show">censor_show<a class="anchor" aria-label="anchor" href="#arg-censor-show"></a></dt>
+<dt id="arg-censor-show">censor_show<a class="anchor" aria-label="anchor" href="#arg-censor-show"></a>
+</dt>
 <dd><p>(<code>flag</code>)<br> whether to show censored observations.</p></dd>
 
 
-<dt id="arg-xlab">xlab<a class="anchor" aria-label="anchor" href="#arg-xlab"></a></dt>
+<dt id="arg-xlab">xlab<a class="anchor" aria-label="anchor" href="#arg-xlab"></a>
+</dt>
 <dd><p>(<code>string</code>)<br> x-axis label.</p></dd>
 
 
-<dt id="arg-ylab">ylab<a class="anchor" aria-label="anchor" href="#arg-ylab"></a></dt>
+<dt id="arg-ylab">ylab<a class="anchor" aria-label="anchor" href="#arg-ylab"></a>
+</dt>
 <dd><p>(<code>string</code>)<br> y-axis label.</p></dd>
 
 
-<dt id="arg-ylim">ylim<a class="anchor" aria-label="anchor" href="#arg-ylim"></a></dt>
+<dt id="arg-ylim">ylim<a class="anchor" aria-label="anchor" href="#arg-ylim"></a>
+</dt>
 <dd><p>(<code>numeric(2)</code>)<br> vector containing lower and upper limits for the y-axis, respectively.
 If <code>NULL</code> (default), the default scale range is used.</p></dd>
 
 
-<dt id="arg-title">title<a class="anchor" aria-label="anchor" href="#arg-title"></a></dt>
+<dt id="arg-title">title<a class="anchor" aria-label="anchor" href="#arg-title"></a>
+</dt>
 <dd><p>(<code>string</code>)<br> plot title.</p></dd>
 
 
-<dt id="arg-footnotes">footnotes<a class="anchor" aria-label="anchor" href="#arg-footnotes"></a></dt>
+<dt id="arg-footnotes">footnotes<a class="anchor" aria-label="anchor" href="#arg-footnotes"></a>
+</dt>
 <dd><p>(<code>string</code>)<br> plot footnotes.</p></dd>
 
 
-<dt id="arg-max-time">max_time<a class="anchor" aria-label="anchor" href="#arg-max-time"></a></dt>
+<dt id="arg-max-time">max_time<a class="anchor" aria-label="anchor" href="#arg-max-time"></a>
+</dt>
 <dd><p>(<code>numeric(1)</code>)<br> maximum value to show on x-axis. Only data values less than or up to
 this threshold value will be plotted (defaults to <code>NULL</code>).</p></dd>
 
 
-<dt id="arg-lwd">lwd<a class="anchor" aria-label="anchor" href="#arg-lwd"></a></dt>
+<dt id="arg-lwd">lwd<a class="anchor" aria-label="anchor" href="#arg-lwd"></a>
+</dt>
 <dd><p>(<code>numeric</code>)<br> line width. If a vector is given, its length should be equal to the number of strata from
 <code><a href="https://rdrr.io/pkg/survival/man/survfit.html" class="external-link">survival::survfit()</a></code>.</p></dd>
 
 
-<dt id="arg-lty">lty<a class="anchor" aria-label="anchor" href="#arg-lty"></a></dt>
+<dt id="arg-lty">lty<a class="anchor" aria-label="anchor" href="#arg-lty"></a>
+</dt>
 <dd><p>(<code>numeric</code>)<br> line type. If a vector is given, its length should be equal to the number of strata from
 <code><a href="https://rdrr.io/pkg/survival/man/survfit.html" class="external-link">survival::survfit()</a></code>.</p></dd>
 
 
-<dt id="arg-pch">pch<a class="anchor" aria-label="anchor" href="#arg-pch"></a></dt>
+<dt id="arg-pch">pch<a class="anchor" aria-label="anchor" href="#arg-pch"></a>
+</dt>
 <dd><p>(<code>string</code>)<br> name of symbol or character to use as point symbol to indicate censored cases.</p></dd>
 
 
-<dt id="arg-size">size<a class="anchor" aria-label="anchor" href="#arg-size"></a></dt>
+<dt id="arg-size">size<a class="anchor" aria-label="anchor" href="#arg-size"></a>
+</dt>
 <dd><p>(<code>numeric(1)</code>)<br> size of censored point symbols.</p></dd>
 
 
-<dt id="arg-col">col<a class="anchor" aria-label="anchor" href="#arg-col"></a></dt>
+<dt id="arg-col">col<a class="anchor" aria-label="anchor" href="#arg-col"></a>
+</dt>
 <dd><p>(<code>character</code>)<br> lines colors. Length of a vector should be equal
 to number of strata from <code><a href="https://rdrr.io/pkg/survival/man/survfit.html" class="external-link">survival::survfit()</a></code>.</p></dd>
 
 
-<dt id="arg-ci-ribbon">ci_ribbon<a class="anchor" aria-label="anchor" href="#arg-ci-ribbon"></a></dt>
+<dt id="arg-ci-ribbon">ci_ribbon<a class="anchor" aria-label="anchor" href="#arg-ci-ribbon"></a>
+</dt>
 <dd><p>(<code>flag</code>)<br> whether the confidence interval should be drawn around the Kaplan-Meier curve.</p></dd>
 
 
-<dt id="arg-ggtheme">ggtheme<a class="anchor" aria-label="anchor" href="#arg-ggtheme"></a></dt>
+<dt id="arg-ggtheme">ggtheme<a class="anchor" aria-label="anchor" href="#arg-ggtheme"></a>
+</dt>
 <dd><p>(<code>theme</code>)<br> a graphical theme as provided by <code>ggplot2</code> to format the Kaplan-Meier plot.</p></dd>
 
-</dl></div>
+</dl>
+</div>
     <div class="section level2">
-    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
+    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a>
+</h2>
     <p>A <code>ggplot</code> object.</p>
     </div>
 
     <div class="section level2">
-    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
+    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="co"># \donttest{</span></span></span>
 <span class="r-in"><span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://dplyr.tidyverse.org" class="external-link">dplyr</a></span><span class="op">)</span></span></span>
 <span class="r-in"><span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://github.com/therneau/survival" class="external-link">survival</a></span><span class="op">)</span></span></span>
@@ -188,17 +274,19 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 </code></pre></div>
     </div>
   </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
-    </nav></aside></div>
+    </nav></aside>
+</div>
 
 
     <footer><div class="nest">
   <p>tern is a part of the <strong>NEST</strong> and <a href="https://pharmaverse.org/" class="external-link"><strong>pharmaverse</strong></a>.</p>
 </div>
-<script type="text/javascript" src="../analytics.js"></script></footer></div>
-
+<script type="text/javascript" src="../analytics.js"></script></footer>
+</div>
 
 
 
 
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+  </body>
+</html>
diff --git a/main/reference/h_glm_count.html b/main/reference/h_glm_count.html
index 677e707c19..57fe020708 100644
--- a/main/reference/h_glm_count.html
+++ b/main/reference/h_glm_count.html
@@ -1,11 +1,34 @@
-<!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Helper functions for Poisson models — h_glm_count • tern</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Helper functions for Poisson models — h_glm_count"><meta name="description" content="
+<html lang="en">
+<head>
+<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+<meta charset="utf-8">
+<meta http-equiv="X-UA-Compatible" content="IE=edge">
+<meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<title>Helper functions for Poisson models — h_glm_count • tern</title>
+<!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png">
+<link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png">
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+<link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet">
+<script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet">
+<link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet">
+<script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Helper functions for Poisson models — h_glm_count">
+<meta name="description" content="
 Helper functions that returns the results of stats::glm() when Poisson or Quasi-Poisson
 distributions are needed (see family parameter), or MASS::glm.nb() for Negative Binomial
-distributions. Link function for the GLM is log."><meta property="og:description" content="
+distributions. Link function for the GLM is log.">
+<meta property="og:description" content="
 Helper functions that returns the results of stats::glm() when Poisson or Quasi-Poisson
 distributions are needed (see family parameter), or MASS::glm.nb() for Negative Binomial
-distributions. Link function for the GLM is log."><meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png"><link rel="stylesheet" href="../consent.css"><script src="../consent.js" type="text/javascript" charset="utf-8"></script></head><body>
+distributions. Link function for the GLM is log.">
+<meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png">
+<link rel="stylesheet" href="../consent.css">
+<script src="../consent.js" type="text/javascript" charset="utf-8"></script>
+</head>
+<body>
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+</li></div>
+</ul>
+<ul class="navbar-nav">
+<li class="nav-item"><form class="form-inline" role="search">
+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json">
+</form></li>
 <li class="nav-item"><a class="external-link nav-link" href="https://github.com/insightsengineering/tern" aria-label="GitHub"><span class="fa fa-github"></span></a></li>
-      </ul></div>
+      </ul>
+</div>
 
 
   </div>
@@ -60,7 +123,8 @@
     </div>
 
     <div class="section level2">
-    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
+    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">h_glm_count</span><span class="op">(</span><span class="va">.var</span>, <span class="va">.df_row</span>, <span class="va">variables</span>, <span class="va">distribution</span>, <span class="va">weights</span><span class="op">)</span></span>
 <span></span>
 <span><span class="fu">h_glm_poisson</span><span class="op">(</span><span class="va">.var</span>, <span class="va">.df_row</span>, <span class="va">variables</span>, <span class="va">weights</span><span class="op">)</span></span>
@@ -71,75 +135,102 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
     </div>
 
     <div class="section level2">
-    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
+    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a>
+</h2>
 
 
-<dl><dt id="arg--var">.var<a class="anchor" aria-label="anchor" href="#arg--var"></a></dt>
+<dl>
+<dt id="arg--var">.var<a class="anchor" aria-label="anchor" href="#arg--var"></a>
+</dt>
 <dd><p>(<code>string</code>)<br> single variable name that is passed by <code>rtables</code> when requested
 by a statistics function.</p></dd>
 
 
-<dt id="arg--df-row">.df_row<a class="anchor" aria-label="anchor" href="#arg--df-row"></a></dt>
+<dt id="arg--df-row">.df_row<a class="anchor" aria-label="anchor" href="#arg--df-row"></a>
+</dt>
 <dd><p>(<code>data.frame</code>)<br> dataset that includes all the variables that are called
 in <code>.var</code> and <code>variables</code>.</p></dd>
 
 
-<dt id="arg-variables">variables<a class="anchor" aria-label="anchor" href="#arg-variables"></a></dt>
-<dd><p>(named <code>list</code> of <code>string</code>)<br> list of additional analysis variables, with
-expected elements:</p><ul><li><p><code>arm</code> (<code>string</code>)<br> group variable, for which the covariate adjusted means of multiple
+<dt id="arg-variables">variables<a class="anchor" aria-label="anchor" href="#arg-variables"></a>
+</dt>
+<dd>
+<p>(named <code>list</code> of <code>string</code>)<br> list of additional analysis variables, with
+expected elements:</p>
+<ul>
+<li><p><code>arm</code> (<code>string</code>)<br> group variable, for which the covariate adjusted means of multiple
 groups will be summarized. Specifically, the first level of <code>arm</code> variable is taken as the
 reference group.</p></li>
 <li><p><code>covariates</code> (<code>character</code>)<br> a vector that can contain single variable names (such as
 <code>"X1"</code>), and/or interaction terms indicated by <code>"X1 * X2"</code>.</p></li>
 <li><p><code>offset</code> (<code>numeric</code>)<br> a numeric vector or scalar adding an offset.</p></li>
-</ul></dd>
+</ul>
+</dd>
 
 
-<dt id="arg-distribution">distribution<a class="anchor" aria-label="anchor" href="#arg-distribution"></a></dt>
+<dt id="arg-distribution">distribution<a class="anchor" aria-label="anchor" href="#arg-distribution"></a>
+</dt>
 <dd><p>(<code>character</code>)<br> a character value specifying the distribution
 used in the regression (Poisson, Quasi-Poisson, negative binomial).</p></dd>
 
 
-<dt id="arg-weights">weights<a class="anchor" aria-label="anchor" href="#arg-weights"></a></dt>
+<dt id="arg-weights">weights<a class="anchor" aria-label="anchor" href="#arg-weights"></a>
+</dt>
 <dd><p>(<code>character</code>)<br> a character vector specifying weights used
 in averaging predictions. Number of weights must equal the number of levels included in the covariates.
 Weights option passed to <code><a href="https://rvlenth.github.io/emmeans/reference/emmeans.html" class="external-link">emmeans::emmeans()</a></code>.</p></dd>
 
-</dl></div>
+</dl>
+</div>
     <div class="section level2">
-    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
-
-<ul><li><p><code>h_glm_count()</code> returns the results of the selected model.</p></li>
-</ul><ul><li><p><code>h_glm_poisson()</code> returns the results of a Poisson model.</p></li>
-</ul><ul><li><p><code>h_glm_quasipoisson()</code> returns the results of a Quasi-Poisson model.</p></li>
-</ul><ul><li><p><code>h_glm_negbin()</code> returns the results of a negative binomial model.</p></li>
-</ul></div>
+    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a>
+</h2>
+
+<ul>
+<li><p><code>h_glm_count()</code> returns the results of the selected model.</p></li>
+</ul>
+<ul>
+<li><p><code>h_glm_poisson()</code> returns the results of a Poisson model.</p></li>
+</ul>
+<ul>
+<li><p><code>h_glm_quasipoisson()</code> returns the results of a Quasi-Poisson model.</p></li>
+</ul>
+<ul>
+<li><p><code>h_glm_negbin()</code> returns the results of a negative binomial model.</p></li>
+</ul>
+</div>
     <div class="section level2">
-    <h2 id="functions">Functions<a class="anchor" aria-label="anchor" href="#functions"></a></h2>
+    <h2 id="functions">Functions<a class="anchor" aria-label="anchor" href="#functions"></a>
+</h2>
 
-<ul><li><p><code>h_glm_count()</code>: Helper function to return the results of the
+<ul>
+<li><p><code>h_glm_count()</code>: Helper function to return the results of the
 selected model (Poisson, Quasi-Poisson, negative binomial).</p></li>
 <li><p><code>h_glm_poisson()</code>: Helper function to return results of a Poisson model.</p></li>
 <li><p><code>h_glm_quasipoisson()</code>: Helper function to return results of a Quasi-Poisson model.</p></li>
 <li><p><code>h_glm_negbin()</code>: Helper function to return results of a negative binomial model.</p></li>
-</ul></div>
+</ul>
+</div>
     <div class="section level2">
-    <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"></a></h2>
+    <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"></a>
+</h2>
     <div class="dont-index"><p><a href="summarize_glm_count.html">summarize_glm_count</a></p></div>
     </div>
 
   </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
-    </nav></aside></div>
+    </nav></aside>
+</div>
 
 
     <footer><div class="nest">
   <p>tern is a part of the <strong>NEST</strong> and <a href="https://pharmaverse.org/" class="external-link"><strong>pharmaverse</strong></a>.</p>
 </div>
-<script type="text/javascript" src="../analytics.js"></script></footer></div>
-
+<script type="text/javascript" src="../analytics.js"></script></footer>
+</div>
 
 
 
 
-  </body></html>
 
+  </body>
+</html>
diff --git a/main/reference/h_grob_coxph.html b/main/reference/h_grob_coxph.html
index d0e019fc82..9af9b5b7a5 100644
--- a/main/reference/h_grob_coxph.html
+++ b/main/reference/h_grob_coxph.html
@@ -1,7 +1,30 @@
-<!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Helper function to create Cox-PH grobs — h_grob_coxph • tern</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Helper function to create Cox-PH grobs — h_grob_coxph"><meta name="description" content="
-Grob of rtable output from h_tbl_coxph_pairwise()"><meta property="og:description" content="
-Grob of rtable output from h_tbl_coxph_pairwise()"><meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png"><link rel="stylesheet" href="../consent.css"><script src="../consent.js" type="text/javascript" charset="utf-8"></script></head><body>
+<html lang="en">
+<head>
+<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+<meta charset="utf-8">
+<meta http-equiv="X-UA-Compatible" content="IE=edge">
+<meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<title>Helper function to create Cox-PH grobs — h_grob_coxph • tern</title>
+<!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png">
+<link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png">
+<link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png">
+<link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png">
+<link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png">
+<link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png">
+<script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet">
+<script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet">
+<link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet">
+<script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Helper function to create Cox-PH grobs — h_grob_coxph">
+<meta name="description" content="
+Grob of rtable output from h_tbl_coxph_pairwise()">
+<meta property="og:description" content="
+Grob of rtable output from h_tbl_coxph_pairwise()">
+<meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png">
+<link rel="stylesheet" href="../consent.css">
+<script src="../consent.js" type="text/javascript" charset="utf-8"></script>
+</head>
+<body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
 
 
@@ -17,26 +40,66 @@
     </button>
 
     <div id="navbar" class="collapse navbar-collapse ms-3">
-      <ul class="navbar-nav me-auto"><li class="nav-item"><a class="nav-link" href="../articles/tern.html">Get started</a></li>
+      <ul class="navbar-nav me-auto">
+<li class="nav-item"><a class="nav-link" href="../articles/tern.html">Get started</a></li>
 <li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
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   <button class="nav-link dropdown-toggle" type="button" id="dropdown-articles" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Articles</button>
-  <ul class="dropdown-menu" aria-labelledby="dropdown-articles"><li><a class="dropdown-item" href="../articles/missing_values.html">Missing Values in Tern</a></li>
+  <ul class="dropdown-menu" aria-labelledby="dropdown-articles">
+<li><a class="dropdown-item" href="../articles/missing_values.html">Missing Values in Tern</a></li>
     <li><a class="dropdown-item" href="../articles/tables.html">Tabulation</a></li>
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     <li><a class="dropdown-item" href="../articles/tern_functions_guide.html">Understanding `tern` functions</a></li>
-  </ul></li>
+  </ul>
+</li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
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   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
-  <ul class="dropdown-menu" aria-labelledby="dropdown-reports"><li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
+  <ul class="dropdown-menu" aria-labelledby="dropdown-reports">
+<li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
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-      </ul><ul class="navbar-nav"><li class="nav-item"><form class="form-inline" role="search">
- <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json"></form></li>
+  </ul>
+</li>
+      <div><li class="nav-item dropdown">
+    <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-versions">Versions</a>
+    <div class="dropdown-menu" aria-labelledby="dropdown-versions">
+    <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/main">main</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.5">v0.9.5</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.4">v0.9.4</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.3">v0.9.3</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1-rc3">v0.9.1-rc3</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a>
+</div>
+</li></div>
+</ul>
+<ul class="navbar-nav">
+<li class="nav-item"><form class="form-inline" role="search">
+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json">
+</form></li>
 <li class="nav-item"><a class="external-link nav-link" href="https://github.com/insightsengineering/tern" aria-label="GitHub"><span class="fa fa-github"></span></a></li>
-      </ul></div>
+      </ul>
+</div>
 
 
   </div>
@@ -54,7 +117,8 @@
     </div>
 
     <div class="section level2">
-    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
+    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">h_grob_coxph</span><span class="op">(</span></span>
 <span>  <span class="va">...</span>,</span>
 <span>  x <span class="op">=</span> <span class="fl">0</span>,</span>
@@ -66,37 +130,47 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
     </div>
 
     <div class="section level2">
-    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
+    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a>
+</h2>
 
 
-<dl><dt id="arg--">...<a class="anchor" aria-label="anchor" href="#arg--"></a></dt>
+<dl>
+<dt id="arg--">...<a class="anchor" aria-label="anchor" href="#arg--"></a>
+</dt>
 <dd><p>arguments to pass to <code><a href="h_tbl_coxph_pairwise.html">h_tbl_coxph_pairwise()</a></code>.</p></dd>
 
 
-<dt id="arg-x">x<a class="anchor" aria-label="anchor" href="#arg-x"></a></dt>
+<dt id="arg-x">x<a class="anchor" aria-label="anchor" href="#arg-x"></a>
+</dt>
 <dd><p>(<code>proportion</code>)<br> a value between 0 and 1 specifying x-location.</p></dd>
 
 
-<dt id="arg-y">y<a class="anchor" aria-label="anchor" href="#arg-y"></a></dt>
+<dt id="arg-y">y<a class="anchor" aria-label="anchor" href="#arg-y"></a>
+</dt>
 <dd><p>(<code>proportion</code>)<br> a value between 0 and 1 specifying y-location.</p></dd>
 
 
-<dt id="arg-width">width<a class="anchor" aria-label="anchor" href="#arg-width"></a></dt>
+<dt id="arg-width">width<a class="anchor" aria-label="anchor" href="#arg-width"></a>
+</dt>
 <dd><p>(<code><a href="https://rdrr.io/r/grid/unit.html" class="external-link">grid::unit</a></code>)<br> width (as a unit) to use when printing the grob.</p></dd>
 
 
-<dt id="arg-ttheme">ttheme<a class="anchor" aria-label="anchor" href="#arg-ttheme"></a></dt>
+<dt id="arg-ttheme">ttheme<a class="anchor" aria-label="anchor" href="#arg-ttheme"></a>
+</dt>
 <dd><p>(<code>list</code>)<br> see <code><a href="https://rdrr.io/pkg/gridExtra/man/tableGrob.html" class="external-link">gridExtra::ttheme_default()</a></code>.</p></dd>
 
-</dl></div>
+</dl>
+</div>
     <div class="section level2">
-    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
+    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a>
+</h2>
     <p>A <code>grob</code> of a table containing statistics <code>HR</code>, <code>XX% CI</code> (<code>XX</code> taken from <code>control_coxph_pw</code>),
 and <code>p-value (log-rank)</code>.</p>
     </div>
 
     <div class="section level2">
-    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
+    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="co"># \donttest{</span></span></span>
 <span class="r-in"><span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://dplyr.tidyverse.org" class="external-link">dplyr</a></span><span class="op">)</span></span></span>
 <span class="r-in"><span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://github.com/therneau/survival" class="external-link">survival</a></span><span class="op">)</span></span></span>
@@ -122,17 +196,19 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 </code></pre></div>
     </div>
   </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
-    </nav></aside></div>
+    </nav></aside>
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diff --git a/main/reference/h_grob_median_surv.html b/main/reference/h_grob_median_surv.html
index 03780f4578..1b6a7859f5 100644
--- a/main/reference/h_grob_median_surv.html
+++ b/main/reference/h_grob_median_surv.html
@@ -1,9 +1,32 @@
-<!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Helper function to create survival estimation grobs — h_grob_median_surv • tern</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Helper function to create survival estimation grobs — h_grob_median_surv"><meta name="description" content="
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+<title>Helper function to create survival estimation grobs — h_grob_median_surv • tern</title>
+<!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png">
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+<meta name="description" content="
 The survival fit is transformed in a grob containing a table with groups in
-rows characterized by N, median and 95% confidence interval."><meta property="og:description" content="
+rows characterized by N, median and 95% confidence interval.">
+<meta property="og:description" content="
 The survival fit is transformed in a grob containing a table with groups in
-rows characterized by N, median and 95% confidence interval."><meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png"><link rel="stylesheet" href="../consent.css"><script src="../consent.js" type="text/javascript" charset="utf-8"></script></head><body>
+rows characterized by N, median and 95% confidence interval.">
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   </div>
@@ -57,7 +120,8 @@
     </div>
 
     <div class="section level2">
-    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
+    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">h_grob_median_surv</span><span class="op">(</span></span>
 <span>  <span class="va">fit_km</span>,</span>
 <span>  armval <span class="op">=</span> <span class="st">"All"</span>,</span>
@@ -69,40 +133,51 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
     </div>
 
     <div class="section level2">
-    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
+    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a>
+</h2>
 
 
-<dl><dt id="arg-fit-km">fit_km<a class="anchor" aria-label="anchor" href="#arg-fit-km"></a></dt>
+<dl>
+<dt id="arg-fit-km">fit_km<a class="anchor" aria-label="anchor" href="#arg-fit-km"></a>
+</dt>
 <dd><p>(<code>survfit</code>)<br> result of <code><a href="https://rdrr.io/pkg/survival/man/survfit.html" class="external-link">survival::survfit()</a></code>.</p></dd>
 
 
-<dt id="arg-armval">armval<a class="anchor" aria-label="anchor" href="#arg-armval"></a></dt>
+<dt id="arg-armval">armval<a class="anchor" aria-label="anchor" href="#arg-armval"></a>
+</dt>
 <dd><p>(<code>string</code>)<br> used as strata name when treatment arm variable only has one level. Default is <code>"All"</code>.</p></dd>
 
 
-<dt id="arg-x">x<a class="anchor" aria-label="anchor" href="#arg-x"></a></dt>
+<dt id="arg-x">x<a class="anchor" aria-label="anchor" href="#arg-x"></a>
+</dt>
 <dd><p>(<code>proportion</code>)<br> a value between 0 and 1 specifying x-location.</p></dd>
 
 
-<dt id="arg-y">y<a class="anchor" aria-label="anchor" href="#arg-y"></a></dt>
+<dt id="arg-y">y<a class="anchor" aria-label="anchor" href="#arg-y"></a>
+</dt>
 <dd><p>(<code>proportion</code>)<br> a value between 0 and 1 specifying y-location.</p></dd>
 
 
-<dt id="arg-width">width<a class="anchor" aria-label="anchor" href="#arg-width"></a></dt>
+<dt id="arg-width">width<a class="anchor" aria-label="anchor" href="#arg-width"></a>
+</dt>
 <dd><p>(<code><a href="https://rdrr.io/r/grid/unit.html" class="external-link">grid::unit</a></code>)<br> width (as a unit) to use when printing the grob.</p></dd>
 
 
-<dt id="arg-ttheme">ttheme<a class="anchor" aria-label="anchor" href="#arg-ttheme"></a></dt>
+<dt id="arg-ttheme">ttheme<a class="anchor" aria-label="anchor" href="#arg-ttheme"></a>
+</dt>
 <dd><p>(<code>list</code>)<br> see <code><a href="https://rdrr.io/pkg/gridExtra/man/tableGrob.html" class="external-link">gridExtra::ttheme_default()</a></code>.</p></dd>
 
-</dl></div>
+</dl>
+</div>
     <div class="section level2">
-    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
+    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a>
+</h2>
     <p>A <code>grob</code> of a table containing statistics <code>N</code>, <code>Median</code>, and <code>XX% CI</code> (<code>XX</code> taken from <code>fit_km</code>).</p>
     </div>
 
     <div class="section level2">
-    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
+    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="co"># \donttest{</span></span></span>
 <span class="r-in"><span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://dplyr.tidyverse.org" class="external-link">dplyr</a></span><span class="op">)</span></span></span>
 <span class="r-in"><span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://github.com/therneau/survival" class="external-link">survival</a></span><span class="op">)</span></span></span>
@@ -124,17 +199,19 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 </code></pre></div>
     </div>
   </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
-    </nav></aside></div>
+    </nav></aside>
+</div>
 
 
     <footer><div class="nest">
   <p>tern is a part of the <strong>NEST</strong> and <a href="https://pharmaverse.org/" class="external-link"><strong>pharmaverse</strong></a>.</p>
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-<script type="text/javascript" src="../analytics.js"></script></footer></div>
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diff --git a/main/reference/h_grob_tbl_at_risk.html b/main/reference/h_grob_tbl_at_risk.html
index fa056bcfb6..42aa0f4d9e 100644
--- a/main/reference/h_grob_tbl_at_risk.html
+++ b/main/reference/h_grob_tbl_at_risk.html
@@ -1,11 +1,34 @@
-<!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Helper function to create patient-at-risk grobs — h_grob_tbl_at_risk • tern</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Helper function to create patient-at-risk grobs — h_grob_tbl_at_risk"><meta name="description" content="
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+<!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png">
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+<script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet">
+<script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet">
+<link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet">
+<script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Helper function to create patient-at-risk grobs — h_grob_tbl_at_risk">
+<meta name="description" content="
 Two graphical objects are obtained, one corresponding to row labeling and the second to the table of
 numbers of patients at risk. If title = TRUE, a third object corresponding to the table title is
-also obtained."><meta property="og:description" content="
+also obtained.">
+<meta property="og:description" content="
 Two graphical objects are obtained, one corresponding to row labeling and the second to the table of
 numbers of patients at risk. If title = TRUE, a third object corresponding to the table title is
-also obtained."><meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png"><link rel="stylesheet" href="../consent.css"><script src="../consent.js" type="text/javascript" charset="utf-8"></script></head><body>
+also obtained.">
+<meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png">
+<link rel="stylesheet" href="../consent.css">
+<script src="../consent.js" type="text/javascript" charset="utf-8"></script>
+</head>
+<body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
 
 
@@ -21,26 +44,66 @@
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-      <ul class="navbar-nav me-auto"><li class="nav-item"><a class="nav-link" href="../articles/tern.html">Get started</a></li>
+      <ul class="navbar-nav me-auto">
+<li class="nav-item"><a class="nav-link" href="../articles/tern.html">Get started</a></li>
 <li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
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   <button class="nav-link dropdown-toggle" type="button" id="dropdown-articles" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Articles</button>
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+  <ul class="dropdown-menu" aria-labelledby="dropdown-articles">
+<li><a class="dropdown-item" href="../articles/missing_values.html">Missing Values in Tern</a></li>
     <li><a class="dropdown-item" href="../articles/tables.html">Tabulation</a></li>
     <li><a class="dropdown-item" href="../articles/tern_formats.html">Formatting Functions</a></li>
     <li><a class="dropdown-item" href="../articles/tern_functions_guide.html">Understanding `tern` functions</a></li>
-  </ul></li>
+  </ul>
+</li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
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   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
-  <ul class="dropdown-menu" aria-labelledby="dropdown-reports"><li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
+  <ul class="dropdown-menu" aria-labelledby="dropdown-reports">
+<li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
     <li><a class="dropdown-item" href="../unit-test-report/">Unit test report</a></li>
     <li><a class="dropdown-item" href="../unit-test-report-non-cran/">Non-CRAN unit test report</a></li>
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- <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json"></form></li>
+  </ul>
+</li>
+      <div><li class="nav-item dropdown">
+    <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-versions">Versions</a>
+    <div class="dropdown-menu" aria-labelledby="dropdown-versions">
+    <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/main">main</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.5">v0.9.5</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.4">v0.9.4</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.3">v0.9.3</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1-rc3">v0.9.1-rc3</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a>
+</div>
+</li></div>
+</ul>
+<ul class="navbar-nav">
+<li class="nav-item"><form class="form-inline" role="search">
+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json">
+</form></li>
 <li class="nav-item"><a class="external-link nav-link" href="https://github.com/insightsengineering/tern" aria-label="GitHub"><span class="fa fa-github"></span></a></li>
-      </ul></div>
+      </ul>
+</div>
 
 
   </div>
@@ -60,41 +123,51 @@
     </div>
 
     <div class="section level2">
-    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
+    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">h_grob_tbl_at_risk</span><span class="op">(</span><span class="va">data</span>, <span class="va">annot_tbl</span>, <span class="va">xlim</span>, title <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></code></pre></div>
     </div>
 
     <div class="section level2">
-    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
+    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a>
+</h2>
 
 
-<dl><dt id="arg-data">data<a class="anchor" aria-label="anchor" href="#arg-data"></a></dt>
+<dl>
+<dt id="arg-data">data<a class="anchor" aria-label="anchor" href="#arg-data"></a>
+</dt>
 <dd><p>(<code>data.frame</code>)<br> survival data as pre-processed by <code>h_data_plot</code>.</p></dd>
 
 
-<dt id="arg-annot-tbl">annot_tbl<a class="anchor" aria-label="anchor" href="#arg-annot-tbl"></a></dt>
+<dt id="arg-annot-tbl">annot_tbl<a class="anchor" aria-label="anchor" href="#arg-annot-tbl"></a>
+</dt>
 <dd><p>(<code>data.frame</code>)<br> annotation as prepared by <code><a href="https://rdrr.io/pkg/survival/man/summary.survfit.html" class="external-link">survival::summary.survfit()</a></code> which
 includes the number of patients at risk at given time points.</p></dd>
 
 
-<dt id="arg-xlim">xlim<a class="anchor" aria-label="anchor" href="#arg-xlim"></a></dt>
+<dt id="arg-xlim">xlim<a class="anchor" aria-label="anchor" href="#arg-xlim"></a>
+</dt>
 <dd><p>(<code>numeric(1)</code>)<br> the maximum value on the x-axis (used to ensure the at risk table aligns with the KM
 graph).</p></dd>
 
 
-<dt id="arg-title">title<a class="anchor" aria-label="anchor" href="#arg-title"></a></dt>
+<dt id="arg-title">title<a class="anchor" aria-label="anchor" href="#arg-title"></a>
+</dt>
 <dd><p>(<code>flag</code>)<br> whether the "Patients at Risk" title should be added above the <code>annot_at_risk</code>
 table. Has no effect if <code>annot_at_risk</code> is <code>FALSE</code>. Defaults to <code>TRUE</code>.</p></dd>
 
-</dl></div>
+</dl>
+</div>
     <div class="section level2">
-    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
+    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a>
+</h2>
     <p>A named <code>list</code> of two <code>gTree</code> objects if <code>title = FALSE</code>: <code>at_risk</code> and <code>label</code>, or three
 <code>gTree</code> objects if <code>title = TRUE</code>: <code>at_risk</code>, <code>label</code>, and <code>title</code>.</p>
     </div>
 
     <div class="section level2">
-    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
+    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="co"># \donttest{</span></span></span>
 <span class="r-in"><span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://dplyr.tidyverse.org" class="external-link">dplyr</a></span><span class="op">)</span></span></span>
 <span class="r-in"><span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://github.com/therneau/survival" class="external-link">survival</a></span><span class="op">)</span></span></span>
@@ -160,17 +233,19 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 </code></pre></div>
     </div>
   </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
-    </nav></aside></div>
+    </nav></aside>
+</div>
 
 
     <footer><div class="nest">
   <p>tern is a part of the <strong>NEST</strong> and <a href="https://pharmaverse.org/" class="external-link"><strong>pharmaverse</strong></a>.</p>
 </div>
-<script type="text/javascript" src="../analytics.js"></script></footer></div>
-
+<script type="text/javascript" src="../analytics.js"></script></footer>
+</div>
 
 
 
 
-  </body></html>
 
+  </body>
+</html>
diff --git a/main/reference/h_grob_y_annot.html b/main/reference/h_grob_y_annot.html
index a6f891ace5..6d7bffd772 100644
--- a/main/reference/h_grob_y_annot.html
+++ b/main/reference/h_grob_y_annot.html
@@ -1,7 +1,30 @@
-<!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Helper function to create grid object with y-axis annotation — h_grob_y_annot • tern</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Helper function to create grid object with y-axis annotation — h_grob_y_annot"><meta name="description" content="
-Build the y-axis annotation from a decomposed ggplot."><meta property="og:description" content="
-Build the y-axis annotation from a decomposed ggplot."><meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png"><link rel="stylesheet" href="../consent.css"><script src="../consent.js" type="text/javascript" charset="utf-8"></script></head><body>
+<html lang="en">
+<head>
+<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+<meta charset="utf-8">
+<meta http-equiv="X-UA-Compatible" content="IE=edge">
+<meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<title>Helper function to create grid object with y-axis annotation — h_grob_y_annot • tern</title>
+<!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png">
+<link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png">
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+<link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png">
+<link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png">
+<link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png">
+<script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet">
+<script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet">
+<link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet">
+<script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Helper function to create grid object with y-axis annotation — h_grob_y_annot">
+<meta name="description" content="
+Build the y-axis annotation from a decomposed ggplot.">
+<meta property="og:description" content="
+Build the y-axis annotation from a decomposed ggplot.">
+<meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png">
+<link rel="stylesheet" href="../consent.css">
+<script src="../consent.js" type="text/javascript" charset="utf-8"></script>
+</head>
+<body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
 
 
@@ -17,26 +40,66 @@
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   <button class="nav-link dropdown-toggle" type="button" id="dropdown-articles" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Articles</button>
-  <ul class="dropdown-menu" aria-labelledby="dropdown-articles"><li><a class="dropdown-item" href="../articles/missing_values.html">Missing Values in Tern</a></li>
+  <ul class="dropdown-menu" aria-labelledby="dropdown-articles">
+<li><a class="dropdown-item" href="../articles/missing_values.html">Missing Values in Tern</a></li>
     <li><a class="dropdown-item" href="../articles/tables.html">Tabulation</a></li>
     <li><a class="dropdown-item" href="../articles/tern_formats.html">Formatting Functions</a></li>
     <li><a class="dropdown-item" href="../articles/tern_functions_guide.html">Understanding `tern` functions</a></li>
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+</li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
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+  <ul class="dropdown-menu" aria-labelledby="dropdown-reports">
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-      </ul><ul class="navbar-nav"><li class="nav-item"><form class="form-inline" role="search">
- <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json"></form></li>
+  </ul>
+</li>
+      <div><li class="nav-item dropdown">
+    <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-versions">Versions</a>
+    <div class="dropdown-menu" aria-labelledby="dropdown-versions">
+    <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
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+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
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+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.3">v0.9.3</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1-rc3">v0.9.1-rc3</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a>
+</div>
+</li></div>
+</ul>
+<ul class="navbar-nav">
+<li class="nav-item"><form class="form-inline" role="search">
+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json">
+</form></li>
 <li class="nav-item"><a class="external-link nav-link" href="https://github.com/insightsengineering/tern" aria-label="GitHub"><span class="fa fa-github"></span></a></li>
-      </ul></div>
+      </ul>
+</div>
 
 
   </div>
@@ -54,29 +117,37 @@
     </div>
 
     <div class="section level2">
-    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
+    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">h_grob_y_annot</span><span class="op">(</span><span class="va">ylab</span>, <span class="va">yaxis</span><span class="op">)</span></span></code></pre></div>
     </div>
 
     <div class="section level2">
-    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
+    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a>
+</h2>
 
 
-<dl><dt id="arg-ylab">ylab<a class="anchor" aria-label="anchor" href="#arg-ylab"></a></dt>
+<dl>
+<dt id="arg-ylab">ylab<a class="anchor" aria-label="anchor" href="#arg-ylab"></a>
+</dt>
 <dd><p>(<code>gtable</code>)<br> the y-lab as a graphical object derived from a <code>ggplot</code>.</p></dd>
 
 
-<dt id="arg-yaxis">yaxis<a class="anchor" aria-label="anchor" href="#arg-yaxis"></a></dt>
+<dt id="arg-yaxis">yaxis<a class="anchor" aria-label="anchor" href="#arg-yaxis"></a>
+</dt>
 <dd><p>(<code>gtable</code>)<br> the y-axis as a graphical object derived from a <code>ggplot</code>.</p></dd>
 
-</dl></div>
+</dl>
+</div>
     <div class="section level2">
-    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
+    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a>
+</h2>
     <p>A <code>gTree</code> object containing the y-axis annotation from a <code>ggplot</code>.</p>
     </div>
 
     <div class="section level2">
-    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
+    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="co"># \donttest{</span></span></span>
 <span class="r-in"><span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://dplyr.tidyverse.org" class="external-link">dplyr</a></span><span class="op">)</span></span></span>
 <span class="r-in"><span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://github.com/therneau/survival" class="external-link">survival</a></span><span class="op">)</span></span></span>
@@ -110,17 +181,19 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 </code></pre></div>
     </div>
   </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
-    </nav></aside></div>
+    </nav></aside>
+</div>
 
 
     <footer><div class="nest">
   <p>tern is a part of the <strong>NEST</strong> and <a href="https://pharmaverse.org/" class="external-link"><strong>pharmaverse</strong></a>.</p>
 </div>
-<script type="text/javascript" src="../analytics.js"></script></footer></div>
-
+<script type="text/javascript" src="../analytics.js"></script></footer>
+</div>
 
 
 
 
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+  </body>
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diff --git a/main/reference/h_incidence_rate.html b/main/reference/h_incidence_rate.html
index 57afcab1d3..b7dbd96404 100644
--- a/main/reference/h_incidence_rate.html
+++ b/main/reference/h_incidence_rate.html
@@ -1,5 +1,28 @@
-<!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Helper functions for incidence rate — h_incidence_rate • tern</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Helper functions for incidence rate — h_incidence_rate"><meta name="description" content=""><meta property="og:description" content=""><meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png"><link rel="stylesheet" href="../consent.css"><script src="../consent.js" type="text/javascript" charset="utf-8"></script></head><body>
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+<script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
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+<script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet">
+<link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet">
+<script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Helper functions for incidence rate — h_incidence_rate">
+<meta name="description" content="">
+<meta property="og:description" content="">
+<meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png">
+<link rel="stylesheet" href="../consent.css">
+<script src="../consent.js" type="text/javascript" charset="utf-8"></script>
+</head>
+<body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
 
 
@@ -15,26 +38,66 @@
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     <div id="navbar" class="collapse navbar-collapse ms-3">
-      <ul class="navbar-nav me-auto"><li class="nav-item"><a class="nav-link" href="../articles/tern.html">Get started</a></li>
+      <ul class="navbar-nav me-auto">
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+  <ul class="dropdown-menu" aria-labelledby="dropdown-articles">
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+  </ul>
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- <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json"></form></li>
+  </ul>
+</li>
+      <div><li class="nav-item dropdown">
+    <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-versions">Versions</a>
+    <div class="dropdown-menu" aria-labelledby="dropdown-versions">
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+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
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+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
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+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a>
+</div>
+</li></div>
+</ul>
+<ul class="navbar-nav">
+<li class="nav-item"><form class="form-inline" role="search">
+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json">
+</form></li>
 <li class="nav-item"><a class="external-link nav-link" href="https://github.com/insightsengineering/tern" aria-label="GitHub"><span class="fa fa-github"></span></a></li>
-      </ul></div>
+      </ul>
+</div>
 
 
   </div>
@@ -51,7 +114,8 @@
     </div>
 
     <div class="section level2">
-    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
+    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">h_incidence_rate</span><span class="op">(</span><span class="va">person_years</span>, <span class="va">n_events</span>, control <span class="op">=</span> <span class="fu"><a href="control_incidence_rate.html">control_incidence_rate</a></span><span class="op">(</span><span class="op">)</span><span class="op">)</span></span>
 <span></span>
 <span><span class="fu">h_incidence_rate_normal</span><span class="op">(</span><span class="va">person_years</span>, <span class="va">n_events</span>, alpha <span class="op">=</span> <span class="fl">0.05</span><span class="op">)</span></span>
@@ -64,40 +128,54 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
     </div>
 
     <div class="section level2">
-    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
+    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a>
+</h2>
 
 
-<dl><dt id="arg-person-years">person_years<a class="anchor" aria-label="anchor" href="#arg-person-years"></a></dt>
+<dl>
+<dt id="arg-person-years">person_years<a class="anchor" aria-label="anchor" href="#arg-person-years"></a>
+</dt>
 <dd><p>(<code>numeric(1)</code>)<br> total person-years at risk.</p></dd>
 
 
-<dt id="arg-n-events">n_events<a class="anchor" aria-label="anchor" href="#arg-n-events"></a></dt>
+<dt id="arg-n-events">n_events<a class="anchor" aria-label="anchor" href="#arg-n-events"></a>
+</dt>
 <dd><p>(<code>integer(1)</code>)<br> number of events observed.</p></dd>
 
 
-<dt id="arg-control">control<a class="anchor" aria-label="anchor" href="#arg-control"></a></dt>
-<dd><p>(<code>list</code>)<br> parameters for estimation details, specified by using
-the helper function <code><a href="control_incidence_rate.html">control_incidence_rate()</a></code>. Possible parameter options are:</p><ul><li><p><code>conf_level</code>: (<code>proportion</code>)<br> confidence level for the estimated incidence rate.</p></li>
+<dt id="arg-control">control<a class="anchor" aria-label="anchor" href="#arg-control"></a>
+</dt>
+<dd>
+<p>(<code>list</code>)<br> parameters for estimation details, specified by using
+the helper function <code><a href="control_incidence_rate.html">control_incidence_rate()</a></code>. Possible parameter options are:</p>
+<ul>
+<li><p><code>conf_level</code>: (<code>proportion</code>)<br> confidence level for the estimated incidence rate.</p></li>
 <li><p><code>conf_type</code>: (<code>string</code>)<br><code>normal</code> (default), <code>normal_log</code>, <code>exact</code>, or <code>byar</code>
 for confidence interval type.</p></li>
 <li><p><code>input_time_unit</code>: (<code>string</code>)<br><code>day</code>, <code>week</code>, <code>month</code>, or <code>year</code> (default)
 indicating time unit for data input.</p></li>
 <li><p><code>num_pt_year</code>: (<code>numeric</code>)<br> time unit for desired output (in person-years).</p></li>
-</ul></dd>
+</ul>
+</dd>
 
 
-<dt id="arg-alpha">alpha<a class="anchor" aria-label="anchor" href="#arg-alpha"></a></dt>
+<dt id="arg-alpha">alpha<a class="anchor" aria-label="anchor" href="#arg-alpha"></a>
+</dt>
 <dd><p>(<code>numeric(1)</code>)<br> two-sided alpha-level for confidence interval.</p></dd>
 
-</dl></div>
+</dl>
+</div>
     <div class="section level2">
-    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
+    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a>
+</h2>
     <p>Estimated incidence rate, <code>rate</code>, and associated confidence interval, <code>rate_ci</code>.</p>
     </div>
     <div class="section level2">
-    <h2 id="functions">Functions<a class="anchor" aria-label="anchor" href="#functions"></a></h2>
+    <h2 id="functions">Functions<a class="anchor" aria-label="anchor" href="#functions"></a>
+</h2>
 
-<ul><li><p><code>h_incidence_rate()</code>: Helper function to estimate the incidence rate and
+<ul>
+<li><p><code>h_incidence_rate()</code>: Helper function to estimate the incidence rate and
 associated confidence interval.</p></li>
 <li><p><code>h_incidence_rate_normal()</code>: Helper function to estimate the incidence rate and
 associated confidence interval based on the normal approximation for the
@@ -109,14 +187,17 @@ <h2 id="functions">Functions<a class="anchor" aria-label="anchor" href="#functio
 associated exact confidence interval. Unit is one person-year.</p></li>
 <li><p><code>h_incidence_rate_byar()</code>: Helper function to estimate the incidence rate and
 associated Byar's confidence interval. Unit is one person-year.</p></li>
-</ul></div>
+</ul>
+</div>
     <div class="section level2">
-    <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"></a></h2>
+    <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"></a>
+</h2>
     <div class="dont-index"><p><a href="incidence_rate.html">incidence_rate</a></p></div>
     </div>
 
     <div class="section level2">
-    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
+    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="fu">h_incidence_rate_normal</span><span class="op">(</span><span class="fl">200</span>, <span class="fl">2</span><span class="op">)</span></span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> $rate</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0.01</span>
@@ -152,17 +233,19 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 </code></pre></div>
     </div>
   </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
-    </nav></aside></div>
+    </nav></aside>
+</div>
 
 
     <footer><div class="nest">
   <p>tern is a part of the <strong>NEST</strong> and <a href="https://pharmaverse.org/" class="external-link"><strong>pharmaverse</strong></a>.</p>
 </div>
-<script type="text/javascript" src="../analytics.js"></script></footer></div>
-
+<script type="text/javascript" src="../analytics.js"></script></footer>
+</div>
 
 
 
 
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+  </body>
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diff --git a/main/reference/h_km_layout.html b/main/reference/h_km_layout.html
index c09d9ee679..a04245a47b 100644
--- a/main/reference/h_km_layout.html
+++ b/main/reference/h_km_layout.html
@@ -1,7 +1,30 @@
-<!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Helper function to prepare a KM layout — h_km_layout • tern</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Helper function to prepare a KM layout — h_km_layout"><meta name="description" content="
-Prepares a (5 rows) x (2 cols) layout for the Kaplan-Meier curve."><meta property="og:description" content="
-Prepares a (5 rows) x (2 cols) layout for the Kaplan-Meier curve."><meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png"><link rel="stylesheet" href="../consent.css"><script src="../consent.js" type="text/javascript" charset="utf-8"></script></head><body>
+<html lang="en">
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+<meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<title>Helper function to prepare a KM layout — h_km_layout • tern</title>
+<!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png">
+<link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png">
+<link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png">
+<link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png">
+<link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png">
+<link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png">
+<script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet">
+<script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet">
+<link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet">
+<script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Helper function to prepare a KM layout — h_km_layout">
+<meta name="description" content="
+Prepares a (5 rows) x (2 cols) layout for the Kaplan-Meier curve.">
+<meta property="og:description" content="
+Prepares a (5 rows) x (2 cols) layout for the Kaplan-Meier curve.">
+<meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png">
+<link rel="stylesheet" href="../consent.css">
+<script src="../consent.js" type="text/javascript" charset="utf-8"></script>
+</head>
+<body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
 
 
@@ -17,26 +40,66 @@
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 <li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
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-  <ul class="dropdown-menu" aria-labelledby="dropdown-articles"><li><a class="dropdown-item" href="../articles/missing_values.html">Missing Values in Tern</a></li>
+  <ul class="dropdown-menu" aria-labelledby="dropdown-articles">
+<li><a class="dropdown-item" href="../articles/missing_values.html">Missing Values in Tern</a></li>
     <li><a class="dropdown-item" href="../articles/tables.html">Tabulation</a></li>
     <li><a class="dropdown-item" href="../articles/tern_formats.html">Formatting Functions</a></li>
     <li><a class="dropdown-item" href="../articles/tern_functions_guide.html">Understanding `tern` functions</a></li>
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+  </ul>
+</li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
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+  <ul class="dropdown-menu" aria-labelledby="dropdown-reports">
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+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
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+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
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+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a>
+</div>
+</li></div>
+</ul>
+<ul class="navbar-nav">
+<li class="nav-item"><form class="form-inline" role="search">
+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json">
+</form></li>
 <li class="nav-item"><a class="external-link nav-link" href="https://github.com/insightsengineering/tern" aria-label="GitHub"><span class="fa fa-github"></span></a></li>
-      </ul></div>
+      </ul>
+</div>
 
 
   </div>
@@ -54,7 +117,8 @@
     </div>
 
     <div class="section level2">
-    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
+    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">h_km_layout</span><span class="op">(</span></span>
 <span>  <span class="va">data</span>,</span>
 <span>  <span class="va">g_el</span>,</span>
@@ -66,50 +130,65 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
     </div>
 
     <div class="section level2">
-    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
+    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a>
+</h2>
 
 
-<dl><dt id="arg-data">data<a class="anchor" aria-label="anchor" href="#arg-data"></a></dt>
+<dl>
+<dt id="arg-data">data<a class="anchor" aria-label="anchor" href="#arg-data"></a>
+</dt>
 <dd><p>(<code>data.frame</code>)<br> survival data as pre-processed by <code>h_data_plot</code>.</p></dd>
 
 
-<dt id="arg-g-el">g_el<a class="anchor" aria-label="anchor" href="#arg-g-el"></a></dt>
+<dt id="arg-g-el">g_el<a class="anchor" aria-label="anchor" href="#arg-g-el"></a>
+</dt>
 <dd><p>(<code>list</code> of <code>gtable</code>)<br> list as obtained by <code><a href="h_decompose_gg.html">h_decompose_gg()</a></code>.</p></dd>
 
 
-<dt id="arg-title">title<a class="anchor" aria-label="anchor" href="#arg-title"></a></dt>
+<dt id="arg-title">title<a class="anchor" aria-label="anchor" href="#arg-title"></a>
+</dt>
 <dd><p>(<code>string</code>)<br> plot title.</p></dd>
 
 
-<dt id="arg-footnotes">footnotes<a class="anchor" aria-label="anchor" href="#arg-footnotes"></a></dt>
+<dt id="arg-footnotes">footnotes<a class="anchor" aria-label="anchor" href="#arg-footnotes"></a>
+</dt>
 <dd><p>(<code>string</code>)<br> plot footnotes.</p></dd>
 
 
-<dt id="arg-annot-at-risk">annot_at_risk<a class="anchor" aria-label="anchor" href="#arg-annot-at-risk"></a></dt>
+<dt id="arg-annot-at-risk">annot_at_risk<a class="anchor" aria-label="anchor" href="#arg-annot-at-risk"></a>
+</dt>
 <dd><p>(<code>flag</code>)<br> compute and add the annotation table reporting the number of
 patient at risk matching the main grid of the Kaplan-Meier curve.</p></dd>
 
 
-<dt id="arg-annot-at-risk-title">annot_at_risk_title<a class="anchor" aria-label="anchor" href="#arg-annot-at-risk-title"></a></dt>
+<dt id="arg-annot-at-risk-title">annot_at_risk_title<a class="anchor" aria-label="anchor" href="#arg-annot-at-risk-title"></a>
+</dt>
 <dd><p>(<code>flag</code>)<br> whether the "Patients at Risk" title should be added above the <code>annot_at_risk</code>
 table. Has no effect if <code>annot_at_risk</code> is <code>FALSE</code>. Defaults to <code>TRUE</code>.</p></dd>
 
-</dl></div>
+</dl>
+</div>
     <div class="section level2">
-    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
+    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a>
+</h2>
     <p>A grid layout.</p>
     </div>
     <div class="section level2">
-    <h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a></h2>
+    <h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a>
+</h2>
     <p>The layout corresponds to a grid of two columns and five rows of unequal dimensions. Most of the
-dimension are fixed, only the curve is flexible and will accommodate with the remaining free space.</p><ul><li><p>The left column gets the annotation of the <code>ggplot</code> (y-axis) and the names of the strata for the patient
+dimension are fixed, only the curve is flexible and will accommodate with the remaining free space.</p>
+<ul>
+<li><p>The left column gets the annotation of the <code>ggplot</code> (y-axis) and the names of the strata for the patient
 at risk tabulation. The main constraint is about the width of the columns which must allow the writing of
 the strata name.</p></li>
 <li><p>The right column receive the <code>ggplot</code>, the legend, the x-axis and the patient at risk table.</p></li>
-</ul></div>
+</ul>
+</div>
 
     <div class="section level2">
-    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
+    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="co"># \donttest{</span></span></span>
 <span class="r-in"><span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://dplyr.tidyverse.org" class="external-link">dplyr</a></span><span class="op">)</span></span></span>
 <span class="r-in"><span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://github.com/therneau/survival" class="external-link">survival</a></span><span class="op">)</span></span></span>
@@ -135,17 +214,19 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 </code></pre></div>
     </div>
   </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
-    </nav></aside></div>
+    </nav></aside>
+</div>
 
 
     <footer><div class="nest">
   <p>tern is a part of the <strong>NEST</strong> and <a href="https://pharmaverse.org/" class="external-link"><strong>pharmaverse</strong></a>.</p>
 </div>
-<script type="text/javascript" src="../analytics.js"></script></footer></div>
-
+<script type="text/javascript" src="../analytics.js"></script></footer>
+</div>
 
 
 
 
-  </body></html>
 
+  </body>
+</html>
diff --git a/main/reference/h_logistic_regression.html b/main/reference/h_logistic_regression.html
index d8c302c25c..78a23992cc 100644
--- a/main/reference/h_logistic_regression.html
+++ b/main/reference/h_logistic_regression.html
@@ -1,7 +1,30 @@
-<!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Helper functions for multivariate logistic regression — h_logistic_regression • tern</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Helper functions for multivariate logistic regression — h_logistic_regression"><meta name="description" content="
-Helper functions used in calculations for logistic regression."><meta property="og:description" content="
-Helper functions used in calculations for logistic regression."><meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png"><link rel="stylesheet" href="../consent.css"><script src="../consent.js" type="text/javascript" charset="utf-8"></script></head><body>
+<html lang="en">
+<head>
+<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+<meta charset="utf-8">
+<meta http-equiv="X-UA-Compatible" content="IE=edge">
+<meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<title>Helper functions for multivariate logistic regression — h_logistic_regression • tern</title>
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+</div>
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-      </ul></div>
+      </ul>
+</div>
 
 
   </div>
@@ -54,7 +117,8 @@
     </div>
 
     <div class="section level2">
-    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
+    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">h_get_interaction_vars</span><span class="op">(</span><span class="va">fit_glm</span><span class="op">)</span></span>
 <span></span>
 <span><span class="fu">h_interaction_coef_name</span><span class="op">(</span></span>
@@ -102,75 +166,94 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
     </div>
 
     <div class="section level2">
-    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
+    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a>
+</h2>
 
 
-<dl><dt id="arg-fit-glm">fit_glm<a class="anchor" aria-label="anchor" href="#arg-fit-glm"></a></dt>
+<dl>
+<dt id="arg-fit-glm">fit_glm<a class="anchor" aria-label="anchor" href="#arg-fit-glm"></a>
+</dt>
 <dd><p>(<code>glm</code>)<br> logistic regression model fitted by <code><a href="https://rdrr.io/r/stats/glm.html" class="external-link">stats::glm()</a></code> with "binomial" family.
 Limited functionality is also available for conditional logistic regression models fitted by
 <code><a href="https://rdrr.io/pkg/survival/man/clogit.html" class="external-link">survival::clogit()</a></code>, currently this is used only by <code><a href="extract_rsp_biomarkers.html">extract_rsp_biomarkers()</a></code>.</p></dd>
 
 
-<dt id="arg-interaction-vars">interaction_vars<a class="anchor" aria-label="anchor" href="#arg-interaction-vars"></a></dt>
+<dt id="arg-interaction-vars">interaction_vars<a class="anchor" aria-label="anchor" href="#arg-interaction-vars"></a>
+</dt>
 <dd><p>(<code>character(2)</code>)<br> interaction variable names.</p></dd>
 
 
-<dt id="arg-first-var-with-level">first_var_with_level<a class="anchor" aria-label="anchor" href="#arg-first-var-with-level"></a></dt>
+<dt id="arg-first-var-with-level">first_var_with_level<a class="anchor" aria-label="anchor" href="#arg-first-var-with-level"></a>
+</dt>
 <dd><p>(<code>character(2)</code>)<br> the first variable name with the interaction level.</p></dd>
 
 
-<dt id="arg-second-var-with-level">second_var_with_level<a class="anchor" aria-label="anchor" href="#arg-second-var-with-level"></a></dt>
+<dt id="arg-second-var-with-level">second_var_with_level<a class="anchor" aria-label="anchor" href="#arg-second-var-with-level"></a>
+</dt>
 <dd><p>(<code>character(2)</code>)<br> the second variable name with the interaction level.</p></dd>
 
 
-<dt id="arg-odds-ratio-var">odds_ratio_var<a class="anchor" aria-label="anchor" href="#arg-odds-ratio-var"></a></dt>
+<dt id="arg-odds-ratio-var">odds_ratio_var<a class="anchor" aria-label="anchor" href="#arg-odds-ratio-var"></a>
+</dt>
 <dd><p>(<code>string</code>)<br> the odds ratio variable.</p></dd>
 
 
-<dt id="arg-interaction-var">interaction_var<a class="anchor" aria-label="anchor" href="#arg-interaction-var"></a></dt>
+<dt id="arg-interaction-var">interaction_var<a class="anchor" aria-label="anchor" href="#arg-interaction-var"></a>
+</dt>
 <dd><p>(<code>string</code>)<br> the interaction variable.</p></dd>
 
 
-<dt id="arg-conf-level">conf_level<a class="anchor" aria-label="anchor" href="#arg-conf-level"></a></dt>
+<dt id="arg-conf-level">conf_level<a class="anchor" aria-label="anchor" href="#arg-conf-level"></a>
+</dt>
 <dd><p>(<code>proportion</code>)<br> confidence level of the interval.</p></dd>
 
 
-<dt id="arg-at">at<a class="anchor" aria-label="anchor" href="#arg-at"></a></dt>
+<dt id="arg-at">at<a class="anchor" aria-label="anchor" href="#arg-at"></a>
+</dt>
 <dd><p>(<code>numeric</code> or <code>NULL</code>)<br> optional values for the interaction variable. Otherwise
 the median is used.</p></dd>
 
 
-<dt id="arg-terms">terms<a class="anchor" aria-label="anchor" href="#arg-terms"></a></dt>
+<dt id="arg-terms">terms<a class="anchor" aria-label="anchor" href="#arg-terms"></a>
+</dt>
 <dd><p>(<code>character</code>)<br> simple terms.</p></dd>
 
 
-<dt id="arg-table">table<a class="anchor" aria-label="anchor" href="#arg-table"></a></dt>
+<dt id="arg-table">table<a class="anchor" aria-label="anchor" href="#arg-table"></a>
+</dt>
 <dd><p>(<code>table</code>)<br> table containing numbers for terms.</p></dd>
 
 
-<dt id="arg-terms-">terms1<a class="anchor" aria-label="anchor" href="#arg-terms-"></a></dt>
+<dt id="arg-terms-">terms1<a class="anchor" aria-label="anchor" href="#arg-terms-"></a>
+</dt>
 <dd><p>(<code>character</code>)<br> terms for first dimension (rows).</p></dd>
 
 
-<dt id="arg-terms-">terms2<a class="anchor" aria-label="anchor" href="#arg-terms-"></a></dt>
+<dt id="arg-terms-">terms2<a class="anchor" aria-label="anchor" href="#arg-terms-"></a>
+</dt>
 <dd><p>(<code>character</code>)<br> terms for second dimension (rows).</p></dd>
 
 
-<dt id="arg-any">any<a class="anchor" aria-label="anchor" href="#arg-any"></a></dt>
+<dt id="arg-any">any<a class="anchor" aria-label="anchor" href="#arg-any"></a>
+</dt>
 <dd><p>(<code>flag</code>)<br> whether any of <code>term1</code> and <code>term2</code> can be fulfilled to count the
 number of patients. In that case they can only be scalar (strings).</p></dd>
 
 
-<dt id="arg-x">x<a class="anchor" aria-label="anchor" href="#arg-x"></a></dt>
+<dt id="arg-x">x<a class="anchor" aria-label="anchor" href="#arg-x"></a>
+</dt>
 <dd><p>(<code>character</code>)<br> a variable or interaction term in <code>fit_glm</code> (depending on the helper function used).</p></dd>
 
 
-<dt id="arg--">...<a class="anchor" aria-label="anchor" href="#arg--"></a></dt>
+<dt id="arg--">...<a class="anchor" aria-label="anchor" href="#arg--"></a>
+</dt>
 <dd><p>additional arguments for the lower level functions.</p></dd>
 
-</dl></div>
+</dl>
+</div>
     <div class="section level2">
-    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
+    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a>
+</h2>
     <p>Vector of names of interaction variables.</p>
 <p>Name of coefficient.</p>
 <p>Odds ratio.</p>
@@ -185,9 +268,11 @@ <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2
 <p>Tabulated statistics for the given variable(s) from the logistic regression model.</p>
     </div>
     <div class="section level2">
-    <h2 id="functions">Functions<a class="anchor" aria-label="anchor" href="#functions"></a></h2>
+    <h2 id="functions">Functions<a class="anchor" aria-label="anchor" href="#functions"></a>
+</h2>
 
-<ul><li><p><code>h_get_interaction_vars()</code>: Helper function to extract interaction variable names from a fitted
+<ul>
+<li><p><code>h_get_interaction_vars()</code>: Helper function to extract interaction variable names from a fitted
 model assuming only one interaction term.</p></li>
 <li><p><code>h_interaction_coef_name()</code>: Helper function to get the right coefficient name from the
 interaction variable names and the given levels. The main value here is that the order
@@ -215,16 +300,19 @@ <h2 id="functions">Functions<a class="anchor" aria-label="anchor" href="#functio
 odds ratios and confidence intervals of simple terms.</p></li>
 <li><p><code>h_logistic_inter_terms()</code>: Helper function to tabulate the results including
 odds ratios and confidence intervals of interaction terms.</p></li>
-</ul></div>
+</ul>
+</div>
     <div class="section level2">
-    <h2 id="note">Note<a class="anchor" aria-label="anchor" href="#note"></a></h2>
+    <h2 id="note">Note<a class="anchor" aria-label="anchor" href="#note"></a>
+</h2>
     <p>We don't provide a function for the case when both variables are continuous because
 this does not arise in this table, as the treatment arm variable will always be involved
 and categorical.</p>
     </div>
 
     <div class="section level2">
-    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
+    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://dplyr.tidyverse.org" class="external-link">dplyr</a></span><span class="op">)</span></span></span>
 <span class="r-in"><span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://broom.tidymodels.org/" class="external-link">broom</a></span><span class="op">)</span></span></span>
 <span class="r-in"><span></span></span>
@@ -404,17 +492,19 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 </code></pre></div>
     </div>
   </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
-    </nav></aside></div>
+    </nav></aside>
+</div>
 
 
     <footer><div class="nest">
   <p>tern is a part of the <strong>NEST</strong> and <a href="https://pharmaverse.org/" class="external-link"><strong>pharmaverse</strong></a>.</p>
 </div>
-<script type="text/javascript" src="../analytics.js"></script></footer></div>
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+<script type="text/javascript" src="../analytics.js"></script></footer>
+</div>
 
 
 
 
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diff --git a/main/reference/h_map_for_count_abnormal.html b/main/reference/h_map_for_count_abnormal.html
index 0c363ea5aa..6232e713ea 100644
--- a/main/reference/h_map_for_count_abnormal.html
+++ b/main/reference/h_map_for_count_abnormal.html
@@ -1,9 +1,32 @@
-<!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Helper function to create a map data frame for trim_levels_to_map() — h_map_for_count_abnormal • tern</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Helper function to create a map data frame for trim_levels_to_map() — h_map_for_count_abnormal"><meta name="description" content="
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+<title>Helper function to create a map data frame for trim_levels_to_map() — h_map_for_count_abnormal • tern</title>
+<!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png">
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+<meta name="description" content="
 Helper function to create a map data frame from the input dataset, which can be used as an argument in the
-trim_levels_to_map split function. Based on different method, the map is constructed differently."><meta property="og:description" content="
+trim_levels_to_map split function. Based on different method, the map is constructed differently.">
+<meta property="og:description" content="
 Helper function to create a map data frame from the input dataset, which can be used as an argument in the
-trim_levels_to_map split function. Based on different method, the map is constructed differently."><meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png"><link rel="stylesheet" href="../consent.css"><script src="../consent.js" type="text/javascript" charset="utf-8"></script></head><body>
+trim_levels_to_map split function. Based on different method, the map is constructed differently.">
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   <main id="main" class="col-md-9"><div class="page-header">
-      <img src="../logo.png" class="logo" alt=""><h1>Helper function to create a map data frame for <code>trim_levels_to_map()</code></h1>
+      <img src="../logo.png" class="logo" alt=""><h1>Helper function to create a map data frame for <code>trim_levels_to_map()</code>
+</h1>
       <small class="dont-index">Source: <a href="https://github.com/insightsengineering/tern/blob/main/R/h_map_for_count_abnormal.R" class="external-link"><code>R/h_map_for_count_abnormal.R</code></a></small>
       <div class="d-none name"><code>h_map_for_count_abnormal.Rd</code></div>
     </div>
@@ -57,7 +121,8 @@
     </div>
 
     <div class="section level2">
-    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
+    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">h_map_for_count_abnormal</span><span class="op">(</span></span>
 <span>  <span class="va">df</span>,</span>
 <span>  variables <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span>anl <span class="op">=</span> <span class="st">"ANRIND"</span>, split_rows <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"PARAM"</span><span class="op">)</span>, range_low <span class="op">=</span> <span class="st">"ANRLO"</span>,</span>
@@ -69,37 +134,47 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
     </div>
 
     <div class="section level2">
-    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
+    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a>
+</h2>
 
 
-<dl><dt id="arg-df">df<a class="anchor" aria-label="anchor" href="#arg-df"></a></dt>
+<dl>
+<dt id="arg-df">df<a class="anchor" aria-label="anchor" href="#arg-df"></a>
+</dt>
 <dd><p>(<code>data.frame</code>)<br> data set containing all analysis variables.</p></dd>
 
 
-<dt id="arg-variables">variables<a class="anchor" aria-label="anchor" href="#arg-variables"></a></dt>
+<dt id="arg-variables">variables<a class="anchor" aria-label="anchor" href="#arg-variables"></a>
+</dt>
 <dd><p>(named <code>list</code> of <code>string</code>)<br> list of additional analysis variables.</p></dd>
 
 
-<dt id="arg-abnormal">abnormal<a class="anchor" aria-label="anchor" href="#arg-abnormal"></a></dt>
+<dt id="arg-abnormal">abnormal<a class="anchor" aria-label="anchor" href="#arg-abnormal"></a>
+</dt>
 <dd><p>(named <code>list</code>)<br> identifying the abnormal range level(s) in <code>df</code>. Based on the levels of
 abnormality of the input dataset, it can be something like <code>list(Low = "LOW LOW", High = "HIGH HIGH")</code> or
 <code>abnormal = list(Low = "LOW", High = "HIGH"))</code></p></dd>
 
 
-<dt id="arg-method">method<a class="anchor" aria-label="anchor" href="#arg-method"></a></dt>
+<dt id="arg-method">method<a class="anchor" aria-label="anchor" href="#arg-method"></a>
+</dt>
 <dd><p>(<code>string</code>)<br> indicates how the returned map will be constructed. Can be <code>"default"</code> or <code>"range"</code>.</p></dd>
 
 
-<dt id="arg-na-str">na_str<a class="anchor" aria-label="anchor" href="#arg-na-str"></a></dt>
+<dt id="arg-na-str">na_str<a class="anchor" aria-label="anchor" href="#arg-na-str"></a>
+</dt>
 <dd><p>(<code>string</code>)<br> string used to replace all <code>NA</code> or empty values in the output.</p></dd>
 
-</dl></div>
+</dl>
+</div>
     <div class="section level2">
-    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
+    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a>
+</h2>
     <p>A map <code>data.frame</code>.</p>
     </div>
     <div class="section level2">
-    <h2 id="note">Note<a class="anchor" aria-label="anchor" href="#note"></a></h2>
+    <h2 id="note">Note<a class="anchor" aria-label="anchor" href="#note"></a>
+</h2>
     <p>If method is <code>"default"</code>, the returned map will only have the abnormal directions that are observed in the
 <code>df</code>, and records with all normal values will be excluded to avoid error in creating layout. If method is
 <code>"range"</code>, the returned map will be based on the rule that at least one observation with low range &gt; 0
@@ -107,7 +182,8 @@ <h2 id="note">Note<a class="anchor" aria-label="anchor" href="#note"></a></h2>
     </div>
 
     <div class="section level2">
-    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
+    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">adlb</span> <span class="op">&lt;-</span> <span class="fu"><a href="df_explicit_na.html">df_explicit_na</a></span><span class="op">(</span><span class="va">tern_ex_adlb</span><span class="op">)</span></span></span>
 <span class="r-in"><span></span></span>
 <span class="r-in"><span><span class="fu">h_map_for_count_abnormal</span><span class="op">(</span></span></span>
@@ -170,17 +246,19 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 </code></pre></div>
     </div>
   </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
-    </nav></aside></div>
+    </nav></aside>
+</div>
 
 
     <footer><div class="nest">
   <p>tern is a part of the <strong>NEST</strong> and <a href="https://pharmaverse.org/" class="external-link"><strong>pharmaverse</strong></a>.</p>
 </div>
-<script type="text/javascript" src="../analytics.js"></script></footer></div>
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+<script type="text/javascript" src="../analytics.js"></script></footer>
+</div>
 
 
 
 
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diff --git a/main/reference/h_odds_ratio.html b/main/reference/h_odds_ratio.html
index 3c7851dd8d..c673a97e7e 100644
--- a/main/reference/h_odds_ratio.html
+++ b/main/reference/h_odds_ratio.html
@@ -1,7 +1,30 @@
-<!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Helper functions for odds ratio estimation — h_odds_ratio • tern</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Helper functions for odds ratio estimation — h_odds_ratio"><meta name="description" content="
-Functions to calculate odds ratios in estimate_odds_ratio()."><meta property="og:description" content="
-Functions to calculate odds ratios in estimate_odds_ratio()."><meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png"><link rel="stylesheet" href="../consent.css"><script src="../consent.js" type="text/javascript" charset="utf-8"></script></head><body>
+<html lang="en">
+<head>
+<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+<meta charset="utf-8">
+<meta http-equiv="X-UA-Compatible" content="IE=edge">
+<meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<title>Helper functions for odds ratio estimation — h_odds_ratio • tern</title>
+<!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png">
+<link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png">
+<link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png">
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+<link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png">
+<link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png">
+<script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet">
+<script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet">
+<link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet">
+<script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Helper functions for odds ratio estimation — h_odds_ratio">
+<meta name="description" content="
+Functions to calculate odds ratios in estimate_odds_ratio().">
+<meta property="og:description" content="
+Functions to calculate odds ratios in estimate_odds_ratio().">
+<meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png">
+<link rel="stylesheet" href="../consent.css">
+<script src="../consent.js" type="text/javascript" charset="utf-8"></script>
+</head>
+<body>
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@@ -17,26 +40,66 @@
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+  <ul class="dropdown-menu" aria-labelledby="dropdown-articles">
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+    <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/main">main</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.5">v0.9.5</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.4">v0.9.4</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.3">v0.9.3</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1-rc3">v0.9.1-rc3</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a>
+</div>
+</li></div>
+</ul>
+<ul class="navbar-nav">
+<li class="nav-item"><form class="form-inline" role="search">
+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json">
+</form></li>
 <li class="nav-item"><a class="external-link nav-link" href="https://github.com/insightsengineering/tern" aria-label="GitHub"><span class="fa fa-github"></span></a></li>
-      </ul></div>
+      </ul>
+</div>
 
 
   </div>
@@ -54,50 +117,63 @@
     </div>
 
     <div class="section level2">
-    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
+    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">or_glm</span><span class="op">(</span><span class="va">data</span>, <span class="va">conf_level</span><span class="op">)</span></span>
 <span></span>
 <span><span class="fu">or_clogit</span><span class="op">(</span><span class="va">data</span>, <span class="va">conf_level</span>, method <span class="op">=</span> <span class="st">"exact"</span><span class="op">)</span></span></code></pre></div>
     </div>
 
     <div class="section level2">
-    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
+    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a>
+</h2>
 
 
-<dl><dt id="arg-data">data<a class="anchor" aria-label="anchor" href="#arg-data"></a></dt>
+<dl>
+<dt id="arg-data">data<a class="anchor" aria-label="anchor" href="#arg-data"></a>
+</dt>
 <dd><p>(<code>data.frame</code>)<br> data frame containing at least the variables <code>rsp</code> and <code>grp</code>, and optionally
 <code>strata</code> for <code>or_clogit()</code>.</p></dd>
 
 
-<dt id="arg-conf-level">conf_level<a class="anchor" aria-label="anchor" href="#arg-conf-level"></a></dt>
+<dt id="arg-conf-level">conf_level<a class="anchor" aria-label="anchor" href="#arg-conf-level"></a>
+</dt>
 <dd><p>(<code>proportion</code>)<br> confidence level of the interval.</p></dd>
 
 
-<dt id="arg-method">method<a class="anchor" aria-label="anchor" href="#arg-method"></a></dt>
+<dt id="arg-method">method<a class="anchor" aria-label="anchor" href="#arg-method"></a>
+</dt>
 <dd><p>(<code>string</code>)<br> whether to use the correct (<code>"exact"</code>) calculation in the conditional likelihood or one
 of the approximations. See <code><a href="https://rdrr.io/pkg/survival/man/clogit.html" class="external-link">survival::clogit()</a></code> for details.</p></dd>
 
-</dl></div>
+</dl>
+</div>
     <div class="section level2">
-    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
+    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a>
+</h2>
     <p>A named <code>list</code> of elements <code>or_ci</code> and <code>n_tot</code>.</p>
     </div>
     <div class="section level2">
-    <h2 id="functions">Functions<a class="anchor" aria-label="anchor" href="#functions"></a></h2>
+    <h2 id="functions">Functions<a class="anchor" aria-label="anchor" href="#functions"></a>
+</h2>
 
-<ul><li><p><code>or_glm()</code>: Estimates the odds ratio based on <code><a href="https://rdrr.io/r/stats/glm.html" class="external-link">stats::glm()</a></code>. Note that there must be
+<ul>
+<li><p><code>or_glm()</code>: Estimates the odds ratio based on <code><a href="https://rdrr.io/r/stats/glm.html" class="external-link">stats::glm()</a></code>. Note that there must be
 exactly 2 groups in <code>data</code> as specified by the <code>grp</code> variable.</p></li>
 <li><p><code>or_clogit()</code>: Estimates the odds ratio based on <code><a href="https://rdrr.io/pkg/survival/man/clogit.html" class="external-link">survival::clogit()</a></code>. This is done for
 the whole data set including all groups, since the results are not the same as when doing
 pairwise comparisons between the groups.</p></li>
-</ul></div>
+</ul>
+</div>
     <div class="section level2">
-    <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"></a></h2>
+    <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"></a>
+</h2>
     <div class="dont-index"><p><a href="odds_ratio.html">odds_ratio</a></p></div>
     </div>
 
     <div class="section level2">
-    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
+    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="co"># Data with 2 groups.</span></span></span>
 <span class="r-in"><span><span class="va">data</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a></span><span class="op">(</span></span></span>
 <span class="r-in"><span>  rsp <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/logical.html" class="external-link">as.logical</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">1</span>, <span class="fl">1</span>, <span class="fl">0</span>, <span class="fl">1</span>, <span class="fl">0</span>, <span class="fl">0</span>, <span class="fl">1</span>, <span class="fl">1</span><span class="op">)</span><span class="op">)</span>,</span></span>
@@ -145,17 +221,19 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 </code></pre></div>
     </div>
   </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
-    </nav></aside></div>
+    </nav></aside>
+</div>
 
 
     <footer><div class="nest">
   <p>tern is a part of the <strong>NEST</strong> and <a href="https://pharmaverse.org/" class="external-link"><strong>pharmaverse</strong></a>.</p>
 </div>
-<script type="text/javascript" src="../analytics.js"></script></footer></div>
-
+<script type="text/javascript" src="../analytics.js"></script></footer>
+</div>
 
 
 
 
-  </body></html>
 
+  </body>
+</html>
diff --git a/main/reference/h_pkparam_sort.html b/main/reference/h_pkparam_sort.html
index 22a9de65be..d23d861fe0 100644
--- a/main/reference/h_pkparam_sort.html
+++ b/main/reference/h_pkparam_sort.html
@@ -1,5 +1,28 @@
-<!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Sort pharmacokinetic data by PARAM variable — h_pkparam_sort • tern</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Sort pharmacokinetic data by PARAM variable — h_pkparam_sort"><meta name="description" content=""><meta property="og:description" content=""><meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png"><link rel="stylesheet" href="../consent.css"><script src="../consent.js" type="text/javascript" charset="utf-8"></script></head><body>
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+<head>
+<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+<meta charset="utf-8">
+<meta http-equiv="X-UA-Compatible" content="IE=edge">
+<meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<title>Sort pharmacokinetic data by PARAM variable — h_pkparam_sort • tern</title>
+<!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png">
+<link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png">
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+<link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png">
+<script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet">
+<script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet">
+<link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet">
+<script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Sort pharmacokinetic data by PARAM variable — h_pkparam_sort">
+<meta name="description" content="">
+<meta property="og:description" content="">
+<meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png">
+<link rel="stylesheet" href="../consent.css">
+<script src="../consent.js" type="text/javascript" charset="utf-8"></script>
+</head>
+<body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
 
 
@@ -15,26 +38,66 @@
     </button>
 
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-      <ul class="navbar-nav me-auto"><li class="nav-item"><a class="nav-link" href="../articles/tern.html">Get started</a></li>
+      <ul class="navbar-nav me-auto">
+<li class="nav-item"><a class="nav-link" href="../articles/tern.html">Get started</a></li>
 <li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
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   <button class="nav-link dropdown-toggle" type="button" id="dropdown-articles" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Articles</button>
-  <ul class="dropdown-menu" aria-labelledby="dropdown-articles"><li><a class="dropdown-item" href="../articles/missing_values.html">Missing Values in Tern</a></li>
+  <ul class="dropdown-menu" aria-labelledby="dropdown-articles">
+<li><a class="dropdown-item" href="../articles/missing_values.html">Missing Values in Tern</a></li>
     <li><a class="dropdown-item" href="../articles/tables.html">Tabulation</a></li>
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     <li><a class="dropdown-item" href="../articles/tern_functions_guide.html">Understanding `tern` functions</a></li>
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+  </ul>
+</li>
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+  </ul>
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+      <div><li class="nav-item dropdown">
+    <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-versions">Versions</a>
+    <div class="dropdown-menu" aria-labelledby="dropdown-versions">
+    <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
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+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
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+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1-rc3">v0.9.1-rc3</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a>
+</div>
+</li></div>
+</ul>
+<ul class="navbar-nav">
+<li class="nav-item"><form class="form-inline" role="search">
+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json">
+</form></li>
 <li class="nav-item"><a class="external-link nav-link" href="https://github.com/insightsengineering/tern" aria-label="GitHub"><span class="fa fa-github"></span></a></li>
-      </ul></div>
+      </ul>
+</div>
 
 
   </div>
@@ -51,29 +114,37 @@
     </div>
 
     <div class="section level2">
-    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
+    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">h_pkparam_sort</span><span class="op">(</span><span class="va">pk_data</span>, key_var <span class="op">=</span> <span class="st">"PARAMCD"</span><span class="op">)</span></span></code></pre></div>
     </div>
 
     <div class="section level2">
-    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
+    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a>
+</h2>
 
 
-<dl><dt id="arg-pk-data">pk_data<a class="anchor" aria-label="anchor" href="#arg-pk-data"></a></dt>
+<dl>
+<dt id="arg-pk-data">pk_data<a class="anchor" aria-label="anchor" href="#arg-pk-data"></a>
+</dt>
 <dd><p>(<code>data.frame</code>)<br> pharmacokinetic data frame.</p></dd>
 
 
-<dt id="arg-key-var">key_var<a class="anchor" aria-label="anchor" href="#arg-key-var"></a></dt>
+<dt id="arg-key-var">key_var<a class="anchor" aria-label="anchor" href="#arg-key-var"></a>
+</dt>
 <dd><p>(<code>string</code>)<br> key variable used to merge pk_data and metadata created by <code><a href="d_pkparam.html">d_pkparam()</a></code>.</p></dd>
 
-</dl></div>
+</dl>
+</div>
     <div class="section level2">
-    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
+    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a>
+</h2>
     <p>A pharmacokinetic <code>data.frame</code> sorted by a <code>PARAM</code> variable.</p>
     </div>
 
     <div class="section level2">
-    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
+    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://dplyr.tidyverse.org" class="external-link">dplyr</a></span><span class="op">)</span></span></span>
 <span class="r-in"><span></span></span>
 <span class="r-in"><span><span class="va">adpp</span> <span class="op">&lt;-</span> <span class="va">tern_ex_adpp</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate.html" class="external-link">mutate</a></span><span class="op">(</span>PKPARAM <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/factor.html" class="external-link">factor</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/paste.html" class="external-link">paste0</a></span><span class="op">(</span><span class="va">PARAM</span>, <span class="st">" ("</span>, <span class="va">AVALU</span>, <span class="st">")"</span><span class="op">)</span><span class="op">)</span><span class="op">)</span></span></span>
@@ -82,17 +153,19 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 </code></pre></div>
     </div>
   </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
-    </nav></aside></div>
+    </nav></aside>
+</div>
 
 
     <footer><div class="nest">
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diff --git a/main/reference/h_ppmeans.html b/main/reference/h_ppmeans.html
index 7d248c1ea1..935ff33798 100644
--- a/main/reference/h_ppmeans.html
+++ b/main/reference/h_ppmeans.html
@@ -1,9 +1,32 @@
-<!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Function to return the estimated means using predicted probabilities — h_ppmeans • tern</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Function to return the estimated means using predicted probabilities — h_ppmeans"><meta name="description" content="For each arm level, the predicted mean rate is calculated using the fitted model object, with newdata
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+<meta name="description" content="For each arm level, the predicted mean rate is calculated using the fitted model object, with newdata
 set to the result of stats::model.frame, a reconstructed data or the original data, depending on the
-object formula (coming from the fit). The confidence interval is derived using the conf_level parameter."><meta property="og:description" content="For each arm level, the predicted mean rate is calculated using the fitted model object, with newdata
+object formula (coming from the fit). The confidence interval is derived using the conf_level parameter.">
+<meta property="og:description" content="For each arm level, the predicted mean rate is calculated using the fitted model object, with newdata
 set to the result of stats::model.frame, a reconstructed data or the original data, depending on the
-object formula (coming from the fit). The confidence interval is derived using the conf_level parameter."><meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png"><link rel="stylesheet" href="../consent.css"><script src="../consent.js" type="text/javascript" charset="utf-8"></script></head><body>
+object formula (coming from the fit). The confidence interval is derived using the conf_level parameter.">
+<meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png">
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+</head>
+<body>
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+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
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+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a>
+</div>
+</li></div>
+</ul>
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+<li class="nav-item"><form class="form-inline" role="search">
+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json">
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+      </ul>
+</div>
 
 
   </div>
@@ -57,53 +120,67 @@
     </div>
 
     <div class="section level2">
-    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
+    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">h_ppmeans</span><span class="op">(</span><span class="va">obj</span>, <span class="va">.df_row</span>, <span class="va">arm</span>, <span class="va">conf_level</span><span class="op">)</span></span></code></pre></div>
     </div>
 
     <div class="section level2">
-    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
+    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a>
+</h2>
 
 
-<dl><dt id="arg-obj">obj<a class="anchor" aria-label="anchor" href="#arg-obj"></a></dt>
+<dl>
+<dt id="arg-obj">obj<a class="anchor" aria-label="anchor" href="#arg-obj"></a>
+</dt>
 <dd><p>(<code>glm.fit</code>)<br> fitted model object used to derive the mean rate estimates in each treatment arm.</p></dd>
 
 
-<dt id="arg--df-row">.df_row<a class="anchor" aria-label="anchor" href="#arg--df-row"></a></dt>
+<dt id="arg--df-row">.df_row<a class="anchor" aria-label="anchor" href="#arg--df-row"></a>
+</dt>
 <dd><p>(<code>data.frame</code>)<br> dataset that includes all the variables that are called in <code>.var</code> and <code>variables</code>.</p></dd>
 
 
-<dt id="arg-arm">arm<a class="anchor" aria-label="anchor" href="#arg-arm"></a></dt>
+<dt id="arg-arm">arm<a class="anchor" aria-label="anchor" href="#arg-arm"></a>
+</dt>
 <dd><p>(<code>string</code>)<br> group variable, for which the covariate adjusted means of multiple groups will be
 summarized. Specifically, the first level of <code>arm</code> variable is taken as the reference group.</p></dd>
 
 
-<dt id="arg-conf-level">conf_level<a class="anchor" aria-label="anchor" href="#arg-conf-level"></a></dt>
+<dt id="arg-conf-level">conf_level<a class="anchor" aria-label="anchor" href="#arg-conf-level"></a>
+</dt>
 <dd><p>(<code>proportion</code>)<br> value used to derive the confidence interval for the rate.</p></dd>
 
-</dl></div>
+</dl>
+</div>
     <div class="section level2">
-    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
+    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a>
+</h2>
 
-<ul><li><p><code>h_ppmeans()</code> returns the estimated means.</p></li>
-</ul></div>
+<ul>
+<li><p><code>h_ppmeans()</code> returns the estimated means.</p></li>
+</ul>
+</div>
     <div class="section level2">
-    <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"></a></h2>
+    <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"></a>
+</h2>
     <div class="dont-index"><p><code><a href="summarize_glm_count.html">summarize_glm_count()</a></code>.</p></div>
     </div>
 
   </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
-    </nav></aside></div>
+    </nav></aside>
+</div>
 
 
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   <p>tern is a part of the <strong>NEST</strong> and <a href="https://pharmaverse.org/" class="external-link"><strong>pharmaverse</strong></a>.</p>
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diff --git a/main/reference/h_prop_diff.html b/main/reference/h_prop_diff.html
index 94c7233ebb..f658f4fab2 100644
--- a/main/reference/h_prop_diff.html
+++ b/main/reference/h_prop_diff.html
@@ -1,5 +1,28 @@
-<!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Helper functions to calculate proportion difference — h_prop_diff • tern</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Helper functions to calculate proportion difference — h_prop_diff"><meta name="description" content=""><meta property="og:description" content=""><meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png"><link rel="stylesheet" href="../consent.css"><script src="../consent.js" type="text/javascript" charset="utf-8"></script></head><body>
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+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
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+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a>
+</div>
+</li></div>
+</ul>
+<ul class="navbar-nav">
+<li class="nav-item"><form class="form-inline" role="search">
+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json">
+</form></li>
 <li class="nav-item"><a class="external-link nav-link" href="https://github.com/insightsengineering/tern" aria-label="GitHub"><span class="fa fa-github"></span></a></li>
-      </ul></div>
+      </ul>
+</div>
 
 
   </div>
@@ -51,7 +114,8 @@
     </div>
 
     <div class="section level2">
-    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
+    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">prop_diff_wald</span><span class="op">(</span><span class="va">rsp</span>, <span class="va">grp</span>, conf_level <span class="op">=</span> <span class="fl">0.95</span>, correct <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span>
 <span></span>
 <span><span class="fu">prop_diff_ha</span><span class="op">(</span><span class="va">rsp</span>, <span class="va">grp</span>, <span class="va">conf_level</span><span class="op">)</span></span>
@@ -71,45 +135,57 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
     </div>
 
     <div class="section level2">
-    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
+    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a>
+</h2>
 
 
-<dl><dt id="arg-rsp">rsp<a class="anchor" aria-label="anchor" href="#arg-rsp"></a></dt>
+<dl>
+<dt id="arg-rsp">rsp<a class="anchor" aria-label="anchor" href="#arg-rsp"></a>
+</dt>
 <dd><p>(<code>logical</code>)<br> vector indicating whether each subject is a responder or not.</p></dd>
 
 
-<dt id="arg-grp">grp<a class="anchor" aria-label="anchor" href="#arg-grp"></a></dt>
+<dt id="arg-grp">grp<a class="anchor" aria-label="anchor" href="#arg-grp"></a>
+</dt>
 <dd><p>(<code>factor</code>)<br> vector assigning observations to one out of two groups
 (e.g. reference and treatment group).</p></dd>
 
 
-<dt id="arg-conf-level">conf_level<a class="anchor" aria-label="anchor" href="#arg-conf-level"></a></dt>
+<dt id="arg-conf-level">conf_level<a class="anchor" aria-label="anchor" href="#arg-conf-level"></a>
+</dt>
 <dd><p>(<code>proportion</code>)<br> confidence level of the interval.</p></dd>
 
 
-<dt id="arg-correct">correct<a class="anchor" aria-label="anchor" href="#arg-correct"></a></dt>
+<dt id="arg-correct">correct<a class="anchor" aria-label="anchor" href="#arg-correct"></a>
+</dt>
 <dd><p>(<code>flag</code>)<br> whether to include the continuity correction. For further
 information, see <code><a href="https://rdrr.io/r/stats/prop.test.html" class="external-link">stats::prop.test()</a></code>.</p></dd>
 
 
-<dt id="arg-strata">strata<a class="anchor" aria-label="anchor" href="#arg-strata"></a></dt>
+<dt id="arg-strata">strata<a class="anchor" aria-label="anchor" href="#arg-strata"></a>
+</dt>
 <dd><p>(<code>factor</code>)<br> variable with one level per stratum and same length as <code>rsp</code>.</p></dd>
 
 
-<dt id="arg-weights-method">weights_method<a class="anchor" aria-label="anchor" href="#arg-weights-method"></a></dt>
+<dt id="arg-weights-method">weights_method<a class="anchor" aria-label="anchor" href="#arg-weights-method"></a>
+</dt>
 <dd><p>(<code>string</code>)<br> weights method. Can be either <code>"cmh"</code> or <code>"heuristic"</code>
 and directs the way weights are estimated.</p></dd>
 
-</dl></div>
+</dl>
+</div>
     <div class="section level2">
-    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
+    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a>
+</h2>
     <p>A named <code>list</code> of elements <code>diff</code> (proportion difference) and <code>diff_ci</code>
 (proportion difference confidence interval).</p>
     </div>
     <div class="section level2">
-    <h2 id="functions">Functions<a class="anchor" aria-label="anchor" href="#functions"></a></h2>
+    <h2 id="functions">Functions<a class="anchor" aria-label="anchor" href="#functions"></a>
+</h2>
 
-<ul><li><p><code>prop_diff_wald()</code>: The Wald interval follows the usual textbook
+<ul>
+<li><p><code>prop_diff_wald()</code>: The Wald interval follows the usual textbook
 definition for a single proportion confidence interval using the normal
 approximation. It is possible to include a continuity correction for Wald's
 interval.</p></li>
@@ -125,18 +201,22 @@ <h2 id="functions">Functions<a class="anchor" aria-label="anchor" href="#functio
 factors. This implementation follows closely the one proposed by Yan2010-jt;textualtern.
 Weights can be estimated from the heuristic proposed in <code><a href="h_proportions.html">prop_strat_wilson()</a></code> or from CMH-derived weights
 (see <code>prop_diff_cmh()</code>).</p></li>
-</ul></div>
+</ul>
+</div>
     <div class="section level2">
-    <h2 id="references">References<a class="anchor" aria-label="anchor" href="#references"></a></h2>
+    <h2 id="references">References<a class="anchor" aria-label="anchor" href="#references"></a>
+</h2>
     <p>Yan2010-jttern</p>
     </div>
     <div class="section level2">
-    <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"></a></h2>
+    <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"></a>
+</h2>
     <div class="dont-index"><p><code><a href="prop_diff.html">prop_diff()</a></code> for implementation of these helper functions.</p></div>
     </div>
 
     <div class="section level2">
-    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
+    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="co"># Wald confidence interval</span></span></span>
 <span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/Random.html" class="external-link">set.seed</a></span><span class="op">(</span><span class="fl">2</span><span class="op">)</span></span></span>
 <span class="r-in"><span><span class="va">rsp</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/sample.html" class="external-link">sample</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="cn">TRUE</span>, <span class="cn">FALSE</span><span class="op">)</span>, replace <span class="op">=</span> <span class="cn">TRUE</span>, size <span class="op">=</span> <span class="fl">20</span><span class="op">)</span></span></span>
@@ -284,17 +364,19 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 </code></pre></div>
     </div>
   </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
-    </nav></aside></div>
+    </nav></aside>
+</div>
 
 
     <footer><div class="nest">
   <p>tern is a part of the <strong>NEST</strong> and <a href="https://pharmaverse.org/" class="external-link"><strong>pharmaverse</strong></a>.</p>
 </div>
-<script type="text/javascript" src="../analytics.js"></script></footer></div>
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+<script type="text/javascript" src="../analytics.js"></script></footer>
+</div>
 
 
 
 
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diff --git a/main/reference/h_prop_diff_test.html b/main/reference/h_prop_diff_test.html
index 6217bcc314..5c5509178f 100644
--- a/main/reference/h_prop_diff_test.html
+++ b/main/reference/h_prop_diff_test.html
@@ -1,5 +1,28 @@
-<!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Helper functions to test proportion differences — h_prop_diff_test • tern</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Helper functions to test proportion differences — h_prop_diff_test"><meta name="description" content="Helper functions to implement various tests on the difference between two proportions."><meta property="og:description" content="Helper functions to implement various tests on the difference between two proportions."><meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png"><link rel="stylesheet" href="../consent.css"><script src="../consent.js" type="text/javascript" charset="utf-8"></script></head><body>
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+<meta name="description" content="Helper functions to implement various tests on the difference between two proportions.">
+<meta property="og:description" content="Helper functions to implement various tests on the difference between two proportions.">
+<meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png">
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@@ -15,26 +38,66 @@
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- <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json"></form></li>
+  </ul>
+</li>
+      <div><li class="nav-item dropdown">
+    <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-versions">Versions</a>
+    <div class="dropdown-menu" aria-labelledby="dropdown-versions">
+    <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/main">main</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.5">v0.9.5</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.4">v0.9.4</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.3">v0.9.3</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1-rc3">v0.9.1-rc3</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a>
+</div>
+</li></div>
+</ul>
+<ul class="navbar-nav">
+<li class="nav-item"><form class="form-inline" role="search">
+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json">
+</form></li>
 <li class="nav-item"><a class="external-link nav-link" href="https://github.com/insightsengineering/tern" aria-label="GitHub"><span class="fa fa-github"></span></a></li>
-      </ul></div>
+      </ul>
+</div>
 
 
   </div>
@@ -51,7 +114,8 @@
     </div>
 
     <div class="section level2">
-    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
+    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">prop_chisq</span><span class="op">(</span><span class="va">tbl</span><span class="op">)</span></span>
 <span></span>
 <span><span class="fu">prop_cmh</span><span class="op">(</span><span class="va">ary</span><span class="op">)</span></span>
@@ -62,49 +126,63 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
     </div>
 
     <div class="section level2">
-    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
+    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a>
+</h2>
 
 
-<dl><dt id="arg-tbl">tbl<a class="anchor" aria-label="anchor" href="#arg-tbl"></a></dt>
+<dl>
+<dt id="arg-tbl">tbl<a class="anchor" aria-label="anchor" href="#arg-tbl"></a>
+</dt>
 <dd><p>(<code>matrix</code>)<br> matrix with two groups in rows and the binary response (<code>TRUE</code>/<code>FALSE</code>) in columns.</p></dd>
 
 
-<dt id="arg-ary">ary<a class="anchor" aria-label="anchor" href="#arg-ary"></a></dt>
+<dt id="arg-ary">ary<a class="anchor" aria-label="anchor" href="#arg-ary"></a>
+</dt>
 <dd><p>(<code>array</code>, 3 dimensions)<br> array with two groups in rows, the binary response
 (<code>TRUE</code>/<code>FALSE</code>) in columns, and the strata in the third dimension.</p></dd>
 
-</dl></div>
+</dl>
+</div>
     <div class="section level2">
-    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
+    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a>
+</h2>
     <p>A p-value.</p>
     </div>
     <div class="section level2">
-    <h2 id="functions">Functions<a class="anchor" aria-label="anchor" href="#functions"></a></h2>
+    <h2 id="functions">Functions<a class="anchor" aria-label="anchor" href="#functions"></a>
+</h2>
 
-<ul><li><p><code>prop_chisq()</code>: Performs Chi-Squared test. Internally calls <code><a href="https://rdrr.io/r/stats/prop.test.html" class="external-link">stats::prop.test()</a></code>.</p></li>
+<ul>
+<li><p><code>prop_chisq()</code>: Performs Chi-Squared test. Internally calls <code><a href="https://rdrr.io/r/stats/prop.test.html" class="external-link">stats::prop.test()</a></code>.</p></li>
 <li><p><code>prop_cmh()</code>: Performs stratified Cochran-Mantel-Haenszel test. Internally calls
 <code><a href="https://rdrr.io/r/stats/mantelhaen.test.html" class="external-link">stats::mantelhaen.test()</a></code>. Note that strata with less than two observations are automatically discarded.</p></li>
 <li><p><code>prop_schouten()</code>: Performs the Chi-Squared test with Schouten correction.</p></li>
 <li><p><code>prop_fisher()</code>: Performs the Fisher's exact test. Internally calls <code><a href="https://rdrr.io/r/stats/fisher.test.html" class="external-link">stats::fisher.test()</a></code>.</p></li>
-</ul></div>
+</ul>
+</div>
     <div class="section level2">
-    <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"></a></h2>
-    <div class="dont-index"><p><code><a href="prop_diff_test.html">prop_diff_test()</a></code> for implementation of these helper functions.</p>
-<p>Schouten correction is based upon Schouten1980-kd;textualtern.</p></div>
+    <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"></a>
+</h2>
+    <div class="dont-index">
+<p><code><a href="prop_diff_test.html">prop_diff_test()</a></code> for implementation of these helper functions.</p>
+<p>Schouten correction is based upon Schouten1980-kd;textualtern.</p>
+</div>
     </div>
 
   </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
-    </nav></aside></div>
+    </nav></aside>
+</div>
 
 
     <footer><div class="nest">
   <p>tern is a part of the <strong>NEST</strong> and <a href="https://pharmaverse.org/" class="external-link"><strong>pharmaverse</strong></a>.</p>
 </div>
-<script type="text/javascript" src="../analytics.js"></script></footer></div>
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+<script type="text/javascript" src="../analytics.js"></script></footer>
+</div>
 
 
 
 
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+  </body>
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diff --git a/main/reference/h_proportions.html b/main/reference/h_proportions.html
index c607a8bd99..0d6570ac85 100644
--- a/main/reference/h_proportions.html
+++ b/main/reference/h_proportions.html
@@ -1,7 +1,30 @@
-<!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Helper functions for calculating proportion confidence intervals — h_proportions • tern</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Helper functions for calculating proportion confidence intervals — h_proportions"><meta name="description" content="
-Functions to calculate different proportion confidence intervals for use in estimate_proportion()."><meta property="og:description" content="
-Functions to calculate different proportion confidence intervals for use in estimate_proportion()."><meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png"><link rel="stylesheet" href="../consent.css"><script src="../consent.js" type="text/javascript" charset="utf-8"></script></head><body>
+<html lang="en">
+<head>
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+<meta http-equiv="X-UA-Compatible" content="IE=edge">
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+<title>Helper functions for calculating proportion confidence intervals — h_proportions • tern</title>
+<!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png">
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+<link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png">
+<link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png">
+<script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet">
+<script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet">
+<link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet">
+<script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Helper functions for calculating proportion confidence intervals — h_proportions">
+<meta name="description" content="
+Functions to calculate different proportion confidence intervals for use in estimate_proportion().">
+<meta property="og:description" content="
+Functions to calculate different proportion confidence intervals for use in estimate_proportion().">
+<meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png">
+<link rel="stylesheet" href="../consent.css">
+<script src="../consent.js" type="text/javascript" charset="utf-8"></script>
+</head>
+<body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
 
 
@@ -17,26 +40,66 @@
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-      <ul class="navbar-nav me-auto"><li class="nav-item"><a class="nav-link" href="../articles/tern.html">Get started</a></li>
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+<li class="nav-item"><a class="nav-link" href="../articles/tern.html">Get started</a></li>
 <li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
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+  <ul class="dropdown-menu" aria-labelledby="dropdown-articles">
+<li><a class="dropdown-item" href="../articles/missing_values.html">Missing Values in Tern</a></li>
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     <li><a class="dropdown-item" href="../articles/tern_functions_guide.html">Understanding `tern` functions</a></li>
-  </ul></li>
+  </ul>
+</li>
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- <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json"></form></li>
+  </ul>
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+      <div><li class="nav-item dropdown">
+    <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-versions">Versions</a>
+    <div class="dropdown-menu" aria-labelledby="dropdown-versions">
+    <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
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+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
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+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.3">v0.9.3</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1-rc3">v0.9.1-rc3</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a>
+</div>
+</li></div>
+</ul>
+<ul class="navbar-nav">
+<li class="nav-item"><form class="form-inline" role="search">
+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json">
+</form></li>
 <li class="nav-item"><a class="external-link nav-link" href="https://github.com/insightsengineering/tern" aria-label="GitHub"><span class="fa fa-github"></span></a></li>
-      </ul></div>
+      </ul>
+</div>
 
 
   </div>
@@ -54,7 +117,8 @@
     </div>
 
     <div class="section level2">
-    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
+    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">prop_wilson</span><span class="op">(</span><span class="va">rsp</span>, <span class="va">conf_level</span>, correct <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span>
 <span></span>
 <span><span class="fu">prop_strat_wilson</span><span class="op">(</span></span>
@@ -76,44 +140,56 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
     </div>
 
     <div class="section level2">
-    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
+    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a>
+</h2>
 
 
-<dl><dt id="arg-rsp">rsp<a class="anchor" aria-label="anchor" href="#arg-rsp"></a></dt>
+<dl>
+<dt id="arg-rsp">rsp<a class="anchor" aria-label="anchor" href="#arg-rsp"></a>
+</dt>
 <dd><p>(<code>logical</code>)<br> vector indicating whether each subject is a responder or not.</p></dd>
 
 
-<dt id="arg-conf-level">conf_level<a class="anchor" aria-label="anchor" href="#arg-conf-level"></a></dt>
+<dt id="arg-conf-level">conf_level<a class="anchor" aria-label="anchor" href="#arg-conf-level"></a>
+</dt>
 <dd><p>(<code>proportion</code>)<br> confidence level of the interval.</p></dd>
 
 
-<dt id="arg-correct">correct<a class="anchor" aria-label="anchor" href="#arg-correct"></a></dt>
+<dt id="arg-correct">correct<a class="anchor" aria-label="anchor" href="#arg-correct"></a>
+</dt>
 <dd><p>(<code>flag</code>)<br> whether to apply continuity correction.</p></dd>
 
 
-<dt id="arg-strata">strata<a class="anchor" aria-label="anchor" href="#arg-strata"></a></dt>
+<dt id="arg-strata">strata<a class="anchor" aria-label="anchor" href="#arg-strata"></a>
+</dt>
 <dd><p>(<code>factor</code>)<br> variable with one level per stratum and same length as <code>rsp</code>.</p></dd>
 
 
-<dt id="arg-weights">weights<a class="anchor" aria-label="anchor" href="#arg-weights"></a></dt>
+<dt id="arg-weights">weights<a class="anchor" aria-label="anchor" href="#arg-weights"></a>
+</dt>
 <dd><p>(<code>numeric</code> or <code>NULL</code>)<br> weights for each level of the strata. If <code>NULL</code>, they are
 estimated using the iterative algorithm proposed in Yan2010-jt;textualtern that
 minimizes the weighted squared length of the confidence interval.</p></dd>
 
 
-<dt id="arg-max-iterations">max_iterations<a class="anchor" aria-label="anchor" href="#arg-max-iterations"></a></dt>
+<dt id="arg-max-iterations">max_iterations<a class="anchor" aria-label="anchor" href="#arg-max-iterations"></a>
+</dt>
 <dd><p>(<code>count</code>)<br> maximum number of iterations for the iterative procedure used
 to find estimates of optimal weights.</p></dd>
 
-</dl></div>
+</dl>
+</div>
     <div class="section level2">
-    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
+    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a>
+</h2>
     <p>Confidence interval of a proportion.</p>
     </div>
     <div class="section level2">
-    <h2 id="functions">Functions<a class="anchor" aria-label="anchor" href="#functions"></a></h2>
+    <h2 id="functions">Functions<a class="anchor" aria-label="anchor" href="#functions"></a>
+</h2>
 
-<ul><li><p><code>prop_wilson()</code>: Calculates the Wilson interval by calling <code><a href="https://rdrr.io/r/stats/prop.test.html" class="external-link">stats::prop.test()</a></code>.
+<ul>
+<li><p><code>prop_wilson()</code>: Calculates the Wilson interval by calling <code><a href="https://rdrr.io/r/stats/prop.test.html" class="external-link">stats::prop.test()</a></code>.
 Also referred to as Wilson score interval.</p></li>
 <li><p><code>prop_strat_wilson()</code>: Calculates the stratified Wilson confidence
 interval for unequal proportions as described in Yan2010-jt;textualtern</p></li>
@@ -125,19 +201,23 @@ <h2 id="functions">Functions<a class="anchor" aria-label="anchor" href="#functio
 and two failures to the data and then using the Wald formula to construct a CI.</p></li>
 <li><p><code>prop_jeffreys()</code>: Calculates the Jeffreys interval, an equal-tailed interval based on the
 non-informative Jeffreys prior for a binomial proportion.</p></li>
-</ul></div>
+</ul>
+</div>
     <div class="section level2">
-    <h2 id="references">References<a class="anchor" aria-label="anchor" href="#references"></a></h2>
+    <h2 id="references">References<a class="anchor" aria-label="anchor" href="#references"></a>
+</h2>
     <p>Yan2010-jttern</p>
     </div>
     <div class="section level2">
-    <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"></a></h2>
+    <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"></a>
+</h2>
     <div class="dont-index"><p><a href="estimate_proportion.html">estimate_proportion</a>, descriptive function <code><a href="d_proportion.html">d_proportion()</a></code>,
 and helper functions <code><a href="strata_normal_quantile.html">strata_normal_quantile()</a></code> and <code><a href="update_weights_strat_wilson.html">update_weights_strat_wilson()</a></code>.</p></div>
     </div>
 
     <div class="section level2">
-    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
+    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">rsp</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span></span></span>
 <span class="r-in"><span>  <span class="cn">TRUE</span>, <span class="cn">TRUE</span>, <span class="cn">TRUE</span>, <span class="cn">TRUE</span>, <span class="cn">TRUE</span>,</span></span>
 <span class="r-in"><span>  <span class="cn">FALSE</span>, <span class="cn">FALSE</span>, <span class="cn">FALSE</span>, <span class="cn">FALSE</span>, <span class="cn">FALSE</span></span></span>
@@ -198,17 +278,19 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 </code></pre></div>
     </div>
   </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
-    </nav></aside></div>
+    </nav></aside>
+</div>
 
 
     <footer><div class="nest">
   <p>tern is a part of the <strong>NEST</strong> and <a href="https://pharmaverse.org/" class="external-link"><strong>pharmaverse</strong></a>.</p>
 </div>
-<script type="text/javascript" src="../analytics.js"></script></footer></div>
-
+<script type="text/javascript" src="../analytics.js"></script></footer>
+</div>
 
 
 
 
-  </body></html>
 
+  </body>
+</html>
diff --git a/main/reference/h_response_biomarkers_subgroups.html b/main/reference/h_response_biomarkers_subgroups.html
index d2575e6892..08a6200385 100644
--- a/main/reference/h_response_biomarkers_subgroups.html
+++ b/main/reference/h_response_biomarkers_subgroups.html
@@ -1,9 +1,32 @@
-<!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Helper functions for tabulating biomarker effects on binary response by subgroup — h_response_biomarkers_subgroups • tern</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Helper functions for tabulating biomarker effects on binary response by subgroup — h_response_biomarkers_subgroups"><meta name="description" content="
+<html lang="en">
+<head>
+<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
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+<meta http-equiv="X-UA-Compatible" content="IE=edge">
+<meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<title>Helper functions for tabulating biomarker effects on binary response by subgroup — h_response_biomarkers_subgroups • tern</title>
+<!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png">
+<link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png">
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+<script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet">
+<script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet">
+<link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet">
+<script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Helper functions for tabulating biomarker effects on binary response by subgroup — h_response_biomarkers_subgroups">
+<meta name="description" content="
 Helper functions which are documented here separately to not confuse the user
-when reading about the user-facing functions."><meta property="og:description" content="
+when reading about the user-facing functions.">
+<meta property="og:description" content="
 Helper functions which are documented here separately to not confuse the user
-when reading about the user-facing functions."><meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png"><link rel="stylesheet" href="../consent.css"><script src="../consent.js" type="text/javascript" charset="utf-8"></script></head><body>
+when reading about the user-facing functions.">
+<meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png">
+<link rel="stylesheet" href="../consent.css">
+<script src="../consent.js" type="text/javascript" charset="utf-8"></script>
+</head>
+<body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
 
 
@@ -19,26 +42,66 @@
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     <li><a class="dropdown-item" href="../articles/tern_functions_guide.html">Understanding `tern` functions</a></li>
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+  </ul>
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+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
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+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
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+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a>
+</div>
+</li></div>
+</ul>
+<ul class="navbar-nav">
+<li class="nav-item"><form class="form-inline" role="search">
+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json">
+</form></li>
 <li class="nav-item"><a class="external-link nav-link" href="https://github.com/insightsengineering/tern" aria-label="GitHub"><span class="fa fa-github"></span></a></li>
-      </ul></div>
+      </ul>
+</div>
 
 
   </div>
@@ -57,7 +120,8 @@
     </div>
 
     <div class="section level2">
-    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
+    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">h_rsp_to_logistic_variables</span><span class="op">(</span><span class="va">variables</span>, <span class="va">biomarker</span><span class="op">)</span></span>
 <span></span>
 <span><span class="fu">h_logistic_mult_cont_df</span><span class="op">(</span><span class="va">variables</span>, <span class="va">data</span>, control <span class="op">=</span> <span class="fu"><a href="control_logistic.html">control_logistic</a></span><span class="op">(</span><span class="op">)</span><span class="op">)</span></span>
@@ -66,64 +130,88 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
     </div>
 
     <div class="section level2">
-    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
+    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a>
+</h2>
 
 
-<dl><dt id="arg-variables">variables<a class="anchor" aria-label="anchor" href="#arg-variables"></a></dt>
+<dl>
+<dt id="arg-variables">variables<a class="anchor" aria-label="anchor" href="#arg-variables"></a>
+</dt>
 <dd><p>(named <code>list</code> of <code>string</code>)<br> list of additional analysis variables.</p></dd>
 
 
-<dt id="arg-biomarker">biomarker<a class="anchor" aria-label="anchor" href="#arg-biomarker"></a></dt>
+<dt id="arg-biomarker">biomarker<a class="anchor" aria-label="anchor" href="#arg-biomarker"></a>
+</dt>
 <dd><p>(<code>string</code>)<br> the name of the biomarker variable.</p></dd>
 
 
-<dt id="arg-data">data<a class="anchor" aria-label="anchor" href="#arg-data"></a></dt>
+<dt id="arg-data">data<a class="anchor" aria-label="anchor" href="#arg-data"></a>
+</dt>
 <dd><p>(<code>data.frame</code>)<br> the dataset containing the variables to summarize.</p></dd>
 
 
-<dt id="arg-control">control<a class="anchor" aria-label="anchor" href="#arg-control"></a></dt>
+<dt id="arg-control">control<a class="anchor" aria-label="anchor" href="#arg-control"></a>
+</dt>
 <dd><p>(named <code>list</code>)<br> controls for the response definition and the
 confidence level produced by <code><a href="control_logistic.html">control_logistic()</a></code>.</p></dd>
 
 
-<dt id="arg-df">df<a class="anchor" aria-label="anchor" href="#arg-df"></a></dt>
+<dt id="arg-df">df<a class="anchor" aria-label="anchor" href="#arg-df"></a>
+</dt>
 <dd><p>(<code>data.frame</code>)<br> results for a single biomarker, as part of what is
 returned by <code><a href="extract_rsp_biomarkers.html">extract_rsp_biomarkers()</a></code> (it needs a couple of columns which are
 added by that high-level function relative to what is returned by <code>h_logistic_mult_cont_df()</code>,
 see the example).</p></dd>
 
 
-<dt id="arg-vars">vars<a class="anchor" aria-label="anchor" href="#arg-vars"></a></dt>
-<dd><p>(<code>character</code>)<br> the names of statistics to be reported among:</p><ul><li><p><code>n_tot</code>: Total number of patients per group.</p></li>
+<dt id="arg-vars">vars<a class="anchor" aria-label="anchor" href="#arg-vars"></a>
+</dt>
+<dd>
+<p>(<code>character</code>)<br> the names of statistics to be reported among:</p>
+<ul>
+<li><p><code>n_tot</code>: Total number of patients per group.</p></li>
 <li><p><code>n_rsp</code>: Total number of responses per group.</p></li>
 <li><p><code>prop</code>: Total response proportion per group.</p></li>
 <li><p><code>or</code>: Odds ratio.</p></li>
 <li><p><code>ci</code>: Confidence interval of odds ratio.</p></li>
 <li><p><code>pval</code>: p-value of the effect.
 Note, the statistics <code>n_tot</code>, <code>or</code> and <code>ci</code> are required.</p></li>
-</ul></dd>
+</ul>
+</dd>
 
 
-<dt id="arg-na-str">na_str<a class="anchor" aria-label="anchor" href="#arg-na-str"></a></dt>
+<dt id="arg-na-str">na_str<a class="anchor" aria-label="anchor" href="#arg-na-str"></a>
+</dt>
 <dd><p>(<code>string</code>)<br> string used to replace all <code>NA</code> or empty values in the output.</p></dd>
 
 
-<dt id="arg--indent-mods">.indent_mods<a class="anchor" aria-label="anchor" href="#arg--indent-mods"></a></dt>
+<dt id="arg--indent-mods">.indent_mods<a class="anchor" aria-label="anchor" href="#arg--indent-mods"></a>
+</dt>
 <dd><p>(named <code>integer</code>)<br> indent modifiers for the labels. Defaults to 0, which corresponds to the
 unmodified default behavior. Can be negative.</p></dd>
 
-</dl></div>
+</dl>
+</div>
     <div class="section level2">
-    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
-
-<ul><li><p><code>h_rsp_to_logistic_variables()</code> returns a named <code>list</code> of elements <code>response</code>, <code>arm</code>, <code>covariates</code>, and <code>strata</code>.</p></li>
-</ul><ul><li><p><code>h_logistic_mult_cont_df()</code> returns a <code>data.frame</code> containing estimates and statistics for the selected biomarkers.</p></li>
-</ul><ul><li><p><code>h_tab_rsp_one_biomarker()</code> returns an <code>rtables</code> table object with the given statistics arranged in columns.</p></li>
-</ul></div>
+    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a>
+</h2>
+
+<ul>
+<li><p><code>h_rsp_to_logistic_variables()</code> returns a named <code>list</code> of elements <code>response</code>, <code>arm</code>, <code>covariates</code>, and <code>strata</code>.</p></li>
+</ul>
+<ul>
+<li><p><code>h_logistic_mult_cont_df()</code> returns a <code>data.frame</code> containing estimates and statistics for the selected biomarkers.</p></li>
+</ul>
+<ul>
+<li><p><code>h_tab_rsp_one_biomarker()</code> returns an <code>rtables</code> table object with the given statistics arranged in columns.</p></li>
+</ul>
+</div>
     <div class="section level2">
-    <h2 id="functions">Functions<a class="anchor" aria-label="anchor" href="#functions"></a></h2>
+    <h2 id="functions">Functions<a class="anchor" aria-label="anchor" href="#functions"></a>
+</h2>
 
-<ul><li><p><code>h_rsp_to_logistic_variables()</code>: helps with converting the "response" function variable list
+<ul>
+<li><p><code>h_rsp_to_logistic_variables()</code>: helps with converting the "response" function variable list
 to the "logistic regression" variable list. The reason is that currently there is an
 inconsistency between the variable names accepted by <code><a href="extract_rsp_subgroups.html">extract_rsp_subgroups()</a></code> and <code><a href="fit_logistic.html">fit_logistic()</a></code>.</p></li>
 <li><p><code>h_logistic_mult_cont_df()</code>: prepares estimates for number of responses, patients and
@@ -134,10 +222,12 @@ <h2 id="functions">Functions<a class="anchor" aria-label="anchor" href="#functio
 and <code>strata</code>.</p></li>
 <li><p><code>h_tab_rsp_one_biomarker()</code>: Prepares a single sub-table given a <code>df_sub</code> containing
 the results for a single biomarker.</p></li>
-</ul></div>
+</ul>
+</div>
 
     <div class="section level2">
-    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
+    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://dplyr.tidyverse.org" class="external-link">dplyr</a></span><span class="op">)</span></span></span>
 <span class="r-in"><span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://forcats.tidyverse.org/" class="external-link">forcats</a></span><span class="op">)</span></span></span>
 <span class="r-in"><span></span></span>
@@ -224,17 +314,19 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 </code></pre></div>
     </div>
   </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
-    </nav></aside></div>
+    </nav></aside>
+</div>
 
 
     <footer><div class="nest">
   <p>tern is a part of the <strong>NEST</strong> and <a href="https://pharmaverse.org/" class="external-link"><strong>pharmaverse</strong></a>.</p>
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-<script type="text/javascript" src="../analytics.js"></script></footer></div>
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+<script type="text/javascript" src="../analytics.js"></script></footer>
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diff --git a/main/reference/h_response_subgroups.html b/main/reference/h_response_subgroups.html
index 3f70db271e..ac36c769c5 100644
--- a/main/reference/h_response_subgroups.html
+++ b/main/reference/h_response_subgroups.html
@@ -1,9 +1,32 @@
-<!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Helper functions for tabulating binary response by subgroup — h_response_subgroups • tern</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Helper functions for tabulating binary response by subgroup — h_response_subgroups"><meta name="description" content="
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+<title>Helper functions for tabulating binary response by subgroup — h_response_subgroups • tern</title>
+<!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png">
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+<meta name="description" content="
 Helper functions that tabulate in a data frame statistics such as response rate
-and odds ratio for population subgroups."><meta property="og:description" content="
+and odds ratio for population subgroups.">
+<meta property="og:description" content="
 Helper functions that tabulate in a data frame statistics such as response rate
-and odds ratio for population subgroups."><meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png"><link rel="stylesheet" href="../consent.css"><script src="../consent.js" type="text/javascript" charset="utf-8"></script></head><body>
+and odds ratio for population subgroups.">
+<meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png">
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+</div>
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-      </ul></div>
+      </ul>
+</div>
 
 
   </div>
@@ -57,7 +120,8 @@
     </div>
 
     <div class="section level2">
-    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
+    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">h_proportion_df</span><span class="op">(</span><span class="va">rsp</span>, <span class="va">arm</span><span class="op">)</span></span>
 <span></span>
 <span><span class="fu">h_proportion_subgroups_df</span><span class="op">(</span></span>
@@ -80,67 +144,91 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
     </div>
 
     <div class="section level2">
-    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
+    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a>
+</h2>
 
 
-<dl><dt id="arg-rsp">rsp<a class="anchor" aria-label="anchor" href="#arg-rsp"></a></dt>
+<dl>
+<dt id="arg-rsp">rsp<a class="anchor" aria-label="anchor" href="#arg-rsp"></a>
+</dt>
 <dd><p>(<code>logical</code>)<br> vector indicating whether each subject is a responder or not.</p></dd>
 
 
-<dt id="arg-arm">arm<a class="anchor" aria-label="anchor" href="#arg-arm"></a></dt>
+<dt id="arg-arm">arm<a class="anchor" aria-label="anchor" href="#arg-arm"></a>
+</dt>
 <dd><p>(<code>factor</code>)<br> the treatment group variable.</p></dd>
 
 
-<dt id="arg-variables">variables<a class="anchor" aria-label="anchor" href="#arg-variables"></a></dt>
+<dt id="arg-variables">variables<a class="anchor" aria-label="anchor" href="#arg-variables"></a>
+</dt>
 <dd><p>(named <code>list</code> of <code>string</code>)<br> list of additional analysis variables.</p></dd>
 
 
-<dt id="arg-data">data<a class="anchor" aria-label="anchor" href="#arg-data"></a></dt>
+<dt id="arg-data">data<a class="anchor" aria-label="anchor" href="#arg-data"></a>
+</dt>
 <dd><p>(<code>data.frame</code>)<br> the dataset containing the variables to summarize.</p></dd>
 
 
-<dt id="arg-groups-lists">groups_lists<a class="anchor" aria-label="anchor" href="#arg-groups-lists"></a></dt>
+<dt id="arg-groups-lists">groups_lists<a class="anchor" aria-label="anchor" href="#arg-groups-lists"></a>
+</dt>
 <dd><p>(named <code>list</code> of <code>list</code>)<br> optionally contains for each <code>subgroups</code> variable a
 list, which specifies the new group levels via the names and the
 levels that belong to it in the character vectors that are elements of the list.</p></dd>
 
 
-<dt id="arg-label-all">label_all<a class="anchor" aria-label="anchor" href="#arg-label-all"></a></dt>
+<dt id="arg-label-all">label_all<a class="anchor" aria-label="anchor" href="#arg-label-all"></a>
+</dt>
 <dd><p>(<code>string</code>)<br> label for the total population analysis.</p></dd>
 
 
-<dt id="arg-strata-data">strata_data<a class="anchor" aria-label="anchor" href="#arg-strata-data"></a></dt>
+<dt id="arg-strata-data">strata_data<a class="anchor" aria-label="anchor" href="#arg-strata-data"></a>
+</dt>
 <dd><p>(<code>factor</code>, <code>data.frame</code>, or <code>NULL</code>)<br> required if stratified analysis is performed.</p></dd>
 
 
-<dt id="arg-conf-level">conf_level<a class="anchor" aria-label="anchor" href="#arg-conf-level"></a></dt>
+<dt id="arg-conf-level">conf_level<a class="anchor" aria-label="anchor" href="#arg-conf-level"></a>
+</dt>
 <dd><p>(<code>proportion</code>)<br> confidence level of the interval.</p></dd>
 
 
-<dt id="arg-method">method<a class="anchor" aria-label="anchor" href="#arg-method"></a></dt>
+<dt id="arg-method">method<a class="anchor" aria-label="anchor" href="#arg-method"></a>
+</dt>
 <dd><p>(<code>string</code> or <code>NULL</code>)<br> specifies the test used to calculate the p-value for the difference between
 two proportions. For options, see <code><a href="prop_diff_test.html">test_proportion_diff()</a></code>. Default is <code>NULL</code> so no test is performed.</p></dd>
 
-</dl></div>
+</dl>
+</div>
     <div class="section level2">
-    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
-
-<ul><li><p><code>h_proportion_df()</code> returns a <code>data.frame</code> with columns <code>arm</code>, <code>n</code>, <code>n_rsp</code>, and <code>prop</code>.</p></li>
-</ul><ul><li><p><code>h_proportion_subgroups_df()</code> returns a <code>data.frame</code> with columns <code>arm</code>, <code>n</code>, <code>n_rsp</code>, <code>prop</code>, <code>subgroup</code>,
+    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a>
+</h2>
+
+<ul>
+<li><p><code>h_proportion_df()</code> returns a <code>data.frame</code> with columns <code>arm</code>, <code>n</code>, <code>n_rsp</code>, and <code>prop</code>.</p></li>
+</ul>
+<ul>
+<li><p><code>h_proportion_subgroups_df()</code> returns a <code>data.frame</code> with columns <code>arm</code>, <code>n</code>, <code>n_rsp</code>, <code>prop</code>, <code>subgroup</code>,
 <code>var</code>, <code>var_label</code>, and <code>row_type</code>.</p></li>
-</ul><ul><li><p><code>h_odds_ratio_df()</code> returns a <code>data.frame</code> with columns <code>arm</code>, <code>n_tot</code>, <code>or</code>, <code>lcl</code>, <code>ucl</code>, <code>conf_level</code>, and
+</ul>
+<ul>
+<li><p><code>h_odds_ratio_df()</code> returns a <code>data.frame</code> with columns <code>arm</code>, <code>n_tot</code>, <code>or</code>, <code>lcl</code>, <code>ucl</code>, <code>conf_level</code>, and
 optionally <code>pval</code> and <code>pval_label</code>.</p></li>
-</ul><ul><li><p><code>h_odds_ratio_subgroups_df()</code> returns a <code>data.frame</code> with columns <code>arm</code>, <code>n_tot</code>, <code>or</code>, <code>lcl</code>, <code>ucl</code>,
+</ul>
+<ul>
+<li><p><code>h_odds_ratio_subgroups_df()</code> returns a <code>data.frame</code> with columns <code>arm</code>, <code>n_tot</code>, <code>or</code>, <code>lcl</code>, <code>ucl</code>,
 <code>conf_level</code>, <code>subgroup</code>, <code>var</code>, <code>var_label</code>, and <code>row_type</code>.</p></li>
-</ul></div>
+</ul>
+</div>
     <div class="section level2">
-    <h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a></h2>
+    <h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a>
+</h2>
     <p>Main functionality is to prepare data for use in a layout-creating function.</p>
     </div>
     <div class="section level2">
-    <h2 id="functions">Functions<a class="anchor" aria-label="anchor" href="#functions"></a></h2>
+    <h2 id="functions">Functions<a class="anchor" aria-label="anchor" href="#functions"></a>
+</h2>
 
-<ul><li><p><code>h_proportion_df()</code>: Helper to prepare a data frame of binary responses by arm.</p></li>
+<ul>
+<li><p><code>h_proportion_df()</code>: Helper to prepare a data frame of binary responses by arm.</p></li>
 <li><p><code>h_proportion_subgroups_df()</code>: Summarizes proportion of binary responses by arm and across subgroups
 in a data frame. <code>variables</code> corresponds to the names of variables found in <code>data</code>, passed as a named list and
 requires elements <code>rsp</code>, <code>arm</code> and optionally <code>subgroups</code>. <code>groups_lists</code> optionally specifies
@@ -151,10 +239,12 @@ <h2 id="functions">Functions<a class="anchor" aria-label="anchor" href="#functio
 arm across subgroups in a data frame. <code>variables</code> corresponds to the names of variables found in
 <code>data</code>, passed as a named list and requires elements <code>rsp</code>, <code>arm</code> and optionally <code>subgroups</code>
 and <code>strata</code>. <code>groups_lists</code> optionally specifies groupings for <code>subgroups</code> variables.</p></li>
-</ul></div>
+</ul>
+</div>
 
     <div class="section level2">
-    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
+    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://dplyr.tidyverse.org" class="external-link">dplyr</a></span><span class="op">)</span></span></span>
 <span class="r-in"><span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://forcats.tidyverse.org/" class="external-link">forcats</a></span><span class="op">)</span></span></span>
 <span class="r-in"><span></span></span>
@@ -356,17 +446,19 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 </code></pre></div>
     </div>
   </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
-    </nav></aside></div>
+    </nav></aside>
+</div>
 
 
     <footer><div class="nest">
   <p>tern is a part of the <strong>NEST</strong> and <a href="https://pharmaverse.org/" class="external-link"><strong>pharmaverse</strong></a>.</p>
 </div>
-<script type="text/javascript" src="../analytics.js"></script></footer></div>
-
+<script type="text/javascript" src="../analytics.js"></script></footer>
+</div>
 
 
 
 
-  </body></html>
 
+  </body>
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diff --git a/main/reference/h_split_by_subgroups.html b/main/reference/h_split_by_subgroups.html
index 277d0b98d4..c5d2a5ff2c 100644
--- a/main/reference/h_split_by_subgroups.html
+++ b/main/reference/h_split_by_subgroups.html
@@ -1,7 +1,30 @@
-<!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Split data frame by subgroups — h_split_by_subgroups • tern</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Split data frame by subgroups — h_split_by_subgroups"><meta name="description" content="
-Split a data frame into a non-nested list of subsets."><meta property="og:description" content="
-Split a data frame into a non-nested list of subsets."><meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png"><link rel="stylesheet" href="../consent.css"><script src="../consent.js" type="text/javascript" charset="utf-8"></script></head><body>
+<html lang="en">
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+<link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png">
+<script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet">
+<script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet">
+<link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet">
+<script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Split data frame by subgroups — h_split_by_subgroups">
+<meta name="description" content="
+Split a data frame into a non-nested list of subsets.">
+<meta property="og:description" content="
+Split a data frame into a non-nested list of subsets.">
+<meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png">
+<link rel="stylesheet" href="../consent.css">
+<script src="../consent.js" type="text/javascript" charset="utf-8"></script>
+</head>
+<body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
 
 
@@ -17,26 +40,66 @@
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+  <ul class="dropdown-menu" aria-labelledby="dropdown-articles">
+<li><a class="dropdown-item" href="../articles/missing_values.html">Missing Values in Tern</a></li>
     <li><a class="dropdown-item" href="../articles/tables.html">Tabulation</a></li>
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     <li><a class="dropdown-item" href="../articles/tern_functions_guide.html">Understanding `tern` functions</a></li>
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+  </ul>
+</li>
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+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a>
+</div>
+</li></div>
+</ul>
+<ul class="navbar-nav">
+<li class="nav-item"><form class="form-inline" role="search">
+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json">
+</form></li>
 <li class="nav-item"><a class="external-link nav-link" href="https://github.com/insightsengineering/tern" aria-label="GitHub"><span class="fa fa-github"></span></a></li>
-      </ul></div>
+      </ul>
+</div>
 
 
   </div>
@@ -54,41 +117,51 @@
     </div>
 
     <div class="section level2">
-    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
+    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">h_split_by_subgroups</span><span class="op">(</span><span class="va">data</span>, <span class="va">subgroups</span>, groups_lists <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span><span class="op">)</span><span class="op">)</span></span></code></pre></div>
     </div>
 
     <div class="section level2">
-    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
+    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a>
+</h2>
 
 
-<dl><dt id="arg-data">data<a class="anchor" aria-label="anchor" href="#arg-data"></a></dt>
+<dl>
+<dt id="arg-data">data<a class="anchor" aria-label="anchor" href="#arg-data"></a>
+</dt>
 <dd><p>(<code>data.frame</code>)<br> dataset to split.</p></dd>
 
 
-<dt id="arg-subgroups">subgroups<a class="anchor" aria-label="anchor" href="#arg-subgroups"></a></dt>
+<dt id="arg-subgroups">subgroups<a class="anchor" aria-label="anchor" href="#arg-subgroups"></a>
+</dt>
 <dd><p>(<code>character</code>)<br> names of factor variables from <code>data</code> used to create subsets.
 Unused levels not present in <code>data</code> are dropped. Note that the order in this vector
 determines the order in the downstream table.</p></dd>
 
 
-<dt id="arg-groups-lists">groups_lists<a class="anchor" aria-label="anchor" href="#arg-groups-lists"></a></dt>
+<dt id="arg-groups-lists">groups_lists<a class="anchor" aria-label="anchor" href="#arg-groups-lists"></a>
+</dt>
 <dd><p>(named <code>list</code> of <code>list</code>)<br> optionally contains for each <code>subgroups</code> variable a
 list, which specifies the new group levels via the names and the
 levels that belong to it in the character vectors that are elements of the list.</p></dd>
 
-</dl></div>
+</dl>
+</div>
     <div class="section level2">
-    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
+    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a>
+</h2>
     <p>A list with subset data (<code>df</code>) and metadata about the subset (<code>df_labels</code>).</p>
     </div>
     <div class="section level2">
-    <h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a></h2>
+    <h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a>
+</h2>
     <p>Main functionality is to prepare data for use in forest plot layouts.</p>
     </div>
 
     <div class="section level2">
-    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
+    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">df</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a></span><span class="op">(</span></span></span>
 <span class="r-in"><span>  x <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">1</span><span class="op">:</span><span class="fl">5</span><span class="op">)</span>,</span></span>
 <span class="r-in"><span>  y <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/factor.html" class="external-link">factor</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"A"</span>, <span class="st">"B"</span>, <span class="st">"A"</span>, <span class="st">"B"</span>, <span class="st">"A"</span><span class="op">)</span>, levels <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"A"</span>, <span class="st">"B"</span>, <span class="st">"C"</span><span class="op">)</span><span class="op">)</span>,</span></span>
@@ -195,17 +268,19 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 </code></pre></div>
     </div>
   </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
-    </nav></aside></div>
+    </nav></aside>
+</div>
 
 
     <footer><div class="nest">
   <p>tern is a part of the <strong>NEST</strong> and <a href="https://pharmaverse.org/" class="external-link"><strong>pharmaverse</strong></a>.</p>
 </div>
-<script type="text/javascript" src="../analytics.js"></script></footer></div>
-
+<script type="text/javascript" src="../analytics.js"></script></footer>
+</div>
 
 
 
 
-  </body></html>
 
+  </body>
+</html>
diff --git a/main/reference/h_split_param.html b/main/reference/h_split_param.html
index 2b4dcfd190..7cd6354bed 100644
--- a/main/reference/h_split_param.html
+++ b/main/reference/h_split_param.html
@@ -1,11 +1,34 @@
-<!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Split parameters — h_split_param • tern</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Split parameters — h_split_param"><meta name="description" content="
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+<meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<title>Split parameters — h_split_param • tern</title>
+<!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png">
+<link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png">
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+<link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png">
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+<script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet">
+<script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet">
+<link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet">
+<script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Split parameters — h_split_param">
+<meta name="description" content="
 It divides the data in the vector param into the groups defined by f based on specified values. It is relevant
 in rtables layers so as to distribute parameters .stats or' .formats into lists with items corresponding to
-specific analysis function."><meta property="og:description" content="
+specific analysis function.">
+<meta property="og:description" content="
 It divides the data in the vector param into the groups defined by f based on specified values. It is relevant
 in rtables layers so as to distribute parameters .stats or' .formats into lists with items corresponding to
-specific analysis function."><meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png"><link rel="stylesheet" href="../consent.css"><script src="../consent.js" type="text/javascript" charset="utf-8"></script></head><body>
+specific analysis function.">
+<meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png">
+<link rel="stylesheet" href="../consent.css">
+<script src="../consent.js" type="text/javascript" charset="utf-8"></script>
+</head>
+<body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
 
 
@@ -21,26 +44,66 @@
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-      <ul class="navbar-nav me-auto"><li class="nav-item"><a class="nav-link" href="../articles/tern.html">Get started</a></li>
+      <ul class="navbar-nav me-auto">
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+  <ul class="dropdown-menu" aria-labelledby="dropdown-articles">
+<li><a class="dropdown-item" href="../articles/missing_values.html">Missing Values in Tern</a></li>
     <li><a class="dropdown-item" href="../articles/tables.html">Tabulation</a></li>
     <li><a class="dropdown-item" href="../articles/tern_formats.html">Formatting Functions</a></li>
     <li><a class="dropdown-item" href="../articles/tern_functions_guide.html">Understanding `tern` functions</a></li>
-  </ul></li>
+  </ul>
+</li>
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   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
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+  <ul class="dropdown-menu" aria-labelledby="dropdown-reports">
+<li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
     <li><a class="dropdown-item" href="../unit-test-report/">Unit test report</a></li>
     <li><a class="dropdown-item" href="../unit-test-report-non-cran/">Non-CRAN unit test report</a></li>
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-      </ul><ul class="navbar-nav"><li class="nav-item"><form class="form-inline" role="search">
- <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json"></form></li>
+  </ul>
+</li>
+      <div><li class="nav-item dropdown">
+    <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-versions">Versions</a>
+    <div class="dropdown-menu" aria-labelledby="dropdown-versions">
+    <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/main">main</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.5">v0.9.5</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.4">v0.9.4</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.3">v0.9.3</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1-rc3">v0.9.1-rc3</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a>
+</div>
+</li></div>
+</ul>
+<ul class="navbar-nav">
+<li class="nav-item"><form class="form-inline" role="search">
+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json">
+</form></li>
 <li class="nav-item"><a class="external-link nav-link" href="https://github.com/insightsengineering/tern" aria-label="GitHub"><span class="fa fa-github"></span></a></li>
-      </ul></div>
+      </ul>
+</div>
 
 
   </div>
@@ -60,33 +123,42 @@
     </div>
 
     <div class="section level2">
-    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
+    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">h_split_param</span><span class="op">(</span><span class="va">param</span>, <span class="va">value</span>, <span class="va">f</span><span class="op">)</span></span></code></pre></div>
     </div>
 
     <div class="section level2">
-    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
+    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a>
+</h2>
 
 
-<dl><dt id="arg-param">param<a class="anchor" aria-label="anchor" href="#arg-param"></a></dt>
+<dl>
+<dt id="arg-param">param<a class="anchor" aria-label="anchor" href="#arg-param"></a>
+</dt>
 <dd><p>(<code>vector</code>)<br> the parameter to be split.</p></dd>
 
 
-<dt id="arg-value">value<a class="anchor" aria-label="anchor" href="#arg-value"></a></dt>
+<dt id="arg-value">value<a class="anchor" aria-label="anchor" href="#arg-value"></a>
+</dt>
 <dd><p>(<code>vector</code>)<br> the value used to split.</p></dd>
 
 
-<dt id="arg-f">f<a class="anchor" aria-label="anchor" href="#arg-f"></a></dt>
+<dt id="arg-f">f<a class="anchor" aria-label="anchor" href="#arg-f"></a>
+</dt>
 <dd><p>(<code>list</code>)<br> the reference to make the split.</p></dd>
 
-</dl></div>
+</dl>
+</div>
     <div class="section level2">
-    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
+    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a>
+</h2>
     <p>A named <code>list</code> with the same element names as <code>f</code>, each containing the elements specified in <code>.stats</code>.</p>
     </div>
 
     <div class="section level2">
-    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
+    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">f</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span></span></span>
 <span class="r-in"><span>  surv <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"pt_at_risk"</span>, <span class="st">"event_free_rate"</span>, <span class="st">"rate_se"</span>, <span class="st">"rate_ci"</span><span class="op">)</span>,</span></span>
 <span class="r-in"><span>  surv_diff <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"rate_diff"</span>, <span class="st">"rate_diff_ci"</span>, <span class="st">"ztest_pval"</span><span class="op">)</span></span></span>
@@ -127,17 +199,19 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 </code></pre></div>
     </div>
   </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
-    </nav></aside></div>
+    </nav></aside>
+</div>
 
 
     <footer><div class="nest">
   <p>tern is a part of the <strong>NEST</strong> and <a href="https://pharmaverse.org/" class="external-link"><strong>pharmaverse</strong></a>.</p>
 </div>
-<script type="text/javascript" src="../analytics.js"></script></footer></div>
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+<script type="text/javascript" src="../analytics.js"></script></footer>
+</div>
 
 
 
 
-  </body></html>
 
+  </body>
+</html>
diff --git a/main/reference/h_stack_by_baskets.html b/main/reference/h_stack_by_baskets.html
index a4f8b1699d..e7ee96e1b3 100644
--- a/main/reference/h_stack_by_baskets.html
+++ b/main/reference/h_stack_by_baskets.html
@@ -1,13 +1,36 @@
-<!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Helper function to create a new SMQ variable in ADAE by stacking SMQ and/or CQ records. — h_stack_by_baskets • tern</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Helper function to create a new SMQ variable in ADAE by stacking SMQ and/or CQ records. — h_stack_by_baskets"><meta name="description" content="
+<html lang="en">
+<head>
+<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+<meta charset="utf-8">
+<meta http-equiv="X-UA-Compatible" content="IE=edge">
+<meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<title>Helper function to create a new SMQ variable in ADAE by stacking SMQ and/or CQ records. — h_stack_by_baskets • tern</title>
+<!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png">
+<link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png">
+<link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png">
+<link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png">
+<link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png">
+<link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png">
+<script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet">
+<script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet">
+<link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet">
+<script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Helper function to create a new SMQ variable in ADAE by stacking SMQ and/or CQ records. — h_stack_by_baskets">
+<meta name="description" content="
 Helper function to create a new SMQ variable in ADAE that consists of all adverse events belonging to
 selected Standardized/Customized queries. The new dataset will only contain records of the adverse events
 belonging to any of the selected baskets. Remember that na_str must match the needed pre-processing
-done with df_explicit_na() to have the desired output."><meta property="og:description" content="
+done with df_explicit_na() to have the desired output.">
+<meta property="og:description" content="
 Helper function to create a new SMQ variable in ADAE that consists of all adverse events belonging to
 selected Standardized/Customized queries. The new dataset will only contain records of the adverse events
 belonging to any of the selected baskets. Remember that na_str must match the needed pre-processing
-done with df_explicit_na() to have the desired output."><meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png"><link rel="stylesheet" href="../consent.css"><script src="../consent.js" type="text/javascript" charset="utf-8"></script></head><body>
+done with df_explicit_na() to have the desired output.">
+<meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png">
+<link rel="stylesheet" href="../consent.css">
+<script src="../consent.js" type="text/javascript" charset="utf-8"></script>
+</head>
+<body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
 
 
@@ -23,26 +46,66 @@
     </button>
 
     <div id="navbar" class="collapse navbar-collapse ms-3">
-      <ul class="navbar-nav me-auto"><li class="nav-item"><a class="nav-link" href="../articles/tern.html">Get started</a></li>
+      <ul class="navbar-nav me-auto">
+<li class="nav-item"><a class="nav-link" href="../articles/tern.html">Get started</a></li>
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   <button class="nav-link dropdown-toggle" type="button" id="dropdown-articles" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Articles</button>
-  <ul class="dropdown-menu" aria-labelledby="dropdown-articles"><li><a class="dropdown-item" href="../articles/missing_values.html">Missing Values in Tern</a></li>
+  <ul class="dropdown-menu" aria-labelledby="dropdown-articles">
+<li><a class="dropdown-item" href="../articles/missing_values.html">Missing Values in Tern</a></li>
     <li><a class="dropdown-item" href="../articles/tables.html">Tabulation</a></li>
     <li><a class="dropdown-item" href="../articles/tern_formats.html">Formatting Functions</a></li>
     <li><a class="dropdown-item" href="../articles/tern_functions_guide.html">Understanding `tern` functions</a></li>
-  </ul></li>
+  </ul>
+</li>
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- <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json"></form></li>
+  </ul>
+</li>
+      <div><li class="nav-item dropdown">
+    <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-versions">Versions</a>
+    <div class="dropdown-menu" aria-labelledby="dropdown-versions">
+    <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/main">main</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.5">v0.9.5</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.4">v0.9.4</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.3">v0.9.3</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1-rc3">v0.9.1-rc3</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a>
+</div>
+</li></div>
+</ul>
+<ul class="navbar-nav">
+<li class="nav-item"><form class="form-inline" role="search">
+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json">
+</form></li>
 <li class="nav-item"><a class="external-link nav-link" href="https://github.com/insightsengineering/tern" aria-label="GitHub"><span class="fa fa-github"></span></a></li>
-      </ul></div>
+      </ul>
+</div>
 
 
   </div>
@@ -63,7 +126,8 @@
     </div>
 
     <div class="section level2">
-    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
+    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">h_stack_by_baskets</span><span class="op">(</span></span>
 <span>  <span class="va">df</span>,</span>
 <span>  baskets <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/grep.html" class="external-link">grep</a></span><span class="op">(</span><span class="st">"^(SMQ|CQ).+NAM$"</span>, <span class="fu"><a href="https://rdrr.io/r/base/names.html" class="external-link">names</a></span><span class="op">(</span><span class="va">df</span><span class="op">)</span>, value <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span>,</span>
@@ -75,43 +139,54 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
     </div>
 
     <div class="section level2">
-    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
+    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a>
+</h2>
 
 
-<dl><dt id="arg-df">df<a class="anchor" aria-label="anchor" href="#arg-df"></a></dt>
+<dl>
+<dt id="arg-df">df<a class="anchor" aria-label="anchor" href="#arg-df"></a>
+</dt>
 <dd><p>(<code>data.frame</code>)<br> data set containing all analysis variables.</p></dd>
 
 
-<dt id="arg-baskets">baskets<a class="anchor" aria-label="anchor" href="#arg-baskets"></a></dt>
+<dt id="arg-baskets">baskets<a class="anchor" aria-label="anchor" href="#arg-baskets"></a>
+</dt>
 <dd><p>(<code>character</code>)<br> variable names of the selected Standardized/Customized queries.</p></dd>
 
 
-<dt id="arg-smq-varlabel">smq_varlabel<a class="anchor" aria-label="anchor" href="#arg-smq-varlabel"></a></dt>
+<dt id="arg-smq-varlabel">smq_varlabel<a class="anchor" aria-label="anchor" href="#arg-smq-varlabel"></a>
+</dt>
 <dd><p>(<code>string</code>)<br> a label for the new variable created.</p></dd>
 
 
-<dt id="arg-keys">keys<a class="anchor" aria-label="anchor" href="#arg-keys"></a></dt>
+<dt id="arg-keys">keys<a class="anchor" aria-label="anchor" href="#arg-keys"></a>
+</dt>
 <dd><p>(<code>character</code>)<br> names of the key variables to be returned along with the new variable created.</p></dd>
 
 
-<dt id="arg-aag-summary">aag_summary<a class="anchor" aria-label="anchor" href="#arg-aag-summary"></a></dt>
+<dt id="arg-aag-summary">aag_summary<a class="anchor" aria-label="anchor" href="#arg-aag-summary"></a>
+</dt>
 <dd><p>(<code>data.frame</code>)<br> containing the SMQ baskets and the levels of interest for the final SMQ
 variable. This is useful when there are some levels of interest that are not observed in the <code>df</code> dataset.
 The two columns of this dataset should be named <code>basket</code> and <code>basket_name</code>.</p></dd>
 
 
-<dt id="arg-na-str">na_str<a class="anchor" aria-label="anchor" href="#arg-na-str"></a></dt>
+<dt id="arg-na-str">na_str<a class="anchor" aria-label="anchor" href="#arg-na-str"></a>
+</dt>
 <dd><p>(<code>string</code>)<br> string used to replace all <code>NA</code> or empty values in the output.</p></dd>
 
-</dl></div>
+</dl>
+</div>
     <div class="section level2">
-    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
+    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a>
+</h2>
     <p>A <code>data.frame</code> with variables in <code>keys</code> taken from <code>df</code> and new variable SMQ containing
 records belonging to the baskets selected via the <code>baskets</code> argument.</p>
     </div>
 
     <div class="section level2">
-    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
+    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">adae</span> <span class="op">&lt;-</span> <span class="va">tern_ex_adae</span><span class="op">[</span><span class="fl">1</span><span class="op">:</span><span class="fl">20</span>, <span class="op">]</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> <span class="fu"><a href="df_explicit_na.html">df_explicit_na</a></span><span class="op">(</span><span class="op">)</span></span></span>
 <span class="r-in"><span><span class="fu">h_stack_by_baskets</span><span class="op">(</span>df <span class="op">=</span> <span class="va">adae</span><span class="op">)</span></span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 8 × 6</span></span>
@@ -173,17 +248,19 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 </code></pre></div>
     </div>
   </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
-    </nav></aside></div>
+    </nav></aside>
+</div>
 
 
     <footer><div class="nest">
   <p>tern is a part of the <strong>NEST</strong> and <a href="https://pharmaverse.org/" class="external-link"><strong>pharmaverse</strong></a>.</p>
 </div>
-<script type="text/javascript" src="../analytics.js"></script></footer></div>
-
+<script type="text/javascript" src="../analytics.js"></script></footer>
+</div>
 
 
 
 
-  </body></html>
 
+  </body>
+</html>
diff --git a/main/reference/h_step.html b/main/reference/h_step.html
index c4388a4a45..2ad7a78b02 100644
--- a/main/reference/h_step.html
+++ b/main/reference/h_step.html
@@ -1,7 +1,30 @@
-<!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Helper functions for subgroup treatment effect pattern (STEP) calculations — h_step • tern</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Helper functions for subgroup treatment effect pattern (STEP) calculations — h_step"><meta name="description" content="
-Helper functions that are used internally for the STEP calculations."><meta property="og:description" content="
-Helper functions that are used internally for the STEP calculations."><meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png"><link rel="stylesheet" href="../consent.css"><script src="../consent.js" type="text/javascript" charset="utf-8"></script></head><body>
+<html lang="en">
+<head>
+<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+<meta charset="utf-8">
+<meta http-equiv="X-UA-Compatible" content="IE=edge">
+<meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<title>Helper functions for subgroup treatment effect pattern (STEP) calculations — h_step • tern</title>
+<!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png">
+<link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png">
+<link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png">
+<link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png">
+<link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png">
+<link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png">
+<script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet">
+<script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet">
+<link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet">
+<script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Helper functions for subgroup treatment effect pattern (STEP) calculations — h_step">
+<meta name="description" content="
+Helper functions that are used internally for the STEP calculations.">
+<meta property="og:description" content="
+Helper functions that are used internally for the STEP calculations.">
+<meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png">
+<link rel="stylesheet" href="../consent.css">
+<script src="../consent.js" type="text/javascript" charset="utf-8"></script>
+</head>
+<body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
 
 
@@ -17,26 +40,66 @@
     </button>
 
     <div id="navbar" class="collapse navbar-collapse ms-3">
-      <ul class="navbar-nav me-auto"><li class="nav-item"><a class="nav-link" href="../articles/tern.html">Get started</a></li>
+      <ul class="navbar-nav me-auto">
+<li class="nav-item"><a class="nav-link" href="../articles/tern.html">Get started</a></li>
 <li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
 <li class="nav-item dropdown">
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-articles" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Articles</button>
-  <ul class="dropdown-menu" aria-labelledby="dropdown-articles"><li><a class="dropdown-item" href="../articles/missing_values.html">Missing Values in Tern</a></li>
+  <ul class="dropdown-menu" aria-labelledby="dropdown-articles">
+<li><a class="dropdown-item" href="../articles/missing_values.html">Missing Values in Tern</a></li>
     <li><a class="dropdown-item" href="../articles/tables.html">Tabulation</a></li>
     <li><a class="dropdown-item" href="../articles/tern_formats.html">Formatting Functions</a></li>
     <li><a class="dropdown-item" href="../articles/tern_functions_guide.html">Understanding `tern` functions</a></li>
-  </ul></li>
+  </ul>
+</li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
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   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
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+  <ul class="dropdown-menu" aria-labelledby="dropdown-reports">
+<li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
     <li><a class="dropdown-item" href="../unit-test-report/">Unit test report</a></li>
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-      </ul><ul class="navbar-nav"><li class="nav-item"><form class="form-inline" role="search">
- <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json"></form></li>
+  </ul>
+</li>
+      <div><li class="nav-item dropdown">
+    <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-versions">Versions</a>
+    <div class="dropdown-menu" aria-labelledby="dropdown-versions">
+    <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/main">main</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.5">v0.9.5</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.4">v0.9.4</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.3">v0.9.3</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1-rc3">v0.9.1-rc3</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a>
+</div>
+</li></div>
+</ul>
+<ul class="navbar-nav">
+<li class="nav-item"><form class="form-inline" role="search">
+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json">
+</form></li>
 <li class="nav-item"><a class="external-link nav-link" href="https://github.com/insightsengineering/tern" aria-label="GitHub"><span class="fa fa-github"></span></a></li>
-      </ul></div>
+      </ul>
+</div>
 
 
   </div>
@@ -54,7 +117,8 @@
     </div>
 
     <div class="section level2">
-    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
+    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">h_step_window</span><span class="op">(</span><span class="va">x</span>, control <span class="op">=</span> <span class="fu"><a href="control_step.html">control_step</a></span><span class="op">(</span><span class="op">)</span><span class="op">)</span></span>
 <span></span>
 <span><span class="fu">h_step_trt_effect</span><span class="op">(</span><span class="va">data</span>, <span class="va">model</span>, <span class="va">variables</span>, <span class="va">x</span><span class="op">)</span></span>
@@ -83,57 +147,82 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
     </div>
 
     <div class="section level2">
-    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
+    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a>
+</h2>
 
 
-<dl><dt id="arg-x">x<a class="anchor" aria-label="anchor" href="#arg-x"></a></dt>
+<dl>
+<dt id="arg-x">x<a class="anchor" aria-label="anchor" href="#arg-x"></a>
+</dt>
 <dd><p>(<code>numeric</code>)<br> biomarker value(s) to use (without <code>NA</code>).</p></dd>
 
 
-<dt id="arg-control">control<a class="anchor" aria-label="anchor" href="#arg-control"></a></dt>
+<dt id="arg-control">control<a class="anchor" aria-label="anchor" href="#arg-control"></a>
+</dt>
 <dd><p>(named <code>list</code>)<br> output from <code><a href="control_step.html">control_step()</a></code>.</p></dd>
 
 
-<dt id="arg-data">data<a class="anchor" aria-label="anchor" href="#arg-data"></a></dt>
+<dt id="arg-data">data<a class="anchor" aria-label="anchor" href="#arg-data"></a>
+</dt>
 <dd><p>(<code>data.frame</code>)<br> the dataset containing the variables to summarize.</p></dd>
 
 
-<dt id="arg-model">model<a class="anchor" aria-label="anchor" href="#arg-model"></a></dt>
+<dt id="arg-model">model<a class="anchor" aria-label="anchor" href="#arg-model"></a>
+</dt>
 <dd><p>(<code>coxph</code> or <code>glm</code>)<br> the regression model object.</p></dd>
 
 
-<dt id="arg-variables">variables<a class="anchor" aria-label="anchor" href="#arg-variables"></a></dt>
+<dt id="arg-variables">variables<a class="anchor" aria-label="anchor" href="#arg-variables"></a>
+</dt>
 <dd><p>(named <code>list</code> of <code>string</code>)<br> list of additional analysis variables.</p></dd>
 
 
-<dt id="arg-formula">formula<a class="anchor" aria-label="anchor" href="#arg-formula"></a></dt>
+<dt id="arg-formula">formula<a class="anchor" aria-label="anchor" href="#arg-formula"></a>
+</dt>
 <dd><p>(<code>formula</code>)<br> the regression model formula.</p></dd>
 
 
-<dt id="arg-subset">subset<a class="anchor" aria-label="anchor" href="#arg-subset"></a></dt>
+<dt id="arg-subset">subset<a class="anchor" aria-label="anchor" href="#arg-subset"></a>
+</dt>
 <dd><p>(<code>logical</code>)<br> subset vector.</p></dd>
 
-</dl></div>
+</dl>
+</div>
     <div class="section level2">
-    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
+    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a>
+</h2>
 
-<ul><li><p><code>h_step_window()</code> returns a list containing the window-selection matrix <code>sel</code>
+<ul>
+<li><p><code>h_step_window()</code> returns a list containing the window-selection matrix <code>sel</code>
 and the interval information matrix <code>interval</code>.</p></li>
-</ul><ul><li><p><code>h_step_trt_effect()</code> returns a vector with elements <code>est</code> and <code>se</code>.</p></li>
-</ul><ul><li><p><code>h_step_survival_formula()</code> returns a model formula.</p></li>
-</ul><ul><li><p><code>h_step_survival_est()</code> returns a matrix of number of observations <code>n</code>,
+</ul>
+<ul>
+<li><p><code>h_step_trt_effect()</code> returns a vector with elements <code>est</code> and <code>se</code>.</p></li>
+</ul>
+<ul>
+<li><p><code>h_step_survival_formula()</code> returns a model formula.</p></li>
+</ul>
+<ul>
+<li><p><code>h_step_survival_est()</code> returns a matrix of number of observations <code>n</code>,
 <code>events</code>, log hazard ratio estimates <code>loghr</code>, standard error <code>se</code>,
 and Wald confidence interval bounds <code>ci_lower</code> and <code>ci_upper</code>. One row is
 included for each biomarker value in <code>x</code>.</p></li>
-</ul><ul><li><p><code>h_step_rsp_formula()</code> returns a model formula.</p></li>
-</ul><ul><li><p><code>h_step_rsp_est()</code> returns a matrix of number of observations <code>n</code>, log odds
+</ul>
+<ul>
+<li><p><code>h_step_rsp_formula()</code> returns a model formula.</p></li>
+</ul>
+<ul>
+<li><p><code>h_step_rsp_est()</code> returns a matrix of number of observations <code>n</code>, log odds
 ratio estimates <code>logor</code>, standard error <code>se</code>, and Wald confidence interval bounds
 <code>ci_lower</code> and <code>ci_upper</code>. One row is included for each biomarker value in <code>x</code>.</p></li>
-</ul></div>
+</ul>
+</div>
     <div class="section level2">
-    <h2 id="functions">Functions<a class="anchor" aria-label="anchor" href="#functions"></a></h2>
+    <h2 id="functions">Functions<a class="anchor" aria-label="anchor" href="#functions"></a>
+</h2>
 
-<ul><li><p><code>h_step_window()</code>: Creates the windows for STEP, based on the control settings
+<ul>
+<li><p><code>h_step_window()</code>: Creates the windows for STEP, based on the control settings
 provided.</p></li>
 <li><p><code>h_step_trt_effect()</code>: Calculates the estimated treatment effect estimate
 on the linear predictor scale and corresponding standard error from a STEP <code>model</code> fitted
@@ -148,20 +237,23 @@ <h2 id="functions">Functions<a class="anchor" aria-label="anchor" href="#functio
 <li><p><code>h_step_rsp_est()</code>: Estimates the model with <code>formula</code> built based on
 <code>variables</code> in <code>data</code> for a given <code>subset</code> and <code>control</code> parameters for the
 logistic regression.</p></li>
-</ul></div>
+</ul>
+</div>
 
   </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
-    </nav></aside></div>
+    </nav></aside>
+</div>
 
 
     <footer><div class="nest">
   <p>tern is a part of the <strong>NEST</strong> and <a href="https://pharmaverse.org/" class="external-link"><strong>pharmaverse</strong></a>.</p>
 </div>
-<script type="text/javascript" src="../analytics.js"></script></footer></div>
-
+<script type="text/javascript" src="../analytics.js"></script></footer>
+</div>
 
 
 
 
-  </body></html>
 
+  </body>
+</html>
diff --git a/main/reference/h_survival_biomarkers_subgroups.html b/main/reference/h_survival_biomarkers_subgroups.html
index e91bda3db2..ebf7265546 100644
--- a/main/reference/h_survival_biomarkers_subgroups.html
+++ b/main/reference/h_survival_biomarkers_subgroups.html
@@ -1,9 +1,32 @@
-<!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Helper functions for tabulating biomarker effects on survival by subgroup — h_survival_biomarkers_subgroups • tern</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Helper functions for tabulating biomarker effects on survival by subgroup — h_survival_biomarkers_subgroups"><meta name="description" content="
+<html lang="en">
+<head>
+<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+<meta charset="utf-8">
+<meta http-equiv="X-UA-Compatible" content="IE=edge">
+<meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<title>Helper functions for tabulating biomarker effects on survival by subgroup — h_survival_biomarkers_subgroups • tern</title>
+<!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png">
+<link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png">
+<link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png">
+<link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png">
+<link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png">
+<link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png">
+<script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet">
+<script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet">
+<link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet">
+<script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Helper functions for tabulating biomarker effects on survival by subgroup — h_survival_biomarkers_subgroups">
+<meta name="description" content="
 Helper functions which are documented here separately to not confuse the user
-when reading about the user-facing functions."><meta property="og:description" content="
+when reading about the user-facing functions.">
+<meta property="og:description" content="
 Helper functions which are documented here separately to not confuse the user
-when reading about the user-facing functions."><meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png"><link rel="stylesheet" href="../consent.css"><script src="../consent.js" type="text/javascript" charset="utf-8"></script></head><body>
+when reading about the user-facing functions.">
+<meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png">
+<link rel="stylesheet" href="../consent.css">
+<script src="../consent.js" type="text/javascript" charset="utf-8"></script>
+</head>
+<body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
 
 
@@ -19,26 +42,66 @@
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-      <ul class="navbar-nav me-auto"><li class="nav-item"><a class="nav-link" href="../articles/tern.html">Get started</a></li>
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+<li class="nav-item"><a class="nav-link" href="../articles/tern.html">Get started</a></li>
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+  <ul class="dropdown-menu" aria-labelledby="dropdown-articles">
+<li><a class="dropdown-item" href="../articles/missing_values.html">Missing Values in Tern</a></li>
     <li><a class="dropdown-item" href="../articles/tables.html">Tabulation</a></li>
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     <li><a class="dropdown-item" href="../articles/tern_functions_guide.html">Understanding `tern` functions</a></li>
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+  </ul>
+</li>
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+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
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+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a>
+</div>
+</li></div>
+</ul>
+<ul class="navbar-nav">
+<li class="nav-item"><form class="form-inline" role="search">
+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json">
+</form></li>
 <li class="nav-item"><a class="external-link nav-link" href="https://github.com/insightsengineering/tern" aria-label="GitHub"><span class="fa fa-github"></span></a></li>
-      </ul></div>
+      </ul>
+</div>
 
 
   </div>
@@ -57,7 +120,8 @@
     </div>
 
     <div class="section level2">
-    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
+    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">h_surv_to_coxreg_variables</span><span class="op">(</span><span class="va">variables</span>, <span class="va">biomarker</span><span class="op">)</span></span>
 <span></span>
 <span><span class="fu">h_coxreg_mult_cont_df</span><span class="op">(</span><span class="va">variables</span>, <span class="va">data</span>, control <span class="op">=</span> <span class="fu"><a href="control_coxreg.html">control_coxreg</a></span><span class="op">(</span><span class="op">)</span><span class="op">)</span></span>
@@ -73,72 +137,98 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
     </div>
 
     <div class="section level2">
-    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
+    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a>
+</h2>
 
 
-<dl><dt id="arg-variables">variables<a class="anchor" aria-label="anchor" href="#arg-variables"></a></dt>
+<dl>
+<dt id="arg-variables">variables<a class="anchor" aria-label="anchor" href="#arg-variables"></a>
+</dt>
 <dd><p>(named <code>list</code> of <code>string</code>)<br> list of additional analysis variables.</p></dd>
 
 
-<dt id="arg-biomarker">biomarker<a class="anchor" aria-label="anchor" href="#arg-biomarker"></a></dt>
+<dt id="arg-biomarker">biomarker<a class="anchor" aria-label="anchor" href="#arg-biomarker"></a>
+</dt>
 <dd><p>(<code>string</code>)<br> the name of the biomarker variable.</p></dd>
 
 
-<dt id="arg-data">data<a class="anchor" aria-label="anchor" href="#arg-data"></a></dt>
+<dt id="arg-data">data<a class="anchor" aria-label="anchor" href="#arg-data"></a>
+</dt>
 <dd><p>(<code>data.frame</code>)<br> the dataset containing the variables to summarize.</p></dd>
 
 
-<dt id="arg-control">control<a class="anchor" aria-label="anchor" href="#arg-control"></a></dt>
+<dt id="arg-control">control<a class="anchor" aria-label="anchor" href="#arg-control"></a>
+</dt>
 <dd><p>(<code>list</code>)<br> a list of parameters as returned by the helper function <code><a href="control_coxreg.html">control_coxreg()</a></code>.</p></dd>
 
 
-<dt id="arg-df">df<a class="anchor" aria-label="anchor" href="#arg-df"></a></dt>
+<dt id="arg-df">df<a class="anchor" aria-label="anchor" href="#arg-df"></a>
+</dt>
 <dd><p>(<code>data.frame</code>)<br> results for a single biomarker, as part of what is
 returned by <code><a href="extract_survival_biomarkers.html">extract_survival_biomarkers()</a></code> (it needs a couple of columns which are
 added by that high-level function relative to what is returned by <code>h_coxreg_mult_cont_df()</code>,
 see the example).</p></dd>
 
 
-<dt id="arg-vars">vars<a class="anchor" aria-label="anchor" href="#arg-vars"></a></dt>
-<dd><p>(<code>character</code>)<br> the names of statistics to be reported among:</p><ul><li><p><code>n_tot_events</code>: Total number of events per group.</p></li>
+<dt id="arg-vars">vars<a class="anchor" aria-label="anchor" href="#arg-vars"></a>
+</dt>
+<dd>
+<p>(<code>character</code>)<br> the names of statistics to be reported among:</p>
+<ul>
+<li><p><code>n_tot_events</code>: Total number of events per group.</p></li>
 <li><p><code>n_tot</code>: Total number of observations per group.</p></li>
 <li><p><code>median</code>: Median survival time.</p></li>
 <li><p><code>hr</code>: Hazard ratio.</p></li>
 <li><p><code>ci</code>: Confidence interval of hazard ratio.</p></li>
 <li><p><code>pval</code>: p-value of the effect.
 Note, one of the statistics <code>n_tot</code> and <code>n_tot_events</code>, as well as both <code>hr</code> and <code>ci</code> are required.</p></li>
-</ul></dd>
+</ul>
+</dd>
 
 
-<dt id="arg-time-unit">time_unit<a class="anchor" aria-label="anchor" href="#arg-time-unit"></a></dt>
+<dt id="arg-time-unit">time_unit<a class="anchor" aria-label="anchor" href="#arg-time-unit"></a>
+</dt>
 <dd><p>(<code>string</code>)<br> label with unit of median survival time. Default <code>NULL</code> skips displaying unit.</p></dd>
 
 
-<dt id="arg-na-str">na_str<a class="anchor" aria-label="anchor" href="#arg-na-str"></a></dt>
+<dt id="arg-na-str">na_str<a class="anchor" aria-label="anchor" href="#arg-na-str"></a>
+</dt>
 <dd><p>(<code>string</code>)<br> string used to replace all <code>NA</code> or empty values in the output.</p></dd>
 
 
-<dt id="arg--indent-mods">.indent_mods<a class="anchor" aria-label="anchor" href="#arg--indent-mods"></a></dt>
+<dt id="arg--indent-mods">.indent_mods<a class="anchor" aria-label="anchor" href="#arg--indent-mods"></a>
+</dt>
 <dd><p>(named <code>integer</code>)<br> indent modifiers for the labels. Defaults to 0, which corresponds to the
 unmodified default behavior. Can be negative.</p></dd>
 
 
-<dt id="arg--">...<a class="anchor" aria-label="anchor" href="#arg--"></a></dt>
+<dt id="arg--">...<a class="anchor" aria-label="anchor" href="#arg--"></a>
+</dt>
 <dd><p>additional arguments for the lower level functions.</p></dd>
 
-</dl></div>
+</dl>
+</div>
     <div class="section level2">
-    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
+    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a>
+</h2>
 
-<ul><li><p><code>h_surv_to_coxreg_variables()</code> returns a named <code>list</code> of elements <code>time</code>, <code>event</code>, <code>arm</code>,
+<ul>
+<li><p><code>h_surv_to_coxreg_variables()</code> returns a named <code>list</code> of elements <code>time</code>, <code>event</code>, <code>arm</code>,
 <code>covariates</code>, and <code>strata</code>.</p></li>
-</ul><ul><li><p><code>h_coxreg_mult_cont_df()</code> returns a <code>data.frame</code> containing estimates and statistics for the selected biomarkers.</p></li>
-</ul><ul><li><p><code>h_tab_surv_one_biomarker()</code> returns an <code>rtables</code> table object with the given statistics arranged in columns.</p></li>
-</ul></div>
+</ul>
+<ul>
+<li><p><code>h_coxreg_mult_cont_df()</code> returns a <code>data.frame</code> containing estimates and statistics for the selected biomarkers.</p></li>
+</ul>
+<ul>
+<li><p><code>h_tab_surv_one_biomarker()</code> returns an <code>rtables</code> table object with the given statistics arranged in columns.</p></li>
+</ul>
+</div>
     <div class="section level2">
-    <h2 id="functions">Functions<a class="anchor" aria-label="anchor" href="#functions"></a></h2>
+    <h2 id="functions">Functions<a class="anchor" aria-label="anchor" href="#functions"></a>
+</h2>
 
-<ul><li><p><code>h_surv_to_coxreg_variables()</code>: Helps with converting the "survival" function variable list
+<ul>
+<li><p><code>h_surv_to_coxreg_variables()</code>: Helps with converting the "survival" function variable list
 to the "Cox regression" variable list. The reason is that currently there is an inconsistency between the variable
 names accepted by <code><a href="extract_survival_subgroups.html">extract_survival_subgroups()</a></code> and <code><a href="fit_coxreg.html">fit_coxreg_multivar()</a></code>.</p></li>
 <li><p><code>h_coxreg_mult_cont_df()</code>: Prepares estimates for number of events, patients and median survival
@@ -148,10 +238,12 @@ <h2 id="functions">Functions<a class="anchor" aria-label="anchor" href="#functio
 <code>tte</code>, <code>is_event</code>, <code>biomarkers</code> (vector of continuous biomarker variables) and optionally <code>subgroups</code> and <code>strata</code>.</p></li>
 <li><p><code>h_tab_surv_one_biomarker()</code>: Prepares a single sub-table given a <code>df_sub</code> containing
 the results for a single biomarker.</p></li>
-</ul></div>
+</ul>
+</div>
 
     <div class="section level2">
-    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
+    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://dplyr.tidyverse.org" class="external-link">dplyr</a></span><span class="op">)</span></span></span>
 <span class="r-in"><span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://forcats.tidyverse.org/" class="external-link">forcats</a></span><span class="op">)</span></span></span>
 <span class="r-in"><span></span></span>
@@ -251,17 +343,19 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 </code></pre></div>
     </div>
   </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
-    </nav></aside></div>
+    </nav></aside>
+</div>
 
 
     <footer><div class="nest">
   <p>tern is a part of the <strong>NEST</strong> and <a href="https://pharmaverse.org/" class="external-link"><strong>pharmaverse</strong></a>.</p>
 </div>
-<script type="text/javascript" src="../analytics.js"></script></footer></div>
-
+<script type="text/javascript" src="../analytics.js"></script></footer>
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diff --git a/main/reference/h_survival_duration_subgroups.html b/main/reference/h_survival_duration_subgroups.html
index 80bfd73556..028a0643e5 100644
--- a/main/reference/h_survival_duration_subgroups.html
+++ b/main/reference/h_survival_duration_subgroups.html
@@ -1,9 +1,32 @@
-<!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Helper functions for tabulating survival duration by subgroup — h_survival_duration_subgroups • tern</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Helper functions for tabulating survival duration by subgroup — h_survival_duration_subgroups"><meta name="description" content="
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+<title>Helper functions for tabulating survival duration by subgroup — h_survival_duration_subgroups • tern</title>
+<!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png">
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+<link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet">
+<script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Helper functions for tabulating survival duration by subgroup — h_survival_duration_subgroups">
+<meta name="description" content="
 Helper functions that tabulate in a data frame statistics such as median survival
-time and hazard ratio for population subgroups."><meta property="og:description" content="
+time and hazard ratio for population subgroups.">
+<meta property="og:description" content="
 Helper functions that tabulate in a data frame statistics such as median survival
-time and hazard ratio for population subgroups."><meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png"><link rel="stylesheet" href="../consent.css"><script src="../consent.js" type="text/javascript" charset="utf-8"></script></head><body>
+time and hazard ratio for population subgroups.">
+<meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png">
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+</head>
+<body>
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@@ -19,26 +42,66 @@
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+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
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+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a>
+</div>
+</li></div>
+</ul>
+<ul class="navbar-nav">
+<li class="nav-item"><form class="form-inline" role="search">
+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json">
+</form></li>
 <li class="nav-item"><a class="external-link nav-link" href="https://github.com/insightsengineering/tern" aria-label="GitHub"><span class="fa fa-github"></span></a></li>
-      </ul></div>
+      </ul>
+</div>
 
 
   </div>
@@ -57,7 +120,8 @@
     </div>
 
     <div class="section level2">
-    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
+    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">h_survtime_df</span><span class="op">(</span><span class="va">tte</span>, <span class="va">is_event</span>, <span class="va">arm</span><span class="op">)</span></span>
 <span></span>
 <span><span class="fu">h_survtime_subgroups_df</span><span class="op">(</span></span>
@@ -79,73 +143,101 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
     </div>
 
     <div class="section level2">
-    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
+    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a>
+</h2>
 
 
-<dl><dt id="arg-tte">tte<a class="anchor" aria-label="anchor" href="#arg-tte"></a></dt>
+<dl>
+<dt id="arg-tte">tte<a class="anchor" aria-label="anchor" href="#arg-tte"></a>
+</dt>
 <dd><p>(<code>numeric</code>)<br> vector of time-to-event duration values.</p></dd>
 
 
-<dt id="arg-is-event">is_event<a class="anchor" aria-label="anchor" href="#arg-is-event"></a></dt>
+<dt id="arg-is-event">is_event<a class="anchor" aria-label="anchor" href="#arg-is-event"></a>
+</dt>
 <dd><p>(<code>flag</code>)<br><code>TRUE</code> if event, <code>FALSE</code> if time to event is censored.</p></dd>
 
 
-<dt id="arg-arm">arm<a class="anchor" aria-label="anchor" href="#arg-arm"></a></dt>
+<dt id="arg-arm">arm<a class="anchor" aria-label="anchor" href="#arg-arm"></a>
+</dt>
 <dd><p>(<code>factor</code>)<br> the treatment group variable.</p></dd>
 
 
-<dt id="arg-variables">variables<a class="anchor" aria-label="anchor" href="#arg-variables"></a></dt>
+<dt id="arg-variables">variables<a class="anchor" aria-label="anchor" href="#arg-variables"></a>
+</dt>
 <dd><p>(named <code>list</code> of <code>string</code>)<br> list of additional analysis variables.</p></dd>
 
 
-<dt id="arg-data">data<a class="anchor" aria-label="anchor" href="#arg-data"></a></dt>
+<dt id="arg-data">data<a class="anchor" aria-label="anchor" href="#arg-data"></a>
+</dt>
 <dd><p>(<code>data.frame</code>)<br> the dataset containing the variables to summarize.</p></dd>
 
 
-<dt id="arg-groups-lists">groups_lists<a class="anchor" aria-label="anchor" href="#arg-groups-lists"></a></dt>
+<dt id="arg-groups-lists">groups_lists<a class="anchor" aria-label="anchor" href="#arg-groups-lists"></a>
+</dt>
 <dd><p>(named <code>list</code> of <code>list</code>)<br> optionally contains for each <code>subgroups</code> variable a
 list, which specifies the new group levels via the names and the
 levels that belong to it in the character vectors that are elements of the list.</p></dd>
 
 
-<dt id="arg-label-all">label_all<a class="anchor" aria-label="anchor" href="#arg-label-all"></a></dt>
+<dt id="arg-label-all">label_all<a class="anchor" aria-label="anchor" href="#arg-label-all"></a>
+</dt>
 <dd><p>(<code>string</code>)<br> label for the total population analysis.</p></dd>
 
 
-<dt id="arg-strata-data">strata_data<a class="anchor" aria-label="anchor" href="#arg-strata-data"></a></dt>
+<dt id="arg-strata-data">strata_data<a class="anchor" aria-label="anchor" href="#arg-strata-data"></a>
+</dt>
 <dd><p>(<code>factor</code>, <code>data.frame</code>, or <code>NULL</code>)<br> required if stratified analysis is performed.</p></dd>
 
 
-<dt id="arg-control">control<a class="anchor" aria-label="anchor" href="#arg-control"></a></dt>
-<dd><p>(<code>list</code>)<br> parameters for comparison details, specified by using the helper function
-<code><a href="control_coxph.html">control_coxph()</a></code>. Some possible parameter options are:</p><ul><li><p><code>pval_method</code> (<code>string</code>)<br> p-value method for testing the null hypothesis that hazard ratio = 1. Default
+<dt id="arg-control">control<a class="anchor" aria-label="anchor" href="#arg-control"></a>
+</dt>
+<dd>
+<p>(<code>list</code>)<br> parameters for comparison details, specified by using the helper function
+<code><a href="control_coxph.html">control_coxph()</a></code>. Some possible parameter options are:</p>
+<ul>
+<li><p><code>pval_method</code> (<code>string</code>)<br> p-value method for testing the null hypothesis that hazard ratio = 1. Default
 method is <code>"log-rank"</code> which comes from <code><a href="https://rdrr.io/pkg/survival/man/survdiff.html" class="external-link">survival::survdiff()</a></code>, can also be set to <code>"wald"</code> or <code>"likelihood"</code>
 (from <code><a href="https://rdrr.io/pkg/survival/man/coxph.html" class="external-link">survival::coxph()</a></code>).</p></li>
 <li><p><code>ties</code> (<code>string</code>)<br> specifying the method for tie handling. Default is <code>"efron"</code>,
 can also be set to <code>"breslow"</code> or <code>"exact"</code>. See more in <code><a href="https://rdrr.io/pkg/survival/man/coxph.html" class="external-link">survival::coxph()</a></code>.</p></li>
 <li><p><code>conf_level</code> (<code>proportion</code>)<br> confidence level of the interval for HR.</p></li>
-</ul></dd>
+</ul>
+</dd>
 
-</dl></div>
+</dl>
+</div>
     <div class="section level2">
-    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
-
-<ul><li><p><code>h_survtime_df()</code> returns a <code>data.frame</code> with columns <code>arm</code>, <code>n</code>, <code>n_events</code>, and <code>median</code>.</p></li>
-</ul><ul><li><p><code>h_survtime_subgroups_df()</code> returns a <code>data.frame</code> with columns <code>arm</code>, <code>n</code>, <code>n_events</code>, <code>median</code>, <code>subgroup</code>,
+    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a>
+</h2>
+
+<ul>
+<li><p><code>h_survtime_df()</code> returns a <code>data.frame</code> with columns <code>arm</code>, <code>n</code>, <code>n_events</code>, and <code>median</code>.</p></li>
+</ul>
+<ul>
+<li><p><code>h_survtime_subgroups_df()</code> returns a <code>data.frame</code> with columns <code>arm</code>, <code>n</code>, <code>n_events</code>, <code>median</code>, <code>subgroup</code>,
 <code>var</code>, <code>var_label</code>, and <code>row_type</code>.</p></li>
-</ul><ul><li><p><code>h_coxph_df()</code> returns a <code>data.frame</code> with columns <code>arm</code>, <code>n_tot</code>, <code>n_tot_events</code>, <code>hr</code>, <code>lcl</code>, <code>ucl</code>,
+</ul>
+<ul>
+<li><p><code>h_coxph_df()</code> returns a <code>data.frame</code> with columns <code>arm</code>, <code>n_tot</code>, <code>n_tot_events</code>, <code>hr</code>, <code>lcl</code>, <code>ucl</code>,
 <code>conf_level</code>, <code>pval</code> and <code>pval_label</code>.</p></li>
-</ul><ul><li><p><code>h_coxph_subgroups_df()</code> returns a <code>data.frame</code> with columns <code>arm</code>, <code>n_tot</code>, <code>n_tot_events</code>, <code>hr</code>,
+</ul>
+<ul>
+<li><p><code>h_coxph_subgroups_df()</code> returns a <code>data.frame</code> with columns <code>arm</code>, <code>n_tot</code>, <code>n_tot_events</code>, <code>hr</code>,
 <code>lcl</code>, <code>ucl</code>, <code>conf_level</code>, <code>pval</code>, <code>pval_label</code>, <code>subgroup</code>, <code>var</code>, <code>var_label</code>, and <code>row_type</code>.</p></li>
-</ul></div>
+</ul>
+</div>
     <div class="section level2">
-    <h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a></h2>
+    <h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a>
+</h2>
     <p>Main functionality is to prepare data for use in a layout-creating function.</p>
     </div>
     <div class="section level2">
-    <h2 id="functions">Functions<a class="anchor" aria-label="anchor" href="#functions"></a></h2>
+    <h2 id="functions">Functions<a class="anchor" aria-label="anchor" href="#functions"></a>
+</h2>
 
-<ul><li><p><code>h_survtime_df()</code>: Helper to prepare a data frame of median survival times by arm.</p></li>
+<ul>
+<li><p><code>h_survtime_df()</code>: Helper to prepare a data frame of median survival times by arm.</p></li>
 <li><p><code>h_survtime_subgroups_df()</code>: Summarizes median survival times by arm and across subgroups
 in a data frame. <code>variables</code> corresponds to the names of variables found in <code>data</code>, passed as a named list and
 requires elements <code>tte</code>, <code>is_event</code>, <code>arm</code> and optionally <code>subgroups</code>. <code>groups_lists</code> optionally specifies
@@ -157,10 +249,12 @@ <h2 id="functions">Functions<a class="anchor" aria-label="anchor" href="#functio
 <code>data</code>, passed as a named list and requires elements <code>tte</code>, <code>is_event</code>, <code>arm</code> and
 optionally <code>subgroups</code> and <code>strata</code>. <code>groups_lists</code> optionally specifies
 groupings for <code>subgroups</code> variables.</p></li>
-</ul></div>
+</ul>
+</div>
 
     <div class="section level2">
-    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
+    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://dplyr.tidyverse.org" class="external-link">dplyr</a></span><span class="op">)</span></span></span>
 <span class="r-in"><span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://forcats.tidyverse.org/" class="external-link">forcats</a></span><span class="op">)</span></span></span>
 <span class="r-in"><span></span></span>
@@ -382,17 +476,19 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 </code></pre></div>
     </div>
   </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
-    </nav></aside></div>
+    </nav></aside>
+</div>
 
 
     <footer><div class="nest">
   <p>tern is a part of the <strong>NEST</strong> and <a href="https://pharmaverse.org/" class="external-link"><strong>pharmaverse</strong></a>.</p>
 </div>
-<script type="text/javascript" src="../analytics.js"></script></footer></div>
-
+<script type="text/javascript" src="../analytics.js"></script></footer>
+</div>
 
 
 
 
-  </body></html>
 
+  </body>
+</html>
diff --git a/main/reference/h_tab_one_biomarker.html b/main/reference/h_tab_one_biomarker.html
index 383f029318..6912939544 100644
--- a/main/reference/h_tab_one_biomarker.html
+++ b/main/reference/h_tab_one_biomarker.html
@@ -1,9 +1,32 @@
-<!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Helper function for tabulation of a single biomarker result — h_tab_one_biomarker • tern</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Helper function for tabulation of a single biomarker result — h_tab_one_biomarker"><meta name="description" content="
+<html lang="en">
+<head>
+<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+<meta charset="utf-8">
+<meta http-equiv="X-UA-Compatible" content="IE=edge">
+<meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<title>Helper function for tabulation of a single biomarker result — h_tab_one_biomarker • tern</title>
+<!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png">
+<link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png">
+<link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png">
+<link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png">
+<link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png">
+<link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png">
+<script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet">
+<script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet">
+<link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet">
+<script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Helper function for tabulation of a single biomarker result — h_tab_one_biomarker">
+<meta name="description" content="
 Please see h_tab_surv_one_biomarker() and h_tab_rsp_one_biomarker(), which use this function for examples.
-This function is a wrapper for rtables::summarize_row_groups()."><meta property="og:description" content="
+This function is a wrapper for rtables::summarize_row_groups().">
+<meta property="og:description" content="
 Please see h_tab_surv_one_biomarker() and h_tab_rsp_one_biomarker(), which use this function for examples.
-This function is a wrapper for rtables::summarize_row_groups()."><meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png"><link rel="stylesheet" href="../consent.css"><script src="../consent.js" type="text/javascript" charset="utf-8"></script></head><body>
+This function is a wrapper for rtables::summarize_row_groups().">
+<meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png">
+<link rel="stylesheet" href="../consent.css">
+<script src="../consent.js" type="text/javascript" charset="utf-8"></script>
+</head>
+<body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
 
 
@@ -19,26 +42,66 @@
     </button>
 
     <div id="navbar" class="collapse navbar-collapse ms-3">
-      <ul class="navbar-nav me-auto"><li class="nav-item"><a class="nav-link" href="../articles/tern.html">Get started</a></li>
+      <ul class="navbar-nav me-auto">
+<li class="nav-item"><a class="nav-link" href="../articles/tern.html">Get started</a></li>
 <li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
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   <button class="nav-link dropdown-toggle" type="button" id="dropdown-articles" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Articles</button>
-  <ul class="dropdown-menu" aria-labelledby="dropdown-articles"><li><a class="dropdown-item" href="../articles/missing_values.html">Missing Values in Tern</a></li>
+  <ul class="dropdown-menu" aria-labelledby="dropdown-articles">
+<li><a class="dropdown-item" href="../articles/missing_values.html">Missing Values in Tern</a></li>
     <li><a class="dropdown-item" href="../articles/tables.html">Tabulation</a></li>
     <li><a class="dropdown-item" href="../articles/tern_formats.html">Formatting Functions</a></li>
     <li><a class="dropdown-item" href="../articles/tern_functions_guide.html">Understanding `tern` functions</a></li>
-  </ul></li>
+  </ul>
+</li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
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   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
-  <ul class="dropdown-menu" aria-labelledby="dropdown-reports"><li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
+  <ul class="dropdown-menu" aria-labelledby="dropdown-reports">
+<li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
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-      </ul><ul class="navbar-nav"><li class="nav-item"><form class="form-inline" role="search">
- <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json"></form></li>
+  </ul>
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+      <div><li class="nav-item dropdown">
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+    <div class="dropdown-menu" aria-labelledby="dropdown-versions">
+    <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/main">main</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.5">v0.9.5</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.4">v0.9.4</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.3">v0.9.3</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1-rc3">v0.9.1-rc3</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a>
+</div>
+</li></div>
+</ul>
+<ul class="navbar-nav">
+<li class="nav-item"><form class="form-inline" role="search">
+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json">
+</form></li>
 <li class="nav-item"><a class="external-link nav-link" href="https://github.com/insightsengineering/tern" aria-label="GitHub"><span class="fa fa-github"></span></a></li>
-      </ul></div>
+      </ul>
+</div>
 
 
   </div>
@@ -57,7 +120,8 @@
     </div>
 
     <div class="section level2">
-    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
+    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">h_tab_one_biomarker</span><span class="op">(</span></span>
 <span>  <span class="va">df</span>,</span>
 <span>  <span class="va">afuns</span>,</span>
@@ -69,51 +133,63 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
     </div>
 
     <div class="section level2">
-    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
+    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a>
+</h2>
 
 
-<dl><dt id="arg-df">df<a class="anchor" aria-label="anchor" href="#arg-df"></a></dt>
+<dl>
+<dt id="arg-df">df<a class="anchor" aria-label="anchor" href="#arg-df"></a>
+</dt>
 <dd><p>(<code>data.frame</code>)<br> results for a single biomarker.</p></dd>
 
 
-<dt id="arg-afuns">afuns<a class="anchor" aria-label="anchor" href="#arg-afuns"></a></dt>
+<dt id="arg-afuns">afuns<a class="anchor" aria-label="anchor" href="#arg-afuns"></a>
+</dt>
 <dd><p>(named <code>list</code> of <code>function</code>)<br> analysis functions.</p></dd>
 
 
-<dt id="arg-colvars">colvars<a class="anchor" aria-label="anchor" href="#arg-colvars"></a></dt>
+<dt id="arg-colvars">colvars<a class="anchor" aria-label="anchor" href="#arg-colvars"></a>
+</dt>
 <dd><p>(named <code>list</code>)<br> named list with elements <code>vars</code> (variables to tabulate) and <code>labels</code> (their labels).</p></dd>
 
 
-<dt id="arg-na-str">na_str<a class="anchor" aria-label="anchor" href="#arg-na-str"></a></dt>
+<dt id="arg-na-str">na_str<a class="anchor" aria-label="anchor" href="#arg-na-str"></a>
+</dt>
 <dd><p>(<code>string</code>)<br> string used to replace all <code>NA</code> or empty values in the output.</p></dd>
 
 
-<dt id="arg--indent-mods">.indent_mods<a class="anchor" aria-label="anchor" href="#arg--indent-mods"></a></dt>
+<dt id="arg--indent-mods">.indent_mods<a class="anchor" aria-label="anchor" href="#arg--indent-mods"></a>
+</dt>
 <dd><p>(named <code>integer</code>)<br> indent modifiers for the labels. Defaults to 0, which corresponds to the
 unmodified default behavior. Can be negative.</p></dd>
 
 
-<dt id="arg--">...<a class="anchor" aria-label="anchor" href="#arg--"></a></dt>
+<dt id="arg--">...<a class="anchor" aria-label="anchor" href="#arg--"></a>
+</dt>
 <dd><p>additional arguments for the lower level functions.</p></dd>
 
-</dl></div>
+</dl>
+</div>
     <div class="section level2">
-    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
+    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a>
+</h2>
     <p>An <code>rtables</code> table object with statistics in columns.</p>
     </div>
 
   </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
-    </nav></aside></div>
+    </nav></aside>
+</div>
 
 
     <footer><div class="nest">
   <p>tern is a part of the <strong>NEST</strong> and <a href="https://pharmaverse.org/" class="external-link"><strong>pharmaverse</strong></a>.</p>
 </div>
-<script type="text/javascript" src="../analytics.js"></script></footer></div>
-
+<script type="text/javascript" src="../analytics.js"></script></footer>
+</div>
 
 
 
 
-  </body></html>
 
+  </body>
+</html>
diff --git a/main/reference/h_tbl_coxph_pairwise.html b/main/reference/h_tbl_coxph_pairwise.html
index 76514fb3f9..0e9d4f0468 100644
--- a/main/reference/h_tbl_coxph_pairwise.html
+++ b/main/reference/h_tbl_coxph_pairwise.html
@@ -1,7 +1,30 @@
-<!DOCTYPE html>
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-Create a data.frame of pairwise stratified or unstratified Cox-PH analysis results."><meta property="og:description" content="
-Create a data.frame of pairwise stratified or unstratified Cox-PH analysis results."><meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png"><link rel="stylesheet" href="../consent.css"><script src="../consent.js" type="text/javascript" charset="utf-8"></script></head><body>
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+<meta name="description" content="
+Create a data.frame of pairwise stratified or unstratified Cox-PH analysis results.">
+<meta property="og:description" content="
+Create a data.frame of pairwise stratified or unstratified Cox-PH analysis results.">
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@@ -54,7 +117,8 @@
     </div>
 
     <div class="section level2">
-    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
+    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">h_tbl_coxph_pairwise</span><span class="op">(</span></span>
 <span>  <span class="va">df</span>,</span>
 <span>  <span class="va">variables</span>,</span>
@@ -65,49 +129,67 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
     </div>
 
     <div class="section level2">
-    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
+    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a>
+</h2>
 
 
-<dl><dt id="arg-df">df<a class="anchor" aria-label="anchor" href="#arg-df"></a></dt>
+<dl>
+<dt id="arg-df">df<a class="anchor" aria-label="anchor" href="#arg-df"></a>
+</dt>
 <dd><p>(<code>data.frame</code>)<br> data set containing all analysis variables.</p></dd>
 
 
-<dt id="arg-variables">variables<a class="anchor" aria-label="anchor" href="#arg-variables"></a></dt>
-<dd><p>(named <code>list</code>)<br> variable names. Details are:</p><ul><li><p><code>tte</code> (<code>numeric</code>)<br> variable indicating time-to-event duration values.</p></li>
+<dt id="arg-variables">variables<a class="anchor" aria-label="anchor" href="#arg-variables"></a>
+</dt>
+<dd>
+<p>(named <code>list</code>)<br> variable names. Details are:</p>
+<ul>
+<li><p><code>tte</code> (<code>numeric</code>)<br> variable indicating time-to-event duration values.</p></li>
 <li><p><code>is_event</code> (<code>logical</code>)<br> event variable. <code>TRUE</code> if event, <code>FALSE</code> if time to event is censored.</p></li>
 <li><p><code>arm</code> (<code>factor</code>)<br> the treatment group variable.</p></li>
 <li><p><code>strata</code> (<code>character</code> or <code>NULL</code>)<br> variable names indicating stratification factors.</p></li>
-</ul></dd>
+</ul>
+</dd>
 
 
-<dt id="arg-ref-group-coxph">ref_group_coxph<a class="anchor" aria-label="anchor" href="#arg-ref-group-coxph"></a></dt>
+<dt id="arg-ref-group-coxph">ref_group_coxph<a class="anchor" aria-label="anchor" href="#arg-ref-group-coxph"></a>
+</dt>
 <dd><p>(<code>string</code> or <code>NULL</code>)<br> level of arm variable to use as reference group in calculations for
 <code>annot_coxph</code> table. If <code>NULL</code> (default), uses the first level of the arm variable.</p></dd>
 
 
-<dt id="arg-control-coxph-pw">control_coxph_pw<a class="anchor" aria-label="anchor" href="#arg-control-coxph-pw"></a></dt>
-<dd><p>(<code>list</code>)<br> parameters for comparison details, specified using the helper function
-<code><a href="control_coxph.html">control_coxph()</a></code>. Some possible parameter options are:</p><ul><li><p><code>pval_method</code> (<code>string</code>)<br> p-value method for testing hazard ratio = 1.
+<dt id="arg-control-coxph-pw">control_coxph_pw<a class="anchor" aria-label="anchor" href="#arg-control-coxph-pw"></a>
+</dt>
+<dd>
+<p>(<code>list</code>)<br> parameters for comparison details, specified using the helper function
+<code><a href="control_coxph.html">control_coxph()</a></code>. Some possible parameter options are:</p>
+<ul>
+<li><p><code>pval_method</code> (<code>string</code>)<br> p-value method for testing hazard ratio = 1.
 Default method is <code>"log-rank"</code>, can also be set to <code>"wald"</code> or <code>"likelihood"</code>.</p></li>
 <li><p><code>ties</code> (<code>string</code>)<br> method for tie handling. Default is <code>"efron"</code>,
 can also be set to <code>"breslow"</code> or <code>"exact"</code>. See more in <code><a href="https://rdrr.io/pkg/survival/man/coxph.html" class="external-link">survival::coxph()</a></code></p></li>
 <li><p><code>conf_level</code> (<code>proportion</code>)<br> confidence level of the interval for HR.</p></li>
-</ul></dd>
+</ul>
+</dd>
 
 
-<dt id="arg-annot-coxph-ref-lbls">annot_coxph_ref_lbls<a class="anchor" aria-label="anchor" href="#arg-annot-coxph-ref-lbls"></a></dt>
+<dt id="arg-annot-coxph-ref-lbls">annot_coxph_ref_lbls<a class="anchor" aria-label="anchor" href="#arg-annot-coxph-ref-lbls"></a>
+</dt>
 <dd><p>(<code>flag</code>)<br> whether the reference group should be explicitly printed in labels for the
 <code>annot_coxph</code> table. If <code>FALSE</code> (default), only comparison groups will be printed in <code>annot_coxph</code> table labels.</p></dd>
 
-</dl></div>
+</dl>
+</div>
     <div class="section level2">
-    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
+    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a>
+</h2>
     <p>A <code>data.frame</code> containing statistics <code>HR</code>, <code>XX% CI</code> (<code>XX</code> taken from <code>control_coxph_pw</code>),
 and <code>p-value (log-rank)</code>.</p>
     </div>
 
     <div class="section level2">
-    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
+    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://dplyr.tidyverse.org" class="external-link">dplyr</a></span><span class="op">)</span></span></span>
 <span class="r-in"><span></span></span>
 <span class="r-in"><span><span class="va">adtte</span> <span class="op">&lt;-</span> <span class="va">tern_ex_adtte</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span></span>
@@ -126,17 +208,19 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 </code></pre></div>
     </div>
   </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
-    </nav></aside></div>
+    </nav></aside>
+</div>
 
 
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   <p>tern is a part of the <strong>NEST</strong> and <a href="https://pharmaverse.org/" class="external-link"><strong>pharmaverse</strong></a>.</p>
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+<script type="text/javascript" src="../analytics.js"></script></footer>
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diff --git a/main/reference/h_tbl_median_surv.html b/main/reference/h_tbl_median_surv.html
index 8a4652d6ad..c7bb413f06 100644
--- a/main/reference/h_tbl_median_surv.html
+++ b/main/reference/h_tbl_median_surv.html
@@ -1,7 +1,30 @@
-<!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Helper function for survival estimations — h_tbl_median_surv • tern</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Helper function for survival estimations — h_tbl_median_surv"><meta name="description" content="
-Transform a survival fit to a table with groups in rows characterized by N, median and confidence interval."><meta property="og:description" content="
-Transform a survival fit to a table with groups in rows characterized by N, median and confidence interval."><meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png"><link rel="stylesheet" href="../consent.css"><script src="../consent.js" type="text/javascript" charset="utf-8"></script></head><body>
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+<script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet">
+<link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet">
+<script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Helper function for survival estimations — h_tbl_median_surv">
+<meta name="description" content="
+Transform a survival fit to a table with groups in rows characterized by N, median and confidence interval.">
+<meta property="og:description" content="
+Transform a survival fit to a table with groups in rows characterized by N, median and confidence interval.">
+<meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png">
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+</head>
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@@ -17,26 +40,66 @@
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-      <ul class="navbar-nav me-auto"><li class="nav-item"><a class="nav-link" href="../articles/tern.html">Get started</a></li>
+      <ul class="navbar-nav me-auto">
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 <li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
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-  <ul class="dropdown-menu" aria-labelledby="dropdown-articles"><li><a class="dropdown-item" href="../articles/missing_values.html">Missing Values in Tern</a></li>
+  <ul class="dropdown-menu" aria-labelledby="dropdown-articles">
+<li><a class="dropdown-item" href="../articles/missing_values.html">Missing Values in Tern</a></li>
     <li><a class="dropdown-item" href="../articles/tables.html">Tabulation</a></li>
     <li><a class="dropdown-item" href="../articles/tern_formats.html">Formatting Functions</a></li>
     <li><a class="dropdown-item" href="../articles/tern_functions_guide.html">Understanding `tern` functions</a></li>
-  </ul></li>
+  </ul>
+</li>
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-  <ul class="dropdown-menu" aria-labelledby="dropdown-reports"><li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
+  <ul class="dropdown-menu" aria-labelledby="dropdown-reports">
+<li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
     <li><a class="dropdown-item" href="../unit-test-report/">Unit test report</a></li>
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-      </ul><ul class="navbar-nav"><li class="nav-item"><form class="form-inline" role="search">
- <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json"></form></li>
+  </ul>
+</li>
+      <div><li class="nav-item dropdown">
+    <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-versions">Versions</a>
+    <div class="dropdown-menu" aria-labelledby="dropdown-versions">
+    <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/main">main</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.5">v0.9.5</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.4">v0.9.4</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.3">v0.9.3</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1-rc3">v0.9.1-rc3</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a>
+</div>
+</li></div>
+</ul>
+<ul class="navbar-nav">
+<li class="nav-item"><form class="form-inline" role="search">
+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json">
+</form></li>
 <li class="nav-item"><a class="external-link nav-link" href="https://github.com/insightsengineering/tern" aria-label="GitHub"><span class="fa fa-github"></span></a></li>
-      </ul></div>
+      </ul>
+</div>
 
 
   </div>
@@ -54,29 +117,37 @@
     </div>
 
     <div class="section level2">
-    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
+    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">h_tbl_median_surv</span><span class="op">(</span><span class="va">fit_km</span>, armval <span class="op">=</span> <span class="st">"All"</span><span class="op">)</span></span></code></pre></div>
     </div>
 
     <div class="section level2">
-    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
+    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a>
+</h2>
 
 
-<dl><dt id="arg-fit-km">fit_km<a class="anchor" aria-label="anchor" href="#arg-fit-km"></a></dt>
+<dl>
+<dt id="arg-fit-km">fit_km<a class="anchor" aria-label="anchor" href="#arg-fit-km"></a>
+</dt>
 <dd><p>(<code>survfit</code>)<br> result of <code><a href="https://rdrr.io/pkg/survival/man/survfit.html" class="external-link">survival::survfit()</a></code>.</p></dd>
 
 
-<dt id="arg-armval">armval<a class="anchor" aria-label="anchor" href="#arg-armval"></a></dt>
+<dt id="arg-armval">armval<a class="anchor" aria-label="anchor" href="#arg-armval"></a>
+</dt>
 <dd><p>(<code>string</code>)<br> used as strata name when treatment arm variable only has one level. Default is <code>"All"</code>.</p></dd>
 
-</dl></div>
+</dl>
+</div>
     <div class="section level2">
-    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
+    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a>
+</h2>
     <p>A summary table with statistics <code>N</code>, <code>Median</code>, and <code>XX% CI</code> (<code>XX</code> taken from <code>fit_km</code>).</p>
     </div>
 
     <div class="section level2">
-    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
+    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://dplyr.tidyverse.org" class="external-link">dplyr</a></span><span class="op">)</span></span></span>
 <span class="r-in"><span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://github.com/therneau/survival" class="external-link">survival</a></span><span class="op">)</span></span></span>
 <span class="r-in"><span></span></span>
@@ -94,17 +165,19 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 </code></pre></div>
     </div>
   </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
-    </nav></aside></div>
+    </nav></aside>
+</div>
 
 
     <footer><div class="nest">
   <p>tern is a part of the <strong>NEST</strong> and <a href="https://pharmaverse.org/" class="external-link"><strong>pharmaverse</strong></a>.</p>
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-<script type="text/javascript" src="../analytics.js"></script></footer></div>
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+<script type="text/javascript" src="../analytics.js"></script></footer>
+</div>
 
 
 
 
-  </body></html>
 
+  </body>
+</html>
diff --git a/main/reference/h_worsen_counter.html b/main/reference/h_worsen_counter.html
index 31e5df2615..48b3c1d893 100644
--- a/main/reference/h_worsen_counter.html
+++ b/main/reference/h_worsen_counter.html
@@ -1,11 +1,34 @@
-<!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Helper function to analyze patients for s_count_abnormal_lab_worsen_by_baseline() — h_worsen_counter • tern</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Helper function to analyze patients for s_count_abnormal_lab_worsen_by_baseline() — h_worsen_counter"><meta name="description" content="
+<html lang="en">
+<head>
+<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+<meta charset="utf-8">
+<meta http-equiv="X-UA-Compatible" content="IE=edge">
+<meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<title>Helper function to analyze patients for s_count_abnormal_lab_worsen_by_baseline() — h_worsen_counter • tern</title>
+<!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png">
+<link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png">
+<link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png">
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+<script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet">
+<script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet">
+<link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet">
+<script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Helper function to analyze patients for s_count_abnormal_lab_worsen_by_baseline() — h_worsen_counter">
+<meta name="description" content="
 Helper function to count the number of patients and the fraction of patients according to
 highest post-baseline lab grade variable .var, baseline lab grade variable baseline_var,
-and the direction of interest specified in direction_var."><meta property="og:description" content="
+and the direction of interest specified in direction_var.">
+<meta property="og:description" content="
 Helper function to count the number of patients and the fraction of patients according to
 highest post-baseline lab grade variable .var, baseline lab grade variable baseline_var,
-and the direction of interest specified in direction_var."><meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png"><link rel="stylesheet" href="../consent.css"><script src="../consent.js" type="text/javascript" charset="utf-8"></script></head><body>
+and the direction of interest specified in direction_var.">
+<meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png">
+<link rel="stylesheet" href="../consent.css">
+<script src="../consent.js" type="text/javascript" charset="utf-8"></script>
+</head>
+<body>
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@@ -21,33 +44,74 @@
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+  <ul class="dropdown-menu" aria-labelledby="dropdown-articles">
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     <li><a class="dropdown-item" href="../articles/tern_formats.html">Formatting Functions</a></li>
     <li><a class="dropdown-item" href="../articles/tern_functions_guide.html">Understanding `tern` functions</a></li>
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+  <ul class="dropdown-menu" aria-labelledby="dropdown-reports">
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+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.5">v0.9.5</a>
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+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1-rc3">v0.9.1-rc3</a>
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+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
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+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a>
+</div>
+</li></div>
+</ul>
+<ul class="navbar-nav">
+<li class="nav-item"><form class="form-inline" role="search">
+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json">
+</form></li>
 <li class="nav-item"><a class="external-link nav-link" href="https://github.com/insightsengineering/tern" aria-label="GitHub"><span class="fa fa-github"></span></a></li>
-      </ul></div>
+      </ul>
+</div>
 
 
   </div>
 </nav><div class="container template-reference-topic">
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
-      <img src="../logo.png" class="logo" alt=""><h1>Helper function to analyze patients for <code>s_count_abnormal_lab_worsen_by_baseline()</code></h1>
+      <img src="../logo.png" class="logo" alt=""><h1>Helper function to analyze patients for <code>s_count_abnormal_lab_worsen_by_baseline()</code>
+</h1>
       <small class="dont-index">Source: <a href="https://github.com/insightsengineering/tern/blob/main/R/abnormal_by_worst_grade_worsen.R" class="external-link"><code>R/abnormal_by_worst_grade_worsen.R</code></a></small>
       <div class="d-none name"><code>h_worsen_counter.Rd</code></div>
     </div>
@@ -60,52 +124,68 @@
     </div>
 
     <div class="section level2">
-    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
+    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">h_worsen_counter</span><span class="op">(</span><span class="va">df</span>, <span class="va">id</span>, <span class="va">.var</span>, <span class="va">baseline_var</span>, <span class="va">direction_var</span><span class="op">)</span></span></code></pre></div>
     </div>
 
     <div class="section level2">
-    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
+    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a>
+</h2>
 
 
-<dl><dt id="arg-df">df<a class="anchor" aria-label="anchor" href="#arg-df"></a></dt>
+<dl>
+<dt id="arg-df">df<a class="anchor" aria-label="anchor" href="#arg-df"></a>
+</dt>
 <dd><p>(<code>data.frame</code>)<br> data set containing all analysis variables.</p></dd>
 
 
-<dt id="arg-id">id<a class="anchor" aria-label="anchor" href="#arg-id"></a></dt>
+<dt id="arg-id">id<a class="anchor" aria-label="anchor" href="#arg-id"></a>
+</dt>
 <dd><p>(<code>string</code>)<br> subject variable name.</p></dd>
 
 
-<dt id="arg--var">.var<a class="anchor" aria-label="anchor" href="#arg--var"></a></dt>
+<dt id="arg--var">.var<a class="anchor" aria-label="anchor" href="#arg--var"></a>
+</dt>
 <dd><p>(<code>string</code>)<br> single variable name that is passed by <code>rtables</code> when requested
 by a statistics function.</p></dd>
 
 
-<dt id="arg-baseline-var">baseline_var<a class="anchor" aria-label="anchor" href="#arg-baseline-var"></a></dt>
+<dt id="arg-baseline-var">baseline_var<a class="anchor" aria-label="anchor" href="#arg-baseline-var"></a>
+</dt>
 <dd><p>(<code>string</code>)<br> name of the baseline lab grade variable.</p></dd>
 
 
-<dt id="arg-direction-var">direction_var<a class="anchor" aria-label="anchor" href="#arg-direction-var"></a></dt>
-<dd><p>(<code>string</code>)<br> name of the direction variable specifying the direction of the shift table of
-interest. Only lab records flagged by <code>L</code>, <code>H</code> or <code>B</code> are included in the shift table.</p><ul><li><p><code>L</code>: low direction only</p></li>
+<dt id="arg-direction-var">direction_var<a class="anchor" aria-label="anchor" href="#arg-direction-var"></a>
+</dt>
+<dd>
+<p>(<code>string</code>)<br> name of the direction variable specifying the direction of the shift table of
+interest. Only lab records flagged by <code>L</code>, <code>H</code> or <code>B</code> are included in the shift table.</p>
+<ul>
+<li><p><code>L</code>: low direction only</p></li>
 <li><p><code>H</code>: high direction only</p></li>
 <li><p><code>B</code>: both low and high directions</p></li>
-</ul></dd>
+</ul>
+</dd>
 
-</dl></div>
+</dl>
+</div>
     <div class="section level2">
-    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
+    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a>
+</h2>
     <p>The counts and fraction of patients
 whose worst post-baseline lab grades are worse than their baseline grades, for
 post-baseline worst grades "1", "2", "3", "4" and "Any".</p>
     </div>
     <div class="section level2">
-    <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"></a></h2>
+    <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"></a>
+</h2>
     <div class="dont-index"><p><a href="abnormal_by_worst_grade_worsen.html">abnormal_by_worst_grade_worsen</a></p></div>
     </div>
 
     <div class="section level2">
-    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
+    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://dplyr.tidyverse.org" class="external-link">dplyr</a></span><span class="op">)</span></span></span>
 <span class="r-in"><span></span></span>
 <span class="r-in"><span><span class="co"># The direction variable, GRADDR, is based on metadata</span></span></span>
@@ -160,17 +240,19 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 </code></pre></div>
     </div>
   </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
-    </nav></aside></div>
+    </nav></aside>
+</div>
 
 
     <footer><div class="nest">
   <p>tern is a part of the <strong>NEST</strong> and <a href="https://pharmaverse.org/" class="external-link"><strong>pharmaverse</strong></a>.</p>
 </div>
-<script type="text/javascript" src="../analytics.js"></script></footer></div>
-
+<script type="text/javascript" src="../analytics.js"></script></footer>
+</div>
 
 
 
 
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+  </body>
+</html>
diff --git a/main/reference/h_xticks.html b/main/reference/h_xticks.html
index 307dc62f03..900c65a017 100644
--- a/main/reference/h_xticks.html
+++ b/main/reference/h_xticks.html
@@ -1,11 +1,34 @@
-<!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Helper function to calculate x-tick positions — h_xticks • tern</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Helper function to calculate x-tick positions — h_xticks"><meta name="description" content="
+<html lang="en">
+<head>
+<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+<meta charset="utf-8">
+<meta http-equiv="X-UA-Compatible" content="IE=edge">
+<meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<title>Helper function to calculate x-tick positions — h_xticks • tern</title>
+<!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png">
+<link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png">
+<link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png">
+<link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png">
+<link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png">
+<link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png">
+<script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet">
+<script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet">
+<link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet">
+<script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Helper function to calculate x-tick positions — h_xticks">
+<meta name="description" content="
 Calculate the positions of ticks on the x-axis. However, if xticks already
 exists it is kept as is. It is based on the same function ggplot2 relies on,
-and is required in the graphic and the patient-at-risk annotation table."><meta property="og:description" content="
+and is required in the graphic and the patient-at-risk annotation table.">
+<meta property="og:description" content="
 Calculate the positions of ticks on the x-axis. However, if xticks already
 exists it is kept as is. It is based on the same function ggplot2 relies on,
-and is required in the graphic and the patient-at-risk annotation table."><meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png"><link rel="stylesheet" href="../consent.css"><script src="../consent.js" type="text/javascript" charset="utf-8"></script></head><body>
+and is required in the graphic and the patient-at-risk annotation table.">
+<meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png">
+<link rel="stylesheet" href="../consent.css">
+<script src="../consent.js" type="text/javascript" charset="utf-8"></script>
+</head>
+<body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
 
 
@@ -21,26 +44,66 @@
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-      <ul class="navbar-nav me-auto"><li class="nav-item"><a class="nav-link" href="../articles/tern.html">Get started</a></li>
+      <ul class="navbar-nav me-auto">
+<li class="nav-item"><a class="nav-link" href="../articles/tern.html">Get started</a></li>
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   <button class="nav-link dropdown-toggle" type="button" id="dropdown-articles" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Articles</button>
-  <ul class="dropdown-menu" aria-labelledby="dropdown-articles"><li><a class="dropdown-item" href="../articles/missing_values.html">Missing Values in Tern</a></li>
+  <ul class="dropdown-menu" aria-labelledby="dropdown-articles">
+<li><a class="dropdown-item" href="../articles/missing_values.html">Missing Values in Tern</a></li>
     <li><a class="dropdown-item" href="../articles/tables.html">Tabulation</a></li>
     <li><a class="dropdown-item" href="../articles/tern_formats.html">Formatting Functions</a></li>
     <li><a class="dropdown-item" href="../articles/tern_functions_guide.html">Understanding `tern` functions</a></li>
-  </ul></li>
+  </ul>
+</li>
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- <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json"></form></li>
+  </ul>
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+    <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/main">main</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.5">v0.9.5</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.4">v0.9.4</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.3">v0.9.3</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1-rc3">v0.9.1-rc3</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a>
+</div>
+</li></div>
+</ul>
+<ul class="navbar-nav">
+<li class="nav-item"><form class="form-inline" role="search">
+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json">
+</form></li>
 <li class="nav-item"><a class="external-link nav-link" href="https://github.com/insightsengineering/tern" aria-label="GitHub"><span class="fa fa-github"></span></a></li>
-      </ul></div>
+      </ul>
+</div>
 
 
   </div>
@@ -60,36 +123,45 @@
     </div>
 
     <div class="section level2">
-    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
+    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">h_xticks</span><span class="op">(</span><span class="va">data</span>, xticks <span class="op">=</span> <span class="cn">NULL</span>, max_time <span class="op">=</span> <span class="cn">NULL</span><span class="op">)</span></span></code></pre></div>
     </div>
 
     <div class="section level2">
-    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
+    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a>
+</h2>
 
 
-<dl><dt id="arg-data">data<a class="anchor" aria-label="anchor" href="#arg-data"></a></dt>
+<dl>
+<dt id="arg-data">data<a class="anchor" aria-label="anchor" href="#arg-data"></a>
+</dt>
 <dd><p>(<code>data.frame</code>)<br> survival data as pre-processed by <code>h_data_plot</code>.</p></dd>
 
 
-<dt id="arg-xticks">xticks<a class="anchor" aria-label="anchor" href="#arg-xticks"></a></dt>
+<dt id="arg-xticks">xticks<a class="anchor" aria-label="anchor" href="#arg-xticks"></a>
+</dt>
 <dd><p>(<code>numeric</code> or <code>NULL</code>)<br> numeric vector of tick positions or a single number with spacing
 between ticks on the x-axis. If <code>NULL</code> (default), <code><a href="https://rdrr.io/pkg/labeling/man/extended.html" class="external-link">labeling::extended()</a></code> is used to determine
 optimal tick positions on the x-axis.</p></dd>
 
 
-<dt id="arg-max-time">max_time<a class="anchor" aria-label="anchor" href="#arg-max-time"></a></dt>
+<dt id="arg-max-time">max_time<a class="anchor" aria-label="anchor" href="#arg-max-time"></a>
+</dt>
 <dd><p>(<code>numeric(1)</code>)<br> maximum value to show on x-axis. Only data values less than or up to
 this threshold value will be plotted (defaults to <code>NULL</code>).</p></dd>
 
-</dl></div>
+</dl>
+</div>
     <div class="section level2">
-    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
+    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a>
+</h2>
     <p>A vector of positions to use for x-axis ticks on a <code>ggplot</code> object.</p>
     </div>
 
     <div class="section level2">
-    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
+    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://dplyr.tidyverse.org" class="external-link">dplyr</a></span><span class="op">)</span></span></span>
 <span class="r-in"><span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://github.com/therneau/survival" class="external-link">survival</a></span><span class="op">)</span></span></span>
 <span class="r-in"><span></span></span>
@@ -114,17 +186,19 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 </code></pre></div>
     </div>
   </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
-    </nav></aside></div>
+    </nav></aside>
+</div>
 
 
     <footer><div class="nest">
   <p>tern is a part of the <strong>NEST</strong> and <a href="https://pharmaverse.org/" class="external-link"><strong>pharmaverse</strong></a>.</p>
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-<script type="text/javascript" src="../analytics.js"></script></footer></div>
-
+<script type="text/javascript" src="../analytics.js"></script></footer>
+</div>
 
 
 
 
-  </body></html>
 
+  </body>
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diff --git a/main/reference/imputation_rule.html b/main/reference/imputation_rule.html
index 504e5c2a95..327c2f0f08 100644
--- a/main/reference/imputation_rule.html
+++ b/main/reference/imputation_rule.html
@@ -1,5 +1,28 @@
-<!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Apply 1/3 or 1/2 imputation rule to data — imputation_rule • tern</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Apply 1/3 or 1/2 imputation rule to data — imputation_rule"><meta name="description" content=""><meta property="og:description" content=""><meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png"><link rel="stylesheet" href="../consent.css"><script src="../consent.js" type="text/javascript" charset="utf-8"></script></head><body>
+<html lang="en">
+<head>
+<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+<meta charset="utf-8">
+<meta http-equiv="X-UA-Compatible" content="IE=edge">
+<meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<title>Apply 1/3 or 1/2 imputation rule to data — imputation_rule • tern</title>
+<!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png">
+<link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png">
+<link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png">
+<link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png">
+<link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png">
+<link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png">
+<script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet">
+<script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet">
+<link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet">
+<script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Apply 1/3 or 1/2 imputation rule to data — imputation_rule">
+<meta name="description" content="">
+<meta property="og:description" content="">
+<meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png">
+<link rel="stylesheet" href="../consent.css">
+<script src="../consent.js" type="text/javascript" charset="utf-8"></script>
+</head>
+<body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
 
 
@@ -15,26 +38,66 @@
     </button>
 
     <div id="navbar" class="collapse navbar-collapse ms-3">
-      <ul class="navbar-nav me-auto"><li class="nav-item"><a class="nav-link" href="../articles/tern.html">Get started</a></li>
+      <ul class="navbar-nav me-auto">
+<li class="nav-item"><a class="nav-link" href="../articles/tern.html">Get started</a></li>
 <li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
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   <button class="nav-link dropdown-toggle" type="button" id="dropdown-articles" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Articles</button>
-  <ul class="dropdown-menu" aria-labelledby="dropdown-articles"><li><a class="dropdown-item" href="../articles/missing_values.html">Missing Values in Tern</a></li>
+  <ul class="dropdown-menu" aria-labelledby="dropdown-articles">
+<li><a class="dropdown-item" href="../articles/missing_values.html">Missing Values in Tern</a></li>
     <li><a class="dropdown-item" href="../articles/tables.html">Tabulation</a></li>
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     <li><a class="dropdown-item" href="../articles/tern_functions_guide.html">Understanding `tern` functions</a></li>
-  </ul></li>
+  </ul>
+</li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
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+  <ul class="dropdown-menu" aria-labelledby="dropdown-reports">
+<li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
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- <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json"></form></li>
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+    <div class="dropdown-menu" aria-labelledby="dropdown-versions">
+    <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/main">main</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
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+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1-rc3">v0.9.1-rc3</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a>
+</div>
+</li></div>
+</ul>
+<ul class="navbar-nav">
+<li class="nav-item"><form class="form-inline" role="search">
+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json">
+</form></li>
 <li class="nav-item"><a class="external-link nav-link" href="https://github.com/insightsengineering/tern" aria-label="GitHub"><span class="fa fa-github"></span></a></li>
-      </ul></div>
+      </ul>
+</div>
 
 
   </div>
@@ -51,7 +114,8 @@
     </div>
 
     <div class="section level2">
-    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
+    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">imputation_rule</span><span class="op">(</span></span>
 <span>  <span class="va">df</span>,</span>
 <span>  <span class="va">x_stats</span>,</span>
@@ -63,51 +127,63 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
     </div>
 
     <div class="section level2">
-    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
+    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a>
+</h2>
 
 
-<dl><dt id="arg-df">df<a class="anchor" aria-label="anchor" href="#arg-df"></a></dt>
+<dl>
+<dt id="arg-df">df<a class="anchor" aria-label="anchor" href="#arg-df"></a>
+</dt>
 <dd><p>(<code>data.frame</code>)<br> data set containing all analysis variables.</p></dd>
 
 
-<dt id="arg-x-stats">x_stats<a class="anchor" aria-label="anchor" href="#arg-x-stats"></a></dt>
+<dt id="arg-x-stats">x_stats<a class="anchor" aria-label="anchor" href="#arg-x-stats"></a>
+</dt>
 <dd><p>(named <code>list</code>)<br> a named list of statistics, typically the results of <code><a href="analyze_variables.html">s_summary()</a></code>.</p></dd>
 
 
-<dt id="arg-stat">stat<a class="anchor" aria-label="anchor" href="#arg-stat"></a></dt>
+<dt id="arg-stat">stat<a class="anchor" aria-label="anchor" href="#arg-stat"></a>
+</dt>
 <dd><p>(<code>string</code>)<br> statistic to return the value/NA level of according to the imputation
 rule applied.</p></dd>
 
 
-<dt id="arg-imp-rule">imp_rule<a class="anchor" aria-label="anchor" href="#arg-imp-rule"></a></dt>
+<dt id="arg-imp-rule">imp_rule<a class="anchor" aria-label="anchor" href="#arg-imp-rule"></a>
+</dt>
 <dd><p>(<code>string</code>)<br> imputation rule setting. Set to <code>"1/3"</code> to implement 1/3 imputation
 rule or <code>"1/2"</code> to implement 1/2 imputation rule.</p></dd>
 
 
-<dt id="arg-post">post<a class="anchor" aria-label="anchor" href="#arg-post"></a></dt>
+<dt id="arg-post">post<a class="anchor" aria-label="anchor" href="#arg-post"></a>
+</dt>
 <dd><p>(<code>flag</code>)<br> whether the data corresponds to a post-dose time-point (defaults to <code>FALSE</code>).
 This parameter is only used when <code>imp_rule</code> is set to <code>"1/3"</code>.</p></dd>
 
 
-<dt id="arg-avalcat-var">avalcat_var<a class="anchor" aria-label="anchor" href="#arg-avalcat-var"></a></dt>
+<dt id="arg-avalcat-var">avalcat_var<a class="anchor" aria-label="anchor" href="#arg-avalcat-var"></a>
+</dt>
 <dd><p>(<code>string</code>)<br> name of variable that indicates whether a row in <code>df</code> corresponds
 to an analysis value in category <code>"BLQ"</code>, <code>"LTR"</code>, <code>"&lt;PCLLOQ"</code>, or none of the above
 (defaults to <code>"AVALCAT1"</code>). Variable <code>avalcat_var</code> must be present in <code>df</code>.</p></dd>
 
-</dl></div>
+</dl>
+</div>
     <div class="section level2">
-    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
+    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a>
+</h2>
     <p>A <code>list</code> containing statistic value (<code>val</code>) and NA level (<code>na_str</code>) that should be displayed
 according to the specified imputation rule.</p>
     </div>
     <div class="section level2">
-    <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"></a></h2>
+    <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"></a>
+</h2>
     <div class="dont-index"><p><code><a href="analyze_vars_in_cols.html">analyze_vars_in_cols()</a></code> where this function can be implemented by setting the <code>imp_rule</code>
 argument.</p></div>
     </div>
 
     <div class="section level2">
-    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
+    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/Random.html" class="external-link">set.seed</a></span><span class="op">(</span><span class="fl">1</span><span class="op">)</span></span></span>
 <span class="r-in"><span><span class="va">df</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a></span><span class="op">(</span></span></span>
 <span class="r-in"><span>  AVAL <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/stats/Uniform.html" class="external-link">runif</a></span><span class="op">(</span><span class="fl">50</span>, <span class="fl">0</span>, <span class="fl">1</span><span class="op">)</span>,</span></span>
@@ -140,17 +216,19 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 </code></pre></div>
     </div>
   </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
-    </nav></aside></div>
+    </nav></aside>
+</div>
 
 
     <footer><div class="nest">
   <p>tern is a part of the <strong>NEST</strong> and <a href="https://pharmaverse.org/" class="external-link"><strong>pharmaverse</strong></a>.</p>
 </div>
-<script type="text/javascript" src="../analytics.js"></script></footer></div>
-
+<script type="text/javascript" src="../analytics.js"></script></footer>
+</div>
 
 
 
 
-  </body></html>
 
+  </body>
+</html>
diff --git a/main/reference/incidence_rate.html b/main/reference/incidence_rate.html
index d19ca29888..6559912451 100644
--- a/main/reference/incidence_rate.html
+++ b/main/reference/incidence_rate.html
@@ -1,13 +1,36 @@
-<!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Incidence rate estimation — incidence_rate • tern</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Incidence rate estimation — incidence_rate"><meta name="description" content="
+<html lang="en">
+<head>
+<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+<meta charset="utf-8">
+<meta http-equiv="X-UA-Compatible" content="IE=edge">
+<meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<title>Incidence rate estimation — incidence_rate • tern</title>
+<!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png">
+<link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png">
+<link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png">
+<link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png">
+<link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png">
+<link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png">
+<script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet">
+<script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet">
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+<script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Incidence rate estimation — incidence_rate">
+<meta name="description" content="
 The analyze function estimate_incidence_rate() creates a layout element to estimate an event rate adjusted for
 person-years at risk, otherwise known as incidence rate. The primary analysis variable specified via vars is
 the person-years at risk. In addition to this variable, the n_events variable for number of events observed (where
-a value of 1 means an event was observed and 0 means that no event was observed) must also be specified."><meta property="og:description" content="
+a value of 1 means an event was observed and 0 means that no event was observed) must also be specified.">
+<meta property="og:description" content="
 The analyze function estimate_incidence_rate() creates a layout element to estimate an event rate adjusted for
 person-years at risk, otherwise known as incidence rate. The primary analysis variable specified via vars is
 the person-years at risk. In addition to this variable, the n_events variable for number of events observed (where
-a value of 1 means an event was observed and 0 means that no event was observed) must also be specified."><meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png"><link rel="stylesheet" href="../consent.css"><script src="../consent.js" type="text/javascript" charset="utf-8"></script></head><body>
+a value of 1 means an event was observed and 0 means that no event was observed) must also be specified.">
+<meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png">
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     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
 
 
@@ -23,26 +46,66 @@
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+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json">
+</form></li>
 <li class="nav-item"><a class="external-link nav-link" href="https://github.com/insightsengineering/tern" aria-label="GitHub"><span class="fa fa-github"></span></a></li>
-      </ul></div>
+      </ul>
+</div>
 
 
   </div>
@@ -63,7 +126,8 @@
     </div>
 
     <div class="section level2">
-    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
+    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">estimate_incidence_rate</span><span class="op">(</span></span>
 <span>  <span class="va">lyt</span>,</span>
 <span>  <span class="va">vars</span>,</span>
@@ -111,144 +175,190 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
     </div>
 
     <div class="section level2">
-    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
+    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a>
+</h2>
 
 
-<dl><dt id="arg-lyt">lyt<a class="anchor" aria-label="anchor" href="#arg-lyt"></a></dt>
+<dl>
+<dt id="arg-lyt">lyt<a class="anchor" aria-label="anchor" href="#arg-lyt"></a>
+</dt>
 <dd><p>(<code>PreDataTableLayouts</code>)<br> layout that analyses will be added to.</p></dd>
 
 
-<dt id="arg-vars">vars<a class="anchor" aria-label="anchor" href="#arg-vars"></a></dt>
+<dt id="arg-vars">vars<a class="anchor" aria-label="anchor" href="#arg-vars"></a>
+</dt>
 <dd><p>(<code>character</code>)<br> variable names for the primary analysis variable to be iterated over.</p></dd>
 
 
-<dt id="arg-n-events">n_events<a class="anchor" aria-label="anchor" href="#arg-n-events"></a></dt>
+<dt id="arg-n-events">n_events<a class="anchor" aria-label="anchor" href="#arg-n-events"></a>
+</dt>
 <dd><p>(<code>string</code>)<br> name of integer variable indicating whether an event has been observed (1) or not (0).</p></dd>
 
 
-<dt id="arg-id-var">id_var<a class="anchor" aria-label="anchor" href="#arg-id-var"></a></dt>
+<dt id="arg-id-var">id_var<a class="anchor" aria-label="anchor" href="#arg-id-var"></a>
+</dt>
 <dd><p>(<code>string</code>)<br> name of variable used as patient identifier if <code>"n_unique"</code> is included in <code>.stats</code>.
 Defaults to <code>"USUBJID"</code>.</p></dd>
 
 
-<dt id="arg-control">control<a class="anchor" aria-label="anchor" href="#arg-control"></a></dt>
-<dd><p>(<code>list</code>)<br> parameters for estimation details, specified by using
-the helper function <code><a href="control_incidence_rate.html">control_incidence_rate()</a></code>. Possible parameter options are:</p><ul><li><p><code>conf_level</code> (<code>proportion</code>)<br> confidence level for the estimated incidence rate.</p></li>
+<dt id="arg-control">control<a class="anchor" aria-label="anchor" href="#arg-control"></a>
+</dt>
+<dd>
+<p>(<code>list</code>)<br> parameters for estimation details, specified by using
+the helper function <code><a href="control_incidence_rate.html">control_incidence_rate()</a></code>. Possible parameter options are:</p>
+<ul>
+<li><p><code>conf_level</code> (<code>proportion</code>)<br> confidence level for the estimated incidence rate.</p></li>
 <li><p><code>conf_type</code> (<code>string</code>)<br><code>normal</code> (default), <code>normal_log</code>, <code>exact</code>, or <code>byar</code>
 for confidence interval type.</p></li>
 <li><p><code>input_time_unit</code> (<code>string</code>)<br><code>day</code>, <code>week</code>, <code>month</code>, or <code>year</code> (default)
 indicating time unit for data input.</p></li>
 <li><p><code>num_pt_year</code> (<code>numeric</code>)<br> time unit for desired output (in person-years).</p></li>
-</ul></dd>
+</ul>
+</dd>
 
 
-<dt id="arg-na-str">na_str<a class="anchor" aria-label="anchor" href="#arg-na-str"></a></dt>
+<dt id="arg-na-str">na_str<a class="anchor" aria-label="anchor" href="#arg-na-str"></a>
+</dt>
 <dd><p>(<code>string</code>)<br> string used to replace all <code>NA</code> or empty values in the output.</p></dd>
 
 
-<dt id="arg-nested">nested<a class="anchor" aria-label="anchor" href="#arg-nested"></a></dt>
+<dt id="arg-nested">nested<a class="anchor" aria-label="anchor" href="#arg-nested"></a>
+</dt>
 <dd><p>(<code>flag</code>)<br> whether this layout instruction should be applied within the existing layout structure _if
 possible (<code>TRUE</code>, the default) or as a new top-level element (<code>FALSE</code>). Ignored if it would nest a split.
 underneath analyses, which is not allowed.</p></dd>
 
 
-<dt id="arg-summarize">summarize<a class="anchor" aria-label="anchor" href="#arg-summarize"></a></dt>
+<dt id="arg-summarize">summarize<a class="anchor" aria-label="anchor" href="#arg-summarize"></a>
+</dt>
 <dd><p>(<code>flag</code>)<br> whether the function should act as an analyze function (<code>summarize = FALSE</code>), or a
 summarize function (<code>summarize = TRUE</code>). Defaults to <code>FALSE</code>.</p></dd>
 
 
-<dt id="arg-label-fmt">label_fmt<a class="anchor" aria-label="anchor" href="#arg-label-fmt"></a></dt>
+<dt id="arg-label-fmt">label_fmt<a class="anchor" aria-label="anchor" href="#arg-label-fmt"></a>
+</dt>
 <dd><p>(<code>string</code>)<br> how labels should be formatted after a row split occurs if <code>summarize = TRUE</code>. The
 string should use <code>"%s"</code> to represent row split levels, and <code>"%.labels"</code> to represent labels supplied to the
 <code>.labels</code> argument. Defaults to <code>"%s - %.labels"</code>.</p></dd>
 
 
-<dt id="arg--">...<a class="anchor" aria-label="anchor" href="#arg--"></a></dt>
+<dt id="arg--">...<a class="anchor" aria-label="anchor" href="#arg--"></a>
+</dt>
 <dd><p>additional arguments for the lower level functions.</p></dd>
 
 
-<dt id="arg-show-labels">show_labels<a class="anchor" aria-label="anchor" href="#arg-show-labels"></a></dt>
+<dt id="arg-show-labels">show_labels<a class="anchor" aria-label="anchor" href="#arg-show-labels"></a>
+</dt>
 <dd><p>(<code>string</code>)<br> label visibility: one of "default", "visible" and "hidden".</p></dd>
 
 
-<dt id="arg-table-names">table_names<a class="anchor" aria-label="anchor" href="#arg-table-names"></a></dt>
+<dt id="arg-table-names">table_names<a class="anchor" aria-label="anchor" href="#arg-table-names"></a>
+</dt>
 <dd><p>(<code>character</code>)<br> this can be customized in the case that the same <code>vars</code> are analyzed multiple
 times, to avoid warnings from <code>rtables</code>.</p></dd>
 
 
-<dt id="arg--stats">.stats<a class="anchor" aria-label="anchor" href="#arg--stats"></a></dt>
-<dd><p>(<code>character</code>)<br> statistics to select for the table.</p>
-<p>Options are: <code>'person_years', 'n_events', 'rate', 'rate_ci', 'n_unique', 'n_rate'</code></p></dd>
+<dt id="arg--stats">.stats<a class="anchor" aria-label="anchor" href="#arg--stats"></a>
+</dt>
+<dd>
+<p>(<code>character</code>)<br> statistics to select for the table.</p>
+<p>Options are: <code>'person_years', 'n_events', 'rate', 'rate_ci', 'n_unique', 'n_rate'</code></p>
+</dd>
 
 
-<dt id="arg--formats">.formats<a class="anchor" aria-label="anchor" href="#arg--formats"></a></dt>
+<dt id="arg--formats">.formats<a class="anchor" aria-label="anchor" href="#arg--formats"></a>
+</dt>
 <dd><p>(named <code>character</code> or <code>list</code>)<br> formats for the statistics. See Details in <code>analyze_vars</code> for more
 information on the <code>"auto"</code> setting.</p></dd>
 
 
-<dt id="arg--labels">.labels<a class="anchor" aria-label="anchor" href="#arg--labels"></a></dt>
+<dt id="arg--labels">.labels<a class="anchor" aria-label="anchor" href="#arg--labels"></a>
+</dt>
 <dd><p>(named <code>character</code>)<br> labels for the statistics (without indent).</p></dd>
 
 
-<dt id="arg--indent-mods">.indent_mods<a class="anchor" aria-label="anchor" href="#arg--indent-mods"></a></dt>
+<dt id="arg--indent-mods">.indent_mods<a class="anchor" aria-label="anchor" href="#arg--indent-mods"></a>
+</dt>
 <dd><p>(named <code>integer</code>)<br> indent modifiers for the labels. Defaults to 0, which corresponds to the
 unmodified default behavior. Can be negative.</p></dd>
 
 
-<dt id="arg-df">df<a class="anchor" aria-label="anchor" href="#arg-df"></a></dt>
+<dt id="arg-df">df<a class="anchor" aria-label="anchor" href="#arg-df"></a>
+</dt>
 <dd><p>(<code>data.frame</code>)<br> data set containing all analysis variables.</p></dd>
 
 
-<dt id="arg--var">.var<a class="anchor" aria-label="anchor" href="#arg--var"></a></dt>
+<dt id="arg--var">.var<a class="anchor" aria-label="anchor" href="#arg--var"></a>
+</dt>
 <dd><p>(<code>string</code>)<br> single variable name that is passed by <code>rtables</code> when requested
 by a statistics function.</p></dd>
 
 
-<dt id="arg-is-event">is_event<a class="anchor" aria-label="anchor" href="#arg-is-event"></a></dt>
+<dt id="arg-is-event">is_event<a class="anchor" aria-label="anchor" href="#arg-is-event"></a>
+</dt>
 <dd><p>(<code>flag</code>)<br><code>TRUE</code> if event, <code>FALSE</code> if time to event is censored.</p></dd>
 
 
-<dt id="arg-labelstr">labelstr<a class="anchor" aria-label="anchor" href="#arg-labelstr"></a></dt>
+<dt id="arg-labelstr">labelstr<a class="anchor" aria-label="anchor" href="#arg-labelstr"></a>
+</dt>
 <dd><p>(<code>string</code>)<br> label of the level of the parent split currently being summarized
 (must be present as second argument in Content Row Functions). See <code><a href="https://insightsengineering.github.io/rtables/latest-tag/reference/summarize_row_groups.html" class="external-link">rtables::summarize_row_groups()</a></code>
 for more information.</p></dd>
 
 
-<dt id="arg--df-row">.df_row<a class="anchor" aria-label="anchor" href="#arg--df-row"></a></dt>
+<dt id="arg--df-row">.df_row<a class="anchor" aria-label="anchor" href="#arg--df-row"></a>
+</dt>
 <dd><p>(<code>data.frame</code>)<br> data frame across all of the columns for the given row split.</p></dd>
 
-</dl></div>
+</dl>
+</div>
     <div class="section level2">
-    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
+    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a>
+</h2>
 
-<ul><li><p><code>estimate_incidence_rate()</code> returns a layout object suitable for passing to further layouting functions,
+<ul>
+<li><p><code>estimate_incidence_rate()</code> returns a layout object suitable for passing to further layouting functions,
 or to <code><a href="https://insightsengineering.github.io/rtables/latest-tag/reference/build_table.html" class="external-link">rtables::build_table()</a></code>. Adding this function to an <code>rtable</code> layout will add formatted rows containing
 the statistics from <code>s_incidence_rate()</code> to the table layout.</p></li>
-</ul><ul><li><p><code>s_incidence_rate()</code> returns the following statistics:</p><ul><li><p><code>person_years</code>: Total person-years at risk.</p></li>
+</ul>
+<ul>
+<li>
+<p><code>s_incidence_rate()</code> returns the following statistics:</p>
+<ul>
+<li><p><code>person_years</code>: Total person-years at risk.</p></li>
 <li><p><code>n_events</code>: Total number of events observed.</p></li>
 <li><p><code>rate</code>: Estimated incidence rate.</p></li>
 <li><p><code>rate_ci</code>: Confidence interval for the incidence rate.</p></li>
 <li><p><code>n_unique</code>: Total number of patients with at least one event observed.</p></li>
 <li><p><code>n_rate</code>: Total number of events observed &amp; estimated incidence rate.</p></li>
-</ul></li>
-</ul><ul><li><p><code>a_incidence_rate()</code> returns the corresponding list with formatted <code><a href="https://insightsengineering.github.io/rtables/latest-tag/reference/CellValue.html" class="external-link">rtables::CellValue()</a></code>.</p></li>
-</ul></div>
+</ul>
+</li>
+</ul>
+<ul>
+<li><p><code>a_incidence_rate()</code> returns the corresponding list with formatted <code><a href="https://insightsengineering.github.io/rtables/latest-tag/reference/CellValue.html" class="external-link">rtables::CellValue()</a></code>.</p></li>
+</ul>
+</div>
     <div class="section level2">
-    <h2 id="functions">Functions<a class="anchor" aria-label="anchor" href="#functions"></a></h2>
+    <h2 id="functions">Functions<a class="anchor" aria-label="anchor" href="#functions"></a>
+</h2>
 
-<ul><li><p><code>estimate_incidence_rate()</code>: Layout-creating function which can take statistics function arguments
+<ul>
+<li><p><code>estimate_incidence_rate()</code>: Layout-creating function which can take statistics function arguments
 and additional format arguments. This function is a wrapper for <code><a href="https://insightsengineering.github.io/rtables/latest-tag/reference/analyze.html" class="external-link">rtables::analyze()</a></code>.</p></li>
 <li><p><code>s_incidence_rate()</code>: Statistics function which estimates the incidence rate and the
 associated confidence interval.</p></li>
 <li><p><code>a_incidence_rate()</code>: Formatted analysis function which is used as <code>afun</code> in <code>estimate_incidence_rate()</code>.</p></li>
-</ul></div>
+</ul>
+</div>
     <div class="section level2">
-    <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"></a></h2>
+    <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"></a>
+</h2>
     <div class="dont-index"><p><code><a href="control_incidence_rate.html">control_incidence_rate()</a></code> and helper functions <a href="h_incidence_rate.html">h_incidence_rate</a>.</p></div>
     </div>
 
     <div class="section level2">
-    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
+    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">df</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a></span><span class="op">(</span></span></span>
 <span class="r-in"><span>  USUBJID <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/character.html" class="external-link">as.character</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/seq.html" class="external-link">seq</a></span><span class="op">(</span><span class="fl">6</span><span class="op">)</span><span class="op">)</span>,</span></span>
 <span class="r-in"><span>  CNSR <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">0</span>, <span class="fl">1</span>, <span class="fl">1</span>, <span class="fl">0</span>, <span class="fl">0</span>, <span class="fl">0</span><span class="op">)</span>,</span></span>
@@ -325,17 +435,19 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 </code></pre></div>
     </div>
   </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
-    </nav></aside></div>
+    </nav></aside>
+</div>
 
 
     <footer><div class="nest">
   <p>tern is a part of the <strong>NEST</strong> and <a href="https://pharmaverse.org/" class="external-link"><strong>pharmaverse</strong></a>.</p>
 </div>
-<script type="text/javascript" src="../analytics.js"></script></footer></div>
-
+<script type="text/javascript" src="../analytics.js"></script></footer>
+</div>
 
 
 
 
-  </body></html>
 
+  </body>
+</html>
diff --git a/main/reference/index.html b/main/reference/index.html
index 2fac5e618a..a29d60d0a5 100644
--- a/main/reference/index.html
+++ b/main/reference/index.html
@@ -1,5 +1,26 @@
-<!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Package index • tern</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Package index"><meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png"><link rel="stylesheet" href="../consent.css"><script src="../consent.js" type="text/javascript" charset="utf-8"></script></head><body>
+<html lang="en">
+<head>
+<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+<meta charset="utf-8">
+<meta http-equiv="X-UA-Compatible" content="IE=edge">
+<meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<title>Package index • tern</title>
+<!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png">
+<link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png">
+<link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png">
+<link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png">
+<link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png">
+<link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png">
+<script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet">
+<script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet">
+<link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet">
+<script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Package index">
+<meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png">
+<link rel="stylesheet" href="../consent.css">
+<script src="../consent.js" type="text/javascript" charset="utf-8"></script>
+</head>
+<body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
 
 
@@ -15,26 +36,66 @@
     </button>
 
     <div id="navbar" class="collapse navbar-collapse ms-3">
-      <ul class="navbar-nav me-auto"><li class="nav-item"><a class="nav-link" href="../articles/tern.html">Get started</a></li>
+      <ul class="navbar-nav me-auto">
+<li class="nav-item"><a class="nav-link" href="../articles/tern.html">Get started</a></li>
 <li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
 <li class="nav-item dropdown">
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-articles" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Articles</button>
-  <ul class="dropdown-menu" aria-labelledby="dropdown-articles"><li><a class="dropdown-item" href="../articles/missing_values.html">Missing Values in Tern</a></li>
+  <ul class="dropdown-menu" aria-labelledby="dropdown-articles">
+<li><a class="dropdown-item" href="../articles/missing_values.html">Missing Values in Tern</a></li>
     <li><a class="dropdown-item" href="../articles/tables.html">Tabulation</a></li>
     <li><a class="dropdown-item" href="../articles/tern_formats.html">Formatting Functions</a></li>
     <li><a class="dropdown-item" href="../articles/tern_functions_guide.html">Understanding `tern` functions</a></li>
-  </ul></li>
+  </ul>
+</li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
-  <ul class="dropdown-menu" aria-labelledby="dropdown-reports"><li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
+  <ul class="dropdown-menu" aria-labelledby="dropdown-reports">
+<li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
     <li><a class="dropdown-item" href="../unit-test-report/">Unit test report</a></li>
     <li><a class="dropdown-item" href="../unit-test-report-non-cran/">Non-CRAN unit test report</a></li>
-  </ul></li>
-      </ul><ul class="navbar-nav"><li class="nav-item"><form class="form-inline" role="search">
- <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json"></form></li>
+  </ul>
+</li>
+      <div><li class="nav-item dropdown">
+    <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-versions">Versions</a>
+    <div class="dropdown-menu" aria-labelledby="dropdown-versions">
+    <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/main">main</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.5">v0.9.5</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.4">v0.9.4</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.3">v0.9.3</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1-rc3">v0.9.1-rc3</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a>
+</div>
+</li></div>
+</ul>
+<ul class="navbar-nav">
+<li class="nav-item"><form class="form-inline" role="search">
+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json">
+</form></li>
 <li class="nav-item"><a class="external-link nav-link" href="https://github.com/insightsengineering/tern" aria-label="GitHub"><span class="fa fa-github"></span></a></li>
-      </ul></div>
+      </ul>
+</div>
 
 
   </div>
@@ -45,1350 +106,1806 @@
     </div>
 
     <div class="section level2">
-      <h2 id="overview-pages">Overview Pages<a class="anchor" aria-label="anchor" href="#overview-pages"></a></h2>
+      <h2 id="overview-pages">Overview Pages<a class="anchor" aria-label="anchor" href="#overview-pages"></a>
+</h2>
 
 
 
 
-    </div><div class="section level2">
+    </div>
+<div class="section level2">
 
 
 
 
-      <dl><dt>
+      <dl>
+<dt>
 
           <code><a href="tern-package.html">tern</a></code> <code><a href="tern-package.html">tern-package</a></code>
 
         </dt>
         <dd>tern Package</dd>
-      </dl><dl><dt>
+      </dl>
+<dl>
+<dt>
 
           <code><a href="analyze_functions.html">analyze_functions</a></code>
 
         </dt>
         <dd>Analyze functions</dd>
-      </dl><dl><dt>
+      </dl>
+<dl>
+<dt>
 
           <code><a href="analyze_colvars_functions.html">analyze_colvars_functions</a></code>
 
         </dt>
         <dd>Analyze functions in columns</dd>
-      </dl><dl><dt>
+      </dl>
+<dl>
+<dt>
 
           <code><a href="summarize_functions.html">summarize_functions</a></code>
 
         </dt>
         <dd>Summarize functions</dd>
-      </dl><dl><dt>
+      </dl>
+<dl>
+<dt>
 
           <code><a href="formatting_functions.html">formatting_functions</a></code>
 
         </dt>
         <dd>Formatting functions</dd>
-      </dl></div><div class="section level2">
-      <h2 id="analysis-functions">Analysis Functions<a class="anchor" aria-label="anchor" href="#analysis-functions"></a></h2>
-
-      <div class="section-desc"><p>Analyze functions with their corresponding statistics functions and formatted analysis functions.</p><ul><li><p><strong>Analyze functions</strong> are used in combination with <code>rtables</code> layout functions in the pipeline which creates the table.</p></li>
+      </dl>
+</div>
+<div class="section level2">
+      <h2 id="analysis-functions">Analysis Functions<a class="anchor" aria-label="anchor" href="#analysis-functions"></a>
+</h2>
+
+      <div class="section-desc">
+<p>Analyze functions with their corresponding statistics functions and formatted analysis functions.</p>
+<ul>
+<li><p><strong>Analyze functions</strong> are used in combination with <code>rtables</code> layout functions in the pipeline which creates the table.</p></li>
 <li><p><strong>Statistics functions</strong> (denoted by <code>s_</code> prefix) compute the numbers that are tabulated later. In order to separate computation from formatting, they do not take care of <code>rcell</code> type formatting themselves.</p></li>
 <li><p><strong>Formatted analysis functions</strong> (denoted by <code>a_</code> prefix) have the same arguments as the corresponding statistics functions, and can be further customized by calling <code><a href="https://insightsengineering.github.io/rtables/latest-tag/reference/make_afun.html" class="external-link">rtables::make_afun()</a></code> on them. They are used as <code>afun</code> in <code><a href="https://insightsengineering.github.io/rtables/latest-tag/reference/analyze.html" class="external-link">rtables::analyze()</a></code>.</p></li>
-</ul></div>
+</ul>
+</div>
 
 
-    </div><div class="section level2">
+    </div>
+<div class="section level2">
 
 
 
 
-      <dl><dt>
+      <dl>
+<dt>
 
           <code><a href="analyze_variables.html">analyze_vars()</a></code> <code><a href="analyze_variables.html">s_summary()</a></code> <code><a href="analyze_variables.html">a_summary()</a></code>
           <span class="badge lifecycle lifecycle-stable">stable</span>
         </dt>
         <dd>Analyze variables</dd>
-      </dl><dl><dt>
+      </dl>
+<dl>
+<dt>
 
           <code><a href="analyze_vars_in_cols.html">analyze_vars_in_cols()</a></code>
           <span class="badge lifecycle lifecycle-experimental">experimental</span>
         </dt>
         <dd>Analyze numeric variables in columns</dd>
-      </dl><dl><dt>
+      </dl>
+<dl>
+<dt>
 
           <code><a href="summarize_num_patients.html">analyze_num_patients()</a></code> <code><a href="summarize_num_patients.html">summarize_num_patients()</a></code> <code><a href="summarize_num_patients.html">s_num_patients()</a></code> <code><a href="summarize_num_patients.html">s_num_patients_content()</a></code>
           <span class="badge lifecycle lifecycle-stable">stable</span>
         </dt>
         <dd>Count number of patients</dd>
-      </dl><dl><dt>
+      </dl>
+<dl>
+<dt>
 
           <code><a href="summarize_patients_exposure_in_cols.html">analyze_patients_exposure_in_cols()</a></code> <code><a href="summarize_patients_exposure_in_cols.html">summarize_patients_exposure_in_cols()</a></code> <code><a href="summarize_patients_exposure_in_cols.html">s_count_patients_sum_exposure()</a></code> <code><a href="summarize_patients_exposure_in_cols.html">a_count_patients_sum_exposure()</a></code>
           <span class="badge lifecycle lifecycle-stable">stable</span>
         </dt>
         <dd>Count number of patients and sum exposure across all patients in columns</dd>
-      </dl><dl><dt>
+      </dl>
+<dl>
+<dt>
 
           <code><a href="compare_variables.html">compare_vars()</a></code> <code><a href="compare_variables.html">s_compare()</a></code>
           <span class="badge lifecycle lifecycle-stable">stable</span>
         </dt>
         <dd>Compare variables between groups</dd>
-      </dl><dl><dt>
+      </dl>
+<dl>
+<dt>
 
           <code><a href="abnormal.html">count_abnormal()</a></code> <code><a href="abnormal.html">s_count_abnormal()</a></code> <code><a href="abnormal.html">a_count_abnormal()</a></code>
           <span class="badge lifecycle lifecycle-stable">stable</span>
         </dt>
         <dd>Count patients with abnormal range values</dd>
-      </dl><dl><dt>
+      </dl>
+<dl>
+<dt>
 
           <code><a href="abnormal_by_baseline.html">count_abnormal_by_baseline()</a></code> <code><a href="abnormal_by_baseline.html">s_count_abnormal_by_baseline()</a></code> <code><a href="abnormal_by_baseline.html">a_count_abnormal_by_baseline()</a></code>
           <span class="badge lifecycle lifecycle-stable">stable</span>
         </dt>
         <dd>Count patients with abnormal analysis range values by baseline status</dd>
-      </dl><dl><dt>
+      </dl>
+<dl>
+<dt>
 
           <code><a href="abnormal_by_marked.html">count_abnormal_by_marked()</a></code> <code><a href="abnormal_by_marked.html">s_count_abnormal_by_marked()</a></code> <code><a href="abnormal_by_marked.html">a_count_abnormal_by_marked()</a></code>
           <span class="badge lifecycle lifecycle-stable">stable</span>
         </dt>
         <dd>Count patients with marked laboratory abnormalities</dd>
-      </dl><dl><dt>
+      </dl>
+<dl>
+<dt>
 
           <code><a href="abnormal_by_worst_grade.html">count_abnormal_by_worst_grade()</a></code> <code><a href="abnormal_by_worst_grade.html">s_count_abnormal_by_worst_grade()</a></code> <code><a href="abnormal_by_worst_grade.html">a_count_abnormal_by_worst_grade()</a></code>
           <span class="badge lifecycle lifecycle-stable">stable</span>
         </dt>
         <dd>Count patients by most extreme post-baseline toxicity grade per direction of abnormality</dd>
-      </dl><dl><dt>
+      </dl>
+<dl>
+<dt>
 
           <code><a href="abnormal_by_worst_grade_worsen.html">count_abnormal_lab_worsen_by_baseline()</a></code> <code><a href="abnormal_by_worst_grade_worsen.html">s_count_abnormal_lab_worsen_by_baseline()</a></code> <code><a href="abnormal_by_worst_grade_worsen.html">a_count_abnormal_lab_worsen_by_baseline()</a></code>
           <span class="badge lifecycle lifecycle-stable">stable</span>
         </dt>
         <dd>Count patients with toxicity grades that have worsened from baseline by highest grade post-baseline</dd>
-      </dl><dl><dt>
+      </dl>
+<dl>
+<dt>
 
           <code><a href="count_cumulative.html">count_cumulative()</a></code> <code><a href="count_cumulative.html">s_count_cumulative()</a></code> <code><a href="count_cumulative.html">a_count_cumulative()</a></code>
           <span class="badge lifecycle lifecycle-stable">stable</span>
         </dt>
         <dd>Cumulative counts of numeric variable by thresholds</dd>
-      </dl><dl><dt>
+      </dl>
+<dl>
+<dt>
 
           <code><a href="count_missed_doses.html">count_missed_doses()</a></code> <code><a href="count_missed_doses.html">s_count_nonmissing()</a></code> <code><a href="count_missed_doses.html">s_count_missed_doses()</a></code> <code><a href="count_missed_doses.html">a_count_missed_doses()</a></code>
           <span class="badge lifecycle lifecycle-stable">stable</span>
         </dt>
         <dd>Count number of patients with missed doses by thresholds</dd>
-      </dl><dl><dt>
+      </dl>
+<dl>
+<dt>
 
           <code><a href="count_occurrences.html">count_occurrences()</a></code> <code><a href="count_occurrences.html">summarize_occurrences()</a></code> <code><a href="count_occurrences.html">s_count_occurrences()</a></code> <code><a href="count_occurrences.html">a_count_occurrences()</a></code>
           <span class="badge lifecycle lifecycle-stable">stable</span>
         </dt>
         <dd>Count occurrences</dd>
-      </dl><dl><dt>
+      </dl>
+<dl>
+<dt>
 
           <code><a href="count_occurrences_by_grade.html">count_occurrences_by_grade()</a></code> <code><a href="count_occurrences_by_grade.html">summarize_occurrences_by_grade()</a></code> <code><a href="count_occurrences_by_grade.html">s_count_occurrences_by_grade()</a></code> <code><a href="count_occurrences_by_grade.html">a_count_occurrences_by_grade()</a></code>
           <span class="badge lifecycle lifecycle-stable">stable</span>
         </dt>
         <dd>Count occurrences by grade</dd>
-      </dl><dl><dt>
+      </dl>
+<dl>
+<dt>
 
           <code><a href="count_patients_events_in_cols.html">summarize_patients_events_in_cols()</a></code> <code><a href="count_patients_events_in_cols.html">s_count_patients_and_multiple_events()</a></code>
           <span class="badge lifecycle lifecycle-stable">stable</span>
         </dt>
         <dd>Count patient events in columns</dd>
-      </dl><dl><dt>
+      </dl>
+<dl>
+<dt>
 
           <code><a href="count_patients_with_event.html">count_patients_with_event()</a></code> <code><a href="count_patients_with_event.html">s_count_patients_with_event()</a></code> <code><a href="count_patients_with_event.html">a_count_patients_with_event()</a></code>
           <span class="badge lifecycle lifecycle-stable">stable</span>
         </dt>
         <dd>Count the number of patients with a particular event</dd>
-      </dl><dl><dt>
+      </dl>
+<dl>
+<dt>
 
           <code><a href="count_patients_with_flags.html">count_patients_with_flags()</a></code> <code><a href="count_patients_with_flags.html">s_count_patients_with_flags()</a></code> <code><a href="count_patients_with_flags.html">a_count_patients_with_flags()</a></code>
           <span class="badge lifecycle lifecycle-stable">stable</span>
         </dt>
         <dd>Count the number of patients with particular flags</dd>
-      </dl><dl><dt>
+      </dl>
+<dl>
+<dt>
 
           <code><a href="count_values.html">count_values()</a></code> <code><a href="count_values.html">s_count_values()</a></code> <code><a href="count_values.html">a_count_values()</a></code>
           <span class="badge lifecycle lifecycle-stable">stable</span>
         </dt>
         <dd>Count specific values</dd>
-      </dl><dl><dt>
+      </dl>
+<dl>
+<dt>
 
           <code><a href="estimate_multinomial_rsp.html">estimate_multinomial_response()</a></code> <code><a href="estimate_multinomial_rsp.html">s_length_proportion()</a></code> <code><a href="estimate_multinomial_rsp.html">a_length_proportion()</a></code>
           <span class="badge lifecycle lifecycle-stable">stable</span>
         </dt>
         <dd>Estimate proportions of each level of a variable</dd>
-      </dl><dl><dt>
+      </dl>
+<dl>
+<dt>
 
           <code><a href="estimate_proportion.html">estimate_proportion()</a></code> <code><a href="estimate_proportion.html">s_proportion()</a></code> <code><a href="estimate_proportion.html">a_proportion()</a></code>
           <span class="badge lifecycle lifecycle-stable">stable</span>
         </dt>
         <dd>Proportion estimation</dd>
-      </dl><dl><dt>
+      </dl>
+<dl>
+<dt>
 
           <code><a href="incidence_rate.html">estimate_incidence_rate()</a></code> <code><a href="incidence_rate.html">s_incidence_rate()</a></code> <code><a href="incidence_rate.html">a_incidence_rate()</a></code>
           <span class="badge lifecycle lifecycle-stable">stable</span>
         </dt>
         <dd>Incidence rate estimation</dd>
-      </dl><dl><dt>
+      </dl>
+<dl>
+<dt>
 
           <code><a href="odds_ratio.html">estimate_odds_ratio()</a></code> <code><a href="odds_ratio.html">s_odds_ratio()</a></code> <code><a href="odds_ratio.html">a_odds_ratio()</a></code>
           <span class="badge lifecycle lifecycle-stable">stable</span>
         </dt>
         <dd>Odds ratio estimation</dd>
-      </dl><dl><dt>
+      </dl>
+<dl>
+<dt>
 
           <code><a href="prop_diff.html">estimate_proportion_diff()</a></code> <code><a href="prop_diff.html">s_proportion_diff()</a></code> <code><a href="prop_diff.html">a_proportion_diff()</a></code>
           <span class="badge lifecycle lifecycle-stable">stable</span>
         </dt>
         <dd>Proportion difference estimation</dd>
-      </dl><dl><dt>
+      </dl>
+<dl>
+<dt>
 
           <code><a href="s_bland_altman.html">s_bland_altman()</a></code>
           <span class="badge lifecycle lifecycle-experimental">experimental</span>
         </dt>
         <dd>Bland-Altman analysis</dd>
-      </dl><dl><dt>
+      </dl>
+<dl>
+<dt>
 
           <code><a href="cox_regression.html">summarize_coxreg()</a></code> <code><a href="cox_regression.html">s_coxreg()</a></code> <code><a href="cox_regression.html">a_coxreg()</a></code>
           <span class="badge lifecycle lifecycle-stable">stable</span>
         </dt>
         <dd>Cox proportional hazards regression</dd>
-      </dl><dl><dt>
+      </dl>
+<dl>
+<dt>
 
           <code><a href="summarize_ancova.html">summarize_ancova()</a></code> <code><a href="summarize_ancova.html">s_ancova()</a></code> <code><a href="summarize_ancova.html">a_ancova()</a></code>
           <span class="badge lifecycle lifecycle-stable">stable</span>
         </dt>
         <dd>Summarize analysis of covariance (ANCOVA) results</dd>
-      </dl><dl><dt>
+      </dl>
+<dl>
+<dt>
 
           <code><a href="summarize_change.html">summarize_change()</a></code> <code><a href="summarize_change.html">s_change_from_baseline()</a></code> <code><a href="summarize_change.html">a_change_from_baseline()</a></code>
           <span class="badge lifecycle lifecycle-stable">stable</span>
         </dt>
         <dd>Summarize change from baseline values or absolute baseline values</dd>
-      </dl><dl><dt>
+      </dl>
+<dl>
+<dt>
 
           <code><a href="summarize_colvars.html">summarize_colvars()</a></code>
           <span class="badge lifecycle lifecycle-stable">stable</span>
         </dt>
         <dd>Summarize variables in columns</dd>
-      </dl><dl><dt>
+      </dl>
+<dl>
+<dt>
 
           <code><a href="summarize_glm_count.html">summarize_glm_count()</a></code> <code><a href="summarize_glm_count.html">s_glm_count()</a></code>
           <span class="badge lifecycle lifecycle-experimental">experimental</span>
         </dt>
         <dd>Summarize Poisson negative binomial regression</dd>
-      </dl><dl><dt>
+      </dl>
+<dl>
+<dt>
 
           <code><a href="summarize_logistic.html">summarize_logistic()</a></code>
           <span class="badge lifecycle lifecycle-stable">stable</span>
         </dt>
         <dd>Multivariate logistic regression table</dd>
-      </dl><dl><dt>
+      </dl>
+<dl>
+<dt>
 
           <code><a href="survival_time.html">surv_time()</a></code> <code><a href="survival_time.html">s_surv_time()</a></code> <code><a href="survival_time.html">a_surv_time()</a></code>
           <span class="badge lifecycle lifecycle-stable">stable</span>
         </dt>
         <dd>Survival time analysis</dd>
-      </dl><dl><dt>
+      </dl>
+<dl>
+<dt>
 
           <code><a href="survival_timepoint.html">surv_timepoint()</a></code> <code><a href="survival_timepoint.html">s_surv_timepoint()</a></code> <code><a href="survival_timepoint.html">a_surv_timepoint()</a></code> <code><a href="survival_timepoint.html">s_surv_timepoint_diff()</a></code> <code><a href="survival_timepoint.html">a_surv_timepoint_diff()</a></code>
           <span class="badge lifecycle lifecycle-stable">stable</span>
         </dt>
         <dd>Survival time point analysis</dd>
-      </dl><dl><dt>
+      </dl>
+<dl>
+<dt>
 
           <code><a href="response_biomarkers_subgroups.html">tabulate_rsp_biomarkers()</a></code>
           <span class="badge lifecycle lifecycle-stable">stable</span>
         </dt>
         <dd>Tabulate biomarker effects on binary response by subgroup</dd>
-      </dl><dl><dt>
+      </dl>
+<dl>
+<dt>
 
           <code><a href="response_subgroups.html">tabulate_rsp_subgroups()</a></code> <code><a href="response_subgroups.html">a_response_subgroups()</a></code>
           <span class="badge lifecycle lifecycle-stable">stable</span>
         </dt>
         <dd>Tabulate binary response by subgroup</dd>
-      </dl><dl><dt>
+      </dl>
+<dl>
+<dt>
 
           <code><a href="survival_biomarkers_subgroups.html">tabulate_survival_biomarkers()</a></code>
           <span class="badge lifecycle lifecycle-stable">stable</span>
         </dt>
         <dd>Tabulate biomarker effects on survival by subgroup</dd>
-      </dl><dl><dt>
+      </dl>
+<dl>
+<dt>
 
           <code><a href="survival_duration_subgroups.html">tabulate_survival_subgroups()</a></code> <code><a href="survival_duration_subgroups.html">a_survival_subgroups()</a></code>
           <span class="badge lifecycle lifecycle-stable">stable</span>
         </dt>
         <dd>Tabulate survival duration by subgroup</dd>
-      </dl><dl><dt>
+      </dl>
+<dl>
+<dt>
 
           <code><a href="prop_diff_test.html">test_proportion_diff()</a></code> <code><a href="prop_diff_test.html">s_test_proportion_diff()</a></code> <code><a href="prop_diff_test.html">a_test_proportion_diff()</a></code>
           <span class="badge lifecycle lifecycle-stable">stable</span>
         </dt>
         <dd>Difference test for two proportions</dd>
-      </dl></div><div class="section level2">
-      <h2 id="model-specific-functions">Model-Specific Functions<a class="anchor" aria-label="anchor" href="#model-specific-functions"></a></h2>
+      </dl>
+</div>
+<div class="section level2">
+      <h2 id="model-specific-functions">Model-Specific Functions<a class="anchor" aria-label="anchor" href="#model-specific-functions"></a>
+</h2>
 
       <div class="section-desc"><p>These functions help with fitting or extracting results from specific models.</p></div>
 
 
-    </div><div class="section level2">
+    </div>
+<div class="section level2">
 
 
 
 
-      <dl><dt>
+      <dl>
+<dt>
 
           <code><a href="estimate_coef.html">estimate_coef()</a></code>
 
         </dt>
         <dd>Hazard ratio estimation in interactions</dd>
-      </dl><dl><dt>
+      </dl>
+<dl>
+<dt>
 
           <code><a href="extract_rsp_biomarkers.html">extract_rsp_biomarkers()</a></code>
           <span class="badge lifecycle lifecycle-stable">stable</span>
         </dt>
         <dd>Prepare response data estimates for multiple biomarkers in a single data frame</dd>
-      </dl><dl><dt>
+      </dl>
+<dl>
+<dt>
 
           <code><a href="extract_rsp_subgroups.html">extract_rsp_subgroups()</a></code>
           <span class="badge lifecycle lifecycle-stable">stable</span>
         </dt>
         <dd>Prepare response data for population subgroups in data frames</dd>
-      </dl><dl><dt>
+      </dl>
+<dl>
+<dt>
 
           <code><a href="extract_survival_biomarkers.html">extract_survival_biomarkers()</a></code>
           <span class="badge lifecycle lifecycle-stable">stable</span>
         </dt>
         <dd>Prepare survival data estimates for multiple biomarkers in a single data frame</dd>
-      </dl><dl><dt>
+      </dl>
+<dl>
+<dt>
 
           <code><a href="extract_survival_subgroups.html">extract_survival_subgroups()</a></code>
           <span class="badge lifecycle lifecycle-stable">stable</span>
         </dt>
         <dd>Prepare survival data for population subgroups in data frames</dd>
-      </dl><dl><dt>
+      </dl>
+<dl>
+<dt>
 
           <code><a href="fit_coxreg.html">fit_coxreg_univar()</a></code> <code><a href="fit_coxreg.html">fit_coxreg_multivar()</a></code>
           <span class="badge lifecycle lifecycle-stable">stable</span>
         </dt>
         <dd>Fitting functions for Cox proportional hazards regression</dd>
-      </dl><dl><dt>
+      </dl>
+<dl>
+<dt>
 
           <code><a href="fit_logistic.html">fit_logistic()</a></code>
           <span class="badge lifecycle lifecycle-stable">stable</span>
         </dt>
         <dd>Fit for logistic regression</dd>
-      </dl><dl><dt>
+      </dl>
+<dl>
+<dt>
 
           <code><a href="fit_rsp_step.html">fit_rsp_step()</a></code>
           <span class="badge lifecycle lifecycle-stable">stable</span>
         </dt>
         <dd>Subgroup treatment effect pattern (STEP) fit for binary (response) outcome</dd>
-      </dl><dl><dt>
+      </dl>
+<dl>
+<dt>
 
           <code><a href="fit_survival_step.html">fit_survival_step()</a></code>
           <span class="badge lifecycle lifecycle-stable">stable</span>
         </dt>
         <dd>Subgroup treatment effect pattern (STEP) fit for survival outcome</dd>
-      </dl><dl><dt>
+      </dl>
+<dl>
+<dt>
 
           <code><a href="get_smooths.html">get_smooths()</a></code>
           <span class="badge lifecycle lifecycle-stable">stable</span>
         </dt>
         <dd>Smooth function with optional grouping</dd>
-      </dl><dl><dt>
+      </dl>
+<dl>
+<dt>
 
           <code><a href="logistic_regression_cols.html">logistic_regression_cols()</a></code>
           <span class="badge lifecycle lifecycle-stable">stable</span>
         </dt>
         <dd>Logistic regression multivariate column layout function</dd>
-      </dl><dl><dt>
+      </dl>
+<dl>
+<dt>
 
           <code><a href="logistic_summary_by_flag.html">logistic_summary_by_flag()</a></code>
           <span class="badge lifecycle lifecycle-stable">stable</span>
         </dt>
         <dd>Logistic regression summary table</dd>
-      </dl><dl><dt>
+      </dl>
+<dl>
+<dt>
 
           <code><a href="tidy.glm.html">tidy(<i>&lt;glm&gt;</i>)</a></code>
           <span class="badge lifecycle lifecycle-stable">stable</span>
         </dt>
         <dd>Custom tidy method for binomial GLM results</dd>
-      </dl><dl><dt>
+      </dl>
+<dl>
+<dt>
 
           <code><a href="tidy.step.html">tidy(<i>&lt;step&gt;</i>)</a></code>
           <span class="badge lifecycle lifecycle-stable">stable</span>
         </dt>
         <dd>Custom tidy method for STEP results</dd>
-      </dl><dl><dt>
+      </dl>
+<dl>
+<dt>
 
           <code><a href="tidy_coxreg.html">tidy(<i>&lt;summary.coxph&gt;</i>)</a></code> <code><a href="tidy_coxreg.html">tidy(<i>&lt;coxreg.univar&gt;</i>)</a></code> <code><a href="tidy_coxreg.html">tidy(<i>&lt;coxreg.multivar&gt;</i>)</a></code>
           <span class="badge lifecycle lifecycle-stable">stable</span>
         </dt>
         <dd>Custom tidy methods for Cox regression</dd>
-      </dl><dl><dt>
+      </dl>
+<dl>
+<dt>
 
           <code><a href="univariate.html">univariate()</a></code>
           <span class="badge lifecycle lifecycle-stable">stable</span>
         </dt>
         <dd>Univariate formula special term</dd>
-      </dl></div><div class="section level2">
-      <h2 id="graphs">Graphs<a class="anchor" aria-label="anchor" href="#graphs"></a></h2>
+      </dl>
+</div>
+<div class="section level2">
+      <h2 id="graphs">Graphs<a class="anchor" aria-label="anchor" href="#graphs"></a>
+</h2>
 
       <div class="section-desc"><p>These function create graphical type output.</p></div>
 
 
-    </div><div class="section level2">
+    </div>
+<div class="section level2">
 
 
 
 
-      <dl><dt>
+      <dl>
+<dt>
 
           <code><a href="g_bland_altman.html">g_bland_altman()</a></code>
           <span class="badge lifecycle lifecycle-experimental">experimental</span>
         </dt>
         <dd>Bland-Altman plot</dd>
-      </dl><dl><dt>
+      </dl>
+<dl>
+<dt>
 
           <code><a href="g_forest.html">g_forest()</a></code>
           <span class="badge lifecycle lifecycle-stable">stable</span>
         </dt>
-        <dd>Create a forest plot from an <code>rtable</code></dd>
-      </dl><dl><dt>
+        <dd>Create a forest plot from an <code>rtable</code>
+</dd>
+      </dl>
+<dl>
+<dt>
 
           <code><a href="g_ipp.html">g_ipp()</a></code>
           <span class="badge lifecycle lifecycle-stable">stable</span>
         </dt>
         <dd>Individual patient plots</dd>
-      </dl><dl><dt>
+      </dl>
+<dl>
+<dt>
 
           <code><a href="g_km.html">g_km()</a></code>
           <span class="badge lifecycle lifecycle-stable">stable</span>
         </dt>
         <dd>Kaplan-Meier plot</dd>
-      </dl><dl><dt>
+      </dl>
+<dl>
+<dt>
 
           <code><a href="g_lineplot.html">g_lineplot()</a></code>
           <span class="badge lifecycle lifecycle-stable">stable</span>
         </dt>
         <dd>Line plot with optional table</dd>
-      </dl><dl><dt>
+      </dl>
+<dl>
+<dt>
 
           <code><a href="g_step.html">g_step()</a></code>
           <span class="badge lifecycle lifecycle-stable">stable</span>
         </dt>
         <dd>Create a STEP graph</dd>
-      </dl><dl><dt>
+      </dl>
+<dl>
+<dt>
 
           <code><a href="g_waterfall.html">g_waterfall()</a></code>
           <span class="badge lifecycle lifecycle-stable">stable</span>
         </dt>
         <dd>Horizontal waterfall plot</dd>
-      </dl></div><div class="section level2">
-      <h2 id="control-functions">Control Functions<a class="anchor" aria-label="anchor" href="#control-functions"></a></h2>
+      </dl>
+</div>
+<div class="section level2">
+      <h2 id="control-functions">Control Functions<a class="anchor" aria-label="anchor" href="#control-functions"></a>
+</h2>
 
       <div class="section-desc"><p>These functions capture options in lists and take care of defaults (and checks where applicable). They avoid cluttering of function signatures with long lists of single arguments.</p></div>
 
 
-    </div><div class="section level2">
+    </div>
+<div class="section level2">
 
 
 
 
-      <dl><dt>
+      <dl>
+<dt>
 
           <code><a href="control_analyze_vars.html">control_analyze_vars()</a></code>
           <span class="badge lifecycle lifecycle-stable">stable</span>
         </dt>
         <dd>Control function for descriptive statistics</dd>
-      </dl><dl><dt>
+      </dl>
+<dl>
+<dt>
 
           <code><a href="control_annot.html">control_surv_med_annot()</a></code> <code><a href="control_annot.html">control_coxph_annot()</a></code>
           <span class="badge lifecycle lifecycle-stable">stable</span>
         </dt>
         <dd>Control functions for Kaplan-Meier plot annotation tables</dd>
-      </dl><dl><dt>
+      </dl>
+<dl>
+<dt>
 
           <code><a href="control_coxph.html">control_coxph()</a></code>
           <span class="badge lifecycle lifecycle-stable">stable</span>
         </dt>
         <dd>Control function for Cox-PH model</dd>
-      </dl><dl><dt>
+      </dl>
+<dl>
+<dt>
 
           <code><a href="control_coxreg.html">control_coxreg()</a></code>
           <span class="badge lifecycle lifecycle-stable">stable</span>
         </dt>
         <dd>Control function for Cox regression</dd>
-      </dl><dl><dt>
+      </dl>
+<dl>
+<dt>
 
           <code><a href="control_incidence_rate.html">control_incidence_rate()</a></code>
           <span class="badge lifecycle lifecycle-stable">stable</span>
         </dt>
         <dd>Control function for incidence rate</dd>
-      </dl><dl><dt>
+      </dl>
+<dl>
+<dt>
 
           <code><a href="control_lineplot_vars.html">control_lineplot_vars()</a></code>
           <span class="badge lifecycle lifecycle-stable">stable</span>
         </dt>
-        <dd>Control function for <code><a href="../reference/g_lineplot.html">g_lineplot()</a></code></dd>
-      </dl><dl><dt>
+        <dd>Control function for <code><a href="../reference/g_lineplot.html">g_lineplot()</a></code>
+</dd>
+      </dl>
+<dl>
+<dt>
 
           <code><a href="control_logistic.html">control_logistic()</a></code>
           <span class="badge lifecycle lifecycle-stable">stable</span>
         </dt>
         <dd>Control function for logistic regression model fitting</dd>
-      </dl><dl><dt>
+      </dl>
+<dl>
+<dt>
 
           <code><a href="control_riskdiff.html">control_riskdiff()</a></code>
           <span class="badge lifecycle lifecycle-stable">stable</span>
         </dt>
         <dd>Control function for risk difference column</dd>
-      </dl><dl><dt>
+      </dl>
+<dl>
+<dt>
 
           <code><a href="control_step.html">control_step()</a></code>
           <span class="badge lifecycle lifecycle-stable">stable</span>
         </dt>
         <dd>Control function for subgroup treatment effect pattern (STEP) calculations</dd>
-      </dl><dl><dt>
+      </dl>
+<dl>
+<dt>
 
           <code><a href="control_surv_time.html">control_surv_time()</a></code>
           <span class="badge lifecycle lifecycle-stable">stable</span>
         </dt>
         <dd>Control function for <code>survfit</code> models for survival time</dd>
-      </dl><dl><dt>
+      </dl>
+<dl>
+<dt>
 
           <code><a href="control_surv_timepoint.html">control_surv_timepoint()</a></code>
           <span class="badge lifecycle lifecycle-stable">stable</span>
         </dt>
         <dd>Control function for <code>survfit</code> models for patients' survival rate at time points</dd>
-      </dl></div><div class="section level2">
-      <h2 id="analysis-helper-functions">Analysis Helper Functions<a class="anchor" aria-label="anchor" href="#analysis-helper-functions"></a></h2>
+      </dl>
+</div>
+<div class="section level2">
+      <h2 id="analysis-helper-functions">Analysis Helper Functions<a class="anchor" aria-label="anchor" href="#analysis-helper-functions"></a>
+</h2>
 
       <div class="section-desc"><p>These functions are useful in defining an analysis.</p></div>
 
 
-    </div><div class="section level2">
+    </div>
+<div class="section level2">
 
 
 
 
-      <dl><dt>
+      <dl>
+<dt>
 
           <code><a href="default_stats_formats_labels.html">get_stats()</a></code> <code><a href="default_stats_formats_labels.html">get_formats_from_stats()</a></code> <code><a href="default_stats_formats_labels.html">get_labels_from_stats()</a></code> <code><a href="default_stats_formats_labels.html">get_indents_from_stats()</a></code> <code><a href="default_stats_formats_labels.html">tern_default_stats</a></code> <code><a href="default_stats_formats_labels.html">tern_default_formats</a></code> <code><a href="default_stats_formats_labels.html">tern_default_labels</a></code> <code><a href="default_stats_formats_labels.html">summary_formats()</a></code> <code><a href="default_stats_formats_labels.html">summary_labels()</a></code>
           <span class="badge lifecycle lifecycle-stable">stable</span>
         </dt>
         <dd>Get default statistical methods and their associated formats, labels, and indent modifiers</dd>
-      </dl><dl><dt>
+      </dl>
+<dl>
+<dt>
 
           <code><a href="cox_regression_inter.html">h_coxreg_inter_effect()</a></code> <code><a href="cox_regression_inter.html">h_coxreg_extract_interaction()</a></code> <code><a href="cox_regression_inter.html">h_coxreg_inter_estimations()</a></code>
           <span class="badge lifecycle lifecycle-stable">stable</span>
         </dt>
         <dd>Cox regression helper function for interactions</dd>
-      </dl><dl><dt>
+      </dl>
+<dl>
+<dt>
 
           <code><a href="extreme_format.html">h_get_format_threshold()</a></code> <code><a href="extreme_format.html">h_format_threshold()</a></code>
           <span class="badge lifecycle lifecycle-stable">stable</span>
         </dt>
         <dd>Format extreme values</dd>
-      </dl><dl><dt>
+      </dl>
+<dl>
+<dt>
 
           <code><a href="h_adlb_abnormal_by_worst_grade.html">h_adlb_abnormal_by_worst_grade()</a></code>
           <span class="badge lifecycle lifecycle-stable">stable</span>
         </dt>
-        <dd>Helper function to prepare ADLB for <code><a href="../reference/abnormal_by_worst_grade.html">count_abnormal_by_worst_grade()</a></code></dd>
-      </dl><dl><dt>
+        <dd>Helper function to prepare ADLB for <code><a href="../reference/abnormal_by_worst_grade.html">count_abnormal_by_worst_grade()</a></code>
+</dd>
+      </dl>
+<dl>
+<dt>
 
           <code><a href="h_adlb_worsen.html">h_adlb_worsen()</a></code>
           <span class="badge lifecycle lifecycle-stable">stable</span>
         </dt>
         <dd>Helper function to prepare ADLB with worst labs</dd>
-      </dl><dl><dt>
+      </dl>
+<dl>
+<dt>
 
           <code><a href="h_adsl_adlb_merge_using_worst_flag.html">h_adsl_adlb_merge_using_worst_flag()</a></code>
           <span class="badge lifecycle lifecycle-stable">stable</span>
         </dt>
         <dd>Helper function for deriving analysis datasets for select laboratory tables</dd>
-      </dl><dl><dt>
+      </dl>
+<dl>
+<dt>
 
           <code><a href="h_ancova.html">h_ancova()</a></code>
           <span class="badge lifecycle lifecycle-stable">stable</span>
         </dt>
         <dd>Helper function to return results of a linear model</dd>
-      </dl><dl><dt>
+      </dl>
+<dl>
+<dt>
 
           <code><a href="h_append_grade_groups.html">h_append_grade_groups()</a></code>
           <span class="badge lifecycle lifecycle-stable">stable</span>
         </dt>
-        <dd>Helper function for <code><a href="../reference/count_occurrences_by_grade.html">s_count_occurrences_by_grade()</a></code></dd>
-      </dl><dl><dt>
+        <dd>Helper function for <code><a href="../reference/count_occurrences_by_grade.html">s_count_occurrences_by_grade()</a></code>
+</dd>
+      </dl>
+<dl>
+<dt>
 
           <code><a href="h_count_cumulative.html">h_count_cumulative()</a></code>
           <span class="badge lifecycle lifecycle-stable">stable</span>
         </dt>
-        <dd>Helper function for <code><a href="../reference/count_cumulative.html">s_count_cumulative()</a></code></dd>
-      </dl><dl><dt>
+        <dd>Helper function for <code><a href="../reference/count_cumulative.html">s_count_cumulative()</a></code>
+</dd>
+      </dl>
+<dl>
+<dt>
 
           <code><a href="h_cox_regression.html">h_coxreg_univar_formulas()</a></code> <code><a href="h_cox_regression.html">h_coxreg_multivar_formula()</a></code> <code><a href="h_cox_regression.html">h_coxreg_univar_extract()</a></code> <code><a href="h_cox_regression.html">h_coxreg_multivar_extract()</a></code>
           <span class="badge lifecycle lifecycle-stable">stable</span>
         </dt>
         <dd>Helper functions for Cox proportional hazards regression</dd>
-      </dl><dl><dt>
+      </dl>
+<dl>
+<dt>
 
           <code><a href="h_decompose_gg.html">h_decompose_gg()</a></code>
           <span class="badge lifecycle lifecycle-deprecated">deprecated</span>
         </dt>
-        <dd><code>ggplot</code> decomposition</dd>
-      </dl><dl><dt>
+        <dd>
+<code>ggplot</code> decomposition</dd>
+      </dl>
+<dl>
+<dt>
 
           <code><a href="h_format_row.html">h_format_row()</a></code>
           <span class="badge lifecycle lifecycle-stable">stable</span>
         </dt>
         <dd>Helper function to format the optional <code>g_lineplot</code> table</dd>
-      </dl><dl><dt>
+      </dl>
+<dl>
+<dt>
 
           <code><a href="h_ggkm.html">h_ggkm()</a></code>
           <span class="badge lifecycle lifecycle-deprecated">deprecated</span>
         </dt>
         <dd>Helper function to create a KM plot</dd>
-      </dl><dl><dt>
+      </dl>
+<dl>
+<dt>
 
           <code><a href="h_km_layout.html">h_km_layout()</a></code>
           <span class="badge lifecycle lifecycle-deprecated">deprecated</span>
         </dt>
         <dd>Helper function to prepare a KM layout</dd>
-      </dl><dl><dt>
+      </dl>
+<dl>
+<dt>
 
           <code><a href="h_logistic_regression.html">h_get_interaction_vars()</a></code> <code><a href="h_logistic_regression.html">h_interaction_coef_name()</a></code> <code><a href="h_logistic_regression.html">h_or_cat_interaction()</a></code> <code><a href="h_logistic_regression.html">h_or_cont_interaction()</a></code> <code><a href="h_logistic_regression.html">h_or_interaction()</a></code> <code><a href="h_logistic_regression.html">h_simple_term_labels()</a></code> <code><a href="h_logistic_regression.html">h_interaction_term_labels()</a></code> <code><a href="h_logistic_regression.html">h_glm_simple_term_extract()</a></code> <code><a href="h_logistic_regression.html">h_glm_interaction_extract()</a></code> <code><a href="h_logistic_regression.html">h_glm_inter_term_extract()</a></code> <code><a href="h_logistic_regression.html">h_logistic_simple_terms()</a></code> <code><a href="h_logistic_regression.html">h_logistic_inter_terms()</a></code>
           <span class="badge lifecycle lifecycle-stable">stable</span>
         </dt>
         <dd>Helper functions for multivariate logistic regression</dd>
-      </dl><dl><dt>
+      </dl>
+<dl>
+<dt>
 
           <code><a href="h_map_for_count_abnormal.html">h_map_for_count_abnormal()</a></code>
           <span class="badge lifecycle lifecycle-stable">stable</span>
         </dt>
-        <dd>Helper function to create a map data frame for <code>trim_levels_to_map()</code></dd>
-      </dl><dl><dt>
+        <dd>Helper function to create a map data frame for <code>trim_levels_to_map()</code>
+</dd>
+      </dl>
+<dl>
+<dt>
 
           <code><a href="h_odds_ratio.html">or_glm()</a></code> <code><a href="h_odds_ratio.html">or_clogit()</a></code>
           <span class="badge lifecycle lifecycle-stable">stable</span>
         </dt>
         <dd>Helper functions for odds ratio estimation</dd>
-      </dl><dl><dt>
+      </dl>
+<dl>
+<dt>
 
           <code><a href="h_pkparam_sort.html">h_pkparam_sort()</a></code>
           <span class="badge lifecycle lifecycle-stable">stable</span>
         </dt>
         <dd>Sort pharmacokinetic data by <code>PARAM</code> variable</dd>
-      </dl><dl><dt>
+      </dl>
+<dl>
+<dt>
 
           <code><a href="h_ppmeans.html">h_ppmeans()</a></code>
 
         </dt>
         <dd>Function to return the estimated means using predicted probabilities</dd>
-      </dl><dl><dt>
+      </dl>
+<dl>
+<dt>
 
           <code><a href="h_prop_diff.html">prop_diff_wald()</a></code> <code><a href="h_prop_diff.html">prop_diff_ha()</a></code> <code><a href="h_prop_diff.html">prop_diff_nc()</a></code> <code><a href="h_prop_diff.html">prop_diff_cmh()</a></code> <code><a href="h_prop_diff.html">prop_diff_strat_nc()</a></code>
           <span class="badge lifecycle lifecycle-stable">stable</span>
         </dt>
         <dd>Helper functions to calculate proportion difference</dd>
-      </dl><dl><dt>
+      </dl>
+<dl>
+<dt>
 
           <code><a href="h_proportions.html">prop_wilson()</a></code> <code><a href="h_proportions.html">prop_strat_wilson()</a></code> <code><a href="h_proportions.html">prop_clopper_pearson()</a></code> <code><a href="h_proportions.html">prop_wald()</a></code> <code><a href="h_proportions.html">prop_agresti_coull()</a></code> <code><a href="h_proportions.html">prop_jeffreys()</a></code>
           <span class="badge lifecycle lifecycle-stable">stable</span>
         </dt>
         <dd>Helper functions for calculating proportion confidence intervals</dd>
-      </dl><dl><dt>
+      </dl>
+<dl>
+<dt>
 
           <code><a href="h_response_biomarkers_subgroups.html">h_rsp_to_logistic_variables()</a></code> <code><a href="h_response_biomarkers_subgroups.html">h_logistic_mult_cont_df()</a></code> <code><a href="h_response_biomarkers_subgroups.html">h_tab_rsp_one_biomarker()</a></code>
           <span class="badge lifecycle lifecycle-stable">stable</span>
         </dt>
         <dd>Helper functions for tabulating biomarker effects on binary response by subgroup</dd>
-      </dl><dl><dt>
+      </dl>
+<dl>
+<dt>
 
           <code><a href="h_response_subgroups.html">h_proportion_df()</a></code> <code><a href="h_response_subgroups.html">h_proportion_subgroups_df()</a></code> <code><a href="h_response_subgroups.html">h_odds_ratio_df()</a></code> <code><a href="h_response_subgroups.html">h_odds_ratio_subgroups_df()</a></code>
           <span class="badge lifecycle lifecycle-stable">stable</span>
         </dt>
         <dd>Helper functions for tabulating binary response by subgroup</dd>
-      </dl><dl><dt>
+      </dl>
+<dl>
+<dt>
 
           <code><a href="h_split_by_subgroups.html">h_split_by_subgroups()</a></code>
           <span class="badge lifecycle lifecycle-stable">stable</span>
         </dt>
         <dd>Split data frame by subgroups</dd>
-      </dl><dl><dt>
+      </dl>
+<dl>
+<dt>
 
           <code><a href="h_split_param.html">h_split_param()</a></code>
           <span class="badge lifecycle lifecycle-stable">stable</span>
         </dt>
         <dd>Split parameters</dd>
-      </dl><dl><dt>
+      </dl>
+<dl>
+<dt>
 
           <code><a href="h_stack_by_baskets.html">h_stack_by_baskets()</a></code>
           <span class="badge lifecycle lifecycle-stable">stable</span>
         </dt>
         <dd>Helper function to create a new SMQ variable in ADAE by stacking SMQ and/or CQ records.</dd>
-      </dl><dl><dt>
+      </dl>
+<dl>
+<dt>
 
           <code><a href="h_step.html">h_step_window()</a></code> <code><a href="h_step.html">h_step_trt_effect()</a></code> <code><a href="h_step.html">h_step_survival_formula()</a></code> <code><a href="h_step.html">h_step_survival_est()</a></code> <code><a href="h_step.html">h_step_rsp_formula()</a></code> <code><a href="h_step.html">h_step_rsp_est()</a></code>
           <span class="badge lifecycle lifecycle-stable">stable</span>
         </dt>
         <dd>Helper functions for subgroup treatment effect pattern (STEP) calculations</dd>
-      </dl><dl><dt>
+      </dl>
+<dl>
+<dt>
 
           <code><a href="h_survival_biomarkers_subgroups.html">h_surv_to_coxreg_variables()</a></code> <code><a href="h_survival_biomarkers_subgroups.html">h_coxreg_mult_cont_df()</a></code> <code><a href="h_survival_biomarkers_subgroups.html">h_tab_surv_one_biomarker()</a></code>
           <span class="badge lifecycle lifecycle-stable">stable</span>
         </dt>
         <dd>Helper functions for tabulating biomarker effects on survival by subgroup</dd>
-      </dl><dl><dt>
+      </dl>
+<dl>
+<dt>
 
           <code><a href="h_survival_duration_subgroups.html">h_survtime_df()</a></code> <code><a href="h_survival_duration_subgroups.html">h_survtime_subgroups_df()</a></code> <code><a href="h_survival_duration_subgroups.html">h_coxph_df()</a></code> <code><a href="h_survival_duration_subgroups.html">h_coxph_subgroups_df()</a></code>
           <span class="badge lifecycle lifecycle-stable">stable</span>
         </dt>
         <dd>Helper functions for tabulating survival duration by subgroup</dd>
-      </dl><dl><dt>
+      </dl>
+<dl>
+<dt>
 
           <code><a href="h_tab_one_biomarker.html">h_tab_one_biomarker()</a></code>
           <span class="badge lifecycle lifecycle-stable">stable</span>
         </dt>
         <dd>Helper function for tabulation of a single biomarker result</dd>
-      </dl><dl><dt>
+      </dl>
+<dl>
+<dt>
 
           <code><a href="h_tbl_coxph_pairwise.html">h_tbl_coxph_pairwise()</a></code>
           <span class="badge lifecycle lifecycle-stable">stable</span>
         </dt>
         <dd>Helper function for generating a pairwise Cox-PH table</dd>
-      </dl><dl><dt>
+      </dl>
+<dl>
+<dt>
 
           <code><a href="h_tbl_median_surv.html">h_tbl_median_surv()</a></code>
           <span class="badge lifecycle lifecycle-stable">stable</span>
         </dt>
         <dd>Helper function for survival estimations</dd>
-      </dl><dl><dt>
+      </dl>
+<dl>
+<dt>
 
           <code><a href="h_worsen_counter.html">h_worsen_counter()</a></code>
           <span class="badge lifecycle lifecycle-stable">stable</span>
         </dt>
-        <dd>Helper function to analyze patients for <code><a href="../reference/abnormal_by_worst_grade_worsen.html">s_count_abnormal_lab_worsen_by_baseline()</a></code></dd>
-      </dl><dl><dt>
+        <dd>Helper function to analyze patients for <code><a href="../reference/abnormal_by_worst_grade_worsen.html">s_count_abnormal_lab_worsen_by_baseline()</a></code>
+</dd>
+      </dl>
+<dl>
+<dt>
 
           <code><a href="imputation_rule.html">imputation_rule()</a></code>
           <span class="badge lifecycle lifecycle-stable">stable</span>
         </dt>
         <dd>Apply 1/3 or 1/2 imputation rule to data</dd>
-      </dl><dl><dt>
+      </dl>
+<dl>
+<dt>
 
           <code><a href="labels_use_control.html">labels_use_control()</a></code>
           <span class="badge lifecycle lifecycle-stable">stable</span>
         </dt>
         <dd>Update labels according to control specifications</dd>
-      </dl></div><div class="section level2">
-      <h2 id="rtables-helper-functions">rtables Helper Functions<a class="anchor" aria-label="anchor" href="#rtables-helper-functions"></a></h2>
+      </dl>
+</div>
+<div class="section level2">
+      <h2 id="rtables-helper-functions">rtables Helper Functions<a class="anchor" aria-label="anchor" href="#rtables-helper-functions"></a>
+</h2>
 
       <div class="section-desc"><p>These functions help to work with the <code>rtables</code> package and may be moved there later.</p></div>
 
 
-    </div><div class="section level2">
+    </div>
+<div class="section level2">
 
 
 
 
-      <dl><dt>
+      <dl>
+<dt>
 
           <code><a href="add_riskdiff.html">add_riskdiff()</a></code>
           <span class="badge lifecycle lifecycle-stable">stable</span>
         </dt>
         <dd>Split function to configure risk difference column</dd>
-      </dl><dl><dt>
+      </dl>
+<dl>
+<dt>
 
           <code><a href="add_rowcounts.html">add_rowcounts()</a></code>
           <span class="badge lifecycle lifecycle-stable">stable</span>
         </dt>
         <dd>Layout-creating function to add row total counts</dd>
-      </dl><dl><dt>
+      </dl>
+<dl>
+<dt>
 
           <code><a href="append_varlabels.html">append_varlabels()</a></code>
           <span class="badge lifecycle lifecycle-stable">stable</span>
         </dt>
         <dd>Add variable labels to top left corner in table</dd>
-      </dl><dl><dt>
+      </dl>
+<dl>
+<dt>
 
           <code><a href="default_na_str.html">default_na_str()</a></code> <code><a href="default_na_str.html">set_default_na_str()</a></code>
           <span class="badge lifecycle lifecycle-stable">stable</span>
         </dt>
         <dd>Default string replacement for <code>NA</code> values</dd>
-      </dl><dl><dt>
+      </dl>
+<dl>
+<dt>
 
           <code><a href="as.rtable.html">as.rtable()</a></code>
           <span class="badge lifecycle lifecycle-stable">stable</span>
         </dt>
-        <dd>Convert to <code>rtable</code></dd>
-      </dl><dl><dt>
+        <dd>Convert to <code>rtable</code>
+</dd>
+      </dl>
+<dl>
+<dt>
 
           <code><a href="combine_counts.html">combine_counts()</a></code>
 
         </dt>
         <dd>Combine counts</dd>
-      </dl><dl><dt>
+      </dl>
+<dl>
+<dt>
 
           <code><a href="combine_groups.html">combine_groups()</a></code>
           <span class="badge lifecycle lifecycle-stable">stable</span>
         </dt>
         <dd>Reference and treatment group combination</dd>
-      </dl><dl><dt>
+      </dl>
+<dl>
+<dt>
 
           <code><a href="combine_levels.html">combine_levels()</a></code>
           <span class="badge lifecycle lifecycle-stable">stable</span>
         </dt>
         <dd>Combine factor levels</dd>
-      </dl><dl><dt>
+      </dl>
+<dl>
+<dt>
 
           <code><a href="combine_vectors.html">combine_vectors()</a></code>
 
         </dt>
         <dd>Element-wise combination of two vectors</dd>
-      </dl><dl><dt>
+      </dl>
+<dl>
+<dt>
 
           <code><a href="h_col_indices.html">h_col_indices()</a></code>
           <span class="badge lifecycle lifecycle-stable">stable</span>
         </dt>
         <dd>Obtain column indices</dd>
-      </dl><dl><dt>
+      </dl>
+<dl>
+<dt>
 
           <code><a href="rtables_access.html">h_row_first_values()</a></code> <code><a href="rtables_access.html">h_row_counts()</a></code> <code><a href="rtables_access.html">h_row_fractions()</a></code> <code><a href="rtables_access.html">h_col_counts()</a></code> <code><a href="rtables_access.html">h_content_first_row()</a></code> <code><a href="rtables_access.html">is_leaf_table()</a></code> <code><a href="rtables_access.html">check_names_indices()</a></code>
           <span class="badge lifecycle lifecycle-stable">stable</span>
         </dt>
-        <dd>Helper functions for accessing information from <code>rtables</code></dd>
-      </dl><dl><dt>
+        <dd>Helper functions for accessing information from <code>rtables</code>
+</dd>
+      </dl>
+<dl>
+<dt>
 
           <code><a href="rtable2gg.html">rtable2gg()</a></code>
           <span class="badge lifecycle lifecycle-experimental">experimental</span>
         </dt>
         <dd>Convert <code>rtable</code> objects to <code>ggplot</code> objects</dd>
-      </dl><dl><dt>
+      </dl>
+<dl>
+<dt>
 
           <code><a href="split_cols_by_groups.html">split_cols_by_groups()</a></code>
           <span class="badge lifecycle lifecycle-stable">stable</span>
         </dt>
         <dd>Split columns by groups of levels</dd>
-      </dl><dl><dt>
+      </dl>
+<dl>
+<dt>
 
           <code><a href="to_string_matrix.html">to_string_matrix()</a></code>
           <span class="badge lifecycle lifecycle-stable">stable</span>
         </dt>
         <dd>Convert table into matrix of strings</dd>
-      </dl><dl><dt>
+      </dl>
+<dl>
+<dt>
 
           <code><a href="groups_list_to_df.html">groups_list_to_df()</a></code>
 
         </dt>
         <dd>Convert list of groups to a data frame</dd>
-      </dl><dl><dt>
+      </dl>
+<dl>
+<dt>
 
           <code><a href="utils_split_funs.html">ref_group_position()</a></code> <code><a href="utils_split_funs.html">level_order()</a></code>
           <span class="badge lifecycle lifecycle-stable">stable</span>
         </dt>
         <dd>Custom split functions</dd>
-      </dl></div><div class="section level2">
-      <h2 id="rtables-formatting-functions">rtables Formatting Functions<a class="anchor" aria-label="anchor" href="#rtables-formatting-functions"></a></h2>
+      </dl>
+</div>
+<div class="section level2">
+      <h2 id="rtables-formatting-functions">rtables Formatting Functions<a class="anchor" aria-label="anchor" href="#rtables-formatting-functions"></a>
+</h2>
 
       <div class="section-desc"><p>These functions provide customized formatting rules to work with the <code>rtables</code> package.</p></div>
 
 
-    </div><div class="section level2">
+    </div>
+<div class="section level2">
 
 
 
 
-      <dl><dt>
+      <dl>
+<dt>
 
           <code><a href="format_auto.html">format_auto()</a></code>
           <span class="badge lifecycle lifecycle-stable">stable</span>
         </dt>
         <dd>Format automatically using data significant digits</dd>
-      </dl><dl><dt>
+      </dl>
+<dl>
+<dt>
 
           <code><a href="format_count_fraction.html">format_count_fraction()</a></code>
           <span class="badge lifecycle lifecycle-stable">stable</span>
         </dt>
         <dd>Format count and fraction</dd>
-      </dl><dl><dt>
+      </dl>
+<dl>
+<dt>
 
           <code><a href="format_count_fraction_fixed_dp.html">format_count_fraction_fixed_dp()</a></code>
           <span class="badge lifecycle lifecycle-experimental">experimental</span>
         </dt>
         <dd>Format count and percentage with fixed single decimal place</dd>
-      </dl><dl><dt>
+      </dl>
+<dl>
+<dt>
 
           <code><a href="format_count_fraction_lt10.html">format_count_fraction_lt10()</a></code>
           <span class="badge lifecycle lifecycle-stable">stable</span>
         </dt>
         <dd>Format count and fraction with special case for count &lt; 10</dd>
-      </dl><dl><dt>
+      </dl>
+<dl>
+<dt>
 
           <code><a href="format_extreme_values.html">format_extreme_values()</a></code>
           <span class="badge lifecycle lifecycle-stable">stable</span>
         </dt>
         <dd>Format a single extreme value</dd>
-      </dl><dl><dt>
+      </dl>
+<dl>
+<dt>
 
           <code><a href="format_extreme_values_ci.html">format_extreme_values_ci()</a></code>
           <span class="badge lifecycle lifecycle-stable">stable</span>
         </dt>
         <dd>Format extreme values part of a confidence interval</dd>
-      </dl><dl><dt>
+      </dl>
+<dl>
+<dt>
 
           <code><a href="format_fraction.html">format_fraction()</a></code>
           <span class="badge lifecycle lifecycle-stable">stable</span>
         </dt>
         <dd>Format fraction and percentage</dd>
-      </dl><dl><dt>
+      </dl>
+<dl>
+<dt>
 
           <code><a href="format_fraction_fixed_dp.html">format_fraction_fixed_dp()</a></code>
           <span class="badge lifecycle lifecycle-stable">stable</span>
         </dt>
         <dd>Format fraction and percentage with fixed single decimal place</dd>
-      </dl><dl><dt>
+      </dl>
+<dl>
+<dt>
 
           <code><a href="format_fraction_threshold.html">format_fraction_threshold()</a></code>
           <span class="badge lifecycle lifecycle-stable">stable</span>
         </dt>
         <dd>Format fraction with lower threshold</dd>
-      </dl><dl><dt>
+      </dl>
+<dl>
+<dt>
 
           <code><a href="format_sigfig.html">format_sigfig()</a></code>
 
         </dt>
         <dd>Format numeric values by significant figures</dd>
-      </dl><dl><dt>
+      </dl>
+<dl>
+<dt>
 
           <code><a href="format_xx.html">format_xx()</a></code>
 
         </dt>
         <dd>Format XX as a formatting function</dd>
-      </dl></div><div class="section level2">
-      <h2 id="rtables-scoring-functions">rtables Scoring Functions<a class="anchor" aria-label="anchor" href="#rtables-scoring-functions"></a></h2>
+      </dl>
+</div>
+<div class="section level2">
+      <h2 id="rtables-scoring-functions">rtables Scoring Functions<a class="anchor" aria-label="anchor" href="#rtables-scoring-functions"></a>
+</h2>
 
       <div class="section-desc"><p>These functions can help with table sorting.</p></div>
 
 
-    </div><div class="section level2">
+    </div>
+<div class="section level2">
 
 
 
 
-      <dl><dt>
+      <dl>
+<dt>
 
           <code><a href="score_occurrences.html">score_occurrences()</a></code> <code><a href="score_occurrences.html">score_occurrences_cols()</a></code> <code><a href="score_occurrences.html">score_occurrences_subtable()</a></code> <code><a href="score_occurrences.html">score_occurrences_cont_cols()</a></code>
           <span class="badge lifecycle lifecycle-stable">stable</span>
         </dt>
         <dd>Occurrence table sorting</dd>
-      </dl></div><div class="section level2">
-      <h2 id="rtables-pruning-functions">rtables Pruning Functions<a class="anchor" aria-label="anchor" href="#rtables-pruning-functions"></a></h2>
+      </dl>
+</div>
+<div class="section level2">
+      <h2 id="rtables-pruning-functions">rtables Pruning Functions<a class="anchor" aria-label="anchor" href="#rtables-pruning-functions"></a>
+</h2>
 
       <div class="section-desc"><p>These functions and classes help with flexible pruning of tables.</p></div>
 
 
-    </div><div class="section level2">
+    </div>
+<div class="section level2">
 
 
 
 
-      <dl><dt>
+      <dl>
+<dt>
 
           <code><a href="combination_function.html">`&amp;`(<i>&lt;CombinationFunction&gt;</i>,<i>&lt;CombinationFunction&gt;</i>)</a></code> <code><a href="combination_function.html">`|`(<i>&lt;CombinationFunction&gt;</i>,<i>&lt;CombinationFunction&gt;</i>)</a></code> <code><a href="combination_function.html">`!`(<i>&lt;CombinationFunction&gt;</i>)</a></code>
           <span class="badge lifecycle lifecycle-stable">stable</span>
         </dt>
-        <dd>Class for <code>CombinationFunction</code></dd>
-      </dl><dl><dt>
+        <dd>Class for <code>CombinationFunction</code>
+</dd>
+      </dl>
+<dl>
+<dt>
 
           <code><a href="prune_occurrences.html">keep_rows()</a></code> <code><a href="prune_occurrences.html">keep_content_rows()</a></code> <code><a href="prune_occurrences.html">has_count_in_cols()</a></code> <code><a href="prune_occurrences.html">has_count_in_any_col()</a></code> <code><a href="prune_occurrences.html">has_fraction_in_cols()</a></code> <code><a href="prune_occurrences.html">has_fraction_in_any_col()</a></code> <code><a href="prune_occurrences.html">has_fractions_difference()</a></code> <code><a href="prune_occurrences.html">has_counts_difference()</a></code>
           <span class="badge lifecycle lifecycle-stable">stable</span>
         </dt>
         <dd>Occurrence table pruning</dd>
-      </dl></div><div class="section level2">
-      <h2 id="graph-helper-functions">Graph Helper Functions<a class="anchor" aria-label="anchor" href="#graph-helper-functions"></a></h2>
+      </dl>
+</div>
+<div class="section level2">
+      <h2 id="graph-helper-functions">Graph Helper Functions<a class="anchor" aria-label="anchor" href="#graph-helper-functions"></a>
+</h2>
 
       <div class="section-desc"><p>These functions are useful to modify graphs.</p></div>
 
 
-    </div><div class="section level2">
+    </div>
+<div class="section level2">
 
 
 
 
-      <dl><dt>
+      <dl>
+<dt>
 
           <code><a href="decorate_grob.html">decorate_grob()</a></code>
           <span class="badge lifecycle lifecycle-stable">stable</span>
         </dt>
         <dd>Add titles, footnotes, page Number, and a bounding box to a grid grob</dd>
-      </dl><dl><dt>
+      </dl>
+<dl>
+<dt>
 
           <code><a href="split_text_grob.html">split_text_grob()</a></code>
 
         </dt>
         <dd>Split text according to available text width</dd>
-      </dl><dl><dt>
+      </dl>
+<dl>
+<dt>
 
           <code><a href="decorate_grob_factory.html">decorate_grob_factory()</a></code>
 
         </dt>
         <dd>Update page number</dd>
-      </dl><dl><dt>
+      </dl>
+<dl>
+<dt>
 
           <code><a href="decorate_grob_set.html">decorate_grob_set()</a></code>
           <span class="badge lifecycle lifecycle-stable">stable</span>
         </dt>
         <dd>Decorate set of <code>grob</code>s and add page numbering</dd>
-      </dl><dl><dt>
+      </dl>
+<dl>
+<dt>
 
           <code><a href="h_g_ipp.html">h_g_ipp()</a></code>
           <span class="badge lifecycle lifecycle-stable">stable</span>
         </dt>
         <dd>Helper function to create simple line plot over time</dd>
-      </dl><dl><dt>
+      </dl>
+<dl>
+<dt>
 
           <code><a href="h_xticks.html">h_xticks()</a></code>
           <span class="badge lifecycle lifecycle-stable">stable</span>
         </dt>
         <dd>Helper function to calculate x-tick positions</dd>
-      </dl></div><div class="section level2">
-      <h2 id="data-helper-functions">Data Helper Functions<a class="anchor" aria-label="anchor" href="#data-helper-functions"></a></h2>
+      </dl>
+</div>
+<div class="section level2">
+      <h2 id="data-helper-functions">Data Helper Functions<a class="anchor" aria-label="anchor" href="#data-helper-functions"></a>
+</h2>
 
       <div class="section-desc"><p>These functions are used by other functions to derive data.</p></div>
 
 
-    </div><div class="section level2">
+    </div>
+<div class="section level2">
 
 
 
 
-      <dl><dt>
+      <dl>
+<dt>
 
           <code><a href="aesi_label.html">aesi_label()</a></code>
           <span class="badge lifecycle lifecycle-stable">stable</span>
         </dt>
         <dd>Labels for adverse event baskets</dd>
-      </dl><dl><dt>
+      </dl>
+<dl>
+<dt>
 
           <code><a href="as_factor_keep_attributes.html">as_factor_keep_attributes()</a></code>
 
         </dt>
         <dd>Conversion of a vector to a factor</dd>
-      </dl><dl><dt>
+      </dl>
+<dl>
+<dt>
 
           <code><a href="bins_percent_labels.html">bins_percent_labels()</a></code>
 
         </dt>
         <dd>Labels for bins in percent</dd>
-      </dl><dl><dt>
+      </dl>
+<dl>
+<dt>
 
           <code><a href="combine_levels.html">combine_levels()</a></code>
           <span class="badge lifecycle lifecycle-stable">stable</span>
         </dt>
         <dd>Combine factor levels</dd>
-      </dl><dl><dt>
+      </dl>
+<dl>
+<dt>
 
           <code><a href="cut_quantile_bins.html">cut_quantile_bins()</a></code>
           <span class="badge lifecycle lifecycle-stable">stable</span>
         </dt>
         <dd>Cut numeric vector into empirical quantile bins</dd>
-      </dl><dl><dt>
+      </dl>
+<dl>
+<dt>
 
           <code><a href="day2month.html">day2month()</a></code>
 
         </dt>
         <dd>Conversion of days to months</dd>
-      </dl><dl><dt>
+      </dl>
+<dl>
+<dt>
 
           <code><a href="df_explicit_na.html">df_explicit_na()</a></code>
           <span class="badge lifecycle lifecycle-stable">stable</span>
         </dt>
         <dd>Encode categorical missing values in a data frame</dd>
-      </dl><dl><dt>
+      </dl>
+<dl>
+<dt>
 
           <code><a href="d_count_abnormal_by_baseline.html">d_count_abnormal_by_baseline()</a></code>
           <span class="badge lifecycle lifecycle-stable">stable</span>
         </dt>
-        <dd>Description function for <code><a href="../reference/abnormal_by_baseline.html">s_count_abnormal_by_baseline()</a></code></dd>
-      </dl><dl><dt>
+        <dd>Description function for <code><a href="../reference/abnormal_by_baseline.html">s_count_abnormal_by_baseline()</a></code>
+</dd>
+      </dl>
+<dl>
+<dt>
 
           <code><a href="d_count_cumulative.html">d_count_cumulative()</a></code>
           <span class="badge lifecycle lifecycle-stable">stable</span>
         </dt>
         <dd>Description of cumulative count</dd>
-      </dl><dl><dt>
+      </dl>
+<dl>
+<dt>
 
           <code><a href="d_count_missed_doses.html">d_count_missed_doses()</a></code>
           <span class="badge lifecycle lifecycle-stable">stable</span>
         </dt>
-        <dd>Description function that calculates labels for <code><a href="../reference/count_missed_doses.html">s_count_missed_doses()</a></code></dd>
-      </dl><dl><dt>
+        <dd>Description function that calculates labels for <code><a href="../reference/count_missed_doses.html">s_count_missed_doses()</a></code>
+</dd>
+      </dl>
+<dl>
+<dt>
 
           <code><a href="d_onco_rsp_label.html">d_onco_rsp_label()</a></code>
           <span class="badge lifecycle lifecycle-stable">stable</span>
         </dt>
         <dd>Description of standard oncology response</dd>
-      </dl><dl><dt>
+      </dl>
+<dl>
+<dt>
 
           <code><a href="d_pkparam.html">d_pkparam()</a></code>
           <span class="badge lifecycle lifecycle-stable">stable</span>
         </dt>
         <dd>Generate PK reference dataset</dd>
-      </dl><dl><dt>
+      </dl>
+<dl>
+<dt>
 
           <code><a href="d_proportion.html">d_proportion()</a></code>
           <span class="badge lifecycle lifecycle-stable">stable</span>
         </dt>
         <dd>Description of the proportion summary</dd>
-      </dl><dl><dt>
+      </dl>
+<dl>
+<dt>
 
           <code><a href="d_proportion_diff.html">d_proportion_diff()</a></code>
           <span class="badge lifecycle lifecycle-stable">stable</span>
         </dt>
         <dd>Description of method used for proportion comparison</dd>
-      </dl><dl><dt>
+      </dl>
+<dl>
+<dt>
 
           <code><a href="d_rsp_subgroups_colvars.html">d_rsp_subgroups_colvars()</a></code>
           <span class="badge lifecycle lifecycle-stable">stable</span>
         </dt>
         <dd>Labels for column variables in binary response by subgroup table</dd>
-      </dl><dl><dt>
+      </dl>
+<dl>
+<dt>
 
           <code><a href="d_survival_subgroups_colvars.html">d_survival_subgroups_colvars()</a></code>
           <span class="badge lifecycle lifecycle-stable">stable</span>
         </dt>
         <dd>Labels for column variables in survival duration by subgroup table</dd>
-      </dl><dl><dt>
+      </dl>
+<dl>
+<dt>
 
           <code><a href="d_test_proportion_diff.html">d_test_proportion_diff()</a></code>
           <span class="badge lifecycle lifecycle-stable">stable</span>
         </dt>
         <dd>Description of the difference test between two proportions</dd>
-      </dl><dl><dt>
+      </dl>
+<dl>
+<dt>
 
           <code><a href="explicit_na.html">explicit_na()</a></code>
           <span class="badge lifecycle lifecycle-stable">stable</span>
         </dt>
         <dd>Missing data</dd>
-      </dl><dl><dt>
+      </dl>
+<dl>
+<dt>
 
           <code><a href="fct_collapse_only.html">fct_collapse_only()</a></code>
           <span class="badge lifecycle lifecycle-stable">stable</span>
         </dt>
         <dd>Collapse factor levels and keep only those new group levels</dd>
-      </dl><dl><dt>
+      </dl>
+<dl>
+<dt>
 
           <code><a href="fct_discard.html">fct_discard()</a></code>
           <span class="badge lifecycle lifecycle-stable">stable</span>
         </dt>
         <dd>Discard specified levels of a factor</dd>
-      </dl><dl><dt>
+      </dl>
+<dl>
+<dt>
 
           <code><a href="fct_explicit_na_if.html">fct_explicit_na_if()</a></code>
           <span class="badge lifecycle lifecycle-stable">stable</span>
         </dt>
         <dd>Insertion of explicit missing values in a factor</dd>
-      </dl><dl><dt>
+      </dl>
+<dl>
+<dt>
 
           <code><a href="f_conf_level.html">f_conf_level()</a></code>
           <span class="badge lifecycle lifecycle-stable">stable</span>
         </dt>
         <dd>Utility function to create label for confidence interval</dd>
-      </dl><dl><dt>
+      </dl>
+<dl>
+<dt>
 
           <code><a href="f_pval.html">f_pval()</a></code>
           <span class="badge lifecycle lifecycle-stable">stable</span>
         </dt>
         <dd>Utility function to create label for p-value</dd>
-      </dl><dl><dt>
+      </dl>
+<dl>
+<dt>
 
           <code><a href="h_data_plot.html">h_data_plot()</a></code>
           <span class="badge lifecycle lifecycle-stable">stable</span>
         </dt>
         <dd>Helper function to tidy survival fit data</dd>
-      </dl><dl><dt>
+      </dl>
+<dl>
+<dt>
 
           <code><a href="month2day.html">month2day()</a></code>
           <span class="badge lifecycle lifecycle-stable">stable</span>
         </dt>
         <dd>Conversion of months to days</dd>
-      </dl><dl><dt>
+      </dl>
+<dl>
+<dt>
 
           <code><a href="reapply_varlabels.html">reapply_varlabels()</a></code>
 
         </dt>
         <dd>Reapply variable labels</dd>
-      </dl><dl><dt>
+      </dl>
+<dl>
+<dt>
 
           <code><a href="sas_na.html">sas_na()</a></code>
           <span class="badge lifecycle lifecycle-stable">stable</span>
         </dt>
-        <dd>Convert strings to <code>NA</code></dd>
-      </dl><dl><dt>
+        <dd>Convert strings to <code>NA</code>
+</dd>
+      </dl>
+<dl>
+<dt>
 
           <code><a href="stat_mean_ci.html">stat_mean_ci()</a></code>
           <span class="badge lifecycle lifecycle-stable">stable</span>
         </dt>
         <dd>Confidence interval for mean</dd>
-      </dl><dl><dt>
+      </dl>
+<dl>
+<dt>
 
           <code><a href="stat_mean_pval.html">stat_mean_pval()</a></code>
           <span class="badge lifecycle lifecycle-stable">stable</span>
         </dt>
         <dd>p-Value of the mean</dd>
-      </dl><dl><dt>
+      </dl>
+<dl>
+<dt>
 
           <code><a href="stat_median_ci.html">stat_median_ci()</a></code>
           <span class="badge lifecycle lifecycle-stable">stable</span>
         </dt>
         <dd>Confidence interval for median</dd>
-      </dl><dl><dt>
+      </dl>
+<dl>
+<dt>
 
           <code><a href="stat_propdiff_ci.html">stat_propdiff_ci()</a></code>
           <span class="badge lifecycle lifecycle-stable">stable</span>
         </dt>
         <dd>Proportion difference and confidence interval</dd>
-      </dl><dl><dt>
+      </dl>
+<dl>
+<dt>
 
           <code><a href="strata_normal_quantile.html">strata_normal_quantile()</a></code>
           <span class="badge lifecycle lifecycle-stable">stable</span>
         </dt>
         <dd>Helper function for the estimation of stratified quantiles</dd>
-      </dl><dl><dt>
+      </dl>
+<dl>
+<dt>
 
           <code><a href="to_n.html">to_n()</a></code>
           <span class="badge lifecycle lifecycle-stable">stable</span>
         </dt>
         <dd>Replicate entries of a vector if required</dd>
-      </dl><dl><dt>
+      </dl>
+<dl>
+<dt>
 
           <code><a href="update_weights_strat_wilson.html">update_weights_strat_wilson()</a></code>
           <span class="badge lifecycle lifecycle-stable">stable</span>
         </dt>
-        <dd>Helper function for the estimation of weights for <code><a href="../reference/h_proportions.html">prop_strat_wilson()</a></code></dd>
-      </dl></div><div class="section level2">
-      <h2 id="assertion-functions">Assertion Functions<a class="anchor" aria-label="anchor" href="#assertion-functions"></a></h2>
+        <dd>Helper function for the estimation of weights for <code><a href="../reference/h_proportions.html">prop_strat_wilson()</a></code>
+</dd>
+      </dl>
+</div>
+<div class="section level2">
+      <h2 id="assertion-functions">Assertion Functions<a class="anchor" aria-label="anchor" href="#assertion-functions"></a>
+</h2>
 
       <div class="section-desc"><p>These functions supplement those in the <code>checkmate</code> package.</p></div>
 
 
-    </div><div class="section level2">
+    </div>
+<div class="section level2">
 
 
 
 
-      <dl><dt>
+      <dl>
+<dt>
 
           <code><a href="assertions.html">assert_list_of_variables()</a></code> <code><a href="assertions.html">assert_df_with_variables()</a></code> <code><a href="assertions.html">assert_valid_factor()</a></code> <code><a href="assertions.html">assert_df_with_factors()</a></code> <code><a href="assertions.html">assert_proportion_value()</a></code>
 
         </dt>
-        <dd>Additional assertions to use with <code>checkmate</code></dd>
-      </dl></div><div class="section level2">
-      <h2 id="data">Data<a class="anchor" aria-label="anchor" href="#data"></a></h2>
+        <dd>Additional assertions to use with <code>checkmate</code>
+</dd>
+      </dl>
+</div>
+<div class="section level2">
+      <h2 id="data">Data<a class="anchor" aria-label="anchor" href="#data"></a>
+</h2>
 
       <div class="section-desc"><p>Data included in the package.</p></div>
 
 
-    </div><div class="section level2">
+    </div>
+<div class="section level2">
 
 
 
 
-      <dl><dt>
+      <dl>
+<dt>
 
           <code><a href="ex_data.html">tern_ex_adsl</a></code> <code><a href="ex_data.html">tern_ex_adae</a></code> <code><a href="ex_data.html">tern_ex_adlb</a></code> <code><a href="ex_data.html">tern_ex_adpp</a></code> <code><a href="ex_data.html">tern_ex_adrs</a></code> <code><a href="ex_data.html">tern_ex_adtte</a></code>
 
         </dt>
         <dd>Simulated CDISC data for examples</dd>
-      </dl></div><div class="section level2">
-      <h2 id="deprecated-functions">Deprecated Functions<a class="anchor" aria-label="anchor" href="#deprecated-functions"></a></h2>
+      </dl>
+</div>
+<div class="section level2">
+      <h2 id="deprecated-functions">Deprecated Functions<a class="anchor" aria-label="anchor" href="#deprecated-functions"></a>
+</h2>
 
       <div class="section-desc"><p>Functions that are currently deprecated within <code>tern</code>.</p></div>
 
 
-    </div><div class="section level2">
+    </div>
+<div class="section level2">
 
 
 
 
-      <dl><dt>
+      <dl>
+<dt>
 
           <code><a href="forest_viewport.html">forest_viewport()</a></code>
           <span class="badge lifecycle lifecycle-deprecated">deprecated</span>
         </dt>
         <dd>Create a viewport tree for the forest plot</dd>
-      </dl><dl><dt>
+      </dl>
+<dl>
+<dt>
 
           <code><a href="h_decompose_gg.html">h_decompose_gg()</a></code>
           <span class="badge lifecycle lifecycle-deprecated">deprecated</span>
         </dt>
-        <dd><code>ggplot</code> decomposition</dd>
-      </dl><dl><dt>
+        <dd>
+<code>ggplot</code> decomposition</dd>
+      </dl>
+<dl>
+<dt>
 
           <code><a href="h_ggkm.html">h_ggkm()</a></code>
           <span class="badge lifecycle lifecycle-deprecated">deprecated</span>
         </dt>
         <dd>Helper function to create a KM plot</dd>
-      </dl><dl><dt>
+      </dl>
+<dl>
+<dt>
 
           <code><a href="h_grob_coxph.html">h_grob_coxph()</a></code>
           <span class="badge lifecycle lifecycle-deprecated">deprecated</span>
         </dt>
         <dd>Helper function to create Cox-PH grobs</dd>
-      </dl><dl><dt>
+      </dl>
+<dl>
+<dt>
 
           <code><a href="h_grob_median_surv.html">h_grob_median_surv()</a></code>
           <span class="badge lifecycle lifecycle-deprecated">deprecated</span>
         </dt>
         <dd>Helper function to create survival estimation grobs</dd>
-      </dl><dl><dt>
+      </dl>
+<dl>
+<dt>
 
           <code><a href="h_grob_tbl_at_risk.html">h_grob_tbl_at_risk()</a></code>
           <span class="badge lifecycle lifecycle-deprecated">deprecated</span>
         </dt>
         <dd>Helper function to create patient-at-risk grobs</dd>
-      </dl><dl><dt>
+      </dl>
+<dl>
+<dt>
 
           <code><a href="h_grob_y_annot.html">h_grob_y_annot()</a></code>
           <span class="badge lifecycle lifecycle-deprecated">deprecated</span>
         </dt>
         <dd>Helper function to create grid object with y-axis annotation</dd>
-      </dl><dl><dt>
+      </dl>
+<dl>
+<dt>
 
           <code><a href="h_km_layout.html">h_km_layout()</a></code>
           <span class="badge lifecycle lifecycle-deprecated">deprecated</span>
         </dt>
         <dd>Helper function to prepare a KM layout</dd>
-      </dl><dl><dt>
+      </dl>
+<dl>
+<dt>
 
           <code><a href="stack_grobs.html">stack_grobs()</a></code>
           <span class="badge lifecycle lifecycle-deprecated">deprecated</span>
         </dt>
         <dd>Stack multiple grobs</dd>
-      </dl><dl><dt>
+      </dl>
+<dl>
+<dt>
 
           <code><a href="arrange_grobs.html">arrange_grobs()</a></code>
           <span class="badge lifecycle lifecycle-deprecated">deprecated</span>
         </dt>
         <dd>Arrange multiple grobs</dd>
-      </dl><dl><dt>
+      </dl>
+<dl>
+<dt>
 
           <code><a href="draw_grob.html">draw_grob()</a></code>
           <span class="badge lifecycle lifecycle-deprecated">deprecated</span>
         </dt>
-        <dd>Draw <code>grob</code></dd>
-      </dl></div>
+        <dd>Draw <code>grob</code>
+</dd>
+      </dl>
+</div>
   </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
-    </nav></aside></div>
+    </nav></aside>
+</div>
 
 
     <footer><div class="nest">
   <p>tern is a part of the <strong>NEST</strong> and <a href="https://pharmaverse.org/" class="external-link"><strong>pharmaverse</strong></a>.</p>
 </div>
-<script type="text/javascript" src="../analytics.js"></script></footer></div>
-
+<script type="text/javascript" src="../analytics.js"></script></footer>
+</div>
 
 
 
 
-  </body></html>
 
+  </body>
+</html>
diff --git a/main/reference/labels_or_names.html b/main/reference/labels_or_names.html
index 29503f35b8..27e1bd6154 100644
--- a/main/reference/labels_or_names.html
+++ b/main/reference/labels_or_names.html
@@ -1,7 +1,30 @@
-<!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Labels or names of list elements — labels_or_names • tern</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Labels or names of list elements — labels_or_names"><meta name="description" content="Internal helper function for working with nested statistic function results which typically
-don't have labels but names that we can use."><meta property="og:description" content="Internal helper function for working with nested statistic function results which typically
-don't have labels but names that we can use."><meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png"><link rel="stylesheet" href="../consent.css"><script src="../consent.js" type="text/javascript" charset="utf-8"></script></head><body>
+<html lang="en">
+<head>
+<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+<meta charset="utf-8">
+<meta http-equiv="X-UA-Compatible" content="IE=edge">
+<meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<title>Labels or names of list elements — labels_or_names • tern</title>
+<!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png">
+<link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png">
+<link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png">
+<link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png">
+<link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png">
+<link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png">
+<script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet">
+<script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet">
+<link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet">
+<script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Labels or names of list elements — labels_or_names">
+<meta name="description" content="Internal helper function for working with nested statistic function results which typically
+don't have labels but names that we can use.">
+<meta property="og:description" content="Internal helper function for working with nested statistic function results which typically
+don't have labels but names that we can use.">
+<meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png">
+<link rel="stylesheet" href="../consent.css">
+<script src="../consent.js" type="text/javascript" charset="utf-8"></script>
+</head>
+<body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
 
 
@@ -17,26 +40,66 @@
     </button>
 
     <div id="navbar" class="collapse navbar-collapse ms-3">
-      <ul class="navbar-nav me-auto"><li class="nav-item"><a class="nav-link" href="../articles/tern.html">Get started</a></li>
+      <ul class="navbar-nav me-auto">
+<li class="nav-item"><a class="nav-link" href="../articles/tern.html">Get started</a></li>
 <li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
 <li class="nav-item dropdown">
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-articles" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Articles</button>
-  <ul class="dropdown-menu" aria-labelledby="dropdown-articles"><li><a class="dropdown-item" href="../articles/missing_values.html">Missing Values in Tern</a></li>
+  <ul class="dropdown-menu" aria-labelledby="dropdown-articles">
+<li><a class="dropdown-item" href="../articles/missing_values.html">Missing Values in Tern</a></li>
     <li><a class="dropdown-item" href="../articles/tables.html">Tabulation</a></li>
     <li><a class="dropdown-item" href="../articles/tern_formats.html">Formatting Functions</a></li>
     <li><a class="dropdown-item" href="../articles/tern_functions_guide.html">Understanding `tern` functions</a></li>
-  </ul></li>
+  </ul>
+</li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
-  <ul class="dropdown-menu" aria-labelledby="dropdown-reports"><li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
+  <ul class="dropdown-menu" aria-labelledby="dropdown-reports">
+<li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
     <li><a class="dropdown-item" href="../unit-test-report/">Unit test report</a></li>
     <li><a class="dropdown-item" href="../unit-test-report-non-cran/">Non-CRAN unit test report</a></li>
-  </ul></li>
-      </ul><ul class="navbar-nav"><li class="nav-item"><form class="form-inline" role="search">
- <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json"></form></li>
+  </ul>
+</li>
+      <div><li class="nav-item dropdown">
+    <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-versions">Versions</a>
+    <div class="dropdown-menu" aria-labelledby="dropdown-versions">
+    <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/main">main</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.5">v0.9.5</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.4">v0.9.4</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.3">v0.9.3</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1-rc3">v0.9.1-rc3</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a>
+</div>
+</li></div>
+</ul>
+<ul class="navbar-nav">
+<li class="nav-item"><form class="form-inline" role="search">
+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json">
+</form></li>
 <li class="nav-item"><a class="external-link nav-link" href="https://github.com/insightsengineering/tern" aria-label="GitHub"><span class="fa fa-github"></span></a></li>
-      </ul></div>
+      </ul>
+</div>
 
 
   </div>
@@ -54,35 +117,43 @@
     </div>
 
     <div class="section level2">
-    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
+    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">labels_or_names</span><span class="op">(</span><span class="va">x</span><span class="op">)</span></span></code></pre></div>
     </div>
 
     <div class="section level2">
-    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
+    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a>
+</h2>
 
 
-<dl><dt id="arg-x">x<a class="anchor" aria-label="anchor" href="#arg-x"></a></dt>
+<dl>
+<dt id="arg-x">x<a class="anchor" aria-label="anchor" href="#arg-x"></a>
+</dt>
 <dd><p>(<code>list</code>)<br> a list.</p></dd>
 
-</dl></div>
+</dl>
+</div>
     <div class="section level2">
-    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
+    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a>
+</h2>
     <p>A <code>character</code> vector with the labels or names for the list elements.</p>
     </div>
 
   </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
-    </nav></aside></div>
+    </nav></aside>
+</div>
 
 
     <footer><div class="nest">
   <p>tern is a part of the <strong>NEST</strong> and <a href="https://pharmaverse.org/" class="external-link"><strong>pharmaverse</strong></a>.</p>
 </div>
-<script type="text/javascript" src="../analytics.js"></script></footer></div>
-
+<script type="text/javascript" src="../analytics.js"></script></footer>
+</div>
 
 
 
 
-  </body></html>
 
+  </body>
+</html>
diff --git a/main/reference/labels_use_control.html b/main/reference/labels_use_control.html
index b54a212902..d405a9daa7 100644
--- a/main/reference/labels_use_control.html
+++ b/main/reference/labels_use_control.html
@@ -1,13 +1,36 @@
-<!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Update labels according to control specifications — labels_use_control • tern</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Update labels according to control specifications — labels_use_control"><meta name="description" content='
+<html lang="en">
+<head>
+<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+<meta charset="utf-8">
+<meta http-equiv="X-UA-Compatible" content="IE=edge">
+<meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<title>Update labels according to control specifications — labels_use_control • tern</title>
+<!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png">
+<link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png">
+<link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png">
+<link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png">
+<link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png">
+<link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png">
+<script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet">
+<script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet">
+<link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet">
+<script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Update labels according to control specifications — labels_use_control">
+<meta name="description" content='
 Given a list of statistic labels and and a list of control parameters, updates labels with a relevant
 control specification. For example, if control has element conf_level set to 0.9, the default
 label for statistic mean_ci will be updated to "Mean 90% CI". Any labels that are supplied
-via labels_custom will not be updated regardless of control.'><meta property="og:description" content='
+via labels_custom will not be updated regardless of control.'>
+<meta property="og:description" content='
 Given a list of statistic labels and and a list of control parameters, updates labels with a relevant
 control specification. For example, if control has element conf_level set to 0.9, the default
 label for statistic mean_ci will be updated to "Mean 90% CI". Any labels that are supplied
-via labels_custom will not be updated regardless of control.'><meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png"><link rel="stylesheet" href="../consent.css"><script src="../consent.js" type="text/javascript" charset="utf-8"></script></head><body>
+via labels_custom will not be updated regardless of control.'>
+<meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png">
+<link rel="stylesheet" href="../consent.css">
+<script src="../consent.js" type="text/javascript" charset="utf-8"></script>
+</head>
+<body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
 
 
@@ -23,26 +46,66 @@
     </button>
 
     <div id="navbar" class="collapse navbar-collapse ms-3">
-      <ul class="navbar-nav me-auto"><li class="nav-item"><a class="nav-link" href="../articles/tern.html">Get started</a></li>
+      <ul class="navbar-nav me-auto">
+<li class="nav-item"><a class="nav-link" href="../articles/tern.html">Get started</a></li>
 <li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
 <li class="nav-item dropdown">
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-articles" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Articles</button>
-  <ul class="dropdown-menu" aria-labelledby="dropdown-articles"><li><a class="dropdown-item" href="../articles/missing_values.html">Missing Values in Tern</a></li>
+  <ul class="dropdown-menu" aria-labelledby="dropdown-articles">
+<li><a class="dropdown-item" href="../articles/missing_values.html">Missing Values in Tern</a></li>
     <li><a class="dropdown-item" href="../articles/tables.html">Tabulation</a></li>
     <li><a class="dropdown-item" href="../articles/tern_formats.html">Formatting Functions</a></li>
     <li><a class="dropdown-item" href="../articles/tern_functions_guide.html">Understanding `tern` functions</a></li>
-  </ul></li>
+  </ul>
+</li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
-  <ul class="dropdown-menu" aria-labelledby="dropdown-reports"><li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
+  <ul class="dropdown-menu" aria-labelledby="dropdown-reports">
+<li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
     <li><a class="dropdown-item" href="../unit-test-report/">Unit test report</a></li>
     <li><a class="dropdown-item" href="../unit-test-report-non-cran/">Non-CRAN unit test report</a></li>
-  </ul></li>
-      </ul><ul class="navbar-nav"><li class="nav-item"><form class="form-inline" role="search">
- <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json"></form></li>
+  </ul>
+</li>
+      <div><li class="nav-item dropdown">
+    <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-versions">Versions</a>
+    <div class="dropdown-menu" aria-labelledby="dropdown-versions">
+    <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/main">main</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.5">v0.9.5</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.4">v0.9.4</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.3">v0.9.3</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1-rc3">v0.9.1-rc3</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a>
+</div>
+</li></div>
+</ul>
+<ul class="navbar-nav">
+<li class="nav-item"><form class="form-inline" role="search">
+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json">
+</form></li>
 <li class="nav-item"><a class="external-link nav-link" href="https://github.com/insightsengineering/tern" aria-label="GitHub"><span class="fa fa-github"></span></a></li>
-      </ul></div>
+      </ul>
+</div>
 
 
   </div>
@@ -63,36 +126,45 @@
     </div>
 
     <div class="section level2">
-    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
+    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">labels_use_control</span><span class="op">(</span><span class="va">labels_default</span>, <span class="va">control</span>, labels_custom <span class="op">=</span> <span class="cn">NULL</span><span class="op">)</span></span></code></pre></div>
     </div>
 
     <div class="section level2">
-    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
+    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a>
+</h2>
 
 
-<dl><dt id="arg-labels-default">labels_default<a class="anchor" aria-label="anchor" href="#arg-labels-default"></a></dt>
+<dl>
+<dt id="arg-labels-default">labels_default<a class="anchor" aria-label="anchor" href="#arg-labels-default"></a>
+</dt>
 <dd><p>(named <code>character</code>)<br> a named vector of statistic labels to modify
 according to the control specifications. Labels that are explicitly defined in <code>labels_custom</code> will
 not be affected.</p></dd>
 
 
-<dt id="arg-control">control<a class="anchor" aria-label="anchor" href="#arg-control"></a></dt>
+<dt id="arg-control">control<a class="anchor" aria-label="anchor" href="#arg-control"></a>
+</dt>
 <dd><p>(named <code>list</code>)<br> list of control parameters to apply to adjust default labels.</p></dd>
 
 
-<dt id="arg-labels-custom">labels_custom<a class="anchor" aria-label="anchor" href="#arg-labels-custom"></a></dt>
+<dt id="arg-labels-custom">labels_custom<a class="anchor" aria-label="anchor" href="#arg-labels-custom"></a>
+</dt>
 <dd><p>(named <code>character</code>)<br> named vector of labels that are customized by
 the user and should not be affected by <code>control</code>.</p></dd>
 
-</dl></div>
+</dl>
+</div>
     <div class="section level2">
-    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
+    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a>
+</h2>
     <p>A named character vector of labels with control specifications applied to relevant labels.</p>
     </div>
 
     <div class="section level2">
-    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
+    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">control</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span>conf_level <span class="op">=</span> <span class="fl">0.80</span>, quantiles <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">0.1</span>, <span class="fl">0.83</span><span class="op">)</span>, test_mean <span class="op">=</span> <span class="fl">0.57</span><span class="op">)</span></span></span>
 <span class="r-in"><span><span class="fu"><a href="default_stats_formats_labels.html">get_labels_from_stats</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"mean_ci"</span>, <span class="st">"quantiles"</span>, <span class="st">"mean_pval"</span><span class="op">)</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span></span>
 <span class="r-in"><span>  <span class="fu">labels_use_control</span><span class="op">(</span>control <span class="op">=</span> <span class="va">control</span><span class="op">)</span></span></span>
@@ -104,17 +176,19 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 </code></pre></div>
     </div>
   </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
-    </nav></aside></div>
+    </nav></aside>
+</div>
 
 
     <footer><div class="nest">
   <p>tern is a part of the <strong>NEST</strong> and <a href="https://pharmaverse.org/" class="external-link"><strong>pharmaverse</strong></a>.</p>
 </div>
-<script type="text/javascript" src="../analytics.js"></script></footer></div>
-
+<script type="text/javascript" src="../analytics.js"></script></footer>
+</div>
 
 
 
 
-  </body></html>
 
+  </body>
+</html>
diff --git a/main/reference/logistic_regression_cols.html b/main/reference/logistic_regression_cols.html
index 29a3226ebd..bd776033a0 100644
--- a/main/reference/logistic_regression_cols.html
+++ b/main/reference/logistic_regression_cols.html
@@ -1,9 +1,32 @@
-<!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Logistic regression multivariate column layout function — logistic_regression_cols • tern</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Logistic regression multivariate column layout function — logistic_regression_cols"><meta name="description" content="
+<html lang="en">
+<head>
+<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+<meta charset="utf-8">
+<meta http-equiv="X-UA-Compatible" content="IE=edge">
+<meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<title>Logistic regression multivariate column layout function — logistic_regression_cols • tern</title>
+<!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png">
+<link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png">
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+<script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet">
+<script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet">
+<link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet">
+<script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Logistic regression multivariate column layout function — logistic_regression_cols">
+<meta name="description" content="
 Layout-creating function which creates a multivariate column layout summarizing logistic
-regression results. This function is a wrapper for rtables::split_cols_by_multivar()."><meta property="og:description" content="
+regression results. This function is a wrapper for rtables::split_cols_by_multivar().">
+<meta property="og:description" content="
 Layout-creating function which creates a multivariate column layout summarizing logistic
-regression results. This function is a wrapper for rtables::split_cols_by_multivar()."><meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png"><link rel="stylesheet" href="../consent.css"><script src="../consent.js" type="text/javascript" charset="utf-8"></script></head><body>
+regression results. This function is a wrapper for rtables::split_cols_by_multivar().">
+<meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png">
+<link rel="stylesheet" href="../consent.css">
+<script src="../consent.js" type="text/javascript" charset="utf-8"></script>
+</head>
+<body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
 
 
@@ -19,26 +42,66 @@
     </button>
 
     <div id="navbar" class="collapse navbar-collapse ms-3">
-      <ul class="navbar-nav me-auto"><li class="nav-item"><a class="nav-link" href="../articles/tern.html">Get started</a></li>
+      <ul class="navbar-nav me-auto">
+<li class="nav-item"><a class="nav-link" href="../articles/tern.html">Get started</a></li>
 <li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
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   <button class="nav-link dropdown-toggle" type="button" id="dropdown-articles" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Articles</button>
-  <ul class="dropdown-menu" aria-labelledby="dropdown-articles"><li><a class="dropdown-item" href="../articles/missing_values.html">Missing Values in Tern</a></li>
+  <ul class="dropdown-menu" aria-labelledby="dropdown-articles">
+<li><a class="dropdown-item" href="../articles/missing_values.html">Missing Values in Tern</a></li>
     <li><a class="dropdown-item" href="../articles/tables.html">Tabulation</a></li>
     <li><a class="dropdown-item" href="../articles/tern_formats.html">Formatting Functions</a></li>
     <li><a class="dropdown-item" href="../articles/tern_functions_guide.html">Understanding `tern` functions</a></li>
-  </ul></li>
+  </ul>
+</li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
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- <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json"></form></li>
+  </ul>
+</li>
+      <div><li class="nav-item dropdown">
+    <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-versions">Versions</a>
+    <div class="dropdown-menu" aria-labelledby="dropdown-versions">
+    <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
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+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.5">v0.9.5</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.4">v0.9.4</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.3">v0.9.3</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1-rc3">v0.9.1-rc3</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a>
+</div>
+</li></div>
+</ul>
+<ul class="navbar-nav">
+<li class="nav-item"><form class="form-inline" role="search">
+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json">
+</form></li>
 <li class="nav-item"><a class="external-link nav-link" href="https://github.com/insightsengineering/tern" aria-label="GitHub"><span class="fa fa-github"></span></a></li>
-      </ul></div>
+      </ul>
+</div>
 
 
   </div>
@@ -57,41 +120,50 @@
     </div>
 
     <div class="section level2">
-    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
+    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">logistic_regression_cols</span><span class="op">(</span><span class="va">lyt</span>, conf_level <span class="op">=</span> <span class="fl">0.95</span><span class="op">)</span></span></code></pre></div>
     </div>
 
     <div class="section level2">
-    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
+    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a>
+</h2>
 
 
-<dl><dt id="arg-lyt">lyt<a class="anchor" aria-label="anchor" href="#arg-lyt"></a></dt>
+<dl>
+<dt id="arg-lyt">lyt<a class="anchor" aria-label="anchor" href="#arg-lyt"></a>
+</dt>
 <dd><p>(<code>PreDataTableLayouts</code>)<br> layout that analyses will be added to.</p></dd>
 
 
-<dt id="arg-conf-level">conf_level<a class="anchor" aria-label="anchor" href="#arg-conf-level"></a></dt>
+<dt id="arg-conf-level">conf_level<a class="anchor" aria-label="anchor" href="#arg-conf-level"></a>
+</dt>
 <dd><p>(<code>proportion</code>)<br> confidence level of the interval.</p></dd>
 
-</dl></div>
+</dl>
+</div>
     <div class="section level2">
-    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
+    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a>
+</h2>
     <p>A layout object suitable for passing to further layouting functions. Adding this
 function to an <code>rtable</code> layout will split the table into columns corresponding to
 statistics <code>df</code>, <code>estimate</code>, <code>std_error</code>, <code>odds_ratio</code>, <code>ci</code>, and <code>pvalue</code>.</p>
     </div>
 
   </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
-    </nav></aside></div>
+    </nav></aside>
+</div>
 
 
     <footer><div class="nest">
   <p>tern is a part of the <strong>NEST</strong> and <a href="https://pharmaverse.org/" class="external-link"><strong>pharmaverse</strong></a>.</p>
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+</div>
 
 
 
 
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diff --git a/main/reference/logistic_summary_by_flag.html b/main/reference/logistic_summary_by_flag.html
index 41888b875c..30adb11463 100644
--- a/main/reference/logistic_summary_by_flag.html
+++ b/main/reference/logistic_summary_by_flag.html
@@ -1,9 +1,32 @@
-<!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Logistic regression summary table — logistic_summary_by_flag • tern</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Logistic regression summary table — logistic_summary_by_flag"><meta name="description" content="
+<html lang="en">
+<head>
+<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
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+<meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<title>Logistic regression summary table — logistic_summary_by_flag • tern</title>
+<!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png">
+<link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png">
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+<script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet">
+<script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet">
+<link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet">
+<script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Logistic regression summary table — logistic_summary_by_flag">
+<meta name="description" content="
 Constructor for content functions to be used in summarize_logistic() to summarize
-logistic regression results. This function is a wrapper for rtables::summarize_row_groups()."><meta property="og:description" content="
+logistic regression results. This function is a wrapper for rtables::summarize_row_groups().">
+<meta property="og:description" content="
 Constructor for content functions to be used in summarize_logistic() to summarize
-logistic regression results. This function is a wrapper for rtables::summarize_row_groups()."><meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png"><link rel="stylesheet" href="../consent.css"><script src="../consent.js" type="text/javascript" charset="utf-8"></script></head><body>
+logistic regression results. This function is a wrapper for rtables::summarize_row_groups().">
+<meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png">
+<link rel="stylesheet" href="../consent.css">
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+</head>
+<body>
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@@ -19,26 +42,66 @@
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+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a>
+</div>
+</li></div>
+</ul>
+<ul class="navbar-nav">
+<li class="nav-item"><form class="form-inline" role="search">
+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json">
+</form></li>
 <li class="nav-item"><a class="external-link nav-link" href="https://github.com/insightsengineering/tern" aria-label="GitHub"><span class="fa fa-github"></span></a></li>
-      </ul></div>
+      </ul>
+</div>
 
 
   </div>
@@ -57,7 +120,8 @@
     </div>
 
     <div class="section level2">
-    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
+    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">logistic_summary_by_flag</span><span class="op">(</span></span>
 <span>  <span class="va">flag_var</span>,</span>
 <span>  na_str <span class="op">=</span> <span class="fu"><a href="default_na_str.html">default_na_str</a></span><span class="op">(</span><span class="op">)</span>,</span>
@@ -66,40 +130,49 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
     </div>
 
     <div class="section level2">
-    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
+    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a>
+</h2>
 
 
-<dl><dt id="arg-flag-var">flag_var<a class="anchor" aria-label="anchor" href="#arg-flag-var"></a></dt>
+<dl>
+<dt id="arg-flag-var">flag_var<a class="anchor" aria-label="anchor" href="#arg-flag-var"></a>
+</dt>
 <dd><p>(<code>string</code>)<br> variable name identifying which row should be used in this
 content function.</p></dd>
 
 
-<dt id="arg-na-str">na_str<a class="anchor" aria-label="anchor" href="#arg-na-str"></a></dt>
+<dt id="arg-na-str">na_str<a class="anchor" aria-label="anchor" href="#arg-na-str"></a>
+</dt>
 <dd><p>(<code>string</code>)<br> string used to replace all <code>NA</code> or empty values in the output.</p></dd>
 
 
-<dt id="arg--indent-mods">.indent_mods<a class="anchor" aria-label="anchor" href="#arg--indent-mods"></a></dt>
+<dt id="arg--indent-mods">.indent_mods<a class="anchor" aria-label="anchor" href="#arg--indent-mods"></a>
+</dt>
 <dd><p>(named <code>integer</code>)<br> indent modifiers for the labels. Defaults to 0, which corresponds to the
 unmodified default behavior. Can be negative.</p></dd>
 
-</dl></div>
+</dl>
+</div>
     <div class="section level2">
-    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
+    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a>
+</h2>
     <p>A content function.</p>
     </div>
 
   </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
-    </nav></aside></div>
+    </nav></aside>
+</div>
 
 
     <footer><div class="nest">
   <p>tern is a part of the <strong>NEST</strong> and <a href="https://pharmaverse.org/" class="external-link"><strong>pharmaverse</strong></a>.</p>
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diff --git a/main/reference/make_names.html b/main/reference/make_names.html
index ca8d329e97..222a590dd6 100644
--- a/main/reference/make_names.html
+++ b/main/reference/make_names.html
@@ -1,5 +1,28 @@
-<!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Make names without dots — make_names • tern</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Make names without dots — make_names"><meta name="description" content="Make names without dots"><meta property="og:description" content="Make names without dots"><meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png"><link rel="stylesheet" href="../consent.css"><script src="../consent.js" type="text/javascript" charset="utf-8"></script></head><body>
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+<meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<title>Make names without dots — make_names • tern</title>
+<!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png">
+<link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png">
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+<link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet">
+<script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Make names without dots — make_names">
+<meta name="description" content="Make names without dots">
+<meta property="og:description" content="Make names without dots">
+<meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png">
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@@ -15,26 +38,66 @@
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+  <ul class="dropdown-menu" aria-labelledby="dropdown-articles">
+<li><a class="dropdown-item" href="../articles/missing_values.html">Missing Values in Tern</a></li>
     <li><a class="dropdown-item" href="../articles/tables.html">Tabulation</a></li>
     <li><a class="dropdown-item" href="../articles/tern_formats.html">Formatting Functions</a></li>
     <li><a class="dropdown-item" href="../articles/tern_functions_guide.html">Understanding `tern` functions</a></li>
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+  </ul>
+</li>
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+    <div class="dropdown-menu" aria-labelledby="dropdown-versions">
+    <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/main">main</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.5">v0.9.5</a>
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+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1-rc3">v0.9.1-rc3</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a>
+</div>
+</li></div>
+</ul>
+<ul class="navbar-nav">
+<li class="nav-item"><form class="form-inline" role="search">
+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json">
+</form></li>
 <li class="nav-item"><a class="external-link nav-link" href="https://github.com/insightsengineering/tern" aria-label="GitHub"><span class="fa fa-github"></span></a></li>
-      </ul></div>
+      </ul>
+</div>
 
 
   </div>
@@ -51,35 +114,43 @@
     </div>
 
     <div class="section level2">
-    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
+    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">make_names</span><span class="op">(</span><span class="va">nams</span><span class="op">)</span></span></code></pre></div>
     </div>
 
     <div class="section level2">
-    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
+    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a>
+</h2>
 
 
-<dl><dt id="arg-nams">nams<a class="anchor" aria-label="anchor" href="#arg-nams"></a></dt>
+<dl>
+<dt id="arg-nams">nams<a class="anchor" aria-label="anchor" href="#arg-nams"></a>
+</dt>
 <dd><p>(<code>character</code>)<br> vector of original names.</p></dd>
 
-</dl></div>
+</dl>
+</div>
     <div class="section level2">
-    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
+    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a>
+</h2>
     <p>A <code>character</code> <code>vector</code> of proper names, which does not use dots in contrast to <code><a href="https://rdrr.io/r/base/make.names.html" class="external-link">make.names()</a></code>.</p>
     </div>
 
   </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
-    </nav></aside></div>
+    </nav></aside>
+</div>
 
 
     <footer><div class="nest">
   <p>tern is a part of the <strong>NEST</strong> and <a href="https://pharmaverse.org/" class="external-link"><strong>pharmaverse</strong></a>.</p>
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-<script type="text/javascript" src="../analytics.js"></script></footer></div>
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+<script type="text/javascript" src="../analytics.js"></script></footer>
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diff --git a/main/reference/month2day.html b/main/reference/month2day.html
index 263df5031f..8a8233fc62 100644
--- a/main/reference/month2day.html
+++ b/main/reference/month2day.html
@@ -1,9 +1,32 @@
-<!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Conversion of months to days — month2day • tern</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Conversion of months to days — month2day"><meta name="description" content="
+<html lang="en">
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+<meta http-equiv="X-UA-Compatible" content="IE=edge">
+<meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<title>Conversion of months to days — month2day • tern</title>
+<!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png">
+<link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png">
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+<link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png">
+<link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png">
+<script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet">
+<script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet">
+<link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet">
+<script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Conversion of months to days — month2day">
+<meta name="description" content="
 Conversion of months to days. This is an approximative calculation because it
-considers each month as having an average of 30.4375 days."><meta property="og:description" content="
+considers each month as having an average of 30.4375 days.">
+<meta property="og:description" content="
 Conversion of months to days. This is an approximative calculation because it
-considers each month as having an average of 30.4375 days."><meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png"><link rel="stylesheet" href="../consent.css"><script src="../consent.js" type="text/javascript" charset="utf-8"></script></head><body>
+considers each month as having an average of 30.4375 days.">
+<meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png">
+<link rel="stylesheet" href="../consent.css">
+<script src="../consent.js" type="text/javascript" charset="utf-8"></script>
+</head>
+<body>
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@@ -19,26 +42,66 @@
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-  <ul class="dropdown-menu" aria-labelledby="dropdown-articles"><li><a class="dropdown-item" href="../articles/missing_values.html">Missing Values in Tern</a></li>
+  <ul class="dropdown-menu" aria-labelledby="dropdown-articles">
+<li><a class="dropdown-item" href="../articles/missing_values.html">Missing Values in Tern</a></li>
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+  </ul>
+</li>
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+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
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+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
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+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a>
+</div>
+</li></div>
+</ul>
+<ul class="navbar-nav">
+<li class="nav-item"><form class="form-inline" role="search">
+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json">
+</form></li>
 <li class="nav-item"><a class="external-link nav-link" href="https://github.com/insightsengineering/tern" aria-label="GitHub"><span class="fa fa-github"></span></a></li>
-      </ul></div>
+      </ul>
+</div>
 
 
   </div>
@@ -57,25 +120,32 @@
     </div>
 
     <div class="section level2">
-    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
+    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">month2day</span><span class="op">(</span><span class="va">x</span><span class="op">)</span></span></code></pre></div>
     </div>
 
     <div class="section level2">
-    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
+    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a>
+</h2>
 
 
-<dl><dt id="arg-x">x<a class="anchor" aria-label="anchor" href="#arg-x"></a></dt>
+<dl>
+<dt id="arg-x">x<a class="anchor" aria-label="anchor" href="#arg-x"></a>
+</dt>
 <dd><p>(<code>numeric(1)</code>)<br> time in months.</p></dd>
 
-</dl></div>
+</dl>
+</div>
     <div class="section level2">
-    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
+    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a>
+</h2>
     <p>A <code>numeric</code> vector with the time in days.</p>
     </div>
 
     <div class="section level2">
-    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
+    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">x</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">13.25</span>, <span class="fl">8.15</span>, <span class="fl">1</span>, <span class="fl">2.834</span><span class="op">)</span></span></span>
 <span class="r-in"><span><span class="fu">month2day</span><span class="op">(</span><span class="va">x</span><span class="op">)</span></span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> [1] 403.29688 248.06563  30.43750  86.25988</span>
@@ -83,17 +153,19 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 </code></pre></div>
     </div>
   </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
-    </nav></aside></div>
+    </nav></aside>
+</div>
 
 
     <footer><div class="nest">
   <p>tern is a part of the <strong>NEST</strong> and <a href="https://pharmaverse.org/" class="external-link"><strong>pharmaverse</strong></a>.</p>
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+</div>
 
 
 
 
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diff --git a/main/reference/muffled_car_anova.html b/main/reference/muffled_car_anova.html
index b59e370d67..896939847b 100644
--- a/main/reference/muffled_car_anova.html
+++ b/main/reference/muffled_car_anova.html
@@ -1,7 +1,30 @@
-<!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Muffled car::Anova — muffled_car_anova • tern</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Muffled car::Anova — muffled_car_anova"><meta name="description" content="Applied on survival models, car::Anova() signal that the strata terms is dropped from the model formula when
-present, this function deliberately muffles this message."><meta property="og:description" content="Applied on survival models, car::Anova() signal that the strata terms is dropped from the model formula when
-present, this function deliberately muffles this message."><meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png"><link rel="stylesheet" href="../consent.css"><script src="../consent.js" type="text/javascript" charset="utf-8"></script></head><body>
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+<meta name="description" content="Applied on survival models, car::Anova() signal that the strata terms is dropped from the model formula when
+present, this function deliberately muffles this message.">
+<meta property="og:description" content="Applied on survival models, car::Anova() signal that the strata terms is dropped from the model formula when
+present, this function deliberately muffles this message.">
+<meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png">
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+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a>
+</div>
+</li></div>
+</ul>
+<ul class="navbar-nav">
+<li class="nav-item"><form class="form-inline" role="search">
+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json">
+</form></li>
 <li class="nav-item"><a class="external-link nav-link" href="https://github.com/insightsengineering/tern" aria-label="GitHub"><span class="fa fa-github"></span></a></li>
-      </ul></div>
+      </ul>
+</div>
 
 
   </div>
 </nav><div class="container template-reference-topic">
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
-      <img src="../logo.png" class="logo" alt=""><h1>Muffled <code>car::Anova</code></h1>
+      <img src="../logo.png" class="logo" alt=""><h1>Muffled <code>car::Anova</code>
+</h1>
       <small class="dont-index">Source: <a href="https://github.com/insightsengineering/tern/blob/main/R/cox_regression.R" class="external-link"><code>R/cox_regression.R</code></a></small>
       <div class="d-none name"><code>muffled_car_anova.Rd</code></div>
     </div>
@@ -54,39 +118,48 @@
     </div>
 
     <div class="section level2">
-    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
+    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">muffled_car_anova</span><span class="op">(</span><span class="va">mod</span>, <span class="va">test_statistic</span><span class="op">)</span></span></code></pre></div>
     </div>
 
     <div class="section level2">
-    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
+    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a>
+</h2>
 
 
-<dl><dt id="arg-mod">mod<a class="anchor" aria-label="anchor" href="#arg-mod"></a></dt>
+<dl>
+<dt id="arg-mod">mod<a class="anchor" aria-label="anchor" href="#arg-mod"></a>
+</dt>
 <dd><p>(<code>coxph</code>)<br> Cox regression model fitted by <code><a href="https://rdrr.io/pkg/survival/man/coxph.html" class="external-link">survival::coxph()</a></code>.</p></dd>
 
 
-<dt id="arg-test-statistic">test_statistic<a class="anchor" aria-label="anchor" href="#arg-test-statistic"></a></dt>
+<dt id="arg-test-statistic">test_statistic<a class="anchor" aria-label="anchor" href="#arg-test-statistic"></a>
+</dt>
 <dd><p>(<code>string</code>)<br> the method used for estimation of p.values; <code>wald</code> (default) or <code>likelihood</code>.</p></dd>
 
-</dl></div>
+</dl>
+</div>
     <div class="section level2">
-    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
+    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a>
+</h2>
     <p>The output of <code><a href="https://rdrr.io/pkg/car/man/Anova.html" class="external-link">car::Anova()</a></code>, with convergence message muffled.</p>
     </div>
 
   </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
-    </nav></aside></div>
+    </nav></aside>
+</div>
 
 
     <footer><div class="nest">
   <p>tern is a part of the <strong>NEST</strong> and <a href="https://pharmaverse.org/" class="external-link"><strong>pharmaverse</strong></a>.</p>
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diff --git a/main/reference/n_available.html b/main/reference/n_available.html
index 38588bd910..2c822b0141 100644
--- a/main/reference/n_available.html
+++ b/main/reference/n_available.html
@@ -1,5 +1,28 @@
-<!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Number of available (non-missing entries) in a vector — n_available • tern</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Number of available (non-missing entries) in a vector — n_available"><meta name="description" content="Small utility function for better readability."><meta property="og:description" content="Small utility function for better readability."><meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png"><link rel="stylesheet" href="../consent.css"><script src="../consent.js" type="text/javascript" charset="utf-8"></script></head><body>
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+<meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<title>Number of available (non-missing entries) in a vector — n_available • tern</title>
+<!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png">
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+<script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet">
+<script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet">
+<link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet">
+<script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Number of available (non-missing entries) in a vector — n_available">
+<meta name="description" content="Small utility function for better readability.">
+<meta property="og:description" content="Small utility function for better readability.">
+<meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png">
+<link rel="stylesheet" href="../consent.css">
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+</head>
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@@ -15,26 +38,66 @@
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+  <ul class="dropdown-menu" aria-labelledby="dropdown-articles">
+<li><a class="dropdown-item" href="../articles/missing_values.html">Missing Values in Tern</a></li>
     <li><a class="dropdown-item" href="../articles/tables.html">Tabulation</a></li>
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+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.5">v0.9.5</a>
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+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1-rc3">v0.9.1-rc3</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a>
+</div>
+</li></div>
+</ul>
+<ul class="navbar-nav">
+<li class="nav-item"><form class="form-inline" role="search">
+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json">
+</form></li>
 <li class="nav-item"><a class="external-link nav-link" href="https://github.com/insightsengineering/tern" aria-label="GitHub"><span class="fa fa-github"></span></a></li>
-      </ul></div>
+      </ul>
+</div>
 
 
   </div>
@@ -51,35 +114,43 @@
     </div>
 
     <div class="section level2">
-    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
+    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">n_available</span><span class="op">(</span><span class="va">x</span><span class="op">)</span></span></code></pre></div>
     </div>
 
     <div class="section level2">
-    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
+    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a>
+</h2>
 
 
-<dl><dt id="arg-x">x<a class="anchor" aria-label="anchor" href="#arg-x"></a></dt>
+<dl>
+<dt id="arg-x">x<a class="anchor" aria-label="anchor" href="#arg-x"></a>
+</dt>
 <dd><p>(<code>vector</code>)<br> vector in which to count non-missing values.</p></dd>
 
-</dl></div>
+</dl>
+</div>
     <div class="section level2">
-    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
+    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a>
+</h2>
     <p>Number of non-missing values.</p>
     </div>
 
   </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
-    </nav></aside></div>
+    </nav></aside>
+</div>
 
 
     <footer><div class="nest">
   <p>tern is a part of the <strong>NEST</strong> and <a href="https://pharmaverse.org/" class="external-link"><strong>pharmaverse</strong></a>.</p>
 </div>
-<script type="text/javascript" src="../analytics.js"></script></footer></div>
-
+<script type="text/javascript" src="../analytics.js"></script></footer>
+</div>
 
 
 
 
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+  </body>
+</html>
diff --git a/main/reference/odds_ratio.html b/main/reference/odds_ratio.html
index b563d550a5..cb86cc41ed 100644
--- a/main/reference/odds_ratio.html
+++ b/main/reference/odds_ratio.html
@@ -1,15 +1,38 @@
-<!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Odds ratio estimation — odds_ratio • tern</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Odds ratio estimation — odds_ratio"><meta name="description" content="
+<html lang="en">
+<head>
+<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+<meta charset="utf-8">
+<meta http-equiv="X-UA-Compatible" content="IE=edge">
+<meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<title>Odds ratio estimation — odds_ratio • tern</title>
+<!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png">
+<link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png">
+<link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png">
+<link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png">
+<link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png">
+<link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png">
+<script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet">
+<script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet">
+<link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet">
+<script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Odds ratio estimation — odds_ratio">
+<meta name="description" content="
 The analyze function estimate_odds_ratio() creates a layout element to compare bivariate responses between
 two groups by estimating an odds ratio and its confidence interval.
 The primary analysis variable specified by vars is the group variable. Additional variables can be included in the
 analysis via the variables argument, which accepts arm, an arm variable, and strata, a stratification variable.
-If more than two arm levels are present, they can be combined into two groups using the groups_list argument."><meta property="og:description" content="
+If more than two arm levels are present, they can be combined into two groups using the groups_list argument.">
+<meta property="og:description" content="
 The analyze function estimate_odds_ratio() creates a layout element to compare bivariate responses between
 two groups by estimating an odds ratio and its confidence interval.
 The primary analysis variable specified by vars is the group variable. Additional variables can be included in the
 analysis via the variables argument, which accepts arm, an arm variable, and strata, a stratification variable.
-If more than two arm levels are present, they can be combined into two groups using the groups_list argument."><meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png"><link rel="stylesheet" href="../consent.css"><script src="../consent.js" type="text/javascript" charset="utf-8"></script></head><body>
+If more than two arm levels are present, they can be combined into two groups using the groups_list argument.">
+<meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png">
+<link rel="stylesheet" href="../consent.css">
+<script src="../consent.js" type="text/javascript" charset="utf-8"></script>
+</head>
+<body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
 
 
@@ -25,26 +48,66 @@
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+      <ul class="navbar-nav me-auto">
+<li class="nav-item"><a class="nav-link" href="../articles/tern.html">Get started</a></li>
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+  <ul class="dropdown-menu" aria-labelledby="dropdown-articles">
+<li><a class="dropdown-item" href="../articles/missing_values.html">Missing Values in Tern</a></li>
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+  </ul>
+</li>
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+  <ul class="dropdown-menu" aria-labelledby="dropdown-reports">
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+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
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+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1-rc3">v0.9.1-rc3</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a>
+</div>
+</li></div>
+</ul>
+<ul class="navbar-nav">
+<li class="nav-item"><form class="form-inline" role="search">
+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json">
+</form></li>
 <li class="nav-item"><a class="external-link nav-link" href="https://github.com/insightsengineering/tern" aria-label="GitHub"><span class="fa fa-github"></span></a></li>
-      </ul></div>
+      </ul>
+</div>
 
 
   </div>
@@ -66,7 +129,8 @@
     </div>
 
     <div class="section level2">
-    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
+    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">estimate_odds_ratio</span><span class="op">(</span></span>
 <span>  <span class="va">lyt</span>,</span>
 <span>  <span class="va">vars</span>,</span>
@@ -111,135 +175,175 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
     </div>
 
     <div class="section level2">
-    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
+    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a>
+</h2>
 
 
-<dl><dt id="arg-lyt">lyt<a class="anchor" aria-label="anchor" href="#arg-lyt"></a></dt>
+<dl>
+<dt id="arg-lyt">lyt<a class="anchor" aria-label="anchor" href="#arg-lyt"></a>
+</dt>
 <dd><p>(<code>PreDataTableLayouts</code>)<br> layout that analyses will be added to.</p></dd>
 
 
-<dt id="arg-vars">vars<a class="anchor" aria-label="anchor" href="#arg-vars"></a></dt>
+<dt id="arg-vars">vars<a class="anchor" aria-label="anchor" href="#arg-vars"></a>
+</dt>
 <dd><p>(<code>character</code>)<br> variable names for the primary analysis variable to be iterated over.</p></dd>
 
 
-<dt id="arg-variables">variables<a class="anchor" aria-label="anchor" href="#arg-variables"></a></dt>
+<dt id="arg-variables">variables<a class="anchor" aria-label="anchor" href="#arg-variables"></a>
+</dt>
 <dd><p>(named <code>list</code> of <code>string</code>)<br> list of additional analysis variables.</p></dd>
 
 
-<dt id="arg-conf-level">conf_level<a class="anchor" aria-label="anchor" href="#arg-conf-level"></a></dt>
+<dt id="arg-conf-level">conf_level<a class="anchor" aria-label="anchor" href="#arg-conf-level"></a>
+</dt>
 <dd><p>(<code>proportion</code>)<br> confidence level of the interval.</p></dd>
 
 
-<dt id="arg-groups-list">groups_list<a class="anchor" aria-label="anchor" href="#arg-groups-list"></a></dt>
+<dt id="arg-groups-list">groups_list<a class="anchor" aria-label="anchor" href="#arg-groups-list"></a>
+</dt>
 <dd><p>(named <code>list</code> of <code>character</code>)<br> specifies the new group levels via the names and the
 levels that belong to it in the character vectors that are elements of the list.</p></dd>
 
 
-<dt id="arg-na-str">na_str<a class="anchor" aria-label="anchor" href="#arg-na-str"></a></dt>
+<dt id="arg-na-str">na_str<a class="anchor" aria-label="anchor" href="#arg-na-str"></a>
+</dt>
 <dd><p>(<code>string</code>)<br> string used to replace all <code>NA</code> or empty values in the output.</p></dd>
 
 
-<dt id="arg-nested">nested<a class="anchor" aria-label="anchor" href="#arg-nested"></a></dt>
+<dt id="arg-nested">nested<a class="anchor" aria-label="anchor" href="#arg-nested"></a>
+</dt>
 <dd><p>(<code>flag</code>)<br> whether this layout instruction should be applied within the existing layout structure _if
 possible (<code>TRUE</code>, the default) or as a new top-level element (<code>FALSE</code>). Ignored if it would nest a split.
 underneath analyses, which is not allowed.</p></dd>
 
 
-<dt id="arg-method">method<a class="anchor" aria-label="anchor" href="#arg-method"></a></dt>
+<dt id="arg-method">method<a class="anchor" aria-label="anchor" href="#arg-method"></a>
+</dt>
 <dd><p>(<code>string</code>)<br> whether to use the correct (<code>"exact"</code>) calculation in the conditional likelihood or one
 of the approximations. See <code><a href="https://rdrr.io/pkg/survival/man/clogit.html" class="external-link">survival::clogit()</a></code> for details.</p></dd>
 
 
-<dt id="arg-show-labels">show_labels<a class="anchor" aria-label="anchor" href="#arg-show-labels"></a></dt>
+<dt id="arg-show-labels">show_labels<a class="anchor" aria-label="anchor" href="#arg-show-labels"></a>
+</dt>
 <dd><p>(<code>string</code>)<br> label visibility: one of "default", "visible" and "hidden".</p></dd>
 
 
-<dt id="arg-table-names">table_names<a class="anchor" aria-label="anchor" href="#arg-table-names"></a></dt>
+<dt id="arg-table-names">table_names<a class="anchor" aria-label="anchor" href="#arg-table-names"></a>
+</dt>
 <dd><p>(<code>character</code>)<br> this can be customized in the case that the same <code>vars</code> are analyzed multiple
 times, to avoid warnings from <code>rtables</code>.</p></dd>
 
 
-<dt id="arg-var-labels">var_labels<a class="anchor" aria-label="anchor" href="#arg-var-labels"></a></dt>
+<dt id="arg-var-labels">var_labels<a class="anchor" aria-label="anchor" href="#arg-var-labels"></a>
+</dt>
 <dd><p>(<code>character</code>)<br> variable labels.</p></dd>
 
 
-<dt id="arg--stats">.stats<a class="anchor" aria-label="anchor" href="#arg--stats"></a></dt>
-<dd><p>(<code>character</code>)<br> statistics to select for the table.</p>
-<p>Options are: <code>'or_ci', 'n_tot'</code></p></dd>
+<dt id="arg--stats">.stats<a class="anchor" aria-label="anchor" href="#arg--stats"></a>
+</dt>
+<dd>
+<p>(<code>character</code>)<br> statistics to select for the table.</p>
+<p>Options are: <code>'or_ci', 'n_tot'</code></p>
+</dd>
 
 
-<dt id="arg--formats">.formats<a class="anchor" aria-label="anchor" href="#arg--formats"></a></dt>
+<dt id="arg--formats">.formats<a class="anchor" aria-label="anchor" href="#arg--formats"></a>
+</dt>
 <dd><p>(named <code>character</code> or <code>list</code>)<br> formats for the statistics. See Details in <code>analyze_vars</code> for more
 information on the <code>"auto"</code> setting.</p></dd>
 
 
-<dt id="arg--labels">.labels<a class="anchor" aria-label="anchor" href="#arg--labels"></a></dt>
+<dt id="arg--labels">.labels<a class="anchor" aria-label="anchor" href="#arg--labels"></a>
+</dt>
 <dd><p>(named <code>character</code>)<br> labels for the statistics (without indent).</p></dd>
 
 
-<dt id="arg--indent-mods">.indent_mods<a class="anchor" aria-label="anchor" href="#arg--indent-mods"></a></dt>
+<dt id="arg--indent-mods">.indent_mods<a class="anchor" aria-label="anchor" href="#arg--indent-mods"></a>
+</dt>
 <dd><p>(named <code>integer</code>)<br> indent modifiers for the labels. Defaults to 0, which corresponds to the
 unmodified default behavior. Can be negative.</p></dd>
 
 
-<dt id="arg-df">df<a class="anchor" aria-label="anchor" href="#arg-df"></a></dt>
+<dt id="arg-df">df<a class="anchor" aria-label="anchor" href="#arg-df"></a>
+</dt>
 <dd><p>(<code>data.frame</code>)<br> data set containing all analysis variables.</p></dd>
 
 
-<dt id="arg--var">.var<a class="anchor" aria-label="anchor" href="#arg--var"></a></dt>
+<dt id="arg--var">.var<a class="anchor" aria-label="anchor" href="#arg--var"></a>
+</dt>
 <dd><p>(<code>string</code>)<br> single variable name that is passed by <code>rtables</code> when requested
 by a statistics function.</p></dd>
 
 
-<dt id="arg--ref-group">.ref_group<a class="anchor" aria-label="anchor" href="#arg--ref-group"></a></dt>
+<dt id="arg--ref-group">.ref_group<a class="anchor" aria-label="anchor" href="#arg--ref-group"></a>
+</dt>
 <dd><p>(<code>data.frame</code> or <code>vector</code>)<br> the data corresponding to the reference group.</p></dd>
 
 
-<dt id="arg--in-ref-col">.in_ref_col<a class="anchor" aria-label="anchor" href="#arg--in-ref-col"></a></dt>
+<dt id="arg--in-ref-col">.in_ref_col<a class="anchor" aria-label="anchor" href="#arg--in-ref-col"></a>
+</dt>
 <dd><p>(<code>flag</code>)<br><code>TRUE</code> when working with the reference level, <code>FALSE</code> otherwise.</p></dd>
 
 
-<dt id="arg--df-row">.df_row<a class="anchor" aria-label="anchor" href="#arg--df-row"></a></dt>
+<dt id="arg--df-row">.df_row<a class="anchor" aria-label="anchor" href="#arg--df-row"></a>
+</dt>
 <dd><p>(<code>data.frame</code>)<br> data frame across all of the columns for the given row split.</p></dd>
 
-</dl></div>
+</dl>
+</div>
     <div class="section level2">
-    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
+    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a>
+</h2>
 
-<ul><li><p><code>estimate_odds_ratio()</code> returns a layout object suitable for passing to further layouting functions,
+<ul>
+<li><p><code>estimate_odds_ratio()</code> returns a layout object suitable for passing to further layouting functions,
 or to <code><a href="https://insightsengineering.github.io/rtables/latest-tag/reference/build_table.html" class="external-link">rtables::build_table()</a></code>. Adding this function to an <code>rtable</code> layout will add formatted rows containing
 the statistics from <code>s_odds_ratio()</code> to the table layout.</p></li>
-</ul><ul><li><p><code>s_odds_ratio()</code> returns a named list with the statistics <code>or_ci</code>
+</ul>
+<ul>
+<li><p><code>s_odds_ratio()</code> returns a named list with the statistics <code>or_ci</code>
 (containing <code>est</code>, <code>lcl</code>, and <code>ucl</code>) and <code>n_tot</code>.</p></li>
-</ul><ul><li><p><code>a_odds_ratio()</code> returns the corresponding list with formatted <code><a href="https://insightsengineering.github.io/rtables/latest-tag/reference/CellValue.html" class="external-link">rtables::CellValue()</a></code>.</p></li>
-</ul></div>
+</ul>
+<ul>
+<li><p><code>a_odds_ratio()</code> returns the corresponding list with formatted <code><a href="https://insightsengineering.github.io/rtables/latest-tag/reference/CellValue.html" class="external-link">rtables::CellValue()</a></code>.</p></li>
+</ul>
+</div>
     <div class="section level2">
-    <h2 id="functions">Functions<a class="anchor" aria-label="anchor" href="#functions"></a></h2>
+    <h2 id="functions">Functions<a class="anchor" aria-label="anchor" href="#functions"></a>
+</h2>
 
-<ul><li><p><code>estimate_odds_ratio()</code>: Layout-creating function which can take statistics function arguments
+<ul>
+<li><p><code>estimate_odds_ratio()</code>: Layout-creating function which can take statistics function arguments
 and additional format arguments. This function is a wrapper for <code><a href="https://insightsengineering.github.io/rtables/latest-tag/reference/analyze.html" class="external-link">rtables::analyze()</a></code>.</p></li>
 <li><p><code>s_odds_ratio()</code>: Statistics function which estimates the odds ratio
 between a treatment and a control. A <code>variables</code> list with <code>arm</code> and <code>strata</code>
 variable names must be passed if a stratified analysis is required.</p></li>
 <li><p><code>a_odds_ratio()</code>: Formatted analysis function which is used as <code>afun</code> in <code>estimate_odds_ratio()</code>.</p></li>
-</ul></div>
+</ul>
+</div>
     <div class="section level2">
-    <h2 id="note">Note<a class="anchor" aria-label="anchor" href="#note"></a></h2>
+    <h2 id="note">Note<a class="anchor" aria-label="anchor" href="#note"></a>
+</h2>
 
-<ul><li><p>This function uses logistic regression for unstratified analyses, and conditional logistic regression for
+<ul>
+<li><p>This function uses logistic regression for unstratified analyses, and conditional logistic regression for
 stratified analyses. The Wald confidence interval is calculated with the specified confidence level.</p></li>
 <li><p>For stratified analyses, there is currently no implementation for conditional likelihood confidence intervals,
 therefore the likelihood confidence interval is not available as an option.</p></li>
 <li><p>When <code>vars</code> contains only responders or non-responders no odds ratio estimation is possible so the returned
 values will be <code>NA</code>.</p></li>
-</ul></div>
+</ul>
+</div>
     <div class="section level2">
-    <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"></a></h2>
+    <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"></a>
+</h2>
     <div class="dont-index"><p>Relevant helper function <code><a href="h_odds_ratio.html">h_odds_ratio()</a></code>.</p></div>
     </div>
 
     <div class="section level2">
-    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
+    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/Random.html" class="external-link">set.seed</a></span><span class="op">(</span><span class="fl">12</span><span class="op">)</span></span></span>
 <span class="r-in"><span><span class="va">dta</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a></span><span class="op">(</span></span></span>
 <span class="r-in"><span>  rsp <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/sample.html" class="external-link">sample</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="cn">TRUE</span>, <span class="cn">FALSE</span><span class="op">)</span>, <span class="fl">100</span>, <span class="cn">TRUE</span><span class="op">)</span>,</span></span>
@@ -315,17 +419,19 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 </code></pre></div>
     </div>
   </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
-    </nav></aside></div>
+    </nav></aside>
+</div>
 
 
     <footer><div class="nest">
   <p>tern is a part of the <strong>NEST</strong> and <a href="https://pharmaverse.org/" class="external-link"><strong>pharmaverse</strong></a>.</p>
 </div>
-<script type="text/javascript" src="../analytics.js"></script></footer></div>
-
+<script type="text/javascript" src="../analytics.js"></script></footer>
+</div>
 
 
 
 
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+  </body>
+</html>
diff --git a/main/reference/prop_diff.html b/main/reference/prop_diff.html
index 09d3d91c96..159fde5ed3 100644
--- a/main/reference/prop_diff.html
+++ b/main/reference/prop_diff.html
@@ -1,15 +1,38 @@
-<!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Proportion difference estimation — prop_diff • tern</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Proportion difference estimation — prop_diff"><meta name="description" content="
+<html lang="en">
+<head>
+<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+<meta charset="utf-8">
+<meta http-equiv="X-UA-Compatible" content="IE=edge">
+<meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<title>Proportion difference estimation — prop_diff • tern</title>
+<!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png">
+<link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png">
+<link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png">
+<link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png">
+<link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png">
+<link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png">
+<script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet">
+<script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet">
+<link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet">
+<script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Proportion difference estimation — prop_diff">
+<meta name="description" content="
 The analysis function estimate_proportion_diff() creates a layout element to estimate the difference in proportion
 of responders within a studied population. The primary analysis variable, vars, is a logical variable indicating
 whether a response has occurred for each record. See the method parameter for options of methods to use when
 constructing the confidence interval of the proportion difference. A stratification variable can be supplied via the
-strata element of the variables argument."><meta property="og:description" content="
+strata element of the variables argument.">
+<meta property="og:description" content="
 The analysis function estimate_proportion_diff() creates a layout element to estimate the difference in proportion
 of responders within a studied population. The primary analysis variable, vars, is a logical variable indicating
 whether a response has occurred for each record. See the method parameter for options of methods to use when
 constructing the confidence interval of the proportion difference. A stratification variable can be supplied via the
-strata element of the variables argument."><meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png"><link rel="stylesheet" href="../consent.css"><script src="../consent.js" type="text/javascript" charset="utf-8"></script></head><body>
+strata element of the variables argument.">
+<meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png">
+<link rel="stylesheet" href="../consent.css">
+<script src="../consent.js" type="text/javascript" charset="utf-8"></script>
+</head>
+<body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
 
 
@@ -25,26 +48,66 @@
     </button>
 
     <div id="navbar" class="collapse navbar-collapse ms-3">
-      <ul class="navbar-nav me-auto"><li class="nav-item"><a class="nav-link" href="../articles/tern.html">Get started</a></li>
+      <ul class="navbar-nav me-auto">
+<li class="nav-item"><a class="nav-link" href="../articles/tern.html">Get started</a></li>
 <li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
 <li class="nav-item dropdown">
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-articles" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Articles</button>
-  <ul class="dropdown-menu" aria-labelledby="dropdown-articles"><li><a class="dropdown-item" href="../articles/missing_values.html">Missing Values in Tern</a></li>
+  <ul class="dropdown-menu" aria-labelledby="dropdown-articles">
+<li><a class="dropdown-item" href="../articles/missing_values.html">Missing Values in Tern</a></li>
     <li><a class="dropdown-item" href="../articles/tables.html">Tabulation</a></li>
     <li><a class="dropdown-item" href="../articles/tern_formats.html">Formatting Functions</a></li>
     <li><a class="dropdown-item" href="../articles/tern_functions_guide.html">Understanding `tern` functions</a></li>
-  </ul></li>
+  </ul>
+</li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
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   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
-  <ul class="dropdown-menu" aria-labelledby="dropdown-reports"><li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
+  <ul class="dropdown-menu" aria-labelledby="dropdown-reports">
+<li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
     <li><a class="dropdown-item" href="../unit-test-report/">Unit test report</a></li>
     <li><a class="dropdown-item" href="../unit-test-report-non-cran/">Non-CRAN unit test report</a></li>
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- <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json"></form></li>
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+</li>
+      <div><li class="nav-item dropdown">
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+    <div class="dropdown-menu" aria-labelledby="dropdown-versions">
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+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/main">main</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.5">v0.9.5</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.4">v0.9.4</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.3">v0.9.3</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1-rc3">v0.9.1-rc3</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a>
+</div>
+</li></div>
+</ul>
+<ul class="navbar-nav">
+<li class="nav-item"><form class="form-inline" role="search">
+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json">
+</form></li>
 <li class="nav-item"><a class="external-link nav-link" href="https://github.com/insightsengineering/tern" aria-label="GitHub"><span class="fa fa-github"></span></a></li>
-      </ul></div>
+      </ul>
+</div>
 
 
   </div>
@@ -66,7 +129,8 @@
     </div>
 
     <div class="section level2">
-    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
+    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">estimate_proportion_diff</span><span class="op">(</span></span>
 <span>  <span class="va">lyt</span>,</span>
 <span>  <span class="va">vars</span>,</span>
@@ -113,127 +177,165 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
     </div>
 
     <div class="section level2">
-    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
+    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a>
+</h2>
 
 
-<dl><dt id="arg-lyt">lyt<a class="anchor" aria-label="anchor" href="#arg-lyt"></a></dt>
+<dl>
+<dt id="arg-lyt">lyt<a class="anchor" aria-label="anchor" href="#arg-lyt"></a>
+</dt>
 <dd><p>(<code>PreDataTableLayouts</code>)<br> layout that analyses will be added to.</p></dd>
 
 
-<dt id="arg-vars">vars<a class="anchor" aria-label="anchor" href="#arg-vars"></a></dt>
+<dt id="arg-vars">vars<a class="anchor" aria-label="anchor" href="#arg-vars"></a>
+</dt>
 <dd><p>(<code>character</code>)<br> variable names for the primary analysis variable to be iterated over.</p></dd>
 
 
-<dt id="arg-variables">variables<a class="anchor" aria-label="anchor" href="#arg-variables"></a></dt>
+<dt id="arg-variables">variables<a class="anchor" aria-label="anchor" href="#arg-variables"></a>
+</dt>
 <dd><p>(named <code>list</code> of <code>string</code>)<br> list of additional analysis variables.</p></dd>
 
 
-<dt id="arg-conf-level">conf_level<a class="anchor" aria-label="anchor" href="#arg-conf-level"></a></dt>
+<dt id="arg-conf-level">conf_level<a class="anchor" aria-label="anchor" href="#arg-conf-level"></a>
+</dt>
 <dd><p>(<code>proportion</code>)<br> confidence level of the interval.</p></dd>
 
 
-<dt id="arg-method">method<a class="anchor" aria-label="anchor" href="#arg-method"></a></dt>
+<dt id="arg-method">method<a class="anchor" aria-label="anchor" href="#arg-method"></a>
+</dt>
 <dd><p>(<code>string</code>)<br> the method used for the confidence interval estimation.</p></dd>
 
 
-<dt id="arg-weights-method">weights_method<a class="anchor" aria-label="anchor" href="#arg-weights-method"></a></dt>
+<dt id="arg-weights-method">weights_method<a class="anchor" aria-label="anchor" href="#arg-weights-method"></a>
+</dt>
 <dd><p>(<code>string</code>)<br> weights method. Can be either <code>"cmh"</code> or <code>"heuristic"</code>
 and directs the way weights are estimated.</p></dd>
 
 
-<dt id="arg-na-str">na_str<a class="anchor" aria-label="anchor" href="#arg-na-str"></a></dt>
+<dt id="arg-na-str">na_str<a class="anchor" aria-label="anchor" href="#arg-na-str"></a>
+</dt>
 <dd><p>(<code>string</code>)<br> string used to replace all <code>NA</code> or empty values in the output.</p></dd>
 
 
-<dt id="arg-nested">nested<a class="anchor" aria-label="anchor" href="#arg-nested"></a></dt>
+<dt id="arg-nested">nested<a class="anchor" aria-label="anchor" href="#arg-nested"></a>
+</dt>
 <dd><p>(<code>flag</code>)<br> whether this layout instruction should be applied within the existing layout structure _if
 possible (<code>TRUE</code>, the default) or as a new top-level element (<code>FALSE</code>). Ignored if it would nest a split.
 underneath analyses, which is not allowed.</p></dd>
 
 
-<dt id="arg--">...<a class="anchor" aria-label="anchor" href="#arg--"></a></dt>
+<dt id="arg--">...<a class="anchor" aria-label="anchor" href="#arg--"></a>
+</dt>
 <dd><p>additional arguments for the lower level functions.</p></dd>
 
 
-<dt id="arg-var-labels">var_labels<a class="anchor" aria-label="anchor" href="#arg-var-labels"></a></dt>
+<dt id="arg-var-labels">var_labels<a class="anchor" aria-label="anchor" href="#arg-var-labels"></a>
+</dt>
 <dd><p>(<code>character</code>)<br> variable labels.</p></dd>
 
 
-<dt id="arg-show-labels">show_labels<a class="anchor" aria-label="anchor" href="#arg-show-labels"></a></dt>
+<dt id="arg-show-labels">show_labels<a class="anchor" aria-label="anchor" href="#arg-show-labels"></a>
+</dt>
 <dd><p>(<code>string</code>)<br> label visibility: one of "default", "visible" and "hidden".</p></dd>
 
 
-<dt id="arg-table-names">table_names<a class="anchor" aria-label="anchor" href="#arg-table-names"></a></dt>
+<dt id="arg-table-names">table_names<a class="anchor" aria-label="anchor" href="#arg-table-names"></a>
+</dt>
 <dd><p>(<code>character</code>)<br> this can be customized in the case that the same <code>vars</code> are analyzed multiple
 times, to avoid warnings from <code>rtables</code>.</p></dd>
 
 
-<dt id="arg--stats">.stats<a class="anchor" aria-label="anchor" href="#arg--stats"></a></dt>
-<dd><p>(<code>character</code>)<br> statistics to select for the table.</p>
-<p>Options are: <code>'diff', 'diff_ci'</code></p></dd>
+<dt id="arg--stats">.stats<a class="anchor" aria-label="anchor" href="#arg--stats"></a>
+</dt>
+<dd>
+<p>(<code>character</code>)<br> statistics to select for the table.</p>
+<p>Options are: <code>'diff', 'diff_ci'</code></p>
+</dd>
 
 
-<dt id="arg--formats">.formats<a class="anchor" aria-label="anchor" href="#arg--formats"></a></dt>
+<dt id="arg--formats">.formats<a class="anchor" aria-label="anchor" href="#arg--formats"></a>
+</dt>
 <dd><p>(named <code>character</code> or <code>list</code>)<br> formats for the statistics. See Details in <code>analyze_vars</code> for more
 information on the <code>"auto"</code> setting.</p></dd>
 
 
-<dt id="arg--labels">.labels<a class="anchor" aria-label="anchor" href="#arg--labels"></a></dt>
+<dt id="arg--labels">.labels<a class="anchor" aria-label="anchor" href="#arg--labels"></a>
+</dt>
 <dd><p>(named <code>character</code>)<br> labels for the statistics (without indent).</p></dd>
 
 
-<dt id="arg--indent-mods">.indent_mods<a class="anchor" aria-label="anchor" href="#arg--indent-mods"></a></dt>
+<dt id="arg--indent-mods">.indent_mods<a class="anchor" aria-label="anchor" href="#arg--indent-mods"></a>
+</dt>
 <dd><p>(named <code>integer</code>)<br> indent modifiers for the labels. Defaults to 0, which corresponds to the
 unmodified default behavior. Can be negative.</p></dd>
 
 
-<dt id="arg-df">df<a class="anchor" aria-label="anchor" href="#arg-df"></a></dt>
+<dt id="arg-df">df<a class="anchor" aria-label="anchor" href="#arg-df"></a>
+</dt>
 <dd><p>(<code>data.frame</code>)<br> data set containing all analysis variables.</p></dd>
 
 
-<dt id="arg--var">.var<a class="anchor" aria-label="anchor" href="#arg--var"></a></dt>
+<dt id="arg--var">.var<a class="anchor" aria-label="anchor" href="#arg--var"></a>
+</dt>
 <dd><p>(<code>string</code>)<br> single variable name that is passed by <code>rtables</code> when requested
 by a statistics function.</p></dd>
 
 
-<dt id="arg--ref-group">.ref_group<a class="anchor" aria-label="anchor" href="#arg--ref-group"></a></dt>
+<dt id="arg--ref-group">.ref_group<a class="anchor" aria-label="anchor" href="#arg--ref-group"></a>
+</dt>
 <dd><p>(<code>data.frame</code> or <code>vector</code>)<br> the data corresponding to the reference group.</p></dd>
 
 
-<dt id="arg--in-ref-col">.in_ref_col<a class="anchor" aria-label="anchor" href="#arg--in-ref-col"></a></dt>
+<dt id="arg--in-ref-col">.in_ref_col<a class="anchor" aria-label="anchor" href="#arg--in-ref-col"></a>
+</dt>
 <dd><p>(<code>flag</code>)<br><code>TRUE</code> when working with the reference level, <code>FALSE</code> otherwise.</p></dd>
 
-</dl></div>
+</dl>
+</div>
     <div class="section level2">
-    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
+    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a>
+</h2>
 
-<ul><li><p><code>estimate_proportion_diff()</code> returns a layout object suitable for passing to further layouting functions,
+<ul>
+<li><p><code>estimate_proportion_diff()</code> returns a layout object suitable for passing to further layouting functions,
 or to <code><a href="https://insightsengineering.github.io/rtables/latest-tag/reference/build_table.html" class="external-link">rtables::build_table()</a></code>. Adding this function to an <code>rtable</code> layout will add formatted rows containing
 the statistics from <code>s_proportion_diff()</code> to the table layout.</p></li>
-</ul><ul><li><p><code>s_proportion_diff()</code> returns a named list of elements <code>diff</code> and <code>diff_ci</code>.</p></li>
-</ul><ul><li><p><code>a_proportion_diff()</code> returns the corresponding list with formatted <code><a href="https://insightsengineering.github.io/rtables/latest-tag/reference/CellValue.html" class="external-link">rtables::CellValue()</a></code>.</p></li>
-</ul></div>
+</ul>
+<ul>
+<li><p><code>s_proportion_diff()</code> returns a named list of elements <code>diff</code> and <code>diff_ci</code>.</p></li>
+</ul>
+<ul>
+<li><p><code>a_proportion_diff()</code> returns the corresponding list with formatted <code><a href="https://insightsengineering.github.io/rtables/latest-tag/reference/CellValue.html" class="external-link">rtables::CellValue()</a></code>.</p></li>
+</ul>
+</div>
     <div class="section level2">
-    <h2 id="functions">Functions<a class="anchor" aria-label="anchor" href="#functions"></a></h2>
+    <h2 id="functions">Functions<a class="anchor" aria-label="anchor" href="#functions"></a>
+</h2>
 
-<ul><li><p><code>estimate_proportion_diff()</code>: Layout-creating function which can take statistics function arguments
+<ul>
+<li><p><code>estimate_proportion_diff()</code>: Layout-creating function which can take statistics function arguments
 and additional format arguments. This function is a wrapper for <code><a href="https://insightsengineering.github.io/rtables/latest-tag/reference/analyze.html" class="external-link">rtables::analyze()</a></code>.</p></li>
 <li><p><code>s_proportion_diff()</code>: Statistics function estimating the difference
 in terms of responder proportion.</p></li>
 <li><p><code>a_proportion_diff()</code>: Formatted analysis function which is used as <code>afun</code> in <code>estimate_proportion_diff()</code>.</p></li>
-</ul></div>
+</ul>
+</div>
     <div class="section level2">
-    <h2 id="note">Note<a class="anchor" aria-label="anchor" href="#note"></a></h2>
+    <h2 id="note">Note<a class="anchor" aria-label="anchor" href="#note"></a>
+</h2>
     <p>When performing an unstratified analysis, methods <code>"cmh"</code>, <code>"strat_newcombe"</code>, and <code>"strat_newcombecc"</code> are
 not permitted.</p>
     </div>
     <div class="section level2">
-    <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"></a></h2>
+    <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"></a>
+</h2>
     <div class="dont-index"><p><code><a href="d_proportion_diff.html">d_proportion_diff()</a></code></p></div>
     </div>
 
     <div class="section level2">
-    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
+    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="co">## "Mid" case: 4/4 respond in group A, 1/2 respond in group B.</span></span></span>
 <span class="r-in"><span><span class="va">nex</span> <span class="op">&lt;-</span> <span class="fl">100</span> <span class="co"># Number of example rows</span></span></span>
 <span class="r-in"><span><span class="va">dta</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a></span><span class="op">(</span></span></span>
@@ -315,17 +417,19 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 </code></pre></div>
     </div>
   </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
-    </nav></aside></div>
+    </nav></aside>
+</div>
 
 
     <footer><div class="nest">
   <p>tern is a part of the <strong>NEST</strong> and <a href="https://pharmaverse.org/" class="external-link"><strong>pharmaverse</strong></a>.</p>
 </div>
-<script type="text/javascript" src="../analytics.js"></script></footer></div>
-
+<script type="text/javascript" src="../analytics.js"></script></footer>
+</div>
 
 
 
 
-  </body></html>
 
+  </body>
+</html>
diff --git a/main/reference/prop_diff_test.html b/main/reference/prop_diff_test.html
index b78fe5ea08..c04b96189a 100644
--- a/main/reference/prop_diff_test.html
+++ b/main/reference/prop_diff_test.html
@@ -1,13 +1,36 @@
-<!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Difference test for two proportions — prop_diff_test • tern</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Difference test for two proportions — prop_diff_test"><meta name="description" content="
+<html lang="en">
+<head>
+<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+<meta charset="utf-8">
+<meta http-equiv="X-UA-Compatible" content="IE=edge">
+<meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<title>Difference test for two proportions — prop_diff_test • tern</title>
+<!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png">
+<link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png">
+<link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png">
+<link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png">
+<link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png">
+<link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png">
+<script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet">
+<script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet">
+<link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet">
+<script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Difference test for two proportions — prop_diff_test">
+<meta name="description" content="
 The analyze function test_proportion_diff() creates a layout element to test the difference between two
 proportions. The primary analysis variable, vars, indicates whether a response has occurred for each record. See
 the method parameter for options of methods to use to calculate the p-value. Additionally, a stratification
-variable can be supplied via the strata element of the variables argument."><meta property="og:description" content="
+variable can be supplied via the strata element of the variables argument.">
+<meta property="og:description" content="
 The analyze function test_proportion_diff() creates a layout element to test the difference between two
 proportions. The primary analysis variable, vars, indicates whether a response has occurred for each record. See
 the method parameter for options of methods to use to calculate the p-value. Additionally, a stratification
-variable can be supplied via the strata element of the variables argument."><meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png"><link rel="stylesheet" href="../consent.css"><script src="../consent.js" type="text/javascript" charset="utf-8"></script></head><body>
+variable can be supplied via the strata element of the variables argument.">
+<meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png">
+<link rel="stylesheet" href="../consent.css">
+<script src="../consent.js" type="text/javascript" charset="utf-8"></script>
+</head>
+<body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
 
 
@@ -23,26 +46,66 @@
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+      <ul class="navbar-nav me-auto">
+<li class="nav-item"><a class="nav-link" href="../articles/tern.html">Get started</a></li>
 <li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
 <li class="nav-item dropdown">
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+  <ul class="dropdown-menu" aria-labelledby="dropdown-articles">
+<li><a class="dropdown-item" href="../articles/missing_values.html">Missing Values in Tern</a></li>
     <li><a class="dropdown-item" href="../articles/tables.html">Tabulation</a></li>
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     <li><a class="dropdown-item" href="../articles/tern_functions_guide.html">Understanding `tern` functions</a></li>
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+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a>
+</div>
+</li></div>
+</ul>
+<ul class="navbar-nav">
+<li class="nav-item"><form class="form-inline" role="search">
+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json">
+</form></li>
 <li class="nav-item"><a class="external-link nav-link" href="https://github.com/insightsengineering/tern" aria-label="GitHub"><span class="fa fa-github"></span></a></li>
-      </ul></div>
+      </ul>
+</div>
 
 
   </div>
@@ -63,7 +126,8 @@
     </div>
 
     <div class="section level2">
-    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
+    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">test_proportion_diff</span><span class="op">(</span></span>
 <span>  <span class="va">lyt</span>,</span>
 <span>  <span class="va">vars</span>,</span>
@@ -101,114 +165,149 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
     </div>
 
     <div class="section level2">
-    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
+    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a>
+</h2>
 
 
-<dl><dt id="arg-lyt">lyt<a class="anchor" aria-label="anchor" href="#arg-lyt"></a></dt>
+<dl>
+<dt id="arg-lyt">lyt<a class="anchor" aria-label="anchor" href="#arg-lyt"></a>
+</dt>
 <dd><p>(<code>PreDataTableLayouts</code>)<br> layout that analyses will be added to.</p></dd>
 
 
-<dt id="arg-vars">vars<a class="anchor" aria-label="anchor" href="#arg-vars"></a></dt>
+<dt id="arg-vars">vars<a class="anchor" aria-label="anchor" href="#arg-vars"></a>
+</dt>
 <dd><p>(<code>character</code>)<br> variable names for the primary analysis variable to be iterated over.</p></dd>
 
 
-<dt id="arg-variables">variables<a class="anchor" aria-label="anchor" href="#arg-variables"></a></dt>
+<dt id="arg-variables">variables<a class="anchor" aria-label="anchor" href="#arg-variables"></a>
+</dt>
 <dd><p>(named <code>list</code> of <code>string</code>)<br> list of additional analysis variables.</p></dd>
 
 
-<dt id="arg-method">method<a class="anchor" aria-label="anchor" href="#arg-method"></a></dt>
+<dt id="arg-method">method<a class="anchor" aria-label="anchor" href="#arg-method"></a>
+</dt>
 <dd><p>(<code>string</code>)<br> one of <code>chisq</code>, <code>cmh</code>, <code>fisher</code>, or <code>schouten</code>; specifies the test used
 to calculate the p-value.</p></dd>
 
 
-<dt id="arg-na-str">na_str<a class="anchor" aria-label="anchor" href="#arg-na-str"></a></dt>
+<dt id="arg-na-str">na_str<a class="anchor" aria-label="anchor" href="#arg-na-str"></a>
+</dt>
 <dd><p>(<code>string</code>)<br> string used to replace all <code>NA</code> or empty values in the output.</p></dd>
 
 
-<dt id="arg-nested">nested<a class="anchor" aria-label="anchor" href="#arg-nested"></a></dt>
+<dt id="arg-nested">nested<a class="anchor" aria-label="anchor" href="#arg-nested"></a>
+</dt>
 <dd><p>(<code>flag</code>)<br> whether this layout instruction should be applied within the existing layout structure _if
 possible (<code>TRUE</code>, the default) or as a new top-level element (<code>FALSE</code>). Ignored if it would nest a split.
 underneath analyses, which is not allowed.</p></dd>
 
 
-<dt id="arg--">...<a class="anchor" aria-label="anchor" href="#arg--"></a></dt>
+<dt id="arg--">...<a class="anchor" aria-label="anchor" href="#arg--"></a>
+</dt>
 <dd><p>additional arguments for the lower level functions.</p></dd>
 
 
-<dt id="arg-var-labels">var_labels<a class="anchor" aria-label="anchor" href="#arg-var-labels"></a></dt>
+<dt id="arg-var-labels">var_labels<a class="anchor" aria-label="anchor" href="#arg-var-labels"></a>
+</dt>
 <dd><p>(<code>character</code>)<br> variable labels.</p></dd>
 
 
-<dt id="arg-show-labels">show_labels<a class="anchor" aria-label="anchor" href="#arg-show-labels"></a></dt>
+<dt id="arg-show-labels">show_labels<a class="anchor" aria-label="anchor" href="#arg-show-labels"></a>
+</dt>
 <dd><p>(<code>string</code>)<br> label visibility: one of "default", "visible" and "hidden".</p></dd>
 
 
-<dt id="arg-table-names">table_names<a class="anchor" aria-label="anchor" href="#arg-table-names"></a></dt>
+<dt id="arg-table-names">table_names<a class="anchor" aria-label="anchor" href="#arg-table-names"></a>
+</dt>
 <dd><p>(<code>character</code>)<br> this can be customized in the case that the same <code>vars</code> are analyzed multiple
 times, to avoid warnings from <code>rtables</code>.</p></dd>
 
 
-<dt id="arg--stats">.stats<a class="anchor" aria-label="anchor" href="#arg--stats"></a></dt>
-<dd><p>(<code>character</code>)<br> statistics to select for the table.</p>
-<p>Options are: <code>'pval'</code></p></dd>
+<dt id="arg--stats">.stats<a class="anchor" aria-label="anchor" href="#arg--stats"></a>
+</dt>
+<dd>
+<p>(<code>character</code>)<br> statistics to select for the table.</p>
+<p>Options are: <code>'pval'</code></p>
+</dd>
 
 
-<dt id="arg--formats">.formats<a class="anchor" aria-label="anchor" href="#arg--formats"></a></dt>
+<dt id="arg--formats">.formats<a class="anchor" aria-label="anchor" href="#arg--formats"></a>
+</dt>
 <dd><p>(named <code>character</code> or <code>list</code>)<br> formats for the statistics. See Details in <code>analyze_vars</code> for more
 information on the <code>"auto"</code> setting.</p></dd>
 
 
-<dt id="arg--labels">.labels<a class="anchor" aria-label="anchor" href="#arg--labels"></a></dt>
+<dt id="arg--labels">.labels<a class="anchor" aria-label="anchor" href="#arg--labels"></a>
+</dt>
 <dd><p>(named <code>character</code>)<br> labels for the statistics (without indent).</p></dd>
 
 
-<dt id="arg--indent-mods">.indent_mods<a class="anchor" aria-label="anchor" href="#arg--indent-mods"></a></dt>
+<dt id="arg--indent-mods">.indent_mods<a class="anchor" aria-label="anchor" href="#arg--indent-mods"></a>
+</dt>
 <dd><p>(named <code>integer</code>)<br> indent modifiers for the labels. Defaults to 0, which corresponds to the
 unmodified default behavior. Can be negative.</p></dd>
 
 
-<dt id="arg-df">df<a class="anchor" aria-label="anchor" href="#arg-df"></a></dt>
+<dt id="arg-df">df<a class="anchor" aria-label="anchor" href="#arg-df"></a>
+</dt>
 <dd><p>(<code>data.frame</code>)<br> data set containing all analysis variables.</p></dd>
 
 
-<dt id="arg--var">.var<a class="anchor" aria-label="anchor" href="#arg--var"></a></dt>
+<dt id="arg--var">.var<a class="anchor" aria-label="anchor" href="#arg--var"></a>
+</dt>
 <dd><p>(<code>string</code>)<br> single variable name that is passed by <code>rtables</code> when requested
 by a statistics function.</p></dd>
 
 
-<dt id="arg--ref-group">.ref_group<a class="anchor" aria-label="anchor" href="#arg--ref-group"></a></dt>
+<dt id="arg--ref-group">.ref_group<a class="anchor" aria-label="anchor" href="#arg--ref-group"></a>
+</dt>
 <dd><p>(<code>data.frame</code> or <code>vector</code>)<br> the data corresponding to the reference group.</p></dd>
 
 
-<dt id="arg--in-ref-col">.in_ref_col<a class="anchor" aria-label="anchor" href="#arg--in-ref-col"></a></dt>
+<dt id="arg--in-ref-col">.in_ref_col<a class="anchor" aria-label="anchor" href="#arg--in-ref-col"></a>
+</dt>
 <dd><p>(<code>flag</code>)<br><code>TRUE</code> when working with the reference level, <code>FALSE</code> otherwise.</p></dd>
 
-</dl></div>
+</dl>
+</div>
     <div class="section level2">
-    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
+    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a>
+</h2>
 
-<ul><li><p><code>test_proportion_diff()</code> returns a layout object suitable for passing to further layouting functions,
+<ul>
+<li><p><code>test_proportion_diff()</code> returns a layout object suitable for passing to further layouting functions,
 or to <code><a href="https://insightsengineering.github.io/rtables/latest-tag/reference/build_table.html" class="external-link">rtables::build_table()</a></code>. Adding this function to an <code>rtable</code> layout will add formatted rows containing
 the statistics from <code>s_test_proportion_diff()</code> to the table layout.</p></li>
-</ul><ul><li><p><code>s_test_proportion_diff()</code> returns a named <code>list</code> with a single item <code>pval</code> with an attribute <code>label</code>
+</ul>
+<ul>
+<li><p><code>s_test_proportion_diff()</code> returns a named <code>list</code> with a single item <code>pval</code> with an attribute <code>label</code>
 describing the method used. The p-value tests the null hypothesis that proportions in two groups are the same.</p></li>
-</ul><ul><li><p><code>a_test_proportion_diff()</code> returns the corresponding list with formatted <code><a href="https://insightsengineering.github.io/rtables/latest-tag/reference/CellValue.html" class="external-link">rtables::CellValue()</a></code>.</p></li>
-</ul></div>
+</ul>
+<ul>
+<li><p><code>a_test_proportion_diff()</code> returns the corresponding list with formatted <code><a href="https://insightsengineering.github.io/rtables/latest-tag/reference/CellValue.html" class="external-link">rtables::CellValue()</a></code>.</p></li>
+</ul>
+</div>
     <div class="section level2">
-    <h2 id="functions">Functions<a class="anchor" aria-label="anchor" href="#functions"></a></h2>
+    <h2 id="functions">Functions<a class="anchor" aria-label="anchor" href="#functions"></a>
+</h2>
 
-<ul><li><p><code>test_proportion_diff()</code>: Layout-creating function which can take statistics function arguments
+<ul>
+<li><p><code>test_proportion_diff()</code>: Layout-creating function which can take statistics function arguments
 and additional format arguments. This function is a wrapper for <code><a href="https://insightsengineering.github.io/rtables/latest-tag/reference/analyze.html" class="external-link">rtables::analyze()</a></code>.</p></li>
 <li><p><code>s_test_proportion_diff()</code>: Statistics function which tests the difference between two proportions.</p></li>
 <li><p><code>a_test_proportion_diff()</code>: Formatted analysis function which is used as <code>afun</code> in <code>test_proportion_diff()</code>.</p></li>
-</ul></div>
+</ul>
+</div>
     <div class="section level2">
-    <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"></a></h2>
+    <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"></a>
+</h2>
     <div class="dont-index"><p><a href="h_prop_diff_test.html">h_prop_diff_test</a></p></div>
     </div>
 
     <div class="section level2">
-    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
+    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">dta</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a></span><span class="op">(</span></span></span>
 <span class="r-in"><span>  rsp <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/sample.html" class="external-link">sample</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="cn">TRUE</span>, <span class="cn">FALSE</span><span class="op">)</span>, <span class="fl">100</span>, <span class="cn">TRUE</span><span class="op">)</span>,</span></span>
 <span class="r-in"><span>  grp <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/factor.html" class="external-link">factor</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/rep.html" class="external-link">rep</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"A"</span>, <span class="st">"B"</span><span class="op">)</span>, each <span class="op">=</span> <span class="fl">50</span><span class="op">)</span><span class="op">)</span>,</span></span>
@@ -231,17 +330,19 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 </code></pre></div>
     </div>
   </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
-    </nav></aside></div>
+    </nav></aside>
+</div>
 
 
     <footer><div class="nest">
   <p>tern is a part of the <strong>NEST</strong> and <a href="https://pharmaverse.org/" class="external-link"><strong>pharmaverse</strong></a>.</p>
 </div>
-<script type="text/javascript" src="../analytics.js"></script></footer></div>
-
+<script type="text/javascript" src="../analytics.js"></script></footer>
+</div>
 
 
 
 
-  </body></html>
 
+  </body>
+</html>
diff --git a/main/reference/prune_occurrences.html b/main/reference/prune_occurrences.html
index 5d018df8b8..f67cfe9aa5 100644
--- a/main/reference/prune_occurrences.html
+++ b/main/reference/prune_occurrences.html
@@ -1,13 +1,36 @@
-<!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Occurrence table pruning — prune_occurrences • tern</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Occurrence table pruning — prune_occurrences"><meta name="description" content="
+<html lang="en">
+<head>
+<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+<meta charset="utf-8">
+<meta http-equiv="X-UA-Compatible" content="IE=edge">
+<meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<title>Occurrence table pruning — prune_occurrences • tern</title>
+<!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png">
+<link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png">
+<link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png">
+<link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png">
+<link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png">
+<link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png">
+<script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet">
+<script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet">
+<link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet">
+<script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Occurrence table pruning — prune_occurrences">
+<meta name="description" content="
 Family of constructor and condition functions to flexibly prune occurrence tables.
 The condition functions always return whether the row result is higher than the threshold.
 Since they are of class CombinationFunction() they can be logically combined with other condition
-functions."><meta property="og:description" content="
+functions.">
+<meta property="og:description" content="
 Family of constructor and condition functions to flexibly prune occurrence tables.
 The condition functions always return whether the row result is higher than the threshold.
 Since they are of class CombinationFunction() they can be logically combined with other condition
-functions."><meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png"><link rel="stylesheet" href="../consent.css"><script src="../consent.js" type="text/javascript" charset="utf-8"></script></head><body>
+functions.">
+<meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png">
+<link rel="stylesheet" href="../consent.css">
+<script src="../consent.js" type="text/javascript" charset="utf-8"></script>
+</head>
+<body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
 
 
@@ -23,26 +46,66 @@
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     <div id="navbar" class="collapse navbar-collapse ms-3">
-      <ul class="navbar-nav me-auto"><li class="nav-item"><a class="nav-link" href="../articles/tern.html">Get started</a></li>
+      <ul class="navbar-nav me-auto">
+<li class="nav-item"><a class="nav-link" href="../articles/tern.html">Get started</a></li>
 <li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
 <li class="nav-item dropdown">
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-articles" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Articles</button>
-  <ul class="dropdown-menu" aria-labelledby="dropdown-articles"><li><a class="dropdown-item" href="../articles/missing_values.html">Missing Values in Tern</a></li>
+  <ul class="dropdown-menu" aria-labelledby="dropdown-articles">
+<li><a class="dropdown-item" href="../articles/missing_values.html">Missing Values in Tern</a></li>
     <li><a class="dropdown-item" href="../articles/tables.html">Tabulation</a></li>
     <li><a class="dropdown-item" href="../articles/tern_formats.html">Formatting Functions</a></li>
     <li><a class="dropdown-item" href="../articles/tern_functions_guide.html">Understanding `tern` functions</a></li>
-  </ul></li>
+  </ul>
+</li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
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   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
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+  <ul class="dropdown-menu" aria-labelledby="dropdown-reports">
+<li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
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-      </ul><ul class="navbar-nav"><li class="nav-item"><form class="form-inline" role="search">
- <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json"></form></li>
+  </ul>
+</li>
+      <div><li class="nav-item dropdown">
+    <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-versions">Versions</a>
+    <div class="dropdown-menu" aria-labelledby="dropdown-versions">
+    <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/main">main</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.5">v0.9.5</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.4">v0.9.4</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.3">v0.9.3</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1-rc3">v0.9.1-rc3</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a>
+</div>
+</li></div>
+</ul>
+<ul class="navbar-nav">
+<li class="nav-item"><form class="form-inline" role="search">
+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json">
+</form></li>
 <li class="nav-item"><a class="external-link nav-link" href="https://github.com/insightsengineering/tern" aria-label="GitHub"><span class="fa fa-github"></span></a></li>
-      </ul></div>
+      </ul>
+</div>
 
 
   </div>
@@ -63,7 +126,8 @@
     </div>
 
     <div class="section level2">
-    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
+    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">keep_rows</span><span class="op">(</span><span class="va">row_condition</span><span class="op">)</span></span>
 <span></span>
 <span><span class="fu">keep_content_rows</span><span class="op">(</span><span class="va">content_row_condition</span><span class="op">)</span></span>
@@ -82,52 +146,78 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
     </div>
 
     <div class="section level2">
-    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
+    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a>
+</h2>
 
 
-<dl><dt id="arg-row-condition">row_condition<a class="anchor" aria-label="anchor" href="#arg-row-condition"></a></dt>
+<dl>
+<dt id="arg-row-condition">row_condition<a class="anchor" aria-label="anchor" href="#arg-row-condition"></a>
+</dt>
 <dd><p>(<code>CombinationFunction</code>)<br> condition function which works on individual
 analysis rows and flags whether these should be kept in the pruned table.</p></dd>
 
 
-<dt id="arg-content-row-condition">content_row_condition<a class="anchor" aria-label="anchor" href="#arg-content-row-condition"></a></dt>
+<dt id="arg-content-row-condition">content_row_condition<a class="anchor" aria-label="anchor" href="#arg-content-row-condition"></a>
+</dt>
 <dd><p>(<code>CombinationFunction</code>)<br> condition function which works on individual
 first content rows of leaf tables and flags whether these leaf tables should be kept in the pruned table.</p></dd>
 
 
-<dt id="arg-atleast">atleast<a class="anchor" aria-label="anchor" href="#arg-atleast"></a></dt>
+<dt id="arg-atleast">atleast<a class="anchor" aria-label="anchor" href="#arg-atleast"></a>
+</dt>
 <dd><p>(<code>numeric(1)</code>)<br> threshold which should be met in order to keep the row.</p></dd>
 
 
-<dt id="arg--">...<a class="anchor" aria-label="anchor" href="#arg--"></a></dt>
+<dt id="arg--">...<a class="anchor" aria-label="anchor" href="#arg--"></a>
+</dt>
 <dd><p>arguments for row or column access, see <code><a href="rtables_access.html">rtables_access</a></code>: either <code>col_names</code> (<code>character</code>) including
 the names of the columns which should be used, or alternatively <code>col_indices</code> (<code>integer</code>) giving the indices
 directly instead.</p></dd>
 
-</dl></div>
+</dl>
+</div>
     <div class="section level2">
-    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
+    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a>
+</h2>
 
-<ul><li><p><code>keep_rows()</code> returns a pruning function that can be used with <code><a href="https://insightsengineering.github.io/rtables/latest-tag/reference/prune_table.html" class="external-link">rtables::prune_table()</a></code>
+<ul>
+<li><p><code>keep_rows()</code> returns a pruning function that can be used with <code><a href="https://insightsengineering.github.io/rtables/latest-tag/reference/prune_table.html" class="external-link">rtables::prune_table()</a></code>
 to prune an <code>rtables</code> table.</p></li>
-</ul><ul><li><p><code>keep_content_rows()</code> returns a pruning function that checks the condition on the first content
+</ul>
+<ul>
+<li><p><code>keep_content_rows()</code> returns a pruning function that checks the condition on the first content
 row of leaf tables in the table.</p></li>
-</ul><ul><li><p><code>has_count_in_cols()</code> returns a condition function that sums the counts in the specified column.</p></li>
-</ul><ul><li><p><code>has_count_in_any_col()</code> returns a condition function that compares the counts in the
+</ul>
+<ul>
+<li><p><code>has_count_in_cols()</code> returns a condition function that sums the counts in the specified column.</p></li>
+</ul>
+<ul>
+<li><p><code>has_count_in_any_col()</code> returns a condition function that compares the counts in the
 specified columns with the threshold.</p></li>
-</ul><ul><li><p><code>has_fraction_in_cols()</code> returns a condition function that sums the counts in the
+</ul>
+<ul>
+<li><p><code>has_fraction_in_cols()</code> returns a condition function that sums the counts in the
 specified column, and computes the fraction by dividing by the total column counts.</p></li>
-</ul><ul><li><p><code>has_fraction_in_any_col()</code> returns a condition function that looks at the fractions
+</ul>
+<ul>
+<li><p><code>has_fraction_in_any_col()</code> returns a condition function that looks at the fractions
 in the specified columns and checks whether any of them fulfill the threshold.</p></li>
-</ul><ul><li><p><code>has_fractions_difference()</code> returns a condition function that extracts the fractions of each
+</ul>
+<ul>
+<li><p><code>has_fractions_difference()</code> returns a condition function that extracts the fractions of each
 specified column, and computes the difference of the minimum and maximum.</p></li>
-</ul><ul><li><p><code>has_counts_difference()</code> returns a condition function that extracts the counts of each
+</ul>
+<ul>
+<li><p><code>has_counts_difference()</code> returns a condition function that extracts the counts of each
 specified column, and computes the difference of the minimum and maximum.</p></li>
-</ul></div>
+</ul>
+</div>
     <div class="section level2">
-    <h2 id="functions">Functions<a class="anchor" aria-label="anchor" href="#functions"></a></h2>
+    <h2 id="functions">Functions<a class="anchor" aria-label="anchor" href="#functions"></a>
+</h2>
 
-<ul><li><p><code>keep_rows()</code>: Constructor for creating pruning functions based on
+<ul>
+<li><p><code>keep_rows()</code>: Constructor for creating pruning functions based on
 a row condition function. This removes all analysis rows (<code>TableRow</code>) that should be
 pruned, i.e., don't fulfill the row condition. It removes the sub-tree if there are no
 children left.</p></li>
@@ -146,16 +236,19 @@ <h2 id="functions">Functions<a class="anchor" aria-label="anchor" href="#functio
 between the fractions reported in each specified column.</p></li>
 <li><p><code>has_counts_difference()</code>: Constructor for creating condition function that checks the difference
 between the counts reported in each specified column.</p></li>
-</ul></div>
+</ul>
+</div>
     <div class="section level2">
-    <h2 id="note">Note<a class="anchor" aria-label="anchor" href="#note"></a></h2>
+    <h2 id="note">Note<a class="anchor" aria-label="anchor" href="#note"></a>
+</h2>
     <p>Since most table specifications are worded positively, we name our constructor and condition
 functions positively, too. However, note that the result of <code>keep_rows()</code> says what
 should be pruned, to conform with the <code><a href="https://insightsengineering.github.io/rtables/latest-tag/reference/prune_table.html" class="external-link">rtables::prune_table()</a></code> interface.</p>
     </div>
 
     <div class="section level2">
-    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
+    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="co"># \donttest{</span></span></span>
 <span class="r-in"><span><span class="va">tab</span> <span class="op">&lt;-</span> <span class="fu">basic_table</span><span class="op">(</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span></span>
 <span class="r-in"><span>  <span class="fu">split_cols_by</span><span class="op">(</span><span class="st">"ARM"</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span></span>
@@ -753,17 +846,19 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 </code></pre></div>
     </div>
   </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
-    </nav></aside></div>
+    </nav></aside>
+</div>
 
 
     <footer><div class="nest">
   <p>tern is a part of the <strong>NEST</strong> and <a href="https://pharmaverse.org/" class="external-link"><strong>pharmaverse</strong></a>.</p>
 </div>
-<script type="text/javascript" src="../analytics.js"></script></footer></div>
-
+<script type="text/javascript" src="../analytics.js"></script></footer>
+</div>
 
 
 
 
-  </body></html>
 
+  </body>
+</html>
diff --git a/main/reference/range_noinf.html b/main/reference/range_noinf.html
index 036106b435..22784708ea 100644
--- a/main/reference/range_noinf.html
+++ b/main/reference/range_noinf.html
@@ -1,7 +1,30 @@
-<!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Re-implemented range() default S3 method for numerical objects — range_noinf • tern</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Re-implemented range() default S3 method for numerical objects — range_noinf"><meta name="description" content="This function returns c(NA, NA) instead of c(-Inf, Inf) for zero-length data
-without any warnings."><meta property="og:description" content="This function returns c(NA, NA) instead of c(-Inf, Inf) for zero-length data
-without any warnings."><meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png"><link rel="stylesheet" href="../consent.css"><script src="../consent.js" type="text/javascript" charset="utf-8"></script></head><body>
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+<script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet">
+<script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet">
+<link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet">
+<script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Re-implemented range() default S3 method for numerical objects — range_noinf">
+<meta name="description" content="This function returns c(NA, NA) instead of c(-Inf, Inf) for zero-length data
+without any warnings.">
+<meta property="og:description" content="This function returns c(NA, NA) instead of c(-Inf, Inf) for zero-length data
+without any warnings.">
+<meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png">
+<link rel="stylesheet" href="../consent.css">
+<script src="../consent.js" type="text/javascript" charset="utf-8"></script>
+</head>
+<body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
 
 
@@ -17,26 +40,66 @@
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+<li class="nav-item"><a class="nav-link" href="../articles/tern.html">Get started</a></li>
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+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a>
+</div>
+</li></div>
+</ul>
+<ul class="navbar-nav">
+<li class="nav-item"><form class="form-inline" role="search">
+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json">
+</form></li>
 <li class="nav-item"><a class="external-link nav-link" href="https://github.com/insightsengineering/tern" aria-label="GitHub"><span class="fa fa-github"></span></a></li>
-      </ul></div>
+      </ul>
+</div>
 
 
   </div>
@@ -54,43 +117,53 @@
     </div>
 
     <div class="section level2">
-    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
+    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">range_noinf</span><span class="op">(</span><span class="va">x</span>, na.rm <span class="op">=</span> <span class="cn">FALSE</span>, finite <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span></code></pre></div>
     </div>
 
     <div class="section level2">
-    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
+    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a>
+</h2>
 
 
-<dl><dt id="arg-x">x<a class="anchor" aria-label="anchor" href="#arg-x"></a></dt>
+<dl>
+<dt id="arg-x">x<a class="anchor" aria-label="anchor" href="#arg-x"></a>
+</dt>
 <dd><p>(<code>numeric</code>)<br> a sequence of numbers for which the range is computed.</p></dd>
 
 
-<dt id="arg-na-rm">na.rm<a class="anchor" aria-label="anchor" href="#arg-na-rm"></a></dt>
+<dt id="arg-na-rm">na.rm<a class="anchor" aria-label="anchor" href="#arg-na-rm"></a>
+</dt>
 <dd><p>(<code>flag</code>)<br> flag indicating if <code>NA</code> should be omitted.</p></dd>
 
 
-<dt id="arg-finite">finite<a class="anchor" aria-label="anchor" href="#arg-finite"></a></dt>
+<dt id="arg-finite">finite<a class="anchor" aria-label="anchor" href="#arg-finite"></a>
+</dt>
 <dd><p>(<code>flag</code>)<br> flag indicating if non-finite elements should be removed.</p></dd>
 
-</dl></div>
+</dl>
+</div>
     <div class="section level2">
-    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
+    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a>
+</h2>
     <p>A 2-element vector of class <code>numeric</code>.</p>
     </div>
 
   </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
-    </nav></aside></div>
+    </nav></aside>
+</div>
 
 
     <footer><div class="nest">
   <p>tern is a part of the <strong>NEST</strong> and <a href="https://pharmaverse.org/" class="external-link"><strong>pharmaverse</strong></a>.</p>
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-<script type="text/javascript" src="../analytics.js"></script></footer></div>
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+<script type="text/javascript" src="../analytics.js"></script></footer>
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+  </body>
+</html>
diff --git a/main/reference/reapply_varlabels.html b/main/reference/reapply_varlabels.html
index 19098f41a4..c65e1a0499 100644
--- a/main/reference/reapply_varlabels.html
+++ b/main/reference/reapply_varlabels.html
@@ -1,5 +1,28 @@
-<!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Reapply variable labels — reapply_varlabels • tern</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Reapply variable labels — reapply_varlabels"><meta name="description" content="This is a helper function that is used in tests."><meta property="og:description" content="This is a helper function that is used in tests."><meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png"><link rel="stylesheet" href="../consent.css"><script src="../consent.js" type="text/javascript" charset="utf-8"></script></head><body>
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+<meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<title>Reapply variable labels — reapply_varlabels • tern</title>
+<!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png">
+<link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png">
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+<script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet">
+<link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet">
+<script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Reapply variable labels — reapply_varlabels">
+<meta name="description" content="This is a helper function that is used in tests.">
+<meta property="og:description" content="This is a helper function that is used in tests.">
+<meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png">
+<link rel="stylesheet" href="../consent.css">
+<script src="../consent.js" type="text/javascript" charset="utf-8"></script>
+</head>
+<body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
 
 
@@ -15,26 +38,66 @@
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+  <ul class="dropdown-menu" aria-labelledby="dropdown-articles">
+<li><a class="dropdown-item" href="../articles/missing_values.html">Missing Values in Tern</a></li>
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+  </ul>
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+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
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+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a>
+</div>
+</li></div>
+</ul>
+<ul class="navbar-nav">
+<li class="nav-item"><form class="form-inline" role="search">
+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json">
+</form></li>
 <li class="nav-item"><a class="external-link nav-link" href="https://github.com/insightsengineering/tern" aria-label="GitHub"><span class="fa fa-github"></span></a></li>
-      </ul></div>
+      </ul>
+</div>
 
 
   </div>
@@ -51,43 +114,53 @@
     </div>
 
     <div class="section level2">
-    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
+    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">reapply_varlabels</span><span class="op">(</span><span class="va">x</span>, <span class="va">varlabels</span>, <span class="va">...</span><span class="op">)</span></span></code></pre></div>
     </div>
 
     <div class="section level2">
-    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
+    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a>
+</h2>
 
 
-<dl><dt id="arg-x">x<a class="anchor" aria-label="anchor" href="#arg-x"></a></dt>
+<dl>
+<dt id="arg-x">x<a class="anchor" aria-label="anchor" href="#arg-x"></a>
+</dt>
 <dd><p>(<code>vector</code>)<br> vector of elements that needs new labels.</p></dd>
 
 
-<dt id="arg-varlabels">varlabels<a class="anchor" aria-label="anchor" href="#arg-varlabels"></a></dt>
+<dt id="arg-varlabels">varlabels<a class="anchor" aria-label="anchor" href="#arg-varlabels"></a>
+</dt>
 <dd><p>(<code>character</code>)<br> vector of labels for <code>x</code>.</p></dd>
 
 
-<dt id="arg--">...<a class="anchor" aria-label="anchor" href="#arg--"></a></dt>
+<dt id="arg--">...<a class="anchor" aria-label="anchor" href="#arg--"></a>
+</dt>
 <dd><p>further parameters to be added to the list.</p></dd>
 
-</dl></div>
+</dl>
+</div>
     <div class="section level2">
-    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
+    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a>
+</h2>
     <p><code>x</code> with variable labels reapplied.</p>
     </div>
 
   </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
-    </nav></aside></div>
+    </nav></aside>
+</div>
 
 
     <footer><div class="nest">
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diff --git a/main/reference/response_biomarkers_subgroups.html b/main/reference/response_biomarkers_subgroups.html
index a49afa47d5..bddd44c7e5 100644
--- a/main/reference/response_biomarkers_subgroups.html
+++ b/main/reference/response_biomarkers_subgroups.html
@@ -1,15 +1,38 @@
-<!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Tabulate biomarker effects on binary response by subgroup — response_biomarkers_subgroups • tern</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Tabulate biomarker effects on binary response by subgroup — response_biomarkers_subgroups"><meta name="description" content="
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+<meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<title>Tabulate biomarker effects on binary response by subgroup — response_biomarkers_subgroups • tern</title>
+<!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png">
+<link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png">
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+<link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png">
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+<script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet">
+<link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet">
+<script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Tabulate biomarker effects on binary response by subgroup — response_biomarkers_subgroups">
+<meta name="description" content="
 The tabulate_rsp_biomarkers() function creates a layout element to tabulate the estimated biomarker effects on a
 binary response endpoint across subgroups, returning statistics including response rate and odds ratio for each
 population subgroup. The table is created from df, a list of data frames returned by extract_rsp_biomarkers(),
 with the statistics to include specified via the vars parameter.
-A forest plot can be created from the resulting table using the g_forest() function."><meta property="og:description" content="
+A forest plot can be created from the resulting table using the g_forest() function.">
+<meta property="og:description" content="
 The tabulate_rsp_biomarkers() function creates a layout element to tabulate the estimated biomarker effects on a
 binary response endpoint across subgroups, returning statistics including response rate and odds ratio for each
 population subgroup. The table is created from df, a list of data frames returned by extract_rsp_biomarkers(),
 with the statistics to include specified via the vars parameter.
-A forest plot can be created from the resulting table using the g_forest() function."><meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png"><link rel="stylesheet" href="../consent.css"><script src="../consent.js" type="text/javascript" charset="utf-8"></script></head><body>
+A forest plot can be created from the resulting table using the g_forest() function.">
+<meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png">
+<link rel="stylesheet" href="../consent.css">
+<script src="../consent.js" type="text/javascript" charset="utf-8"></script>
+</head>
+<body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
 
 
@@ -25,26 +48,66 @@
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     <div id="navbar" class="collapse navbar-collapse ms-3">
-      <ul class="navbar-nav me-auto"><li class="nav-item"><a class="nav-link" href="../articles/tern.html">Get started</a></li>
+      <ul class="navbar-nav me-auto">
+<li class="nav-item"><a class="nav-link" href="../articles/tern.html">Get started</a></li>
 <li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
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-  <ul class="dropdown-menu" aria-labelledby="dropdown-articles"><li><a class="dropdown-item" href="../articles/missing_values.html">Missing Values in Tern</a></li>
+  <ul class="dropdown-menu" aria-labelledby="dropdown-articles">
+<li><a class="dropdown-item" href="../articles/missing_values.html">Missing Values in Tern</a></li>
     <li><a class="dropdown-item" href="../articles/tables.html">Tabulation</a></li>
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     <li><a class="dropdown-item" href="../articles/tern_functions_guide.html">Understanding `tern` functions</a></li>
-  </ul></li>
+  </ul>
+</li>
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+  <ul class="dropdown-menu" aria-labelledby="dropdown-reports">
+<li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
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- <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json"></form></li>
+  </ul>
+</li>
+      <div><li class="nav-item dropdown">
+    <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-versions">Versions</a>
+    <div class="dropdown-menu" aria-labelledby="dropdown-versions">
+    <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/main">main</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.5">v0.9.5</a>
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+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1-rc3">v0.9.1-rc3</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a>
+</div>
+</li></div>
+</ul>
+<ul class="navbar-nav">
+<li class="nav-item"><form class="form-inline" role="search">
+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json">
+</form></li>
 <li class="nav-item"><a class="external-link nav-link" href="https://github.com/insightsengineering/tern" aria-label="GitHub"><span class="fa fa-github"></span></a></li>
-      </ul></div>
+      </ul>
+</div>
 
 
   </div>
@@ -66,7 +129,8 @@
     </div>
 
     <div class="section level2">
-    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
+    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">tabulate_rsp_biomarkers</span><span class="op">(</span></span>
 <span>  <span class="va">df</span>,</span>
 <span>  vars <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"n_tot"</span>, <span class="st">"n_rsp"</span>, <span class="st">"prop"</span>, <span class="st">"or"</span>, <span class="st">"ci"</span>, <span class="st">"pval"</span><span class="op">)</span>,</span>
@@ -76,56 +140,72 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
     </div>
 
     <div class="section level2">
-    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
+    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a>
+</h2>
 
 
-<dl><dt id="arg-df">df<a class="anchor" aria-label="anchor" href="#arg-df"></a></dt>
+<dl>
+<dt id="arg-df">df<a class="anchor" aria-label="anchor" href="#arg-df"></a>
+</dt>
 <dd><p>(<code>data.frame</code>)<br> containing all analysis variables, as returned by
 <code><a href="extract_rsp_biomarkers.html">extract_rsp_biomarkers()</a></code>.</p></dd>
 
 
-<dt id="arg-vars">vars<a class="anchor" aria-label="anchor" href="#arg-vars"></a></dt>
-<dd><p>(<code>character</code>)<br> the names of statistics to be reported among:</p><ul><li><p><code>n_tot</code>: Total number of patients per group.</p></li>
+<dt id="arg-vars">vars<a class="anchor" aria-label="anchor" href="#arg-vars"></a>
+</dt>
+<dd>
+<p>(<code>character</code>)<br> the names of statistics to be reported among:</p>
+<ul>
+<li><p><code>n_tot</code>: Total number of patients per group.</p></li>
 <li><p><code>n_rsp</code>: Total number of responses per group.</p></li>
 <li><p><code>prop</code>: Total response proportion per group.</p></li>
 <li><p><code>or</code>: Odds ratio.</p></li>
 <li><p><code>ci</code>: Confidence interval of odds ratio.</p></li>
 <li><p><code>pval</code>: p-value of the effect.
 Note, the statistics <code>n_tot</code>, <code>or</code> and <code>ci</code> are required.</p></li>
-</ul></dd>
+</ul>
+</dd>
 
 
-<dt id="arg-na-str">na_str<a class="anchor" aria-label="anchor" href="#arg-na-str"></a></dt>
+<dt id="arg-na-str">na_str<a class="anchor" aria-label="anchor" href="#arg-na-str"></a>
+</dt>
 <dd><p>(<code>string</code>)<br> string used to replace all <code>NA</code> or empty values in the output.</p></dd>
 
 
-<dt id="arg--indent-mods">.indent_mods<a class="anchor" aria-label="anchor" href="#arg--indent-mods"></a></dt>
+<dt id="arg--indent-mods">.indent_mods<a class="anchor" aria-label="anchor" href="#arg--indent-mods"></a>
+</dt>
 <dd><p>(named <code>integer</code>)<br> indent modifiers for the labels. Defaults to 0, which corresponds to the
 unmodified default behavior. Can be negative.</p></dd>
 
-</dl></div>
+</dl>
+</div>
     <div class="section level2">
-    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
+    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a>
+</h2>
     <p>An <code>rtables</code> table summarizing biomarker effects on binary response by subgroup.</p>
     </div>
     <div class="section level2">
-    <h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a></h2>
+    <h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a>
+</h2>
     <p>These functions create a layout starting from a data frame which contains
 the required statistics. The tables are then typically used as input for forest plots.</p>
     </div>
     <div class="section level2">
-    <h2 id="note">Note<a class="anchor" aria-label="anchor" href="#note"></a></h2>
+    <h2 id="note">Note<a class="anchor" aria-label="anchor" href="#note"></a>
+</h2>
     <p>In contrast to <code><a href="response_subgroups.html">tabulate_rsp_subgroups()</a></code> this tabulation function does
 not start from an input layout <code>lyt</code>. This is because internally the table is
 created by combining multiple subtables.</p>
     </div>
     <div class="section level2">
-    <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"></a></h2>
+    <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"></a>
+</h2>
     <div class="dont-index"><p><code><a href="h_response_biomarkers_subgroups.html">h_tab_rsp_one_biomarker()</a></code> which is used internally, <code><a href="extract_rsp_biomarkers.html">extract_rsp_biomarkers()</a></code>.</p></div>
     </div>
 
     <div class="section level2">
-    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
+    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://dplyr.tidyverse.org" class="external-link">dplyr</a></span><span class="op">)</span></span></span>
 <span class="r-in"><span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://forcats.tidyverse.org/" class="external-link">forcats</a></span><span class="op">)</span></span></span>
 <span class="r-in"><span></span></span>
@@ -179,17 +259,19 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 </code></pre></div>
     </div>
   </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
-    </nav></aside></div>
+    </nav></aside>
+</div>
 
 
     <footer><div class="nest">
   <p>tern is a part of the <strong>NEST</strong> and <a href="https://pharmaverse.org/" class="external-link"><strong>pharmaverse</strong></a>.</p>
 </div>
-<script type="text/javascript" src="../analytics.js"></script></footer></div>
-
+<script type="text/javascript" src="../analytics.js"></script></footer>
+</div>
 
 
 
 
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diff --git a/main/reference/response_subgroups.html b/main/reference/response_subgroups.html
index f85daf788e..19c74b4733 100644
--- a/main/reference/response_subgroups.html
+++ b/main/reference/response_subgroups.html
@@ -1,15 +1,38 @@
-<!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Tabulate binary response by subgroup — response_subgroups • tern</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Tabulate binary response by subgroup — response_subgroups"><meta name="description" content="
+<html lang="en">
+<head>
+<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+<meta charset="utf-8">
+<meta http-equiv="X-UA-Compatible" content="IE=edge">
+<meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<title>Tabulate binary response by subgroup — response_subgroups • tern</title>
+<!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png">
+<link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png">
+<link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png">
+<link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png">
+<link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png">
+<link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png">
+<script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet">
+<script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet">
+<link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet">
+<script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Tabulate binary response by subgroup — response_subgroups">
+<meta name="description" content="
 The tabulate_rsp_subgroups() function creates a layout element to tabulate binary response by subgroup, returning
 statistics including response rate and odds ratio for each population subgroup. The table is created from df, a
 list of data frames returned by extract_rsp_subgroups(), with the statistics to include specified via the vars
 parameter.
-A forest plot can be created from the resulting table using the g_forest() function."><meta property="og:description" content="
+A forest plot can be created from the resulting table using the g_forest() function.">
+<meta property="og:description" content="
 The tabulate_rsp_subgroups() function creates a layout element to tabulate binary response by subgroup, returning
 statistics including response rate and odds ratio for each population subgroup. The table is created from df, a
 list of data frames returned by extract_rsp_subgroups(), with the statistics to include specified via the vars
 parameter.
-A forest plot can be created from the resulting table using the g_forest() function."><meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png"><link rel="stylesheet" href="../consent.css"><script src="../consent.js" type="text/javascript" charset="utf-8"></script></head><body>
+A forest plot can be created from the resulting table using the g_forest() function.">
+<meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png">
+<link rel="stylesheet" href="../consent.css">
+<script src="../consent.js" type="text/javascript" charset="utf-8"></script>
+</head>
+<body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
 
 
@@ -25,26 +48,66 @@
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+      <ul class="navbar-nav me-auto">
+<li class="nav-item"><a class="nav-link" href="../articles/tern.html">Get started</a></li>
 <li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
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   <button class="nav-link dropdown-toggle" type="button" id="dropdown-articles" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Articles</button>
-  <ul class="dropdown-menu" aria-labelledby="dropdown-articles"><li><a class="dropdown-item" href="../articles/missing_values.html">Missing Values in Tern</a></li>
+  <ul class="dropdown-menu" aria-labelledby="dropdown-articles">
+<li><a class="dropdown-item" href="../articles/missing_values.html">Missing Values in Tern</a></li>
     <li><a class="dropdown-item" href="../articles/tables.html">Tabulation</a></li>
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     <li><a class="dropdown-item" href="../articles/tern_functions_guide.html">Understanding `tern` functions</a></li>
-  </ul></li>
+  </ul>
+</li>
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   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
-  <ul class="dropdown-menu" aria-labelledby="dropdown-reports"><li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
+  <ul class="dropdown-menu" aria-labelledby="dropdown-reports">
+<li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
     <li><a class="dropdown-item" href="../unit-test-report/">Unit test report</a></li>
     <li><a class="dropdown-item" href="../unit-test-report-non-cran/">Non-CRAN unit test report</a></li>
-  </ul></li>
-      </ul><ul class="navbar-nav"><li class="nav-item"><form class="form-inline" role="search">
- <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json"></form></li>
+  </ul>
+</li>
+      <div><li class="nav-item dropdown">
+    <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-versions">Versions</a>
+    <div class="dropdown-menu" aria-labelledby="dropdown-versions">
+    <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/main">main</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.5">v0.9.5</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.4">v0.9.4</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.3">v0.9.3</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1-rc3">v0.9.1-rc3</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a>
+</div>
+</li></div>
+</ul>
+<ul class="navbar-nav">
+<li class="nav-item"><form class="form-inline" role="search">
+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json">
+</form></li>
 <li class="nav-item"><a class="external-link nav-link" href="https://github.com/insightsengineering/tern" aria-label="GitHub"><span class="fa fa-github"></span></a></li>
-      </ul></div>
+      </ul>
+</div>
 
 
   </div>
@@ -66,7 +129,8 @@
     </div>
 
     <div class="section level2">
-    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
+    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">tabulate_rsp_subgroups</span><span class="op">(</span></span>
 <span>  <span class="va">lyt</span>,</span>
 <span>  <span class="va">df</span>,</span>
@@ -89,20 +153,28 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
     </div>
 
     <div class="section level2">
-    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
+    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a>
+</h2>
 
 
-<dl><dt id="arg-lyt">lyt<a class="anchor" aria-label="anchor" href="#arg-lyt"></a></dt>
+<dl>
+<dt id="arg-lyt">lyt<a class="anchor" aria-label="anchor" href="#arg-lyt"></a>
+</dt>
 <dd><p>(<code>PreDataTableLayouts</code>)<br> layout that analyses will be added to.</p></dd>
 
 
-<dt id="arg-df">df<a class="anchor" aria-label="anchor" href="#arg-df"></a></dt>
+<dt id="arg-df">df<a class="anchor" aria-label="anchor" href="#arg-df"></a>
+</dt>
 <dd><p>(<code>list</code>)<br> a list of data frames containing all analysis variables. List should be
 created using <code><a href="extract_rsp_subgroups.html">extract_rsp_subgroups()</a></code>.</p></dd>
 
 
-<dt id="arg-vars">vars<a class="anchor" aria-label="anchor" href="#arg-vars"></a></dt>
-<dd><p>(<code>character</code>)<br> the names of statistics to be reported among:</p><ul><li><p><code>n</code>: Total number of observations per group.</p></li>
+<dt id="arg-vars">vars<a class="anchor" aria-label="anchor" href="#arg-vars"></a>
+</dt>
+<dd>
+<p>(<code>character</code>)<br> the names of statistics to be reported among:</p>
+<ul>
+<li><p><code>n</code>: Total number of observations per group.</p></li>
 <li><p><code>n_rsp</code>: Number of responders per group.</p></li>
 <li><p><code>prop</code>: Proportion of responders.</p></li>
 <li><p><code>n_tot</code>: Total number of observations.</p></li>
@@ -110,60 +182,76 @@ <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#argumen
 <li><p><code>ci</code> : Confidence interval of odds ratio.</p></li>
 <li><p><code>pval</code>: p-value of the effect.
 Note, the statistics <code>n_tot</code>, <code>or</code>, and <code>ci</code> are required.</p></li>
-</ul></dd>
+</ul>
+</dd>
 
 
-<dt id="arg-groups-lists">groups_lists<a class="anchor" aria-label="anchor" href="#arg-groups-lists"></a></dt>
+<dt id="arg-groups-lists">groups_lists<a class="anchor" aria-label="anchor" href="#arg-groups-lists"></a>
+</dt>
 <dd><p>(named <code>list</code> of <code>list</code>)<br> optionally contains for each <code>subgroups</code> variable a
 list, which specifies the new group levels via the names and the
 levels that belong to it in the character vectors that are elements of the list.</p></dd>
 
 
-<dt id="arg-label-all">label_all<a class="anchor" aria-label="anchor" href="#arg-label-all"></a></dt>
+<dt id="arg-label-all">label_all<a class="anchor" aria-label="anchor" href="#arg-label-all"></a>
+</dt>
 <dd><p>(<code>string</code>)<br> label for the total population analysis.</p></dd>
 
 
-<dt id="arg-riskdiff">riskdiff<a class="anchor" aria-label="anchor" href="#arg-riskdiff"></a></dt>
+<dt id="arg-riskdiff">riskdiff<a class="anchor" aria-label="anchor" href="#arg-riskdiff"></a>
+</dt>
 <dd><p>(<code>list</code>)<br> if a risk (proportion) difference column should be added, a list of settings to apply
 within the column. See <code><a href="control_riskdiff.html">control_riskdiff()</a></code> for details. If <code>NULL</code>, no risk difference column will be added. If
 <code>riskdiff$arm_x</code> and <code>riskdiff$arm_y</code> are <code>NULL</code>, the first level of <code>df$prop$arm</code> will be used as <code>arm_x</code> and
 the second level as <code>arm_y</code>.</p></dd>
 
 
-<dt id="arg-na-str">na_str<a class="anchor" aria-label="anchor" href="#arg-na-str"></a></dt>
+<dt id="arg-na-str">na_str<a class="anchor" aria-label="anchor" href="#arg-na-str"></a>
+</dt>
 <dd><p>(<code>string</code>)<br> string used to replace all <code>NA</code> or empty values in the output.</p></dd>
 
 
-<dt id="arg--formats">.formats<a class="anchor" aria-label="anchor" href="#arg--formats"></a></dt>
+<dt id="arg--formats">.formats<a class="anchor" aria-label="anchor" href="#arg--formats"></a>
+</dt>
 <dd><p>(named <code>character</code> or <code>list</code>)<br> formats for the statistics. See Details in <code>analyze_vars</code> for more
 information on the <code>"auto"</code> setting.</p></dd>
 
-</dl></div>
+</dl>
+</div>
     <div class="section level2">
-    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
+    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a>
+</h2>
     <p>An <code>rtables</code> table summarizing binary response by subgroup.</p>
-<ul><li><p><code>a_response_subgroups()</code> returns the corresponding list with formatted <code><a href="https://insightsengineering.github.io/rtables/latest-tag/reference/CellValue.html" class="external-link">rtables::CellValue()</a></code>.</p></li>
-</ul></div>
+<ul>
+<li><p><code>a_response_subgroups()</code> returns the corresponding list with formatted <code><a href="https://insightsengineering.github.io/rtables/latest-tag/reference/CellValue.html" class="external-link">rtables::CellValue()</a></code>.</p></li>
+</ul>
+</div>
     <div class="section level2">
-    <h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a></h2>
+    <h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a>
+</h2>
     <p>These functions create a layout starting from a data frame which contains
 the required statistics. Tables typically used as part of forest plot.</p>
     </div>
     <div class="section level2">
-    <h2 id="functions">Functions<a class="anchor" aria-label="anchor" href="#functions"></a></h2>
+    <h2 id="functions">Functions<a class="anchor" aria-label="anchor" href="#functions"></a>
+</h2>
 
-<ul><li><p><code>tabulate_rsp_subgroups()</code>: Table-creating function which creates a table
+<ul>
+<li><p><code>tabulate_rsp_subgroups()</code>: Table-creating function which creates a table
 summarizing binary response by subgroup. This function is a wrapper for <code><a href="https://insightsengineering.github.io/rtables/latest-tag/reference/analyze_colvars.html" class="external-link">rtables::analyze_colvars()</a></code>
 and <code><a href="https://insightsengineering.github.io/rtables/latest-tag/reference/summarize_row_groups.html" class="external-link">rtables::summarize_row_groups()</a></code>.</p></li>
 <li><p><code>a_response_subgroups()</code>: Formatted analysis function which is used as <code>afun</code> in <code>tabulate_rsp_subgroups()</code>.</p></li>
-</ul></div>
+</ul>
+</div>
     <div class="section level2">
-    <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"></a></h2>
+    <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"></a>
+</h2>
     <div class="dont-index"><p><code><a href="extract_rsp_subgroups.html">extract_rsp_subgroups()</a></code></p></div>
     </div>
 
     <div class="section level2">
-    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
+    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://dplyr.tidyverse.org" class="external-link">dplyr</a></span><span class="op">)</span></span></span>
 <span class="r-in"><span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://forcats.tidyverse.org/" class="external-link">forcats</a></span><span class="op">)</span></span></span>
 <span class="r-in"><span></span></span>
@@ -398,17 +486,19 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 </code></pre></div>
     </div>
   </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
-    </nav></aside></div>
+    </nav></aside>
+</div>
 
 
     <footer><div class="nest">
   <p>tern is a part of the <strong>NEST</strong> and <a href="https://pharmaverse.org/" class="external-link"><strong>pharmaverse</strong></a>.</p>
 </div>
-<script type="text/javascript" src="../analytics.js"></script></footer></div>
-
+<script type="text/javascript" src="../analytics.js"></script></footer>
+</div>
 
 
 
 
-  </body></html>
 
+  </body>
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diff --git a/main/reference/rtable2gg.html b/main/reference/rtable2gg.html
index 371e112509..cf24b8b31c 100644
--- a/main/reference/rtable2gg.html
+++ b/main/reference/rtable2gg.html
@@ -1,9 +1,32 @@
-<!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Convert rtable objects to ggplot objects — rtable2gg • tern</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Convert rtable objects to ggplot objects — rtable2gg"><meta name="description" content="
+<html lang="en">
+<head>
+<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+<meta charset="utf-8">
+<meta http-equiv="X-UA-Compatible" content="IE=edge">
+<meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<title>Convert rtable objects to ggplot objects — rtable2gg • tern</title>
+<!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png">
+<link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png">
+<link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png">
+<link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png">
+<link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png">
+<link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png">
+<script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet">
+<script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet">
+<link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet">
+<script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Convert rtable objects to ggplot objects — rtable2gg">
+<meta name="description" content="
 Given a rtables::rtable() object, performs basic conversion to a ggplot2::ggplot() object built using
-functions from the ggplot2 package. Any table titles and/or footnotes are ignored."><meta property="og:description" content="
+functions from the ggplot2 package. Any table titles and/or footnotes are ignored.">
+<meta property="og:description" content="
 Given a rtables::rtable() object, performs basic conversion to a ggplot2::ggplot() object built using
-functions from the ggplot2 package. Any table titles and/or footnotes are ignored."><meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png"><link rel="stylesheet" href="../consent.css"><script src="../consent.js" type="text/javascript" charset="utf-8"></script></head><body>
+functions from the ggplot2 package. Any table titles and/or footnotes are ignored.">
+<meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png">
+<link rel="stylesheet" href="../consent.css">
+<script src="../consent.js" type="text/javascript" charset="utf-8"></script>
+</head>
+<body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
 
 
@@ -19,26 +42,66 @@
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-      <ul class="navbar-nav me-auto"><li class="nav-item"><a class="nav-link" href="../articles/tern.html">Get started</a></li>
+      <ul class="navbar-nav me-auto">
+<li class="nav-item"><a class="nav-link" href="../articles/tern.html">Get started</a></li>
 <li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
 <li class="nav-item dropdown">
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-articles" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Articles</button>
-  <ul class="dropdown-menu" aria-labelledby="dropdown-articles"><li><a class="dropdown-item" href="../articles/missing_values.html">Missing Values in Tern</a></li>
+  <ul class="dropdown-menu" aria-labelledby="dropdown-articles">
+<li><a class="dropdown-item" href="../articles/missing_values.html">Missing Values in Tern</a></li>
     <li><a class="dropdown-item" href="../articles/tables.html">Tabulation</a></li>
     <li><a class="dropdown-item" href="../articles/tern_formats.html">Formatting Functions</a></li>
     <li><a class="dropdown-item" href="../articles/tern_functions_guide.html">Understanding `tern` functions</a></li>
-  </ul></li>
+  </ul>
+</li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
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-  <ul class="dropdown-menu" aria-labelledby="dropdown-reports"><li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
+  <ul class="dropdown-menu" aria-labelledby="dropdown-reports">
+<li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
     <li><a class="dropdown-item" href="../unit-test-report/">Unit test report</a></li>
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- <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json"></form></li>
+  </ul>
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+      <div><li class="nav-item dropdown">
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+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/main">main</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.5">v0.9.5</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.4">v0.9.4</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.3">v0.9.3</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1-rc3">v0.9.1-rc3</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a>
+</div>
+</li></div>
+</ul>
+<ul class="navbar-nav">
+<li class="nav-item"><form class="form-inline" role="search">
+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json">
+</form></li>
 <li class="nav-item"><a class="external-link nav-link" href="https://github.com/insightsengineering/tern" aria-label="GitHub"><span class="fa fa-github"></span></a></li>
-      </ul></div>
+      </ul>
+</div>
 
 
   </div>
@@ -57,41 +120,51 @@
     </div>
 
     <div class="section level2">
-    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
+    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">rtable2gg</span><span class="op">(</span><span class="va">tbl</span>, fontsize <span class="op">=</span> <span class="fl">12</span>, colwidths <span class="op">=</span> <span class="cn">NULL</span>, lbl_col_padding <span class="op">=</span> <span class="fl">0</span><span class="op">)</span></span></code></pre></div>
     </div>
 
     <div class="section level2">
-    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
+    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a>
+</h2>
 
 
-<dl><dt id="arg-tbl">tbl<a class="anchor" aria-label="anchor" href="#arg-tbl"></a></dt>
+<dl>
+<dt id="arg-tbl">tbl<a class="anchor" aria-label="anchor" href="#arg-tbl"></a>
+</dt>
 <dd><p>(<code>VTableTree</code>)<br><code>rtables</code> table object.</p></dd>
 
 
-<dt id="arg-fontsize">fontsize<a class="anchor" aria-label="anchor" href="#arg-fontsize"></a></dt>
+<dt id="arg-fontsize">fontsize<a class="anchor" aria-label="anchor" href="#arg-fontsize"></a>
+</dt>
 <dd><p>(<code>numeric(1)</code>)<br> font size.</p></dd>
 
 
-<dt id="arg-colwidths">colwidths<a class="anchor" aria-label="anchor" href="#arg-colwidths"></a></dt>
+<dt id="arg-colwidths">colwidths<a class="anchor" aria-label="anchor" href="#arg-colwidths"></a>
+</dt>
 <dd><p>(<code>numeric</code> or <code>NULL</code>)<br> a vector of column widths. Each element's position in
 <code>colwidths</code> corresponds to the column of <code>tbl</code> in the same position. If <code>NULL</code>, column widths
 are calculated according to maximum number of characters per column.</p></dd>
 
 
-<dt id="arg-lbl-col-padding">lbl_col_padding<a class="anchor" aria-label="anchor" href="#arg-lbl-col-padding"></a></dt>
+<dt id="arg-lbl-col-padding">lbl_col_padding<a class="anchor" aria-label="anchor" href="#arg-lbl-col-padding"></a>
+</dt>
 <dd><p>(<code>numeric</code>)<br> additional padding to use when calculating spacing between
 the first (label) column and the second column of <code>tbl</code>. If <code>colwidths</code> is specified,
 the width of the first column becomes <code>colwidths[1] + lbl_col_padding</code>. Defaults to 0.</p></dd>
 
-</dl></div>
+</dl>
+</div>
     <div class="section level2">
-    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
+    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a>
+</h2>
     <p>A <code>ggplot</code> object.</p>
     </div>
 
     <div class="section level2">
-    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
+    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">dta</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a></span><span class="op">(</span></span></span>
 <span class="r-in"><span>  ARM     <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/rep.html" class="external-link">rep</a></span><span class="op">(</span><span class="va">LETTERS</span><span class="op">[</span><span class="fl">1</span><span class="op">:</span><span class="fl">3</span><span class="op">]</span>, <span class="fu"><a href="https://rdrr.io/r/base/rep.html" class="external-link">rep</a></span><span class="op">(</span><span class="fl">6</span>, <span class="fl">3</span><span class="op">)</span><span class="op">)</span>,</span></span>
 <span class="r-in"><span>  AVISIT  <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/rep.html" class="external-link">rep</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/paste.html" class="external-link">paste0</a></span><span class="op">(</span><span class="st">"V"</span>, <span class="fl">1</span><span class="op">:</span><span class="fl">3</span><span class="op">)</span>, <span class="fl">6</span><span class="op">)</span>,</span></span>
@@ -114,17 +187,19 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 </code></pre></div>
     </div>
   </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
-    </nav></aside></div>
+    </nav></aside>
+</div>
 
 
     <footer><div class="nest">
   <p>tern is a part of the <strong>NEST</strong> and <a href="https://pharmaverse.org/" class="external-link"><strong>pharmaverse</strong></a>.</p>
 </div>
-<script type="text/javascript" src="../analytics.js"></script></footer></div>
-
+<script type="text/javascript" src="../analytics.js"></script></footer>
+</div>
 
 
 
 
-  </body></html>
 
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diff --git a/main/reference/rtables_access.html b/main/reference/rtables_access.html
index ab033628ea..1b06369a85 100644
--- a/main/reference/rtables_access.html
+++ b/main/reference/rtables_access.html
@@ -1,11 +1,34 @@
-<!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Helper functions for accessing information from rtables — rtables_access • tern</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Helper functions for accessing information from rtables — rtables_access"><meta name="description" content="
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+<meta http-equiv="X-UA-Compatible" content="IE=edge">
+<meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<title>Helper functions for accessing information from rtables — rtables_access • tern</title>
+<!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png">
+<link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png">
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+<link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet">
+<script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet">
+<link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet">
+<script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Helper functions for accessing information from rtables — rtables_access">
+<meta name="description" content="
 These are a couple of functions that help with accessing the data in rtables objects.
 Currently these work for occurrence tables, which are defined as having a count as the first
-element and a fraction as the second element in each cell."><meta property="og:description" content="
+element and a fraction as the second element in each cell.">
+<meta property="og:description" content="
 These are a couple of functions that help with accessing the data in rtables objects.
 Currently these work for occurrence tables, which are defined as having a count as the first
-element and a fraction as the second element in each cell."><meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png"><link rel="stylesheet" href="../consent.css"><script src="../consent.js" type="text/javascript" charset="utf-8"></script></head><body>
+element and a fraction as the second element in each cell.">
+<meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png">
+<link rel="stylesheet" href="../consent.css">
+<script src="../consent.js" type="text/javascript" charset="utf-8"></script>
+</head>
+<body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
 
 
@@ -21,33 +44,74 @@
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+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
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+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a>
+</div>
+</li></div>
+</ul>
+<ul class="navbar-nav">
+<li class="nav-item"><form class="form-inline" role="search">
+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json">
+</form></li>
 <li class="nav-item"><a class="external-link nav-link" href="https://github.com/insightsengineering/tern" aria-label="GitHub"><span class="fa fa-github"></span></a></li>
-      </ul></div>
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+</div>
 
 
   </div>
 </nav><div class="container template-reference-topic">
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
-      <img src="../logo.png" class="logo" alt=""><h1>Helper functions for accessing information from <code>rtables</code></h1>
+      <img src="../logo.png" class="logo" alt=""><h1>Helper functions for accessing information from <code>rtables</code>
+</h1>
       <small class="dont-index">Source: <a href="https://github.com/insightsengineering/tern/blob/main/R/rtables_access.R" class="external-link"><code>R/rtables_access.R</code></a></small>
       <div class="d-none name"><code>rtables_access.Rd</code></div>
     </div>
@@ -60,7 +124,8 @@
     </div>
 
     <div class="section level2">
-    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
+    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">h_row_first_values</span><span class="op">(</span><span class="va">table_row</span>, col_names <span class="op">=</span> <span class="cn">NULL</span>, col_indices <span class="op">=</span> <span class="cn">NULL</span><span class="op">)</span></span>
 <span></span>
 <span><span class="fu">h_row_counts</span><span class="op">(</span><span class="va">table_row</span>, col_names <span class="op">=</span> <span class="cn">NULL</span>, col_indices <span class="op">=</span> <span class="cn">NULL</span><span class="op">)</span></span>
@@ -77,42 +142,66 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
     </div>
 
     <div class="section level2">
-    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
+    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a>
+</h2>
 
 
-<dl><dt id="arg-table-row">table_row<a class="anchor" aria-label="anchor" href="#arg-table-row"></a></dt>
+<dl>
+<dt id="arg-table-row">table_row<a class="anchor" aria-label="anchor" href="#arg-table-row"></a>
+</dt>
 <dd><p>(<code>TableRow</code>)<br> an analysis row in a occurrence table.</p></dd>
 
 
-<dt id="arg-col-names">col_names<a class="anchor" aria-label="anchor" href="#arg-col-names"></a></dt>
+<dt id="arg-col-names">col_names<a class="anchor" aria-label="anchor" href="#arg-col-names"></a>
+</dt>
 <dd><p>(<code>character</code>)<br> the names of the columns to extract from.</p></dd>
 
 
-<dt id="arg-col-indices">col_indices<a class="anchor" aria-label="anchor" href="#arg-col-indices"></a></dt>
+<dt id="arg-col-indices">col_indices<a class="anchor" aria-label="anchor" href="#arg-col-indices"></a>
+</dt>
 <dd><p>(<code>integer</code>)<br> the indices of the columns to extract from. If <code>col_names</code> are provided,
 then these are inferred from the names of <code>table_row</code>. Note that this currently only works well with a single
 column split.</p></dd>
 
 
-<dt id="arg-table">table<a class="anchor" aria-label="anchor" href="#arg-table"></a></dt>
+<dt id="arg-table">table<a class="anchor" aria-label="anchor" href="#arg-table"></a>
+</dt>
 <dd><p>(<code>VTableNodeInfo</code>)<br> an occurrence table or row.</p></dd>
 
-</dl></div>
+</dl>
+</div>
     <div class="section level2">
-    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
-
-<ul><li><p><code>h_row_first_values()</code> returns a <code>vector</code> of numeric values.</p></li>
-</ul><ul><li><p><code>h_row_counts()</code> returns a <code>vector</code> of numeric values.</p></li>
-</ul><ul><li><p><code>h_row_fractions()</code> returns a <code>vector</code> of proportions.</p></li>
-</ul><ul><li><p><code>h_col_counts()</code> returns a <code>vector</code> of column counts.</p></li>
-</ul><ul><li><p><code>h_content_first_row()</code> returns a row from an <code>rtables</code> table.</p></li>
-</ul><ul><li><p><code>is_leaf_table()</code> returns a <code>logical</code> value indicating whether current table is a leaf.</p></li>
-</ul><ul><li><p><code>check_names_indices</code> returns column indices.</p></li>
-</ul></div>
+    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a>
+</h2>
+
+<ul>
+<li><p><code>h_row_first_values()</code> returns a <code>vector</code> of numeric values.</p></li>
+</ul>
+<ul>
+<li><p><code>h_row_counts()</code> returns a <code>vector</code> of numeric values.</p></li>
+</ul>
+<ul>
+<li><p><code>h_row_fractions()</code> returns a <code>vector</code> of proportions.</p></li>
+</ul>
+<ul>
+<li><p><code>h_col_counts()</code> returns a <code>vector</code> of column counts.</p></li>
+</ul>
+<ul>
+<li><p><code>h_content_first_row()</code> returns a row from an <code>rtables</code> table.</p></li>
+</ul>
+<ul>
+<li><p><code>is_leaf_table()</code> returns a <code>logical</code> value indicating whether current table is a leaf.</p></li>
+</ul>
+<ul>
+<li><p><code>check_names_indices</code> returns column indices.</p></li>
+</ul>
+</div>
     <div class="section level2">
-    <h2 id="functions">Functions<a class="anchor" aria-label="anchor" href="#functions"></a></h2>
+    <h2 id="functions">Functions<a class="anchor" aria-label="anchor" href="#functions"></a>
+</h2>
 
-<ul><li><p><code>h_row_first_values()</code>: Helper function to extract the first values from each content
+<ul>
+<li><p><code>h_row_first_values()</code>: Helper function to extract the first values from each content
 cell and from specified columns in a <code>TableRow</code>. Defaults to all columns.</p></li>
 <li><p><code>h_row_counts()</code>: Helper function that extracts row values and checks if they are
 convertible to integers (<code>integerish</code> values).</p></li>
@@ -122,14 +211,17 @@ <h2 id="functions">Functions<a class="anchor" aria-label="anchor" href="#functio
 <li><p><code>h_content_first_row()</code>: Helper function to get first row of content table of current table.</p></li>
 <li><p><code>is_leaf_table()</code>: Helper function which says whether current table is a leaf in the tree.</p></li>
 <li><p><code>check_names_indices()</code>: Internal helper function that tests standard inputs for column indices.</p></li>
-</ul></div>
+</ul>
+</div>
     <div class="section level2">
-    <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"></a></h2>
+    <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"></a>
+</h2>
     <div class="dont-index"><p><a href="prune_occurrences.html">prune_occurrences</a> for usage of these functions.</p></div>
     </div>
 
     <div class="section level2">
-    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
+    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">tbl</span> <span class="op">&lt;-</span> <span class="fu">basic_table</span><span class="op">(</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span></span>
 <span class="r-in"><span>  <span class="fu">split_cols_by</span><span class="op">(</span><span class="st">"ARM"</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span></span>
 <span class="r-in"><span>  <span class="fu">split_rows_by</span><span class="op">(</span><span class="st">"RACE"</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span></span>
@@ -163,17 +255,19 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 </code></pre></div>
     </div>
   </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
-    </nav></aside></div>
+    </nav></aside>
+</div>
 
 
     <footer><div class="nest">
   <p>tern is a part of the <strong>NEST</strong> and <a href="https://pharmaverse.org/" class="external-link"><strong>pharmaverse</strong></a>.</p>
 </div>
-<script type="text/javascript" src="../analytics.js"></script></footer></div>
-
+<script type="text/javascript" src="../analytics.js"></script></footer>
+</div>
 
 
 
 
-  </body></html>
 
+  </body>
+</html>
diff --git a/main/reference/s_bland_altman.html b/main/reference/s_bland_altman.html
index 5890552e38..056be209e4 100644
--- a/main/reference/s_bland_altman.html
+++ b/main/reference/s_bland_altman.html
@@ -1,9 +1,32 @@
-<!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Bland-Altman analysis — s_bland_altman • tern</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Bland-Altman analysis — s_bland_altman"><meta name="description" content="
+<html lang="en">
+<head>
+<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+<meta charset="utf-8">
+<meta http-equiv="X-UA-Compatible" content="IE=edge">
+<meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<title>Bland-Altman analysis — s_bland_altman • tern</title>
+<!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png">
+<link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png">
+<link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png">
+<link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png">
+<link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png">
+<link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png">
+<script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet">
+<script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet">
+<link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet">
+<script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Bland-Altman analysis — s_bland_altman">
+<meta name="description" content="
 Statistics function that uses the Bland-Altman method to assess the agreement between two numerical vectors
-and calculates a variety of statistics."><meta property="og:description" content="
+and calculates a variety of statistics.">
+<meta property="og:description" content="
 Statistics function that uses the Bland-Altman method to assess the agreement between two numerical vectors
-and calculates a variety of statistics."><meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png"><link rel="stylesheet" href="../consent.css"><script src="../consent.js" type="text/javascript" charset="utf-8"></script></head><body>
+and calculates a variety of statistics.">
+<meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png">
+<link rel="stylesheet" href="../consent.css">
+<script src="../consent.js" type="text/javascript" charset="utf-8"></script>
+</head>
+<body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
 
 
@@ -19,26 +42,66 @@
     </button>
 
     <div id="navbar" class="collapse navbar-collapse ms-3">
-      <ul class="navbar-nav me-auto"><li class="nav-item"><a class="nav-link" href="../articles/tern.html">Get started</a></li>
+      <ul class="navbar-nav me-auto">
+<li class="nav-item"><a class="nav-link" href="../articles/tern.html">Get started</a></li>
 <li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
 <li class="nav-item dropdown">
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-articles" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Articles</button>
-  <ul class="dropdown-menu" aria-labelledby="dropdown-articles"><li><a class="dropdown-item" href="../articles/missing_values.html">Missing Values in Tern</a></li>
+  <ul class="dropdown-menu" aria-labelledby="dropdown-articles">
+<li><a class="dropdown-item" href="../articles/missing_values.html">Missing Values in Tern</a></li>
     <li><a class="dropdown-item" href="../articles/tables.html">Tabulation</a></li>
     <li><a class="dropdown-item" href="../articles/tern_formats.html">Formatting Functions</a></li>
     <li><a class="dropdown-item" href="../articles/tern_functions_guide.html">Understanding `tern` functions</a></li>
-  </ul></li>
+  </ul>
+</li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
-  <ul class="dropdown-menu" aria-labelledby="dropdown-reports"><li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
+  <ul class="dropdown-menu" aria-labelledby="dropdown-reports">
+<li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
     <li><a class="dropdown-item" href="../unit-test-report/">Unit test report</a></li>
     <li><a class="dropdown-item" href="../unit-test-report-non-cran/">Non-CRAN unit test report</a></li>
-  </ul></li>
-      </ul><ul class="navbar-nav"><li class="nav-item"><form class="form-inline" role="search">
- <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json"></form></li>
+  </ul>
+</li>
+      <div><li class="nav-item dropdown">
+    <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-versions">Versions</a>
+    <div class="dropdown-menu" aria-labelledby="dropdown-versions">
+    <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/main">main</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.5">v0.9.5</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.4">v0.9.4</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.3">v0.9.3</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1-rc3">v0.9.1-rc3</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a>
+</div>
+</li></div>
+</ul>
+<ul class="navbar-nav">
+<li class="nav-item"><form class="form-inline" role="search">
+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json">
+</form></li>
 <li class="nav-item"><a class="external-link nav-link" href="https://github.com/insightsengineering/tern" aria-label="GitHub"><span class="fa fa-github"></span></a></li>
-      </ul></div>
+      </ul>
+</div>
 
 
   </div>
@@ -57,29 +120,39 @@
     </div>
 
     <div class="section level2">
-    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
+    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">s_bland_altman</span><span class="op">(</span><span class="va">x</span>, <span class="va">y</span>, conf_level <span class="op">=</span> <span class="fl">0.95</span><span class="op">)</span></span></code></pre></div>
     </div>
 
     <div class="section level2">
-    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
+    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a>
+</h2>
 
 
-<dl><dt id="arg-x">x<a class="anchor" aria-label="anchor" href="#arg-x"></a></dt>
+<dl>
+<dt id="arg-x">x<a class="anchor" aria-label="anchor" href="#arg-x"></a>
+</dt>
 <dd><p>(<code>numeric</code>)<br> vector of numbers we want to analyze.</p></dd>
 
 
-<dt id="arg-y">y<a class="anchor" aria-label="anchor" href="#arg-y"></a></dt>
+<dt id="arg-y">y<a class="anchor" aria-label="anchor" href="#arg-y"></a>
+</dt>
 <dd><p>(<code>numeric</code>)<br> vector of numbers we want to analyze, to be compared with <code>x</code>.</p></dd>
 
 
-<dt id="arg-conf-level">conf_level<a class="anchor" aria-label="anchor" href="#arg-conf-level"></a></dt>
+<dt id="arg-conf-level">conf_level<a class="anchor" aria-label="anchor" href="#arg-conf-level"></a>
+</dt>
 <dd><p>(<code>proportion</code>)<br> confidence level of the interval.</p></dd>
 
-</dl></div>
+</dl>
+</div>
     <div class="section level2">
-    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
-    <p>A named list of the following elements:</p><ul><li><p><code>df</code></p></li>
+    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a>
+</h2>
+    <p>A named list of the following elements:</p>
+<ul>
+<li><p><code>df</code></p></li>
 <li><p><code>difference_mean</code></p></li>
 <li><p><code>ci_mean</code></p></li>
 <li><p><code>difference_sd</code></p></li>
@@ -91,10 +164,12 @@ <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2
 <li><p><code>lower_agreement_limit_ci</code></p></li>
 <li><p><code>t_value</code></p></li>
 <li><p><code>n</code></p></li>
-</ul></div>
+</ul>
+</div>
 
     <div class="section level2">
-    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
+    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">x</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/seq.html" class="external-link">seq</a></span><span class="op">(</span><span class="fl">1</span>, <span class="fl">60</span>, <span class="fl">5</span><span class="op">)</span></span></span>
 <span class="r-in"><span><span class="va">y</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/seq.html" class="external-link">seq</a></span><span class="op">(</span><span class="fl">5</span>, <span class="fl">50</span>, <span class="fl">4</span><span class="op">)</span></span></span>
 <span class="r-in"><span></span></span>
@@ -151,17 +226,19 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 </code></pre></div>
     </div>
   </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
-    </nav></aside></div>
+    </nav></aside>
+</div>
 
 
     <footer><div class="nest">
   <p>tern is a part of the <strong>NEST</strong> and <a href="https://pharmaverse.org/" class="external-link"><strong>pharmaverse</strong></a>.</p>
 </div>
-<script type="text/javascript" src="../analytics.js"></script></footer></div>
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+<script type="text/javascript" src="../analytics.js"></script></footer>
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diff --git a/main/reference/s_cox_multivariate.html b/main/reference/s_cox_multivariate.html
index 893148ea20..cb1cfdd97f 100644
--- a/main/reference/s_cox_multivariate.html
+++ b/main/reference/s_cox_multivariate.html
@@ -1,19 +1,42 @@
-<!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Multivariate Cox model - summarized results — s_cox_multivariate • tern</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Multivariate Cox model - summarized results — s_cox_multivariate"><meta name="description" content="Analyses based on multivariate Cox model are usually not performed for the Controlled Substance Reporting or
+<html lang="en">
+<head>
+<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+<meta charset="utf-8">
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+<meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<title>Multivariate Cox model - summarized results — s_cox_multivariate • tern</title>
+<!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png">
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+<script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet">
+<script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet">
+<link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet">
+<script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Multivariate Cox model - summarized results — s_cox_multivariate">
+<meta name="description" content="Analyses based on multivariate Cox model are usually not performed for the Controlled Substance Reporting or
 regulatory documents but serve exploratory purposes only (e.g., for publication). In practice, the model usually
 includes only the main effects (without interaction terms). It produces the hazard ratio estimates for each of the
 covariates included in the model.
 The analysis follows the same principles (e.g., stratified vs. unstratified analysis and tie handling) as the
 usual Cox model analysis. Since there is usually no pre-specified hypothesis testing for such analysis,
 the p.values need to be interpreted with caution. (Statistical Analysis of Clinical Trials Data with R,
-NEST's bookdown)"><meta property="og:description" content="Analyses based on multivariate Cox model are usually not performed for the Controlled Substance Reporting or
+NEST's bookdown)">
+<meta property="og:description" content="Analyses based on multivariate Cox model are usually not performed for the Controlled Substance Reporting or
 regulatory documents but serve exploratory purposes only (e.g., for publication). In practice, the model usually
 includes only the main effects (without interaction terms). It produces the hazard ratio estimates for each of the
 covariates included in the model.
 The analysis follows the same principles (e.g., stratified vs. unstratified analysis and tie handling) as the
 usual Cox model analysis. Since there is usually no pre-specified hypothesis testing for such analysis,
 the p.values need to be interpreted with caution. (Statistical Analysis of Clinical Trials Data with R,
-NEST's bookdown)"><meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png"><link rel="stylesheet" href="../consent.css"><script src="../consent.js" type="text/javascript" charset="utf-8"></script></head><body>
+NEST's bookdown)">
+<meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png">
+<link rel="stylesheet" href="../consent.css">
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+</head>
+<body>
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@@ -29,26 +52,66 @@
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+</div>
+</li></div>
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+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json">
+</form></li>
 <li class="nav-item"><a class="external-link nav-link" href="https://github.com/insightsengineering/tern" aria-label="GitHub"><span class="fa fa-github"></span></a></li>
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+      </ul>
+</div>
 
 
   </div>
@@ -72,7 +135,8 @@
     </div>
 
     <div class="section level2">
-    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
+    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">s_cox_multivariate</span><span class="op">(</span></span>
 <span>  <span class="va">formula</span>,</span>
 <span>  <span class="va">data</span>,</span>
@@ -83,49 +147,61 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
     </div>
 
     <div class="section level2">
-    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
+    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a>
+</h2>
 
 
-<dl><dt id="arg-formula">formula<a class="anchor" aria-label="anchor" href="#arg-formula"></a></dt>
+<dl>
+<dt id="arg-formula">formula<a class="anchor" aria-label="anchor" href="#arg-formula"></a>
+</dt>
 <dd><p>(<code>formula</code>)<br> a formula corresponding to the investigated <code><a href="https://rdrr.io/pkg/survival/man/Surv.html" class="external-link">survival::Surv()</a></code> survival model
 including covariates.</p></dd>
 
 
-<dt id="arg-data">data<a class="anchor" aria-label="anchor" href="#arg-data"></a></dt>
+<dt id="arg-data">data<a class="anchor" aria-label="anchor" href="#arg-data"></a>
+</dt>
 <dd><p>(<code>data.frame</code>)<br> a data frame which includes the variable in formula and covariates.</p></dd>
 
 
-<dt id="arg-conf-level">conf_level<a class="anchor" aria-label="anchor" href="#arg-conf-level"></a></dt>
+<dt id="arg-conf-level">conf_level<a class="anchor" aria-label="anchor" href="#arg-conf-level"></a>
+</dt>
 <dd><p>(<code>proportion</code>)<br> the confidence level for the hazard ratio interval estimations. Default is 0.95.</p></dd>
 
 
-<dt id="arg-pval-method">pval_method<a class="anchor" aria-label="anchor" href="#arg-pval-method"></a></dt>
+<dt id="arg-pval-method">pval_method<a class="anchor" aria-label="anchor" href="#arg-pval-method"></a>
+</dt>
 <dd><p>(<code>string</code>)<br> the method used for the estimation of p-values, should be one of
 <code>"wald"</code> (default) or <code>"likelihood"</code>.</p></dd>
 
 
-<dt id="arg--">...<a class="anchor" aria-label="anchor" href="#arg--"></a></dt>
+<dt id="arg--">...<a class="anchor" aria-label="anchor" href="#arg--"></a>
+</dt>
 <dd><p>optional parameters passed to <code><a href="https://rdrr.io/pkg/survival/man/coxph.html" class="external-link">survival::coxph()</a></code>. Can include <code>ties</code>, a character string specifying the
 method for tie handling, one of <code>exact</code> (default), <code>efron</code>, <code>breslow</code>.</p></dd>
 
-</dl></div>
+</dl>
+</div>
     <div class="section level2">
-    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
+    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a>
+</h2>
     <p>A <code>list</code> with elements <code>mod</code>, <code>msum</code>, <code>aov</code>, and <code>coef_inter</code>.</p>
     </div>
     <div class="section level2">
-    <h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a></h2>
+    <h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a>
+</h2>
     <p>The output is limited to single effect terms. Work in ongoing for estimation of interaction terms
 but is out of scope as defined by the  Global Data Standards Repository
 (<strong><code>GDS_Standard_TLG_Specs_Tables_2.doc</code></strong>).</p>
     </div>
     <div class="section level2">
-    <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"></a></h2>
+    <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"></a>
+</h2>
     <div class="dont-index"><p><code><a href="estimate_coef.html">estimate_coef()</a></code>.</p></div>
     </div>
 
     <div class="section level2">
-    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
+    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://dplyr.tidyverse.org" class="external-link">dplyr</a></span><span class="op">)</span></span></span>
 <span class="r-in"><span></span></span>
 <span class="r-in"><span><span class="va">adtte</span> <span class="op">&lt;-</span> <span class="va">tern_ex_adtte</span></span></span>
@@ -142,17 +218,19 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 </code></pre></div>
     </div>
   </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
-    </nav></aside></div>
+    </nav></aside>
+</div>
 
 
     <footer><div class="nest">
   <p>tern is a part of the <strong>NEST</strong> and <a href="https://pharmaverse.org/" class="external-link"><strong>pharmaverse</strong></a>.</p>
 </div>
-<script type="text/javascript" src="../analytics.js"></script></footer></div>
-
+<script type="text/javascript" src="../analytics.js"></script></footer>
+</div>
 
 
 
 
-  </body></html>
 
+  </body>
+</html>
diff --git a/main/reference/sas_na.html b/main/reference/sas_na.html
index 437fb67c5b..549d8b2b85 100644
--- a/main/reference/sas_na.html
+++ b/main/reference/sas_na.html
@@ -1,9 +1,32 @@
-<!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Convert strings to NA — sas_na • tern</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Convert strings to NA — sas_na"><meta name="description" content="
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+<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
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+<meta http-equiv="X-UA-Compatible" content="IE=edge">
+<meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<title>Convert strings to NA — sas_na • tern</title>
+<!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png">
+<link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png">
+<link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png">
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+<link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png">
+<script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet">
+<script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet">
+<link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet">
+<script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Convert strings to NA — sas_na">
+<meta name="description" content="
 SAS imports missing data as empty strings or strings with whitespaces only. This helper function can be used to
-convert these values to NAs."><meta property="og:description" content="
+convert these values to NAs.">
+<meta property="og:description" content="
 SAS imports missing data as empty strings or strings with whitespaces only. This helper function can be used to
-convert these values to NAs."><meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png"><link rel="stylesheet" href="../consent.css"><script src="../consent.js" type="text/javascript" charset="utf-8"></script></head><body>
+convert these values to NAs.">
+<meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png">
+<link rel="stylesheet" href="../consent.css">
+<script src="../consent.js" type="text/javascript" charset="utf-8"></script>
+</head>
+<body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
 
 
@@ -19,33 +42,74 @@
     </button>
 
     <div id="navbar" class="collapse navbar-collapse ms-3">
-      <ul class="navbar-nav me-auto"><li class="nav-item"><a class="nav-link" href="../articles/tern.html">Get started</a></li>
+      <ul class="navbar-nav me-auto">
+<li class="nav-item"><a class="nav-link" href="../articles/tern.html">Get started</a></li>
 <li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
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-  <ul class="dropdown-menu" aria-labelledby="dropdown-articles"><li><a class="dropdown-item" href="../articles/missing_values.html">Missing Values in Tern</a></li>
+  <ul class="dropdown-menu" aria-labelledby="dropdown-articles">
+<li><a class="dropdown-item" href="../articles/missing_values.html">Missing Values in Tern</a></li>
     <li><a class="dropdown-item" href="../articles/tables.html">Tabulation</a></li>
     <li><a class="dropdown-item" href="../articles/tern_formats.html">Formatting Functions</a></li>
     <li><a class="dropdown-item" href="../articles/tern_functions_guide.html">Understanding `tern` functions</a></li>
-  </ul></li>
+  </ul>
+</li>
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   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
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+  <ul class="dropdown-menu" aria-labelledby="dropdown-reports">
+<li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
     <li><a class="dropdown-item" href="../unit-test-report/">Unit test report</a></li>
     <li><a class="dropdown-item" href="../unit-test-report-non-cran/">Non-CRAN unit test report</a></li>
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-      </ul><ul class="navbar-nav"><li class="nav-item"><form class="form-inline" role="search">
- <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json"></form></li>
+  </ul>
+</li>
+      <div><li class="nav-item dropdown">
+    <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-versions">Versions</a>
+    <div class="dropdown-menu" aria-labelledby="dropdown-versions">
+    <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/main">main</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.5">v0.9.5</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.4">v0.9.4</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.3">v0.9.3</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1-rc3">v0.9.1-rc3</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a>
+</div>
+</li></div>
+</ul>
+<ul class="navbar-nav">
+<li class="nav-item"><form class="form-inline" role="search">
+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json">
+</form></li>
 <li class="nav-item"><a class="external-link nav-link" href="https://github.com/insightsengineering/tern" aria-label="GitHub"><span class="fa fa-github"></span></a></li>
-      </ul></div>
+      </ul>
+</div>
 
 
   </div>
 </nav><div class="container template-reference-topic">
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
-      <img src="../logo.png" class="logo" alt=""><h1>Convert strings to <code>NA</code></h1>
+      <img src="../logo.png" class="logo" alt=""><h1>Convert strings to <code>NA</code>
+</h1>
       <small class="dont-index">Source: <a href="https://github.com/insightsengineering/tern/blob/main/R/missing_data.R" class="external-link"><code>R/missing_data.R</code></a></small>
       <div class="d-none name"><code>sas_na.Rd</code></div>
     </div>
@@ -57,34 +121,43 @@
     </div>
 
     <div class="section level2">
-    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
+    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">sas_na</span><span class="op">(</span><span class="va">x</span>, empty <span class="op">=</span> <span class="cn">TRUE</span>, whitespaces <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></code></pre></div>
     </div>
 
     <div class="section level2">
-    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
+    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a>
+</h2>
 
 
-<dl><dt id="arg-x">x<a class="anchor" aria-label="anchor" href="#arg-x"></a></dt>
+<dl>
+<dt id="arg-x">x<a class="anchor" aria-label="anchor" href="#arg-x"></a>
+</dt>
 <dd><p>(<code>factor</code> or <code>character</code>)<br> values for which any missing values should be substituted.</p></dd>
 
 
-<dt id="arg-empty">empty<a class="anchor" aria-label="anchor" href="#arg-empty"></a></dt>
+<dt id="arg-empty">empty<a class="anchor" aria-label="anchor" href="#arg-empty"></a>
+</dt>
 <dd><p>(<code>flag</code>)<br> if <code>TRUE</code>, empty strings get replaced by <code>NA</code>.</p></dd>
 
 
-<dt id="arg-whitespaces">whitespaces<a class="anchor" aria-label="anchor" href="#arg-whitespaces"></a></dt>
+<dt id="arg-whitespaces">whitespaces<a class="anchor" aria-label="anchor" href="#arg-whitespaces"></a>
+</dt>
 <dd><p>(<code>flag</code>)<br> if <code>TRUE</code>, strings made from only whitespaces get replaced with <code>NA</code>.</p></dd>
 
-</dl></div>
+</dl>
+</div>
     <div class="section level2">
-    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
+    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a>
+</h2>
     <p><code>x</code> with <code>""</code> and/or whitespace-only values substituted by <code>NA</code>, depending on the values of
 <code>empty</code> and <code>whitespaces</code>.</p>
     </div>
 
     <div class="section level2">
-    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
+    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="fu">sas_na</span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"1"</span>, <span class="st">""</span>, <span class="st">" "</span>, <span class="st">"   "</span>, <span class="st">"b"</span><span class="op">)</span><span class="op">)</span></span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> [1] "1" NA  NA  NA  "b"</span>
 <span class="r-in"><span><span class="fu">sas_na</span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/factor.html" class="external-link">factor</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">""</span>, <span class="st">" "</span>, <span class="st">"b"</span><span class="op">)</span><span class="op">)</span><span class="op">)</span></span></span>
@@ -97,17 +170,19 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 </code></pre></div>
     </div>
   </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
-    </nav></aside></div>
+    </nav></aside>
+</div>
 
 
     <footer><div class="nest">
   <p>tern is a part of the <strong>NEST</strong> and <a href="https://pharmaverse.org/" class="external-link"><strong>pharmaverse</strong></a>.</p>
 </div>
-<script type="text/javascript" src="../analytics.js"></script></footer></div>
-
+<script type="text/javascript" src="../analytics.js"></script></footer>
+</div>
 
 
 
 
-  </body></html>
 
+  </body>
+</html>
diff --git a/main/reference/score_occurrences.html b/main/reference/score_occurrences.html
index 95d46f902b..21a2455f6c 100644
--- a/main/reference/score_occurrences.html
+++ b/main/reference/score_occurrences.html
@@ -1,9 +1,32 @@
-<!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Occurrence table sorting — score_occurrences • tern</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Occurrence table sorting — score_occurrences"><meta name="description" content="
+<html lang="en">
+<head>
+<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+<meta charset="utf-8">
+<meta http-equiv="X-UA-Compatible" content="IE=edge">
+<meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<title>Occurrence table sorting — score_occurrences • tern</title>
+<!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png">
+<link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png">
+<link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png">
+<link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png">
+<link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png">
+<link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png">
+<script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet">
+<script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet">
+<link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet">
+<script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Occurrence table sorting — score_occurrences">
+<meta name="description" content="
 Functions to score occurrence table subtables and rows which can be used in the
-sorting of occurrence tables."><meta property="og:description" content="
+sorting of occurrence tables.">
+<meta property="og:description" content="
 Functions to score occurrence table subtables and rows which can be used in the
-sorting of occurrence tables."><meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png"><link rel="stylesheet" href="../consent.css"><script src="../consent.js" type="text/javascript" charset="utf-8"></script></head><body>
+sorting of occurrence tables.">
+<meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png">
+<link rel="stylesheet" href="../consent.css">
+<script src="../consent.js" type="text/javascript" charset="utf-8"></script>
+</head>
+<body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
 
 
@@ -19,26 +42,66 @@
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-      <ul class="navbar-nav me-auto"><li class="nav-item"><a class="nav-link" href="../articles/tern.html">Get started</a></li>
+      <ul class="navbar-nav me-auto">
+<li class="nav-item"><a class="nav-link" href="../articles/tern.html">Get started</a></li>
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   <button class="nav-link dropdown-toggle" type="button" id="dropdown-articles" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Articles</button>
-  <ul class="dropdown-menu" aria-labelledby="dropdown-articles"><li><a class="dropdown-item" href="../articles/missing_values.html">Missing Values in Tern</a></li>
+  <ul class="dropdown-menu" aria-labelledby="dropdown-articles">
+<li><a class="dropdown-item" href="../articles/missing_values.html">Missing Values in Tern</a></li>
     <li><a class="dropdown-item" href="../articles/tables.html">Tabulation</a></li>
     <li><a class="dropdown-item" href="../articles/tern_formats.html">Formatting Functions</a></li>
     <li><a class="dropdown-item" href="../articles/tern_functions_guide.html">Understanding `tern` functions</a></li>
-  </ul></li>
+  </ul>
+</li>
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+  <ul class="dropdown-menu" aria-labelledby="dropdown-reports">
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- <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json"></form></li>
+  </ul>
+</li>
+      <div><li class="nav-item dropdown">
+    <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-versions">Versions</a>
+    <div class="dropdown-menu" aria-labelledby="dropdown-versions">
+    <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
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+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
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+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.4">v0.9.4</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.3">v0.9.3</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1-rc3">v0.9.1-rc3</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a>
+</div>
+</li></div>
+</ul>
+<ul class="navbar-nav">
+<li class="nav-item"><form class="form-inline" role="search">
+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json">
+</form></li>
 <li class="nav-item"><a class="external-link nav-link" href="https://github.com/insightsengineering/tern" aria-label="GitHub"><span class="fa fa-github"></span></a></li>
-      </ul></div>
+      </ul>
+</div>
 
 
   </div>
@@ -57,7 +120,8 @@
     </div>
 
     <div class="section level2">
-    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
+    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">score_occurrences</span><span class="op">(</span><span class="va">table_row</span><span class="op">)</span></span>
 <span></span>
 <span><span class="fu">score_occurrences_cols</span><span class="op">(</span><span class="va">...</span><span class="op">)</span></span>
@@ -68,34 +132,50 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
     </div>
 
     <div class="section level2">
-    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
+    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a>
+</h2>
 
 
-<dl><dt id="arg-table-row">table_row<a class="anchor" aria-label="anchor" href="#arg-table-row"></a></dt>
+<dl>
+<dt id="arg-table-row">table_row<a class="anchor" aria-label="anchor" href="#arg-table-row"></a>
+</dt>
 <dd><p>(<code>TableRow</code>)<br> an analysis row in a occurrence table.</p></dd>
 
 
-<dt id="arg--">...<a class="anchor" aria-label="anchor" href="#arg--"></a></dt>
+<dt id="arg--">...<a class="anchor" aria-label="anchor" href="#arg--"></a>
+</dt>
 <dd><p>arguments for row or column access, see <code><a href="rtables_access.html">rtables_access</a></code>: either <code>col_names</code> (<code>character</code>) including
 the names of the columns which should be used, or alternatively <code>col_indices</code> (<code>integer</code>) giving the indices
 directly instead.</p></dd>
 
-</dl></div>
+</dl>
+</div>
     <div class="section level2">
-    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
+    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a>
+</h2>
 
-<ul><li><p><code>score_occurrences()</code> returns the sum of counts across all columns of a table row.</p></li>
-</ul><ul><li><p><code>score_occurrences_cols()</code> returns a function that sums counts across all specified columns
+<ul>
+<li><p><code>score_occurrences()</code> returns the sum of counts across all columns of a table row.</p></li>
+</ul>
+<ul>
+<li><p><code>score_occurrences_cols()</code> returns a function that sums counts across all specified columns
 of a table row.</p></li>
-</ul><ul><li><p><code>score_occurrences_subtable()</code> returns a function that sums counts in each subtable
+</ul>
+<ul>
+<li><p><code>score_occurrences_subtable()</code> returns a function that sums counts in each subtable
 across all specified columns.</p></li>
-</ul><ul><li><p><code>score_occurrences_cont_cols()</code> returns a function that sums counts in the first content row in
+</ul>
+<ul>
+<li><p><code>score_occurrences_cont_cols()</code> returns a function that sums counts in the first content row in
 specified columns.</p></li>
-</ul></div>
+</ul>
+</div>
     <div class="section level2">
-    <h2 id="functions">Functions<a class="anchor" aria-label="anchor" href="#functions"></a></h2>
+    <h2 id="functions">Functions<a class="anchor" aria-label="anchor" href="#functions"></a>
+</h2>
 
-<ul><li><p><code>score_occurrences()</code>: Scoring function which sums the counts across all
+<ul>
+<li><p><code>score_occurrences()</code>: Scoring function which sums the counts across all
 columns. It will fail if anything else but counts are used.</p></li>
 <li><p><code>score_occurrences_cols()</code>: Scoring functions can be produced by this constructor to only include
 specific columns in the scoring. See <code><a href="rtables_access.html">h_row_counts()</a></code> for further information.</p></li>
@@ -104,15 +184,20 @@ <h2 id="functions">Functions<a class="anchor" aria-label="anchor" href="#functio
 there is no available content row summing up these counts.</p></li>
 <li><p><code>score_occurrences_cont_cols()</code>: Produces a score function for sorting table by summing the first content row in
 specified columns. Note that this is extending <code><a href="https://insightsengineering.github.io/rtables/latest-tag/reference/score_funs.html" class="external-link">rtables::cont_n_onecol()</a></code> and <code><a href="https://insightsengineering.github.io/rtables/latest-tag/reference/score_funs.html" class="external-link">rtables::cont_n_allcols()</a></code>.</p></li>
-</ul></div>
+</ul>
+</div>
     <div class="section level2">
-    <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"></a></h2>
-    <div class="dont-index"><p><code><a href="rtables_access.html">h_row_first_values()</a></code></p>
-<p><code><a href="rtables_access.html">h_row_counts()</a></code></p></div>
+    <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"></a>
+</h2>
+    <div class="dont-index">
+<p><code><a href="rtables_access.html">h_row_first_values()</a></code></p>
+<p><code><a href="rtables_access.html">h_row_counts()</a></code></p>
+</div>
     </div>
 
     <div class="section level2">
-    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
+    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">lyt</span> <span class="op">&lt;-</span> <span class="fu">basic_table</span><span class="op">(</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span></span>
 <span class="r-in"><span>  <span class="fu">split_cols_by</span><span class="op">(</span><span class="st">"ARM"</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span></span>
 <span class="r-in"><span>  <span class="fu">add_colcounts</span><span class="op">(</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span></span>
@@ -266,17 +351,19 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 </code></pre></div>
     </div>
   </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
-    </nav></aside></div>
+    </nav></aside>
+</div>
 
 
     <footer><div class="nest">
   <p>tern is a part of the <strong>NEST</strong> and <a href="https://pharmaverse.org/" class="external-link"><strong>pharmaverse</strong></a>.</p>
 </div>
-<script type="text/javascript" src="../analytics.js"></script></footer></div>
-
+<script type="text/javascript" src="../analytics.js"></script></footer>
+</div>
 
 
 
 
-  </body></html>
 
+  </body>
+</html>
diff --git a/main/reference/split_cols_by_groups.html b/main/reference/split_cols_by_groups.html
index 1c9a306352..1a83812aca 100644
--- a/main/reference/split_cols_by_groups.html
+++ b/main/reference/split_cols_by_groups.html
@@ -1,5 +1,28 @@
-<!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Split columns by groups of levels — split_cols_by_groups • tern</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Split columns by groups of levels — split_cols_by_groups"><meta name="description" content=""><meta property="og:description" content=""><meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png"><link rel="stylesheet" href="../consent.css"><script src="../consent.js" type="text/javascript" charset="utf-8"></script></head><body>
+<html lang="en">
+<head>
+<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+<meta charset="utf-8">
+<meta http-equiv="X-UA-Compatible" content="IE=edge">
+<meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<title>Split columns by groups of levels — split_cols_by_groups • tern</title>
+<!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png">
+<link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png">
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+<link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png">
+<link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png">
+<link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png">
+<script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet">
+<script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet">
+<link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet">
+<script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Split columns by groups of levels — split_cols_by_groups">
+<meta name="description" content="">
+<meta property="og:description" content="">
+<meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png">
+<link rel="stylesheet" href="../consent.css">
+<script src="../consent.js" type="text/javascript" charset="utf-8"></script>
+</head>
+<body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
 
 
@@ -15,26 +38,66 @@
     </button>
 
     <div id="navbar" class="collapse navbar-collapse ms-3">
-      <ul class="navbar-nav me-auto"><li class="nav-item"><a class="nav-link" href="../articles/tern.html">Get started</a></li>
+      <ul class="navbar-nav me-auto">
+<li class="nav-item"><a class="nav-link" href="../articles/tern.html">Get started</a></li>
 <li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
 <li class="nav-item dropdown">
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-articles" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Articles</button>
-  <ul class="dropdown-menu" aria-labelledby="dropdown-articles"><li><a class="dropdown-item" href="../articles/missing_values.html">Missing Values in Tern</a></li>
+  <ul class="dropdown-menu" aria-labelledby="dropdown-articles">
+<li><a class="dropdown-item" href="../articles/missing_values.html">Missing Values in Tern</a></li>
     <li><a class="dropdown-item" href="../articles/tables.html">Tabulation</a></li>
     <li><a class="dropdown-item" href="../articles/tern_formats.html">Formatting Functions</a></li>
     <li><a class="dropdown-item" href="../articles/tern_functions_guide.html">Understanding `tern` functions</a></li>
-  </ul></li>
+  </ul>
+</li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
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+  <ul class="dropdown-menu" aria-labelledby="dropdown-reports">
+<li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
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- <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json"></form></li>
+  </ul>
+</li>
+      <div><li class="nav-item dropdown">
+    <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-versions">Versions</a>
+    <div class="dropdown-menu" aria-labelledby="dropdown-versions">
+    <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/main">main</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.5">v0.9.5</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.4">v0.9.4</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.3">v0.9.3</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1-rc3">v0.9.1-rc3</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a>
+</div>
+</li></div>
+</ul>
+<ul class="navbar-nav">
+<li class="nav-item"><form class="form-inline" role="search">
+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json">
+</form></li>
 <li class="nav-item"><a class="external-link nav-link" href="https://github.com/insightsengineering/tern" aria-label="GitHub"><span class="fa fa-github"></span></a></li>
-      </ul></div>
+      </ul>
+</div>
 
 
   </div>
@@ -51,50 +114,62 @@
     </div>
 
     <div class="section level2">
-    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
+    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">split_cols_by_groups</span><span class="op">(</span><span class="va">lyt</span>, <span class="va">var</span>, groups_list <span class="op">=</span> <span class="cn">NULL</span>, ref_group <span class="op">=</span> <span class="cn">NULL</span>, <span class="va">...</span><span class="op">)</span></span></code></pre></div>
     </div>
 
     <div class="section level2">
-    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
+    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a>
+</h2>
 
 
-<dl><dt id="arg-lyt">lyt<a class="anchor" aria-label="anchor" href="#arg-lyt"></a></dt>
+<dl>
+<dt id="arg-lyt">lyt<a class="anchor" aria-label="anchor" href="#arg-lyt"></a>
+</dt>
 <dd><p>(<code>PreDataTableLayouts</code>)<br> layout that analyses will be added to.</p></dd>
 
 
-<dt id="arg-var">var<a class="anchor" aria-label="anchor" href="#arg-var"></a></dt>
+<dt id="arg-var">var<a class="anchor" aria-label="anchor" href="#arg-var"></a>
+</dt>
 <dd><p>(<code>string</code>)<br> single variable name that is passed by <code>rtables</code> when requested
 by a statistics function.</p></dd>
 
 
-<dt id="arg-groups-list">groups_list<a class="anchor" aria-label="anchor" href="#arg-groups-list"></a></dt>
+<dt id="arg-groups-list">groups_list<a class="anchor" aria-label="anchor" href="#arg-groups-list"></a>
+</dt>
 <dd><p>(named <code>list</code> of <code>character</code>)<br> specifies the new group levels via the names and the
 levels that belong to it in the character vectors that are elements of the list.</p></dd>
 
 
-<dt id="arg-ref-group">ref_group<a class="anchor" aria-label="anchor" href="#arg-ref-group"></a></dt>
+<dt id="arg-ref-group">ref_group<a class="anchor" aria-label="anchor" href="#arg-ref-group"></a>
+</dt>
 <dd><p>(<code>data.frame</code> or <code>vector</code>)<br> the data corresponding to the reference group.</p></dd>
 
 
-<dt id="arg--">...<a class="anchor" aria-label="anchor" href="#arg--"></a></dt>
+<dt id="arg--">...<a class="anchor" aria-label="anchor" href="#arg--"></a>
+</dt>
 <dd><p>additional arguments to <code><a href="https://insightsengineering.github.io/rtables/latest-tag/reference/split_cols_by.html" class="external-link">rtables::split_cols_by()</a></code> in order. For instance, to
 control formats (<code>format</code>), add a joint column for all groups (<code>incl_all</code>).</p></dd>
 
-</dl></div>
+</dl>
+</div>
     <div class="section level2">
-    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
+    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a>
+</h2>
     <p>A layout object suitable for passing to further layouting functions. Adding
 this function to an <code>rtable</code> layout will add a column split including the given
 groups to the table layout.</p>
     </div>
     <div class="section level2">
-    <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"></a></h2>
+    <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"></a>
+</h2>
     <div class="dont-index"><p><code><a href="https://insightsengineering.github.io/rtables/latest-tag/reference/split_cols_by.html" class="external-link">rtables::split_cols_by()</a></code></p></div>
     </div>
 
     <div class="section level2">
-    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
+    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="co"># 1 - Basic use</span></span></span>
 <span class="r-in"><span></span></span>
 <span class="r-in"><span><span class="co"># Without group combination `split_cols_by_groups` is</span></span></span>
@@ -215,17 +290,19 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 </code></pre></div>
     </div>
   </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
-    </nav></aside></div>
+    </nav></aside>
+</div>
 
 
     <footer><div class="nest">
   <p>tern is a part of the <strong>NEST</strong> and <a href="https://pharmaverse.org/" class="external-link"><strong>pharmaverse</strong></a>.</p>
 </div>
-<script type="text/javascript" src="../analytics.js"></script></footer></div>
-
+<script type="text/javascript" src="../analytics.js"></script></footer>
+</div>
 
 
 
 
-  </body></html>
 
+  </body>
+</html>
diff --git a/main/reference/split_text_grob.html b/main/reference/split_text_grob.html
index 2571e8a606..e9fcc9c893 100644
--- a/main/reference/split_text_grob.html
+++ b/main/reference/split_text_grob.html
@@ -1,5 +1,28 @@
-<!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Split text according to available text width — split_text_grob • tern</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Split text according to available text width — split_text_grob"><meta name="description" content="Dynamically wrap text."><meta property="og:description" content="Dynamically wrap text."><meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png"><link rel="stylesheet" href="../consent.css"><script src="../consent.js" type="text/javascript" charset="utf-8"></script></head><body>
+<html lang="en">
+<head>
+<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+<meta charset="utf-8">
+<meta http-equiv="X-UA-Compatible" content="IE=edge">
+<meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<title>Split text according to available text width — split_text_grob • tern</title>
+<!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png">
+<link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png">
+<link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png">
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+<link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png">
+<link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png">
+<script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet">
+<script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet">
+<link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet">
+<script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Split text according to available text width — split_text_grob">
+<meta name="description" content="Dynamically wrap text.">
+<meta property="og:description" content="Dynamically wrap text.">
+<meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png">
+<link rel="stylesheet" href="../consent.css">
+<script src="../consent.js" type="text/javascript" charset="utf-8"></script>
+</head>
+<body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
 
 
@@ -15,26 +38,66 @@
     </button>
 
     <div id="navbar" class="collapse navbar-collapse ms-3">
-      <ul class="navbar-nav me-auto"><li class="nav-item"><a class="nav-link" href="../articles/tern.html">Get started</a></li>
+      <ul class="navbar-nav me-auto">
+<li class="nav-item"><a class="nav-link" href="../articles/tern.html">Get started</a></li>
 <li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
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   <button class="nav-link dropdown-toggle" type="button" id="dropdown-articles" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Articles</button>
-  <ul class="dropdown-menu" aria-labelledby="dropdown-articles"><li><a class="dropdown-item" href="../articles/missing_values.html">Missing Values in Tern</a></li>
+  <ul class="dropdown-menu" aria-labelledby="dropdown-articles">
+<li><a class="dropdown-item" href="../articles/missing_values.html">Missing Values in Tern</a></li>
     <li><a class="dropdown-item" href="../articles/tables.html">Tabulation</a></li>
     <li><a class="dropdown-item" href="../articles/tern_formats.html">Formatting Functions</a></li>
     <li><a class="dropdown-item" href="../articles/tern_functions_guide.html">Understanding `tern` functions</a></li>
-  </ul></li>
+  </ul>
+</li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
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   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
-  <ul class="dropdown-menu" aria-labelledby="dropdown-reports"><li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
+  <ul class="dropdown-menu" aria-labelledby="dropdown-reports">
+<li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
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- <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json"></form></li>
+  </ul>
+</li>
+      <div><li class="nav-item dropdown">
+    <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-versions">Versions</a>
+    <div class="dropdown-menu" aria-labelledby="dropdown-versions">
+    <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
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+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.5">v0.9.5</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.4">v0.9.4</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.3">v0.9.3</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1-rc3">v0.9.1-rc3</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a>
+</div>
+</li></div>
+</ul>
+<ul class="navbar-nav">
+<li class="nav-item"><form class="form-inline" role="search">
+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json">
+</form></li>
 <li class="nav-item"><a class="external-link nav-link" href="https://github.com/insightsengineering/tern" aria-label="GitHub"><span class="fa fa-github"></span></a></li>
-      </ul></div>
+      </ul>
+</div>
 
 
   </div>
@@ -51,7 +114,8 @@
     </div>
 
     <div class="section level2">
-    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
+    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">split_text_grob</span><span class="op">(</span></span>
 <span>  <span class="va">text</span>,</span>
 <span>  x <span class="op">=</span> <span class="fu">grid</span><span class="fu">::</span><span class="fu"><a href="https://rdrr.io/r/grid/unit.html" class="external-link">unit</a></span><span class="op">(</span><span class="fl">0.5</span>, <span class="st">"npc"</span><span class="op">)</span>,</span>
@@ -68,26 +132,33 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
     </div>
 
     <div class="section level2">
-    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
+    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a>
+</h2>
 
 
-<dl><dt id="arg-text">text<a class="anchor" aria-label="anchor" href="#arg-text"></a></dt>
+<dl>
+<dt id="arg-text">text<a class="anchor" aria-label="anchor" href="#arg-text"></a>
+</dt>
 <dd><p>(<code>string</code>)<br> the text to wrap.</p></dd>
 
 
-<dt id="arg-x">x<a class="anchor" aria-label="anchor" href="#arg-x"></a></dt>
+<dt id="arg-x">x<a class="anchor" aria-label="anchor" href="#arg-x"></a>
+</dt>
 <dd><p>A numeric vector or unit object specifying x-values.</p></dd>
 
 
-<dt id="arg-y">y<a class="anchor" aria-label="anchor" href="#arg-y"></a></dt>
+<dt id="arg-y">y<a class="anchor" aria-label="anchor" href="#arg-y"></a>
+</dt>
 <dd><p>A numeric vector or unit object specifying y-values.</p></dd>
 
 
-<dt id="arg-width">width<a class="anchor" aria-label="anchor" href="#arg-width"></a></dt>
+<dt id="arg-width">width<a class="anchor" aria-label="anchor" href="#arg-width"></a>
+</dt>
 <dd><p>(<code><a href="https://rdrr.io/r/grid/unit.html" class="external-link">grid::unit</a></code>)<br> a unit object specifying maximum width of text.</p></dd>
 
 
-<dt id="arg-just">just<a class="anchor" aria-label="anchor" href="#arg-just"></a></dt>
+<dt id="arg-just">just<a class="anchor" aria-label="anchor" href="#arg-just"></a>
+</dt>
 <dd><p>The justification of the text
     relative to its (x, y) location.  If there are two values, the first
     value specifies horizontal justification and the second value specifies
@@ -97,57 +168,68 @@ <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#argumen
     and 1 means right (top) alignment.</p></dd>
 
 
-<dt id="arg-hjust">hjust<a class="anchor" aria-label="anchor" href="#arg-hjust"></a></dt>
+<dt id="arg-hjust">hjust<a class="anchor" aria-label="anchor" href="#arg-hjust"></a>
+</dt>
 <dd><p>A numeric vector specifying horizontal justification.
     If specified, overrides the <code>just</code> setting.</p></dd>
 
 
-<dt id="arg-vjust">vjust<a class="anchor" aria-label="anchor" href="#arg-vjust"></a></dt>
+<dt id="arg-vjust">vjust<a class="anchor" aria-label="anchor" href="#arg-vjust"></a>
+</dt>
 <dd><p>A numeric vector specifying vertical justification.
     If specified, overrides the <code>just</code> setting.</p></dd>
 
 
-<dt id="arg-default-units">default.units<a class="anchor" aria-label="anchor" href="#arg-default-units"></a></dt>
+<dt id="arg-default-units">default.units<a class="anchor" aria-label="anchor" href="#arg-default-units"></a>
+</dt>
 <dd><p>A string indicating the default units to use
     if <code>x</code> or <code>y</code>
     are only given as numeric vectors.</p></dd>
 
 
-<dt id="arg-name">name<a class="anchor" aria-label="anchor" href="#arg-name"></a></dt>
+<dt id="arg-name">name<a class="anchor" aria-label="anchor" href="#arg-name"></a>
+</dt>
 <dd><p>A character identifier.</p></dd>
 
 
-<dt id="arg-gp">gp<a class="anchor" aria-label="anchor" href="#arg-gp"></a></dt>
+<dt id="arg-gp">gp<a class="anchor" aria-label="anchor" href="#arg-gp"></a>
+</dt>
 <dd><p>An object of class <code>"gpar"</code>, typically the output
     from a call to the function <code><a href="https://rdrr.io/r/grid/gpar.html" class="external-link">gpar</a></code>.  This is basically
     a list of graphical parameter settings.</p></dd>
 
 
-<dt id="arg-vp">vp<a class="anchor" aria-label="anchor" href="#arg-vp"></a></dt>
+<dt id="arg-vp">vp<a class="anchor" aria-label="anchor" href="#arg-vp"></a>
+</dt>
 <dd><p>A Grid viewport object (or NULL).</p></dd>
 
-</dl></div>
+</dl>
+</div>
     <div class="section level2">
-    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
+    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a>
+</h2>
     <p>A text <code>grob</code>.</p>
     </div>
     <div class="section level2">
-    <h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a></h2>
+    <h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a>
+</h2>
     <p>This code is taken from <code>R Graphics by Paul Murell, 2nd edition</code></p>
     </div>
 
   </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
-    </nav></aside></div>
+    </nav></aside>
+</div>
 
 
     <footer><div class="nest">
   <p>tern is a part of the <strong>NEST</strong> and <a href="https://pharmaverse.org/" class="external-link"><strong>pharmaverse</strong></a>.</p>
 </div>
-<script type="text/javascript" src="../analytics.js"></script></footer></div>
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+<script type="text/javascript" src="../analytics.js"></script></footer>
+</div>
 
 
 
 
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+  </body>
+</html>
diff --git a/main/reference/stack_grobs.html b/main/reference/stack_grobs.html
index 0a428444c5..650dcfbecb 100644
--- a/main/reference/stack_grobs.html
+++ b/main/reference/stack_grobs.html
@@ -1,7 +1,30 @@
-<!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Stack multiple grobs — stack_grobs • tern</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Stack multiple grobs — stack_grobs"><meta name="description" content="
-Stack grobs as a new grob with 1 column and multiple rows layout."><meta property="og:description" content="
-Stack grobs as a new grob with 1 column and multiple rows layout."><meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png"><link rel="stylesheet" href="../consent.css"><script src="../consent.js" type="text/javascript" charset="utf-8"></script></head><body>
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+<script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Stack multiple grobs — stack_grobs">
+<meta name="description" content="
+Stack grobs as a new grob with 1 column and multiple rows layout.">
+<meta property="og:description" content="
+Stack grobs as a new grob with 1 column and multiple rows layout.">
+<meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png">
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@@ -17,26 +40,66 @@
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+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
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+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a>
+</div>
+</li></div>
+</ul>
+<ul class="navbar-nav">
+<li class="nav-item"><form class="form-inline" role="search">
+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json">
+</form></li>
 <li class="nav-item"><a class="external-link nav-link" href="https://github.com/insightsengineering/tern" aria-label="GitHub"><span class="fa fa-github"></span></a></li>
-      </ul></div>
+      </ul>
+</div>
 
 
   </div>
@@ -54,7 +117,8 @@
     </div>
 
     <div class="section level2">
-    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
+    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">stack_grobs</span><span class="op">(</span></span>
 <span>  <span class="va">...</span>,</span>
 <span>  grobs <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span><span class="va">...</span><span class="op">)</span>,</span>
@@ -66,40 +130,51 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
     </div>
 
     <div class="section level2">
-    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
+    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a>
+</h2>
 
 
-<dl><dt id="arg--">...<a class="anchor" aria-label="anchor" href="#arg--"></a></dt>
+<dl>
+<dt id="arg--">...<a class="anchor" aria-label="anchor" href="#arg--"></a>
+</dt>
 <dd><p>grobs.</p></dd>
 
 
-<dt id="arg-grobs">grobs<a class="anchor" aria-label="anchor" href="#arg-grobs"></a></dt>
+<dt id="arg-grobs">grobs<a class="anchor" aria-label="anchor" href="#arg-grobs"></a>
+</dt>
 <dd><p>(<code>list</code> of <code>grob</code>)<br> a list of grobs.</p></dd>
 
 
-<dt id="arg-padding">padding<a class="anchor" aria-label="anchor" href="#arg-padding"></a></dt>
+<dt id="arg-padding">padding<a class="anchor" aria-label="anchor" href="#arg-padding"></a>
+</dt>
 <dd><p>(<code><a href="https://rdrr.io/r/grid/unit.html" class="external-link">grid::unit</a></code>)<br> unit of length 1, space between each grob.</p></dd>
 
 
-<dt id="arg-vp">vp<a class="anchor" aria-label="anchor" href="#arg-vp"></a></dt>
+<dt id="arg-vp">vp<a class="anchor" aria-label="anchor" href="#arg-vp"></a>
+</dt>
 <dd><p>(<code>viewport</code> or <code>NULL</code>)<br> a <code><a href="https://rdrr.io/r/grid/viewport.html" class="external-link">viewport()</a></code> object (or <code>NULL</code>).</p></dd>
 
 
-<dt id="arg-gp">gp<a class="anchor" aria-label="anchor" href="#arg-gp"></a></dt>
+<dt id="arg-gp">gp<a class="anchor" aria-label="anchor" href="#arg-gp"></a>
+</dt>
 <dd><p>(<code>gpar</code>)<br> a <code><a href="https://rdrr.io/r/grid/gpar.html" class="external-link">gpar()</a></code> object.</p></dd>
 
 
-<dt id="arg-name">name<a class="anchor" aria-label="anchor" href="#arg-name"></a></dt>
+<dt id="arg-name">name<a class="anchor" aria-label="anchor" href="#arg-name"></a>
+</dt>
 <dd><p>(<code>string</code>)<br> a character identifier for the grob.</p></dd>
 
-</dl></div>
+</dl>
+</div>
     <div class="section level2">
-    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
+    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a>
+</h2>
     <p>A <code>grob</code>.</p>
     </div>
 
     <div class="section level2">
-    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
+    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va">grid</span><span class="op">)</span></span></span>
 <span class="r-in"><span></span></span>
 <span class="r-in"><span><span class="va">g1</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/grid/grid.circle.html" class="external-link">circleGrob</a></span><span class="op">(</span>gp <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/grid/gpar.html" class="external-link">gpar</a></span><span class="op">(</span>col <span class="op">=</span> <span class="st">"blue"</span><span class="op">)</span><span class="op">)</span></span></span>
@@ -123,17 +198,19 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 </code></pre></div>
     </div>
   </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
-    </nav></aside></div>
+    </nav></aside>
+</div>
 
 
     <footer><div class="nest">
   <p>tern is a part of the <strong>NEST</strong> and <a href="https://pharmaverse.org/" class="external-link"><strong>pharmaverse</strong></a>.</p>
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-<script type="text/javascript" src="../analytics.js"></script></footer></div>
-
+<script type="text/javascript" src="../analytics.js"></script></footer>
+</div>
 
 
 
 
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+</html>
diff --git a/main/reference/stat_mean_ci.html b/main/reference/stat_mean_ci.html
index 897b5c1060..0c5214c9fe 100644
--- a/main/reference/stat_mean_ci.html
+++ b/main/reference/stat_mean_ci.html
@@ -1,9 +1,32 @@
-<!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Confidence interval for mean — stat_mean_ci • tern</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Confidence interval for mean — stat_mean_ci"><meta name="description" content="
+<html lang="en">
+<head>
+<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+<meta charset="utf-8">
+<meta http-equiv="X-UA-Compatible" content="IE=edge">
+<meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<title>Confidence interval for mean — stat_mean_ci • tern</title>
+<!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png">
+<link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png">
+<link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png">
+<link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png">
+<link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png">
+<link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png">
+<script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet">
+<script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet">
+<link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet">
+<script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Confidence interval for mean — stat_mean_ci">
+<meta name="description" content="
 Convenient function for calculating the mean confidence interval. It calculates the arithmetic as well as the
-geometric mean. It can be used as a ggplot helper function for plotting."><meta property="og:description" content="
+geometric mean. It can be used as a ggplot helper function for plotting.">
+<meta property="og:description" content="
 Convenient function for calculating the mean confidence interval. It calculates the arithmetic as well as the
-geometric mean. It can be used as a ggplot helper function for plotting."><meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png"><link rel="stylesheet" href="../consent.css"><script src="../consent.js" type="text/javascript" charset="utf-8"></script></head><body>
+geometric mean. It can be used as a ggplot helper function for plotting.">
+<meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png">
+<link rel="stylesheet" href="../consent.css">
+<script src="../consent.js" type="text/javascript" charset="utf-8"></script>
+</head>
+<body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
 
 
@@ -19,26 +42,66 @@
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+      <ul class="navbar-nav me-auto">
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   <button class="nav-link dropdown-toggle" type="button" id="dropdown-articles" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Articles</button>
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+  <ul class="dropdown-menu" aria-labelledby="dropdown-articles">
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+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
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+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
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+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a>
+</div>
+</li></div>
+</ul>
+<ul class="navbar-nav">
+<li class="nav-item"><form class="form-inline" role="search">
+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json">
+</form></li>
 <li class="nav-item"><a class="external-link nav-link" href="https://github.com/insightsengineering/tern" aria-label="GitHub"><span class="fa fa-github"></span></a></li>
-      </ul></div>
+      </ul>
+</div>
 
 
   </div>
@@ -57,7 +120,8 @@
     </div>
 
     <div class="section level2">
-    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
+    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">stat_mean_ci</span><span class="op">(</span></span>
 <span>  <span class="va">x</span>,</span>
 <span>  conf_level <span class="op">=</span> <span class="fl">0.95</span>,</span>
@@ -69,40 +133,51 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
     </div>
 
     <div class="section level2">
-    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
+    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a>
+</h2>
 
 
-<dl><dt id="arg-x">x<a class="anchor" aria-label="anchor" href="#arg-x"></a></dt>
+<dl>
+<dt id="arg-x">x<a class="anchor" aria-label="anchor" href="#arg-x"></a>
+</dt>
 <dd><p>(<code>numeric</code>)<br> vector of numbers we want to analyze.</p></dd>
 
 
-<dt id="arg-conf-level">conf_level<a class="anchor" aria-label="anchor" href="#arg-conf-level"></a></dt>
+<dt id="arg-conf-level">conf_level<a class="anchor" aria-label="anchor" href="#arg-conf-level"></a>
+</dt>
 <dd><p>(<code>proportion</code>)<br> confidence level of the interval.</p></dd>
 
 
-<dt id="arg-na-rm">na.rm<a class="anchor" aria-label="anchor" href="#arg-na-rm"></a></dt>
+<dt id="arg-na-rm">na.rm<a class="anchor" aria-label="anchor" href="#arg-na-rm"></a>
+</dt>
 <dd><p>(<code>flag</code>)<br> whether <code>NA</code> values should be removed from <code>x</code> prior to analysis.</p></dd>
 
 
-<dt id="arg-n-min">n_min<a class="anchor" aria-label="anchor" href="#arg-n-min"></a></dt>
+<dt id="arg-n-min">n_min<a class="anchor" aria-label="anchor" href="#arg-n-min"></a>
+</dt>
 <dd><p>(<code>numeric(1)</code>)<br> a minimum number of non-missing <code>x</code> to estimate the confidence interval for mean.</p></dd>
 
 
-<dt id="arg-gg-helper">gg_helper<a class="anchor" aria-label="anchor" href="#arg-gg-helper"></a></dt>
+<dt id="arg-gg-helper">gg_helper<a class="anchor" aria-label="anchor" href="#arg-gg-helper"></a>
+</dt>
 <dd><p>(<code>flag</code>)<br> whether output should be aligned for use with <code>ggplot</code>s.</p></dd>
 
 
-<dt id="arg-geom-mean">geom_mean<a class="anchor" aria-label="anchor" href="#arg-geom-mean"></a></dt>
+<dt id="arg-geom-mean">geom_mean<a class="anchor" aria-label="anchor" href="#arg-geom-mean"></a>
+</dt>
 <dd><p>(<code>flag</code>)<br> whether the geometric mean should be calculated.</p></dd>
 
-</dl></div>
+</dl>
+</div>
     <div class="section level2">
-    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
+    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a>
+</h2>
     <p>A named <code>vector</code> of values <code>mean_ci_lwr</code> and <code>mean_ci_upr</code>.</p>
     </div>
 
     <div class="section level2">
-    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
+    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="fu">stat_mean_ci</span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/sample.html" class="external-link">sample</a></span><span class="op">(</span><span class="fl">10</span><span class="op">)</span>, gg_helper <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> mean_ci_lwr mean_ci_upr </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>    3.334149    7.665851 </span>
@@ -133,17 +208,19 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 </code></pre></div>
     </div>
   </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
-    </nav></aside></div>
+    </nav></aside>
+</div>
 
 
     <footer><div class="nest">
   <p>tern is a part of the <strong>NEST</strong> and <a href="https://pharmaverse.org/" class="external-link"><strong>pharmaverse</strong></a>.</p>
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-<script type="text/javascript" src="../analytics.js"></script></footer></div>
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diff --git a/main/reference/stat_mean_pval.html b/main/reference/stat_mean_pval.html
index 0266969e87..91e7f35dc5 100644
--- a/main/reference/stat_mean_pval.html
+++ b/main/reference/stat_mean_pval.html
@@ -1,7 +1,30 @@
-<!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>p-Value of the mean — stat_mean_pval • tern</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="p-Value of the mean — stat_mean_pval"><meta name="description" content="
-Convenient function for calculating the two-sided p-value of the mean."><meta property="og:description" content="
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+<link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet">
+<script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="p-Value of the mean — stat_mean_pval">
+<meta name="description" content="
+Convenient function for calculating the two-sided p-value of the mean.">
+<meta property="og:description" content="
+Convenient function for calculating the two-sided p-value of the mean.">
+<meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png">
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@@ -17,26 +40,66 @@
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+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json">
+</form></li>
 <li class="nav-item"><a class="external-link nav-link" href="https://github.com/insightsengineering/tern" aria-label="GitHub"><span class="fa fa-github"></span></a></li>
-      </ul></div>
+      </ul>
+</div>
 
 
   </div>
@@ -54,37 +117,47 @@
     </div>
 
     <div class="section level2">
-    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
+    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">stat_mean_pval</span><span class="op">(</span><span class="va">x</span>, na.rm <span class="op">=</span> <span class="cn">TRUE</span>, n_min <span class="op">=</span> <span class="fl">2</span>, test_mean <span class="op">=</span> <span class="fl">0</span><span class="op">)</span></span></code></pre></div>
     </div>
 
     <div class="section level2">
-    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
+    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a>
+</h2>
 
 
-<dl><dt id="arg-x">x<a class="anchor" aria-label="anchor" href="#arg-x"></a></dt>
+<dl>
+<dt id="arg-x">x<a class="anchor" aria-label="anchor" href="#arg-x"></a>
+</dt>
 <dd><p>(<code>numeric</code>)<br> vector of numbers we want to analyze.</p></dd>
 
 
-<dt id="arg-na-rm">na.rm<a class="anchor" aria-label="anchor" href="#arg-na-rm"></a></dt>
+<dt id="arg-na-rm">na.rm<a class="anchor" aria-label="anchor" href="#arg-na-rm"></a>
+</dt>
 <dd><p>(<code>flag</code>)<br> whether <code>NA</code> values should be removed from <code>x</code> prior to analysis.</p></dd>
 
 
-<dt id="arg-n-min">n_min<a class="anchor" aria-label="anchor" href="#arg-n-min"></a></dt>
+<dt id="arg-n-min">n_min<a class="anchor" aria-label="anchor" href="#arg-n-min"></a>
+</dt>
 <dd><p>(<code>numeric(1)</code>)<br> a minimum number of non-missing <code>x</code> to estimate the p-value of the mean.</p></dd>
 
 
-<dt id="arg-test-mean">test_mean<a class="anchor" aria-label="anchor" href="#arg-test-mean"></a></dt>
+<dt id="arg-test-mean">test_mean<a class="anchor" aria-label="anchor" href="#arg-test-mean"></a>
+</dt>
 <dd><p>(<code>numeric(1)</code>)<br> mean value to test under the null hypothesis.</p></dd>
 
-</dl></div>
+</dl>
+</div>
     <div class="section level2">
-    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
+    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a>
+</h2>
     <p>A p-value.</p>
     </div>
 
     <div class="section level2">
-    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
+    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="fu">stat_mean_pval</span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/sample.html" class="external-link">sample</a></span><span class="op">(</span><span class="fl">10</span><span class="op">)</span><span class="op">)</span></span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>     p_value </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> 0.000278196 </span>
@@ -96,17 +169,19 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 </code></pre></div>
     </div>
   </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
-    </nav></aside></div>
+    </nav></aside>
+</div>
 
 
     <footer><div class="nest">
   <p>tern is a part of the <strong>NEST</strong> and <a href="https://pharmaverse.org/" class="external-link"><strong>pharmaverse</strong></a>.</p>
 </div>
-<script type="text/javascript" src="../analytics.js"></script></footer></div>
-
+<script type="text/javascript" src="../analytics.js"></script></footer>
+</div>
 
 
 
 
-  </body></html>
 
+  </body>
+</html>
diff --git a/main/reference/stat_median_ci.html b/main/reference/stat_median_ci.html
index cf116f8136..d6ef1bc711 100644
--- a/main/reference/stat_median_ci.html
+++ b/main/reference/stat_median_ci.html
@@ -1,9 +1,32 @@
-<!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Confidence interval for median — stat_median_ci • tern</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Confidence interval for median — stat_median_ci"><meta name="description" content="
+<html lang="en">
+<head>
+<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+<meta charset="utf-8">
+<meta http-equiv="X-UA-Compatible" content="IE=edge">
+<meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<title>Confidence interval for median — stat_median_ci • tern</title>
+<!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png">
+<link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png">
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+<link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png">
+<script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet">
+<script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet">
+<link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet">
+<script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Confidence interval for median — stat_median_ci">
+<meta name="description" content="
 Convenient function for calculating the median confidence interval. It can be used as a ggplot helper
-function for plotting."><meta property="og:description" content="
+function for plotting.">
+<meta property="og:description" content="
 Convenient function for calculating the median confidence interval. It can be used as a ggplot helper
-function for plotting."><meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png"><link rel="stylesheet" href="../consent.css"><script src="../consent.js" type="text/javascript" charset="utf-8"></script></head><body>
+function for plotting.">
+<meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png">
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+</head>
+<body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
 
 
@@ -19,26 +42,66 @@
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+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a>
+</div>
+</li></div>
+</ul>
+<ul class="navbar-nav">
+<li class="nav-item"><form class="form-inline" role="search">
+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json">
+</form></li>
 <li class="nav-item"><a class="external-link nav-link" href="https://github.com/insightsengineering/tern" aria-label="GitHub"><span class="fa fa-github"></span></a></li>
-      </ul></div>
+      </ul>
+</div>
 
 
   </div>
@@ -57,41 +120,52 @@
     </div>
 
     <div class="section level2">
-    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
+    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">stat_median_ci</span><span class="op">(</span><span class="va">x</span>, conf_level <span class="op">=</span> <span class="fl">0.95</span>, na.rm <span class="op">=</span> <span class="cn">TRUE</span>, gg_helper <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></code></pre></div>
     </div>
 
     <div class="section level2">
-    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
+    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a>
+</h2>
 
 
-<dl><dt id="arg-x">x<a class="anchor" aria-label="anchor" href="#arg-x"></a></dt>
+<dl>
+<dt id="arg-x">x<a class="anchor" aria-label="anchor" href="#arg-x"></a>
+</dt>
 <dd><p>(<code>numeric</code>)<br> vector of numbers we want to analyze.</p></dd>
 
 
-<dt id="arg-conf-level">conf_level<a class="anchor" aria-label="anchor" href="#arg-conf-level"></a></dt>
+<dt id="arg-conf-level">conf_level<a class="anchor" aria-label="anchor" href="#arg-conf-level"></a>
+</dt>
 <dd><p>(<code>proportion</code>)<br> confidence level of the interval.</p></dd>
 
 
-<dt id="arg-na-rm">na.rm<a class="anchor" aria-label="anchor" href="#arg-na-rm"></a></dt>
+<dt id="arg-na-rm">na.rm<a class="anchor" aria-label="anchor" href="#arg-na-rm"></a>
+</dt>
 <dd><p>(<code>flag</code>)<br> whether <code>NA</code> values should be removed from <code>x</code> prior to analysis.</p></dd>
 
 
-<dt id="arg-gg-helper">gg_helper<a class="anchor" aria-label="anchor" href="#arg-gg-helper"></a></dt>
+<dt id="arg-gg-helper">gg_helper<a class="anchor" aria-label="anchor" href="#arg-gg-helper"></a>
+</dt>
 <dd><p>(<code>flag</code>)<br> whether output should be aligned for use with <code>ggplot</code>s.</p></dd>
 
-</dl></div>
+</dl>
+</div>
     <div class="section level2">
-    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
+    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a>
+</h2>
     <p>A named <code>vector</code> of values <code>median_ci_lwr</code> and <code>median_ci_upr</code>.</p>
     </div>
     <div class="section level2">
-    <h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a></h2>
+    <h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a>
+</h2>
     <p>This function was adapted from <code>DescTools/versions/0.99.35/source</code></p>
     </div>
 
     <div class="section level2">
-    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
+    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="fu">stat_median_ci</span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/sample.html" class="external-link">sample</a></span><span class="op">(</span><span class="fl">10</span><span class="op">)</span>, gg_helper <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> median_ci_lwr median_ci_upr </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>             2             9 </span>
@@ -109,17 +183,19 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 </code></pre></div>
     </div>
   </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
-    </nav></aside></div>
+    </nav></aside>
+</div>
 
 
     <footer><div class="nest">
   <p>tern is a part of the <strong>NEST</strong> and <a href="https://pharmaverse.org/" class="external-link"><strong>pharmaverse</strong></a>.</p>
 </div>
-<script type="text/javascript" src="../analytics.js"></script></footer></div>
-
+<script type="text/javascript" src="../analytics.js"></script></footer>
+</div>
 
 
 
 
-  </body></html>
 
+  </body>
+</html>
diff --git a/main/reference/stat_propdiff_ci.html b/main/reference/stat_propdiff_ci.html
index 3239bb4872..666ef8cadd 100644
--- a/main/reference/stat_propdiff_ci.html
+++ b/main/reference/stat_propdiff_ci.html
@@ -1,11 +1,34 @@
-<!DOCTYPE html>
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+<title>Proportion difference and confidence interval — stat_propdiff_ci • tern</title>
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+<meta name="description" content="
 Function for calculating the proportion (or risk) difference and confidence interval between arm
 X (reference group) and arm Y. Risk difference is calculated by subtracting cumulative incidence
-in arm Y from cumulative incidence in arm X."><meta property="og:description" content="
+in arm Y from cumulative incidence in arm X.">
+<meta property="og:description" content="
 Function for calculating the proportion (or risk) difference and confidence interval between arm
 X (reference group) and arm Y. Risk difference is calculated by subtracting cumulative incidence
-in arm Y from cumulative incidence in arm X."><meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png"><link rel="stylesheet" href="../consent.css"><script src="../consent.js" type="text/javascript" charset="utf-8"></script></head><body>
+in arm Y from cumulative incidence in arm X.">
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@@ -21,26 +44,66 @@
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+</div>
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 <li class="nav-item"><a class="external-link nav-link" href="https://github.com/insightsengineering/tern" aria-label="GitHub"><span class="fa fa-github"></span></a></li>
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+</div>
 
 
   </div>
@@ -60,7 +123,8 @@
     </div>
 
     <div class="section level2">
-    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
+    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">stat_propdiff_ci</span><span class="op">(</span></span>
 <span>  <span class="va">x</span>,</span>
 <span>  <span class="va">y</span>,</span>
@@ -73,52 +137,65 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
     </div>
 
     <div class="section level2">
-    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
+    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a>
+</h2>
 
 
-<dl><dt id="arg-x">x<a class="anchor" aria-label="anchor" href="#arg-x"></a></dt>
+<dl>
+<dt id="arg-x">x<a class="anchor" aria-label="anchor" href="#arg-x"></a>
+</dt>
 <dd><p>(<code>list</code> of <code>integer</code>)<br> list of number of occurrences in arm X (reference group).</p></dd>
 
 
-<dt id="arg-y">y<a class="anchor" aria-label="anchor" href="#arg-y"></a></dt>
+<dt id="arg-y">y<a class="anchor" aria-label="anchor" href="#arg-y"></a>
+</dt>
 <dd><p>(<code>list</code> of <code>integer</code>)<br> list of number of occurrences in arm Y. Must be of equal length to <code>x</code>.</p></dd>
 
 
-<dt id="arg-n-x">N_x<a class="anchor" aria-label="anchor" href="#arg-n-x"></a></dt>
+<dt id="arg-n-x">N_x<a class="anchor" aria-label="anchor" href="#arg-n-x"></a>
+</dt>
 <dd><p>(<code>numeric(1)</code>)<br> total number of records in arm X.</p></dd>
 
 
-<dt id="arg-n-y">N_y<a class="anchor" aria-label="anchor" href="#arg-n-y"></a></dt>
+<dt id="arg-n-y">N_y<a class="anchor" aria-label="anchor" href="#arg-n-y"></a>
+</dt>
 <dd><p>(<code>numeric(1)</code>)<br> total number of records in arm Y.</p></dd>
 
 
-<dt id="arg-list-names">list_names<a class="anchor" aria-label="anchor" href="#arg-list-names"></a></dt>
+<dt id="arg-list-names">list_names<a class="anchor" aria-label="anchor" href="#arg-list-names"></a>
+</dt>
 <dd><p>(<code>character</code>)<br> names of each variable/level corresponding to pair of proportions in
 <code>x</code> and <code>y</code>. Must be of equal length to <code>x</code> and <code>y</code>.</p></dd>
 
 
-<dt id="arg-conf-level">conf_level<a class="anchor" aria-label="anchor" href="#arg-conf-level"></a></dt>
+<dt id="arg-conf-level">conf_level<a class="anchor" aria-label="anchor" href="#arg-conf-level"></a>
+</dt>
 <dd><p>(<code>proportion</code>)<br> confidence level of the interval.</p></dd>
 
 
-<dt id="arg-pct">pct<a class="anchor" aria-label="anchor" href="#arg-pct"></a></dt>
+<dt id="arg-pct">pct<a class="anchor" aria-label="anchor" href="#arg-pct"></a>
+</dt>
 <dd><p>(<code>flag</code>)<br> whether output should be returned as percentages. Defaults to <code>TRUE</code>.</p></dd>
 
-</dl></div>
+</dl>
+</div>
     <div class="section level2">
-    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
+    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a>
+</h2>
     <p>List of proportion differences and CIs corresponding to each pair of number of occurrences in <code>x</code> and
 <code>y</code>. Each list element consists of 3 statistics: proportion difference, CI lower bound, and CI upper bound.</p>
     </div>
     <div class="section level2">
-    <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"></a></h2>
+    <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"></a>
+</h2>
     <div class="dont-index"><p>Split function <code><a href="add_riskdiff.html">add_riskdiff()</a></code> which, when used as <code>split_fun</code> within <code><a href="https://insightsengineering.github.io/rtables/latest-tag/reference/split_cols_by.html" class="external-link">rtables::split_cols_by()</a></code>
 with <code>riskdiff</code> argument is set to <code>TRUE</code> in subsequent analyze functions, adds a column containing
 proportion (risk) difference to an <code>rtables</code> layout.</p></div>
     </div>
 
     <div class="section level2">
-    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
+    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="fu">stat_propdiff_ci</span><span class="op">(</span></span></span>
 <span class="r-in"><span>  x <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span><span class="fl">0.375</span><span class="op">)</span>, y <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span><span class="fl">0.01</span><span class="op">)</span>, N_x <span class="op">=</span> <span class="fl">5</span>, N_y <span class="op">=</span> <span class="fl">5</span>, list_names <span class="op">=</span> <span class="st">"x"</span>, conf_level <span class="op">=</span> <span class="fl">0.9</span></span></span>
 <span class="r-in"><span><span class="op">)</span></span></span>
@@ -142,17 +219,19 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 </code></pre></div>
     </div>
   </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
-    </nav></aside></div>
+    </nav></aside>
+</div>
 
 
     <footer><div class="nest">
   <p>tern is a part of the <strong>NEST</strong> and <a href="https://pharmaverse.org/" class="external-link"><strong>pharmaverse</strong></a>.</p>
 </div>
-<script type="text/javascript" src="../analytics.js"></script></footer></div>
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+<script type="text/javascript" src="../analytics.js"></script></footer>
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diff --git a/main/reference/strata_normal_quantile.html b/main/reference/strata_normal_quantile.html
index 29661db005..0f56766472 100644
--- a/main/reference/strata_normal_quantile.html
+++ b/main/reference/strata_normal_quantile.html
@@ -1,11 +1,34 @@
-<!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Helper function for the estimation of stratified quantiles — strata_normal_quantile • tern</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Helper function for the estimation of stratified quantiles — strata_normal_quantile"><meta name="description" content="
+<html lang="en">
+<head>
+<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+<meta charset="utf-8">
+<meta http-equiv="X-UA-Compatible" content="IE=edge">
+<meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<title>Helper function for the estimation of stratified quantiles — strata_normal_quantile • tern</title>
+<!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png">
+<link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png">
+<link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png">
+<link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png">
+<link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png">
+<link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png">
+<script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet">
+<script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet">
+<link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet">
+<script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Helper function for the estimation of stratified quantiles — strata_normal_quantile">
+<meta name="description" content="
 This function wraps the estimation of stratified percentiles when we assume
 the approximation for large numbers. This is necessary only in the case
-proportions for each strata are unequal."><meta property="og:description" content="
+proportions for each strata are unequal.">
+<meta property="og:description" content="
 This function wraps the estimation of stratified percentiles when we assume
 the approximation for large numbers. This is necessary only in the case
-proportions for each strata are unequal."><meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png"><link rel="stylesheet" href="../consent.css"><script src="../consent.js" type="text/javascript" charset="utf-8"></script></head><body>
+proportions for each strata are unequal.">
+<meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png">
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@@ -21,26 +44,66 @@
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+    <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
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+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a>
+</div>
+</li></div>
+</ul>
+<ul class="navbar-nav">
+<li class="nav-item"><form class="form-inline" role="search">
+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json">
+</form></li>
 <li class="nav-item"><a class="external-link nav-link" href="https://github.com/insightsengineering/tern" aria-label="GitHub"><span class="fa fa-github"></span></a></li>
-      </ul></div>
+      </ul>
+</div>
 
 
   </div>
@@ -60,39 +123,49 @@
     </div>
 
     <div class="section level2">
-    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
+    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">strata_normal_quantile</span><span class="op">(</span><span class="va">vars</span>, <span class="va">weights</span>, <span class="va">conf_level</span><span class="op">)</span></span></code></pre></div>
     </div>
 
     <div class="section level2">
-    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
+    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a>
+</h2>
 
 
-<dl><dt id="arg-vars">vars<a class="anchor" aria-label="anchor" href="#arg-vars"></a></dt>
+<dl>
+<dt id="arg-vars">vars<a class="anchor" aria-label="anchor" href="#arg-vars"></a>
+</dt>
 <dd><p>(<code>character</code>)<br> variable names for the primary analysis variable to be iterated over.</p></dd>
 
 
-<dt id="arg-weights">weights<a class="anchor" aria-label="anchor" href="#arg-weights"></a></dt>
+<dt id="arg-weights">weights<a class="anchor" aria-label="anchor" href="#arg-weights"></a>
+</dt>
 <dd><p>(<code>numeric</code> or <code>NULL</code>)<br> weights for each level of the strata. If <code>NULL</code>, they are
 estimated using the iterative algorithm proposed in Yan2010-jt;textualtern that
 minimizes the weighted squared length of the confidence interval.</p></dd>
 
 
-<dt id="arg-conf-level">conf_level<a class="anchor" aria-label="anchor" href="#arg-conf-level"></a></dt>
+<dt id="arg-conf-level">conf_level<a class="anchor" aria-label="anchor" href="#arg-conf-level"></a>
+</dt>
 <dd><p>(<code>proportion</code>)<br> confidence level of the interval.</p></dd>
 
-</dl></div>
+</dl>
+</div>
     <div class="section level2">
-    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
+    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a>
+</h2>
     <p>Stratified quantile.</p>
     </div>
     <div class="section level2">
-    <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"></a></h2>
+    <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"></a>
+</h2>
     <div class="dont-index"><p><code><a href="h_proportions.html">prop_strat_wilson()</a></code></p></div>
     </div>
 
     <div class="section level2">
-    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
+    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">strata_data</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/table.html" class="external-link">table</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a></span><span class="op">(</span></span></span>
 <span class="r-in"><span>  <span class="st">"f1"</span> <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/sample.html" class="external-link">sample</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="cn">TRUE</span>, <span class="cn">FALSE</span><span class="op">)</span>, <span class="fl">100</span>, <span class="cn">TRUE</span><span class="op">)</span>,</span></span>
 <span class="r-in"><span>  <span class="st">"f2"</span> <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/sample.html" class="external-link">sample</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"x"</span>, <span class="st">"y"</span>, <span class="st">"z"</span><span class="op">)</span>, <span class="fl">100</span>, <span class="cn">TRUE</span><span class="op">)</span>,</span></span>
@@ -109,17 +182,19 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 </code></pre></div>
     </div>
   </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
-    </nav></aside></div>
+    </nav></aside>
+</div>
 
 
     <footer><div class="nest">
   <p>tern is a part of the <strong>NEST</strong> and <a href="https://pharmaverse.org/" class="external-link"><strong>pharmaverse</strong></a>.</p>
 </div>
-<script type="text/javascript" src="../analytics.js"></script></footer></div>
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+<script type="text/javascript" src="../analytics.js"></script></footer>
+</div>
 
 
 
 
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diff --git a/main/reference/study_arm.html b/main/reference/study_arm.html
index d1a9086a61..e127297de0 100644
--- a/main/reference/study_arm.html
+++ b/main/reference/study_arm.html
@@ -1,5 +1,28 @@
-<!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Indicate study arm variable in formula — study_arm • tern</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Indicate study arm variable in formula — study_arm"><meta name="description" content="We use study_arm to indicate the study arm variable in tern formulas."><meta property="og:description" content="We use study_arm to indicate the study arm variable in tern formulas."><meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png"><link rel="stylesheet" href="../consent.css"><script src="../consent.js" type="text/javascript" charset="utf-8"></script></head><body>
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+<title>Indicate study arm variable in formula — study_arm • tern</title>
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+<link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet">
+<script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Indicate study arm variable in formula — study_arm">
+<meta name="description" content="We use study_arm to indicate the study arm variable in tern formulas.">
+<meta property="og:description" content="We use study_arm to indicate the study arm variable in tern formulas.">
+<meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png">
+<link rel="stylesheet" href="../consent.css">
+<script src="../consent.js" type="text/javascript" charset="utf-8"></script>
+</head>
+<body>
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@@ -15,26 +38,66 @@
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+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a>
+</div>
+</li></div>
+</ul>
+<ul class="navbar-nav">
+<li class="nav-item"><form class="form-inline" role="search">
+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json">
+</form></li>
 <li class="nav-item"><a class="external-link nav-link" href="https://github.com/insightsengineering/tern" aria-label="GitHub"><span class="fa fa-github"></span></a></li>
-      </ul></div>
+      </ul>
+</div>
 
 
   </div>
@@ -51,35 +114,43 @@
     </div>
 
     <div class="section level2">
-    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
+    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">study_arm</span><span class="op">(</span><span class="va">x</span><span class="op">)</span></span></code></pre></div>
     </div>
 
     <div class="section level2">
-    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
+    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a>
+</h2>
 
 
-<dl><dt id="arg-x">x<a class="anchor" aria-label="anchor" href="#arg-x"></a></dt>
+<dl>
+<dt id="arg-x">x<a class="anchor" aria-label="anchor" href="#arg-x"></a>
+</dt>
 <dd><p>arm information</p></dd>
 
-</dl></div>
+</dl>
+</div>
     <div class="section level2">
-    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
+    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a>
+</h2>
     <p><code>x</code></p>
     </div>
 
   </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
-    </nav></aside></div>
+    </nav></aside>
+</div>
 
 
     <footer><div class="nest">
   <p>tern is a part of the <strong>NEST</strong> and <a href="https://pharmaverse.org/" class="external-link"><strong>pharmaverse</strong></a>.</p>
 </div>
-<script type="text/javascript" src="../analytics.js"></script></footer></div>
-
+<script type="text/javascript" src="../analytics.js"></script></footer>
+</div>
 
 
 
 
-  </body></html>
 
+  </body>
+</html>
diff --git a/main/reference/summarize_ancova.html b/main/reference/summarize_ancova.html
index 6e7384ea72..8ab33bc326 100644
--- a/main/reference/summarize_ancova.html
+++ b/main/reference/summarize_ancova.html
@@ -1,5 +1,22 @@
-<!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Summarize analysis of covariance (ANCOVA) results — summarize_ancova • tern</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Summarize analysis of covariance (ANCOVA) results — summarize_ancova"><meta name="description" content="
+<html lang="en">
+<head>
+<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+<meta charset="utf-8">
+<meta http-equiv="X-UA-Compatible" content="IE=edge">
+<meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<title>Summarize analysis of covariance (ANCOVA) results — summarize_ancova • tern</title>
+<!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png">
+<link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png">
+<link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png">
+<link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png">
+<link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png">
+<link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png">
+<script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet">
+<script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet">
+<link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet">
+<script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Summarize analysis of covariance (ANCOVA) results — summarize_ancova">
+<meta name="description" content="
 The analyze function summarize_ancova() creates a layout element to summarize ANCOVA results.
 This function can be used to analyze multiple endpoints and/or multiple timepoints within the response variable(s)
 specified as vars.
@@ -7,7 +24,8 @@
 via the variables argument. See below for more details on how to specify variables. An interaction term can
 be implemented in the model if needed. The interaction variable that should interact with the arm variable is
 specified via the interaction_term parameter, and the specific value of interaction_term for which to extract
-the ANCOVA results via the interaction_y parameter."><meta property="og:description" content="
+the ANCOVA results via the interaction_y parameter.">
+<meta property="og:description" content="
 The analyze function summarize_ancova() creates a layout element to summarize ANCOVA results.
 This function can be used to analyze multiple endpoints and/or multiple timepoints within the response variable(s)
 specified as vars.
@@ -15,7 +33,12 @@
 via the variables argument. See below for more details on how to specify variables. An interaction term can
 be implemented in the model if needed. The interaction variable that should interact with the arm variable is
 specified via the interaction_term parameter, and the specific value of interaction_term for which to extract
-the ANCOVA results via the interaction_y parameter."><meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png"><link rel="stylesheet" href="../consent.css"><script src="../consent.js" type="text/javascript" charset="utf-8"></script></head><body>
+the ANCOVA results via the interaction_y parameter.">
+<meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png">
+<link rel="stylesheet" href="../consent.css">
+<script src="../consent.js" type="text/javascript" charset="utf-8"></script>
+</head>
+<body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
 
 
@@ -31,26 +54,66 @@
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+<li class="nav-item"><a class="nav-link" href="../articles/tern.html">Get started</a></li>
 <li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
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-  <ul class="dropdown-menu" aria-labelledby="dropdown-articles"><li><a class="dropdown-item" href="../articles/missing_values.html">Missing Values in Tern</a></li>
+  <ul class="dropdown-menu" aria-labelledby="dropdown-articles">
+<li><a class="dropdown-item" href="../articles/missing_values.html">Missing Values in Tern</a></li>
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-  </ul></li>
+  </ul>
+</li>
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+  <ul class="dropdown-menu" aria-labelledby="dropdown-reports">
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+  </ul>
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+      <div><li class="nav-item dropdown">
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+    <div class="dropdown-menu" aria-labelledby="dropdown-versions">
+    <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
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+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
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+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a>
+</div>
+</li></div>
+</ul>
+<ul class="navbar-nav">
+<li class="nav-item"><form class="form-inline" role="search">
+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json">
+</form></li>
 <li class="nav-item"><a class="external-link nav-link" href="https://github.com/insightsengineering/tern" aria-label="GitHub"><span class="fa fa-github"></span></a></li>
-      </ul></div>
+      </ul>
+</div>
 
 
   </div>
@@ -75,7 +138,8 @@
     </div>
 
     <div class="section level2">
-    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
+    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">summarize_ancova</span><span class="op">(</span></span>
 <span>  <span class="va">lyt</span>,</span>
 <span>  <span class="va">vars</span>,</span>
@@ -121,134 +185,179 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
     </div>
 
     <div class="section level2">
-    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
+    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a>
+</h2>
 
 
-<dl><dt id="arg-lyt">lyt<a class="anchor" aria-label="anchor" href="#arg-lyt"></a></dt>
+<dl>
+<dt id="arg-lyt">lyt<a class="anchor" aria-label="anchor" href="#arg-lyt"></a>
+</dt>
 <dd><p>(<code>PreDataTableLayouts</code>)<br> layout that analyses will be added to.</p></dd>
 
 
-<dt id="arg-vars">vars<a class="anchor" aria-label="anchor" href="#arg-vars"></a></dt>
+<dt id="arg-vars">vars<a class="anchor" aria-label="anchor" href="#arg-vars"></a>
+</dt>
 <dd><p>(<code>character</code>)<br> variable names for the primary analysis variable to be iterated over.</p></dd>
 
 
-<dt id="arg-variables">variables<a class="anchor" aria-label="anchor" href="#arg-variables"></a></dt>
-<dd><p>(named <code>list</code> of <code>string</code>)<br> list of additional analysis variables, with expected elements:</p><ul><li><p><code>arm</code> (<code>string</code>)<br> group variable, for which the covariate adjusted means of multiple groups will be
+<dt id="arg-variables">variables<a class="anchor" aria-label="anchor" href="#arg-variables"></a>
+</dt>
+<dd>
+<p>(named <code>list</code> of <code>string</code>)<br> list of additional analysis variables, with expected elements:</p>
+<ul>
+<li><p><code>arm</code> (<code>string</code>)<br> group variable, for which the covariate adjusted means of multiple groups will be
 summarized. Specifically, the first level of <code>arm</code> variable is taken as the reference group.</p></li>
 <li><p><code>covariates</code> (<code>character</code>)<br> a vector that can contain single variable names (such as <code>"X1"</code>), and/or
 interaction terms indicated by <code>"X1 * X2"</code>.</p></li>
-</ul></dd>
+</ul>
+</dd>
 
 
-<dt id="arg-conf-level">conf_level<a class="anchor" aria-label="anchor" href="#arg-conf-level"></a></dt>
+<dt id="arg-conf-level">conf_level<a class="anchor" aria-label="anchor" href="#arg-conf-level"></a>
+</dt>
 <dd><p>(<code>proportion</code>)<br> confidence level of the interval.</p></dd>
 
 
-<dt id="arg-interaction-y">interaction_y<a class="anchor" aria-label="anchor" href="#arg-interaction-y"></a></dt>
+<dt id="arg-interaction-y">interaction_y<a class="anchor" aria-label="anchor" href="#arg-interaction-y"></a>
+</dt>
 <dd><p>(<code>string</code> or <code>flag</code>)<br> a selected item inside of the <code>interaction_item</code> variable which will be
 used to select the specific ANCOVA results. if the interaction is not needed, the default option is <code>FALSE</code>.</p></dd>
 
 
-<dt id="arg-interaction-item">interaction_item<a class="anchor" aria-label="anchor" href="#arg-interaction-item"></a></dt>
+<dt id="arg-interaction-item">interaction_item<a class="anchor" aria-label="anchor" href="#arg-interaction-item"></a>
+</dt>
 <dd><p>(<code>string</code> or <code>NULL</code>)<br> name of the variable that should have interactions
 with arm. if the interaction is not needed, the default option is <code>NULL</code>.</p></dd>
 
 
-<dt id="arg-var-labels">var_labels<a class="anchor" aria-label="anchor" href="#arg-var-labels"></a></dt>
+<dt id="arg-var-labels">var_labels<a class="anchor" aria-label="anchor" href="#arg-var-labels"></a>
+</dt>
 <dd><p>(<code>character</code>)<br> variable labels.</p></dd>
 
 
-<dt id="arg-na-str">na_str<a class="anchor" aria-label="anchor" href="#arg-na-str"></a></dt>
+<dt id="arg-na-str">na_str<a class="anchor" aria-label="anchor" href="#arg-na-str"></a>
+</dt>
 <dd><p>(<code>string</code>)<br> string used to replace all <code>NA</code> or empty values in the output.</p></dd>
 
 
-<dt id="arg-nested">nested<a class="anchor" aria-label="anchor" href="#arg-nested"></a></dt>
+<dt id="arg-nested">nested<a class="anchor" aria-label="anchor" href="#arg-nested"></a>
+</dt>
 <dd><p>(<code>flag</code>)<br> whether this layout instruction should be applied within the existing layout structure _if
 possible (<code>TRUE</code>, the default) or as a new top-level element (<code>FALSE</code>). Ignored if it would nest a split.
 underneath analyses, which is not allowed.</p></dd>
 
 
-<dt id="arg--">...<a class="anchor" aria-label="anchor" href="#arg--"></a></dt>
+<dt id="arg--">...<a class="anchor" aria-label="anchor" href="#arg--"></a>
+</dt>
 <dd><p>additional arguments for the lower level functions.</p></dd>
 
 
-<dt id="arg-show-labels">show_labels<a class="anchor" aria-label="anchor" href="#arg-show-labels"></a></dt>
+<dt id="arg-show-labels">show_labels<a class="anchor" aria-label="anchor" href="#arg-show-labels"></a>
+</dt>
 <dd><p>(<code>string</code>)<br> label visibility: one of "default", "visible" and "hidden".</p></dd>
 
 
-<dt id="arg-table-names">table_names<a class="anchor" aria-label="anchor" href="#arg-table-names"></a></dt>
+<dt id="arg-table-names">table_names<a class="anchor" aria-label="anchor" href="#arg-table-names"></a>
+</dt>
 <dd><p>(<code>character</code>)<br> this can be customized in the case that the same <code>vars</code> are analyzed multiple
 times, to avoid warnings from <code>rtables</code>.</p></dd>
 
 
-<dt id="arg--stats">.stats<a class="anchor" aria-label="anchor" href="#arg--stats"></a></dt>
-<dd><p>(<code>character</code>)<br> statistics to select for the table.</p>
-<p>Options are: <code>'n', 'lsmean', 'lsmean_diff', 'lsmean_diff_ci', 'pval'</code></p></dd>
+<dt id="arg--stats">.stats<a class="anchor" aria-label="anchor" href="#arg--stats"></a>
+</dt>
+<dd>
+<p>(<code>character</code>)<br> statistics to select for the table.</p>
+<p>Options are: <code>'n', 'lsmean', 'lsmean_diff', 'lsmean_diff_ci', 'pval'</code></p>
+</dd>
 
 
-<dt id="arg--formats">.formats<a class="anchor" aria-label="anchor" href="#arg--formats"></a></dt>
+<dt id="arg--formats">.formats<a class="anchor" aria-label="anchor" href="#arg--formats"></a>
+</dt>
 <dd><p>(named <code>character</code> or <code>list</code>)<br> formats for the statistics. See Details in <code>analyze_vars</code> for more
 information on the <code>"auto"</code> setting.</p></dd>
 
 
-<dt id="arg--labels">.labels<a class="anchor" aria-label="anchor" href="#arg--labels"></a></dt>
+<dt id="arg--labels">.labels<a class="anchor" aria-label="anchor" href="#arg--labels"></a>
+</dt>
 <dd><p>(named <code>character</code>)<br> labels for the statistics (without indent).</p></dd>
 
 
-<dt id="arg--indent-mods">.indent_mods<a class="anchor" aria-label="anchor" href="#arg--indent-mods"></a></dt>
+<dt id="arg--indent-mods">.indent_mods<a class="anchor" aria-label="anchor" href="#arg--indent-mods"></a>
+</dt>
 <dd><p>(named <code>integer</code>)<br> indent modifiers for the labels. Defaults to 0, which corresponds to the
 unmodified default behavior. Can be negative.</p></dd>
 
 
-<dt id="arg-df">df<a class="anchor" aria-label="anchor" href="#arg-df"></a></dt>
+<dt id="arg-df">df<a class="anchor" aria-label="anchor" href="#arg-df"></a>
+</dt>
 <dd><p>(<code>data.frame</code>)<br> data set containing all analysis variables.</p></dd>
 
 
-<dt id="arg--var">.var<a class="anchor" aria-label="anchor" href="#arg--var"></a></dt>
+<dt id="arg--var">.var<a class="anchor" aria-label="anchor" href="#arg--var"></a>
+</dt>
 <dd><p>(<code>string</code>)<br> single variable name that is passed by <code>rtables</code> when requested
 by a statistics function.</p></dd>
 
 
-<dt id="arg--df-row">.df_row<a class="anchor" aria-label="anchor" href="#arg--df-row"></a></dt>
+<dt id="arg--df-row">.df_row<a class="anchor" aria-label="anchor" href="#arg--df-row"></a>
+</dt>
 <dd><p>(<code>data.frame</code>)<br> data set that includes all the variables that are called in <code>.var</code> and <code>variables</code>.</p></dd>
 
 
-<dt id="arg--ref-group">.ref_group<a class="anchor" aria-label="anchor" href="#arg--ref-group"></a></dt>
+<dt id="arg--ref-group">.ref_group<a class="anchor" aria-label="anchor" href="#arg--ref-group"></a>
+</dt>
 <dd><p>(<code>data.frame</code> or <code>vector</code>)<br> the data corresponding to the reference group.</p></dd>
 
 
-<dt id="arg--in-ref-col">.in_ref_col<a class="anchor" aria-label="anchor" href="#arg--in-ref-col"></a></dt>
+<dt id="arg--in-ref-col">.in_ref_col<a class="anchor" aria-label="anchor" href="#arg--in-ref-col"></a>
+</dt>
 <dd><p>(<code>flag</code>)<br><code>TRUE</code> when working with the reference level, <code>FALSE</code> otherwise.</p></dd>
 
-</dl></div>
+</dl>
+</div>
     <div class="section level2">
-    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
+    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a>
+</h2>
 
-<ul><li><p><code>summarize_ancova()</code> returns a layout object suitable for passing to further layouting functions,
+<ul>
+<li><p><code>summarize_ancova()</code> returns a layout object suitable for passing to further layouting functions,
 or to <code><a href="https://insightsengineering.github.io/rtables/latest-tag/reference/build_table.html" class="external-link">rtables::build_table()</a></code>. Adding this function to an <code>rtable</code> layout will add formatted rows containing
 the statistics from <code>s_ancova()</code> to the table layout.</p></li>
-</ul><ul><li><p><code>s_ancova()</code> returns a named list of 5 statistics:</p><ul><li><p><code>n</code>: Count of complete sample size for the group.</p></li>
+</ul>
+<ul>
+<li>
+<p><code>s_ancova()</code> returns a named list of 5 statistics:</p>
+<ul>
+<li><p><code>n</code>: Count of complete sample size for the group.</p></li>
 <li><p><code>lsmean</code>: Estimated marginal means in the group.</p></li>
 <li><p><code>lsmean_diff</code>: Difference in estimated marginal means in comparison to the reference group.
 If working with the reference group, this will be empty.</p></li>
 <li><p><code>lsmean_diff_ci</code>: Confidence level for difference in estimated marginal means in comparison
 to the reference group.</p></li>
 <li><p><code>pval</code>: p-value (not adjusted for multiple comparisons).</p></li>
-</ul></li>
-</ul><ul><li><p><code>a_ancova()</code> returns the corresponding list with formatted <code><a href="https://insightsengineering.github.io/rtables/latest-tag/reference/CellValue.html" class="external-link">rtables::CellValue()</a></code>.</p></li>
-</ul></div>
+</ul>
+</li>
+</ul>
+<ul>
+<li><p><code>a_ancova()</code> returns the corresponding list with formatted <code><a href="https://insightsengineering.github.io/rtables/latest-tag/reference/CellValue.html" class="external-link">rtables::CellValue()</a></code>.</p></li>
+</ul>
+</div>
     <div class="section level2">
-    <h2 id="functions">Functions<a class="anchor" aria-label="anchor" href="#functions"></a></h2>
+    <h2 id="functions">Functions<a class="anchor" aria-label="anchor" href="#functions"></a>
+</h2>
 
-<ul><li><p><code>summarize_ancova()</code>: Layout-creating function which can take statistics function arguments
+<ul>
+<li><p><code>summarize_ancova()</code>: Layout-creating function which can take statistics function arguments
 and additional format arguments. This function is a wrapper for <code><a href="https://insightsengineering.github.io/rtables/latest-tag/reference/analyze.html" class="external-link">rtables::analyze()</a></code>.</p></li>
 <li><p><code>s_ancova()</code>: Statistics function that produces a named list of results
 of the investigated linear model.</p></li>
 <li><p><code>a_ancova()</code>: Formatted analysis function which is used as <code>afun</code> in <code>summarize_ancova()</code>.</p></li>
-</ul></div>
+</ul>
+</div>
 
     <div class="section level2">
-    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
+    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="fu">basic_table</span><span class="op">(</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span></span>
 <span class="r-in"><span>  <span class="fu">split_cols_by</span><span class="op">(</span><span class="st">"Species"</span>, ref_group <span class="op">=</span> <span class="st">"setosa"</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span></span>
 <span class="r-in"><span>  <span class="fu">add_colcounts</span><span class="op">(</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span></span>
@@ -285,17 +394,19 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 </code></pre></div>
     </div>
   </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
-    </nav></aside></div>
+    </nav></aside>
+</div>
 
 
     <footer><div class="nest">
   <p>tern is a part of the <strong>NEST</strong> and <a href="https://pharmaverse.org/" class="external-link"><strong>pharmaverse</strong></a>.</p>
 </div>
-<script type="text/javascript" src="../analytics.js"></script></footer></div>
-
+<script type="text/javascript" src="../analytics.js"></script></footer>
+</div>
 
 
 
 
-  </body></html>
 
+  </body>
+</html>
diff --git a/main/reference/summarize_change.html b/main/reference/summarize_change.html
index 6dd1e5c502..6ea3a2bada 100644
--- a/main/reference/summarize_change.html
+++ b/main/reference/summarize_change.html
@@ -1,19 +1,42 @@
-<!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Summarize change from baseline values or absolute baseline values — summarize_change • tern</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Summarize change from baseline values or absolute baseline values — summarize_change"><meta name="description" content="
+<html lang="en">
+<head>
+<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+<meta charset="utf-8">
+<meta http-equiv="X-UA-Compatible" content="IE=edge">
+<meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<title>Summarize change from baseline values or absolute baseline values — summarize_change • tern</title>
+<!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png">
+<link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png">
+<link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png">
+<link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png">
+<link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png">
+<link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png">
+<script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet">
+<script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet">
+<link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet">
+<script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Summarize change from baseline values or absolute baseline values — summarize_change">
+<meta name="description" content="
 The analyze function summarize_change() creates a layout element to summarize the change from baseline or absolute
 baseline values. The primary analysis variable vars indicates the numerical change from baseline results.
 Required secondary analysis variables value and baseline_flag can be supplied to the function via
 the variables argument. The value element should be the name of the analysis value variable, and the
 baseline_flag element should be the name of the flag variable that indicates whether or not records contain
 baseline values. Depending on the baseline flag given, either the absolute baseline values (at baseline)
-or the change from baseline values (post-baseline) are then summarized."><meta property="og:description" content="
+or the change from baseline values (post-baseline) are then summarized.">
+<meta property="og:description" content="
 The analyze function summarize_change() creates a layout element to summarize the change from baseline or absolute
 baseline values. The primary analysis variable vars indicates the numerical change from baseline results.
 Required secondary analysis variables value and baseline_flag can be supplied to the function via
 the variables argument. The value element should be the name of the analysis value variable, and the
 baseline_flag element should be the name of the flag variable that indicates whether or not records contain
 baseline values. Depending on the baseline flag given, either the absolute baseline values (at baseline)
-or the change from baseline values (post-baseline) are then summarized."><meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png"><link rel="stylesheet" href="../consent.css"><script src="../consent.js" type="text/javascript" charset="utf-8"></script></head><body>
+or the change from baseline values (post-baseline) are then summarized.">
+<meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png">
+<link rel="stylesheet" href="../consent.css">
+<script src="../consent.js" type="text/javascript" charset="utf-8"></script>
+</head>
+<body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
 
 
@@ -29,26 +52,66 @@
     </button>
 
     <div id="navbar" class="collapse navbar-collapse ms-3">
-      <ul class="navbar-nav me-auto"><li class="nav-item"><a class="nav-link" href="../articles/tern.html">Get started</a></li>
+      <ul class="navbar-nav me-auto">
+<li class="nav-item"><a class="nav-link" href="../articles/tern.html">Get started</a></li>
 <li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
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   <button class="nav-link dropdown-toggle" type="button" id="dropdown-articles" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Articles</button>
-  <ul class="dropdown-menu" aria-labelledby="dropdown-articles"><li><a class="dropdown-item" href="../articles/missing_values.html">Missing Values in Tern</a></li>
+  <ul class="dropdown-menu" aria-labelledby="dropdown-articles">
+<li><a class="dropdown-item" href="../articles/missing_values.html">Missing Values in Tern</a></li>
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-  </ul></li>
+  </ul>
+</li>
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+  <ul class="dropdown-menu" aria-labelledby="dropdown-reports">
+<li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
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- <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json"></form></li>
+  </ul>
+</li>
+      <div><li class="nav-item dropdown">
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+    <div class="dropdown-menu" aria-labelledby="dropdown-versions">
+    <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/main">main</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.5">v0.9.5</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.4">v0.9.4</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.3">v0.9.3</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1-rc3">v0.9.1-rc3</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a>
+</div>
+</li></div>
+</ul>
+<ul class="navbar-nav">
+<li class="nav-item"><form class="form-inline" role="search">
+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json">
+</form></li>
 <li class="nav-item"><a class="external-link nav-link" href="https://github.com/insightsengineering/tern" aria-label="GitHub"><span class="fa fa-github"></span></a></li>
-      </ul></div>
+      </ul>
+</div>
 
 
   </div>
@@ -72,7 +135,8 @@
     </div>
 
     <div class="section level2">
-    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
+    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">summarize_change</span><span class="op">(</span></span>
 <span>  <span class="va">lyt</span>,</span>
 <span>  <span class="va">vars</span>,</span>
@@ -107,95 +171,126 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
     </div>
 
     <div class="section level2">
-    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
+    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a>
+</h2>
 
 
-<dl><dt id="arg-lyt">lyt<a class="anchor" aria-label="anchor" href="#arg-lyt"></a></dt>
+<dl>
+<dt id="arg-lyt">lyt<a class="anchor" aria-label="anchor" href="#arg-lyt"></a>
+</dt>
 <dd><p>(<code>PreDataTableLayouts</code>)<br> layout that analyses will be added to.</p></dd>
 
 
-<dt id="arg-vars">vars<a class="anchor" aria-label="anchor" href="#arg-vars"></a></dt>
+<dt id="arg-vars">vars<a class="anchor" aria-label="anchor" href="#arg-vars"></a>
+</dt>
 <dd><p>(<code>character</code>)<br> variable names for the primary analysis variable to be iterated over.</p></dd>
 
 
-<dt id="arg-variables">variables<a class="anchor" aria-label="anchor" href="#arg-variables"></a></dt>
+<dt id="arg-variables">variables<a class="anchor" aria-label="anchor" href="#arg-variables"></a>
+</dt>
 <dd><p>(named <code>list</code> of <code>string</code>)<br> list of additional analysis variables.</p></dd>
 
 
-<dt id="arg-var-labels">var_labels<a class="anchor" aria-label="anchor" href="#arg-var-labels"></a></dt>
+<dt id="arg-var-labels">var_labels<a class="anchor" aria-label="anchor" href="#arg-var-labels"></a>
+</dt>
 <dd><p>(<code>character</code>)<br> variable labels.</p></dd>
 
 
-<dt id="arg-na-str">na_str<a class="anchor" aria-label="anchor" href="#arg-na-str"></a></dt>
+<dt id="arg-na-str">na_str<a class="anchor" aria-label="anchor" href="#arg-na-str"></a>
+</dt>
 <dd><p>(<code>string</code>)<br> string used to replace all <code>NA</code> or empty values in the output.</p></dd>
 
 
-<dt id="arg-nested">nested<a class="anchor" aria-label="anchor" href="#arg-nested"></a></dt>
+<dt id="arg-nested">nested<a class="anchor" aria-label="anchor" href="#arg-nested"></a>
+</dt>
 <dd><p>(<code>flag</code>)<br> whether this layout instruction should be applied within the existing layout structure _if
 possible (<code>TRUE</code>, the default) or as a new top-level element (<code>FALSE</code>). Ignored if it would nest a split.
 underneath analyses, which is not allowed.</p></dd>
 
 
-<dt id="arg-show-labels">show_labels<a class="anchor" aria-label="anchor" href="#arg-show-labels"></a></dt>
+<dt id="arg-show-labels">show_labels<a class="anchor" aria-label="anchor" href="#arg-show-labels"></a>
+</dt>
 <dd><p>(<code>string</code>)<br> label visibility: one of "default", "visible" and "hidden".</p></dd>
 
 
-<dt id="arg-table-names">table_names<a class="anchor" aria-label="anchor" href="#arg-table-names"></a></dt>
+<dt id="arg-table-names">table_names<a class="anchor" aria-label="anchor" href="#arg-table-names"></a>
+</dt>
 <dd><p>(<code>character</code>)<br> this can be customized in the case that the same <code>vars</code> are analyzed multiple
 times, to avoid warnings from <code>rtables</code>.</p></dd>
 
 
-<dt id="arg-section-div">section_div<a class="anchor" aria-label="anchor" href="#arg-section-div"></a></dt>
+<dt id="arg-section-div">section_div<a class="anchor" aria-label="anchor" href="#arg-section-div"></a>
+</dt>
 <dd><p>(<code>string</code>)<br> string which should be repeated as a section divider after each group
 defined by this split instruction, or <code>NA_character_</code> (the default) for no section divider.</p></dd>
 
 
-<dt id="arg--">...<a class="anchor" aria-label="anchor" href="#arg--"></a></dt>
+<dt id="arg--">...<a class="anchor" aria-label="anchor" href="#arg--"></a>
+</dt>
 <dd><p>additional arguments for the lower level functions.</p></dd>
 
 
-<dt id="arg--stats">.stats<a class="anchor" aria-label="anchor" href="#arg--stats"></a></dt>
-<dd><p>(<code>character</code>)<br> statistics to select for the table.</p>
-<p>Options are: <code>'n', 'sum', 'mean', 'sd', 'se', 'mean_sd', 'mean_se', 'mean_ci', 'mean_sei', 'mean_sdi', 'mean_pval', 'median', 'mad', 'median_ci', 'quantiles', 'iqr', 'range', 'min', 'max', 'median_range', 'cv', 'geom_mean', 'geom_mean_ci', 'geom_cv', 'median_ci_3d', 'mean_ci_3d', 'geom_mean_ci_3d'</code></p></dd>
+<dt id="arg--stats">.stats<a class="anchor" aria-label="anchor" href="#arg--stats"></a>
+</dt>
+<dd>
+<p>(<code>character</code>)<br> statistics to select for the table.</p>
+<p>Options are: <code>'n', 'sum', 'mean', 'sd', 'se', 'mean_sd', 'mean_se', 'mean_ci', 'mean_sei', 'mean_sdi', 'mean_pval', 'median', 'mad', 'median_ci', 'quantiles', 'iqr', 'range', 'min', 'max', 'median_range', 'cv', 'geom_mean', 'geom_mean_ci', 'geom_cv', 'median_ci_3d', 'mean_ci_3d', 'geom_mean_ci_3d'</code></p>
+</dd>
 
 
-<dt id="arg--formats">.formats<a class="anchor" aria-label="anchor" href="#arg--formats"></a></dt>
+<dt id="arg--formats">.formats<a class="anchor" aria-label="anchor" href="#arg--formats"></a>
+</dt>
 <dd><p>(named <code>character</code> or <code>list</code>)<br> formats for the statistics. See Details in <code>analyze_vars</code> for more
 information on the <code>"auto"</code> setting.</p></dd>
 
 
-<dt id="arg--labels">.labels<a class="anchor" aria-label="anchor" href="#arg--labels"></a></dt>
+<dt id="arg--labels">.labels<a class="anchor" aria-label="anchor" href="#arg--labels"></a>
+</dt>
 <dd><p>(named <code>character</code>)<br> labels for the statistics (without indent).</p></dd>
 
 
-<dt id="arg--indent-mods">.indent_mods<a class="anchor" aria-label="anchor" href="#arg--indent-mods"></a></dt>
+<dt id="arg--indent-mods">.indent_mods<a class="anchor" aria-label="anchor" href="#arg--indent-mods"></a>
+</dt>
 <dd><p>(named <code>integer</code>)<br> indent modifiers for the labels. Defaults to 0, which corresponds to the
 unmodified default behavior. Can be negative.</p></dd>
 
 
-<dt id="arg-df">df<a class="anchor" aria-label="anchor" href="#arg-df"></a></dt>
+<dt id="arg-df">df<a class="anchor" aria-label="anchor" href="#arg-df"></a>
+</dt>
 <dd><p>(<code>data.frame</code>)<br> data set containing all analysis variables.</p></dd>
 
-</dl></div>
+</dl>
+</div>
     <div class="section level2">
-    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
+    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a>
+</h2>
 
-<ul><li><p><code>summarize_change()</code> returns a layout object suitable for passing to further layouting functions,
+<ul>
+<li><p><code>summarize_change()</code> returns a layout object suitable for passing to further layouting functions,
 or to <code><a href="https://insightsengineering.github.io/rtables/latest-tag/reference/build_table.html" class="external-link">rtables::build_table()</a></code>. Adding this function to an <code>rtable</code> layout will add formatted rows containing
 the statistics from <code>s_change_from_baseline()</code> to the table layout.</p></li>
-</ul><ul><li><p><code>s_change_from_baseline()</code> returns the same values returned by <code><a href="analyze_variables.html">s_summary.numeric()</a></code>.</p></li>
-</ul><ul><li><p><code>a_change_from_baseline()</code> returns the corresponding list with formatted <code><a href="https://insightsengineering.github.io/rtables/latest-tag/reference/CellValue.html" class="external-link">rtables::CellValue()</a></code>.</p></li>
-</ul></div>
+</ul>
+<ul>
+<li><p><code>s_change_from_baseline()</code> returns the same values returned by <code><a href="analyze_variables.html">s_summary.numeric()</a></code>.</p></li>
+</ul>
+<ul>
+<li><p><code>a_change_from_baseline()</code> returns the corresponding list with formatted <code><a href="https://insightsengineering.github.io/rtables/latest-tag/reference/CellValue.html" class="external-link">rtables::CellValue()</a></code>.</p></li>
+</ul>
+</div>
     <div class="section level2">
-    <h2 id="functions">Functions<a class="anchor" aria-label="anchor" href="#functions"></a></h2>
+    <h2 id="functions">Functions<a class="anchor" aria-label="anchor" href="#functions"></a>
+</h2>
 
-<ul><li><p><code>summarize_change()</code>: Layout-creating function which can take statistics function arguments
+<ul>
+<li><p><code>summarize_change()</code>: Layout-creating function which can take statistics function arguments
 and additional format arguments. This function is a wrapper for <code><a href="https://insightsengineering.github.io/rtables/latest-tag/reference/analyze.html" class="external-link">rtables::analyze()</a></code>.</p></li>
 <li><p><code>s_change_from_baseline()</code>: Statistics function that summarizes baseline or post-baseline visits.</p></li>
 <li><p><code>a_change_from_baseline()</code>: Formatted analysis function which is used as <code>afun</code> in <code>summarize_change()</code>.</p></li>
-</ul></div>
+</ul>
+</div>
     <div class="section level2">
-    <h2 id="note">Note<a class="anchor" aria-label="anchor" href="#note"></a></h2>
+    <h2 id="note">Note<a class="anchor" aria-label="anchor" href="#note"></a>
+</h2>
     <p>To be used after a split on visits in the layout, such that each data subset only contains
 either baseline or post-baseline data.</p>
 <p>The data in <code>df</code> must be either all be from baseline or post-baseline visits. Otherwise
@@ -203,7 +298,8 @@ <h2 id="note">Note<a class="anchor" aria-label="anchor" href="#note"></a></h2>
     </div>
 
     <div class="section level2">
-    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
+    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://dplyr.tidyverse.org" class="external-link">dplyr</a></span><span class="op">)</span></span></span>
 <span class="r-in"><span></span></span>
 <span class="r-in"><span><span class="co"># Fabricate dataset</span></span></span>
@@ -249,17 +345,19 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 </code></pre></div>
     </div>
   </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
-    </nav></aside></div>
+    </nav></aside>
+</div>
 
 
     <footer><div class="nest">
   <p>tern is a part of the <strong>NEST</strong> and <a href="https://pharmaverse.org/" class="external-link"><strong>pharmaverse</strong></a>.</p>
 </div>
-<script type="text/javascript" src="../analytics.js"></script></footer></div>
-
+<script type="text/javascript" src="../analytics.js"></script></footer>
+</div>
 
 
 
 
-  </body></html>
 
+  </body>
+</html>
diff --git a/main/reference/summarize_colvars.html b/main/reference/summarize_colvars.html
index 28608acf99..70878d8a08 100644
--- a/main/reference/summarize_colvars.html
+++ b/main/reference/summarize_colvars.html
@@ -1,17 +1,40 @@
-<!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Summarize variables in columns — summarize_colvars • tern</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Summarize variables in columns — summarize_colvars"><meta name="description" content="
+<html lang="en">
+<head>
+<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+<meta charset="utf-8">
+<meta http-equiv="X-UA-Compatible" content="IE=edge">
+<meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<title>Summarize variables in columns — summarize_colvars • tern</title>
+<!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png">
+<link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png">
+<link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png">
+<link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png">
+<link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png">
+<link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png">
+<script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet">
+<script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet">
+<link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet">
+<script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Summarize variables in columns — summarize_colvars">
+<meta name="description" content="
 The analyze function summarize_colvars() uses the statistics function s_summary() to analyze variables that are
 arranged in columns. The variables to analyze should be specified in the table layout via column splits (see
 rtables::split_cols_by() and rtables::split_cols_by_multivar()) prior to using summarize_colvars().
 The function is a minimal wrapper for rtables::analyze_colvars(), a function typically used to apply different
 analysis methods in rows for each column variable. To use the analysis methods as column labels, please refer to
-the analyze_vars_in_cols() function."><meta property="og:description" content="
+the analyze_vars_in_cols() function.">
+<meta property="og:description" content="
 The analyze function summarize_colvars() uses the statistics function s_summary() to analyze variables that are
 arranged in columns. The variables to analyze should be specified in the table layout via column splits (see
 rtables::split_cols_by() and rtables::split_cols_by_multivar()) prior to using summarize_colvars().
 The function is a minimal wrapper for rtables::analyze_colvars(), a function typically used to apply different
 analysis methods in rows for each column variable. To use the analysis methods as column labels, please refer to
-the analyze_vars_in_cols() function."><meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png"><link rel="stylesheet" href="../consent.css"><script src="../consent.js" type="text/javascript" charset="utf-8"></script></head><body>
+the analyze_vars_in_cols() function.">
+<meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png">
+<link rel="stylesheet" href="../consent.css">
+<script src="../consent.js" type="text/javascript" charset="utf-8"></script>
+</head>
+<body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
 
 
@@ -27,26 +50,66 @@
     </button>
 
     <div id="navbar" class="collapse navbar-collapse ms-3">
-      <ul class="navbar-nav me-auto"><li class="nav-item"><a class="nav-link" href="../articles/tern.html">Get started</a></li>
+      <ul class="navbar-nav me-auto">
+<li class="nav-item"><a class="nav-link" href="../articles/tern.html">Get started</a></li>
 <li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
 <li class="nav-item dropdown">
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-articles" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Articles</button>
-  <ul class="dropdown-menu" aria-labelledby="dropdown-articles"><li><a class="dropdown-item" href="../articles/missing_values.html">Missing Values in Tern</a></li>
+  <ul class="dropdown-menu" aria-labelledby="dropdown-articles">
+<li><a class="dropdown-item" href="../articles/missing_values.html">Missing Values in Tern</a></li>
     <li><a class="dropdown-item" href="../articles/tables.html">Tabulation</a></li>
     <li><a class="dropdown-item" href="../articles/tern_formats.html">Formatting Functions</a></li>
     <li><a class="dropdown-item" href="../articles/tern_functions_guide.html">Understanding `tern` functions</a></li>
-  </ul></li>
+  </ul>
+</li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
-  <ul class="dropdown-menu" aria-labelledby="dropdown-reports"><li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
+  <ul class="dropdown-menu" aria-labelledby="dropdown-reports">
+<li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
     <li><a class="dropdown-item" href="../unit-test-report/">Unit test report</a></li>
     <li><a class="dropdown-item" href="../unit-test-report-non-cran/">Non-CRAN unit test report</a></li>
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-      </ul><ul class="navbar-nav"><li class="nav-item"><form class="form-inline" role="search">
- <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json"></form></li>
+  </ul>
+</li>
+      <div><li class="nav-item dropdown">
+    <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-versions">Versions</a>
+    <div class="dropdown-menu" aria-labelledby="dropdown-versions">
+    <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/main">main</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.5">v0.9.5</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.4">v0.9.4</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.3">v0.9.3</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1-rc3">v0.9.1-rc3</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a>
+</div>
+</li></div>
+</ul>
+<ul class="navbar-nav">
+<li class="nav-item"><form class="form-inline" role="search">
+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json">
+</form></li>
 <li class="nav-item"><a class="external-link nav-link" href="https://github.com/insightsengineering/tern" aria-label="GitHub"><span class="fa fa-github"></span></a></li>
-      </ul></div>
+      </ul>
+</div>
 
 
   </div>
@@ -69,7 +132,8 @@
     </div>
 
     <div class="section level2">
-    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
+    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">summarize_colvars</span><span class="op">(</span></span>
 <span>  <span class="va">lyt</span>,</span>
 <span>  <span class="va">...</span>,</span>
@@ -82,53 +146,66 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
     </div>
 
     <div class="section level2">
-    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
+    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a>
+</h2>
 
 
-<dl><dt id="arg-lyt">lyt<a class="anchor" aria-label="anchor" href="#arg-lyt"></a></dt>
+<dl>
+<dt id="arg-lyt">lyt<a class="anchor" aria-label="anchor" href="#arg-lyt"></a>
+</dt>
 <dd><p>(<code>PreDataTableLayouts</code>)<br> layout that analyses will be added to.</p></dd>
 
 
-<dt id="arg--">...<a class="anchor" aria-label="anchor" href="#arg--"></a></dt>
+<dt id="arg--">...<a class="anchor" aria-label="anchor" href="#arg--"></a>
+</dt>
 <dd><p>arguments passed to <code><a href="analyze_variables.html">s_summary()</a></code>.</p></dd>
 
 
-<dt id="arg-na-str">na_str<a class="anchor" aria-label="anchor" href="#arg-na-str"></a></dt>
+<dt id="arg-na-str">na_str<a class="anchor" aria-label="anchor" href="#arg-na-str"></a>
+</dt>
 <dd><p>(<code>string</code>)<br> string used to replace all <code>NA</code> or empty values in the output.</p></dd>
 
 
-<dt id="arg--stats">.stats<a class="anchor" aria-label="anchor" href="#arg--stats"></a></dt>
+<dt id="arg--stats">.stats<a class="anchor" aria-label="anchor" href="#arg--stats"></a>
+</dt>
 <dd><p>(<code>character</code>)<br> statistics to select for the table.</p></dd>
 
 
-<dt id="arg--formats">.formats<a class="anchor" aria-label="anchor" href="#arg--formats"></a></dt>
+<dt id="arg--formats">.formats<a class="anchor" aria-label="anchor" href="#arg--formats"></a>
+</dt>
 <dd><p>(named <code>character</code> or <code>list</code>)<br> formats for the statistics. See Details in <code>analyze_vars</code> for more
 information on the <code>"auto"</code> setting.</p></dd>
 
 
-<dt id="arg--labels">.labels<a class="anchor" aria-label="anchor" href="#arg--labels"></a></dt>
+<dt id="arg--labels">.labels<a class="anchor" aria-label="anchor" href="#arg--labels"></a>
+</dt>
 <dd><p>(named <code>character</code>)<br> labels for the statistics (without indent).</p></dd>
 
 
-<dt id="arg--indent-mods">.indent_mods<a class="anchor" aria-label="anchor" href="#arg--indent-mods"></a></dt>
+<dt id="arg--indent-mods">.indent_mods<a class="anchor" aria-label="anchor" href="#arg--indent-mods"></a>
+</dt>
 <dd><p>(named <code>vector</code> of <code>integer</code>)<br> indent modifiers for the labels. Each element of the vector
 should be a name-value pair with name corresponding to a statistic specified in <code>.stats</code> and value the indentation
 for that statistic's row label.</p></dd>
 
-</dl></div>
+</dl>
+</div>
     <div class="section level2">
-    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
+    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a>
+</h2>
     <p>A layout object suitable for passing to further layouting functions, or to <code><a href="https://insightsengineering.github.io/rtables/latest-tag/reference/build_table.html" class="external-link">rtables::build_table()</a></code>.
 Adding this function to an <code>rtable</code> layout will summarize the given variables, arrange the output
 in columns, and add it to the table layout.</p>
     </div>
     <div class="section level2">
-    <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"></a></h2>
+    <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"></a>
+</h2>
     <div class="dont-index"><p><code><a href="https://insightsengineering.github.io/rtables/latest-tag/reference/split_cols_by_multivar.html" class="external-link">rtables::split_cols_by_multivar()</a></code> and <code><a href="analyze_colvars_functions.html">analyze_colvars_functions</a></code>.</p></div>
     </div>
 
     <div class="section level2">
-    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
+    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">dta_test</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a></span><span class="op">(</span></span></span>
 <span class="r-in"><span>  USUBJID <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/rep.html" class="external-link">rep</a></span><span class="op">(</span><span class="fl">1</span><span class="op">:</span><span class="fl">6</span>, each <span class="op">=</span> <span class="fl">3</span><span class="op">)</span>,</span></span>
 <span class="r-in"><span>  PARAMCD <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/rep.html" class="external-link">rep</a></span><span class="op">(</span><span class="st">"lab"</span>, <span class="fl">6</span> <span class="op">*</span> <span class="fl">3</span><span class="op">)</span>,</span></span>
@@ -217,17 +294,19 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 </code></pre></div>
     </div>
   </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
-    </nav></aside></div>
+    </nav></aside>
+</div>
 
 
     <footer><div class="nest">
   <p>tern is a part of the <strong>NEST</strong> and <a href="https://pharmaverse.org/" class="external-link"><strong>pharmaverse</strong></a>.</p>
 </div>
-<script type="text/javascript" src="../analytics.js"></script></footer></div>
-
+<script type="text/javascript" src="../analytics.js"></script></footer>
+</div>
 
 
 
 
-  </body></html>
 
+  </body>
+</html>
diff --git a/main/reference/summarize_functions.html b/main/reference/summarize_functions.html
index 80e7ed77c8..729f2beca6 100644
--- a/main/reference/summarize_functions.html
+++ b/main/reference/summarize_functions.html
@@ -1,7 +1,30 @@
-<!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Summarize functions — summarize_functions • tern</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Summarize functions — summarize_functions"><meta name="description" content="These functions are wrappers for rtables::summarize_row_groups(), applying corresponding tern content functions
-to add summary rows to a given table layout:"><meta property="og:description" content="These functions are wrappers for rtables::summarize_row_groups(), applying corresponding tern content functions
-to add summary rows to a given table layout:"><meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png"><link rel="stylesheet" href="../consent.css"><script src="../consent.js" type="text/javascript" charset="utf-8"></script></head><body>
+<html lang="en">
+<head>
+<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+<meta charset="utf-8">
+<meta http-equiv="X-UA-Compatible" content="IE=edge">
+<meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<title>Summarize functions — summarize_functions • tern</title>
+<!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png">
+<link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png">
+<link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png">
+<link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png">
+<link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png">
+<link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png">
+<script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet">
+<script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet">
+<link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet">
+<script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Summarize functions — summarize_functions">
+<meta name="description" content="These functions are wrappers for rtables::summarize_row_groups(), applying corresponding tern content functions
+to add summary rows to a given table layout:">
+<meta property="og:description" content="These functions are wrappers for rtables::summarize_row_groups(), applying corresponding tern content functions
+to add summary rows to a given table layout:">
+<meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png">
+<link rel="stylesheet" href="../consent.css">
+<script src="../consent.js" type="text/javascript" charset="utf-8"></script>
+</head>
+<body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
 
 
@@ -17,26 +40,66 @@
     </button>
 
     <div id="navbar" class="collapse navbar-collapse ms-3">
-      <ul class="navbar-nav me-auto"><li class="nav-item"><a class="nav-link" href="../articles/tern.html">Get started</a></li>
+      <ul class="navbar-nav me-auto">
+<li class="nav-item"><a class="nav-link" href="../articles/tern.html">Get started</a></li>
 <li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
 <li class="nav-item dropdown">
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-articles" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Articles</button>
-  <ul class="dropdown-menu" aria-labelledby="dropdown-articles"><li><a class="dropdown-item" href="../articles/missing_values.html">Missing Values in Tern</a></li>
+  <ul class="dropdown-menu" aria-labelledby="dropdown-articles">
+<li><a class="dropdown-item" href="../articles/missing_values.html">Missing Values in Tern</a></li>
     <li><a class="dropdown-item" href="../articles/tables.html">Tabulation</a></li>
     <li><a class="dropdown-item" href="../articles/tern_formats.html">Formatting Functions</a></li>
     <li><a class="dropdown-item" href="../articles/tern_functions_guide.html">Understanding `tern` functions</a></li>
-  </ul></li>
+  </ul>
+</li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
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   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
-  <ul class="dropdown-menu" aria-labelledby="dropdown-reports"><li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
+  <ul class="dropdown-menu" aria-labelledby="dropdown-reports">
+<li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
     <li><a class="dropdown-item" href="../unit-test-report/">Unit test report</a></li>
     <li><a class="dropdown-item" href="../unit-test-report-non-cran/">Non-CRAN unit test report</a></li>
-  </ul></li>
-      </ul><ul class="navbar-nav"><li class="nav-item"><form class="form-inline" role="search">
- <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json"></form></li>
+  </ul>
+</li>
+      <div><li class="nav-item dropdown">
+    <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-versions">Versions</a>
+    <div class="dropdown-menu" aria-labelledby="dropdown-versions">
+    <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/main">main</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.5">v0.9.5</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.4">v0.9.4</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.3">v0.9.3</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1-rc3">v0.9.1-rc3</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a>
+</div>
+</li></div>
+</ul>
+<ul class="navbar-nav">
+<li class="nav-item"><form class="form-inline" role="search">
+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json">
+</form></li>
 <li class="nav-item"><a class="external-link nav-link" href="https://github.com/insightsengineering/tern" aria-label="GitHub"><span class="fa fa-github"></span></a></li>
-      </ul></div>
+      </ul>
+</div>
 
 
   </div>
@@ -55,9 +118,11 @@
 
 
     <div class="section level2">
-    <h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a></h2>
+    <h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a>
+</h2>
 
-<ul><li><p><code><a href="add_rowcounts.html">add_rowcounts()</a></code></p></li>
+<ul>
+<li><p><code><a href="add_rowcounts.html">add_rowcounts()</a></code></p></li>
 <li><p><code><a href="estimate_multinomial_rsp.html">estimate_multinomial_response()</a></code> (with <code><a href="https://insightsengineering.github.io/rtables/latest-tag/reference/analyze.html" class="external-link">rtables::analyze()</a></code>)</p></li>
 <li><p><code><a href="h_tab_one_biomarker.html">h_tab_one_biomarker()</a></code> (probably to deprecate)</p></li>
 <li><p><code><a href="logistic_summary_by_flag.html">logistic_summary_by_flag()</a></code></p></li>
@@ -66,30 +131,36 @@ <h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></
 <li><p><code><a href="count_occurrences_by_grade.html">summarize_occurrences_by_grade()</a></code></p></li>
 <li><p><code><a href="count_patients_events_in_cols.html">summarize_patients_events_in_cols()</a></code></p></li>
 <li><p><code><a href="summarize_patients_exposure_in_cols.html">summarize_patients_exposure_in_cols()</a></code></p></li>
-</ul><p>Additionally, the <code><a href="cox_regression.html">summarize_coxreg()</a></code> function utilizes <code><a href="https://insightsengineering.github.io/rtables/latest-tag/reference/summarize_row_groups.html" class="external-link">rtables::summarize_row_groups()</a></code>
+</ul>
+<p>Additionally, the <code><a href="cox_regression.html">summarize_coxreg()</a></code> function utilizes <code><a href="https://insightsengineering.github.io/rtables/latest-tag/reference/summarize_row_groups.html" class="external-link">rtables::summarize_row_groups()</a></code>
 (in combination with several other <code>rtables</code> functions like <code><a href="https://insightsengineering.github.io/rtables/latest-tag/reference/analyze_colvars.html" class="external-link">rtables::analyze_colvars()</a></code>) to
 output a Cox regression summary table.</p>
     </div>
     <div class="section level2">
-    <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"></a></h2>
+    <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"></a>
+</h2>
     <div class="dont-index">
-<ul><li><p><a href="analyze_functions.html">analyze_functions</a> for functions which are wrappers for <code><a href="https://insightsengineering.github.io/rtables/latest-tag/reference/analyze.html" class="external-link">rtables::analyze()</a></code>.</p></li>
+<ul>
+<li><p><a href="analyze_functions.html">analyze_functions</a> for functions which are wrappers for <code><a href="https://insightsengineering.github.io/rtables/latest-tag/reference/analyze.html" class="external-link">rtables::analyze()</a></code>.</p></li>
 <li><p><a href="analyze_colvars_functions.html">analyze_colvars_functions</a> for functions that are wrappers for <code><a href="https://insightsengineering.github.io/rtables/latest-tag/reference/analyze_colvars.html" class="external-link">rtables::analyze_colvars()</a></code>.</p></li>
-</ul></div>
+</ul>
+</div>
     </div>
 
   </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
-    </nav></aside></div>
+    </nav></aside>
+</div>
 
 
     <footer><div class="nest">
   <p>tern is a part of the <strong>NEST</strong> and <a href="https://pharmaverse.org/" class="external-link"><strong>pharmaverse</strong></a>.</p>
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-<script type="text/javascript" src="../analytics.js"></script></footer></div>
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+<script type="text/javascript" src="../analytics.js"></script></footer>
+</div>
 
 
 
 
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+  </body>
+</html>
diff --git a/main/reference/summarize_glm_count.html b/main/reference/summarize_glm_count.html
index f65cf3801c..fec8ed3a93 100644
--- a/main/reference/summarize_glm_count.html
+++ b/main/reference/summarize_glm_count.html
@@ -1,15 +1,38 @@
-<!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Summarize Poisson negative binomial regression — summarize_glm_count • tern</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Summarize Poisson negative binomial regression — summarize_glm_count"><meta name="description" content="
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+<title>Summarize Poisson negative binomial regression — summarize_glm_count • tern</title>
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+<meta name="description" content="
 Summarize results of a Poisson negative binomial regression.
 This can be used to analyze count and/or frequency data using a linear model.
 It is specifically useful for analyzing count data (using the Poisson or Negative
 Binomial distribution) that is result of a generalized linear model of one (e.g. arm) or more
-covariates."><meta property="og:description" content="
+covariates.">
+<meta property="og:description" content="
 Summarize results of a Poisson negative binomial regression.
 This can be used to analyze count and/or frequency data using a linear model.
 It is specifically useful for analyzing count data (using the Poisson or Negative
 Binomial distribution) that is result of a generalized linear model of one (e.g. arm) or more
-covariates."><meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png"><link rel="stylesheet" href="../consent.css"><script src="../consent.js" type="text/javascript" charset="utf-8"></script></head><body>
+covariates.">
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   </div>
@@ -66,7 +129,8 @@
     </div>
 
     <div class="section level2">
-    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
+    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">summarize_glm_count</span><span class="op">(</span></span>
 <span>  <span class="va">lyt</span>,</span>
 <span>  <span class="va">vars</span>,</span>
@@ -105,136 +169,178 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
     </div>
 
     <div class="section level2">
-    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
+    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a>
+</h2>
 
 
-<dl><dt id="arg-lyt">lyt<a class="anchor" aria-label="anchor" href="#arg-lyt"></a></dt>
+<dl>
+<dt id="arg-lyt">lyt<a class="anchor" aria-label="anchor" href="#arg-lyt"></a>
+</dt>
 <dd><p>(<code>PreDataTableLayouts</code>)<br> layout that analyses will be added to.</p></dd>
 
 
-<dt id="arg-vars">vars<a class="anchor" aria-label="anchor" href="#arg-vars"></a></dt>
+<dt id="arg-vars">vars<a class="anchor" aria-label="anchor" href="#arg-vars"></a>
+</dt>
 <dd><p>(<code>character</code>)<br> variable names for the primary analysis variable to be iterated over.</p></dd>
 
 
-<dt id="arg-variables">variables<a class="anchor" aria-label="anchor" href="#arg-variables"></a></dt>
-<dd><p>(named <code>list</code> of <code>string</code>)<br> list of additional analysis variables, with
-expected elements:</p><ul><li><p><code>arm</code> (<code>string</code>)<br> group variable, for which the covariate adjusted means of multiple
+<dt id="arg-variables">variables<a class="anchor" aria-label="anchor" href="#arg-variables"></a>
+</dt>
+<dd>
+<p>(named <code>list</code> of <code>string</code>)<br> list of additional analysis variables, with
+expected elements:</p>
+<ul>
+<li><p><code>arm</code> (<code>string</code>)<br> group variable, for which the covariate adjusted means of multiple
 groups will be summarized. Specifically, the first level of <code>arm</code> variable is taken as the
 reference group.</p></li>
 <li><p><code>covariates</code> (<code>character</code>)<br> a vector that can contain single variable names (such as
 <code>"X1"</code>), and/or interaction terms indicated by <code>"X1 * X2"</code>.</p></li>
 <li><p><code>offset</code> (<code>numeric</code>)<br> a numeric vector or scalar adding an offset.</p></li>
-</ul></dd>
+</ul>
+</dd>
 
 
-<dt id="arg-distribution">distribution<a class="anchor" aria-label="anchor" href="#arg-distribution"></a></dt>
+<dt id="arg-distribution">distribution<a class="anchor" aria-label="anchor" href="#arg-distribution"></a>
+</dt>
 <dd><p>(<code>character</code>)<br> a character value specifying the distribution
 used in the regression (Poisson, Quasi-Poisson, negative binomial).</p></dd>
 
 
-<dt id="arg-conf-level">conf_level<a class="anchor" aria-label="anchor" href="#arg-conf-level"></a></dt>
+<dt id="arg-conf-level">conf_level<a class="anchor" aria-label="anchor" href="#arg-conf-level"></a>
+</dt>
 <dd><p>(<code>proportion</code>)<br> confidence level of the interval.</p></dd>
 
 
-<dt id="arg-rate-mean-method">rate_mean_method<a class="anchor" aria-label="anchor" href="#arg-rate-mean-method"></a></dt>
+<dt id="arg-rate-mean-method">rate_mean_method<a class="anchor" aria-label="anchor" href="#arg-rate-mean-method"></a>
+</dt>
 <dd><p>(<code>character(1)</code>)<br> method used to estimate the mean odds ratio. Defaults to <code>emmeans</code>.
 see details for more information.</p></dd>
 
 
-<dt id="arg-weights">weights<a class="anchor" aria-label="anchor" href="#arg-weights"></a></dt>
+<dt id="arg-weights">weights<a class="anchor" aria-label="anchor" href="#arg-weights"></a>
+</dt>
 <dd><p>(<code>character</code>)<br> a character vector specifying weights used
 in averaging predictions. Number of weights must equal the number of levels included in the covariates.
 Weights option passed to <code><a href="https://rvlenth.github.io/emmeans/reference/emmeans.html" class="external-link">emmeans::emmeans()</a></code>.</p></dd>
 
 
-<dt id="arg-scale">scale<a class="anchor" aria-label="anchor" href="#arg-scale"></a></dt>
+<dt id="arg-scale">scale<a class="anchor" aria-label="anchor" href="#arg-scale"></a>
+</dt>
 <dd><p>(<code>numeric(1)</code>)<br> linear scaling factor for rate and confidence intervals. Defaults to <code>1</code>.</p></dd>
 
 
-<dt id="arg-var-labels">var_labels<a class="anchor" aria-label="anchor" href="#arg-var-labels"></a></dt>
+<dt id="arg-var-labels">var_labels<a class="anchor" aria-label="anchor" href="#arg-var-labels"></a>
+</dt>
 <dd><p>(<code>character</code>)<br> variable labels.</p></dd>
 
 
-<dt id="arg-na-str">na_str<a class="anchor" aria-label="anchor" href="#arg-na-str"></a></dt>
+<dt id="arg-na-str">na_str<a class="anchor" aria-label="anchor" href="#arg-na-str"></a>
+</dt>
 <dd><p>(<code>string</code>)<br> string used to replace all <code>NA</code> or empty values in the output.</p></dd>
 
 
-<dt id="arg-nested">nested<a class="anchor" aria-label="anchor" href="#arg-nested"></a></dt>
+<dt id="arg-nested">nested<a class="anchor" aria-label="anchor" href="#arg-nested"></a>
+</dt>
 <dd><p>(<code>flag</code>)<br> whether this layout instruction should be applied within the existing layout structure _if
 possible (<code>TRUE</code>, the default) or as a new top-level element (<code>FALSE</code>). Ignored if it would nest a split.
 underneath analyses, which is not allowed.</p></dd>
 
 
-<dt id="arg--">...<a class="anchor" aria-label="anchor" href="#arg--"></a></dt>
+<dt id="arg--">...<a class="anchor" aria-label="anchor" href="#arg--"></a>
+</dt>
 <dd><p>additional arguments for the lower level functions.</p></dd>
 
 
-<dt id="arg-show-labels">show_labels<a class="anchor" aria-label="anchor" href="#arg-show-labels"></a></dt>
+<dt id="arg-show-labels">show_labels<a class="anchor" aria-label="anchor" href="#arg-show-labels"></a>
+</dt>
 <dd><p>(<code>string</code>)<br> label visibility: one of "default", "visible" and "hidden".</p></dd>
 
 
-<dt id="arg-table-names">table_names<a class="anchor" aria-label="anchor" href="#arg-table-names"></a></dt>
+<dt id="arg-table-names">table_names<a class="anchor" aria-label="anchor" href="#arg-table-names"></a>
+</dt>
 <dd><p>(<code>character</code>)<br> this can be customized in the case that the same <code>vars</code> are analyzed multiple
 times, to avoid warnings from <code>rtables</code>.</p></dd>
 
 
-<dt id="arg--stats">.stats<a class="anchor" aria-label="anchor" href="#arg--stats"></a></dt>
-<dd><p>(<code>character</code>)<br> statistics to select for the table.</p>
-<p>Options are: <code>'n', 'rate', 'rate_ci', 'rate_ratio', 'rate_ratio_ci', 'pval'</code></p></dd>
+<dt id="arg--stats">.stats<a class="anchor" aria-label="anchor" href="#arg--stats"></a>
+</dt>
+<dd>
+<p>(<code>character</code>)<br> statistics to select for the table.</p>
+<p>Options are: <code>'n', 'rate', 'rate_ci', 'rate_ratio', 'rate_ratio_ci', 'pval'</code></p>
+</dd>
 
 
-<dt id="arg--formats">.formats<a class="anchor" aria-label="anchor" href="#arg--formats"></a></dt>
+<dt id="arg--formats">.formats<a class="anchor" aria-label="anchor" href="#arg--formats"></a>
+</dt>
 <dd><p>(named <code>character</code> or <code>list</code>)<br> formats for the statistics. See Details in <code>analyze_vars</code> for more
 information on the <code>"auto"</code> setting.</p></dd>
 
 
-<dt id="arg--labels">.labels<a class="anchor" aria-label="anchor" href="#arg--labels"></a></dt>
+<dt id="arg--labels">.labels<a class="anchor" aria-label="anchor" href="#arg--labels"></a>
+</dt>
 <dd><p>(named <code>character</code>)<br> labels for the statistics (without indent).</p></dd>
 
 
-<dt id="arg--indent-mods">.indent_mods<a class="anchor" aria-label="anchor" href="#arg--indent-mods"></a></dt>
+<dt id="arg--indent-mods">.indent_mods<a class="anchor" aria-label="anchor" href="#arg--indent-mods"></a>
+</dt>
 <dd><p>(named <code>integer</code>)<br> indent modifiers for the labels. Defaults to 0, which corresponds to the
 unmodified default behavior. Can be negative.</p></dd>
 
 
-<dt id="arg-df">df<a class="anchor" aria-label="anchor" href="#arg-df"></a></dt>
+<dt id="arg-df">df<a class="anchor" aria-label="anchor" href="#arg-df"></a>
+</dt>
 <dd><p>(<code>data.frame</code>)<br> data set containing all analysis variables.</p></dd>
 
 
-<dt id="arg--var">.var<a class="anchor" aria-label="anchor" href="#arg--var"></a></dt>
+<dt id="arg--var">.var<a class="anchor" aria-label="anchor" href="#arg--var"></a>
+</dt>
 <dd><p>(<code>string</code>)<br> single variable name that is passed by <code>rtables</code> when requested
 by a statistics function.</p></dd>
 
 
-<dt id="arg--df-row">.df_row<a class="anchor" aria-label="anchor" href="#arg--df-row"></a></dt>
+<dt id="arg--df-row">.df_row<a class="anchor" aria-label="anchor" href="#arg--df-row"></a>
+</dt>
 <dd><p>(<code>data.frame</code>)<br> dataset that includes all the variables that are called
 in <code>.var</code> and <code>variables</code>.</p></dd>
 
 
-<dt id="arg--ref-group">.ref_group<a class="anchor" aria-label="anchor" href="#arg--ref-group"></a></dt>
+<dt id="arg--ref-group">.ref_group<a class="anchor" aria-label="anchor" href="#arg--ref-group"></a>
+</dt>
 <dd><p>(<code>data.frame</code> or <code>vector</code>)<br> the data corresponding to the reference group.</p></dd>
 
 
-<dt id="arg--in-ref-col">.in_ref_col<a class="anchor" aria-label="anchor" href="#arg--in-ref-col"></a></dt>
+<dt id="arg--in-ref-col">.in_ref_col<a class="anchor" aria-label="anchor" href="#arg--in-ref-col"></a>
+</dt>
 <dd><p>(<code>flag</code>)<br><code>TRUE</code> when working with the reference level, <code>FALSE</code> otherwise.</p></dd>
 
-</dl></div>
+</dl>
+</div>
     <div class="section level2">
-    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
+    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a>
+</h2>
 
-<ul><li><p><code>summarize_glm_count()</code> returns a layout object suitable for passing to further layouting functions,
+<ul>
+<li><p><code>summarize_glm_count()</code> returns a layout object suitable for passing to further layouting functions,
 or to <code><a href="https://insightsengineering.github.io/rtables/latest-tag/reference/build_table.html" class="external-link">rtables::build_table()</a></code>. Adding this function to an <code>rtable</code> layout will add formatted rows containing
 the statistics from <code>s_glm_count()</code> to the table layout.</p></li>
-</ul><ul><li><p><code>s_glm_count()</code> returns a named <code>list</code> of 5 statistics:</p><ul><li><p><code>n</code>: Count of complete sample size for the group.</p></li>
+</ul>
+<ul>
+<li>
+<p><code>s_glm_count()</code> returns a named <code>list</code> of 5 statistics:</p>
+<ul>
+<li><p><code>n</code>: Count of complete sample size for the group.</p></li>
 <li><p><code>rate</code>: Estimated event rate per follow-up time.</p></li>
 <li><p><code>rate_ci</code>: Confidence level for estimated rate per follow-up time.</p></li>
 <li><p><code>rate_ratio</code>: Ratio of event rates in each treatment arm to the reference arm.</p></li>
 <li><p><code>rate_ratio_ci</code>: Confidence level for the rate ratio.</p></li>
 <li><p><code>pval</code>: p-value.</p></li>
-</ul></li>
-</ul></div>
+</ul>
+</li>
+</ul>
+</div>
     <div class="section level2">
-    <h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a></h2>
+    <h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a>
+</h2>
     <p><code>summarize_glm_count()</code> uses <code>s_glm_count()</code> to calculate the statistics for the table. This
 analysis function uses <code><a href="h_glm_count.html">h_glm_count()</a></code> to estimate the GLM with <code><a href="https://rdrr.io/r/stats/glm.html" class="external-link">stats::glm()</a></code> for Poisson and Quasi-Poisson
 distributions or <code><a href="https://rdrr.io/pkg/MASS/man/glm.nb.html" class="external-link">MASS::glm.nb()</a></code> for Negative Binomial distribution. All methods assume a
@@ -248,16 +354,20 @@ <h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></
 with <code>method = "trt.vs.ctrl"</code> and <code>ref</code> equal to the first <code>arm</code> value.</p>
     </div>
     <div class="section level2">
-    <h2 id="functions">Functions<a class="anchor" aria-label="anchor" href="#functions"></a></h2>
+    <h2 id="functions">Functions<a class="anchor" aria-label="anchor" href="#functions"></a>
+</h2>
 
-<ul><li><p><code>summarize_glm_count()</code>: Layout-creating function which can take statistics function arguments
+<ul>
+<li><p><code>summarize_glm_count()</code>: Layout-creating function which can take statistics function arguments
 and additional format arguments. This function is a wrapper for <code><a href="https://insightsengineering.github.io/rtables/latest-tag/reference/analyze.html" class="external-link">rtables::analyze()</a></code>.</p></li>
 <li><p><code>s_glm_count()</code>: Statistics function that produces a named list of results
 of the investigated Poisson model.</p></li>
-</ul></div>
+</ul>
+</div>
 
     <div class="section level2">
-    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
+    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://dplyr.tidyverse.org" class="external-link">dplyr</a></span><span class="op">)</span></span></span>
 <span class="r-in"><span></span></span>
 <span class="r-in"><span><span class="va">anl</span> <span class="op">&lt;-</span> <span class="va">tern_ex_adtte</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter</a></span><span class="op">(</span><span class="va">PARAMCD</span> <span class="op">==</span> <span class="st">"TNE"</span><span class="op">)</span></span></span>
@@ -345,17 +455,19 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 </code></pre></div>
     </div>
   </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
-    </nav></aside></div>
+    </nav></aside>
+</div>
 
 
     <footer><div class="nest">
   <p>tern is a part of the <strong>NEST</strong> and <a href="https://pharmaverse.org/" class="external-link"><strong>pharmaverse</strong></a>.</p>
 </div>
-<script type="text/javascript" src="../analytics.js"></script></footer></div>
-
+<script type="text/javascript" src="../analytics.js"></script></footer>
+</div>
 
 
 
 
-  </body></html>
 
+  </body>
+</html>
diff --git a/main/reference/summarize_logistic.html b/main/reference/summarize_logistic.html
index 7f8ff9bae3..9481cac6dd 100644
--- a/main/reference/summarize_logistic.html
+++ b/main/reference/summarize_logistic.html
@@ -1,5 +1,22 @@
-<!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Multivariate logistic regression table — summarize_logistic • tern</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Multivariate logistic regression table — summarize_logistic"><meta name="description" content="
+<html lang="en">
+<head>
+<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
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+<meta http-equiv="X-UA-Compatible" content="IE=edge">
+<meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<title>Multivariate logistic regression table — summarize_logistic • tern</title>
+<!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png">
+<link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png">
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+<link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png">
+<script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet">
+<script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet">
+<link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet">
+<script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Multivariate logistic regression table — summarize_logistic">
+<meta name="description" content="
 Layout-creating function which summarizes a logistic variable regression for binary outcome with
 categorical/continuous covariates in model statement. For each covariate category (if categorical)
 or specified values (if continuous), present degrees of freedom, regression parameter estimate and
@@ -8,7 +25,8 @@
 to specify other confidence levels. Report p-value for Wald chi-square test of the null hypothesis
 that covariate has no effect on response in model containing all specified covariates.
 Allow option to include one two-way interaction and present similar output for
-each interaction degree of freedom."><meta property="og:description" content="
+each interaction degree of freedom.">
+<meta property="og:description" content="
 Layout-creating function which summarizes a logistic variable regression for binary outcome with
 categorical/continuous covariates in model statement. For each covariate category (if categorical)
 or specified values (if continuous), present degrees of freedom, regression parameter estimate and
@@ -17,7 +35,12 @@
 to specify other confidence levels. Report p-value for Wald chi-square test of the null hypothesis
 that covariate has no effect on response in model containing all specified covariates.
 Allow option to include one two-way interaction and present similar output for
-each interaction degree of freedom."><meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png"><link rel="stylesheet" href="../consent.css"><script src="../consent.js" type="text/javascript" charset="utf-8"></script></head><body>
+each interaction degree of freedom.">
+<meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png">
+<link rel="stylesheet" href="../consent.css">
+<script src="../consent.js" type="text/javascript" charset="utf-8"></script>
+</head>
+<body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
 
 
@@ -33,26 +56,66 @@
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-      <ul class="navbar-nav me-auto"><li class="nav-item"><a class="nav-link" href="../articles/tern.html">Get started</a></li>
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+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
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+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
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+</div>
+</li></div>
+</ul>
+<ul class="navbar-nav">
+<li class="nav-item"><form class="form-inline" role="search">
+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json">
+</form></li>
 <li class="nav-item"><a class="external-link nav-link" href="https://github.com/insightsengineering/tern" aria-label="GitHub"><span class="fa fa-github"></span></a></li>
-      </ul></div>
+      </ul>
+</div>
 
 
   </div>
@@ -78,7 +141,8 @@
     </div>
 
     <div class="section level2">
-    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
+    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">summarize_logistic</span><span class="op">(</span></span>
 <span>  <span class="va">lyt</span>,</span>
 <span>  <span class="va">conf_level</span>,</span>
@@ -88,39 +152,49 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
     </div>
 
     <div class="section level2">
-    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
+    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a>
+</h2>
 
 
-<dl><dt id="arg-lyt">lyt<a class="anchor" aria-label="anchor" href="#arg-lyt"></a></dt>
+<dl>
+<dt id="arg-lyt">lyt<a class="anchor" aria-label="anchor" href="#arg-lyt"></a>
+</dt>
 <dd><p>(<code>PreDataTableLayouts</code>)<br> layout that analyses will be added to.</p></dd>
 
 
-<dt id="arg-conf-level">conf_level<a class="anchor" aria-label="anchor" href="#arg-conf-level"></a></dt>
+<dt id="arg-conf-level">conf_level<a class="anchor" aria-label="anchor" href="#arg-conf-level"></a>
+</dt>
 <dd><p>(<code>proportion</code>)<br> confidence level of the interval.</p></dd>
 
 
-<dt id="arg-drop-and-remove-str">drop_and_remove_str<a class="anchor" aria-label="anchor" href="#arg-drop-and-remove-str"></a></dt>
+<dt id="arg-drop-and-remove-str">drop_and_remove_str<a class="anchor" aria-label="anchor" href="#arg-drop-and-remove-str"></a>
+</dt>
 <dd><p>(<code>string</code>)<br> string to be dropped and removed.</p></dd>
 
 
-<dt id="arg--indent-mods">.indent_mods<a class="anchor" aria-label="anchor" href="#arg--indent-mods"></a></dt>
+<dt id="arg--indent-mods">.indent_mods<a class="anchor" aria-label="anchor" href="#arg--indent-mods"></a>
+</dt>
 <dd><p>(named <code>integer</code>)<br> indent modifiers for the labels. Defaults to 0, which corresponds to the
 unmodified default behavior. Can be negative.</p></dd>
 
-</dl></div>
+</dl>
+</div>
     <div class="section level2">
-    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
+    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a>
+</h2>
     <p>A layout object suitable for passing to further layouting functions, or to <code><a href="https://insightsengineering.github.io/rtables/latest-tag/reference/build_table.html" class="external-link">rtables::build_table()</a></code>.
 Adding this function to an <code>rtable</code> layout will add a logistic regression variable summary to the table layout.</p>
     </div>
     <div class="section level2">
-    <h2 id="note">Note<a class="anchor" aria-label="anchor" href="#note"></a></h2>
+    <h2 id="note">Note<a class="anchor" aria-label="anchor" href="#note"></a>
+</h2>
     <p>For the formula, the variable names need to be standard <code>data.frame</code> column names without
 special characters.</p>
     </div>
 
     <div class="section level2">
-    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
+    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://dplyr.tidyverse.org" class="external-link">dplyr</a></span><span class="op">)</span></span></span>
 <span class="r-in"><span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://broom.tidymodels.org/" class="external-link">broom</a></span><span class="op">)</span></span></span>
 <span class="r-in"><span></span></span>
@@ -215,17 +289,19 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 </code></pre></div>
     </div>
   </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
-    </nav></aside></div>
+    </nav></aside>
+</div>
 
 
     <footer><div class="nest">
   <p>tern is a part of the <strong>NEST</strong> and <a href="https://pharmaverse.org/" class="external-link"><strong>pharmaverse</strong></a>.</p>
 </div>
-<script type="text/javascript" src="../analytics.js"></script></footer></div>
-
+<script type="text/javascript" src="../analytics.js"></script></footer>
+</div>
 
 
 
 
-  </body></html>
 
+  </body>
+</html>
diff --git a/main/reference/summarize_num_patients.html b/main/reference/summarize_num_patients.html
index 331bd6215a..ac31fd65c6 100644
--- a/main/reference/summarize_num_patients.html
+++ b/main/reference/summarize_num_patients.html
@@ -1,5 +1,22 @@
-<!DOCTYPE html>
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+<title>Count number of patients — summarize_num_patients • tern</title>
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+<meta name="description" content="
 The analyze function analyze_num_patients() creates a layout element to count total numbers of unique or
 non-unique patients. The primary analysis variable vars is used to uniquely identify patients.
 The count_by variable can be used to identify non-unique patients such that the number of patients with a unique
@@ -7,7 +24,8 @@
 variable can be used to specify a variable required to be non-missing for the record to be included in the counts.
 The summarize function summarize_num_patients() performs the same function as analyze_num_patients() except it
 creates content rows, not data rows, to summarize the current table row/column context and operates on the level of
-the latest row split or the root of the table if no row splits have occurred."><meta property="og:description" content="
+the latest row split or the root of the table if no row splits have occurred.">
+<meta property="og:description" content="
 The analyze function analyze_num_patients() creates a layout element to count total numbers of unique or
 non-unique patients. The primary analysis variable vars is used to uniquely identify patients.
 The count_by variable can be used to identify non-unique patients such that the number of patients with a unique
@@ -15,7 +33,12 @@
 variable can be used to specify a variable required to be non-missing for the record to be included in the counts.
 The summarize function summarize_num_patients() performs the same function as analyze_num_patients() except it
 creates content rows, not data rows, to summarize the current table row/column context and operates on the level of
-the latest row split or the root of the table if no row splits have occurred."><meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png"><link rel="stylesheet" href="../consent.css"><script src="../consent.js" type="text/javascript" charset="utf-8"></script></head><body>
+the latest row split or the root of the table if no row splits have occurred.">
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@@ -31,26 +54,66 @@
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   </div>
@@ -75,7 +138,8 @@
     </div>
 
     <div class="section level2">
-    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
+    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">analyze_num_patients</span><span class="op">(</span></span>
 <span>  <span class="va">lyt</span>,</span>
 <span>  <span class="va">vars</span>,</span>
@@ -130,115 +194,153 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
     </div>
 
     <div class="section level2">
-    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
+    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a>
+</h2>
 
 
-<dl><dt id="arg-lyt">lyt<a class="anchor" aria-label="anchor" href="#arg-lyt"></a></dt>
+<dl>
+<dt id="arg-lyt">lyt<a class="anchor" aria-label="anchor" href="#arg-lyt"></a>
+</dt>
 <dd><p>(<code>PreDataTableLayouts</code>)<br> layout that analyses will be added to.</p></dd>
 
 
-<dt id="arg-vars">vars<a class="anchor" aria-label="anchor" href="#arg-vars"></a></dt>
+<dt id="arg-vars">vars<a class="anchor" aria-label="anchor" href="#arg-vars"></a>
+</dt>
 <dd><p>(<code>character</code>)<br> variable names for the primary analysis variable to be iterated over.</p></dd>
 
 
-<dt id="arg-required">required<a class="anchor" aria-label="anchor" href="#arg-required"></a></dt>
+<dt id="arg-required">required<a class="anchor" aria-label="anchor" href="#arg-required"></a>
+</dt>
 <dd><p>(<code>character</code> or <code>NULL</code>)<br> name of a variable that is required to be non-missing.</p></dd>
 
 
-<dt id="arg-count-by">count_by<a class="anchor" aria-label="anchor" href="#arg-count-by"></a></dt>
+<dt id="arg-count-by">count_by<a class="anchor" aria-label="anchor" href="#arg-count-by"></a>
+</dt>
 <dd><p>(<code>character</code> or <code>NULL</code>)<br> name of a variable to be combined with <code>vars</code> when counting
 <code>nonunique</code> records.</p></dd>
 
 
-<dt id="arg-unique-count-suffix">unique_count_suffix<a class="anchor" aria-label="anchor" href="#arg-unique-count-suffix"></a></dt>
+<dt id="arg-unique-count-suffix">unique_count_suffix<a class="anchor" aria-label="anchor" href="#arg-unique-count-suffix"></a>
+</dt>
 <dd><p>(<code>flag</code>)<br> whether the <code>"(n)"</code> suffix should be added to <code>unique_count</code> labels.
 Defaults to <code>TRUE</code>.</p></dd>
 
 
-<dt id="arg-na-str">na_str<a class="anchor" aria-label="anchor" href="#arg-na-str"></a></dt>
+<dt id="arg-na-str">na_str<a class="anchor" aria-label="anchor" href="#arg-na-str"></a>
+</dt>
 <dd><p>(<code>string</code>)<br> string used to replace all <code>NA</code> or empty values in the output.</p></dd>
 
 
-<dt id="arg-nested">nested<a class="anchor" aria-label="anchor" href="#arg-nested"></a></dt>
+<dt id="arg-nested">nested<a class="anchor" aria-label="anchor" href="#arg-nested"></a>
+</dt>
 <dd><p>(<code>flag</code>)<br> whether this layout instruction should be applied within the existing layout structure _if
 possible (<code>TRUE</code>, the default) or as a new top-level element (<code>FALSE</code>). Ignored if it would nest a split.
 underneath analyses, which is not allowed.</p></dd>
 
 
-<dt id="arg--stats">.stats<a class="anchor" aria-label="anchor" href="#arg--stats"></a></dt>
-<dd><p>(<code>character</code>)<br> statistics to select for the table.</p>
-<p>Options are: <code>'unique', 'nonunique', 'unique_count'</code></p></dd>
+<dt id="arg--stats">.stats<a class="anchor" aria-label="anchor" href="#arg--stats"></a>
+</dt>
+<dd>
+<p>(<code>character</code>)<br> statistics to select for the table.</p>
+<p>Options are: <code>'unique', 'nonunique', 'unique_count'</code></p>
+</dd>
 
 
-<dt id="arg--formats">.formats<a class="anchor" aria-label="anchor" href="#arg--formats"></a></dt>
+<dt id="arg--formats">.formats<a class="anchor" aria-label="anchor" href="#arg--formats"></a>
+</dt>
 <dd><p>(named <code>character</code> or <code>list</code>)<br> formats for the statistics. See Details in <code>analyze_vars</code> for more
 information on the <code>"auto"</code> setting.</p></dd>
 
 
-<dt id="arg--labels">.labels<a class="anchor" aria-label="anchor" href="#arg--labels"></a></dt>
+<dt id="arg--labels">.labels<a class="anchor" aria-label="anchor" href="#arg--labels"></a>
+</dt>
 <dd><p>(named <code>character</code>)<br> labels for the statistics (without indent).</p></dd>
 
 
-<dt id="arg-show-labels">show_labels<a class="anchor" aria-label="anchor" href="#arg-show-labels"></a></dt>
+<dt id="arg-show-labels">show_labels<a class="anchor" aria-label="anchor" href="#arg-show-labels"></a>
+</dt>
 <dd><p>(<code>string</code>)<br> label visibility: one of "default", "visible" and "hidden".</p></dd>
 
 
-<dt id="arg--indent-mods">.indent_mods<a class="anchor" aria-label="anchor" href="#arg--indent-mods"></a></dt>
+<dt id="arg--indent-mods">.indent_mods<a class="anchor" aria-label="anchor" href="#arg--indent-mods"></a>
+</dt>
 <dd><p>(named <code>integer</code>)<br> indent modifiers for the labels. Defaults to 0, which corresponds to the
 unmodified default behavior. Can be negative.</p></dd>
 
 
-<dt id="arg-riskdiff">riskdiff<a class="anchor" aria-label="anchor" href="#arg-riskdiff"></a></dt>
+<dt id="arg-riskdiff">riskdiff<a class="anchor" aria-label="anchor" href="#arg-riskdiff"></a>
+</dt>
 <dd><p>(<code>flag</code>)<br> whether a risk difference column is present. When set to <code>TRUE</code>, <code><a href="add_riskdiff.html">add_riskdiff()</a></code> must be
 used as <code>split_fun</code> in the prior column split of the table layout, specifying which columns should be compared.
 See <code><a href="stat_propdiff_ci.html">stat_propdiff_ci()</a></code> for details on risk difference calculation.</p></dd>
 
 
-<dt id="arg--">...<a class="anchor" aria-label="anchor" href="#arg--"></a></dt>
+<dt id="arg--">...<a class="anchor" aria-label="anchor" href="#arg--"></a>
+</dt>
 <dd><p>additional arguments for the lower level functions.</p></dd>
 
 
-<dt id="arg-x">x<a class="anchor" aria-label="anchor" href="#arg-x"></a></dt>
+<dt id="arg-x">x<a class="anchor" aria-label="anchor" href="#arg-x"></a>
+</dt>
 <dd><p>(<code>character</code> or <code>factor</code>)<br> vector of patient IDs.</p></dd>
 
 
-<dt id="arg-labelstr">labelstr<a class="anchor" aria-label="anchor" href="#arg-labelstr"></a></dt>
+<dt id="arg-labelstr">labelstr<a class="anchor" aria-label="anchor" href="#arg-labelstr"></a>
+</dt>
 <dd><p>(<code>string</code>)<br> label of the level of the parent split currently being summarized
 (must be present as second argument in Content Row Functions). See <code><a href="https://insightsengineering.github.io/rtables/latest-tag/reference/summarize_row_groups.html" class="external-link">rtables::summarize_row_groups()</a></code>
 for more information.</p></dd>
 
 
-<dt id="arg--n-col">.N_col<a class="anchor" aria-label="anchor" href="#arg--n-col"></a></dt>
+<dt id="arg--n-col">.N_col<a class="anchor" aria-label="anchor" href="#arg--n-col"></a>
+</dt>
 <dd><p>(<code>integer(1)</code>)<br> column-wise N (column count) for the full column being analyzed that is typically
 passed by <code>rtables</code>.</p></dd>
 
 
-<dt id="arg-df">df<a class="anchor" aria-label="anchor" href="#arg-df"></a></dt>
+<dt id="arg-df">df<a class="anchor" aria-label="anchor" href="#arg-df"></a>
+</dt>
 <dd><p>(<code>data.frame</code>)<br> data set containing all analysis variables.</p></dd>
 
 
-<dt id="arg--var-var">.var, var<a class="anchor" aria-label="anchor" href="#arg--var-var"></a></dt>
+<dt id="arg--var-var">.var, var<a class="anchor" aria-label="anchor" href="#arg--var-var"></a>
+</dt>
 <dd><p>(<code>string</code>)<br> single variable name that is passed by <code>rtables</code> when requested
 by a statistics function.</p></dd>
 
-</dl></div>
+</dl>
+</div>
     <div class="section level2">
-    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
+    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a>
+</h2>
 
-<ul><li><p><code>analyze_num_patients()</code> returns a layout object suitable for passing to further layouting functions,
+<ul>
+<li><p><code>analyze_num_patients()</code> returns a layout object suitable for passing to further layouting functions,
 or to <code><a href="https://insightsengineering.github.io/rtables/latest-tag/reference/build_table.html" class="external-link">rtables::build_table()</a></code>. Adding this function to an <code>rtable</code> layout will add formatted rows containing
 the statistics from <code>s_num_patients_content()</code> to the table layout.</p></li>
-</ul><ul><li><p><code>summarize_num_patients()</code> returns a layout object suitable for passing to further layouting functions,
+</ul>
+<ul>
+<li><p><code>summarize_num_patients()</code> returns a layout object suitable for passing to further layouting functions,
 or to <code><a href="https://insightsengineering.github.io/rtables/latest-tag/reference/build_table.html" class="external-link">rtables::build_table()</a></code>. Adding this function to an <code>rtable</code> layout will add formatted rows containing
 the statistics from <code>s_num_patients_content()</code> to the table layout.</p></li>
-</ul><ul><li><p><code>s_num_patients()</code> returns a named <code>list</code> of 3 statistics:</p><ul><li><p><code>unique</code>: Vector of counts and percentages.</p></li>
+</ul>
+<ul>
+<li>
+<p><code>s_num_patients()</code> returns a named <code>list</code> of 3 statistics:</p>
+<ul>
+<li><p><code>unique</code>: Vector of counts and percentages.</p></li>
 <li><p><code>nonunique</code>: Vector of counts.</p></li>
 <li><p><code>unique_count</code>: Counts.</p></li>
-</ul></li>
-</ul><ul><li><p><code>s_num_patients_content()</code> returns the same values as <code>s_num_patients()</code>.</p></li>
-</ul></div>
+</ul>
+</li>
+</ul>
+<ul>
+<li><p><code>s_num_patients_content()</code> returns the same values as <code>s_num_patients()</code>.</p></li>
+</ul>
+</div>
     <div class="section level2">
-    <h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a></h2>
+    <h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a>
+</h2>
     <p>In general, functions that starts with <code>analyze*</code> are expected to
 work like <code><a href="https://insightsengineering.github.io/rtables/latest-tag/reference/analyze.html" class="external-link">rtables::analyze()</a></code>, while functions that starts with <code>summarize*</code>
 are based upon <code><a href="https://insightsengineering.github.io/rtables/latest-tag/reference/summarize_row_groups.html" class="external-link">rtables::summarize_row_groups()</a></code>. The latter provides a
@@ -247,9 +349,11 @@ <h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></
 when pagination is involved.</p>
     </div>
     <div class="section level2">
-    <h2 id="functions">Functions<a class="anchor" aria-label="anchor" href="#functions"></a></h2>
+    <h2 id="functions">Functions<a class="anchor" aria-label="anchor" href="#functions"></a>
+</h2>
 
-<ul><li><p><code>analyze_num_patients()</code>: Layout-creating function which can take statistics function arguments
+<ul>
+<li><p><code>analyze_num_patients()</code>: Layout-creating function which can take statistics function arguments
 and additional format arguments. This function is a wrapper for <code><a href="https://insightsengineering.github.io/rtables/latest-tag/reference/analyze.html" class="external-link">rtables::analyze()</a></code>.</p></li>
 <li><p><code>summarize_num_patients()</code>: Layout-creating function which can take statistics function arguments
 and additional format arguments. This function is a wrapper for <code><a href="https://insightsengineering.github.io/rtables/latest-tag/reference/summarize_row_groups.html" class="external-link">rtables::summarize_row_groups()</a></code>.</p></li>
@@ -259,14 +363,17 @@ <h2 id="functions">Functions<a class="anchor" aria-label="anchor" href="#functio
 <li><p><code>s_num_patients_content()</code>: Statistics function which counts the number of unique patients
 in a column (variable), the corresponding percentage taken with respect to the total number of
 patients, and the number of non-unique patients in the column.</p></li>
-</ul></div>
+</ul>
+</div>
     <div class="section level2">
-    <h2 id="note">Note<a class="anchor" aria-label="anchor" href="#note"></a></h2>
+    <h2 id="note">Note<a class="anchor" aria-label="anchor" href="#note"></a>
+</h2>
     <p>As opposed to <code>summarize_num_patients()</code>, this function does not repeat the produced rows.</p>
     </div>
 
     <div class="section level2">
-    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
+    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">df</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a></span><span class="op">(</span></span></span>
 <span class="r-in"><span>  USUBJID <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/character.html" class="external-link">as.character</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">1</span>, <span class="fl">2</span>, <span class="fl">1</span>, <span class="fl">4</span>, <span class="cn">NA</span>, <span class="fl">6</span>, <span class="fl">6</span>, <span class="fl">8</span>, <span class="fl">9</span><span class="op">)</span><span class="op">)</span>,</span></span>
 <span class="r-in"><span>  ARM <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"A"</span>, <span class="st">"A"</span>, <span class="st">"A"</span>, <span class="st">"A"</span>, <span class="st">"A"</span>, <span class="st">"B"</span>, <span class="st">"B"</span>, <span class="st">"B"</span>, <span class="st">"B"</span><span class="op">)</span>,</span></span>
@@ -386,17 +493,19 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 </code></pre></div>
     </div>
   </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
-    </nav></aside></div>
+    </nav></aside>
+</div>
 
 
     <footer><div class="nest">
   <p>tern is a part of the <strong>NEST</strong> and <a href="https://pharmaverse.org/" class="external-link"><strong>pharmaverse</strong></a>.</p>
 </div>
-<script type="text/javascript" src="../analytics.js"></script></footer></div>
-
+<script type="text/javascript" src="../analytics.js"></script></footer>
+</div>
 
 
 
 
-  </body></html>
 
+  </body>
+</html>
diff --git a/main/reference/summarize_patients_exposure_in_cols.html b/main/reference/summarize_patients_exposure_in_cols.html
index cb8e9abdcc..c01bf66b0c 100644
--- a/main/reference/summarize_patients_exposure_in_cols.html
+++ b/main/reference/summarize_patients_exposure_in_cols.html
@@ -1,5 +1,22 @@
-<!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Count number of patients and sum exposure across all patients in columns — summarize_patients_exposure_in_cols • tern</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Count number of patients and sum exposure across all patients in columns — summarize_patients_exposure_in_cols"><meta name="description" content="
+<html lang="en">
+<head>
+<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+<meta charset="utf-8">
+<meta http-equiv="X-UA-Compatible" content="IE=edge">
+<meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<title>Count number of patients and sum exposure across all patients in columns — summarize_patients_exposure_in_cols • tern</title>
+<!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png">
+<link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png">
+<link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png">
+<link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png">
+<link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png">
+<link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png">
+<script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet">
+<script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet">
+<link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet">
+<script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Count number of patients and sum exposure across all patients in columns — summarize_patients_exposure_in_cols">
+<meta name="description" content="
 The analyze function analyze_patients_exposure_in_cols() creates a layout element to count total numbers of
 patients and sum an analysis value (i.e. exposure) across all patients in columns.
 The primary analysis variable ex_var is the exposure variable used to calculate the sum_exposure statistic. The
@@ -11,7 +28,8 @@
 row/column context and operates on the level of the latest row split or the root of the table if no row splits have
 occurred.
 If a column split has not yet been performed in the table, col_split must be set to TRUE for the first call of
-analyze_patients_exposure_in_cols() or summarize_patients_exposure_in_cols()."><meta property="og:description" content="
+analyze_patients_exposure_in_cols() or summarize_patients_exposure_in_cols().">
+<meta property="og:description" content="
 The analyze function analyze_patients_exposure_in_cols() creates a layout element to count total numbers of
 patients and sum an analysis value (i.e. exposure) across all patients in columns.
 The primary analysis variable ex_var is the exposure variable used to calculate the sum_exposure statistic. The
@@ -23,7 +41,12 @@
 row/column context and operates on the level of the latest row split or the root of the table if no row splits have
 occurred.
 If a column split has not yet been performed in the table, col_split must be set to TRUE for the first call of
-analyze_patients_exposure_in_cols() or summarize_patients_exposure_in_cols()."><meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png"><link rel="stylesheet" href="../consent.css"><script src="../consent.js" type="text/javascript" charset="utf-8"></script></head><body>
+analyze_patients_exposure_in_cols() or summarize_patients_exposure_in_cols().">
+<meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png">
+<link rel="stylesheet" href="../consent.css">
+<script src="../consent.js" type="text/javascript" charset="utf-8"></script>
+</head>
+<body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
 
 
@@ -39,26 +62,66 @@
     </button>
 
     <div id="navbar" class="collapse navbar-collapse ms-3">
-      <ul class="navbar-nav me-auto"><li class="nav-item"><a class="nav-link" href="../articles/tern.html">Get started</a></li>
+      <ul class="navbar-nav me-auto">
+<li class="nav-item"><a class="nav-link" href="../articles/tern.html">Get started</a></li>
 <li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
 <li class="nav-item dropdown">
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-articles" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Articles</button>
-  <ul class="dropdown-menu" aria-labelledby="dropdown-articles"><li><a class="dropdown-item" href="../articles/missing_values.html">Missing Values in Tern</a></li>
+  <ul class="dropdown-menu" aria-labelledby="dropdown-articles">
+<li><a class="dropdown-item" href="../articles/missing_values.html">Missing Values in Tern</a></li>
     <li><a class="dropdown-item" href="../articles/tables.html">Tabulation</a></li>
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     <li><a class="dropdown-item" href="../articles/tern_functions_guide.html">Understanding `tern` functions</a></li>
-  </ul></li>
+  </ul>
+</li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
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+  <ul class="dropdown-menu" aria-labelledby="dropdown-reports">
+<li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
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-      </ul><ul class="navbar-nav"><li class="nav-item"><form class="form-inline" role="search">
- <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json"></form></li>
+  </ul>
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+      <div><li class="nav-item dropdown">
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+    <div class="dropdown-menu" aria-labelledby="dropdown-versions">
+    <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/main">main</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.5">v0.9.5</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.4">v0.9.4</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.3">v0.9.3</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1-rc3">v0.9.1-rc3</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a>
+</div>
+</li></div>
+</ul>
+<ul class="navbar-nav">
+<li class="nav-item"><form class="form-inline" role="search">
+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json">
+</form></li>
 <li class="nav-item"><a class="external-link nav-link" href="https://github.com/insightsengineering/tern" aria-label="GitHub"><span class="fa fa-github"></span></a></li>
-      </ul></div>
+      </ul>
+</div>
 
 
   </div>
@@ -87,7 +150,8 @@
     </div>
 
     <div class="section level2">
-    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
+    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">analyze_patients_exposure_in_cols</span><span class="op">(</span></span>
 <span>  <span class="va">lyt</span>,</span>
 <span>  var <span class="op">=</span> <span class="cn">NULL</span>,</span>
@@ -143,102 +207,138 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
     </div>
 
     <div class="section level2">
-    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
+    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a>
+</h2>
 
 
-<dl><dt id="arg-lyt">lyt<a class="anchor" aria-label="anchor" href="#arg-lyt"></a></dt>
+<dl>
+<dt id="arg-lyt">lyt<a class="anchor" aria-label="anchor" href="#arg-lyt"></a>
+</dt>
 <dd><p>(<code>PreDataTableLayouts</code>)<br> layout that analyses will be added to.</p></dd>
 
 
-<dt id="arg-var">var<a class="anchor" aria-label="anchor" href="#arg-var"></a></dt>
+<dt id="arg-var">var<a class="anchor" aria-label="anchor" href="#arg-var"></a>
+</dt>
 <dd><p>(<code>string</code>)<br> single variable name that is passed by <code>rtables</code> when requested
 by a statistics function.</p></dd>
 
 
-<dt id="arg-ex-var">ex_var<a class="anchor" aria-label="anchor" href="#arg-ex-var"></a></dt>
+<dt id="arg-ex-var">ex_var<a class="anchor" aria-label="anchor" href="#arg-ex-var"></a>
+</dt>
 <dd><p>(<code>string</code>)<br> name of the variable in <code>df</code> containing exposure values.</p></dd>
 
 
-<dt id="arg-id">id<a class="anchor" aria-label="anchor" href="#arg-id"></a></dt>
+<dt id="arg-id">id<a class="anchor" aria-label="anchor" href="#arg-id"></a>
+</dt>
 <dd><p>(<code>string</code>)<br> subject variable name.</p></dd>
 
 
-<dt id="arg-add-total-level">add_total_level<a class="anchor" aria-label="anchor" href="#arg-add-total-level"></a></dt>
+<dt id="arg-add-total-level">add_total_level<a class="anchor" aria-label="anchor" href="#arg-add-total-level"></a>
+</dt>
 <dd><p>(<code>flag</code>)<br> adds a "total" level after the others which includes all the levels
 that constitute the split. A custom label can be set for this level via the <code>custom_label</code> argument.</p></dd>
 
 
-<dt id="arg-custom-label">custom_label<a class="anchor" aria-label="anchor" href="#arg-custom-label"></a></dt>
+<dt id="arg-custom-label">custom_label<a class="anchor" aria-label="anchor" href="#arg-custom-label"></a>
+</dt>
 <dd><p>(<code>string</code> or <code>NULL</code>)<br> if provided and <code>labelstr</code> is empty, this will be used as label.</p></dd>
 
 
-<dt id="arg-col-split">col_split<a class="anchor" aria-label="anchor" href="#arg-col-split"></a></dt>
+<dt id="arg-col-split">col_split<a class="anchor" aria-label="anchor" href="#arg-col-split"></a>
+</dt>
 <dd><p>(<code>flag</code>)<br> whether the columns should be split. Set to <code>FALSE</code> when the required
 column split has been done already earlier in the layout pipe.</p></dd>
 
 
-<dt id="arg-na-str">na_str<a class="anchor" aria-label="anchor" href="#arg-na-str"></a></dt>
+<dt id="arg-na-str">na_str<a class="anchor" aria-label="anchor" href="#arg-na-str"></a>
+</dt>
 <dd><p>(<code>string</code>)<br> string used to replace all <code>NA</code> or empty values in the output.</p></dd>
 
 
-<dt id="arg--stats">.stats<a class="anchor" aria-label="anchor" href="#arg--stats"></a></dt>
-<dd><p>(<code>character</code>)<br> statistics to select for the table.</p>
-<p>Options are: <code>'n_patients', 'sum_exposure'</code></p></dd>
+<dt id="arg--stats">.stats<a class="anchor" aria-label="anchor" href="#arg--stats"></a>
+</dt>
+<dd>
+<p>(<code>character</code>)<br> statistics to select for the table.</p>
+<p>Options are: <code>'n_patients', 'sum_exposure'</code></p>
+</dd>
 
 
-<dt id="arg--labels">.labels<a class="anchor" aria-label="anchor" href="#arg--labels"></a></dt>
+<dt id="arg--labels">.labels<a class="anchor" aria-label="anchor" href="#arg--labels"></a>
+</dt>
 <dd><p>(named <code>character</code>)<br> labels for the statistics (without indent).</p></dd>
 
 
-<dt id="arg--indent-mods">.indent_mods<a class="anchor" aria-label="anchor" href="#arg--indent-mods"></a></dt>
+<dt id="arg--indent-mods">.indent_mods<a class="anchor" aria-label="anchor" href="#arg--indent-mods"></a>
+</dt>
 <dd><p>(named <code>integer</code>)<br> indent modifiers for the labels. Defaults to 0, which corresponds to the
 unmodified default behavior. Can be negative.</p></dd>
 
 
-<dt id="arg--">...<a class="anchor" aria-label="anchor" href="#arg--"></a></dt>
+<dt id="arg--">...<a class="anchor" aria-label="anchor" href="#arg--"></a>
+</dt>
 <dd><p>additional arguments for the lower level functions.</p></dd>
 
 
-<dt id="arg-df">df<a class="anchor" aria-label="anchor" href="#arg-df"></a></dt>
+<dt id="arg-df">df<a class="anchor" aria-label="anchor" href="#arg-df"></a>
+</dt>
 <dd><p>(<code>data.frame</code>)<br> data set containing all analysis variables.</p></dd>
 
 
-<dt id="arg-labelstr">labelstr<a class="anchor" aria-label="anchor" href="#arg-labelstr"></a></dt>
+<dt id="arg-labelstr">labelstr<a class="anchor" aria-label="anchor" href="#arg-labelstr"></a>
+</dt>
 <dd><p>(<code>string</code>)<br> label of the level of the parent split currently being summarized
 (must be present as second argument in Content Row Functions). See <code><a href="https://insightsengineering.github.io/rtables/latest-tag/reference/summarize_row_groups.html" class="external-link">rtables::summarize_row_groups()</a></code>
 for more information.</p></dd>
 
 
-<dt id="arg--n-col">.N_col<a class="anchor" aria-label="anchor" href="#arg--n-col"></a></dt>
+<dt id="arg--n-col">.N_col<a class="anchor" aria-label="anchor" href="#arg--n-col"></a>
+</dt>
 <dd><p>(<code>integer(1)</code>)<br> column-wise N (column count) for the full column being analyzed that is typically
 passed by <code>rtables</code>.</p></dd>
 
 
-<dt id="arg--formats">.formats<a class="anchor" aria-label="anchor" href="#arg--formats"></a></dt>
+<dt id="arg--formats">.formats<a class="anchor" aria-label="anchor" href="#arg--formats"></a>
+</dt>
 <dd><p>(named <code>character</code> or <code>list</code>)<br> formats for the statistics. See Details in <code>analyze_vars</code> for more
 information on the <code>"auto"</code> setting.</p></dd>
 
-</dl></div>
+</dl>
+</div>
     <div class="section level2">
-    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
+    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a>
+</h2>
 
-<ul><li><p><code>analyze_patients_exposure_in_cols()</code> returns a layout object suitable for passing to further
+<ul>
+<li><p><code>analyze_patients_exposure_in_cols()</code> returns a layout object suitable for passing to further
 layouting functions, or to <code><a href="https://insightsengineering.github.io/rtables/latest-tag/reference/build_table.html" class="external-link">rtables::build_table()</a></code>. Adding this function to an <code>rtable</code> layout will
 add formatted data rows, with the statistics from <code>s_count_patients_sum_exposure()</code> arranged in
 columns, to the table layout.</p></li>
-</ul><ul><li><p><code>summarize_patients_exposure_in_cols()</code> returns a layout object suitable for passing to further
+</ul>
+<ul>
+<li><p><code>summarize_patients_exposure_in_cols()</code> returns a layout object suitable for passing to further
 layouting functions, or to <code><a href="https://insightsengineering.github.io/rtables/latest-tag/reference/build_table.html" class="external-link">rtables::build_table()</a></code>. Adding this function to an <code>rtable</code> layout will
 add formatted content rows, with the statistics from <code>s_count_patients_sum_exposure()</code> arranged in
 columns, to the table layout.</p></li>
-</ul><ul><li><p><code>s_count_patients_sum_exposure()</code> returns a named <code>list</code> with the statistics:</p><ul><li><p><code>n_patients</code>: Number of unique patients in <code>df</code>.</p></li>
+</ul>
+<ul>
+<li>
+<p><code>s_count_patients_sum_exposure()</code> returns a named <code>list</code> with the statistics:</p>
+<ul>
+<li><p><code>n_patients</code>: Number of unique patients in <code>df</code>.</p></li>
 <li><p><code>sum_exposure</code>: Sum of <code>ex_var</code> across all patients in <code>df</code>.</p></li>
-</ul></li>
-</ul><ul><li><p><code>a_count_patients_sum_exposure()</code> returns formatted <code><a href="https://insightsengineering.github.io/rtables/latest-tag/reference/CellValue.html" class="external-link">rtables::CellValue()</a></code>.</p></li>
-</ul></div>
+</ul>
+</li>
+</ul>
+<ul>
+<li><p><code>a_count_patients_sum_exposure()</code> returns formatted <code><a href="https://insightsengineering.github.io/rtables/latest-tag/reference/CellValue.html" class="external-link">rtables::CellValue()</a></code>.</p></li>
+</ul>
+</div>
     <div class="section level2">
-    <h2 id="functions">Functions<a class="anchor" aria-label="anchor" href="#functions"></a></h2>
+    <h2 id="functions">Functions<a class="anchor" aria-label="anchor" href="#functions"></a>
+</h2>
 
-<ul><li><p><code>analyze_patients_exposure_in_cols()</code>: Layout-creating function which can take statistics
+<ul>
+<li><p><code>analyze_patients_exposure_in_cols()</code>: Layout-creating function which can take statistics
 function arguments and additional format arguments. This function is a wrapper for
 <code><a href="https://insightsengineering.github.io/rtables/latest-tag/reference/split_cols_by_multivar.html" class="external-link">rtables::split_cols_by_multivar()</a></code> and <code><a href="https://insightsengineering.github.io/rtables/latest-tag/reference/analyze_colvars.html" class="external-link">rtables::analyze_colvars()</a></code>.</p></li>
 <li><p><code>summarize_patients_exposure_in_cols()</code>: Layout-creating function which can take statistics
@@ -249,16 +349,19 @@ <h2 id="functions">Functions<a class="anchor" aria-label="anchor" href="#functio
 <li><p><code>a_count_patients_sum_exposure()</code>: Analysis function which is used as <code>afun</code> in
 <code><a href="https://insightsengineering.github.io/rtables/latest-tag/reference/analyze_colvars.html" class="external-link">rtables::analyze_colvars()</a></code> within <code>analyze_patients_exposure_in_cols()</code> and as <code>cfun</code> in
 <code><a href="https://insightsengineering.github.io/rtables/latest-tag/reference/summarize_row_groups.html" class="external-link">rtables::summarize_row_groups()</a></code> within <code>summarize_patients_exposure_in_cols()</code>.</p></li>
-</ul></div>
+</ul>
+</div>
     <div class="section level2">
-    <h2 id="note">Note<a class="anchor" aria-label="anchor" href="#note"></a></h2>
+    <h2 id="note">Note<a class="anchor" aria-label="anchor" href="#note"></a>
+</h2>
     <p>As opposed to <code>summarize_patients_exposure_in_cols()</code> which generates content rows,
 <code>analyze_patients_exposure_in_cols()</code> generates data rows which will <em>not</em> be repeated on multiple
 pages when pagination is used.</p>
     </div>
 
     <div class="section level2">
-    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
+    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/Random.html" class="external-link">set.seed</a></span><span class="op">(</span><span class="fl">1</span><span class="op">)</span></span></span>
 <span class="r-in"><span><span class="va">df</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a></span><span class="op">(</span></span></span>
 <span class="r-in"><span>  USUBJID <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/paste.html" class="external-link">paste</a></span><span class="op">(</span><span class="st">"id"</span>, <span class="fu"><a href="https://rdrr.io/r/base/seq.html" class="external-link">seq</a></span><span class="op">(</span><span class="fl">1</span>, <span class="fl">12</span><span class="op">)</span>, sep <span class="op">=</span> <span class="st">""</span><span class="op">)</span><span class="op">)</span>,</span></span>
@@ -366,17 +469,19 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 </code></pre></div>
     </div>
   </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
-    </nav></aside></div>
+    </nav></aside>
+</div>
 
 
     <footer><div class="nest">
   <p>tern is a part of the <strong>NEST</strong> and <a href="https://pharmaverse.org/" class="external-link"><strong>pharmaverse</strong></a>.</p>
 </div>
-<script type="text/javascript" src="../analytics.js"></script></footer></div>
-
+<script type="text/javascript" src="../analytics.js"></script></footer>
+</div>
 
 
 
 
-  </body></html>
 
+  </body>
+</html>
diff --git a/main/reference/survival_biomarkers_subgroups.html b/main/reference/survival_biomarkers_subgroups.html
index 0b1b9a51be..2782a7e96e 100644
--- a/main/reference/survival_biomarkers_subgroups.html
+++ b/main/reference/survival_biomarkers_subgroups.html
@@ -1,15 +1,38 @@
-<!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Tabulate biomarker effects on survival by subgroup — survival_biomarkers_subgroups • tern</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Tabulate biomarker effects on survival by subgroup — survival_biomarkers_subgroups"><meta name="description" content="
+<html lang="en">
+<head>
+<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+<meta charset="utf-8">
+<meta http-equiv="X-UA-Compatible" content="IE=edge">
+<meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<title>Tabulate biomarker effects on survival by subgroup — survival_biomarkers_subgroups • tern</title>
+<!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png">
+<link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png">
+<link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png">
+<link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png">
+<link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png">
+<link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png">
+<script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet">
+<script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet">
+<link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet">
+<script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Tabulate biomarker effects on survival by subgroup — survival_biomarkers_subgroups">
+<meta name="description" content="
 The tabulate_survival_biomarkers() function creates a layout element to tabulate the estimated effects of multiple
 continuous biomarker variables on survival across subgroups, returning statistics including median survival time and
 hazard ratio for each population subgroup. The table is created from df, a list of data frames returned by
 extract_survival_biomarkers(), with the statistics to include specified via the vars parameter.
-A forest plot can be created from the resulting table using the g_forest() function."><meta property="og:description" content="
+A forest plot can be created from the resulting table using the g_forest() function.">
+<meta property="og:description" content="
 The tabulate_survival_biomarkers() function creates a layout element to tabulate the estimated effects of multiple
 continuous biomarker variables on survival across subgroups, returning statistics including median survival time and
 hazard ratio for each population subgroup. The table is created from df, a list of data frames returned by
 extract_survival_biomarkers(), with the statistics to include specified via the vars parameter.
-A forest plot can be created from the resulting table using the g_forest() function."><meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png"><link rel="stylesheet" href="../consent.css"><script src="../consent.js" type="text/javascript" charset="utf-8"></script></head><body>
+A forest plot can be created from the resulting table using the g_forest() function.">
+<meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png">
+<link rel="stylesheet" href="../consent.css">
+<script src="../consent.js" type="text/javascript" charset="utf-8"></script>
+</head>
+<body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
 
 
@@ -25,26 +48,66 @@
     </button>
 
     <div id="navbar" class="collapse navbar-collapse ms-3">
-      <ul class="navbar-nav me-auto"><li class="nav-item"><a class="nav-link" href="../articles/tern.html">Get started</a></li>
+      <ul class="navbar-nav me-auto">
+<li class="nav-item"><a class="nav-link" href="../articles/tern.html">Get started</a></li>
 <li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
 <li class="nav-item dropdown">
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-articles" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Articles</button>
-  <ul class="dropdown-menu" aria-labelledby="dropdown-articles"><li><a class="dropdown-item" href="../articles/missing_values.html">Missing Values in Tern</a></li>
+  <ul class="dropdown-menu" aria-labelledby="dropdown-articles">
+<li><a class="dropdown-item" href="../articles/missing_values.html">Missing Values in Tern</a></li>
     <li><a class="dropdown-item" href="../articles/tables.html">Tabulation</a></li>
     <li><a class="dropdown-item" href="../articles/tern_formats.html">Formatting Functions</a></li>
     <li><a class="dropdown-item" href="../articles/tern_functions_guide.html">Understanding `tern` functions</a></li>
-  </ul></li>
+  </ul>
+</li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
-  <ul class="dropdown-menu" aria-labelledby="dropdown-reports"><li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
+  <ul class="dropdown-menu" aria-labelledby="dropdown-reports">
+<li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
     <li><a class="dropdown-item" href="../unit-test-report/">Unit test report</a></li>
     <li><a class="dropdown-item" href="../unit-test-report-non-cran/">Non-CRAN unit test report</a></li>
-  </ul></li>
-      </ul><ul class="navbar-nav"><li class="nav-item"><form class="form-inline" role="search">
- <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json"></form></li>
+  </ul>
+</li>
+      <div><li class="nav-item dropdown">
+    <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-versions">Versions</a>
+    <div class="dropdown-menu" aria-labelledby="dropdown-versions">
+    <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/main">main</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.5">v0.9.5</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.4">v0.9.4</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.3">v0.9.3</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1-rc3">v0.9.1-rc3</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a>
+</div>
+</li></div>
+</ul>
+<ul class="navbar-nav">
+<li class="nav-item"><form class="form-inline" role="search">
+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json">
+</form></li>
 <li class="nav-item"><a class="external-link nav-link" href="https://github.com/insightsengineering/tern" aria-label="GitHub"><span class="fa fa-github"></span></a></li>
-      </ul></div>
+      </ul>
+</div>
 
 
   </div>
@@ -66,7 +129,8 @@
     </div>
 
     <div class="section level2">
-    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
+    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">tabulate_survival_biomarkers</span><span class="op">(</span></span>
 <span>  <span class="va">df</span>,</span>
 <span>  vars <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"n_tot"</span>, <span class="st">"n_tot_events"</span>, <span class="st">"median"</span>, <span class="st">"hr"</span>, <span class="st">"ci"</span>, <span class="st">"pval"</span><span class="op">)</span>,</span>
@@ -80,81 +144,104 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
     </div>
 
     <div class="section level2">
-    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
+    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a>
+</h2>
 
 
-<dl><dt id="arg-df">df<a class="anchor" aria-label="anchor" href="#arg-df"></a></dt>
+<dl>
+<dt id="arg-df">df<a class="anchor" aria-label="anchor" href="#arg-df"></a>
+</dt>
 <dd><p>(<code>data.frame</code>)<br> containing all analysis variables, as returned by
 <code><a href="extract_survival_biomarkers.html">extract_survival_biomarkers()</a></code>.</p></dd>
 
 
-<dt id="arg-vars">vars<a class="anchor" aria-label="anchor" href="#arg-vars"></a></dt>
-<dd><p>(<code>character</code>)<br> the names of statistics to be reported among:</p><ul><li><p><code>n_tot_events</code>: Total number of events per group.</p></li>
+<dt id="arg-vars">vars<a class="anchor" aria-label="anchor" href="#arg-vars"></a>
+</dt>
+<dd>
+<p>(<code>character</code>)<br> the names of statistics to be reported among:</p>
+<ul>
+<li><p><code>n_tot_events</code>: Total number of events per group.</p></li>
 <li><p><code>n_tot</code>: Total number of observations per group.</p></li>
 <li><p><code>median</code>: Median survival time.</p></li>
 <li><p><code>hr</code>: Hazard ratio.</p></li>
 <li><p><code>ci</code>: Confidence interval of hazard ratio.</p></li>
 <li><p><code>pval</code>: p-value of the effect.
 Note, one of the statistics <code>n_tot</code> and <code>n_tot_events</code>, as well as both <code>hr</code> and <code>ci</code> are required.</p></li>
-</ul></dd>
+</ul>
+</dd>
 
 
-<dt id="arg-groups-lists">groups_lists<a class="anchor" aria-label="anchor" href="#arg-groups-lists"></a></dt>
+<dt id="arg-groups-lists">groups_lists<a class="anchor" aria-label="anchor" href="#arg-groups-lists"></a>
+</dt>
 <dd><p>(named <code>list</code> of <code>list</code>)<br> optionally contains for each <code>subgroups</code> variable a
 list, which specifies the new group levels via the names and the
 levels that belong to it in the character vectors that are elements of the list.</p></dd>
 
 
-<dt id="arg-control">control<a class="anchor" aria-label="anchor" href="#arg-control"></a></dt>
+<dt id="arg-control">control<a class="anchor" aria-label="anchor" href="#arg-control"></a>
+</dt>
 <dd><p>(<code>list</code>)<br> a list of parameters as returned by the helper function <code><a href="control_coxreg.html">control_coxreg()</a></code>.</p></dd>
 
 
-<dt id="arg-label-all">label_all<a class="anchor" aria-label="anchor" href="#arg-label-all"></a></dt>
+<dt id="arg-label-all">label_all<a class="anchor" aria-label="anchor" href="#arg-label-all"></a>
+</dt>
 <dd><p><a href="https://lifecycle.r-lib.org/articles/stages.html#deprecated" class="external-link"><img src="figures/lifecycle-deprecated.svg" alt="[Deprecated]"></a><br> please assign the <code>label_all</code> parameter within the
 <code><a href="extract_survival_biomarkers.html">extract_survival_biomarkers()</a></code> function when creating <code>df</code>.</p></dd>
 
 
-<dt id="arg-time-unit">time_unit<a class="anchor" aria-label="anchor" href="#arg-time-unit"></a></dt>
+<dt id="arg-time-unit">time_unit<a class="anchor" aria-label="anchor" href="#arg-time-unit"></a>
+</dt>
 <dd><p>(<code>string</code>)<br> label with unit of median survival time. Default <code>NULL</code> skips displaying unit.</p></dd>
 
 
-<dt id="arg-na-str">na_str<a class="anchor" aria-label="anchor" href="#arg-na-str"></a></dt>
+<dt id="arg-na-str">na_str<a class="anchor" aria-label="anchor" href="#arg-na-str"></a>
+</dt>
 <dd><p>(<code>string</code>)<br> string used to replace all <code>NA</code> or empty values in the output.</p></dd>
 
 
-<dt id="arg--indent-mods">.indent_mods<a class="anchor" aria-label="anchor" href="#arg--indent-mods"></a></dt>
+<dt id="arg--indent-mods">.indent_mods<a class="anchor" aria-label="anchor" href="#arg--indent-mods"></a>
+</dt>
 <dd><p>(named <code>integer</code>)<br> indent modifiers for the labels. Defaults to 0, which corresponds to the
 unmodified default behavior. Can be negative.</p></dd>
 
-</dl></div>
+</dl>
+</div>
     <div class="section level2">
-    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
+    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a>
+</h2>
     <p>An <code>rtables</code> table summarizing biomarker effects on survival by subgroup.</p>
     </div>
     <div class="section level2">
-    <h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a></h2>
+    <h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a>
+</h2>
     <p>These functions create a layout starting from a data frame which contains
 the required statistics. The tables are then typically used as input for forest plots.</p>
     </div>
     <div class="section level2">
-    <h2 id="functions">Functions<a class="anchor" aria-label="anchor" href="#functions"></a></h2>
+    <h2 id="functions">Functions<a class="anchor" aria-label="anchor" href="#functions"></a>
+</h2>
 
-<ul><li><p><code>tabulate_survival_biomarkers()</code>: Table-creating function which creates a table
+<ul>
+<li><p><code>tabulate_survival_biomarkers()</code>: Table-creating function which creates a table
 summarizing biomarker effects on survival by subgroup.</p></li>
-</ul></div>
+</ul>
+</div>
     <div class="section level2">
-    <h2 id="note">Note<a class="anchor" aria-label="anchor" href="#note"></a></h2>
+    <h2 id="note">Note<a class="anchor" aria-label="anchor" href="#note"></a>
+</h2>
     <p>In contrast to <code><a href="survival_duration_subgroups.html">tabulate_survival_subgroups()</a></code> this tabulation function does
 not start from an input layout <code>lyt</code>. This is because internally the table is
 created by combining multiple subtables.</p>
     </div>
     <div class="section level2">
-    <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"></a></h2>
+    <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"></a>
+</h2>
     <div class="dont-index"><p><code><a href="h_survival_biomarkers_subgroups.html">h_tab_surv_one_biomarker()</a></code> which is used internally, <code><a href="extract_survival_biomarkers.html">extract_survival_biomarkers()</a></code>.</p></div>
     </div>
 
     <div class="section level2">
-    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
+    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://dplyr.tidyverse.org" class="external-link">dplyr</a></span><span class="op">)</span></span></span>
 <span class="r-in"><span></span></span>
 <span class="r-in"><span><span class="va">adtte</span> <span class="op">&lt;-</span> <span class="va">tern_ex_adtte</span></span></span>
@@ -298,17 +385,19 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 </code></pre></div>
     </div>
   </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
-    </nav></aside></div>
+    </nav></aside>
+</div>
 
 
     <footer><div class="nest">
   <p>tern is a part of the <strong>NEST</strong> and <a href="https://pharmaverse.org/" class="external-link"><strong>pharmaverse</strong></a>.</p>
 </div>
-<script type="text/javascript" src="../analytics.js"></script></footer></div>
-
+<script type="text/javascript" src="../analytics.js"></script></footer>
+</div>
 
 
 
 
-  </body></html>
 
+  </body>
+</html>
diff --git a/main/reference/survival_coxph_pairwise.html b/main/reference/survival_coxph_pairwise.html
index 56bc1d111d..5aec7d56a3 100644
--- a/main/reference/survival_coxph_pairwise.html
+++ b/main/reference/survival_coxph_pairwise.html
@@ -1,13 +1,36 @@
-<!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Analyze a pairwise Cox-PH model — survival_coxph_pairwise • tern</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Analyze a pairwise Cox-PH model — survival_coxph_pairwise"><meta name="description" content="
+<html lang="en">
+<head>
+<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+<meta charset="utf-8">
+<meta http-equiv="X-UA-Compatible" content="IE=edge">
+<meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<title>Analyze a pairwise Cox-PH model — survival_coxph_pairwise • tern</title>
+<!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png">
+<link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png">
+<link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png">
+<link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png">
+<link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png">
+<link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png">
+<script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet">
+<script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet">
+<link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet">
+<script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Analyze a pairwise Cox-PH model — survival_coxph_pairwise">
+<meta name="description" content="
 The analyze function coxph_pairwise() creates a layout element to analyze a pairwise Cox-PH model.
 This function can return statistics including p-value, hazard ratio (HR), and HR confidence intervals from both
 stratified and unstratified Cox-PH models. The variable(s) to be analyzed is specified via the vars argument and
-any stratification factors via the strata argument."><meta property="og:description" content="
+any stratification factors via the strata argument.">
+<meta property="og:description" content="
 The analyze function coxph_pairwise() creates a layout element to analyze a pairwise Cox-PH model.
 This function can return statistics including p-value, hazard ratio (HR), and HR confidence intervals from both
 stratified and unstratified Cox-PH models. The variable(s) to be analyzed is specified via the vars argument and
-any stratification factors via the strata argument."><meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png"><link rel="stylesheet" href="../consent.css"><script src="../consent.js" type="text/javascript" charset="utf-8"></script></head><body>
+any stratification factors via the strata argument.">
+<meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png">
+<link rel="stylesheet" href="../consent.css">
+<script src="../consent.js" type="text/javascript" charset="utf-8"></script>
+</head>
+<body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
 
 
@@ -23,26 +46,66 @@
     </button>
 
     <div id="navbar" class="collapse navbar-collapse ms-3">
-      <ul class="navbar-nav me-auto"><li class="nav-item"><a class="nav-link" href="../articles/tern.html">Get started</a></li>
+      <ul class="navbar-nav me-auto">
+<li class="nav-item"><a class="nav-link" href="../articles/tern.html">Get started</a></li>
 <li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
 <li class="nav-item dropdown">
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-articles" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Articles</button>
-  <ul class="dropdown-menu" aria-labelledby="dropdown-articles"><li><a class="dropdown-item" href="../articles/missing_values.html">Missing Values in Tern</a></li>
+  <ul class="dropdown-menu" aria-labelledby="dropdown-articles">
+<li><a class="dropdown-item" href="../articles/missing_values.html">Missing Values in Tern</a></li>
     <li><a class="dropdown-item" href="../articles/tables.html">Tabulation</a></li>
     <li><a class="dropdown-item" href="../articles/tern_formats.html">Formatting Functions</a></li>
     <li><a class="dropdown-item" href="../articles/tern_functions_guide.html">Understanding `tern` functions</a></li>
-  </ul></li>
+  </ul>
+</li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
-  <ul class="dropdown-menu" aria-labelledby="dropdown-reports"><li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
+  <ul class="dropdown-menu" aria-labelledby="dropdown-reports">
+<li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
     <li><a class="dropdown-item" href="../unit-test-report/">Unit test report</a></li>
     <li><a class="dropdown-item" href="../unit-test-report-non-cran/">Non-CRAN unit test report</a></li>
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- <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json"></form></li>
+  </ul>
+</li>
+      <div><li class="nav-item dropdown">
+    <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-versions">Versions</a>
+    <div class="dropdown-menu" aria-labelledby="dropdown-versions">
+    <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/main">main</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.5">v0.9.5</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.4">v0.9.4</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.3">v0.9.3</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1-rc3">v0.9.1-rc3</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a>
+</div>
+</li></div>
+</ul>
+<ul class="navbar-nav">
+<li class="nav-item"><form class="form-inline" role="search">
+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json">
+</form></li>
 <li class="nav-item"><a class="external-link nav-link" href="https://github.com/insightsengineering/tern" aria-label="GitHub"><span class="fa fa-github"></span></a></li>
-      </ul></div>
+      </ul>
+</div>
 
 
   </div>
@@ -63,7 +126,8 @@
     </div>
 
     <div class="section level2">
-    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
+    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">coxph_pairwise</span><span class="op">(</span></span>
 <span>  <span class="va">lyt</span>,</span>
 <span>  <span class="va">vars</span>,</span>
@@ -105,128 +169,172 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
     </div>
 
     <div class="section level2">
-    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
+    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a>
+</h2>
 
 
-<dl><dt id="arg-lyt">lyt<a class="anchor" aria-label="anchor" href="#arg-lyt"></a></dt>
+<dl>
+<dt id="arg-lyt">lyt<a class="anchor" aria-label="anchor" href="#arg-lyt"></a>
+</dt>
 <dd><p>(<code>PreDataTableLayouts</code>)<br> layout that analyses will be added to.</p></dd>
 
 
-<dt id="arg-vars">vars<a class="anchor" aria-label="anchor" href="#arg-vars"></a></dt>
+<dt id="arg-vars">vars<a class="anchor" aria-label="anchor" href="#arg-vars"></a>
+</dt>
 <dd><p>(<code>character</code>)<br> variable names for the primary analysis variable to be iterated over.</p></dd>
 
 
-<dt id="arg-strata">strata<a class="anchor" aria-label="anchor" href="#arg-strata"></a></dt>
+<dt id="arg-strata">strata<a class="anchor" aria-label="anchor" href="#arg-strata"></a>
+</dt>
 <dd><p>(<code>character</code> or <code>NULL</code>)<br> variable names indicating stratification factors.</p></dd>
 
 
-<dt id="arg-control">control<a class="anchor" aria-label="anchor" href="#arg-control"></a></dt>
-<dd><p>(<code>list</code>)<br> parameters for comparison details, specified by using the helper function
-<code><a href="control_coxph.html">control_coxph()</a></code>. Some possible parameter options are:</p><ul><li><p><code>pval_method</code> (<code>string</code>)<br> p-value method for testing the null hypothesis that hazard ratio = 1. Default
+<dt id="arg-control">control<a class="anchor" aria-label="anchor" href="#arg-control"></a>
+</dt>
+<dd>
+<p>(<code>list</code>)<br> parameters for comparison details, specified by using the helper function
+<code><a href="control_coxph.html">control_coxph()</a></code>. Some possible parameter options are:</p>
+<ul>
+<li><p><code>pval_method</code> (<code>string</code>)<br> p-value method for testing the null hypothesis that hazard ratio = 1. Default
 method is <code>"log-rank"</code> which comes from <code><a href="https://rdrr.io/pkg/survival/man/survdiff.html" class="external-link">survival::survdiff()</a></code>, can also be set to <code>"wald"</code> or <code>"likelihood"</code>
 (from <code><a href="https://rdrr.io/pkg/survival/man/coxph.html" class="external-link">survival::coxph()</a></code>).</p></li>
 <li><p><code>ties</code> (<code>string</code>)<br> specifying the method for tie handling. Default is <code>"efron"</code>,
 can also be set to <code>"breslow"</code> or <code>"exact"</code>. See more in <code><a href="https://rdrr.io/pkg/survival/man/coxph.html" class="external-link">survival::coxph()</a></code>.</p></li>
 <li><p><code>conf_level</code> (<code>proportion</code>)<br> confidence level of the interval for HR.</p></li>
-</ul></dd>
+</ul>
+</dd>
 
 
-<dt id="arg-na-str">na_str<a class="anchor" aria-label="anchor" href="#arg-na-str"></a></dt>
+<dt id="arg-na-str">na_str<a class="anchor" aria-label="anchor" href="#arg-na-str"></a>
+</dt>
 <dd><p>(<code>string</code>)<br> string used to replace all <code>NA</code> or empty values in the output.</p></dd>
 
 
-<dt id="arg-nested">nested<a class="anchor" aria-label="anchor" href="#arg-nested"></a></dt>
+<dt id="arg-nested">nested<a class="anchor" aria-label="anchor" href="#arg-nested"></a>
+</dt>
 <dd><p>(<code>flag</code>)<br> whether this layout instruction should be applied within the existing layout structure _if
 possible (<code>TRUE</code>, the default) or as a new top-level element (<code>FALSE</code>). Ignored if it would nest a split.
 underneath analyses, which is not allowed.</p></dd>
 
 
-<dt id="arg--">...<a class="anchor" aria-label="anchor" href="#arg--"></a></dt>
+<dt id="arg--">...<a class="anchor" aria-label="anchor" href="#arg--"></a>
+</dt>
 <dd><p>additional arguments for the lower level functions.</p></dd>
 
 
-<dt id="arg-var-labels">var_labels<a class="anchor" aria-label="anchor" href="#arg-var-labels"></a></dt>
+<dt id="arg-var-labels">var_labels<a class="anchor" aria-label="anchor" href="#arg-var-labels"></a>
+</dt>
 <dd><p>(<code>character</code>)<br> variable labels.</p></dd>
 
 
-<dt id="arg-show-labels">show_labels<a class="anchor" aria-label="anchor" href="#arg-show-labels"></a></dt>
+<dt id="arg-show-labels">show_labels<a class="anchor" aria-label="anchor" href="#arg-show-labels"></a>
+</dt>
 <dd><p>(<code>string</code>)<br> label visibility: one of "default", "visible" and "hidden".</p></dd>
 
 
-<dt id="arg-table-names">table_names<a class="anchor" aria-label="anchor" href="#arg-table-names"></a></dt>
+<dt id="arg-table-names">table_names<a class="anchor" aria-label="anchor" href="#arg-table-names"></a>
+</dt>
 <dd><p>(<code>character</code>)<br> this can be customized in the case that the same <code>vars</code> are analyzed multiple
 times, to avoid warnings from <code>rtables</code>.</p></dd>
 
 
-<dt id="arg--stats">.stats<a class="anchor" aria-label="anchor" href="#arg--stats"></a></dt>
-<dd><p>(<code>character</code>)<br> statistics to select for the table.</p>
-<p>Options are: <code>'pvalue', 'hr', 'hr_ci', 'n_tot', 'n_tot_events'</code></p></dd>
+<dt id="arg--stats">.stats<a class="anchor" aria-label="anchor" href="#arg--stats"></a>
+</dt>
+<dd>
+<p>(<code>character</code>)<br> statistics to select for the table.</p>
+<p>Options are: <code>'pvalue', 'hr', 'hr_ci', 'n_tot', 'n_tot_events'</code></p>
+</dd>
 
 
-<dt id="arg--formats">.formats<a class="anchor" aria-label="anchor" href="#arg--formats"></a></dt>
+<dt id="arg--formats">.formats<a class="anchor" aria-label="anchor" href="#arg--formats"></a>
+</dt>
 <dd><p>(named <code>character</code> or <code>list</code>)<br> formats for the statistics. See Details in <code>analyze_vars</code> for more
 information on the <code>"auto"</code> setting.</p></dd>
 
 
-<dt id="arg--labels">.labels<a class="anchor" aria-label="anchor" href="#arg--labels"></a></dt>
+<dt id="arg--labels">.labels<a class="anchor" aria-label="anchor" href="#arg--labels"></a>
+</dt>
 <dd><p>(named <code>character</code>)<br> labels for the statistics (without indent).</p></dd>
 
 
-<dt id="arg--indent-mods">.indent_mods<a class="anchor" aria-label="anchor" href="#arg--indent-mods"></a></dt>
+<dt id="arg--indent-mods">.indent_mods<a class="anchor" aria-label="anchor" href="#arg--indent-mods"></a>
+</dt>
 <dd><p>(named <code>integer</code>)<br> indent modifiers for the labels. Defaults to 0, which corresponds to the
 unmodified default behavior. Can be negative.</p></dd>
 
 
-<dt id="arg-df">df<a class="anchor" aria-label="anchor" href="#arg-df"></a></dt>
+<dt id="arg-df">df<a class="anchor" aria-label="anchor" href="#arg-df"></a>
+</dt>
 <dd><p>(<code>data.frame</code>)<br> data set containing all analysis variables.</p></dd>
 
 
-<dt id="arg--ref-group">.ref_group<a class="anchor" aria-label="anchor" href="#arg--ref-group"></a></dt>
+<dt id="arg--ref-group">.ref_group<a class="anchor" aria-label="anchor" href="#arg--ref-group"></a>
+</dt>
 <dd><p>(<code>data.frame</code> or <code>vector</code>)<br> the data corresponding to the reference group.</p></dd>
 
 
-<dt id="arg--in-ref-col">.in_ref_col<a class="anchor" aria-label="anchor" href="#arg--in-ref-col"></a></dt>
+<dt id="arg--in-ref-col">.in_ref_col<a class="anchor" aria-label="anchor" href="#arg--in-ref-col"></a>
+</dt>
 <dd><p>(<code>flag</code>)<br><code>TRUE</code> when working with the reference level, <code>FALSE</code> otherwise.</p></dd>
 
 
-<dt id="arg--var">.var<a class="anchor" aria-label="anchor" href="#arg--var"></a></dt>
+<dt id="arg--var">.var<a class="anchor" aria-label="anchor" href="#arg--var"></a>
+</dt>
 <dd><p>(<code>string</code>)<br> single variable name that is passed by <code>rtables</code> when requested
 by a statistics function.</p></dd>
 
 
-<dt id="arg-is-event">is_event<a class="anchor" aria-label="anchor" href="#arg-is-event"></a></dt>
+<dt id="arg-is-event">is_event<a class="anchor" aria-label="anchor" href="#arg-is-event"></a>
+</dt>
 <dd><p>(<code>flag</code>)<br><code>TRUE</code> if event, <code>FALSE</code> if time to event is censored.</p></dd>
 
 
-<dt id="arg-strat">strat<a class="anchor" aria-label="anchor" href="#arg-strat"></a></dt>
+<dt id="arg-strat">strat<a class="anchor" aria-label="anchor" href="#arg-strat"></a>
+</dt>
 <dd><p><a href="https://lifecycle.r-lib.org/articles/stages.html#deprecated" class="external-link"><img src="figures/lifecycle-deprecated.svg" alt="[Deprecated]"></a> Please use the <code>strata</code> argument instead.</p></dd>
 
-</dl></div>
+</dl>
+</div>
     <div class="section level2">
-    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
+    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a>
+</h2>
 
-<ul><li><p><code>coxph_pairwise()</code> returns a layout object suitable for passing to further layouting functions,
+<ul>
+<li><p><code>coxph_pairwise()</code> returns a layout object suitable for passing to further layouting functions,
 or to <code><a href="https://insightsengineering.github.io/rtables/latest-tag/reference/build_table.html" class="external-link">rtables::build_table()</a></code>. Adding this function to an <code>rtable</code> layout will add formatted rows containing
 the statistics from <code>s_coxph_pairwise()</code> to the table layout.</p></li>
-</ul><ul><li><p><code>s_coxph_pairwise()</code> returns the statistics:</p><ul><li><p><code>pvalue</code>: p-value to test the null hypothesis that hazard ratio = 1.</p></li>
+</ul>
+<ul>
+<li>
+<p><code>s_coxph_pairwise()</code> returns the statistics:</p>
+<ul>
+<li><p><code>pvalue</code>: p-value to test the null hypothesis that hazard ratio = 1.</p></li>
 <li><p><code>hr</code>: Hazard ratio.</p></li>
 <li><p><code>hr_ci</code>: Confidence interval for hazard ratio.</p></li>
 <li><p><code>n_tot</code>: Total number of observations.</p></li>
 <li><p><code>n_tot_events</code>: Total number of events.</p></li>
-</ul></li>
-</ul><ul><li><p><code>a_coxph_pairwise()</code> returns the corresponding list with formatted <code><a href="https://insightsengineering.github.io/rtables/latest-tag/reference/CellValue.html" class="external-link">rtables::CellValue()</a></code>.</p></li>
-</ul></div>
+</ul>
+</li>
+</ul>
+<ul>
+<li><p><code>a_coxph_pairwise()</code> returns the corresponding list with formatted <code><a href="https://insightsengineering.github.io/rtables/latest-tag/reference/CellValue.html" class="external-link">rtables::CellValue()</a></code>.</p></li>
+</ul>
+</div>
     <div class="section level2">
-    <h2 id="functions">Functions<a class="anchor" aria-label="anchor" href="#functions"></a></h2>
+    <h2 id="functions">Functions<a class="anchor" aria-label="anchor" href="#functions"></a>
+</h2>
 
-<ul><li><p><code>coxph_pairwise()</code>: Layout-creating function which can take statistics function arguments
+<ul>
+<li><p><code>coxph_pairwise()</code>: Layout-creating function which can take statistics function arguments
 and additional format arguments. This function is a wrapper for <code><a href="https://insightsengineering.github.io/rtables/latest-tag/reference/analyze.html" class="external-link">rtables::analyze()</a></code>.</p></li>
 <li><p><code>s_coxph_pairwise()</code>: Statistics function which analyzes HR, CIs of HR, and p-value of a Cox-PH model.</p></li>
 <li><p><code>a_coxph_pairwise()</code>: Formatted analysis function which is used as <code>afun</code> in <code>coxph_pairwise()</code>.</p></li>
-</ul></div>
+</ul>
+</div>
 
     <div class="section level2">
-    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
+    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://dplyr.tidyverse.org" class="external-link">dplyr</a></span><span class="op">)</span></span></span>
 <span class="r-in"><span></span></span>
 <span class="r-in"><span><span class="va">adtte_f</span> <span class="op">&lt;-</span> <span class="va">tern_ex_adtte</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span></span>
@@ -275,17 +383,19 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 </code></pre></div>
     </div>
   </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
-    </nav></aside></div>
+    </nav></aside>
+</div>
 
 
     <footer><div class="nest">
   <p>tern is a part of the <strong>NEST</strong> and <a href="https://pharmaverse.org/" class="external-link"><strong>pharmaverse</strong></a>.</p>
 </div>
-<script type="text/javascript" src="../analytics.js"></script></footer></div>
-
+<script type="text/javascript" src="../analytics.js"></script></footer>
+</div>
 
 
 
 
-  </body></html>
 
+  </body>
+</html>
diff --git a/main/reference/survival_duration_subgroups.html b/main/reference/survival_duration_subgroups.html
index 1bba7b4019..8eeb04dad4 100644
--- a/main/reference/survival_duration_subgroups.html
+++ b/main/reference/survival_duration_subgroups.html
@@ -1,15 +1,38 @@
-<!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Tabulate survival duration by subgroup — survival_duration_subgroups • tern</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Tabulate survival duration by subgroup — survival_duration_subgroups"><meta name="description" content="
+<html lang="en">
+<head>
+<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+<meta charset="utf-8">
+<meta http-equiv="X-UA-Compatible" content="IE=edge">
+<meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<title>Tabulate survival duration by subgroup — survival_duration_subgroups • tern</title>
+<!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png">
+<link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png">
+<link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png">
+<link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png">
+<link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png">
+<link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png">
+<script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet">
+<script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet">
+<link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet">
+<script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Tabulate survival duration by subgroup — survival_duration_subgroups">
+<meta name="description" content="
 The tabulate_survival_subgroups() function creates a layout element to tabulate survival duration by subgroup,
 returning statistics including median survival time and hazard ratio for each population subgroup. The table is
 created from df, a list of data frames returned by extract_survival_subgroups(), with the statistics to include
 specified via the vars parameter.
-A forest plot can be created from the resulting table using the g_forest() function."><meta property="og:description" content="
+A forest plot can be created from the resulting table using the g_forest() function.">
+<meta property="og:description" content="
 The tabulate_survival_subgroups() function creates a layout element to tabulate survival duration by subgroup,
 returning statistics including median survival time and hazard ratio for each population subgroup. The table is
 created from df, a list of data frames returned by extract_survival_subgroups(), with the statistics to include
 specified via the vars parameter.
-A forest plot can be created from the resulting table using the g_forest() function."><meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png"><link rel="stylesheet" href="../consent.css"><script src="../consent.js" type="text/javascript" charset="utf-8"></script></head><body>
+A forest plot can be created from the resulting table using the g_forest() function.">
+<meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png">
+<link rel="stylesheet" href="../consent.css">
+<script src="../consent.js" type="text/javascript" charset="utf-8"></script>
+</head>
+<body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
 
 
@@ -25,26 +48,66 @@
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-      <ul class="navbar-nav me-auto"><li class="nav-item"><a class="nav-link" href="../articles/tern.html">Get started</a></li>
+      <ul class="navbar-nav me-auto">
+<li class="nav-item"><a class="nav-link" href="../articles/tern.html">Get started</a></li>
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-  <ul class="dropdown-menu" aria-labelledby="dropdown-articles"><li><a class="dropdown-item" href="../articles/missing_values.html">Missing Values in Tern</a></li>
+  <ul class="dropdown-menu" aria-labelledby="dropdown-articles">
+<li><a class="dropdown-item" href="../articles/missing_values.html">Missing Values in Tern</a></li>
     <li><a class="dropdown-item" href="../articles/tables.html">Tabulation</a></li>
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     <li><a class="dropdown-item" href="../articles/tern_functions_guide.html">Understanding `tern` functions</a></li>
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+  </ul>
+</li>
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+  <ul class="dropdown-menu" aria-labelledby="dropdown-reports">
+<li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
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- <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json"></form></li>
+  </ul>
+</li>
+      <div><li class="nav-item dropdown">
+    <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-versions">Versions</a>
+    <div class="dropdown-menu" aria-labelledby="dropdown-versions">
+    <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/main">main</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.5">v0.9.5</a>
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+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.3">v0.9.3</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
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+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
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+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
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+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a>
+</div>
+</li></div>
+</ul>
+<ul class="navbar-nav">
+<li class="nav-item"><form class="form-inline" role="search">
+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json">
+</form></li>
 <li class="nav-item"><a class="external-link nav-link" href="https://github.com/insightsengineering/tern" aria-label="GitHub"><span class="fa fa-github"></span></a></li>
-      </ul></div>
+      </ul>
+</div>
 
 
   </div>
@@ -66,7 +129,8 @@
     </div>
 
     <div class="section level2">
-    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
+    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">tabulate_survival_subgroups</span><span class="op">(</span></span>
 <span>  <span class="va">lyt</span>,</span>
 <span>  <span class="va">df</span>,</span>
@@ -90,20 +154,28 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
     </div>
 
     <div class="section level2">
-    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
+    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a>
+</h2>
 
 
-<dl><dt id="arg-lyt">lyt<a class="anchor" aria-label="anchor" href="#arg-lyt"></a></dt>
+<dl>
+<dt id="arg-lyt">lyt<a class="anchor" aria-label="anchor" href="#arg-lyt"></a>
+</dt>
 <dd><p>(<code>PreDataTableLayouts</code>)<br> layout that analyses will be added to.</p></dd>
 
 
-<dt id="arg-df">df<a class="anchor" aria-label="anchor" href="#arg-df"></a></dt>
+<dt id="arg-df">df<a class="anchor" aria-label="anchor" href="#arg-df"></a>
+</dt>
 <dd><p>(<code>list</code>)<br> list of data frames containing all analysis variables. List should be
 created using <code><a href="extract_survival_subgroups.html">extract_survival_subgroups()</a></code>.</p></dd>
 
 
-<dt id="arg-vars">vars<a class="anchor" aria-label="anchor" href="#arg-vars"></a></dt>
-<dd><p>(<code>character</code>)<br> the names of statistics to be reported among:</p><ul><li><p><code>n_tot_events</code>: Total number of events per group.</p></li>
+<dt id="arg-vars">vars<a class="anchor" aria-label="anchor" href="#arg-vars"></a>
+</dt>
+<dd>
+<p>(<code>character</code>)<br> the names of statistics to be reported among:</p>
+<ul>
+<li><p><code>n_tot_events</code>: Total number of events per group.</p></li>
 <li><p><code>n_events</code>: Number of events per group.</p></li>
 <li><p><code>n_tot</code>: Total number of observations per group.</p></li>
 <li><p><code>n</code>: Number of observations per group.</p></li>
@@ -113,66 +185,83 @@ <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#argumen
 <li><p><code>pval</code>: p-value of the effect.
 Note, one of the statistics <code>n_tot</code> and <code>n_tot_events</code>, as well as both <code>hr</code> and <code>ci</code>
 are required.</p></li>
-</ul></dd>
+</ul>
+</dd>
 
 
-<dt id="arg-groups-lists">groups_lists<a class="anchor" aria-label="anchor" href="#arg-groups-lists"></a></dt>
+<dt id="arg-groups-lists">groups_lists<a class="anchor" aria-label="anchor" href="#arg-groups-lists"></a>
+</dt>
 <dd><p>(named <code>list</code> of <code>list</code>)<br> optionally contains for each <code>subgroups</code> variable a
 list, which specifies the new group levels via the names and the
 levels that belong to it in the character vectors that are elements of the list.</p></dd>
 
 
-<dt id="arg-label-all">label_all<a class="anchor" aria-label="anchor" href="#arg-label-all"></a></dt>
+<dt id="arg-label-all">label_all<a class="anchor" aria-label="anchor" href="#arg-label-all"></a>
+</dt>
 <dd><p><a href="https://lifecycle.r-lib.org/articles/stages.html#deprecated" class="external-link"><img src="figures/lifecycle-deprecated.svg" alt="[Deprecated]"></a><br> please assign the <code>label_all</code> parameter within the
 <code><a href="extract_survival_subgroups.html">extract_survival_subgroups()</a></code> function when creating <code>df</code>.</p></dd>
 
 
-<dt id="arg-time-unit">time_unit<a class="anchor" aria-label="anchor" href="#arg-time-unit"></a></dt>
+<dt id="arg-time-unit">time_unit<a class="anchor" aria-label="anchor" href="#arg-time-unit"></a>
+</dt>
 <dd><p>(<code>string</code>)<br> label with unit of median survival time. Default <code>NULL</code> skips displaying unit.</p></dd>
 
 
-<dt id="arg-riskdiff">riskdiff<a class="anchor" aria-label="anchor" href="#arg-riskdiff"></a></dt>
+<dt id="arg-riskdiff">riskdiff<a class="anchor" aria-label="anchor" href="#arg-riskdiff"></a>
+</dt>
 <dd><p>(<code>list</code>)<br> if a risk (proportion) difference column should be added, a list of settings to apply
 within the column. See <code><a href="control_riskdiff.html">control_riskdiff()</a></code> for details. If <code>NULL</code>, no risk difference column will be added. If
 <code>riskdiff$arm_x</code> and <code>riskdiff$arm_y</code> are <code>NULL</code>, the first level of <code>df$survtime$arm</code> will be used as <code>arm_x</code>
 and the second level as <code>arm_y</code>.</p></dd>
 
 
-<dt id="arg-na-str">na_str<a class="anchor" aria-label="anchor" href="#arg-na-str"></a></dt>
+<dt id="arg-na-str">na_str<a class="anchor" aria-label="anchor" href="#arg-na-str"></a>
+</dt>
 <dd><p>(<code>string</code>)<br> string used to replace all <code>NA</code> or empty values in the output.</p></dd>
 
 
-<dt id="arg--formats">.formats<a class="anchor" aria-label="anchor" href="#arg--formats"></a></dt>
+<dt id="arg--formats">.formats<a class="anchor" aria-label="anchor" href="#arg--formats"></a>
+</dt>
 <dd><p>(named <code>character</code> or <code>list</code>)<br> formats for the statistics. See Details in <code>analyze_vars</code> for more
 information on the <code>"auto"</code> setting.</p></dd>
 
-</dl></div>
+</dl>
+</div>
     <div class="section level2">
-    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
+    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a>
+</h2>
     <p>An <code>rtables</code> table summarizing survival by subgroup.</p>
-<ul><li><p><code>a_survival_subgroups()</code> returns the corresponding list with formatted <code><a href="https://insightsengineering.github.io/rtables/latest-tag/reference/CellValue.html" class="external-link">rtables::CellValue()</a></code>.</p></li>
-</ul></div>
+<ul>
+<li><p><code>a_survival_subgroups()</code> returns the corresponding list with formatted <code><a href="https://insightsengineering.github.io/rtables/latest-tag/reference/CellValue.html" class="external-link">rtables::CellValue()</a></code>.</p></li>
+</ul>
+</div>
     <div class="section level2">
-    <h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a></h2>
+    <h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a>
+</h2>
     <p>These functions create a layout starting from a data frame which contains
 the required statistics. Tables typically used as part of forest plot.</p>
     </div>
     <div class="section level2">
-    <h2 id="functions">Functions<a class="anchor" aria-label="anchor" href="#functions"></a></h2>
+    <h2 id="functions">Functions<a class="anchor" aria-label="anchor" href="#functions"></a>
+</h2>
 
-<ul><li><p><code>tabulate_survival_subgroups()</code>: Table-creating function which creates a table
+<ul>
+<li><p><code>tabulate_survival_subgroups()</code>: Table-creating function which creates a table
 summarizing survival by subgroup. This function is a wrapper for <code><a href="https://insightsengineering.github.io/rtables/latest-tag/reference/analyze_colvars.html" class="external-link">rtables::analyze_colvars()</a></code>
 and <code><a href="https://insightsengineering.github.io/rtables/latest-tag/reference/summarize_row_groups.html" class="external-link">rtables::summarize_row_groups()</a></code>.</p></li>
 <li><p><code>a_survival_subgroups()</code>: Formatted analysis function which is used as
 <code>afun</code> in <code>tabulate_survival_subgroups()</code>.</p></li>
-</ul></div>
+</ul>
+</div>
     <div class="section level2">
-    <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"></a></h2>
+    <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"></a>
+</h2>
     <div class="dont-index"><p><code><a href="extract_survival_subgroups.html">extract_survival_subgroups()</a></code></p></div>
     </div>
 
     <div class="section level2">
-    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
+    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://dplyr.tidyverse.org" class="external-link">dplyr</a></span><span class="op">)</span></span></span>
 <span class="r-in"><span></span></span>
 <span class="r-in"><span><span class="va">adtte</span> <span class="op">&lt;-</span> <span class="va">tern_ex_adtte</span></span></span>
@@ -368,17 +457,19 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 </code></pre></div>
     </div>
   </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
-    </nav></aside></div>
+    </nav></aside>
+</div>
 
 
     <footer><div class="nest">
   <p>tern is a part of the <strong>NEST</strong> and <a href="https://pharmaverse.org/" class="external-link"><strong>pharmaverse</strong></a>.</p>
 </div>
-<script type="text/javascript" src="../analytics.js"></script></footer></div>
-
+<script type="text/javascript" src="../analytics.js"></script></footer>
+</div>
 
 
 
 
-  </body></html>
 
+  </body>
+</html>
diff --git a/main/reference/survival_time.html b/main/reference/survival_time.html
index 087bf536d1..cb47a56cae 100644
--- a/main/reference/survival_time.html
+++ b/main/reference/survival_time.html
@@ -1,13 +1,36 @@
-<!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Survival time analysis — survival_time • tern</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Survival time analysis — survival_time"><meta name="description" content="
+<html lang="en">
+<head>
+<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+<meta charset="utf-8">
+<meta http-equiv="X-UA-Compatible" content="IE=edge">
+<meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<title>Survival time analysis — survival_time • tern</title>
+<!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png">
+<link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png">
+<link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png">
+<link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png">
+<link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png">
+<link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png">
+<script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet">
+<script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet">
+<link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet">
+<script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Survival time analysis — survival_time">
+<meta name="description" content="
 The analyze function surv_time() creates a layout element to analyze survival time by calculating survival time
 median, median confidence interval, quantiles, and range (for all, censored, or event patients). The primary
 analysis variable vars is the time variable and the secondary analysis variable is_event indicates whether or
-not an event has occurred."><meta property="og:description" content="
+not an event has occurred.">
+<meta property="og:description" content="
 The analyze function surv_time() creates a layout element to analyze survival time by calculating survival time
 median, median confidence interval, quantiles, and range (for all, censored, or event patients). The primary
 analysis variable vars is the time variable and the secondary analysis variable is_event indicates whether or
-not an event has occurred."><meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png"><link rel="stylesheet" href="../consent.css"><script src="../consent.js" type="text/javascript" charset="utf-8"></script></head><body>
+not an event has occurred.">
+<meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png">
+<link rel="stylesheet" href="../consent.css">
+<script src="../consent.js" type="text/javascript" charset="utf-8"></script>
+</head>
+<body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
 
 
@@ -23,26 +46,66 @@
     </button>
 
     <div id="navbar" class="collapse navbar-collapse ms-3">
-      <ul class="navbar-nav me-auto"><li class="nav-item"><a class="nav-link" href="../articles/tern.html">Get started</a></li>
+      <ul class="navbar-nav me-auto">
+<li class="nav-item"><a class="nav-link" href="../articles/tern.html">Get started</a></li>
 <li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
 <li class="nav-item dropdown">
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-articles" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Articles</button>
-  <ul class="dropdown-menu" aria-labelledby="dropdown-articles"><li><a class="dropdown-item" href="../articles/missing_values.html">Missing Values in Tern</a></li>
+  <ul class="dropdown-menu" aria-labelledby="dropdown-articles">
+<li><a class="dropdown-item" href="../articles/missing_values.html">Missing Values in Tern</a></li>
     <li><a class="dropdown-item" href="../articles/tables.html">Tabulation</a></li>
     <li><a class="dropdown-item" href="../articles/tern_formats.html">Formatting Functions</a></li>
     <li><a class="dropdown-item" href="../articles/tern_functions_guide.html">Understanding `tern` functions</a></li>
-  </ul></li>
+  </ul>
+</li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
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-  <ul class="dropdown-menu" aria-labelledby="dropdown-reports"><li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
+  <ul class="dropdown-menu" aria-labelledby="dropdown-reports">
+<li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
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-      </ul><ul class="navbar-nav"><li class="nav-item"><form class="form-inline" role="search">
- <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json"></form></li>
+  </ul>
+</li>
+      <div><li class="nav-item dropdown">
+    <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-versions">Versions</a>
+    <div class="dropdown-menu" aria-labelledby="dropdown-versions">
+    <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/main">main</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.5">v0.9.5</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.4">v0.9.4</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.3">v0.9.3</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1-rc3">v0.9.1-rc3</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a>
+</div>
+</li></div>
+</ul>
+<ul class="navbar-nav">
+<li class="nav-item"><form class="form-inline" role="search">
+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json">
+</form></li>
 <li class="nav-item"><a class="external-link nav-link" href="https://github.com/insightsengineering/tern" aria-label="GitHub"><span class="fa fa-github"></span></a></li>
-      </ul></div>
+      </ul>
+</div>
 
 
   </div>
@@ -63,7 +126,8 @@
     </div>
 
     <div class="section level2">
-    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
+    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">surv_time</span><span class="op">(</span></span>
 <span>  <span class="va">lyt</span>,</span>
 <span>  <span class="va">vars</span>,</span>
@@ -101,108 +165,143 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
     </div>
 
     <div class="section level2">
-    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
+    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a>
+</h2>
 
 
-<dl><dt id="arg-lyt">lyt<a class="anchor" aria-label="anchor" href="#arg-lyt"></a></dt>
+<dl>
+<dt id="arg-lyt">lyt<a class="anchor" aria-label="anchor" href="#arg-lyt"></a>
+</dt>
 <dd><p>(<code>PreDataTableLayouts</code>)<br> layout that analyses will be added to.</p></dd>
 
 
-<dt id="arg-vars">vars<a class="anchor" aria-label="anchor" href="#arg-vars"></a></dt>
+<dt id="arg-vars">vars<a class="anchor" aria-label="anchor" href="#arg-vars"></a>
+</dt>
 <dd><p>(<code>character</code>)<br> variable names for the primary analysis variable to be iterated over.</p></dd>
 
 
-<dt id="arg-is-event">is_event<a class="anchor" aria-label="anchor" href="#arg-is-event"></a></dt>
+<dt id="arg-is-event">is_event<a class="anchor" aria-label="anchor" href="#arg-is-event"></a>
+</dt>
 <dd><p>(<code>flag</code>)<br><code>TRUE</code> if event, <code>FALSE</code> if time to event is censored.</p></dd>
 
 
-<dt id="arg-control">control<a class="anchor" aria-label="anchor" href="#arg-control"></a></dt>
-<dd><p>(<code>list</code>)<br> parameters for comparison details, specified by using the helper function
-<code><a href="control_surv_time.html">control_surv_time()</a></code>. Some possible parameter options are:</p><ul><li><p><code>conf_level</code> (<code>proportion</code>)<br> confidence level of the interval for survival time.</p></li>
+<dt id="arg-control">control<a class="anchor" aria-label="anchor" href="#arg-control"></a>
+</dt>
+<dd>
+<p>(<code>list</code>)<br> parameters for comparison details, specified by using the helper function
+<code><a href="control_surv_time.html">control_surv_time()</a></code>. Some possible parameter options are:</p>
+<ul>
+<li><p><code>conf_level</code> (<code>proportion</code>)<br> confidence level of the interval for survival time.</p></li>
 <li><p><code>conf_type</code> (<code>string</code>)<br> confidence interval type. Options are "plain" (default), "log", or "log-log",
 see more in <code><a href="https://rdrr.io/pkg/survival/man/survfit.html" class="external-link">survival::survfit()</a></code>. Note option "none" is not supported.</p></li>
 <li><p><code>quantiles</code> (<code>numeric</code>)<br> vector of length two to specify the quantiles of survival time.</p></li>
-</ul></dd>
+</ul>
+</dd>
 
 
-<dt id="arg-ref-fn-censor">ref_fn_censor<a class="anchor" aria-label="anchor" href="#arg-ref-fn-censor"></a></dt>
+<dt id="arg-ref-fn-censor">ref_fn_censor<a class="anchor" aria-label="anchor" href="#arg-ref-fn-censor"></a>
+</dt>
 <dd><p>(<code>flag</code>)<br> whether referential footnotes indicating censored observations should be printed
 when the <code>range</code> statistic is included.</p></dd>
 
 
-<dt id="arg-na-str">na_str<a class="anchor" aria-label="anchor" href="#arg-na-str"></a></dt>
+<dt id="arg-na-str">na_str<a class="anchor" aria-label="anchor" href="#arg-na-str"></a>
+</dt>
 <dd><p>(<code>string</code>)<br> string used to replace all <code>NA</code> or empty values in the output.</p></dd>
 
 
-<dt id="arg-nested">nested<a class="anchor" aria-label="anchor" href="#arg-nested"></a></dt>
+<dt id="arg-nested">nested<a class="anchor" aria-label="anchor" href="#arg-nested"></a>
+</dt>
 <dd><p>(<code>flag</code>)<br> whether this layout instruction should be applied within the existing layout structure _if
 possible (<code>TRUE</code>, the default) or as a new top-level element (<code>FALSE</code>). Ignored if it would nest a split.
 underneath analyses, which is not allowed.</p></dd>
 
 
-<dt id="arg--">...<a class="anchor" aria-label="anchor" href="#arg--"></a></dt>
+<dt id="arg--">...<a class="anchor" aria-label="anchor" href="#arg--"></a>
+</dt>
 <dd><p>additional arguments for the lower level functions.</p></dd>
 
 
-<dt id="arg-var-labels">var_labels<a class="anchor" aria-label="anchor" href="#arg-var-labels"></a></dt>
+<dt id="arg-var-labels">var_labels<a class="anchor" aria-label="anchor" href="#arg-var-labels"></a>
+</dt>
 <dd><p>(<code>character</code>)<br> variable labels.</p></dd>
 
 
-<dt id="arg-show-labels">show_labels<a class="anchor" aria-label="anchor" href="#arg-show-labels"></a></dt>
+<dt id="arg-show-labels">show_labels<a class="anchor" aria-label="anchor" href="#arg-show-labels"></a>
+</dt>
 <dd><p>(<code>string</code>)<br> label visibility: one of "default", "visible" and "hidden".</p></dd>
 
 
-<dt id="arg-table-names">table_names<a class="anchor" aria-label="anchor" href="#arg-table-names"></a></dt>
+<dt id="arg-table-names">table_names<a class="anchor" aria-label="anchor" href="#arg-table-names"></a>
+</dt>
 <dd><p>(<code>character</code>)<br> this can be customized in the case that the same <code>vars</code> are analyzed multiple
 times, to avoid warnings from <code>rtables</code>.</p></dd>
 
 
-<dt id="arg--stats">.stats<a class="anchor" aria-label="anchor" href="#arg--stats"></a></dt>
-<dd><p>(<code>character</code>)<br> statistics to select for the table.</p>
-<p>Options are: <code>'median', 'median_ci', 'median_ci_3d', 'quantiles', 'quantiles_lower', 'quantiles_upper', 'range_censor', 'range_event', 'range'</code></p></dd>
+<dt id="arg--stats">.stats<a class="anchor" aria-label="anchor" href="#arg--stats"></a>
+</dt>
+<dd>
+<p>(<code>character</code>)<br> statistics to select for the table.</p>
+<p>Options are: <code>'median', 'median_ci', 'median_ci_3d', 'quantiles', 'quantiles_lower', 'quantiles_upper', 'range_censor', 'range_event', 'range'</code></p>
+</dd>
 
 
-<dt id="arg--formats">.formats<a class="anchor" aria-label="anchor" href="#arg--formats"></a></dt>
+<dt id="arg--formats">.formats<a class="anchor" aria-label="anchor" href="#arg--formats"></a>
+</dt>
 <dd><p>(named <code>character</code> or <code>list</code>)<br> formats for the statistics. See Details in <code>analyze_vars</code> for more
 information on the <code>"auto"</code> setting.</p></dd>
 
 
-<dt id="arg--labels">.labels<a class="anchor" aria-label="anchor" href="#arg--labels"></a></dt>
+<dt id="arg--labels">.labels<a class="anchor" aria-label="anchor" href="#arg--labels"></a>
+</dt>
 <dd><p>(named <code>character</code>)<br> labels for the statistics (without indent).</p></dd>
 
 
-<dt id="arg--indent-mods">.indent_mods<a class="anchor" aria-label="anchor" href="#arg--indent-mods"></a></dt>
+<dt id="arg--indent-mods">.indent_mods<a class="anchor" aria-label="anchor" href="#arg--indent-mods"></a>
+</dt>
 <dd><p>(named <code>integer</code>)<br> indent modifiers for the labels. Each element of the vector
 should be a name-value pair with name corresponding to a statistic specified in <code>.stats</code> and value the indentation
 for that statistic's row label.</p></dd>
 
 
-<dt id="arg-df">df<a class="anchor" aria-label="anchor" href="#arg-df"></a></dt>
+<dt id="arg-df">df<a class="anchor" aria-label="anchor" href="#arg-df"></a>
+</dt>
 <dd><p>(<code>data.frame</code>)<br> data set containing all analysis variables.</p></dd>
 
 
-<dt id="arg--var">.var<a class="anchor" aria-label="anchor" href="#arg--var"></a></dt>
+<dt id="arg--var">.var<a class="anchor" aria-label="anchor" href="#arg--var"></a>
+</dt>
 <dd><p>(<code>string</code>)<br> single variable name that is passed by <code>rtables</code> when requested
 by a statistics function.</p></dd>
 
 
-<dt id="arg-labelstr">labelstr<a class="anchor" aria-label="anchor" href="#arg-labelstr"></a></dt>
+<dt id="arg-labelstr">labelstr<a class="anchor" aria-label="anchor" href="#arg-labelstr"></a>
+</dt>
 <dd><p>(<code>string</code>)<br> label of the level of the parent split currently being summarized
 (must be present as second argument in Content Row Functions). See <code><a href="https://insightsengineering.github.io/rtables/latest-tag/reference/summarize_row_groups.html" class="external-link">rtables::summarize_row_groups()</a></code>
 for more information.</p></dd>
 
 
-<dt id="arg--df-row">.df_row<a class="anchor" aria-label="anchor" href="#arg--df-row"></a></dt>
+<dt id="arg--df-row">.df_row<a class="anchor" aria-label="anchor" href="#arg--df-row"></a>
+</dt>
 <dd><p>(<code>data.frame</code>)<br> data frame across all of the columns for the given row split.</p></dd>
 
-</dl></div>
+</dl>
+</div>
     <div class="section level2">
-    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
+    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a>
+</h2>
 
-<ul><li><p><code>surv_time()</code> returns a layout object suitable for passing to further layouting functions,
+<ul>
+<li><p><code>surv_time()</code> returns a layout object suitable for passing to further layouting functions,
 or to <code><a href="https://insightsengineering.github.io/rtables/latest-tag/reference/build_table.html" class="external-link">rtables::build_table()</a></code>. Adding this function to an <code>rtable</code> layout will add formatted rows containing
 the statistics from <code>s_surv_time()</code> to the table layout.</p></li>
-</ul><ul><li><p><code>s_surv_time()</code> returns the statistics:</p><ul><li><p><code>median</code>: Median survival time.</p></li>
+</ul>
+<ul>
+<li>
+<p><code>s_surv_time()</code> returns the statistics:</p>
+<ul>
+<li><p><code>median</code>: Median survival time.</p></li>
 <li><p><code>median_ci</code>: Confidence interval for median time.</p></li>
 <li><p><code>median_ci_3d</code>: Median with confidence interval for median time.</p></li>
 <li><p><code>quantiles</code>: Survival time for two specified quantiles.</p></li>
@@ -211,20 +310,28 @@ <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2
 <li><p><code>range_censor</code>: Survival time range for censored observations.</p></li>
 <li><p><code>range_event</code>: Survival time range for observations with events.</p></li>
 <li><p><code>range</code>: Survival time range for all observations.</p></li>
-</ul></li>
-</ul><ul><li><p><code>a_surv_time()</code> returns the corresponding list with formatted <code><a href="https://insightsengineering.github.io/rtables/latest-tag/reference/CellValue.html" class="external-link">rtables::CellValue()</a></code>.</p></li>
-</ul></div>
+</ul>
+</li>
+</ul>
+<ul>
+<li><p><code>a_surv_time()</code> returns the corresponding list with formatted <code><a href="https://insightsengineering.github.io/rtables/latest-tag/reference/CellValue.html" class="external-link">rtables::CellValue()</a></code>.</p></li>
+</ul>
+</div>
     <div class="section level2">
-    <h2 id="functions">Functions<a class="anchor" aria-label="anchor" href="#functions"></a></h2>
+    <h2 id="functions">Functions<a class="anchor" aria-label="anchor" href="#functions"></a>
+</h2>
 
-<ul><li><p><code>surv_time()</code>: Layout-creating function which can take statistics function arguments
+<ul>
+<li><p><code>surv_time()</code>: Layout-creating function which can take statistics function arguments
 and additional format arguments. This function is a wrapper for <code><a href="https://insightsengineering.github.io/rtables/latest-tag/reference/analyze.html" class="external-link">rtables::analyze()</a></code>.</p></li>
 <li><p><code>s_surv_time()</code>: Statistics function which analyzes survival times.</p></li>
 <li><p><code>a_surv_time()</code>: Formatted analysis function which is used as <code>afun</code> in <code>surv_time()</code>.</p></li>
-</ul></div>
+</ul>
+</div>
 
     <div class="section level2">
-    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
+    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://dplyr.tidyverse.org" class="external-link">dplyr</a></span><span class="op">)</span></span></span>
 <span class="r-in"><span></span></span>
 <span class="r-in"><span><span class="va">adtte_f</span> <span class="op">&lt;-</span> <span class="va">tern_ex_adtte</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span></span>
@@ -276,17 +383,19 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 </code></pre></div>
     </div>
   </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
-    </nav></aside></div>
+    </nav></aside>
+</div>
 
 
     <footer><div class="nest">
   <p>tern is a part of the <strong>NEST</strong> and <a href="https://pharmaverse.org/" class="external-link"><strong>pharmaverse</strong></a>.</p>
 </div>
-<script type="text/javascript" src="../analytics.js"></script></footer></div>
-
+<script type="text/javascript" src="../analytics.js"></script></footer>
+</div>
 
 
 
 
-  </body></html>
 
+  </body>
+</html>
diff --git a/main/reference/survival_timepoint.html b/main/reference/survival_timepoint.html
index 38f2143cc5..f0bbef2896 100644
--- a/main/reference/survival_timepoint.html
+++ b/main/reference/survival_timepoint.html
@@ -1,17 +1,40 @@
-<!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Survival time point analysis — survival_timepoint • tern</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Survival time point analysis — survival_timepoint"><meta name="description" content='
+<html lang="en">
+<head>
+<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+<meta charset="utf-8">
+<meta http-equiv="X-UA-Compatible" content="IE=edge">
+<meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<title>Survival time point analysis — survival_timepoint • tern</title>
+<!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png">
+<link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png">
+<link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png">
+<link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png">
+<link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png">
+<link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png">
+<script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet">
+<script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet">
+<link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet">
+<script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Survival time point analysis — survival_timepoint">
+<meta name="description" content='
 The analyze function surv_timepoint() creates a layout element to analyze patient survival rates and difference
 of survival rates between groups at a given time point. The primary analysis variable vars is the time variable.
 Other required inputs are time_point, the numeric time point of interest, and is_event, a variable that
 indicates whether or not an event has occurred. The method argument is used to specify whether you want to analyze
 survival estimations ("surv"), difference in survival with the control ("surv_diff"), or both of these
-("both").'><meta property="og:description" content='
+("both").'>
+<meta property="og:description" content='
 The analyze function surv_timepoint() creates a layout element to analyze patient survival rates and difference
 of survival rates between groups at a given time point. The primary analysis variable vars is the time variable.
 Other required inputs are time_point, the numeric time point of interest, and is_event, a variable that
 indicates whether or not an event has occurred. The method argument is used to specify whether you want to analyze
 survival estimations ("surv"), difference in survival with the control ("surv_diff"), or both of these
-("both").'><meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png"><link rel="stylesheet" href="../consent.css"><script src="../consent.js" type="text/javascript" charset="utf-8"></script></head><body>
+("both").'>
+<meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png">
+<link rel="stylesheet" href="../consent.css">
+<script src="../consent.js" type="text/javascript" charset="utf-8"></script>
+</head>
+<body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
 
 
@@ -27,26 +50,66 @@
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+      <ul class="navbar-nav me-auto">
+<li class="nav-item"><a class="nav-link" href="../articles/tern.html">Get started</a></li>
 <li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
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+  <ul class="dropdown-menu" aria-labelledby="dropdown-articles">
+<li><a class="dropdown-item" href="../articles/missing_values.html">Missing Values in Tern</a></li>
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- <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json"></form></li>
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+    <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-versions">Versions</a>
+    <div class="dropdown-menu" aria-labelledby="dropdown-versions">
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+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
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+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.4">v0.9.4</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.3">v0.9.3</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1-rc3">v0.9.1-rc3</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a>
+</div>
+</li></div>
+</ul>
+<ul class="navbar-nav">
+<li class="nav-item"><form class="form-inline" role="search">
+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json">
+</form></li>
 <li class="nav-item"><a class="external-link nav-link" href="https://github.com/insightsengineering/tern" aria-label="GitHub"><span class="fa fa-github"></span></a></li>
-      </ul></div>
+      </ul>
+</div>
 
 
   </div>
@@ -69,7 +132,8 @@
     </div>
 
     <div class="section level2">
-    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
+    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">surv_timepoint</span><span class="op">(</span></span>
 <span>  <span class="va">lyt</span>,</span>
 <span>  <span class="va">vars</span>,</span>
@@ -133,127 +197,177 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
     </div>
 
     <div class="section level2">
-    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
+    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a>
+</h2>
 
 
-<dl><dt id="arg-lyt">lyt<a class="anchor" aria-label="anchor" href="#arg-lyt"></a></dt>
+<dl>
+<dt id="arg-lyt">lyt<a class="anchor" aria-label="anchor" href="#arg-lyt"></a>
+</dt>
 <dd><p>(<code>PreDataTableLayouts</code>)<br> layout that analyses will be added to.</p></dd>
 
 
-<dt id="arg-vars">vars<a class="anchor" aria-label="anchor" href="#arg-vars"></a></dt>
+<dt id="arg-vars">vars<a class="anchor" aria-label="anchor" href="#arg-vars"></a>
+</dt>
 <dd><p>(<code>character</code>)<br> variable names for the primary analysis variable to be iterated over.</p></dd>
 
 
-<dt id="arg-time-point">time_point<a class="anchor" aria-label="anchor" href="#arg-time-point"></a></dt>
+<dt id="arg-time-point">time_point<a class="anchor" aria-label="anchor" href="#arg-time-point"></a>
+</dt>
 <dd><p>(<code>numeric(1)</code>)<br> survival time point of interest.</p></dd>
 
 
-<dt id="arg-is-event">is_event<a class="anchor" aria-label="anchor" href="#arg-is-event"></a></dt>
+<dt id="arg-is-event">is_event<a class="anchor" aria-label="anchor" href="#arg-is-event"></a>
+</dt>
 <dd><p>(<code>flag</code>)<br><code>TRUE</code> if event, <code>FALSE</code> if time to event is censored.</p></dd>
 
 
-<dt id="arg-control">control<a class="anchor" aria-label="anchor" href="#arg-control"></a></dt>
-<dd><p>(<code>list</code>)<br> parameters for comparison details, specified by using the helper function
-<code><a href="control_surv_timepoint.html">control_surv_timepoint()</a></code>. Some possible parameter options are:</p><ul><li><p><code>conf_level</code> (<code>proportion</code>)<br> confidence level of the interval for survival rate.</p></li>
+<dt id="arg-control">control<a class="anchor" aria-label="anchor" href="#arg-control"></a>
+</dt>
+<dd>
+<p>(<code>list</code>)<br> parameters for comparison details, specified by using the helper function
+<code><a href="control_surv_timepoint.html">control_surv_timepoint()</a></code>. Some possible parameter options are:</p>
+<ul>
+<li><p><code>conf_level</code> (<code>proportion</code>)<br> confidence level of the interval for survival rate.</p></li>
 <li><p><code>conf_type</code> (<code>string</code>)<br> confidence interval type. Options are "plain" (default), "log", "log-log",
 see more in <code><a href="https://rdrr.io/pkg/survival/man/survfit.html" class="external-link">survival::survfit()</a></code>. Note option "none" is no longer supported.</p></li>
-</ul></dd>
+</ul>
+</dd>
 
 
-<dt id="arg-method">method<a class="anchor" aria-label="anchor" href="#arg-method"></a></dt>
+<dt id="arg-method">method<a class="anchor" aria-label="anchor" href="#arg-method"></a>
+</dt>
 <dd><p>(<code>string</code>)<br><code>"surv"</code> (survival estimations), <code>"surv_diff"</code> (difference in survival with the
 control), or <code>"both"</code>.</p></dd>
 
 
-<dt id="arg-na-str">na_str<a class="anchor" aria-label="anchor" href="#arg-na-str"></a></dt>
+<dt id="arg-na-str">na_str<a class="anchor" aria-label="anchor" href="#arg-na-str"></a>
+</dt>
 <dd><p>(<code>string</code>)<br> string used to replace all <code>NA</code> or empty values in the output.</p></dd>
 
 
-<dt id="arg-nested">nested<a class="anchor" aria-label="anchor" href="#arg-nested"></a></dt>
+<dt id="arg-nested">nested<a class="anchor" aria-label="anchor" href="#arg-nested"></a>
+</dt>
 <dd><p>(<code>flag</code>)<br> whether this layout instruction should be applied within the existing layout structure _if
 possible (<code>TRUE</code>, the default) or as a new top-level element (<code>FALSE</code>). Ignored if it would nest a split.
 underneath analyses, which is not allowed.</p></dd>
 
 
-<dt id="arg--">...<a class="anchor" aria-label="anchor" href="#arg--"></a></dt>
+<dt id="arg--">...<a class="anchor" aria-label="anchor" href="#arg--"></a>
+</dt>
 <dd><p>additional arguments for the lower level functions.</p></dd>
 
 
-<dt id="arg-table-names-suffix">table_names_suffix<a class="anchor" aria-label="anchor" href="#arg-table-names-suffix"></a></dt>
+<dt id="arg-table-names-suffix">table_names_suffix<a class="anchor" aria-label="anchor" href="#arg-table-names-suffix"></a>
+</dt>
 <dd><p>(<code>string</code>)<br> optional suffix for the <code>table_names</code> used for the <code>rtables</code> to
 avoid warnings from duplicate table names.</p></dd>
 
 
-<dt id="arg-var-labels">var_labels<a class="anchor" aria-label="anchor" href="#arg-var-labels"></a></dt>
+<dt id="arg-var-labels">var_labels<a class="anchor" aria-label="anchor" href="#arg-var-labels"></a>
+</dt>
 <dd><p>(<code>character</code>)<br> variable labels.</p></dd>
 
 
-<dt id="arg-show-labels">show_labels<a class="anchor" aria-label="anchor" href="#arg-show-labels"></a></dt>
+<dt id="arg-show-labels">show_labels<a class="anchor" aria-label="anchor" href="#arg-show-labels"></a>
+</dt>
 <dd><p>(<code>string</code>)<br> label visibility: one of "default", "visible" and "hidden".</p></dd>
 
 
-<dt id="arg--stats">.stats<a class="anchor" aria-label="anchor" href="#arg--stats"></a></dt>
-<dd><p>(<code>character</code>)<br> statistics to select for the table.</p>
-<p>Options are: <code>'pt_at_risk', 'event_free_rate', 'rate_se', 'rate_ci', 'rate_diff', 'rate_diff_ci', 'ztest_pval', 'event_free_rate_3d'</code></p></dd>
+<dt id="arg--stats">.stats<a class="anchor" aria-label="anchor" href="#arg--stats"></a>
+</dt>
+<dd>
+<p>(<code>character</code>)<br> statistics to select for the table.</p>
+<p>Options are: <code>'pt_at_risk', 'event_free_rate', 'rate_se', 'rate_ci', 'rate_diff', 'rate_diff_ci', 'ztest_pval', 'event_free_rate_3d'</code></p>
+</dd>
 
 
-<dt id="arg--formats">.formats<a class="anchor" aria-label="anchor" href="#arg--formats"></a></dt>
+<dt id="arg--formats">.formats<a class="anchor" aria-label="anchor" href="#arg--formats"></a>
+</dt>
 <dd><p>(named <code>character</code> or <code>list</code>)<br> formats for the statistics. See Details in <code>analyze_vars</code> for more
 information on the <code>"auto"</code> setting.</p></dd>
 
 
-<dt id="arg--labels">.labels<a class="anchor" aria-label="anchor" href="#arg--labels"></a></dt>
+<dt id="arg--labels">.labels<a class="anchor" aria-label="anchor" href="#arg--labels"></a>
+</dt>
 <dd><p>(named <code>character</code>)<br> labels for the statistics (without indent).</p></dd>
 
 
-<dt id="arg--indent-mods">.indent_mods<a class="anchor" aria-label="anchor" href="#arg--indent-mods"></a></dt>
+<dt id="arg--indent-mods">.indent_mods<a class="anchor" aria-label="anchor" href="#arg--indent-mods"></a>
+</dt>
 <dd><p>(named <code>integer</code>)<br> indent modifiers for the labels. Each element of the vector
 should be a name-value pair with name corresponding to a statistic specified in <code>.stats</code> and value the indentation
 for that statistic's row label.</p></dd>
 
 
-<dt id="arg-df">df<a class="anchor" aria-label="anchor" href="#arg-df"></a></dt>
+<dt id="arg-df">df<a class="anchor" aria-label="anchor" href="#arg-df"></a>
+</dt>
 <dd><p>(<code>data.frame</code>)<br> data set containing all analysis variables.</p></dd>
 
 
-<dt id="arg--var">.var<a class="anchor" aria-label="anchor" href="#arg--var"></a></dt>
+<dt id="arg--var">.var<a class="anchor" aria-label="anchor" href="#arg--var"></a>
+</dt>
 <dd><p>(<code>string</code>)<br> single variable name that is passed by <code>rtables</code> when requested
 by a statistics function.</p></dd>
 
 
-<dt id="arg--ref-group">.ref_group<a class="anchor" aria-label="anchor" href="#arg--ref-group"></a></dt>
+<dt id="arg--ref-group">.ref_group<a class="anchor" aria-label="anchor" href="#arg--ref-group"></a>
+</dt>
 <dd><p>(<code>data.frame</code> or <code>vector</code>)<br> the data corresponding to the reference group.</p></dd>
 
 
-<dt id="arg--in-ref-col">.in_ref_col<a class="anchor" aria-label="anchor" href="#arg--in-ref-col"></a></dt>
+<dt id="arg--in-ref-col">.in_ref_col<a class="anchor" aria-label="anchor" href="#arg--in-ref-col"></a>
+</dt>
 <dd><p>(<code>flag</code>)<br><code>TRUE</code> when working with the reference level, <code>FALSE</code> otherwise.</p></dd>
 
-</dl></div>
+</dl>
+</div>
     <div class="section level2">
-    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
+    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a>
+</h2>
 
-<ul><li><p><code>surv_timepoint()</code> returns a layout object suitable for passing to further layouting functions,
+<ul>
+<li><p><code>surv_timepoint()</code> returns a layout object suitable for passing to further layouting functions,
 or to <code><a href="https://insightsengineering.github.io/rtables/latest-tag/reference/build_table.html" class="external-link">rtables::build_table()</a></code>. Adding this function to an <code>rtable</code> layout will add formatted rows containing
 the statistics from <code>s_surv_timepoint()</code> and/or <code>s_surv_timepoint_diff()</code> to the table layout depending on
 the value of <code>method</code>.</p></li>
-</ul><ul><li><p><code>s_surv_timepoint()</code> returns the statistics:</p><ul><li><p><code>pt_at_risk</code>: Patients remaining at risk.</p></li>
+</ul>
+<ul>
+<li>
+<p><code>s_surv_timepoint()</code> returns the statistics:</p>
+<ul>
+<li><p><code>pt_at_risk</code>: Patients remaining at risk.</p></li>
 <li><p><code>event_free_rate</code>: Event-free rate (%).</p></li>
 <li><p><code>rate_se</code>: Standard error of event free rate.</p></li>
 <li><p><code>rate_ci</code>: Confidence interval for event free rate.</p></li>
 <li><p><code>event_free_rate_3d</code>: Event-free rate (%) with Confidence interval.</p></li>
-</ul></li>
-</ul><ul><li><p><code>a_surv_timepoint()</code> returns the corresponding list with formatted <code><a href="https://insightsengineering.github.io/rtables/latest-tag/reference/CellValue.html" class="external-link">rtables::CellValue()</a></code>.</p></li>
-</ul><ul><li><p><code>s_surv_timepoint_diff()</code> returns the statistics:</p><ul><li><p><code>rate_diff</code>: Event-free rate difference between two groups.</p></li>
+</ul>
+</li>
+</ul>
+<ul>
+<li><p><code>a_surv_timepoint()</code> returns the corresponding list with formatted <code><a href="https://insightsengineering.github.io/rtables/latest-tag/reference/CellValue.html" class="external-link">rtables::CellValue()</a></code>.</p></li>
+</ul>
+<ul>
+<li>
+<p><code>s_surv_timepoint_diff()</code> returns the statistics:</p>
+<ul>
+<li><p><code>rate_diff</code>: Event-free rate difference between two groups.</p></li>
 <li><p><code>rate_diff_ci</code>: Confidence interval for the difference.</p></li>
 <li><p><code>rate_diff_ci_3d</code>: Event-free rate difference and confidence interval between two groups.</p></li>
 <li><p><code>ztest_pval</code>: p-value to test the difference is 0.</p></li>
-</ul></li>
-</ul><ul><li><p><code>a_surv_timepoint_diff()</code> returns the corresponding list with formatted <code><a href="https://insightsengineering.github.io/rtables/latest-tag/reference/CellValue.html" class="external-link">rtables::CellValue()</a></code>.</p></li>
-</ul></div>
+</ul>
+</li>
+</ul>
+<ul>
+<li><p><code>a_surv_timepoint_diff()</code> returns the corresponding list with formatted <code><a href="https://insightsengineering.github.io/rtables/latest-tag/reference/CellValue.html" class="external-link">rtables::CellValue()</a></code>.</p></li>
+</ul>
+</div>
     <div class="section level2">
-    <h2 id="functions">Functions<a class="anchor" aria-label="anchor" href="#functions"></a></h2>
+    <h2 id="functions">Functions<a class="anchor" aria-label="anchor" href="#functions"></a>
+</h2>
 
-<ul><li><p><code>surv_timepoint()</code>: Layout-creating function which can take statistics function arguments
+<ul>
+<li><p><code>surv_timepoint()</code>: Layout-creating function which can take statistics function arguments
 and additional format arguments. This function is a wrapper for <code><a href="https://insightsengineering.github.io/rtables/latest-tag/reference/analyze.html" class="external-link">rtables::analyze()</a></code>.</p></li>
 <li><p><code>s_surv_timepoint()</code>: Statistics function which analyzes survival rate.</p></li>
 <li><p><code>a_surv_timepoint()</code>: Formatted analysis function which is used as <code>afun</code> in <code>surv_timepoint()</code>
@@ -261,10 +375,12 @@ <h2 id="functions">Functions<a class="anchor" aria-label="anchor" href="#functio
 <li><p><code>s_surv_timepoint_diff()</code>: Statistics function which analyzes difference between two survival rates.</p></li>
 <li><p><code>a_surv_timepoint_diff()</code>: Formatted analysis function which is used as <code>afun</code> in <code>surv_timepoint()</code>
 when <code>method = "surv_diff"</code>.</p></li>
-</ul></div>
+</ul>
+</div>
 
     <div class="section level2">
-    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
+    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://dplyr.tidyverse.org" class="external-link">dplyr</a></span><span class="op">)</span></span></span>
 <span class="r-in"><span></span></span>
 <span class="r-in"><span><span class="va">adtte_f</span> <span class="op">&lt;-</span> <span class="va">tern_ex_adtte</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span></span>
@@ -340,17 +456,19 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 </code></pre></div>
     </div>
   </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
-    </nav></aside></div>
+    </nav></aside>
+</div>
 
 
     <footer><div class="nest">
   <p>tern is a part of the <strong>NEST</strong> and <a href="https://pharmaverse.org/" class="external-link"><strong>pharmaverse</strong></a>.</p>
 </div>
-<script type="text/javascript" src="../analytics.js"></script></footer></div>
-
+<script type="text/javascript" src="../analytics.js"></script></footer>
+</div>
 
 
 
 
-  </body></html>
 
+  </body>
+</html>
diff --git a/main/reference/tern-package.html b/main/reference/tern-package.html
index e96510016c..1389ae400a 100644
--- a/main/reference/tern-package.html
+++ b/main/reference/tern-package.html
@@ -1,5 +1,28 @@
-<!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>tern Package — tern-package • tern</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="tern Package — tern-package"><meta name="description" content="Package to create tables, listings and graphs to analyze clinical trials data."><meta property="og:description" content="Package to create tables, listings and graphs to analyze clinical trials data."><meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png"><link rel="stylesheet" href="../consent.css"><script src="../consent.js" type="text/javascript" charset="utf-8"></script></head><body>
+<html lang="en">
+<head>
+<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+<meta charset="utf-8">
+<meta http-equiv="X-UA-Compatible" content="IE=edge">
+<meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<title>tern Package — tern-package • tern</title>
+<!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png">
+<link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png">
+<link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png">
+<link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png">
+<link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png">
+<link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png">
+<script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet">
+<script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet">
+<link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet">
+<script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="tern Package — tern-package">
+<meta name="description" content="Package to create tables, listings and graphs to analyze clinical trials data.">
+<meta property="og:description" content="Package to create tables, listings and graphs to analyze clinical trials data.">
+<meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png">
+<link rel="stylesheet" href="../consent.css">
+<script src="../consent.js" type="text/javascript" charset="utf-8"></script>
+</head>
+<body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
 
 
@@ -15,26 +38,66 @@
     </button>
 
     <div id="navbar" class="collapse navbar-collapse ms-3">
-      <ul class="navbar-nav me-auto"><li class="nav-item"><a class="nav-link" href="../articles/tern.html">Get started</a></li>
+      <ul class="navbar-nav me-auto">
+<li class="nav-item"><a class="nav-link" href="../articles/tern.html">Get started</a></li>
 <li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
 <li class="nav-item dropdown">
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-articles" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Articles</button>
-  <ul class="dropdown-menu" aria-labelledby="dropdown-articles"><li><a class="dropdown-item" href="../articles/missing_values.html">Missing Values in Tern</a></li>
+  <ul class="dropdown-menu" aria-labelledby="dropdown-articles">
+<li><a class="dropdown-item" href="../articles/missing_values.html">Missing Values in Tern</a></li>
     <li><a class="dropdown-item" href="../articles/tables.html">Tabulation</a></li>
     <li><a class="dropdown-item" href="../articles/tern_formats.html">Formatting Functions</a></li>
     <li><a class="dropdown-item" href="../articles/tern_functions_guide.html">Understanding `tern` functions</a></li>
-  </ul></li>
+  </ul>
+</li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
-  <ul class="dropdown-menu" aria-labelledby="dropdown-reports"><li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
+  <ul class="dropdown-menu" aria-labelledby="dropdown-reports">
+<li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
     <li><a class="dropdown-item" href="../unit-test-report/">Unit test report</a></li>
     <li><a class="dropdown-item" href="../unit-test-report-non-cran/">Non-CRAN unit test report</a></li>
-  </ul></li>
-      </ul><ul class="navbar-nav"><li class="nav-item"><form class="form-inline" role="search">
- <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json"></form></li>
+  </ul>
+</li>
+      <div><li class="nav-item dropdown">
+    <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-versions">Versions</a>
+    <div class="dropdown-menu" aria-labelledby="dropdown-versions">
+    <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/main">main</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.5">v0.9.5</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.4">v0.9.4</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.3">v0.9.3</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1-rc3">v0.9.1-rc3</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a>
+</div>
+</li></div>
+</ul>
+<ul class="navbar-nav">
+<li class="nav-item"><form class="form-inline" role="search">
+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json">
+</form></li>
 <li class="nav-item"><a class="external-link nav-link" href="https://github.com/insightsengineering/tern" aria-label="GitHub"><span class="fa fa-github"></span></a></li>
-      </ul></div>
+      </ul>
+</div>
 
 
   </div>
@@ -52,16 +115,24 @@
 
 
     <div class="section level2">
-    <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"></a></h2>
-    <div class="dont-index"><p>Useful links:</p><ul><li><p><a href="https://insightsengineering.github.io/tern/">https://insightsengineering.github.io/tern/</a></p></li>
+    <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"></a>
+</h2>
+    <div class="dont-index">
+<p>Useful links:</p>
+<ul>
+<li><p><a href="https://insightsengineering.github.io/tern/">https://insightsengineering.github.io/tern/</a></p></li>
 <li><p><a href="https://github.com/insightsengineering/tern/" class="external-link">https://github.com/insightsengineering/tern/</a></p></li>
 <li><p>Report bugs at <a href="https://github.com/insightsengineering/tern/issues" class="external-link">https://github.com/insightsengineering/tern/issues</a></p></li>
-</ul></div>
+</ul>
+</div>
     </div>
     <div class="section level2">
-    <h2 id="author">Author<a class="anchor" aria-label="anchor" href="#author"></a></h2>
+    <h2 id="author">Author<a class="anchor" aria-label="anchor" href="#author"></a>
+</h2>
     <p><strong>Maintainer</strong>: Joe Zhu <a href="mailto:joe.zhu@roche.com">joe.zhu@roche.com</a></p>
-<p>Authors:</p><ul><li><p>Daniel Sabanés Bové <a href="mailto:daniel.sabanes_bove@roche.com">daniel.sabanes_bove@roche.com</a></p></li>
+<p>Authors:</p>
+<ul>
+<li><p>Daniel Sabanés Bové <a href="mailto:daniel.sabanes_bove@roche.com">daniel.sabanes_bove@roche.com</a></p></li>
 <li><p>Jana Stoilova <a href="mailto:jana.stoilova@roche.com">jana.stoilova@roche.com</a></p></li>
 <li><p>Davide Garolini <a href="mailto:davide.garolini@roche.com">davide.garolini@roche.com</a></p></li>
 <li><p>Emily de la Rua <a href="mailto:emily.de_la_rua@contractors.roche.com">emily.de_la_rua@contractors.roche.com</a></p></li>
@@ -72,21 +143,27 @@ <h2 id="author">Author<a class="anchor" aria-label="anchor" href="#author"></a><
 <li><p>Pawel Rucki <a href="mailto:pawel.rucki@roche.com">pawel.rucki@roche.com</a></p></li>
 <li><p>Chendi Liao <a href="mailto:chendi.liao@roche.com">chendi.liao@roche.com</a></p></li>
 <li><p>Jennifer Li <a href="mailto:li.jing@gene.com">li.jing@gene.com</a></p></li>
-</ul><p>Other contributors:</p><ul><li><p>F. Hoffmann-La Roche AG [copyright holder, funder]</p></li>
-</ul></div>
+</ul>
+<p>Other contributors:</p>
+<ul>
+<li><p>F. Hoffmann-La Roche AG [copyright holder, funder]</p></li>
+</ul>
+</div>
 
   </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
-    </nav></aside></div>
+    </nav></aside>
+</div>
 
 
     <footer><div class="nest">
   <p>tern is a part of the <strong>NEST</strong> and <a href="https://pharmaverse.org/" class="external-link"><strong>pharmaverse</strong></a>.</p>
 </div>
-<script type="text/javascript" src="../analytics.js"></script></footer></div>
-
+<script type="text/javascript" src="../analytics.js"></script></footer>
+</div>
 
 
 
 
-  </body></html>
 
+  </body>
+</html>
diff --git a/main/reference/tidy.glm.html b/main/reference/tidy.glm.html
index 86a2acaf44..033e0697ed 100644
--- a/main/reference/tidy.glm.html
+++ b/main/reference/tidy.glm.html
@@ -1,9 +1,32 @@
-<!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Custom tidy method for binomial GLM results — tidy.glm • tern</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Custom tidy method for binomial GLM results — tidy.glm"><meta name="description" content="
+<html lang="en">
+<head>
+<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+<meta charset="utf-8">
+<meta http-equiv="X-UA-Compatible" content="IE=edge">
+<meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<title>Custom tidy method for binomial GLM results — tidy.glm • tern</title>
+<!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png">
+<link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png">
+<link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png">
+<link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png">
+<link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png">
+<link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png">
+<script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet">
+<script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet">
+<link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet">
+<script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Custom tidy method for binomial GLM results — tidy.glm">
+<meta name="description" content="
 Helper method (for broom::tidy()) to prepare a data frame from a glm object
-with binomial family."><meta property="og:description" content="
+with binomial family.">
+<meta property="og:description" content="
 Helper method (for broom::tidy()) to prepare a data frame from a glm object
-with binomial family."><meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png"><link rel="stylesheet" href="../consent.css"><script src="../consent.js" type="text/javascript" charset="utf-8"></script></head><body>
+with binomial family.">
+<meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png">
+<link rel="stylesheet" href="../consent.css">
+<script src="../consent.js" type="text/javascript" charset="utf-8"></script>
+</head>
+<body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
 
 
@@ -19,26 +42,66 @@
     </button>
 
     <div id="navbar" class="collapse navbar-collapse ms-3">
-      <ul class="navbar-nav me-auto"><li class="nav-item"><a class="nav-link" href="../articles/tern.html">Get started</a></li>
+      <ul class="navbar-nav me-auto">
+<li class="nav-item"><a class="nav-link" href="../articles/tern.html">Get started</a></li>
 <li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
 <li class="nav-item dropdown">
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-articles" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Articles</button>
-  <ul class="dropdown-menu" aria-labelledby="dropdown-articles"><li><a class="dropdown-item" href="../articles/missing_values.html">Missing Values in Tern</a></li>
+  <ul class="dropdown-menu" aria-labelledby="dropdown-articles">
+<li><a class="dropdown-item" href="../articles/missing_values.html">Missing Values in Tern</a></li>
     <li><a class="dropdown-item" href="../articles/tables.html">Tabulation</a></li>
     <li><a class="dropdown-item" href="../articles/tern_formats.html">Formatting Functions</a></li>
     <li><a class="dropdown-item" href="../articles/tern_functions_guide.html">Understanding `tern` functions</a></li>
-  </ul></li>
+  </ul>
+</li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
-  <ul class="dropdown-menu" aria-labelledby="dropdown-reports"><li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
+  <ul class="dropdown-menu" aria-labelledby="dropdown-reports">
+<li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
     <li><a class="dropdown-item" href="../unit-test-report/">Unit test report</a></li>
     <li><a class="dropdown-item" href="../unit-test-report-non-cran/">Non-CRAN unit test report</a></li>
-  </ul></li>
-      </ul><ul class="navbar-nav"><li class="nav-item"><form class="form-inline" role="search">
- <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json"></form></li>
+  </ul>
+</li>
+      <div><li class="nav-item dropdown">
+    <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-versions">Versions</a>
+    <div class="dropdown-menu" aria-labelledby="dropdown-versions">
+    <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/main">main</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.5">v0.9.5</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.4">v0.9.4</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.3">v0.9.3</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1-rc3">v0.9.1-rc3</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a>
+</div>
+</li></div>
+</ul>
+<ul class="navbar-nav">
+<li class="nav-item"><form class="form-inline" role="search">
+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json">
+</form></li>
 <li class="nav-item"><a class="external-link nav-link" href="https://github.com/insightsengineering/tern" aria-label="GitHub"><span class="fa fa-github"></span></a></li>
-      </ul></div>
+      </ul>
+</div>
 
 
   </div>
@@ -57,42 +120,53 @@
     </div>
 
     <div class="section level2">
-    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
+    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="co"># S3 method for class 'glm'</span></span>
 <span><span class="fu"><a href="https://generics.r-lib.org/reference/tidy.html" class="external-link">tidy</a></span><span class="op">(</span><span class="va">x</span>, conf_level <span class="op">=</span> <span class="fl">0.95</span>, at <span class="op">=</span> <span class="cn">NULL</span>, <span class="va">...</span><span class="op">)</span></span></code></pre></div>
     </div>
 
     <div class="section level2">
-    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
+    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a>
+</h2>
 
 
-<dl><dt id="arg-x">x<a class="anchor" aria-label="anchor" href="#arg-x"></a></dt>
+<dl>
+<dt id="arg-x">x<a class="anchor" aria-label="anchor" href="#arg-x"></a>
+</dt>
 <dd><p>(<code>glm</code>)<br> logistic regression model fitted by <code><a href="https://rdrr.io/r/stats/glm.html" class="external-link">stats::glm()</a></code> with "binomial" family.</p></dd>
 
 
-<dt id="arg-conf-level">conf_level<a class="anchor" aria-label="anchor" href="#arg-conf-level"></a></dt>
+<dt id="arg-conf-level">conf_level<a class="anchor" aria-label="anchor" href="#arg-conf-level"></a>
+</dt>
 <dd><p>(<code>proportion</code>)<br> confidence level of the interval.</p></dd>
 
 
-<dt id="arg-at">at<a class="anchor" aria-label="anchor" href="#arg-at"></a></dt>
+<dt id="arg-at">at<a class="anchor" aria-label="anchor" href="#arg-at"></a>
+</dt>
 <dd><p>(<code>numeric</code> or <code>NULL</code>)<br> optional values for the interaction variable. Otherwise the median is used.</p></dd>
 
 
-<dt id="arg--">...<a class="anchor" aria-label="anchor" href="#arg--"></a></dt>
+<dt id="arg--">...<a class="anchor" aria-label="anchor" href="#arg--"></a>
+</dt>
 <dd><p>additional arguments for the lower level functions.</p></dd>
 
-</dl></div>
+</dl>
+</div>
     <div class="section level2">
-    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
+    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a>
+</h2>
     <p>A <code>data.frame</code> containing the tidied model.</p>
     </div>
     <div class="section level2">
-    <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"></a></h2>
+    <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"></a>
+</h2>
     <div class="dont-index"><p><a href="h_logistic_regression.html">h_logistic_regression</a> for relevant helper functions.</p></div>
     </div>
 
     <div class="section level2">
-    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
+    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://dplyr.tidyverse.org" class="external-link">dplyr</a></span><span class="op">)</span></span></span>
 <span class="r-in"><span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://broom.tidymodels.org/" class="external-link">broom</a></span><span class="op">)</span></span></span>
 <span class="r-in"><span></span></span>
@@ -131,17 +205,19 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 </code></pre></div>
     </div>
   </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
-    </nav></aside></div>
+    </nav></aside>
+</div>
 
 
     <footer><div class="nest">
   <p>tern is a part of the <strong>NEST</strong> and <a href="https://pharmaverse.org/" class="external-link"><strong>pharmaverse</strong></a>.</p>
 </div>
-<script type="text/javascript" src="../analytics.js"></script></footer></div>
-
+<script type="text/javascript" src="../analytics.js"></script></footer>
+</div>
 
 
 
 
-  </body></html>
 
+  </body>
+</html>
diff --git a/main/reference/tidy.step.html b/main/reference/tidy.step.html
index 341e346b6a..e32fea9fd0 100644
--- a/main/reference/tidy.step.html
+++ b/main/reference/tidy.step.html
@@ -1,7 +1,30 @@
-<!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Custom tidy method for STEP results — tidy.step • tern</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Custom tidy method for STEP results — tidy.step"><meta name="description" content="
-Tidy the STEP results into a tibble format ready for plotting."><meta property="og:description" content="
-Tidy the STEP results into a tibble format ready for plotting."><meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png"><link rel="stylesheet" href="../consent.css"><script src="../consent.js" type="text/javascript" charset="utf-8"></script></head><body>
+<html lang="en">
+<head>
+<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+<meta charset="utf-8">
+<meta http-equiv="X-UA-Compatible" content="IE=edge">
+<meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<title>Custom tidy method for STEP results — tidy.step • tern</title>
+<!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png">
+<link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png">
+<link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png">
+<link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png">
+<link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png">
+<link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png">
+<script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet">
+<script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet">
+<link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet">
+<script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Custom tidy method for STEP results — tidy.step">
+<meta name="description" content="
+Tidy the STEP results into a tibble format ready for plotting.">
+<meta property="og:description" content="
+Tidy the STEP results into a tibble format ready for plotting.">
+<meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png">
+<link rel="stylesheet" href="../consent.css">
+<script src="../consent.js" type="text/javascript" charset="utf-8"></script>
+</head>
+<body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
 
 
@@ -17,26 +40,66 @@
     </button>
 
     <div id="navbar" class="collapse navbar-collapse ms-3">
-      <ul class="navbar-nav me-auto"><li class="nav-item"><a class="nav-link" href="../articles/tern.html">Get started</a></li>
+      <ul class="navbar-nav me-auto">
+<li class="nav-item"><a class="nav-link" href="../articles/tern.html">Get started</a></li>
 <li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
 <li class="nav-item dropdown">
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-articles" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Articles</button>
-  <ul class="dropdown-menu" aria-labelledby="dropdown-articles"><li><a class="dropdown-item" href="../articles/missing_values.html">Missing Values in Tern</a></li>
+  <ul class="dropdown-menu" aria-labelledby="dropdown-articles">
+<li><a class="dropdown-item" href="../articles/missing_values.html">Missing Values in Tern</a></li>
     <li><a class="dropdown-item" href="../articles/tables.html">Tabulation</a></li>
     <li><a class="dropdown-item" href="../articles/tern_formats.html">Formatting Functions</a></li>
     <li><a class="dropdown-item" href="../articles/tern_functions_guide.html">Understanding `tern` functions</a></li>
-  </ul></li>
+  </ul>
+</li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
-  <ul class="dropdown-menu" aria-labelledby="dropdown-reports"><li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
+  <ul class="dropdown-menu" aria-labelledby="dropdown-reports">
+<li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
     <li><a class="dropdown-item" href="../unit-test-report/">Unit test report</a></li>
     <li><a class="dropdown-item" href="../unit-test-report-non-cran/">Non-CRAN unit test report</a></li>
-  </ul></li>
-      </ul><ul class="navbar-nav"><li class="nav-item"><form class="form-inline" role="search">
- <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json"></form></li>
+  </ul>
+</li>
+      <div><li class="nav-item dropdown">
+    <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-versions">Versions</a>
+    <div class="dropdown-menu" aria-labelledby="dropdown-versions">
+    <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/main">main</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.5">v0.9.5</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.4">v0.9.4</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.3">v0.9.3</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1-rc3">v0.9.1-rc3</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a>
+</div>
+</li></div>
+</ul>
+<ul class="navbar-nav">
+<li class="nav-item"><form class="form-inline" role="search">
+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json">
+</form></li>
 <li class="nav-item"><a class="external-link nav-link" href="https://github.com/insightsengineering/tern" aria-label="GitHub"><span class="fa fa-github"></span></a></li>
-      </ul></div>
+      </ul>
+</div>
 
 
   </div>
@@ -54,35 +117,44 @@
     </div>
 
     <div class="section level2">
-    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
+    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="co"># S3 method for class 'step'</span></span>
 <span><span class="fu"><a href="https://generics.r-lib.org/reference/tidy.html" class="external-link">tidy</a></span><span class="op">(</span><span class="va">x</span>, <span class="va">...</span><span class="op">)</span></span></code></pre></div>
     </div>
 
     <div class="section level2">
-    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
+    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a>
+</h2>
 
 
-<dl><dt id="arg-x">x<a class="anchor" aria-label="anchor" href="#arg-x"></a></dt>
+<dl>
+<dt id="arg-x">x<a class="anchor" aria-label="anchor" href="#arg-x"></a>
+</dt>
 <dd><p>(<code>matrix</code>)<br> results from <code><a href="fit_survival_step.html">fit_survival_step()</a></code>.</p></dd>
 
 
-<dt id="arg--">...<a class="anchor" aria-label="anchor" href="#arg--"></a></dt>
+<dt id="arg--">...<a class="anchor" aria-label="anchor" href="#arg--"></a>
+</dt>
 <dd><p>not used.</p></dd>
 
-</dl></div>
+</dl>
+</div>
     <div class="section level2">
-    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
+    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a>
+</h2>
     <p>A <code>tibble</code> with one row per STEP subgroup. The estimates and CIs are on the HR or OR scale,
 respectively. Additional attributes carry metadata also used for plotting.</p>
     </div>
     <div class="section level2">
-    <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"></a></h2>
+    <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"></a>
+</h2>
     <div class="dont-index"><p><code><a href="g_step.html">g_step()</a></code> which consumes the result from this function.</p></div>
     </div>
 
     <div class="section level2">
-    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
+    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://github.com/therneau/survival" class="external-link">survival</a></span><span class="op">)</span></span></span>
 <span class="r-in"><span><span class="va">lung</span><span class="op">$</span><span class="va">sex</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/factor.html" class="external-link">factor</a></span><span class="op">(</span><span class="va">lung</span><span class="op">$</span><span class="va">sex</span><span class="op">)</span></span></span>
 <span class="r-in"><span><span class="va">vars</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span></span></span>
@@ -117,17 +189,19 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 </code></pre></div>
     </div>
   </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
-    </nav></aside></div>
+    </nav></aside>
+</div>
 
 
     <footer><div class="nest">
   <p>tern is a part of the <strong>NEST</strong> and <a href="https://pharmaverse.org/" class="external-link"><strong>pharmaverse</strong></a>.</p>
 </div>
-<script type="text/javascript" src="../analytics.js"></script></footer></div>
-
+<script type="text/javascript" src="../analytics.js"></script></footer>
+</div>
 
 
 
 
-  </body></html>
 
+  </body>
+</html>
diff --git a/main/reference/tidy_coxreg.html b/main/reference/tidy_coxreg.html
index 67d946de79..8fab3fbf78 100644
--- a/main/reference/tidy_coxreg.html
+++ b/main/reference/tidy_coxreg.html
@@ -1,5 +1,28 @@
-<!DOCTYPE html>
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@@ -51,7 +114,8 @@
     </div>
 
     <div class="section level2">
-    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
+    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="co"># S3 method for class 'summary.coxph'</span></span>
 <span><span class="fu"><a href="https://generics.r-lib.org/reference/tidy.html" class="external-link">tidy</a></span><span class="op">(</span><span class="va">x</span>, <span class="va">...</span><span class="op">)</span></span>
 <span></span>
@@ -63,44 +127,64 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
     </div>
 
     <div class="section level2">
-    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
+    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a>
+</h2>
 
 
-<dl><dt id="arg-x">x<a class="anchor" aria-label="anchor" href="#arg-x"></a></dt>
+<dl>
+<dt id="arg-x">x<a class="anchor" aria-label="anchor" href="#arg-x"></a>
+</dt>
 <dd><p>(<code>list</code>)<br> result of the Cox regression model fitted by <code><a href="fit_coxreg.html">fit_coxreg_univar()</a></code> (for univariate models)
 or <code><a href="fit_coxreg.html">fit_coxreg_multivar()</a></code> (for multivariate models).</p></dd>
 
 
-<dt id="arg--">...<a class="anchor" aria-label="anchor" href="#arg--"></a></dt>
+<dt id="arg--">...<a class="anchor" aria-label="anchor" href="#arg--"></a>
+</dt>
 <dd><p>additional arguments for the lower level functions.</p></dd>
 
-</dl></div>
+</dl>
+</div>
     <div class="section level2">
-    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
-    <p><code><a href="https://broom.tidymodels.org/reference/reexports.html" class="external-link">broom::tidy()</a></code> returns:</p><ul><li><p>For <code>summary.coxph</code> objects,  a <code>data.frame</code> with columns: <code>Pr(&gt;|z|)</code>, <code>exp(coef)</code>, <code>exp(-coef)</code>, <code>lower .95</code>,
+    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a>
+</h2>
+    <p><code><a href="https://broom.tidymodels.org/reference/reexports.html" class="external-link">broom::tidy()</a></code> returns:</p>
+<ul>
+<li><p>For <code>summary.coxph</code> objects,  a <code>data.frame</code> with columns: <code>Pr(&gt;|z|)</code>, <code>exp(coef)</code>, <code>exp(-coef)</code>, <code>lower .95</code>,
 <code>upper .95</code>, <code>level</code>, and <code>n</code>.</p></li>
 <li><p>For <code>coxreg.univar</code> objects, a <code>data.frame</code> with columns: <code>effect</code>, <code>term</code>, <code>term_label</code>, <code>level</code>, <code>n</code>, <code>hr</code>,
 <code>lcl</code>, <code>ucl</code>, <code>pval</code>, and <code>ci</code>.</p></li>
 <li><p>For <code>coxreg.multivar</code> objects, a <code>data.frame</code> with columns: <code>term</code>, <code>pval</code>, <code>term_label</code>, <code>hr</code>, <code>lcl</code>, <code>ucl</code>,
 <code>level</code>, and <code>ci</code>.</p></li>
-</ul></div>
+</ul>
+</div>
     <div class="section level2">
-    <h2 id="functions">Functions<a class="anchor" aria-label="anchor" href="#functions"></a></h2>
-
-<ul><li><p><code>tidy(summary.coxph)</code>: Custom tidy method for <code><a href="https://rdrr.io/pkg/survival/man/coxph.html" class="external-link">survival::coxph()</a></code> summary results.</p>
-<p>Tidy the <code><a href="https://rdrr.io/pkg/survival/man/coxph.html" class="external-link">survival::coxph()</a></code> results into a <code>data.frame</code> to extract model results.</p></li>
-<li><p><code>tidy(coxreg.univar)</code>: Custom tidy method for a univariate Cox regression.</p>
-<p>Tidy up the result of a Cox regression model fitted by <code><a href="fit_coxreg.html">fit_coxreg_univar()</a></code>.</p></li>
-<li><p><code>tidy(coxreg.multivar)</code>: Custom tidy method for a multivariate Cox regression.</p>
-<p>Tidy up the result of a Cox regression model fitted by <code><a href="fit_coxreg.html">fit_coxreg_multivar()</a></code>.</p></li>
-</ul></div>
+    <h2 id="functions">Functions<a class="anchor" aria-label="anchor" href="#functions"></a>
+</h2>
+
+<ul>
+<li>
+<p><code>tidy(summary.coxph)</code>: Custom tidy method for <code><a href="https://rdrr.io/pkg/survival/man/coxph.html" class="external-link">survival::coxph()</a></code> summary results.</p>
+<p>Tidy the <code><a href="https://rdrr.io/pkg/survival/man/coxph.html" class="external-link">survival::coxph()</a></code> results into a <code>data.frame</code> to extract model results.</p>
+</li>
+<li>
+<p><code>tidy(coxreg.univar)</code>: Custom tidy method for a univariate Cox regression.</p>
+<p>Tidy up the result of a Cox regression model fitted by <code><a href="fit_coxreg.html">fit_coxreg_univar()</a></code>.</p>
+</li>
+<li>
+<p><code>tidy(coxreg.multivar)</code>: Custom tidy method for a multivariate Cox regression.</p>
+<p>Tidy up the result of a Cox regression model fitted by <code><a href="fit_coxreg.html">fit_coxreg_multivar()</a></code>.</p>
+</li>
+</ul>
+</div>
     <div class="section level2">
-    <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"></a></h2>
+    <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"></a>
+</h2>
     <div class="dont-index"><p><a href="cox_regression.html">cox_regression</a></p></div>
     </div>
 
     <div class="section level2">
-    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
+    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://github.com/therneau/survival" class="external-link">survival</a></span><span class="op">)</span></span></span>
 <span class="r-in"><span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://broom.tidymodels.org/" class="external-link">broom</a></span><span class="op">)</span></span></span>
 <span class="r-in"><span></span></span>
@@ -221,17 +305,19 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 </code></pre></div>
     </div>
   </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
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+<link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet">
+<script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Replicate entries of a vector if required — to_n">
+<meta name="description" content="
+Replicate entries of a vector if required.">
+<meta property="og:description" content="
+Replicate entries of a vector if required.">
+<meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png">
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@@ -17,26 +40,66 @@
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+      <ul class="navbar-nav me-auto">
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+<li><a class="dropdown-item" href="../articles/missing_values.html">Missing Values in Tern</a></li>
     <li><a class="dropdown-item" href="../articles/tables.html">Tabulation</a></li>
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+  </ul>
+</li>
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+<li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
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+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a>
+</div>
+</li></div>
+</ul>
+<ul class="navbar-nav">
+<li class="nav-item"><form class="form-inline" role="search">
+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json">
+</form></li>
 <li class="nav-item"><a class="external-link nav-link" href="https://github.com/insightsengineering/tern" aria-label="GitHub"><span class="fa fa-github"></span></a></li>
-      </ul></div>
+      </ul>
+</div>
 
 
   </div>
@@ -54,44 +117,54 @@
     </div>
 
     <div class="section level2">
-    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
+    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">to_n</span><span class="op">(</span><span class="va">x</span>, <span class="va">n</span><span class="op">)</span></span></code></pre></div>
     </div>
 
     <div class="section level2">
-    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
+    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a>
+</h2>
 
 
-<dl><dt id="arg-x">x<a class="anchor" aria-label="anchor" href="#arg-x"></a></dt>
+<dl>
+<dt id="arg-x">x<a class="anchor" aria-label="anchor" href="#arg-x"></a>
+</dt>
 <dd><p>(<code>numeric</code>)<br> vector of numbers we want to analyze.</p></dd>
 
 
-<dt id="arg-n">n<a class="anchor" aria-label="anchor" href="#arg-n"></a></dt>
+<dt id="arg-n">n<a class="anchor" aria-label="anchor" href="#arg-n"></a>
+</dt>
 <dd><p>(<code>integer(1)</code>)<br> number of entries that are needed.</p></dd>
 
-</dl></div>
+</dl>
+</div>
     <div class="section level2">
-    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
+    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a>
+</h2>
     <p><code>x</code> if it has the required length already or is <code>NULL</code>,
 otherwise if it is scalar the replicated version of it with <code>n</code> entries.</p>
     </div>
     <div class="section level2">
-    <h2 id="note">Note<a class="anchor" aria-label="anchor" href="#note"></a></h2>
+    <h2 id="note">Note<a class="anchor" aria-label="anchor" href="#note"></a>
+</h2>
     <p>This function will fail if <code>x</code> is not of length <code>n</code> and/or is not a scalar.</p>
     </div>
 
   </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
-    </nav></aside></div>
+    </nav></aside>
+</div>
 
 
     <footer><div class="nest">
   <p>tern is a part of the <strong>NEST</strong> and <a href="https://pharmaverse.org/" class="external-link"><strong>pharmaverse</strong></a>.</p>
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-<script type="text/javascript" src="../analytics.js"></script></footer></div>
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+<script type="text/javascript" src="../analytics.js"></script></footer>
+</div>
 
 
 
 
-  </body></html>
 
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diff --git a/main/reference/to_string_matrix.html b/main/reference/to_string_matrix.html
index 81626fcb8e..d64744de27 100644
--- a/main/reference/to_string_matrix.html
+++ b/main/reference/to_string_matrix.html
@@ -1,13 +1,36 @@
-<!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Convert table into matrix of strings — to_string_matrix • tern</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Convert table into matrix of strings — to_string_matrix"><meta name="description" content="
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+<meta http-equiv="X-UA-Compatible" content="IE=edge">
+<meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<title>Convert table into matrix of strings — to_string_matrix • tern</title>
+<!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png">
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+<script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet">
+<script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet">
+<link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet">
+<script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Convert table into matrix of strings — to_string_matrix">
+<meta name="description" content="
 Helper function to use mostly within tests. with_spacesparameter allows
 to test not only for content but also indentation and table structure.
 print_txt_to_copy instead facilitate the testing development by returning a well
-formatted text that needs only to be copied and pasted in the expected output."><meta property="og:description" content="
+formatted text that needs only to be copied and pasted in the expected output.">
+<meta property="og:description" content="
 Helper function to use mostly within tests. with_spacesparameter allows
 to test not only for content but also indentation and table structure.
 print_txt_to_copy instead facilitate the testing development by returning a well
-formatted text that needs only to be copied and pasted in the expected output."><meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png"><link rel="stylesheet" href="../consent.css"><script src="../consent.js" type="text/javascript" charset="utf-8"></script></head><body>
+formatted text that needs only to be copied and pasted in the expected output.">
+<meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png">
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+</head>
+<body>
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@@ -23,26 +46,66 @@
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     <li><a class="dropdown-item" href="../articles/tables.html">Tabulation</a></li>
     <li><a class="dropdown-item" href="../articles/tern_formats.html">Formatting Functions</a></li>
     <li><a class="dropdown-item" href="../articles/tern_functions_guide.html">Understanding `tern` functions</a></li>
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+</li>
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+</li>
+      <div><li class="nav-item dropdown">
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+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
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+</div>
+</li></div>
+</ul>
+<ul class="navbar-nav">
+<li class="nav-item"><form class="form-inline" role="search">
+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json">
+</form></li>
 <li class="nav-item"><a class="external-link nav-link" href="https://github.com/insightsengineering/tern" aria-label="GitHub"><span class="fa fa-github"></span></a></li>
-      </ul></div>
+      </ul>
+</div>
 
 
   </div>
@@ -63,7 +126,8 @@
     </div>
 
     <div class="section level2">
-    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
+    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">to_string_matrix</span><span class="op">(</span></span>
 <span>  <span class="va">x</span>,</span>
 <span>  widths <span class="op">=</span> <span class="cn">NULL</span>,</span>
@@ -75,49 +139,60 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
     </div>
 
     <div class="section level2">
-    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
+    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a>
+</h2>
 
 
-<dl><dt id="arg-x">x<a class="anchor" aria-label="anchor" href="#arg-x"></a></dt>
+<dl>
+<dt id="arg-x">x<a class="anchor" aria-label="anchor" href="#arg-x"></a>
+</dt>
 <dd><p>(<code>VTableTree</code>)<br><code>rtables</code> table object.</p></dd>
 
 
-<dt id="arg-widths">widths<a class="anchor" aria-label="anchor" href="#arg-widths"></a></dt>
+<dt id="arg-widths">widths<a class="anchor" aria-label="anchor" href="#arg-widths"></a>
+</dt>
 <dd><p>(<code>numeric</code> or  <code>NULL</code>)<br> Proposed widths for the columns of <code>x</code>. The expected
 length of this numeric vector can be retrieved with <code>ncol(x) + 1</code> as the column of row names
 must also be considered.</p></dd>
 
 
-<dt id="arg-max-width">max_width<a class="anchor" aria-label="anchor" href="#arg-max-width"></a></dt>
+<dt id="arg-max-width">max_width<a class="anchor" aria-label="anchor" href="#arg-max-width"></a>
+</dt>
 <dd><p>(<code>integer(1)</code>, <code>string</code> or <code>NULL</code>)<br> width that title and footer (including
 footnotes) materials should be word-wrapped to. If <code>NULL</code>, it is set to the current print width of the
 session (<code>getOption("width")</code>). If set to <code>"auto"</code>, the width of the table (plus any table inset) is
 used. Parameter is ignored if <code>tf_wrap = FALSE</code>.</p></dd>
 
 
-<dt id="arg-hsep">hsep<a class="anchor" aria-label="anchor" href="#arg-hsep"></a></dt>
+<dt id="arg-hsep">hsep<a class="anchor" aria-label="anchor" href="#arg-hsep"></a>
+</dt>
 <dd><p>(<code>string</code>)<br> character to repeat to create header/body separator line. If
 <code>NULL</code>, the object value will be used. If <code>" "</code>, an empty separator will be printed. See
 <code><a href="https://insightsengineering.github.io/formatters/latest-tag/reference/default_horizontal_sep.html" class="external-link">default_hsep()</a></code> for more information.</p></dd>
 
 
-<dt id="arg-with-spaces">with_spaces<a class="anchor" aria-label="anchor" href="#arg-with-spaces"></a></dt>
+<dt id="arg-with-spaces">with_spaces<a class="anchor" aria-label="anchor" href="#arg-with-spaces"></a>
+</dt>
 <dd><p>(<code>flag</code>)<br> whether the tested table should keep the indentation and other relevant spaces.</p></dd>
 
 
-<dt id="arg-print-txt-to-copy">print_txt_to_copy<a class="anchor" aria-label="anchor" href="#arg-print-txt-to-copy"></a></dt>
+<dt id="arg-print-txt-to-copy">print_txt_to_copy<a class="anchor" aria-label="anchor" href="#arg-print-txt-to-copy"></a>
+</dt>
 <dd><p>(<code>flag</code>)<br> utility to have a way to copy the input table directly
 into the expected variable instead of copying it too manually.</p></dd>
 
-</dl></div>
+</dl>
+</div>
     <div class="section level2">
-    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
+    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a>
+</h2>
     <p>A <code>matrix</code> of <code>string</code>s. If <code>print_txt_to_copy = TRUE</code> the well formatted printout of the
 table will be printed to console, ready to be copied as a expected value.</p>
     </div>
 
     <div class="section level2">
-    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
+    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">tbl</span> <span class="op">&lt;-</span> <span class="fu">basic_table</span><span class="op">(</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span></span>
 <span class="r-in"><span>  <span class="fu">split_rows_by</span><span class="op">(</span><span class="st">"SEX"</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span></span>
 <span class="r-in"><span>  <span class="fu">split_cols_by</span><span class="op">(</span><span class="st">"ARM"</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span></span>
@@ -136,17 +211,19 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 </code></pre></div>
     </div>
   </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
-    </nav></aside></div>
+    </nav></aside>
+</div>
 
 
     <footer><div class="nest">
   <p>tern is a part of the <strong>NEST</strong> and <a href="https://pharmaverse.org/" class="external-link"><strong>pharmaverse</strong></a>.</p>
 </div>
-<script type="text/javascript" src="../analytics.js"></script></footer></div>
-
+<script type="text/javascript" src="../analytics.js"></script></footer>
+</div>
 
 
 
 
-  </body></html>
 
+  </body>
+</html>
diff --git a/main/reference/try_car_anova.html b/main/reference/try_car_anova.html
index 4caa6ac62b..e087cb592d 100644
--- a/main/reference/try_car_anova.html
+++ b/main/reference/try_car_anova.html
@@ -1,5 +1,28 @@
-<!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>tryCatch around car::Anova — try_car_anova • tern</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="tryCatch around car::Anova — try_car_anova"><meta name="description" content="Captures warnings when executing car::Anova."><meta property="og:description" content="Captures warnings when executing car::Anova."><meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png"><link rel="stylesheet" href="../consent.css"><script src="../consent.js" type="text/javascript" charset="utf-8"></script></head><body>
+<html lang="en">
+<head>
+<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+<meta charset="utf-8">
+<meta http-equiv="X-UA-Compatible" content="IE=edge">
+<meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<title>tryCatch around car::Anova — try_car_anova • tern</title>
+<!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png">
+<link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png">
+<link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png">
+<link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png">
+<link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png">
+<link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png">
+<script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet">
+<script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet">
+<link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet">
+<script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="tryCatch around car::Anova — try_car_anova">
+<meta name="description" content="Captures warnings when executing car::Anova.">
+<meta property="og:description" content="Captures warnings when executing car::Anova.">
+<meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png">
+<link rel="stylesheet" href="../consent.css">
+<script src="../consent.js" type="text/javascript" charset="utf-8"></script>
+</head>
+<body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
 
 
@@ -15,33 +38,75 @@
     </button>
 
     <div id="navbar" class="collapse navbar-collapse ms-3">
-      <ul class="navbar-nav me-auto"><li class="nav-item"><a class="nav-link" href="../articles/tern.html">Get started</a></li>
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+<li class="nav-item"><a class="nav-link" href="../articles/tern.html">Get started</a></li>
 <li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
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+  <ul class="dropdown-menu" aria-labelledby="dropdown-articles">
+<li><a class="dropdown-item" href="../articles/missing_values.html">Missing Values in Tern</a></li>
     <li><a class="dropdown-item" href="../articles/tables.html">Tabulation</a></li>
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     <li><a class="dropdown-item" href="../articles/tern_functions_guide.html">Understanding `tern` functions</a></li>
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+  </ul>
+</li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
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+  <ul class="dropdown-menu" aria-labelledby="dropdown-reports">
+<li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
     <li><a class="dropdown-item" href="../unit-test-report/">Unit test report</a></li>
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- <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json"></form></li>
+  </ul>
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+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.5">v0.9.5</a>
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+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.3">v0.9.3</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1-rc3">v0.9.1-rc3</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a>
+</div>
+</li></div>
+</ul>
+<ul class="navbar-nav">
+<li class="nav-item"><form class="form-inline" role="search">
+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json">
+</form></li>
 <li class="nav-item"><a class="external-link nav-link" href="https://github.com/insightsengineering/tern" aria-label="GitHub"><span class="fa fa-github"></span></a></li>
-      </ul></div>
+      </ul>
+</div>
 
 
   </div>
 </nav><div class="container template-reference-topic">
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
-      <img src="../logo.png" class="logo" alt=""><h1><code>tryCatch</code> around <code>car::Anova</code></h1>
+      <img src="../logo.png" class="logo" alt=""><h1>
+<code>tryCatch</code> around <code>car::Anova</code>
+</h1>
       <small class="dont-index">Source: <a href="https://github.com/insightsengineering/tern/blob/main/R/coxph.R" class="external-link"><code>R/coxph.R</code></a></small>
       <div class="d-none name"><code>try_car_anova.Rd</code></div>
     </div>
@@ -51,21 +116,26 @@
     </div>
 
     <div class="section level2">
-    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
+    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">try_car_anova</span><span class="op">(</span><span class="va">mod</span>, <span class="va">test.statistic</span><span class="op">)</span></span></code></pre></div>
     </div>
 
     <div class="section level2">
-    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
+    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a>
+</h2>
 
 
-<dl><dt id="arg-mod">mod<a class="anchor" aria-label="anchor" href="#arg-mod"></a></dt>
+<dl>
+<dt id="arg-mod">mod<a class="anchor" aria-label="anchor" href="#arg-mod"></a>
+</dt>
 <dd><p><code>lm</code>, <code>aov</code>, <code>glm</code>, <code>multinom</code>, <code>polr</code>
     <code>mlm</code>, <code>coxph</code>, <code>coxme</code>, <code>lme</code>, <code>mer</code>, <code>merMod</code>, <code>svyglm</code>, <code>svycoxph</code>,
     <code>rlm</code>, <code>clm</code>, <code>clmm</code>, or other suitable model object.</p></dd>
 
 
-<dt id="arg-test-statistic">test.statistic<a class="anchor" aria-label="anchor" href="#arg-test-statistic"></a></dt>
+<dt id="arg-test-statistic">test.statistic<a class="anchor" aria-label="anchor" href="#arg-test-statistic"></a>
+</dt>
 <dd><p>for a generalized linear model, whether to calculate
     <code>"LR"</code> (likelihood-ratio), <code>"Wald"</code>, or <code>"F"</code> tests; for a Cox
     or Cox mixed-effects model, whether to calculate <code>"LR"</code> (partial-likelihood ratio) or
@@ -79,14 +149,17 @@ <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#argumen
     objects permits the specification of more than one multivariate
     test statistic, and the default is to report all four.</p></dd>
 
-</dl></div>
+</dl>
+</div>
     <div class="section level2">
-    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
+    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a>
+</h2>
     <p>A list with item <code>aov</code> for the result of the model and <code>error_text</code> for the captured warnings.</p>
     </div>
 
     <div class="section level2">
-    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
+    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="co"># `car::Anova` on cox regression model including strata and expected</span></span></span>
 <span class="r-in"><span><span class="co"># a likelihood ratio test triggers a warning as only Wald method is</span></span></span>
 <span class="r-in"><span><span class="co"># accepted.</span></span></span>
@@ -101,17 +174,19 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 </code></pre></div>
     </div>
   </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
-    </nav></aside></div>
+    </nav></aside>
+</div>
 
 
     <footer><div class="nest">
   <p>tern is a part of the <strong>NEST</strong> and <a href="https://pharmaverse.org/" class="external-link"><strong>pharmaverse</strong></a>.</p>
 </div>
-<script type="text/javascript" src="../analytics.js"></script></footer></div>
-
+<script type="text/javascript" src="../analytics.js"></script></footer>
+</div>
 
 
 
 
-  </body></html>
 
+  </body>
+</html>
diff --git a/main/reference/ungroup_stats.html b/main/reference/ungroup_stats.html
index ef26e78382..207ec33b25 100644
--- a/main/reference/ungroup_stats.html
+++ b/main/reference/ungroup_stats.html
@@ -1,5 +1,28 @@
-<!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Ungroup non-numeric statistics — ungroup_stats • tern</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Ungroup non-numeric statistics — ungroup_stats"><meta name="description" content="Ungroups grouped non-numeric statistics within input vectors .formats, .labels, and .indent_mods."><meta property="og:description" content="Ungroups grouped non-numeric statistics within input vectors .formats, .labels, and .indent_mods."><meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png"><link rel="stylesheet" href="../consent.css"><script src="../consent.js" type="text/javascript" charset="utf-8"></script></head><body>
+<html lang="en">
+<head>
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+<meta charset="utf-8">
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+<meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<title>Ungroup non-numeric statistics — ungroup_stats • tern</title>
+<!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png">
+<link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png">
+<link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png">
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+<link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png">
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+<script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet">
+<script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet">
+<link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet">
+<script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Ungroup non-numeric statistics — ungroup_stats">
+<meta name="description" content="Ungroups grouped non-numeric statistics within input vectors .formats, .labels, and .indent_mods.">
+<meta property="og:description" content="Ungroups grouped non-numeric statistics within input vectors .formats, .labels, and .indent_mods.">
+<meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png">
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+</head>
+<body>
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@@ -15,26 +38,66 @@
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+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a>
+</div>
+</li></div>
+</ul>
+<ul class="navbar-nav">
+<li class="nav-item"><form class="form-inline" role="search">
+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json">
+</form></li>
 <li class="nav-item"><a class="external-link nav-link" href="https://github.com/insightsengineering/tern" aria-label="GitHub"><span class="fa fa-github"></span></a></li>
-      </ul></div>
+      </ul>
+</div>
 
 
   </div>
@@ -51,53 +114,65 @@
     </div>
 
     <div class="section level2">
-    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
+    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">ungroup_stats</span><span class="op">(</span><span class="va">x</span>, <span class="va">.formats</span>, <span class="va">.labels</span>, <span class="va">.indent_mods</span><span class="op">)</span></span></code></pre></div>
     </div>
 
     <div class="section level2">
-    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
+    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a>
+</h2>
 
 
-<dl><dt id="arg-x">x<a class="anchor" aria-label="anchor" href="#arg-x"></a></dt>
+<dl>
+<dt id="arg-x">x<a class="anchor" aria-label="anchor" href="#arg-x"></a>
+</dt>
 <dd><p>(named <code>list</code> of <code>numeric</code>)<br> list of numeric statistics containing the statistics to ungroup.</p></dd>
 
 
-<dt id="arg--formats">.formats<a class="anchor" aria-label="anchor" href="#arg--formats"></a></dt>
+<dt id="arg--formats">.formats<a class="anchor" aria-label="anchor" href="#arg--formats"></a>
+</dt>
 <dd><p>(named <code>character</code> or <code>list</code>)<br> formats for the statistics. See Details in <code>analyze_vars</code> for more
 information on the <code>"auto"</code> setting.</p></dd>
 
 
-<dt id="arg--labels">.labels<a class="anchor" aria-label="anchor" href="#arg--labels"></a></dt>
+<dt id="arg--labels">.labels<a class="anchor" aria-label="anchor" href="#arg--labels"></a>
+</dt>
 <dd><p>(named <code>character</code>)<br> labels for the statistics (without indent).</p></dd>
 
 
-<dt id="arg--indent-mods">.indent_mods<a class="anchor" aria-label="anchor" href="#arg--indent-mods"></a></dt>
+<dt id="arg--indent-mods">.indent_mods<a class="anchor" aria-label="anchor" href="#arg--indent-mods"></a>
+</dt>
 <dd><p>(named <code>integer</code>)<br> indent modifiers for the labels. Defaults to 0, which corresponds to the
 unmodified default behavior. Can be negative.</p></dd>
 
-</dl></div>
+</dl>
+</div>
     <div class="section level2">
-    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
+    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a>
+</h2>
     <p>A <code>list</code> with modified elements <code>x</code>, <code>.formats</code>, <code>.labels</code>, and <code>.indent_mods</code>.</p>
     </div>
     <div class="section level2">
-    <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"></a></h2>
+    <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"></a>
+</h2>
     <div class="dont-index"><p><code><a href="analyze_variables.html">a_summary()</a></code> which uses this function internally.</p></div>
     </div>
 
   </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
-    </nav></aside></div>
+    </nav></aside>
+</div>
 
 
     <footer><div class="nest">
   <p>tern is a part of the <strong>NEST</strong> and <a href="https://pharmaverse.org/" class="external-link"><strong>pharmaverse</strong></a>.</p>
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-<script type="text/javascript" src="../analytics.js"></script></footer></div>
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diff --git a/main/reference/univariate.html b/main/reference/univariate.html
index e09c01bc82..5fcc4a1815 100644
--- a/main/reference/univariate.html
+++ b/main/reference/univariate.html
@@ -1,9 +1,32 @@
-<!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Univariate formula special term — univariate • tern</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Univariate formula special term — univariate"><meta name="description" content="
+<html lang="en">
+<head>
+<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+<meta charset="utf-8">
+<meta http-equiv="X-UA-Compatible" content="IE=edge">
+<meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<title>Univariate formula special term — univariate • tern</title>
+<!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png">
+<link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png">
+<link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png">
+<link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png">
+<link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png">
+<link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png">
+<script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet">
+<script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet">
+<link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet">
+<script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Univariate formula special term — univariate">
+<meta name="description" content="
 The special term univariate indicate that the model should be fitted individually for
-every variable included in univariate."><meta property="og:description" content="
+every variable included in univariate.">
+<meta property="og:description" content="
 The special term univariate indicate that the model should be fitted individually for
-every variable included in univariate."><meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png"><link rel="stylesheet" href="../consent.css"><script src="../consent.js" type="text/javascript" charset="utf-8"></script></head><body>
+every variable included in univariate.">
+<meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png">
+<link rel="stylesheet" href="../consent.css">
+<script src="../consent.js" type="text/javascript" charset="utf-8"></script>
+</head>
+<body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
 
 
@@ -19,26 +42,66 @@
     </button>
 
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-      <ul class="navbar-nav me-auto"><li class="nav-item"><a class="nav-link" href="../articles/tern.html">Get started</a></li>
+      <ul class="navbar-nav me-auto">
+<li class="nav-item"><a class="nav-link" href="../articles/tern.html">Get started</a></li>
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   <button class="nav-link dropdown-toggle" type="button" id="dropdown-articles" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Articles</button>
-  <ul class="dropdown-menu" aria-labelledby="dropdown-articles"><li><a class="dropdown-item" href="../articles/missing_values.html">Missing Values in Tern</a></li>
+  <ul class="dropdown-menu" aria-labelledby="dropdown-articles">
+<li><a class="dropdown-item" href="../articles/missing_values.html">Missing Values in Tern</a></li>
     <li><a class="dropdown-item" href="../articles/tables.html">Tabulation</a></li>
     <li><a class="dropdown-item" href="../articles/tern_formats.html">Formatting Functions</a></li>
     <li><a class="dropdown-item" href="../articles/tern_functions_guide.html">Understanding `tern` functions</a></li>
-  </ul></li>
+  </ul>
+</li>
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   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
-  <ul class="dropdown-menu" aria-labelledby="dropdown-reports"><li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
+  <ul class="dropdown-menu" aria-labelledby="dropdown-reports">
+<li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
     <li><a class="dropdown-item" href="../unit-test-report/">Unit test report</a></li>
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- <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json"></form></li>
+  </ul>
+</li>
+      <div><li class="nav-item dropdown">
+    <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-versions">Versions</a>
+    <div class="dropdown-menu" aria-labelledby="dropdown-versions">
+    <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/main">main</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.5">v0.9.5</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.4">v0.9.4</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.3">v0.9.3</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1-rc3">v0.9.1-rc3</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a>
+</div>
+</li></div>
+</ul>
+<ul class="navbar-nav">
+<li class="nav-item"><form class="form-inline" role="search">
+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json">
+</form></li>
 <li class="nav-item"><a class="external-link nav-link" href="https://github.com/insightsengineering/tern" aria-label="GitHub"><span class="fa fa-github"></span></a></li>
-      </ul></div>
+      </ul>
+</div>
 
 
   </div>
@@ -57,43 +120,55 @@
     </div>
 
     <div class="section level2">
-    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
+    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">univariate</span><span class="op">(</span><span class="va">x</span><span class="op">)</span></span></code></pre></div>
     </div>
 
     <div class="section level2">
-    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
+    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a>
+</h2>
 
 
-<dl><dt id="arg-x">x<a class="anchor" aria-label="anchor" href="#arg-x"></a></dt>
+<dl>
+<dt id="arg-x">x<a class="anchor" aria-label="anchor" href="#arg-x"></a>
+</dt>
 <dd><p>(<code>character</code>)<br> a vector of variable names separated by commas.</p></dd>
 
-</dl></div>
+</dl>
+</div>
     <div class="section level2">
-    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
+    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a>
+</h2>
     <p>When used within a model formula, produces univariate models for each variable provided.</p>
     </div>
     <div class="section level2">
-    <h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a></h2>
+    <h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a>
+</h2>
     <p>If provided alongside with pairwise specification, the model
-<code>y ~ ARM + univariate(SEX, AGE, RACE)</code> lead to the study and comparison of the models</p><ul><li><p><code>y ~ ARM</code></p></li>
+<code>y ~ ARM + univariate(SEX, AGE, RACE)</code> lead to the study and comparison of the models</p>
+<ul>
+<li><p><code>y ~ ARM</code></p></li>
 <li><p><code>y ~ ARM + SEX</code></p></li>
 <li><p><code>y ~ ARM + AGE</code></p></li>
 <li><p><code>y ~ ARM + RACE</code></p></li>
-</ul></div>
+</ul>
+</div>
 
   </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
-    </nav></aside></div>
+    </nav></aside>
+</div>
 
 
     <footer><div class="nest">
   <p>tern is a part of the <strong>NEST</strong> and <a href="https://pharmaverse.org/" class="external-link"><strong>pharmaverse</strong></a>.</p>
 </div>
-<script type="text/javascript" src="../analytics.js"></script></footer></div>
-
+<script type="text/javascript" src="../analytics.js"></script></footer>
+</div>
 
 
 
 
-  </body></html>
 
+  </body>
+</html>
diff --git a/main/reference/unlist_and_blank_na.html b/main/reference/unlist_and_blank_na.html
index a12ee616d7..1b730df58d 100644
--- a/main/reference/unlist_and_blank_na.html
+++ b/main/reference/unlist_and_blank_na.html
@@ -1,5 +1,28 @@
-<!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Blank for missing input — unlist_and_blank_na • tern</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Blank for missing input — unlist_and_blank_na"><meta name="description" content="Helper function to use in tabulating model results."><meta property="og:description" content="Helper function to use in tabulating model results."><meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png"><link rel="stylesheet" href="../consent.css"><script src="../consent.js" type="text/javascript" charset="utf-8"></script></head><body>
+<html lang="en">
+<head>
+<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+<meta charset="utf-8">
+<meta http-equiv="X-UA-Compatible" content="IE=edge">
+<meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<title>Blank for missing input — unlist_and_blank_na • tern</title>
+<!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png">
+<link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png">
+<link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png">
+<link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png">
+<link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png">
+<link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png">
+<script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet">
+<script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet">
+<link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet">
+<script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Blank for missing input — unlist_and_blank_na">
+<meta name="description" content="Helper function to use in tabulating model results.">
+<meta property="og:description" content="Helper function to use in tabulating model results.">
+<meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png">
+<link rel="stylesheet" href="../consent.css">
+<script src="../consent.js" type="text/javascript" charset="utf-8"></script>
+</head>
+<body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
 
 
@@ -15,26 +38,66 @@
     </button>
 
     <div id="navbar" class="collapse navbar-collapse ms-3">
-      <ul class="navbar-nav me-auto"><li class="nav-item"><a class="nav-link" href="../articles/tern.html">Get started</a></li>
+      <ul class="navbar-nav me-auto">
+<li class="nav-item"><a class="nav-link" href="../articles/tern.html">Get started</a></li>
 <li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
 <li class="nav-item dropdown">
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-articles" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Articles</button>
-  <ul class="dropdown-menu" aria-labelledby="dropdown-articles"><li><a class="dropdown-item" href="../articles/missing_values.html">Missing Values in Tern</a></li>
+  <ul class="dropdown-menu" aria-labelledby="dropdown-articles">
+<li><a class="dropdown-item" href="../articles/missing_values.html">Missing Values in Tern</a></li>
     <li><a class="dropdown-item" href="../articles/tables.html">Tabulation</a></li>
     <li><a class="dropdown-item" href="../articles/tern_formats.html">Formatting Functions</a></li>
     <li><a class="dropdown-item" href="../articles/tern_functions_guide.html">Understanding `tern` functions</a></li>
-  </ul></li>
+  </ul>
+</li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
-  <ul class="dropdown-menu" aria-labelledby="dropdown-reports"><li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
+  <ul class="dropdown-menu" aria-labelledby="dropdown-reports">
+<li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
     <li><a class="dropdown-item" href="../unit-test-report/">Unit test report</a></li>
     <li><a class="dropdown-item" href="../unit-test-report-non-cran/">Non-CRAN unit test report</a></li>
-  </ul></li>
-      </ul><ul class="navbar-nav"><li class="nav-item"><form class="form-inline" role="search">
- <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json"></form></li>
+  </ul>
+</li>
+      <div><li class="nav-item dropdown">
+    <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-versions">Versions</a>
+    <div class="dropdown-menu" aria-labelledby="dropdown-versions">
+    <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/main">main</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.5">v0.9.5</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.4">v0.9.4</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.3">v0.9.3</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1-rc3">v0.9.1-rc3</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a>
+</div>
+</li></div>
+</ul>
+<ul class="navbar-nav">
+<li class="nav-item"><form class="form-inline" role="search">
+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json">
+</form></li>
 <li class="nav-item"><a class="external-link nav-link" href="https://github.com/insightsengineering/tern" aria-label="GitHub"><span class="fa fa-github"></span></a></li>
-      </ul></div>
+      </ul>
+</div>
 
 
   </div>
@@ -51,36 +114,44 @@
     </div>
 
     <div class="section level2">
-    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
+    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">unlist_and_blank_na</span><span class="op">(</span><span class="va">x</span><span class="op">)</span></span></code></pre></div>
     </div>
 
     <div class="section level2">
-    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
+    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a>
+</h2>
 
 
-<dl><dt id="arg-x">x<a class="anchor" aria-label="anchor" href="#arg-x"></a></dt>
+<dl>
+<dt id="arg-x">x<a class="anchor" aria-label="anchor" href="#arg-x"></a>
+</dt>
 <dd><p>(<code>vector</code>)<br> input for a cell.</p></dd>
 
-</dl></div>
+</dl>
+</div>
     <div class="section level2">
-    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
+    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a>
+</h2>
     <p>An empty <code>character</code> vector if all entries in <code>x</code> are missing (<code>NA</code>), otherwise
 the unlisted version of <code>x</code>.</p>
     </div>
 
   </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
-    </nav></aside></div>
+    </nav></aside>
+</div>
 
 
     <footer><div class="nest">
   <p>tern is a part of the <strong>NEST</strong> and <a href="https://pharmaverse.org/" class="external-link"><strong>pharmaverse</strong></a>.</p>
 </div>
-<script type="text/javascript" src="../analytics.js"></script></footer></div>
-
+<script type="text/javascript" src="../analytics.js"></script></footer>
+</div>
 
 
 
 
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+  </body>
+</html>
diff --git a/main/reference/update_weights_strat_wilson.html b/main/reference/update_weights_strat_wilson.html
index 44f967e6a4..78dd989374 100644
--- a/main/reference/update_weights_strat_wilson.html
+++ b/main/reference/update_weights_strat_wilson.html
@@ -1,11 +1,34 @@
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+<meta name="description" content="
 This function wraps the iteration procedure that allows you to estimate
 the weights for each proportional strata. This assumes to minimize the
-weighted squared length of the confidence interval."><meta property="og:description" content="
+weighted squared length of the confidence interval.">
+<meta property="og:description" content="
 This function wraps the iteration procedure that allows you to estimate
 the weights for each proportional strata. This assumes to minimize the
-weighted squared length of the confidence interval."><meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png"><link rel="stylesheet" href="../consent.css"><script src="../consent.js" type="text/javascript" charset="utf-8"></script></head><body>
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   <main id="main" class="col-md-9"><div class="page-header">
-      <img src="../logo.png" class="logo" alt=""><h1>Helper function for the estimation of weights for <code>prop_strat_wilson()</code></h1>
+      <img src="../logo.png" class="logo" alt=""><h1>Helper function for the estimation of weights for <code>prop_strat_wilson()</code>
+</h1>
       <small class="dont-index">Source: <a href="https://github.com/insightsengineering/tern/blob/main/R/estimate_proportion.R" class="external-link"><code>R/estimate_proportion.R</code></a></small>
       <div class="d-none name"><code>update_weights_strat_wilson.Rd</code></div>
     </div>
@@ -60,7 +124,8 @@
     </div>
 
     <div class="section level2">
-    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
+    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">update_weights_strat_wilson</span><span class="op">(</span></span>
 <span>  <span class="va">vars</span>,</span>
 <span>  <span class="va">strata_qnorm</span>,</span>
@@ -73,49 +138,62 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
     </div>
 
     <div class="section level2">
-    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
+    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a>
+</h2>
 
 
-<dl><dt id="arg-vars">vars<a class="anchor" aria-label="anchor" href="#arg-vars"></a></dt>
+<dl>
+<dt id="arg-vars">vars<a class="anchor" aria-label="anchor" href="#arg-vars"></a>
+</dt>
 <dd><p>(<code>numeric</code>)<br> normalized proportions for each strata.</p></dd>
 
 
-<dt id="arg-strata-qnorm">strata_qnorm<a class="anchor" aria-label="anchor" href="#arg-strata-qnorm"></a></dt>
+<dt id="arg-strata-qnorm">strata_qnorm<a class="anchor" aria-label="anchor" href="#arg-strata-qnorm"></a>
+</dt>
 <dd><p>(<code>numeric(1)</code>)<br> initial estimation with identical weights of the quantiles.</p></dd>
 
 
-<dt id="arg-initial-weights">initial_weights<a class="anchor" aria-label="anchor" href="#arg-initial-weights"></a></dt>
+<dt id="arg-initial-weights">initial_weights<a class="anchor" aria-label="anchor" href="#arg-initial-weights"></a>
+</dt>
 <dd><p>(<code>numeric</code>)<br> initial weights used to calculate <code>strata_qnorm</code>. This can
 be optimized in the future if we need to estimate better initial weights.</p></dd>
 
 
-<dt id="arg-n-per-strata">n_per_strata<a class="anchor" aria-label="anchor" href="#arg-n-per-strata"></a></dt>
+<dt id="arg-n-per-strata">n_per_strata<a class="anchor" aria-label="anchor" href="#arg-n-per-strata"></a>
+</dt>
 <dd><p>(<code>numeric</code>)<br> number of elements in each strata.</p></dd>
 
 
-<dt id="arg-max-iterations">max_iterations<a class="anchor" aria-label="anchor" href="#arg-max-iterations"></a></dt>
+<dt id="arg-max-iterations">max_iterations<a class="anchor" aria-label="anchor" href="#arg-max-iterations"></a>
+</dt>
 <dd><p>(<code>integer(1)</code>)<br> maximum number of iterations to be tried. Convergence is always checked.</p></dd>
 
 
-<dt id="arg-conf-level">conf_level<a class="anchor" aria-label="anchor" href="#arg-conf-level"></a></dt>
+<dt id="arg-conf-level">conf_level<a class="anchor" aria-label="anchor" href="#arg-conf-level"></a>
+</dt>
 <dd><p>(<code>proportion</code>)<br> confidence level of the interval.</p></dd>
 
 
-<dt id="arg-tol">tol<a class="anchor" aria-label="anchor" href="#arg-tol"></a></dt>
+<dt id="arg-tol">tol<a class="anchor" aria-label="anchor" href="#arg-tol"></a>
+</dt>
 <dd><p>(<code>numeric(1)</code>)<br> tolerance threshold for convergence.</p></dd>
 
-</dl></div>
+</dl>
+</div>
     <div class="section level2">
-    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
+    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a>
+</h2>
     <p>A <code>list</code> of 3 elements: <code>n_it</code>, <code>weights</code>, and <code>diff_v</code>.</p>
     </div>
     <div class="section level2">
-    <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"></a></h2>
+    <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"></a>
+</h2>
     <div class="dont-index"><p>For references and details see <code><a href="h_proportions.html">prop_strat_wilson()</a></code>.</p></div>
     </div>
 
     <div class="section level2">
-    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
+    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">vs</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">0.011</span>, <span class="fl">0.013</span>, <span class="fl">0.012</span>, <span class="fl">0.014</span>, <span class="fl">0.017</span>, <span class="fl">0.018</span><span class="op">)</span></span></span>
 <span class="r-in"><span><span class="va">sq</span> <span class="op">&lt;-</span> <span class="fl">0.674</span></span></span>
 <span class="r-in"><span><span class="va">ws</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/rep.html" class="external-link">rep</a></span><span class="op">(</span><span class="fl">1</span> <span class="op">/</span> <span class="fu"><a href="https://rdrr.io/r/base/length.html" class="external-link">length</a></span><span class="op">(</span><span class="va">vs</span><span class="op">)</span>, <span class="fu"><a href="https://rdrr.io/r/base/length.html" class="external-link">length</a></span><span class="op">(</span><span class="va">vs</span><span class="op">)</span><span class="op">)</span></span></span>
@@ -135,17 +213,19 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 </code></pre></div>
     </div>
   </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
-    </nav></aside></div>
+    </nav></aside>
+</div>
 
 
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diff --git a/main/reference/util_handling_additional_fun_params.html b/main/reference/util_handling_additional_fun_params.html
index 21b80eeb59..13fbf960fa 100644
--- a/main/reference/util_handling_additional_fun_params.html
+++ b/main/reference/util_handling_additional_fun_params.html
@@ -1,15 +1,38 @@
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+<script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet">
+<link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet">
+<script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Utilities to handle extra arguments in analysis functions — util_handling_additional_fun_params">
+<meta name="description" content="
 Important additional parameters, useful to modify behavior of analysis and summary
 functions are listed in rtables::additional_fun_params. With these utility functions
 we can retrieve a curated list of these parameters from the environment, and pass them
 to the analysis functions with dedicated ...; notice that the final s_* function
-will get them through argument matching."><meta property="og:description" content="
+will get them through argument matching.">
+<meta property="og:description" content="
 Important additional parameters, useful to modify behavior of analysis and summary
 functions are listed in rtables::additional_fun_params. With these utility functions
 we can retrieve a curated list of these parameters from the environment, and pass them
 to the analysis functions with dedicated ...; notice that the final s_* function
-will get them through argument matching."><meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png"><link rel="stylesheet" href="../consent.css"><script src="../consent.js" type="text/javascript" charset="utf-8"></script></head><body>
+will get them through argument matching.">
+<meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png">
+<link rel="stylesheet" href="../consent.css">
+<script src="../consent.js" type="text/javascript" charset="utf-8"></script>
+</head>
+<body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
 
 
@@ -25,26 +48,66 @@
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-      <ul class="navbar-nav me-auto"><li class="nav-item"><a class="nav-link" href="../articles/tern.html">Get started</a></li>
+      <ul class="navbar-nav me-auto">
+<li class="nav-item"><a class="nav-link" href="../articles/tern.html">Get started</a></li>
 <li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
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+  <ul class="dropdown-menu" aria-labelledby="dropdown-articles">
+<li><a class="dropdown-item" href="../articles/missing_values.html">Missing Values in Tern</a></li>
     <li><a class="dropdown-item" href="../articles/tables.html">Tabulation</a></li>
     <li><a class="dropdown-item" href="../articles/tern_formats.html">Formatting Functions</a></li>
     <li><a class="dropdown-item" href="../articles/tern_functions_guide.html">Understanding `tern` functions</a></li>
-  </ul></li>
+  </ul>
+</li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
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   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
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+  <ul class="dropdown-menu" aria-labelledby="dropdown-reports">
+<li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
     <li><a class="dropdown-item" href="../unit-test-report/">Unit test report</a></li>
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-      </ul><ul class="navbar-nav"><li class="nav-item"><form class="form-inline" role="search">
- <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json"></form></li>
+  </ul>
+</li>
+      <div><li class="nav-item dropdown">
+    <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-versions">Versions</a>
+    <div class="dropdown-menu" aria-labelledby="dropdown-versions">
+    <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/main">main</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.5">v0.9.5</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.4">v0.9.4</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.3">v0.9.3</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1-rc3">v0.9.1-rc3</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a>
+</div>
+</li></div>
+</ul>
+<ul class="navbar-nav">
+<li class="nav-item"><form class="form-inline" role="search">
+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json">
+</form></li>
 <li class="nav-item"><a class="external-link nav-link" href="https://github.com/insightsengineering/tern" aria-label="GitHub"><span class="fa fa-github"></span></a></li>
-      </ul></div>
+      </ul>
+</div>
 
 
   </div>
@@ -66,52 +129,68 @@
     </div>
 
     <div class="section level2">
-    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
+    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">retrieve_extra_afun_params</span><span class="op">(</span><span class="va">extra_afun_params</span><span class="op">)</span></span>
 <span></span>
 <span><span class="fu">get_additional_afun_params</span><span class="op">(</span>add_alt_df <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span></code></pre></div>
     </div>
 
     <div class="section level2">
-    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
+    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a>
+</h2>
 
 
-<dl><dt id="arg-extra-afun-params">extra_afun_params<a class="anchor" aria-label="anchor" href="#arg-extra-afun-params"></a></dt>
+<dl>
+<dt id="arg-extra-afun-params">extra_afun_params<a class="anchor" aria-label="anchor" href="#arg-extra-afun-params"></a>
+</dt>
 <dd><p>(<code>list</code>)<br> list of additional parameters (<code>character</code>) to be
 retrieved from the environment. Curated list is present in <a href="https://insightsengineering.github.io/rtables/latest-tag/reference/additional_fun_params.html" class="external-link">rtables::additional_fun_params</a>.</p></dd>
 
 
-<dt id="arg-add-alt-df">add_alt_df<a class="anchor" aria-label="anchor" href="#arg-add-alt-df"></a></dt>
+<dt id="arg-add-alt-df">add_alt_df<a class="anchor" aria-label="anchor" href="#arg-add-alt-df"></a>
+</dt>
 <dd><p>(<code>logical</code>)<br> if <code>TRUE</code>, the function will also add <code>.alt_df</code> and <code>.alt_df_row</code>
 parameters.</p></dd>
 
-</dl></div>
+</dl>
+</div>
     <div class="section level2">
-    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
-
-<ul><li><p><code>retrieve_extra_afun_params</code> returns a list of the values of the parameters in the environment.</p></li>
-</ul><ul><li><p><code>get_additional_afun_params</code> returns a list of additional parameters.</p></li>
-</ul></div>
+    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a>
+</h2>
+
+<ul>
+<li><p><code>retrieve_extra_afun_params</code> returns a list of the values of the parameters in the environment.</p></li>
+</ul>
+<ul>
+<li><p><code>get_additional_afun_params</code> returns a list of additional parameters.</p></li>
+</ul>
+</div>
     <div class="section level2">
-    <h2 id="functions">Functions<a class="anchor" aria-label="anchor" href="#functions"></a></h2>
+    <h2 id="functions">Functions<a class="anchor" aria-label="anchor" href="#functions"></a>
+</h2>
 
-<ul><li><p><code>retrieve_extra_afun_params()</code>: Retrieve additional parameters from the environment.</p></li>
+<ul>
+<li><p><code>retrieve_extra_afun_params()</code>: Retrieve additional parameters from the environment.</p></li>
 <li><p><code>get_additional_afun_params()</code>: Curated list of additional parameters for
 analysis functions. Please check <a href="https://insightsengineering.github.io/rtables/latest-tag/reference/additional_fun_params.html" class="external-link">rtables::additional_fun_params</a> for precise descriptions.</p></li>
-</ul></div>
+</ul>
+</div>
 
   </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
-    </nav></aside></div>
+    </nav></aside>
+</div>
 
 
     <footer><div class="nest">
   <p>tern is a part of the <strong>NEST</strong> and <a href="https://pharmaverse.org/" class="external-link"><strong>pharmaverse</strong></a>.</p>
 </div>
-<script type="text/javascript" src="../analytics.js"></script></footer></div>
-
+<script type="text/javascript" src="../analytics.js"></script></footer>
+</div>
 
 
 
 
-  </body></html>
 
+  </body>
+</html>
diff --git a/main/reference/utils_split_funs.html b/main/reference/utils_split_funs.html
index 8fd86f3ce3..a327c6e669 100644
--- a/main/reference/utils_split_funs.html
+++ b/main/reference/utils_split_funs.html
@@ -1,15 +1,38 @@
-<!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Custom split functions — utils_split_funs • tern</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Custom split functions — utils_split_funs"><meta name="description" content="
+<html lang="en">
+<head>
+<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+<meta charset="utf-8">
+<meta http-equiv="X-UA-Compatible" content="IE=edge">
+<meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<title>Custom split functions — utils_split_funs • tern</title>
+<!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png">
+<link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png">
+<link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png">
+<link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png">
+<link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png">
+<link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png">
+<script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet">
+<script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet">
+<link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet">
+<script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Custom split functions — utils_split_funs">
+<meta name="description" content="
 Collection of useful functions that are expanding on the core list of functions
 provided by rtables. See rtables::custom_split_funs and rtables::make_split_fun()
 for more information on how to make a custom split function. All these functions
 work with rtables::split_rows_by() argument split_fun to modify the way the split
-happens. For other split functions, consider consulting rtables::split_funcs."><meta property="og:description" content="
+happens. For other split functions, consider consulting rtables::split_funcs.">
+<meta property="og:description" content="
 Collection of useful functions that are expanding on the core list of functions
 provided by rtables. See rtables::custom_split_funs and rtables::make_split_fun()
 for more information on how to make a custom split function. All these functions
 work with rtables::split_rows_by() argument split_fun to modify the way the split
-happens. For other split functions, consider consulting rtables::split_funcs."><meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png"><link rel="stylesheet" href="../consent.css"><script src="../consent.js" type="text/javascript" charset="utf-8"></script></head><body>
+happens. For other split functions, consider consulting rtables::split_funcs.">
+<meta property="og:image" content="https://insightsengineering.github.io/tern/logo.png">
+<link rel="stylesheet" href="../consent.css">
+<script src="../consent.js" type="text/javascript" charset="utf-8"></script>
+</head>
+<body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
 
 
@@ -25,26 +48,66 @@
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+      <ul class="navbar-nav me-auto">
+<li class="nav-item"><a class="nav-link" href="../articles/tern.html">Get started</a></li>
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+  <ul class="dropdown-menu" aria-labelledby="dropdown-articles">
+<li><a class="dropdown-item" href="../articles/missing_values.html">Missing Values in Tern</a></li>
     <li><a class="dropdown-item" href="../articles/tables.html">Tabulation</a></li>
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     <li><a class="dropdown-item" href="../articles/tern_functions_guide.html">Understanding `tern` functions</a></li>
-  </ul></li>
+  </ul>
+</li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
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+  <ul class="dropdown-menu" aria-labelledby="dropdown-reports">
+<li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
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- <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json"></form></li>
+  </ul>
+</li>
+      <div><li class="nav-item dropdown">
+    <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-versions">Versions</a>
+    <div class="dropdown-menu" aria-labelledby="dropdown-versions">
+    <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/main">main</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.5">v0.9.5</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.4">v0.9.4</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.3">v0.9.3</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1-rc3">v0.9.1-rc3</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a>
+</div>
+</li></div>
+</ul>
+<ul class="navbar-nav">
+<li class="nav-item"><form class="form-inline" role="search">
+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json">
+</form></li>
 <li class="nav-item"><a class="external-link nav-link" href="https://github.com/insightsengineering/tern" aria-label="GitHub"><span class="fa fa-github"></span></a></li>
-      </ul></div>
+      </ul>
+</div>
 
 
   </div>
@@ -66,48 +129,64 @@
     </div>
 
     <div class="section level2">
-    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
+    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">ref_group_position</span><span class="op">(</span>position <span class="op">=</span> <span class="st">"first"</span><span class="op">)</span></span>
 <span></span>
 <span><span class="fu">level_order</span><span class="op">(</span><span class="va">order</span><span class="op">)</span></span></code></pre></div>
     </div>
 
     <div class="section level2">
-    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
+    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a>
+</h2>
 
 
-<dl><dt id="arg-position">position<a class="anchor" aria-label="anchor" href="#arg-position"></a></dt>
+<dl>
+<dt id="arg-position">position<a class="anchor" aria-label="anchor" href="#arg-position"></a>
+</dt>
 <dd><p>(<code>string</code> or <code>integer</code>)<br> position to use for the reference group facet. Can be <code>"first"</code>,
 <code>"last"</code>, or a specific position.</p></dd>
 
 
-<dt id="arg-order">order<a class="anchor" aria-label="anchor" href="#arg-order"></a></dt>
+<dt id="arg-order">order<a class="anchor" aria-label="anchor" href="#arg-order"></a>
+</dt>
 <dd><p>(<code>character</code> or <code>numeric</code>)<br> vector of ordering indices for the split facets.</p></dd>
 
-</dl></div>
+</dl>
+</div>
     <div class="section level2">
-    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
+    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a>
+</h2>
 
-<ul><li><p><code>ref_group_position()</code> returns an utility function that puts the reference group
+<ul>
+<li><p><code>ref_group_position()</code> returns an utility function that puts the reference group
 as first, last or at a certain position and needs to be assigned to <code>split_fun</code>.</p></li>
-</ul><ul><li><p><code>level_order()</code> returns an utility function that changes the original levels' order,
+</ul>
+<ul>
+<li><p><code>level_order()</code> returns an utility function that changes the original levels' order,
 depending on input <code>order</code> and split levels.</p></li>
-</ul></div>
+</ul>
+</div>
     <div class="section level2">
-    <h2 id="functions">Functions<a class="anchor" aria-label="anchor" href="#functions"></a></h2>
+    <h2 id="functions">Functions<a class="anchor" aria-label="anchor" href="#functions"></a>
+</h2>
 
-<ul><li><p><code>ref_group_position()</code>: Split function to place reference group facet at a specific position
+<ul>
+<li><p><code>ref_group_position()</code>: Split function to place reference group facet at a specific position
 during post-processing stage.</p></li>
 <li><p><code>level_order()</code>: Split function to change level order based on an <code>integer</code>
 vector or a <code>character</code> vector that represent the split variable's factor levels.</p></li>
-</ul></div>
+</ul>
+</div>
     <div class="section level2">
-    <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"></a></h2>
+    <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"></a>
+</h2>
     <div class="dont-index"><p><code><a href="https://insightsengineering.github.io/rtables/latest-tag/reference/make_split_fun.html" class="external-link">rtables::make_split_fun()</a></code></p></div>
     </div>
 
     <div class="section level2">
-    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
+    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a>
+</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://dplyr.tidyverse.org" class="external-link">dplyr</a></span><span class="op">)</span></span></span>
 <span class="r-in"><span></span></span>
 <span class="r-in"><span><span class="va">dat</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a></span><span class="op">(</span></span></span>
@@ -191,17 +270,19 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 </code></pre></div>
     </div>
   </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
-    </nav></aside></div>
+    </nav></aside>
+</div>
 
 
     <footer><div class="nest">
   <p>tern is a part of the <strong>NEST</strong> and <a href="https://pharmaverse.org/" class="external-link"><strong>pharmaverse</strong></a>.</p>
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-<script type="text/javascript" src="../analytics.js"></script></footer></div>
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+<script type="text/javascript" src="../analytics.js"></script></footer>
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diff --git a/main/search.json b/main/search.json
index 0e3028a3fe..c2dc3f2eef 100644
--- a/main/search.json
+++ b/main/search.json
@@ -1 +1 @@
-[{"path":[]},{"path":"https://insightsengineering.github.io/tern/CODE_OF_CONDUCT.html","id":"our-pledge","dir":"","previous_headings":"","what":"Our Pledge","title":"Contributor Covenant Code of Conduct","text":"members, contributors, leaders pledge make participation community harassment-free experience everyone, regardless age, body size, visible invisible disability, ethnicity, sex characteristics, gender identity expression, level experience, education, socio-economic status, nationality, personal appearance, race, caste, color, religion, sexual identity orientation. pledge act interact ways contribute open, welcoming, diverse, inclusive, healthy community.","code":""},{"path":"https://insightsengineering.github.io/tern/CODE_OF_CONDUCT.html","id":"our-standards","dir":"","previous_headings":"","what":"Our Standards","title":"Contributor Covenant Code of Conduct","text":"Examples behavior contributes positive environment community include: Demonstrating empathy kindness toward people respectful differing opinions, viewpoints, experiences Giving gracefully accepting constructive feedback Accepting responsibility apologizing affected mistakes, learning experience Focusing best just us individuals, overall community Examples unacceptable behavior include: use sexualized language imagery, sexual attention advances kind Trolling, insulting derogatory comments, personal political attacks Public private harassment Publishing others’ private information, physical email address, without explicit permission conduct reasonably considered inappropriate professional setting","code":""},{"path":"https://insightsengineering.github.io/tern/CODE_OF_CONDUCT.html","id":"enforcement-responsibilities","dir":"","previous_headings":"","what":"Enforcement Responsibilities","title":"Contributor Covenant Code of Conduct","text":"Community leaders responsible clarifying enforcing standards acceptable behavior take appropriate fair corrective action response behavior deem inappropriate, threatening, offensive, harmful. Community leaders right responsibility remove, edit, reject comments, commits, code, wiki edits, issues, contributions aligned Code Conduct, communicate reasons moderation decisions appropriate.","code":""},{"path":"https://insightsengineering.github.io/tern/CODE_OF_CONDUCT.html","id":"scope","dir":"","previous_headings":"","what":"Scope","title":"Contributor Covenant Code of Conduct","text":"Code Conduct applies within community spaces, also applies individual officially representing community public spaces. Examples representing community include using official e-mail address, posting via official social media account, acting appointed representative online offline event.","code":""},{"path":"https://insightsengineering.github.io/tern/CODE_OF_CONDUCT.html","id":"enforcement","dir":"","previous_headings":"","what":"Enforcement","title":"Contributor Covenant Code of Conduct","text":"Instances abusive, harassing, otherwise unacceptable behavior may reported community leaders responsible enforcement [INSERT CONTACT METHOD]. complaints reviewed investigated promptly fairly. community leaders obligated respect privacy security reporter incident.","code":""},{"path":"https://insightsengineering.github.io/tern/CODE_OF_CONDUCT.html","id":"enforcement-guidelines","dir":"","previous_headings":"","what":"Enforcement Guidelines","title":"Contributor Covenant Code of Conduct","text":"Community leaders follow Community Impact Guidelines determining consequences action deem violation Code Conduct:","code":""},{"path":"https://insightsengineering.github.io/tern/CODE_OF_CONDUCT.html","id":"id_1-correction","dir":"","previous_headings":"Enforcement Guidelines","what":"1. Correction","title":"Contributor Covenant Code of Conduct","text":"Community Impact: Use inappropriate language behavior deemed unprofessional unwelcome community. Consequence: private, written warning community leaders, providing clarity around nature violation explanation behavior inappropriate. public apology may requested.","code":""},{"path":"https://insightsengineering.github.io/tern/CODE_OF_CONDUCT.html","id":"id_2-warning","dir":"","previous_headings":"Enforcement Guidelines","what":"2. Warning","title":"Contributor Covenant Code of Conduct","text":"Community Impact: violation single incident series actions. Consequence: warning consequences continued behavior. interaction people involved, including unsolicited interaction enforcing Code Conduct, specified period time. includes avoiding interactions community spaces well external channels like social media. Violating terms may lead temporary permanent ban.","code":""},{"path":"https://insightsengineering.github.io/tern/CODE_OF_CONDUCT.html","id":"id_3-temporary-ban","dir":"","previous_headings":"Enforcement Guidelines","what":"3. Temporary Ban","title":"Contributor Covenant Code of Conduct","text":"Community Impact: serious violation community standards, including sustained inappropriate behavior. Consequence: temporary ban sort interaction public communication community specified period time. public private interaction people involved, including unsolicited interaction enforcing Code Conduct, allowed period. Violating terms may lead permanent ban.","code":""},{"path":"https://insightsengineering.github.io/tern/CODE_OF_CONDUCT.html","id":"id_4-permanent-ban","dir":"","previous_headings":"Enforcement Guidelines","what":"4. Permanent Ban","title":"Contributor Covenant Code of Conduct","text":"Community Impact: Demonstrating pattern violation community standards, including sustained inappropriate behavior, harassment individual, aggression toward disparagement classes individuals. Consequence: permanent ban sort public interaction within community.","code":""},{"path":"https://insightsengineering.github.io/tern/CODE_OF_CONDUCT.html","id":"attribution","dir":"","previous_headings":"","what":"Attribution","title":"Contributor Covenant Code of Conduct","text":"Code Conduct adapted Contributor Covenant, version 2.1, available https://www.contributor-covenant.org/version/2/1/code_of_conduct.html. Community Impact Guidelines inspired Mozilla’s code conduct enforcement ladder. answers common questions code conduct, see FAQ https://www.contributor-covenant.org/faq. Translations available https://www.contributor-covenant.org/translations.","code":""},{"path":"https://insightsengineering.github.io/tern/CONTRIBUTING.html","id":null,"dir":"","previous_headings":"","what":"Contribution Guidelines","title":"Contribution Guidelines","text":"🙏 Thank taking time contribute! input deeply valued, whether issue, pull request, even feedback, regardless size, content scope.","code":""},{"path":"https://insightsengineering.github.io/tern/CONTRIBUTING.html","id":"table-of-contents","dir":"","previous_headings":"","what":"Table of contents","title":"Contribution Guidelines","text":"👶 Getting started 📔 Code Conduct 🗃 License 📜 Issues 🚩 Pull requests 💻 Coding guidelines 🏆 Recognition model ❓ Questions","code":""},{"path":"https://insightsengineering.github.io/tern/CONTRIBUTING.html","id":"getting-started","dir":"","previous_headings":"","what":"Getting started","title":"Contribution Guidelines","text":"Please refer project documentation brief introduction. Please also see articles within project documentation additional information.","code":""},{"path":"https://insightsengineering.github.io/tern/CONTRIBUTING.html","id":"code-of-conduct","dir":"","previous_headings":"","what":"Code of Conduct","title":"Contribution Guidelines","text":"Code Conduct governs project. Participants contributors expected follow rules outlined therein.","code":""},{"path":"https://insightsengineering.github.io/tern/CONTRIBUTING.html","id":"license","dir":"","previous_headings":"","what":"License","title":"Contribution Guidelines","text":"contributions covered project’s license.","code":""},{"path":"https://insightsengineering.github.io/tern/CONTRIBUTING.html","id":"issues","dir":"","previous_headings":"","what":"Issues","title":"Contribution Guidelines","text":"use GitHub track issues, feature requests, bugs. submitting new issue, please check issue already reported. issue already exists, please upvote existing issue 👍. new feature requests, please elaborate context benefit feature users, developers, relevant personas.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/CONTRIBUTING.html","id":"github-flow","dir":"","previous_headings":"Pull requests","what":"GitHub Flow","title":"Contribution Guidelines","text":"repository uses GitHub Flow model collaboration. submit pull request: Create branch Please see branch naming convention . don’t write access repository, please fork . Make changes Make sure code passes checks imposed GitHub Actions well documented well tested unit tests sufficiently covering changes introduced Create pull request (PR) pull request description, please link relevant issue (), provide detailed description change, include assumptions. Address review comments, Post approval Merge PR write access. Otherwise, reviewer merge PR behalf. Pat back Congratulations! 🎉 now official contributor project! grateful contribution.","code":""},{"path":"https://insightsengineering.github.io/tern/CONTRIBUTING.html","id":"branch-naming-convention","dir":"","previous_headings":"Pull requests","what":"Branch naming convention","title":"Contribution Guidelines","text":"Suppose changes related current issue current project; please name branch follows: <issue_id>_<short_description>. Please use underscore (_) delimiter word separation. example, 420_fix_ui_bug suitable branch name change resolving UI-related bug reported issue number 420 current project. change affects multiple repositories, please name branches follows: <issue_id>_<issue_repo>_<short description>. example, 69_awesomeproject_fix_spelling_error reference issue 69 reported project awesomeproject aims resolve one spelling errors multiple (likely related) repositories.","code":""},{"path":"https://insightsengineering.github.io/tern/CONTRIBUTING.html","id":"monorepo-and-stageddependencies","dir":"","previous_headings":"Pull requests","what":"monorepo and staged.dependencies","title":"Contribution Guidelines","text":"Sometimes might need change upstream dependent package(s) able submit meaningful change. using staged.dependencies functionality simulate monorepo behavior. dependency configuration already specified project’s staged_dependencies.yaml file. need name feature branches appropriately. exception branch naming convention described . Please refer staged.dependencies package documentation details.","code":""},{"path":"https://insightsengineering.github.io/tern/CONTRIBUTING.html","id":"coding-guidelines","dir":"","previous_headings":"","what":"Coding guidelines","title":"Contribution Guidelines","text":"repository follows unified processes standards adopted maintainers ensure software development carried consistently within teams cohesively across repositories.","code":""},{"path":"https://insightsengineering.github.io/tern/CONTRIBUTING.html","id":"style-guide","dir":"","previous_headings":"Coding guidelines","what":"Style guide","title":"Contribution Guidelines","text":"repository follows standard tidyverse style guide uses lintr lint checks. Customized lint configurations available repository’s .lintr file.","code":""},{"path":"https://insightsengineering.github.io/tern/CONTRIBUTING.html","id":"dependency-management","dir":"","previous_headings":"Coding guidelines","what":"Dependency management","title":"Contribution Guidelines","text":"Lightweight right weight. repository follows tinyverse recommedations limiting dependencies minimum.","code":""},{"path":"https://insightsengineering.github.io/tern/CONTRIBUTING.html","id":"dependency-version-management","dir":"","previous_headings":"Coding guidelines","what":"Dependency version management","title":"Contribution Guidelines","text":"code compatible (!) historical versions given dependenct package, required specify minimal version DESCRIPTION file. particular: development version requires (imports) development version another package - required put abc (>= 1.2.3.9000).","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/CONTRIBUTING.html","id":"r--package-versions","dir":"","previous_headings":"Coding guidelines > Recommended development environment & tools","what":"R & package versions","title":"Contribution Guidelines","text":"continuously test packages newest R version along recent dependencies CRAN BioConductor. recommend working environment also set way. can find details R version packages used R CMD check GitHub Action execution log - step prints R sessionInfo(). discover bugs older R versions older set dependencies, please create relevant bug reports.","code":""},{"path":"https://insightsengineering.github.io/tern/CONTRIBUTING.html","id":"pre-commit","dir":"","previous_headings":"Coding guidelines > Recommended development environment & tools","what":"pre-commit","title":"Contribution Guidelines","text":"highly recommend use pre-commit tool combined R hooks pre-commit execute checks committing pushing changes. Pre-commit hooks already available repository’s .pre-commit-config.yaml file.","code":""},{"path":"https://insightsengineering.github.io/tern/CONTRIBUTING.html","id":"recognition-model","dir":"","previous_headings":"","what":"Recognition model","title":"Contribution Guidelines","text":"mentioned previously, contributions deeply valued appreciated. contribution data available part repository insights, recognize significant contribution hence add contributor package authors list, following rules enforced: Minimum 5% lines code authored* (determined git blame query) top 5 contributors terms number commits lines added lines removed* *Excluding auto-generated code, including limited roxygen comments renv.lock files. package maintainer also reserves right adjust criteria recognize contributions.","code":""},{"path":"https://insightsengineering.github.io/tern/CONTRIBUTING.html","id":"questions","dir":"","previous_headings":"","what":"Questions","title":"Contribution Guidelines","text":"questions regarding contribution guidelines, please contact package/repository maintainer.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/SECURITY.html","id":"reporting-security-issues","dir":"","previous_headings":"","what":"Reporting Security Issues","title":"Security Policy","text":"believe found security vulnerability repositories organization, please report us coordinated disclosure. Please report security vulnerabilities public GitHub issues, discussions, pull requests. Instead, please send email vulnerability.management[@]roche.com. Please include much information listed can help us better understand resolve issue: type issue (e.g., buffer overflow, SQL injection, cross-site scripting) Full paths source file(s) related manifestation issue location affected source code (tag/branch/commit direct URL) special configuration required reproduce issue Step--step instructions reproduce issue Proof--concept exploit code (possible) Impact issue, including attacker might exploit issue information help us triage report quickly.","code":""},{"path":"https://insightsengineering.github.io/tern/SECURITY.html","id":"data-security-standards-dss","dir":"","previous_headings":"","what":"Data Security Standards (DSS)","title":"Security Policy","text":"Please make sure reporting issues form bug, feature, pull request, sensitive information PII, PHI, PCI completely removed text attachments, including pictures videos.","code":""},{"path":"https://insightsengineering.github.io/tern/articles/missing_values.html","id":"variable-class-conversion","dir":"Articles","previous_headings":"","what":"Variable Class Conversion","title":"Missing Values in Tern","text":"rtables requires split variables factors. try split variable isn’t, warning message appear. purposefully convert SEX variable character demonstrate happens try splitting rows variable. fix , df_explict_na convert factor resulting table generated.","code":"adsl <- tern_ex_adsl adsl$SEX <- as.character(adsl$SEX)  vars <- c(\"AGE\", \"SEX\", \"RACE\", \"BMRKR1\") var_labels <- c(   \"Age (yr)\",   \"Sex\",   \"Race\",   \"Continous Level Biomarker 1\" )  result <- basic_table(show_colcounts = TRUE) %>%   split_cols_by(var = \"ARM\") %>%   add_overall_col(\"All Patients\") %>%   analyze_vars(     vars = vars,     var_labels = var_labels   ) %>%   build_table(adsl) #> Warning in as_factor_keep_attributes(x, verbose = verbose): automatically #> converting character variable x to factor, better manually convert to factor to #> avoid failures #> Warning in as_factor_keep_attributes(x, verbose = verbose): automatically #> converting character variable x to factor, better manually convert to factor to #> avoid failures #> Warning in as_factor_keep_attributes(x, verbose = verbose): automatically #> converting character variable x to factor, better manually convert to factor to #> avoid failures #> Warning in as_factor_keep_attributes(x, verbose = verbose): automatically #> converting character variable x to factor, better manually convert to factor to #> avoid failures result #>                                                A: Drug X    B: Placebo    C: Combination   All Patients #>                                                 (N=69)        (N=73)          (N=58)         (N=200)    #> ——————————————————————————————————————————————————————————————————————————————————————————————————————— #> Age (yr)                                                                                                #>   n                                               69            73              58             200      #>   Mean (SD)                                   34.1 (6.8)    35.8 (7.1)      36.1 (7.4)      35.3 (7.1)  #>   Median                                         32.8          35.4            36.2            34.8     #>   Min - Max                                   22.4 - 48.0   23.3 - 57.5    23.0 - 58.3     22.4 - 58.3  #> Sex                                                                                                     #>   n                                               69            73              58             200      #>   F                                           38 (55.1%)    40 (54.8%)      32 (55.2%)      110 (55%)   #>   M                                           31 (44.9%)    33 (45.2%)      26 (44.8%)       90 (45%)   #> Race                                                                                                    #>   n                                               69            73              58             200      #>   ASIAN                                       38 (55.1%)    43 (58.9%)       29 (50%)       110 (55%)   #>   BLACK OR AFRICAN AMERICAN                   15 (21.7%)    13 (17.8%)      12 (20.7%)       40 (20%)   #>   WHITE                                       11 (15.9%)    12 (16.4%)       11 (19%)        34 (17%)   #>   AMERICAN INDIAN OR ALASKA NATIVE             4 (5.8%)      3 (4.1%)       6 (10.3%)       13 (6.5%)   #>   MULTIPLE                                     1 (1.4%)      1 (1.4%)           0             2 (1%)    #>   NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER        0         1 (1.4%)           0            1 (0.5%)   #>   OTHER                                            0             0              0               0       #>   UNKNOWN                                          0             0              0               0       #> Continous Level Biomarker 1                                                                             #>   n                                               69            73              58             200      #>   Mean (SD)                                    6.3 (3.6)     6.7 (3.5)      6.2 (3.3)       6.4 (3.5)   #>   Median                                          5.4           6.3            5.4             5.6      #>   Min - Max                                   0.4 - 17.8    1.0 - 18.5      2.4 - 19.1      0.4 - 19.1"},{"path":"https://insightsengineering.github.io/tern/articles/missing_values.html","id":"including-missing-values-in-rtables","dir":"Articles","previous_headings":"","what":"Including Missing Values in rtables","title":"Missing Values in Tern","text":"purposefully convert M values NA SEX variable. running df_explicit_na NA values encoded <Missing> included table. well, missing values included n count included denominator value calculating percent values. want Na values displayed table included n count denominator calculating percent values, use na_level argument.","code":"adsl <- tern_ex_adsl adsl$SEX[adsl$SEX == \"M\"] <- NA adsl <- df_explicit_na(adsl)  vars <- c(\"AGE\", \"SEX\") var_labels <- c(   \"Age (yr)\",   \"Sex\" )  result <- basic_table(show_colcounts = TRUE) %>%   split_cols_by(var = \"ARM\") %>%   add_overall_col(\"All Patients\") %>%   analyze_vars(     vars = vars,     var_labels = var_labels   ) %>%   build_table(adsl) result #>                A: Drug X    B: Placebo    C: Combination   All Patients #>                 (N=69)        (N=73)          (N=58)         (N=200)    #> ——————————————————————————————————————————————————————————————————————— #> Age (yr)                                                                #>   n               69            73              58             200      #>   Mean (SD)   34.1 (6.8)    35.8 (7.1)      36.1 (7.4)      35.3 (7.1)  #>   Median         32.8          35.4            36.2            34.8     #>   Min - Max   22.4 - 48.0   23.3 - 57.5    23.0 - 58.3     22.4 - 58.3  #> Sex                                                                     #>   n               38            40              32             110      #>   F            38 (100%)     40 (100%)      32 (100%)       110 (100%)  #>   M                0             0              0               0 adsl <- tern_ex_adsl adsl$SEX[adsl$SEX == \"M\"] <- NA adsl <- df_explicit_na(adsl, na_level = \"Missing Values\")  result <- basic_table(show_colcounts = TRUE) %>%   split_cols_by(var = \"ARM\") %>%   add_overall_col(\"All Patients\") %>%   analyze_vars(     vars = vars,     var_labels = var_labels   ) %>%   build_table(adsl) result #>                     A: Drug X    B: Placebo    C: Combination   All Patients #>                      (N=69)        (N=73)          (N=58)         (N=200)    #> ———————————————————————————————————————————————————————————————————————————— #> Age (yr)                                                                     #>   n                    69            73              58             200      #>   Mean (SD)        34.1 (6.8)    35.8 (7.1)      36.1 (7.4)      35.3 (7.1)  #>   Median              32.8          35.4            36.2            34.8     #>   Min - Max        22.4 - 48.0   23.3 - 57.5    23.0 - 58.3     22.4 - 58.3  #> Sex                                                                          #>   n                    69            73              58             200      #>   F                38 (55.1%)    40 (54.8%)      32 (55.2%)      110 (55%)   #>   M                     0             0              0               0       #>   Missing Values   31 (44.9%)    33 (45.2%)      26 (44.8%)       90 (45%)"},{"path":"https://insightsengineering.github.io/tern/articles/missing_values.html","id":"missing-values-in-numeric-variables","dir":"Articles","previous_headings":"","what":"Missing Values in Numeric Variables","title":"Missing Values in Tern","text":"Numeric variables missing values altered. means NA value numeric variable included summary statistics, included denominator value calculating percent values. make value less 30 missing AGE variable valued greater 30 included table .","code":"adsl <- tern_ex_adsl adsl$AGE[adsl$AGE < 30] <- NA adsl <- df_explicit_na(adsl)  vars <- c(\"AGE\", \"SEX\") var_labels <- c(   \"Age (yr)\",   \"Sex\" )  result <- basic_table(show_colcounts = TRUE) %>%   split_cols_by(var = \"ARM\") %>%   add_overall_col(\"All Patients\") %>%   analyze_vars(     vars = vars,     var_labels = var_labels   ) %>%   build_table(adsl) result #>                A: Drug X    B: Placebo    C: Combination   All Patients #>                 (N=69)        (N=73)          (N=58)         (N=200)    #> ——————————————————————————————————————————————————————————————————————— #> Age (yr)                                                                #>   n               46            56              44             146      #>   Mean (SD)   37.8 (5.2)    38.3 (6.3)      39.1 (5.9)      38.3 (5.8)  #>   Median         37.2          37.3            37.5            37.5     #>   Min - Max   30.3 - 48.0   30.0 - 57.5    30.5 - 58.3     30.0 - 58.3  #> Sex                                                                     #>   n               69            73              58             200      #>   F           38 (55.1%)    40 (54.8%)      32 (55.2%)      110 (55%)   #>   M           31 (44.9%)    33 (45.2%)      26 (44.8%)       90 (45%)"},{"path":"https://insightsengineering.github.io/tern/articles/tables.html","id":"tern-tabulation","dir":"Articles","previous_headings":"","what":"tern Tabulation","title":"Tabulation","text":"tern R package provides functions create common analyses clinical trials R. core functionality tabulation built general purpose rtables package. New users first begin reading “Introduction tern” “Introduction rtables” vignettes. packages used vignette : datasets used vignette :","code":"library(rtables) library(tern) library(dplyr) adsl <- ex_adsl adae <- ex_adae adrs <- ex_adrs"},{"path":"https://insightsengineering.github.io/tern/articles/tables.html","id":"tern-analyze-functions","dir":"Articles","previous_headings":"","what":"tern Analyze Functions","title":"Tabulation","text":"Analyze functions used combination rtables layout functions, pipeline creates rtables table. apply statistical logic layout rtables table. table layout materialized rtables::build_table function data. tern analyze functions wrappers around rtables::analyze function, offer various methods useful perspective clinical trials statistical projects. Examples tern analyze functions count_occurrences, summarize_ancova analyze_vars. one prefix identify tern analyze functions recommended use tern website functions reference.","code":""},{"path":"https://insightsengineering.github.io/tern/articles/tables.html","id":"internals-of-tern-analyze-functions","dir":"Articles","previous_headings":"tern Analyze Functions","what":"Internals of tern Analyze Functions","title":"Tabulation","text":"Please skip subsection interested internals tern analyze functions. Internally tern analyze functions like summarize_ancova mainly built 4 elements chain: descriptions function type: analysis helper functions h_*. functions useful help define analysis. statistics function s_*. Statistics functions computation numbers tabulated later. order separate computation formatting, take care rcell type formatting . formatted analysis functions a_*. arguments corresponding statistics functions, can customized calling rtables::make_afun() . used afun rtables::analyze(). analyze functions rtables::analyze(..., afun = make_afun(tern::a_*)). Analyze functions used combination rtables layout functions, pipeline creates table. last element chain. use native rtables::analyze function tern formatted analysis functions afun parameter. rtables::make_afun function helpful somebody wants attach format formatted analysis function.","code":"h_ancova() -> tern:::s_ancova() -> tern:::a_ancova() -> summarize_ancova() l <- basic_table() %>%     split_cols_by(var = \"ARM\") %>%     split_rows_by(var = \"AVISIT\") %>%     analyze(vars = \"AVAL\", afun = a_summary)  build_table(l, df = adrs) afun <- make_afun(     a_summary,     .stats = NULL,     .formats = c(median = \"xx.\"),     .labels = c(median = \"My median\"),     .indent_mods = c(median = 1L) )  l2 <- basic_table() %>%     split_cols_by(var = \"ARM\") %>%     split_rows_by(var = \"AVISIT\") %>%     analyze(vars = \"AVAL\", afun = afun)  build_table(l2, df = adrs)"},{"path":"https://insightsengineering.github.io/tern/articles/tables.html","id":"tabulation-examples","dir":"Articles","previous_headings":"","what":"Tabulation Examples","title":"Tabulation","text":"going create 3 different tables using tern analyze functions rtables interface.","code":""},{"path":"https://insightsengineering.github.io/tern/articles/tables.html","id":"demographic-table","dir":"Articles","previous_headings":"Tabulation Examples","what":"Demographic Table","title":"Tabulation","text":"Demographic tables provide summary characteristics patients enrolled clinical trial. Typically table columns represent treatment arms variables summarized table demographic properties age, sex, race, etc. example function tern analyze_vars() remaining layout functions rtables. change display order categorical variables table use factor variables explicitly set order levels. case display order columns rows. Note forcats package many useful functions help types data processing steps (used ). tern package includes many functions similar analyze_vars(). functions called layout creating functions used combination rtables layout functions just like examples . Layout creating functions wrapping calls rtables analyze(), analyze_colvars() summarize_row_groups() provide options easy formatting analysis modifications. customize display demographics table, can via arguments analyze_vars(). layout creating functions tern include standard arguments .stats, .formats, .labels .indent_mods control statistics displayed numbers formatted. Refer package help help(\"analyze_vars\") ?analyze_vars see full set options. example change default summary numeric variables include number records, mean standard deviation (single statistic, .e. within single cell). categorical variables modify summary include number records counts categories. also modify display format mean standard deviation print two decimal places instead just one. One feature layout can used different datasets create different summaries. example, can easily create summary demographics Brazil China subgroups, respectively:","code":"# Select variables to include in table. vars <- c(\"AGE\", \"SEX\") var_labels <- c(\"Age (yr)\", \"Sex\")  basic_table() %>%   split_cols_by(var = \"ARM\") %>%   add_overall_col(\"All Patients\") %>%   add_colcounts() %>%   analyze_vars(     vars = vars,     var_labels = var_labels   ) %>%   build_table(adsl) #>                       A: Drug X    B: Placebo    C: Combination   All Patients #>                        (N=134)       (N=134)        (N=132)         (N=400)    #> —————————————————————————————————————————————————————————————————————————————— #> Age (yr)                                                                       #>   n                      134           134            132             400      #>   Mean (SD)          33.8 (6.6)    35.4 (7.9)      35.4 (7.7)      34.9 (7.4)  #>   Median                33.0          35.0            35.0            34.0     #>   Min - Max          21.0 - 50.0   21.0 - 62.0    20.0 - 69.0     20.0 - 69.0  #> Sex                                                                            #>   n                      134           134            132             400      #>   F                   79 (59%)     77 (57.5%)       66 (50%)      222 (55.5%)  #>   M                  51 (38.1%)     55 (41%)       60 (45.5%)     166 (41.5%)  #>   U                   3 (2.2%)      2 (1.5%)         4 (3%)         9 (2.2%)   #>   UNDIFFERENTIATED    1 (0.7%)          0           2 (1.5%)        3 (0.8%) # Reorder the levels in the ARM variable. adsl$ARM <- factor(adsl$ARM, levels = c(\"B: Placebo\", \"A: Drug X\", \"C: Combination\"))  # Reorder the levels in the SEX variable. adsl$SEX <- factor(adsl$SEX, levels = c(\"M\", \"F\", \"U\", \"UNDIFFERENTIATED\"))  basic_table() %>%   split_cols_by(var = \"ARM\") %>%   add_overall_col(\"All Patients\") %>%   add_colcounts() %>%   analyze_vars(     vars = vars,     var_labels = var_labels   ) %>%   build_table(adsl) #>                      B: Placebo     A: Drug X    C: Combination   All Patients #>                        (N=134)       (N=134)        (N=132)         (N=400)    #> —————————————————————————————————————————————————————————————————————————————— #> Age (yr)                                                                       #>   n                      134           134            132             400      #>   Mean (SD)          35.4 (7.9)    33.8 (6.6)      35.4 (7.7)      34.9 (7.4)  #>   Median                35.0          33.0            35.0            34.0     #>   Min - Max          21.0 - 62.0   21.0 - 50.0    20.0 - 69.0     20.0 - 69.0  #> Sex                                                                            #>   n                      134           134            132             400      #>   M                   55 (41%)     51 (38.1%)      60 (45.5%)     166 (41.5%)  #>   F                  77 (57.5%)     79 (59%)        66 (50%)      222 (55.5%)  #>   U                   2 (1.5%)      3 (2.2%)         4 (3%)         9 (2.2%)   #>   UNDIFFERENTIATED        0         1 (0.7%)        2 (1.5%)        3 (0.8%) # Select statistics and modify default formats. basic_table() %>%   split_cols_by(var = \"ARM\") %>%   add_overall_col(\"All Patients\") %>%   add_colcounts() %>%   analyze_vars(     vars = vars,     var_labels = var_labels,     .stats = c(\"n\", \"mean_sd\", \"count\"),     .formats = c(mean_sd = \"xx.xx (xx.xx)\")   ) %>%   build_table(adsl) #>                       B: Placebo     A: Drug X     C: Combination   All Patients #>                        (N=134)        (N=134)         (N=132)         (N=400)    #> ———————————————————————————————————————————————————————————————————————————————— #> Age (yr)                                                                         #>   n                      134            134             132             400      #>   Mean (SD)          35.43 (7.90)   33.77 (6.55)    35.43 (7.72)    34.88 (7.44) #> Sex                                                                              #>   n                      134            134             132             400      #>   M                       55             51              60             166      #>   F                       77             79              66             222      #>   U                       2              3               4               9       #>   UNDIFFERENTIATED        0              1               2               3 lyt <- basic_table() %>%   split_cols_by(var = \"ARM\") %>%   add_overall_col(\"All Patients\") %>%   add_colcounts() %>%   analyze_vars(     vars = vars,     var_labels = var_labels   )  build_table(lyt, df = adsl %>% dplyr::filter(COUNTRY == \"BRA\")) #>                      B: Placebo     A: Drug X    C: Combination   All Patients #>                         (N=7)        (N=13)          (N=10)          (N=30)    #> —————————————————————————————————————————————————————————————————————————————— #> Age (yr)                                                                       #>   n                       7            13              10              30      #>   Mean (SD)          32.0 (6.1)    36.7 (6.4)     38.3 (10.6)      36.1 (8.1)  #>   Median                32.0          37.0            35.0            35.5     #>   Min - Max          25.0 - 42.0   24.0 - 47.0    25.0 - 64.0     24.0 - 64.0  #> Sex                                                                            #>   n                       7            13              10              30      #>   M                   4 (57.1%)     8 (61.5%)       5 (50%)        17 (56.7%)  #>   F                   3 (42.9%)     5 (38.5%)       5 (50%)        13 (43.3%)  #>   U                       0             0              0               0       #>   UNDIFFERENTIATED        0             0              0               0  build_table(lyt, df = adsl %>% dplyr::filter(COUNTRY == \"CHN\")) #>                      B: Placebo     A: Drug X    C: Combination   All Patients #>                        (N=81)        (N=74)          (N=64)         (N=219)    #> —————————————————————————————————————————————————————————————————————————————— #> Age (yr)                                                                       #>   n                      81            74              64             219      #>   Mean (SD)          35.7 (7.3)    33.0 (6.4)      35.2 (6.4)      34.6 (6.8)  #>   Median                36.0          32.0            35.0            34.0     #>   Min - Max          21.0 - 58.0   23.0 - 48.0    21.0 - 49.0     21.0 - 58.0  #> Sex                                                                            #>   n                      81            74              64             219      #>   M                  35 (43.2%)    27 (36.5%)      30 (46.9%)       92 (42%)   #>   F                  45 (55.6%)    44 (59.5%)      29 (45.3%)     118 (53.9%)  #>   U                   1 (1.2%)      2 (2.7%)        3 (4.7%)        6 (2.7%)   #>   UNDIFFERENTIATED        0         1 (1.4%)        2 (3.1%)        3 (1.4%)"},{"path":"https://insightsengineering.github.io/tern/articles/tables.html","id":"adverse-event-table","dir":"Articles","previous_headings":"Tabulation Examples","what":"Adverse Event Table","title":"Tabulation","text":"standard table adverse events summary system organ class preferred term. frequency counts preferred term, multiple occurrences AE individual count . create table need use combination several layout creating functions tabulation pipeline. start creating high-level summary. layout creating function tern can summarize_num_patients(): Note table, denominator used percentages shown header table (N = xx) defined based subject-level dataset adsl. done using alt_df_counts argument build_table(), provides alternative data set deriving counts header. often required work data sets include multiple records per patient df, adae .","code":"basic_table() %>%   split_cols_by(var = \"ACTARM\") %>%   add_colcounts() %>%   add_overall_col(label = \"All Patients\") %>%   summarize_num_patients(     var = \"USUBJID\",     .stats = c(\"unique\", \"nonunique\"),     .labels = c(       unique = \"Total number of patients with at least one AE\",       nonunique = \"Overall total number of events\"     )   ) %>%   build_table(     df = adae,     alt_counts_df = adsl   ) #>                                                  A: Drug X    B: Placebo    C: Combination   All Patients #>                                                   (N=134)       (N=134)        (N=132)         (N=400)    #> ————————————————————————————————————————————————————————————————————————————————————————————————————————— #> Total number of patients with at least one AE   122 (91.0%)   123 (91.8%)    120 (90.9%)     365 (91.2%)  #> Overall total number of events                      609           622            703             1934"},{"path":"https://insightsengineering.github.io/tern/articles/tables.html","id":"statistics-functions","dir":"Articles","previous_headings":"Tabulation Examples > Adverse Event Table","what":"Statistics Functions","title":"Tabulation","text":"building rest AE table helpful introduce tern package design conventions. layout creating function tern wrapper Statistics function. Statistics functions ones actual computation numbers table. functions always return named lists whose elements statistics available include layout via .stats argument layout creating function level. Statistics functions follow naming convention always begin s_* ease use documented page layout creating function counterpart. helpful review Statistic function understand logic used calculate numbers table see options may available modify analysis. example, Statistics function calculating numbers summarize_num_patients() s_num_patients(). results Statistics function list elements unique, nonunique unique_count: results can see unique nonunique statistics displayed “Patients” column initial AE table output . Also can see raw numbers formatted way. formatting functionality handled layout creating function level .formats argument. Now know types statistics can derived s_num_patients(), can try modifying default layout returned summarize_num_patients(). Instead reporting unique nonqunie statistics, specify analysis include unique_count statistic. result show counts unique patients. Note make update .stats .labels argument summarize_num_patients(). Let’s now continue building layout adverse event table. top-level summary, can repeat summary system organ class level. split analysis data split_rows_by() calling summarize_num_patients(). table looks almost ready. final step, need layout creating function can produce count table event frequencies. layout creating function count_occurrences(). Let’s first try using function simpler layout without row splits: Putting everything together, final AE table looks like :","code":"s_num_patients(x = adae$USUBJID, labelstr = \"\", .N_col = nrow(adae)) #> $unique #> [1] 365.000000   0.188728 #> attr(,\"label\") #> [1] \"\" #>  #> $nonunique #> [1] 1934 #> attr(,\"label\") #> [1] \"\" #>  #> $unique_count #> [1] 365 #> attr(,\"label\") #> [1] \"(n)\" basic_table() %>%   split_cols_by(var = \"ACTARM\") %>%   add_colcounts() %>%   add_overall_col(label = \"All Patients\") %>%   summarize_num_patients(     var = \"USUBJID\",     .stats = \"unique_count\",     .labels = c(unique_count = \"Total number of patients with at least one AE\")   ) %>%   build_table(     df = adae,     alt_counts_df = adsl   ) #>                                                 A: Drug X   B: Placebo   C: Combination   All Patients #>                                                  (N=134)     (N=134)        (N=132)         (N=400)    #> —————————————————————————————————————————————————————————————————————————————————————————————————————— #> Total number of patients with at least one AE      122         123            120             365 basic_table() %>%   split_cols_by(var = \"ACTARM\") %>%   add_colcounts() %>%   add_overall_col(label = \"All Patients\") %>%   summarize_num_patients(     var = \"USUBJID\",     .stats = c(\"unique\", \"nonunique\"),     .labels = c(       unique = \"Total number of patients with at least one AE\",       nonunique = \"Overall total number of events\"     )   ) %>%   split_rows_by(     \"AEBODSYS\",     child_labels = \"visible\",     nested = FALSE,     indent_mod = -1L,     split_fun = drop_split_levels   ) %>%   summarize_num_patients(     var = \"USUBJID\",     .stats = c(\"unique\", \"nonunique\"),     .labels = c(       unique = \"Total number of patients with at least one AE\",       nonunique = \"Overall total number of events\"     )   ) %>%   build_table(     df = adae,     alt_counts_df = adsl   ) #>                                                    A: Drug X    B: Placebo    C: Combination   All Patients #>                                                     (N=134)       (N=134)        (N=132)         (N=400)    #> ——————————————————————————————————————————————————————————————————————————————————————————————————————————— #> Total number of patients with at least one AE     122 (91.0%)   123 (91.8%)    120 (90.9%)     365 (91.2%)  #> Overall total number of events                        609           622            703             1934     #> cl A.1                                                                                                      #>   Total number of patients with at least one AE   78 (58.2%)    75 (56.0%)      89 (67.4%)     242 (60.5%)  #>   Overall total number of events                      132           130            160             422      #> cl B.1                                                                                                      #>   Total number of patients with at least one AE   47 (35.1%)    49 (36.6%)      43 (32.6%)     139 (34.8%)  #>   Overall total number of events                      56            60              62             178      #> cl B.2                                                                                                      #>   Total number of patients with at least one AE   79 (59.0%)    74 (55.2%)      85 (64.4%)     238 (59.5%)  #>   Overall total number of events                      129           138            143             410      #> cl C.1                                                                                                      #>   Total number of patients with at least one AE   43 (32.1%)    46 (34.3%)      43 (32.6%)     132 (33.0%)  #>   Overall total number of events                      55            63              64             182      #> cl C.2                                                                                                      #>   Total number of patients with at least one AE   35 (26.1%)    48 (35.8%)      55 (41.7%)     138 (34.5%)  #>   Overall total number of events                      48            53              65             166      #> cl D.1                                                                                                      #>   Total number of patients with at least one AE   79 (59.0%)    67 (50.0%)      80 (60.6%)     226 (56.5%)  #>   Overall total number of events                      127           106            135             368      #> cl D.2                                                                                                      #>   Total number of patients with at least one AE   47 (35.1%)    58 (43.3%)      57 (43.2%)     162 (40.5%)  #>   Overall total number of events                      62            72              74             208 basic_table() %>%   split_cols_by(var = \"ACTARM\") %>%   add_colcounts() %>%   add_overall_col(label = \"All Patients\") %>%   count_occurrences(vars = \"AEDECOD\") %>%   build_table(     df = adae,     alt_counts_df = adsl   ) #>                 A: Drug X    B: Placebo   C: Combination   All Patients #>                  (N=134)      (N=134)        (N=132)         (N=400)    #> ——————————————————————————————————————————————————————————————————————— #> dcd A.1.1.1.1   50 (37.3%)   45 (33.6%)     63 (47.7%)     158 (39.5%)  #> dcd A.1.1.1.2   48 (35.8%)   48 (35.8%)     50 (37.9%)     146 (36.5%)  #> dcd B.1.1.1.1   47 (35.1%)   49 (36.6%)     43 (32.6%)     139 (34.8%)  #> dcd B.2.1.2.1   49 (36.6%)   44 (32.8%)     52 (39.4%)     145 (36.2%)  #> dcd B.2.2.3.1   48 (35.8%)   54 (40.3%)     51 (38.6%)     153 (38.2%)  #> dcd C.1.1.1.3   43 (32.1%)   46 (34.3%)     43 (32.6%)     132 (33.0%)  #> dcd C.2.1.2.1   35 (26.1%)   48 (35.8%)     55 (41.7%)     138 (34.5%)  #> dcd D.1.1.1.1   50 (37.3%)   42 (31.3%)     51 (38.6%)     143 (35.8%)  #> dcd D.1.1.4.2   48 (35.8%)   42 (31.3%)     50 (37.9%)     140 (35.0%)  #> dcd D.2.1.5.3   47 (35.1%)   58 (43.3%)     57 (43.2%)     162 (40.5%) basic_table() %>%   split_cols_by(var = \"ACTARM\") %>%   add_colcounts() %>%   add_overall_col(label = \"All Patients\") %>%   summarize_num_patients(     var = \"USUBJID\",     .stats = c(\"unique\", \"nonunique\"),     .labels = c(       unique = \"Total number of patients with at least one AE\",       nonunique = \"Overall total number of events\"     )   ) %>%   split_rows_by(     \"AEBODSYS\",     child_labels = \"visible\",     nested = FALSE,     indent_mod = -1L,     split_fun = drop_split_levels   ) %>%   summarize_num_patients(     var = \"USUBJID\",     .stats = c(\"unique\", \"nonunique\"),     .labels = c(       unique = \"Total number of patients with at least one AE\",       nonunique = \"Overall total number of events\"     )   ) %>%   count_occurrences(vars = \"AEDECOD\") %>%   build_table(     df = adae,     alt_counts_df = adsl   ) #>                                                    A: Drug X    B: Placebo    C: Combination   All Patients #>                                                     (N=134)       (N=134)        (N=132)         (N=400)    #> ——————————————————————————————————————————————————————————————————————————————————————————————————————————— #> Total number of patients with at least one AE     122 (91.0%)   123 (91.8%)    120 (90.9%)     365 (91.2%)  #> Overall total number of events                        609           622            703             1934     #> cl A.1                                                                                                      #>   Total number of patients with at least one AE   78 (58.2%)    75 (56.0%)      89 (67.4%)     242 (60.5%)  #>   Overall total number of events                      132           130            160             422      #>     dcd A.1.1.1.1                                 50 (37.3%)    45 (33.6%)      63 (47.7%)     158 (39.5%)  #>     dcd A.1.1.1.2                                 48 (35.8%)    48 (35.8%)      50 (37.9%)     146 (36.5%)  #> cl B.1                                                                                                      #>   Total number of patients with at least one AE   47 (35.1%)    49 (36.6%)      43 (32.6%)     139 (34.8%)  #>   Overall total number of events                      56            60              62             178      #>     dcd B.1.1.1.1                                 47 (35.1%)    49 (36.6%)      43 (32.6%)     139 (34.8%)  #> cl B.2                                                                                                      #>   Total number of patients with at least one AE   79 (59.0%)    74 (55.2%)      85 (64.4%)     238 (59.5%)  #>   Overall total number of events                      129           138            143             410      #>     dcd B.2.1.2.1                                 49 (36.6%)    44 (32.8%)      52 (39.4%)     145 (36.2%)  #>     dcd B.2.2.3.1                                 48 (35.8%)    54 (40.3%)      51 (38.6%)     153 (38.2%)  #> cl C.1                                                                                                      #>   Total number of patients with at least one AE   43 (32.1%)    46 (34.3%)      43 (32.6%)     132 (33.0%)  #>   Overall total number of events                      55            63              64             182      #>     dcd C.1.1.1.3                                 43 (32.1%)    46 (34.3%)      43 (32.6%)     132 (33.0%)  #> cl C.2                                                                                                      #>   Total number of patients with at least one AE   35 (26.1%)    48 (35.8%)      55 (41.7%)     138 (34.5%)  #>   Overall total number of events                      48            53              65             166      #>     dcd C.2.1.2.1                                 35 (26.1%)    48 (35.8%)      55 (41.7%)     138 (34.5%)  #> cl D.1                                                                                                      #>   Total number of patients with at least one AE   79 (59.0%)    67 (50.0%)      80 (60.6%)     226 (56.5%)  #>   Overall total number of events                      127           106            135             368      #>     dcd D.1.1.1.1                                 50 (37.3%)    42 (31.3%)      51 (38.6%)     143 (35.8%)  #>     dcd D.1.1.4.2                                 48 (35.8%)    42 (31.3%)      50 (37.9%)     140 (35.0%)  #> cl D.2                                                                                                      #>   Total number of patients with at least one AE   47 (35.1%)    58 (43.3%)      57 (43.2%)     162 (40.5%)  #>   Overall total number of events                      62            72              74             208      #>     dcd D.2.1.5.3                                 47 (35.1%)    58 (43.3%)      57 (43.2%)     162 (40.5%)"},{"path":"https://insightsengineering.github.io/tern/articles/tables.html","id":"response-table","dir":"Articles","previous_headings":"Tabulation Examples","what":"Response Table","title":"Tabulation","text":"typical response table binary clinical trial endpoint may composed several different analyses: Proportion responders treatment group Difference proportion responders comparison groups vs. control group Chi-Square test difference response rates comparison groups vs. control group can build table layout like following approach used AE table: table section produced using different layout creating function tern. First start data preparation steps set analysis dataset. select endpoint analyze PARAMCD define logical variable is_rsp indicates whether patient classified responder . create summary proportion responders treatment group, use estimate_proportion() layout creating function: specify arm table used reference, use argument ref_group split_cols_by(). change reference arm “B: Placebo” arm displayed first column: customize analysis, can use method conf_level arguments modify type confidence interval calculated: next table section needed summarize difference response rates reference arm comparison arm. Use estimate_proportion_diff() layout creating function : final section needed complete table includes statistical test difference response rates. Use test_proportion_diff() layout creating function : customize output, use method argument select Chi-Squared test Schouten correction. Now can put table sections together one layout pipeline. Note one small change needed. Since primary analysis variable table sections (is_rsp), need give sub-table unique name. done adding table_names argument providing unique names :","code":"# Preprocessing to select an analysis endpoint. anl <- adrs %>%   dplyr::filter(PARAMCD == \"BESRSPI\") %>%   dplyr::mutate(is_rsp = AVALC %in% c(\"CR\", \"PR\")) basic_table() %>%   split_cols_by(var = \"ARM\") %>%   add_colcounts() %>%   estimate_proportion(     vars = \"is_rsp\",     table_names = \"est_prop\"   ) %>%   build_table(anl) #>                                   A: Drug X      B: Placebo    C: Combination #>                                    (N=134)        (N=134)         (N=132)     #> ————————————————————————————————————————————————————————————————————————————— #> Responders                       114 (85.1%)     90 (67.2%)     120 (90.9%)   #> 95% CI (Wald, with correction)   (78.7, 91.5)   (58.8, 75.5)    (85.6, 96.2) basic_table() %>%   split_cols_by(var = \"ARM\", ref_group = \"B: Placebo\") %>%   add_colcounts() %>%   estimate_proportion(     vars = \"is_rsp\"   ) %>%   build_table(anl) #>                                   A: Drug X      B: Placebo    C: Combination #>                                    (N=134)        (N=134)         (N=132)     #> ————————————————————————————————————————————————————————————————————————————— #> Responders                       114 (85.1%)     90 (67.2%)     120 (90.9%)   #> 95% CI (Wald, with correction)   (78.7, 91.5)   (58.8, 75.5)    (85.6, 96.2) basic_table() %>%   split_cols_by(var = \"ARM\", ref_group = \"B: Placebo\") %>%   add_colcounts() %>%   estimate_proportion(     vars = \"is_rsp\",     method = \"clopper-pearson\",     conf_level = 0.9   ) %>%   build_table(anl) #>                             A: Drug X      B: Placebo    C: Combination #>                              (N=134)        (N=134)         (N=132)     #> ——————————————————————————————————————————————————————————————————————— #> Responders                 114 (85.1%)     90 (67.2%)     120 (90.9%)   #> 90% CI (Clopper-Pearson)   (79.1, 89.9)   (59.9, 73.9)    (85.7, 94.7) basic_table() %>%   split_cols_by(var = \"ARM\", ref_group = \"B: Placebo\") %>%   add_colcounts() %>%   estimate_proportion_diff(     vars = \"is_rsp\",     show_labels = \"visible\",     var_labels = \"Unstratified Analysis\"   ) %>%   build_table(anl) #>                                       A: Drug X    B: Placebo   C: Combination #>                                        (N=134)      (N=134)        (N=132)     #> —————————————————————————————————————————————————————————————————————————————— #> Unstratified Analysis                                                          #>   Difference in Response rate (%)       17.9                         23.7      #>     95% CI (Wald, with correction)   (7.2, 28.6)                 (13.7, 33.8) basic_table() %>%   split_cols_by(var = \"ARM\", ref_group = \"B: Placebo\") %>%   add_colcounts() %>%   test_proportion_diff(vars = \"is_rsp\") %>%   build_table(anl) #>                                A: Drug X   B: Placebo   C: Combination #>                                 (N=134)     (N=134)        (N=132)     #> —————————————————————————————————————————————————————————————————————— #>   p-value (Chi-Squared Test)    0.0006                     <0.0001 basic_table() %>%   split_cols_by(var = \"ARM\", ref_group = \"B: Placebo\") %>%   add_colcounts() %>%   test_proportion_diff(     vars = \"is_rsp\",     method = \"schouten\"   ) %>%   build_table(anl) #>                                                         A: Drug X   B: Placebo   C: Combination #>                                                          (N=134)     (N=134)        (N=132)     #> ——————————————————————————————————————————————————————————————————————————————————————————————— #>   p-value (Chi-Squared Test with Schouten Correction)    0.0008                     <0.0001 basic_table() %>%   split_cols_by(var = \"ARM\", ref_group = \"B: Placebo\") %>%   add_colcounts() %>%   estimate_proportion(     vars = \"is_rsp\",     method = \"clopper-pearson\",     conf_level = 0.9,     table_names = \"est_prop\"   ) %>%   estimate_proportion_diff(     vars = \"is_rsp\",     show_labels = \"visible\",     var_labels = \"Unstratified Analysis\",     table_names = \"est_prop_diff\"   ) %>%   test_proportion_diff(     vars = \"is_rsp\",     method = \"schouten\",     table_names = \"test_prop_diff\"   ) %>%   build_table(anl) #>                                                          A: Drug X      B: Placebo    C: Combination #>                                                           (N=134)        (N=134)         (N=132)     #> ———————————————————————————————————————————————————————————————————————————————————————————————————— #> Responders                                              114 (85.1%)     90 (67.2%)     120 (90.9%)   #> 90% CI (Clopper-Pearson)                                (79.1, 89.9)   (59.9, 73.9)    (85.7, 94.7)  #> Unstratified Analysis                                                                                #>   Difference in Response rate (%)                           17.9                           23.7      #>     95% CI (Wald, with correction)                      (7.2, 28.6)                    (13.7, 33.8)  #>   p-value (Chi-Squared Test with Schouten Correction)      0.0008                        <0.0001"},{"path":"https://insightsengineering.github.io/tern/articles/tables.html","id":"summary","dir":"Articles","previous_headings":"","what":"Summary","title":"Tabulation","text":"Tabulation tern builds top layout tabulation framework rtables. Complex tables built step step pipeline combining layout creating functions perform specific type analysis. tern analyze functions introduced vignette : analyze_vars() summarize_num_patients() count_occurrences() estimate_proportion() estimate_proportion_diff() test_proportion_diff() Layout creating functions build formatted layout controlling features labels, numerical display formats indentation. functions wrappers Statistics functions calculate raw summaries analysis. can easily spot Statistics functions documentation always begin prefix s_. can helpful inspect run Statistics functions understand ways analysis can customized.","code":""},{"path":"https://insightsengineering.github.io/tern/articles/tern.html","id":"common-clinical-trials-analyses","dir":"Articles","previous_headings":"","what":"Common Clinical Trials Analyses","title":"Introduction to tern","text":"package provides large range functionality create tables graphs used clinical trial statistical analysis. rtables tabulation extended clinical trials specific functions: demographics unique patients exposure across patients change baseline parameters statistical model fits: MMRM, logistic regression, Cox regression, … … rtables tabulation helper functions: pre-processing conversions transformations … data visualizations connected clinical trials: Kaplan-Meier plots forest plots line plots … data visualizations helper functions: arrange/stack multiple graphs embellishing graphs/tables metadata details, adding titles, footnotes, page number, etc. … reference tern functions available tern website functions reference.","code":""},{"path":"https://insightsengineering.github.io/tern/articles/tern.html","id":"analytical-functions-for-rtables","dir":"Articles","previous_headings":"","what":"Analytical Functions for rtables","title":"Introduction to tern","text":"Analytical functions used combination rtables layout functions, pipeline creates rtables table. apply statistical logic layout rtables table. table layout materialized rtables::build_table function data. tern analytical functions wrappers around rtables::analyze function; offer various methods useful perspective clinical trials statistical projects. Examples tern analytical functions count_occurrences, summarize_ancova analyze_vars. one prefix identify tern analytical functions recommended use reference subsection tern website. rtables code first describe two tables assign descriptions variables lyt lyt2. built tables using actual data rtables::build_table. description table called table layout. analyze instruction adds layout ARM variable analyzed mean analysis function result rounded 1 decimal place. Hence, layout “pre-data”; , ’s description build table get data. Defining table layout pure rtables code: , tern function used analyze_vars replaces rtables::analyze function used . see tern offers advanced analysis extending rtables function calls one additional function call. examples tabulation analyze functions presented Tabulation vignette.","code":"library(tern) library(dplyr) # Create table layout pure rtables lyt <- rtables::basic_table() %>%   rtables::split_cols_by(var = \"ARM\") %>%   rtables::split_rows_by(var = \"AVISIT\") %>%   rtables::analyze(vars = \"AVAL\", mean, format = \"xx.x\") # Create table layout with tern analyze_vars analyze function lyt2 <- rtables::basic_table() %>%   rtables::split_cols_by(var = \"ARM\") %>%   rtables::split_rows_by(var = \"AVISIT\") %>%   analyze_vars(vars = \"AVAL\", .formats = c(\"mean_sd\" = \"(xx.xx, xx.xx)\")) # Apply table layout to data and produce `rtables` object  adrs <- formatters::ex_adrs  rtables::build_table(lyt, df = adrs) #>                    A: Drug X   B: Placebo   C: Combination #> —————————————————————————————————————————————————————————— #> SCREENING                                                  #>   mean                3.0         3.0            3.0       #> BASELINE                                                   #>   mean                2.5         2.8            2.5       #> END OF INDUCTION                                           #>   mean                1.7         2.1            1.6       #> FOLLOW UP                                                  #>   mean                2.2         2.9            2.0 rtables::build_table(lyt2, df = adrs) #>                     A: Drug X      B: Placebo    C: Combination #> ——————————————————————————————————————————————————————————————— #> SCREENING                                                       #>   n                    154            178             144       #>   Mean (SD)        (3.00, 0.00)   (3.00, 0.00)    (3.00, 0.00)  #>   Median               3.0            3.0             3.0       #>   Min - Max         3.0 - 3.0      3.0 - 3.0       3.0 - 3.0    #> BASELINE                                                        #>   n                    136            146             124       #>   Mean (SD)        (2.46, 0.88)   (2.77, 1.00)    (2.46, 1.08)  #>   Median               3.0            3.0             3.0       #>   Min - Max         1.0 - 4.0      1.0 - 5.0       1.0 - 5.0    #> END OF INDUCTION                                                #>   n                    218            205             217       #>   Mean (SD)        (1.75, 0.90)   (2.14, 1.28)    (1.65, 1.06)  #>   Median               2.0            2.0             1.0       #>   Min - Max         1.0 - 4.0      1.0 - 5.0       1.0 - 5.0    #> FOLLOW UP                                                       #>   n                    164            153             167       #>   Mean (SD)        (2.23, 1.26)   (2.89, 1.29)    (1.97, 1.01)  #>   Median               2.0            4.0             2.0       #>   Min - Max         1.0 - 4.0      1.0 - 4.0       1.0 - 4.0"},{"path":"https://insightsengineering.github.io/tern/articles/tern.html","id":"clinical-trial-visualizations","dir":"Articles","previous_headings":"","what":"Clinical Trial Visualizations","title":"Introduction to tern","text":"Clinical trial related plots complement rich palette tern tabulation analysis functions. Thus tern package delivers full-featured tool clinical trial reporting. tern plot functions return graphs ggplot2 objects. nestcolor package can loaded apply standardized NEST color palette tern plots. Line plot without table generated g_lineplot function.  Line plot table generated g_lineplot function.  tern functions used plot generation g_ prefixed listed tern website functions reference.","code":"adsl <- formatters::ex_adsl adlb <- formatters::ex_adlb adlb <- dplyr::filter(adlb, PARAMCD == \"ALT\", AVISIT != \"SCREENING\") library(nestcolor) # Mean with CI g_lineplot(adlb, adsl, subtitle = \"Laboratory Test:\") # Mean with CI, table, and customized confidence level g_lineplot(   adlb,   adsl,   table = c(\"n\", \"mean\", \"mean_ci\"),   title = \"Plot of Mean and 80% Confidence Limits by Visit\" )"},{"path":"https://insightsengineering.github.io/tern/articles/tern.html","id":"interactive-apps","dir":"Articles","previous_headings":"","what":"Interactive Apps","title":"Introduction to tern","text":"tern outputs can easily converted shiny apps. recommend building apps using teal package, shiny-based interactive exploration framework analyzing data. variety pre-made teal shiny apps tern outputs available teal.modules.clinical package.","code":""},{"path":"https://insightsengineering.github.io/tern/articles/tern.html","id":"summary","dir":"Articles","previous_headings":"","what":"Summary","title":"Introduction to tern","text":"summary, tern contains many additional functions creating tables, listings, graphs used clinical trials statistical analyses. design package gives users flexibility meet analysis needs regulatory exploratory reporting contexts. information please explore tern website.","code":""},{"path":"https://insightsengineering.github.io/tern/articles/tern_formats.html","id":"tern-formatting-functions-overview","dir":"Articles","previous_headings":"","what":"tern Formatting Functions Overview","title":"Formatting Functions","text":"tern R package provides functions create common analyses clinical trials R functions default formatting arguments displaying values output specific way. tern formatting differs compared formatting available formatters package tern formats capable handling logical statements, allowing fine-tuning output displayed. Depending type value displayed, value , format output change. Whereas using formatters package, specified format applied regardless value. see available formatting functions available tern see ?formatting_functions. see available format strings available formatters see formatters::list_valid_format_labels().","code":""},{"path":"https://insightsengineering.github.io/tern/articles/tern_formats.html","id":"comparing-tern-formatters-formats","dir":"Articles","previous_headings":"","what":"Comparing tern & formatters Formats","title":"Formatting Functions","text":"packages used vignette : example demonstrates use tern formatting count_abnormal() function. example “low” category non-zero numerator value fraction percentage value displayed, “high” value numerator value zero fraction value displayed without also displaying redundant zero percentage value. following example count_abnormal() function utilized . time “low” values “high” values non-zero numerator show percentage. following example demonstrates difference formatters used instead format output. choose use \"xx / xx\" value format. “high” value zero numerator value “low” value non-zero numerator, yet displayed format. concept occurs using available formats formatters package. following example displays result using \"xx.x / xx.x\" format instead. Use formatters::list_valid_format_labels() see full list available formats formatters.","code":"library(rtables) library(formatters) library(tern) library(dplyr) df2 <- data.frame(   ID = as.character(c(1, 1, 2, 2)),   RANGE = factor(c(\"NORMAL\", \"LOW\", \"HIGH\", \"LOW\")),   BL_RANGE = factor(c(\"NORMAL\", \"NORMAL\", \"HIGH\", \"HIGH\")),   ONTRTFL = c(\"\", \"Y\", \"\", \"Y\"),   stringsAsFactors = FALSE )  df2 <- df2 %>%   filter(ONTRTFL == \"Y\")  basic_table() %>%   count_abnormal(     var = \"RANGE\",     abnormal = list(low = \"LOW\", high = \"HIGH\"),     variables = list(id = \"ID\", baseline = \"BL_RANGE\"),     exclude_base_abn = FALSE,     .formats = list(fraction = format_fraction)   ) %>%   build_table(df2) #>         all obs   #> ————————————————— #> low    2/2 (100%) #> high      0/2 df2 <- data.frame(   ID = as.character(c(1, 1, 2, 2)),   RANGE = factor(c(\"NORMAL\", \"LOW\", \"HIGH\", \"HIGH\")),   BL_RANGE = factor(c(\"NORMAL\", \"NORMAL\", \"HIGH\", \"HIGH\")),   ONTRTFL = c(\"\", \"Y\", \"\", \"Y\"),   stringsAsFactors = FALSE )  df2 <- df2 %>%   filter(ONTRTFL == \"Y\")  basic_table() %>%   count_abnormal(     var = \"RANGE\",     abnormal = list(low = \"LOW\", high = \"HIGH\"),     variables = list(id = \"ID\", baseline = \"BL_RANGE\"),     exclude_base_abn = FALSE,     .formats = list(fraction = format_fraction)   ) %>%   build_table(df2) #>         all obs  #> ———————————————— #> low    1/2 (50%) #> high   1/2 (50%) df2 <- data.frame(   ID = as.character(c(1, 1, 2, 2)),   RANGE = factor(c(\"NORMAL\", \"LOW\", \"HIGH\", \"LOW\")),   BL_RANGE = factor(c(\"NORMAL\", \"NORMAL\", \"HIGH\", \"HIGH\")),   ONTRTFL = c(\"\", \"Y\", \"\", \"Y\"),   stringsAsFactors = FALSE ) df2 <- df2 %>%   filter(ONTRTFL == \"Y\")  basic_table() %>%   count_abnormal(     var = \"RANGE\",     abnormal = list(low = \"LOW\", high = \"HIGH\"),     variables = list(id = \"ID\", baseline = \"BL_RANGE\"),     exclude_base_abn = FALSE,     .formats = list(fraction = \"xx / xx\")   ) %>%   build_table(df2) #>        all obs #> —————————————— #> low     2 / 2  #> high    0 / 2 df2 <- data.frame(   ID = as.character(c(1, 1, 2, 2)),   RANGE = factor(c(\"NORMAL\", \"LOW\", \"HIGH\", \"LOW\")),   BL_RANGE = factor(c(\"NORMAL\", \"NORMAL\", \"HIGH\", \"HIGH\")),   ONTRTFL = c(\"\", \"Y\", \"\", \"Y\"),   stringsAsFactors = FALSE ) df2 <- df2 %>%   filter(ONTRTFL == \"Y\")  basic_table() %>%   count_abnormal(     var = \"RANGE\",     abnormal = list(low = \"LOW\", high = \"HIGH\"),     variables = list(id = \"ID\", baseline = \"BL_RANGE\"),     exclude_base_abn = FALSE,     .formats = list(fraction = \"xx.x / xx.x\")   ) %>%   build_table(df2) #>         all obs  #> ———————————————— #> low    2.0 / 2.0 #> high   0.0 / 2.0"},{"path":"https://insightsengineering.github.io/tern/articles/tern_formats.html","id":"formatting-function-basics","dir":"Articles","previous_headings":"","what":"Formatting Function Basics","title":"Formatting Functions","text":"Current tern formatting functions consider following aspects setting custom behaviors: Missing values - custom value string can set display missing values instead NA. 0’s - cell value zero, tern fraction formatting functions exclude accompanying percentage value. Number decimal places display - number decimal places can fixed needed. Value thresholds - different format value can displayed depending whether value within certain threshold.","code":""},{"path":"https://insightsengineering.github.io/tern/articles/tern_formats.html","id":"number-of-decimal-places-to-display","dir":"Articles","previous_headings":"Formatting Function Basics","what":"Number of Decimal Places to Display","title":"Formatting Functions","text":"Two functions set fixed number decimal places (specifically 1) format_fraction_fixed_dp() format_count_fraction_fixed_dp(). default, formatting functions remove trailing zeros, two functions always one decimal place percentage, even digit zero. See following example:","code":"format_fraction_fixed_dp(x = c(num = 1L, denom = 3L)) #> [1] \"1/3 (33.3%)\" format_fraction_fixed_dp(x = c(num = 1L, denom = 2L)) #> [1] \"1/2 (50.0%)\"  format_count_fraction_fixed_dp(x = c(2, 0.6667)) #> [1] \"2 (66.7%)\" format_count_fraction_fixed_dp(x = c(2, 0.25)) #> [1] \"2 (25.0%)\""},{"path":"https://insightsengineering.github.io/tern/articles/tern_formats.html","id":"value-thresholds","dir":"Articles","previous_headings":"Formatting Function Basics","what":"Value Thresholds","title":"Formatting Functions","text":"Functions set custom values according certain threshold include format_extreme_values(), format_extreme_values_ci(), format_fraction_threshold(). extreme value formats work similarly allow user specify maximum number digits include, large small values given special string value. example: format_fraction_threshold() function allows user specify lower percentage threshold, values instead assigned special string value. example: See documentation function specific details behavior customize .","code":"extreme_format <- format_extreme_values(digits = 2) extreme_format(0.235) #> [1] \"0.23\" extreme_format(0.001) #> [1] \"<0.01\" extreme_format(Inf) #> [1] \">999.99\" fraction_format <- format_fraction_threshold(0.05) fraction_format(x = c(20, 0.1)) #> [1] 10 fraction_format(x = c(2, 0.01)) #> [1] \"<5\""},{"path":"https://insightsengineering.github.io/tern/articles/tern_formats.html","id":"creating-custom-formatting-functions","dir":"Articles","previous_headings":"","what":"Creating Custom Formatting Functions","title":"Formatting Functions","text":"table requires customized output displayed using one pre-existing tern formatting functions, may want consider creating new formatting function. creating formatting function important consider aspects listed Formatting Function Customization section . section create custom formatting function derived format_fraction_fixed_dp() function. First take look function detail customize . see numerator value greater 0, fraction percentage displayed. numerator 0, fraction shown. Percent values always display 1 decimal place. create dummy dataset observe output value behavior formatting function applied. Now modify function make custom formatting function, custom_format. want display 3 decimal places percent value, numerator value 0 want display 0 value (without denominator).","code":"# First we will see how the format_fraction_fixed_dp code works and displays the outputs format_fraction_fixed_dp <- function(x, ...) {   attr(x, \"label\") <- NULL   checkmate::assert_vector(x)   checkmate::assert_count(x[\"num\"])   checkmate::assert_count(x[\"denom\"])    result <- if (x[\"num\"] == 0) {     paste0(x[\"num\"], \"/\", x[\"denom\"])   } else {     paste0(       x[\"num\"], \"/\", x[\"denom\"],       \" (\", sprintf(\"%.1f\", round(x[\"num\"] / x[\"denom\"] * 100, 1)), \"%)\"     )   }   return(result) } df2 <- data.frame(   ID = as.character(c(1, 1, 2, 2)),   RANGE = factor(c(\"NORMAL\", \"LOW\", \"HIGH\", \"LOW\")),   BL_RANGE = factor(c(\"NORMAL\", \"NORMAL\", \"HIGH\", \"HIGH\")),   ONTRTFL = c(\"\", \"Y\", \"\", \"Y\"),   stringsAsFactors = FALSE ) %>%   filter(ONTRTFL == \"Y\")  basic_table() %>%   count_abnormal(     var = \"RANGE\",     abnormal = list(low = \"LOW\", high = \"HIGH\"),     variables = list(id = \"ID\", baseline = \"BL_RANGE\"),     exclude_base_abn = FALSE,     .formats = list(fraction = format_fraction_fixed_dp)   ) %>%   build_table(df2) #>          all obs    #> ——————————————————— #> low    2/2 (100.0%) #> high       0/2 custom_format <- function(x, ...) {   attr(x, \"label\") <- NULL   checkmate::assert_vector(x)   checkmate::assert_count(x[\"num\"])   checkmate::assert_count(x[\"denom\"])    result <- if (x[\"num\"] == 0) {     paste0(x[\"num\"]) # We remove the denominator on this line so that only a 0 is displayed   } else {     paste0(       x[\"num\"], \"/\", x[\"denom\"],       \" (\", sprintf(\"%.3f\", round(x[\"num\"] / x[\"denom\"] * 100, 1)), \"%)\" # We include 3 decimal places with %.3f     )   }   return(result) }  basic_table() %>%   count_abnormal(     var = \"RANGE\",     abnormal = list(low = \"LOW\", high = \"HIGH\"),     variables = list(id = \"ID\", baseline = \"BL_RANGE\"),     exclude_base_abn = FALSE,     .formats = list(fraction = custom_format) # Here we implement our new custom_format function   ) %>%   build_table(df2) #>           all obs     #> ————————————————————— #> low    2/2 (100.000%) #> high         0"},{"path":"https://insightsengineering.github.io/tern/articles/tern_formats.html","id":"summary","dir":"Articles","previous_headings":"","what":"Summary","title":"Formatting Functions","text":"tern analysis function pre-specified default format functions implement generating output, taken formatters package custom formatting functions stored tern. tern functions differ compared formatters logical statements can used set value-dependent customized formats. like create custom formatting function use tern, sure carefully consider rules want implement handle different input values.","code":""},{"path":"https://insightsengineering.github.io/tern/articles/tern_functions_guide.html","id":"understanding-tern-functions","dir":"Articles","previous_headings":"","what":"Understanding tern functions","title":"Understanding `tern` functions","text":"Every function tern package designed certain structure can cooperate well every user’s need, maintaining consistent predictable behavior. document guide example function package, explaining purpose many building blocks can used. recently worked consider summarize_change() example. function used calculate change baseline value given variable. realistic example can found LBT03 TLG-catalog. summarize_change() main function available user. can find lists functions ?tern::analyze_functions. build around rtables::analyze() function, core analysis function rtables. wrapper functions call specific analysis functions (always written a_*) meant handle statistic functions (always written s_*) format results rtables::in_row() function. can summarize structure follows: summarize_change() (1)-> a_change_from_baseline() (2)-> [s_change_from_baseline() + rtables::in_row()] main questions may arise : Handling NA. Handling formats. Additional statistics. Data set library loading. Classic use summarize_change(). .formats, .labels, .indent_mods depend names .stats. can change default formatting. want something special format? Adding custom statistic (custom format):","code":"library(dplyr) #>  #> Attaching package: 'dplyr' #> The following objects are masked from 'package:stats': #>  #>     filter, lag #> The following objects are masked from 'package:base': #>  #>     intersect, setdiff, setequal, union library(tern) #> Loading required package: rtables #> Loading required package: formatters #>  #> Attaching package: 'formatters' #> The following object is masked from 'package:base': #>  #>     %||% #> Loading required package: magrittr #>  #> Attaching package: 'rtables' #> The following object is masked from 'package:utils': #>  #>     str #> Registered S3 method overwritten by 'tern': #>   method   from  #>   tidy.glm broom  ## Fabricate dataset dta_test <- data.frame(   USUBJID = rep(1:6, each = 3),   AVISIT = rep(paste0(\"V\", 1:3), 6),   ARM = rep(LETTERS[1:3], rep(6, 3)),   AVAL = c(9:1, rep(NA, 9)) ) %>%   mutate(ABLFLL = AVISIT == \"V1\") %>%   group_by(USUBJID) %>%   mutate(     BLVAL = AVAL[ABLFLL],     CHG = AVAL - BLVAL   ) %>%   ungroup() fix_layout <- basic_table() %>%   split_cols_by(\"ARM\") %>%   split_rows_by(\"AVISIT\")   # Dealing with NAs: na_rm = TRUE fix_layout %>%   summarize_change(\"CHG\", variables = list(value = \"AVAL\", baseline_flag = \"ABLFLL\")) %>%   build_table(dta_test) %>%   print() #>                     A               B         C  #> ———————————————————————————————————————————————— #> V1                                               #>   n                 2               1         0  #>   Mean (SD)    7.50 (2.12)      3.00 (NA)     NA #>   Median          7.50            3.00        NA #>   Min - Max    6.00 - 9.00     3.00 - 3.00    NA #> V2                                               #>   n                 2               1         0  #>   Mean (SD)   -1.00 (0.00)     -1.00 (NA)     NA #>   Median          -1.00           -1.00       NA #>   Min - Max   -1.00 - -1.00   -1.00 - -1.00   NA #> V3                                               #>   n                 2               1         0  #>   Mean (SD)   -2.00 (0.00)     -2.00 (NA)     NA #>   Median          -2.00           -2.00       NA #>   Min - Max   -2.00 - -2.00   -2.00 - -2.00   NA  # Dealing with NAs: na_rm = FALSE fix_layout %>%   summarize_change(\"CHG\", variables = list(value = \"AVAL\", baseline_flag = \"ABLFLL\"), na_rm = FALSE) %>%   build_table(dta_test) %>%   print() #>                     A               B         C  #> ———————————————————————————————————————————————— #> V1                                               #>   n                 2               1         0  #>   Mean (SD)    7.50 (2.12)      3.00 (NA)     NA #>   Median          7.50            3.00        NA #>   Min - Max    6.00 - 9.00     3.00 - 3.00    NA #> V2                                               #>   n                 2               1         0  #>   Mean (SD)   -1.00 (0.00)     -1.00 (NA)     NA #>   Median          -1.00           -1.00       NA #>   Min - Max   -1.00 - -1.00   -1.00 - -1.00   NA #> V3                                               #>   n                 2               1         0  #>   Mean (SD)   -2.00 (0.00)     -2.00 (NA)     NA #>   Median          -2.00           -2.00       NA #>   Min - Max   -2.00 - -2.00   -2.00 - -2.00   NA  # changing the NA string (it is done on all levels) fix_layout %>%   summarize_change(\"CHG\", variables = list(value = \"AVAL\", baseline_flag = \"ABLFLL\"), na_str = \"my_na\") %>%   build_table(dta_test) %>%   print() #>                     A               B           C   #> ——————————————————————————————————————————————————— #> V1                                                  #>   n                 2               1           0   #>   Mean (SD)    7.50 (2.12)    3.00 (my_na)    my_na #>   Median          7.50            3.00        my_na #>   Min - Max    6.00 - 9.00     3.00 - 3.00    my_na #> V2                                                  #>   n                 2               1           0   #>   Mean (SD)   -1.00 (0.00)    -1.00 (my_na)   my_na #>   Median          -1.00           -1.00       my_na #>   Min - Max   -1.00 - -1.00   -1.00 - -1.00   my_na #> V3                                                  #>   n                 2               1           0   #>   Mean (SD)   -2.00 (0.00)    -2.00 (my_na)   my_na #>   Median          -2.00           -2.00       my_na #>   Min - Max   -2.00 - -2.00   -2.00 - -2.00   my_na # changing n count format and label and indentation fix_layout %>%   summarize_change(\"CHG\",     variables = list(value = \"AVAL\", baseline_flag = \"ABLFLL\"),     .stats = c(\"n\", \"mean\"), # reducing the number of stats for visual appreciation     .formats = c(n = \"xx.xx\"),     .labels = c(n = \"NnNn\"),     .indent_mods = c(n = 5), na_str = \"nA\"   ) %>%   build_table(dta_test) %>%   print() #>                     A      B      C   #> ————————————————————————————————————— #> V1                                    #>             NnNn   2.00   1.00   0.00 #>   Mean             7.5    3.0     nA  #> V2                                    #>             NnNn   2.00   1.00   0.00 #>   Mean             -1.0   -1.0    nA  #> V3                                    #>             NnNn   2.00   1.00   0.00 #>   Mean             -2.0   -2.0    nA # changing n count format and label and indentation fix_layout %>%   summarize_change(\"CHG\",     variables = list(value = \"AVAL\", baseline_flag = \"ABLFLL\"),     .stats = c(\"n\", \"mean\"), # reducing the number of stats for visual appreciation     .formats = c(n = function(x, ...) as.character(x * 100))   ) %>% # Note you need ...!!!   build_table(dta_test) %>%   print() #>           A      B     C  #> ————————————————————————— #> V1                        #>   n      200    100    0  #>   Mean   7.5    3.0    NA #> V2                        #>   n      200    100    0  #>   Mean   -1.0   -1.0   NA #> V3                        #>   n      200    100    0  #>   Mean   -2.0   -2.0   NA # changing n count format and label and indentation fix_layout %>%   summarize_change(     \"CHG\",     variables = list(value = \"AVAL\", baseline_flag = \"ABLFLL\"),     .stats = c(\"n\", \"my_stat\" = function(df, ...) {       a <- mean(df$AVAL, na.rm = TRUE)       b <- list(...)$.N_row # It has access at all `?rtables::additional_fun_params`       a / b     }),     .formats = c(\"my_stat\" = function(x, ...) sprintf(\"%.2f\", x))   ) %>%   build_table(dta_test) #>              A      B     C  #> ———————————————————————————— #> V1                           #>   n          2      1     0  #>   my_stat   1.25   0.50   NA #> V2                           #>   n          2      1     0  #>   my_stat   1.08   0.33   NA #> V3                           #>   n          2      1     0  #>   my_stat   0.92   0.17   NA"},{"path":"https://insightsengineering.github.io/tern/articles/tern_functions_guide.html","id":"for-developers","dir":"Articles","previous_headings":"","what":"For Developers","title":"Understanding `tern` functions","text":"layers specific parameters need available, , rtables multiple way handle formatting NA values, decide correctly handle additional extra arguments. follow following scheme: Level 1: summarize_change(): parameters without starting dot .* used added extra_args. Specifically, solve NA values using inclNAs option rtables::analyze(). add ... na.rm = inclNAs. Also na_str set. may want statistic dependent future, still need think accomplish . add rtables::additional_fun_params analysis function make available ... next level. Level 2: a_change_from_baseline(): parameters starting dot . used. Mainly .stats, .formats, .labels, .indent_mods used. also add extra_afun_params ... list statistical function. Notice handling additional parameters .call() function.","code":""},{"path":"https://insightsengineering.github.io/tern/authors.html","id":null,"dir":"","previous_headings":"","what":"Authors","title":"Authors and Citation","text":"Joe Zhu. Author, maintainer. Daniel Sabanés Bové. Author. Jana Stoilova. Author. Davide Garolini. Author. Emily de la Rua. Author. Abinaya Yogasekaram. Author. Heng Wang. Author. Francois Collin. Author. Adrian Waddell. Author. Pawel Rucki. Author. Chendi Liao. Author. Jennifer Li. Author. F. Hoffmann-La Roche AG. Copyright holder, funder.","code":""},{"path":"https://insightsengineering.github.io/tern/authors.html","id":"citation","dir":"","previous_headings":"","what":"Citation","title":"Authors and Citation","text":"Zhu J, Sabanés Bové D, Stoilova J, Garolini D, de la Rua E, Yogasekaram , Wang H, Collin F, Waddell , Rucki P, Liao C, Li J (2024). tern: Create Common TLGs Used Clinical Trials. R package version 0.9.6.9016, https://github.com/insightsengineering/tern/, https://insightsengineering.github.io/tern/.","code":"@Manual{,   title = {tern: Create Common TLGs Used in Clinical Trials},   author = {Joe Zhu and Daniel {Sabanés Bové} and Jana Stoilova and Davide Garolini and Emily {de la Rua} and Abinaya Yogasekaram and Heng Wang and Francois Collin and Adrian Waddell and Pawel Rucki and Chendi Liao and Jennifer Li},   year = {2024},   note = {R package version 0.9.6.9016,     https://github.com/insightsengineering/tern/},   url = {https://insightsengineering.github.io/tern/}, }"},{"path":"https://insightsengineering.github.io/tern/index.html","id":"tern-","dir":"","previous_headings":"","what":"Create Common TLGs Used in Clinical Trials","title":"Create Common TLGs Used in Clinical Trials","text":"tern R package contains analysis functions create tables graphs used clinical trial reporting. package provides large range functionality, : Data visualizations: Line plots (g_lineplot) Kaplan-Meier plots (g_km) Forest plots (g_forest) STEP graphs (g_step) Individual patient plots (g_ipp) Waterfall plots (g_waterfall) Bland-Altman plots (g_bland_altman) Statistical model fit summaries: Logistic regression (summarize_logistic) Cox regression (summarize_coxreg) Analysis tables: See list available analyze functions See list available summarize functions See list available column-wise analysis functions Many outputs available added teal shiny applications interactive exploration data. teal modules available teal.modules.clinical package. See TLG Catalog extensive catalog example clinical trial tables, listings, graphs created using tern functionality.","code":""},{"path":"https://insightsengineering.github.io/tern/index.html","id":"installation","dir":"","previous_headings":"","what":"Installation","title":"Create Common TLGs Used in Clinical Trials","text":"tern available CRAN can install latest released version : can install latest development version directly GitHub running following:","code":"install.packages(\"tern\") # install.packages(\"pak\") pak::pak(\"insightsengineering/tern\")"},{"path":"https://insightsengineering.github.io/tern/index.html","id":"usage","dir":"","previous_headings":"","what":"Usage","title":"Create Common TLGs Used in Clinical Trials","text":"understand use package, please refer Introduction tern article, provides multiple examples code implementation. See package vignettes browseVignettes(package = \"tern\") usage package.","code":""},{"path":"https://insightsengineering.github.io/tern/index.html","id":"related","dir":"","previous_headings":"","what":"Related","title":"Create Common TLGs Used in Clinical Trials","text":"rtables - table engine used tlg-catalog - website showcasing many examples clinical trial tables, listings, graphs teal.modules.clinical - teal modules interactive data analysis","code":""},{"path":"https://insightsengineering.github.io/tern/index.html","id":"acknowledgment","dir":"","previous_headings":"","what":"Acknowledgment","title":"Create Common TLGs Used in Clinical Trials","text":"package result joint efforts many developers stakeholders. like thank everyone contributed far!","code":""},{"path":[]},{"path":[]},{"path":[]},{"path":"https://insightsengineering.github.io/tern/reference/abnormal.html","id":null,"dir":"Reference","previous_headings":"","what":"Count patients with abnormal range values — abnormal","title":"Count patients with abnormal range values — abnormal","text":"analyze function count_abnormal() creates layout element count patients abnormal analysis range values direction. function analyzes primary analysis variable var indicates abnormal range results. Additional analysis variables can supplied list via variables parameter id (defaults USUBJID), variable indicate unique subject identifiers, baseline (defaults BNRIND), variable indicate baseline reference ranges. direction specified via abnormal parameter (e.g. High Low), fraction patient counts returned, numerator denominator calculated follows: num: number patients abnormality recorded treatment. denom: total number patients least one post-baseline assessment. function assumes df filtered include post-baseline records.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/abnormal.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Count patients with abnormal range values — abnormal","text":"","code":"count_abnormal(   lyt,   var,   abnormal = list(Low = \"LOW\", High = \"HIGH\"),   variables = list(id = \"USUBJID\", baseline = \"BNRIND\"),   exclude_base_abn = FALSE,   na_str = default_na_str(),   nested = TRUE,   ...,   table_names = var,   .stats = NULL,   .formats = NULL,   .labels = NULL,   .indent_mods = NULL )  s_count_abnormal(   df,   .var,   abnormal = list(Low = \"LOW\", High = \"HIGH\"),   variables = list(id = \"USUBJID\", baseline = \"BNRIND\"),   exclude_base_abn = FALSE )  a_count_abnormal(   df,   .var,   abnormal = list(Low = \"LOW\", High = \"HIGH\"),   variables = list(id = \"USUBJID\", baseline = \"BNRIND\"),   exclude_base_abn = FALSE )"},{"path":"https://insightsengineering.github.io/tern/reference/abnormal.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Count patients with abnormal range values — abnormal","text":"lyt (PreDataTableLayouts) layout analyses added . abnormal (named list) list identifying abnormal range level(s) var. Defaults list(Low = \"LOW\", High = \"HIGH\") can also group different levels named list, example, abnormal = list(Low = c(\"LOW\", \"LOW LOW\"), High = c(\"HIGH\", \"HIGH HIGH\")). variables (named list string) list additional analysis variables. exclude_base_abn (flag) whether exclude subjects baseline abnormality numerator denominator. na_str (string) string used replace NA empty values output. nested (flag) whether layout instruction applied within existing layout structure _if possible (TRUE, default) new top-level element (FALSE). Ignored nest split. underneath analyses, allowed. ... additional arguments lower level functions. table_names (character) can customized case vars analyzed multiple times, avoid warnings rtables. .stats (character) statistics select table. Options : 'fraction' .formats (named character list) formats statistics. See Details analyze_vars information \"auto\" setting. .labels (named character) labels statistics (without indent). .indent_mods (named integer) indent modifiers labels. Defaults 0, corresponds unmodified default behavior. Can negative. df (data.frame) data set containing analysis variables. .var, var (string) single variable name passed rtables requested statistics function.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/abnormal.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Count patients with abnormal range values — abnormal","text":"count_abnormal() returns layout object suitable passing layouting functions, rtables::build_table(). Adding function rtable layout add formatted rows containing statistics s_count_abnormal() table layout. s_count_abnormal() returns statistic fraction vector num denom counts patients. a_count_abnormal() returns corresponding list formatted rtables::CellValue().","code":""},{"path":"https://insightsengineering.github.io/tern/reference/abnormal.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Count patients with abnormal range values — abnormal","text":"count_abnormal(): Layout-creating function can take statistics function arguments additional format arguments. function wrapper rtables::analyze(). s_count_abnormal(): Statistics function counts patients abnormal range values single abnormal level. a_count_abnormal(): Formatted analysis function used afun count_abnormal().","code":""},{"path":"https://insightsengineering.github.io/tern/reference/abnormal.html","id":"note","dir":"Reference","previous_headings":"","what":"Note","title":"Count patients with abnormal range values — abnormal","text":"count_abnormal() considers single variable contains multiple abnormal levels. df filtered include post-baseline records. denominator includes patients may abnormal levels baseline, patients missing baseline records. Patients abnormalities baseline can optionally excluded numerator denominator via exclude_base_abn parameter.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/abnormal.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Count patients with abnormal range values — abnormal","text":"","code":"library(dplyr) #>  #> Attaching package: ‘dplyr’ #> The following object is masked from ‘package:testthat’: #>  #>     matches #> The following objects are masked from ‘package:stats’: #>  #>     filter, lag #> The following objects are masked from ‘package:base’: #>  #>     intersect, setdiff, setequal, union  df <- data.frame(   USUBJID = as.character(c(1, 1, 2, 2)),   ANRIND = factor(c(\"NORMAL\", \"LOW\", \"HIGH\", \"HIGH\")),   BNRIND = factor(c(\"NORMAL\", \"NORMAL\", \"HIGH\", \"HIGH\")),   ONTRTFL = c(\"\", \"Y\", \"\", \"Y\"),   stringsAsFactors = FALSE )  # Select only post-baseline records. df <- df %>%   filter(ONTRTFL == \"Y\")  # Layout creating function. basic_table() %>%   count_abnormal(var = \"ANRIND\", abnormal = list(high = \"HIGH\", low = \"LOW\")) %>%   build_table(df) #>         all obs  #> ———————————————— #> high   1/2 (50%) #> low    1/2 (50%)  # Passing of statistics function and formatting arguments. df2 <- data.frame(   ID = as.character(c(1, 1, 2, 2)),   RANGE = factor(c(\"NORMAL\", \"LOW\", \"HIGH\", \"HIGH\")),   BL_RANGE = factor(c(\"NORMAL\", \"NORMAL\", \"HIGH\", \"HIGH\")),   ONTRTFL = c(\"\", \"Y\", \"\", \"Y\"),   stringsAsFactors = FALSE )  # Select only post-baseline records. df2 <- df2 %>%   filter(ONTRTFL == \"Y\")  basic_table() %>%   count_abnormal(     var = \"RANGE\",     abnormal = list(low = \"LOW\", high = \"HIGH\"),     variables = list(id = \"ID\", baseline = \"BL_RANGE\")   ) %>%   build_table(df2) #>         all obs  #> ———————————————— #> low    1/2 (50%) #> high   1/2 (50%)"},{"path":"https://insightsengineering.github.io/tern/reference/abnormal_by_baseline.html","id":null,"dir":"Reference","previous_headings":"","what":"Count patients with abnormal analysis range values by baseline status — abnormal_by_baseline","title":"Count patients with abnormal analysis range values by baseline status — abnormal_by_baseline","text":"analyze function count_abnormal_by_baseline() creates layout element count patients abnormal analysis range values, categorized baseline status. function analyzes primary analysis variable var indicates abnormal range results. Additional analysis variables can supplied list via variables parameter id (defaults USUBJID), variable indicate unique subject identifiers, baseline (defaults BNRIND), variable indicate baseline reference ranges. direction specified via abnormal parameter (e.g. High Low), condition baseline range result count patients numerator denominator follows following categories: <abnormality> num:  number patients without abnormality baseline (excluding missing baseline) least one abnormality post-baseline. denom: number patients without abnormality baseline (excluding missing baseline). <Abnormality> num: number patients abnormality baseline least one abnormality post-baseline. denom: number patients abnormality baseline. Total num: number patients least one post-baseline record least one abnormality post-baseline. denom: number patients least one post-baseline record. function assumes df filtered include post-baseline records.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/abnormal_by_baseline.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Count patients with abnormal analysis range values by baseline status — abnormal_by_baseline","text":"","code":"count_abnormal_by_baseline(   lyt,   var,   abnormal,   variables = list(id = \"USUBJID\", baseline = \"BNRIND\"),   na_str = \"<Missing>\",   nested = TRUE,   ...,   table_names = abnormal,   .stats = NULL,   .formats = NULL,   .labels = NULL,   .indent_mods = NULL )  s_count_abnormal_by_baseline(   df,   .var,   abnormal,   na_str = \"<Missing>\",   variables = list(id = \"USUBJID\", baseline = \"BNRIND\") )  a_count_abnormal_by_baseline(   df,   .var,   abnormal,   na_str = \"<Missing>\",   variables = list(id = \"USUBJID\", baseline = \"BNRIND\") )"},{"path":"https://insightsengineering.github.io/tern/reference/abnormal_by_baseline.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Count patients with abnormal analysis range values by baseline status — abnormal_by_baseline","text":"lyt (PreDataTableLayouts) layout analyses added . abnormal (character) values identifying abnormal range level(s) .var. variables (named list string) list additional analysis variables. na_str (string) explicit na_level argument used pre-processing steps (maybe df_explicit_na()). default \"<Missing>\". nested (flag) whether layout instruction applied within existing layout structure _if possible (TRUE, default) new top-level element (FALSE). Ignored nest split. underneath analyses, allowed. ... additional arguments lower level functions. table_names (character) can customized case vars analyzed multiple times, avoid warnings rtables. .stats (character) statistics select table. Options : 'fraction' .formats (named character list) formats statistics. See Details analyze_vars information \"auto\" setting. .labels (named character) labels statistics (without indent). .indent_mods (named integer) indent modifiers labels. Defaults 0, corresponds unmodified default behavior. Can negative. df (data.frame) data set containing analysis variables. .var, var (string) single variable name passed rtables requested statistics function.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/abnormal_by_baseline.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Count patients with abnormal analysis range values by baseline status — abnormal_by_baseline","text":"count_abnormal_by_baseline() returns layout object suitable passing layouting functions, rtables::build_table(). Adding function rtable layout add formatted rows containing statistics s_count_abnormal_by_baseline() table layout. s_count_abnormal_by_baseline() returns statistic fraction named list 3 labeled elements: not_abnormal, abnormal, total. element contains vector num denom patient counts. a_count_abnormal_by_baseline() returns corresponding list formatted rtables::CellValue().","code":""},{"path":"https://insightsengineering.github.io/tern/reference/abnormal_by_baseline.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Count patients with abnormal analysis range values by baseline status — abnormal_by_baseline","text":"count_abnormal_by_baseline(): Layout-creating function can take statistics function arguments additional format arguments. function wrapper rtables::analyze(). s_count_abnormal_by_baseline(): Statistics function single abnormal level. a_count_abnormal_by_baseline(): Formatted analysis function used afun count_abnormal_by_baseline().","code":""},{"path":"https://insightsengineering.github.io/tern/reference/abnormal_by_baseline.html","id":"note","dir":"Reference","previous_headings":"","what":"Note","title":"Count patients with abnormal analysis range values by baseline status — abnormal_by_baseline","text":"df filtered include post-baseline records. baseline variable analysis variable contains NA records, expected df pre-processed using df_explicit_na() explicit_na().","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/reference/abnormal_by_baseline.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Count patients with abnormal analysis range values by baseline status — abnormal_by_baseline","text":"","code":"df <- data.frame(   USUBJID = as.character(c(1:6)),   ANRIND = factor(c(rep(\"LOW\", 4), \"NORMAL\", \"HIGH\")),   BNRIND = factor(c(\"LOW\", \"NORMAL\", \"HIGH\", NA, \"LOW\", \"NORMAL\")) ) df <- df_explicit_na(df)  # Layout creating function. basic_table() %>%   count_abnormal_by_baseline(var = \"ANRIND\", abnormal = c(High = \"HIGH\")) %>%   build_table(df) #>                all obs   #> ———————————————————————— #> High                     #>   Not high    1/4 (25%)  #>   High           0/1     #>   Total      1/6 (16.7%)  # Passing of statistics function and formatting arguments. df2 <- data.frame(   ID = as.character(c(1, 2, 3, 4)),   RANGE = factor(c(\"NORMAL\", \"LOW\", \"HIGH\", \"HIGH\")),   BLRANGE = factor(c(\"LOW\", \"HIGH\", \"HIGH\", \"NORMAL\")) )  basic_table() %>%   count_abnormal_by_baseline(     var = \"RANGE\",     abnormal = c(Low = \"LOW\"),     variables = list(id = \"ID\", baseline = \"BLRANGE\"),     .formats = c(fraction = \"xx / xx\"),     .indent_mods = c(fraction = 2L)   ) %>%   build_table(df2) #>                 all obs #> ——————————————————————— #> Low                     #>       Not low    1 / 3  #>       Low        0 / 1  #>       Total      1 / 4"},{"path":"https://insightsengineering.github.io/tern/reference/abnormal_by_marked.html","id":null,"dir":"Reference","previous_headings":"","what":"Count patients with marked laboratory abnormalities — abnormal_by_marked","title":"Count patients with marked laboratory abnormalities — abnormal_by_marked","text":"analyze function count_abnormal_by_marked() creates layout element count patients marked laboratory abnormalities direction abnormality, categorized parameter value. function analyzes primary analysis variable var indicates whether single, replicated, last marked laboratory abnormality observed. Levels var include marked lab abnormality (single last_replicated) can supplied via category parameter. Additional analysis variables can supplied list via variables parameter id (defaults USUBJID), variable indicate unique subject identifiers, param (defaults PARAM), variable indicate parameter values, direction (defaults abn_dir), variable indicate abnormality directions. combination param direction levels, marked lab abnormality counts calculated follows: Single, last & Last replicated: number patients Single, last Last replicated values, respectively. : number patients either single replicated marked abnormalities. Fractions calculated dividing counts number patients least one valid measurement recorded analysis. Prior using function table layout must use rtables::split_rows_by() create two row splits, one variable param one variable direction.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/abnormal_by_marked.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Count patients with marked laboratory abnormalities — abnormal_by_marked","text":"","code":"count_abnormal_by_marked(   lyt,   var,   category = list(single = \"SINGLE\", last_replicated = c(\"LAST\", \"REPLICATED\")),   variables = list(id = \"USUBJID\", param = \"PARAM\", direction = \"abn_dir\"),   na_str = default_na_str(),   nested = TRUE,   ...,   .stats = NULL,   .formats = NULL,   .labels = NULL,   .indent_mods = NULL )  s_count_abnormal_by_marked(   df,   .var = \"AVALCAT1\",   .spl_context,   category = list(single = \"SINGLE\", last_replicated = c(\"LAST\", \"REPLICATED\")),   variables = list(id = \"USUBJID\", param = \"PARAM\", direction = \"abn_dir\") )  a_count_abnormal_by_marked(   df,   .var = \"AVALCAT1\",   .spl_context,   category = list(single = \"SINGLE\", last_replicated = c(\"LAST\", \"REPLICATED\")),   variables = list(id = \"USUBJID\", param = \"PARAM\", direction = \"abn_dir\") )"},{"path":"https://insightsengineering.github.io/tern/reference/abnormal_by_marked.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Count patients with marked laboratory abnormalities — abnormal_by_marked","text":"lyt (PreDataTableLayouts) layout analyses added . category (list) list different marked category names single last replicated. variables (named list string) list additional analysis variables. na_str (string) string used replace NA empty values output. nested (flag) whether layout instruction applied within existing layout structure _if possible (TRUE, default) new top-level element (FALSE). Ignored nest split. underneath analyses, allowed. ... additional arguments lower level functions. .stats (character) statistics select table. Options : 'count_fraction', 'count_fraction_fixed_dp' .formats (named character list) formats statistics. See Details analyze_vars information \"auto\" setting. .labels (named character) labels statistics (without indent). .indent_mods (named integer) indent modifiers labels. Defaults 0, corresponds unmodified default behavior. Can negative. df (data.frame) data set containing analysis variables. .var, var (string) single variable name passed rtables requested statistics function. .spl_context (data.frame) gives information ancestor split states passed rtables.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/abnormal_by_marked.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Count patients with marked laboratory abnormalities — abnormal_by_marked","text":"count_abnormal_by_marked() returns layout object suitable passing layouting functions, rtables::build_table(). Adding function rtable layout add formatted rows containing statistics s_count_abnormal_by_marked() table layout. s_count_abnormal_by_marked() returns statistic count_fraction Single, last, Last replicated, results. a_count_abnormal_by_marked() returns corresponding list formatted rtables::CellValue().","code":""},{"path":"https://insightsengineering.github.io/tern/reference/abnormal_by_marked.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Count patients with marked laboratory abnormalities — abnormal_by_marked","text":"count_abnormal_by_marked(): Layout-creating function can take statistics function arguments additional format arguments. function wrapper rtables::analyze(). s_count_abnormal_by_marked(): Statistics function patients marked lab abnormalities. a_count_abnormal_by_marked(): Formatted analysis function used afun count_abnormal_by_marked().","code":""},{"path":"https://insightsengineering.github.io/tern/reference/abnormal_by_marked.html","id":"note","dir":"Reference","previous_headings":"","what":"Note","title":"Count patients with marked laboratory abnormalities — abnormal_by_marked","text":"Single, last Last replicated levels mutually exclusive. patient abnormalities meet Single, last Last replicated criteria, patient counted Last replicated category.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/abnormal_by_marked.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Count patients with marked laboratory abnormalities — abnormal_by_marked","text":"","code":"library(dplyr)  df <- data.frame(   USUBJID = as.character(c(rep(1, 5), rep(2, 5), rep(1, 5), rep(2, 5))),   ARMCD = factor(c(rep(\"ARM A\", 5), rep(\"ARM B\", 5), rep(\"ARM A\", 5), rep(\"ARM B\", 5))),   ANRIND = factor(c(     \"NORMAL\", \"HIGH\", \"HIGH\", \"HIGH HIGH\", \"HIGH\",     \"HIGH\", \"HIGH\", \"HIGH HIGH\", \"NORMAL\", \"HIGH HIGH\", \"NORMAL\", \"LOW\", \"LOW\", \"LOW LOW\", \"LOW\",     \"LOW\", \"LOW\", \"LOW LOW\", \"NORMAL\", \"LOW LOW\"   )),   ONTRTFL = rep(c(\"\", \"Y\", \"Y\", \"Y\", \"Y\", \"Y\", \"Y\", \"Y\", \"Y\", \"Y\"), 2),   PARAMCD = factor(c(rep(\"CRP\", 10), rep(\"ALT\", 10))),   AVALCAT1 = factor(rep(c(\"\", \"\", \"\", \"SINGLE\", \"REPLICATED\", \"\", \"\", \"LAST\", \"\", \"SINGLE\"), 2)),   stringsAsFactors = FALSE )  df <- df %>%   mutate(abn_dir = factor(     case_when(       ANRIND == \"LOW LOW\" ~ \"Low\",       ANRIND == \"HIGH HIGH\" ~ \"High\",       TRUE ~ \"\"     ),     levels = c(\"Low\", \"High\")   ))  # Select only post-baseline records. df <- df %>% filter(ONTRTFL == \"Y\") df_crp <- df %>%   filter(PARAMCD == \"CRP\") %>%   droplevels() full_parent_df <- list(df_crp, \"not_needed\") cur_col_subset <- list(rep(TRUE, nrow(df_crp)), \"not_needed\") spl_context <- data.frame(   split = c(\"PARAMCD\", \"GRADE_DIR\"),   full_parent_df = I(full_parent_df),   cur_col_subset = I(cur_col_subset) )  map <- unique(   df[df$abn_dir %in% c(\"Low\", \"High\") & df$AVALCAT1 != \"\", c(\"PARAMCD\", \"abn_dir\")] ) %>%   lapply(as.character) %>%   as.data.frame() %>%   arrange(PARAMCD, abn_dir)  basic_table() %>%   split_cols_by(\"ARMCD\") %>%   split_rows_by(\"PARAMCD\") %>%   summarize_num_patients(     var = \"USUBJID\",     .stats = \"unique_count\"   ) %>%   split_rows_by(     \"abn_dir\",     split_fun = trim_levels_to_map(map)   ) %>%   count_abnormal_by_marked(     var = \"AVALCAT1\",     variables = list(       id = \"USUBJID\",       param = \"PARAMCD\",       direction = \"abn_dir\"     )   ) %>%   build_table(df = df) #>                           ARM A      ARM B   #> ———————————————————————————————————————————— #> ALT (n)                     1          1     #>   Low                                        #>     Single, not last     1 (100%)      0     #>     Last or replicated      0       1 (100%) #>     Any Abnormality      1 (100%)   1 (100%) #> CRP (n)                     1          1     #>   High                                       #>     Single, not last     1 (100%)      0     #>     Last or replicated      0       1 (100%) #>     Any Abnormality      1 (100%)   1 (100%)  basic_table() %>%   split_cols_by(\"ARMCD\") %>%   split_rows_by(\"PARAMCD\") %>%   summarize_num_patients(     var = \"USUBJID\",     .stats = \"unique_count\"   ) %>%   split_rows_by(     \"abn_dir\",     split_fun = trim_levels_in_group(\"abn_dir\")   ) %>%   count_abnormal_by_marked(     var = \"AVALCAT1\",     variables = list(       id = \"USUBJID\",       param = \"PARAMCD\",       direction = \"abn_dir\"     )   ) %>%   build_table(df = df) #>                           ARM A      ARM B   #> ———————————————————————————————————————————— #> ALT (n)                     1          1     #>   Low                                        #>     Single, not last     1 (100%)      0     #>     Last or replicated      0       1 (100%) #>     Any Abnormality      1 (100%)   1 (100%) #> CRP (n)                     1          1     #>   High                                       #>     Single, not last     1 (100%)      0     #>     Last or replicated      0       1 (100%) #>     Any Abnormality      1 (100%)   1 (100%)"},{"path":"https://insightsengineering.github.io/tern/reference/abnormal_by_worst_grade.html","id":null,"dir":"Reference","previous_headings":"","what":"Count patients by most extreme post-baseline toxicity grade per direction of abnormality — abnormal_by_worst_grade","title":"Count patients by most extreme post-baseline toxicity grade per direction of abnormality — abnormal_by_worst_grade","text":"analyze function count_abnormal_by_worst_grade() creates layout element count patients highest (worst) analysis toxicity grade post-baseline direction, categorized parameter value. function analyzes primary analysis variable var indicates toxicity grades. Additional analysis variables can supplied list via variables parameter id (defaults USUBJID), variable indicate unique subject identifiers, param (defaults PARAM), variable indicate parameter values, grade_dir (defaults GRADE_DIR), variable indicate directions (e.g. High Low) toxicity grade supplied var. combination param grade_dir levels, patient counts worst grade calculated follows: 1 4: number patients worst grades 1-4, respectively. : number patients least one abnormality (.e. grade 0). Fractions calculated dividing counts number patients least one valid measurement recorded treatment. Pre-processing crucial using function can done automatically using h_adlb_abnormal_by_worst_grade() helper function. See description function details necessary pre-processing steps. Prior using function table layout must use rtables::split_rows_by() create two row splits, one variable param one variable grade_dir.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/abnormal_by_worst_grade.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Count patients by most extreme post-baseline toxicity grade per direction of abnormality — abnormal_by_worst_grade","text":"","code":"count_abnormal_by_worst_grade(   lyt,   var,   variables = list(id = \"USUBJID\", param = \"PARAM\", grade_dir = \"GRADE_DIR\"),   na_str = default_na_str(),   nested = TRUE,   ...,   .stats = NULL,   .formats = NULL,   .labels = NULL,   .indent_mods = NULL )  s_count_abnormal_by_worst_grade(   df,   .var = \"GRADE_ANL\",   .spl_context,   variables = list(id = \"USUBJID\", param = \"PARAM\", grade_dir = \"GRADE_DIR\") )  a_count_abnormal_by_worst_grade(   df,   .var = \"GRADE_ANL\",   .spl_context,   variables = list(id = \"USUBJID\", param = \"PARAM\", grade_dir = \"GRADE_DIR\") )"},{"path":"https://insightsengineering.github.io/tern/reference/abnormal_by_worst_grade.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Count patients by most extreme post-baseline toxicity grade per direction of abnormality — abnormal_by_worst_grade","text":"lyt (PreDataTableLayouts) layout analyses added . variables (named list string) list additional analysis variables. na_str (string) string used replace NA empty values output. nested (flag) whether layout instruction applied within existing layout structure _if possible (TRUE, default) new top-level element (FALSE). Ignored nest split. underneath analyses, allowed. ... additional arguments lower level functions. .stats (character) statistics select table. Options : 'count_fraction', 'count_fraction_fixed_dp' .formats (named character list) formats statistics. See Details analyze_vars information \"auto\" setting. .labels (named character) labels statistics (without indent). .indent_mods (named integer) indent modifiers labels. Defaults 0, corresponds unmodified default behavior. Can negative. df (data.frame) data set containing analysis variables. .var, var (string) single variable name passed rtables requested statistics function. .spl_context (data.frame) gives information ancestor split states passed rtables.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/abnormal_by_worst_grade.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Count patients by most extreme post-baseline toxicity grade per direction of abnormality — abnormal_by_worst_grade","text":"count_abnormal_by_worst_grade() returns layout object suitable passing layouting functions, rtables::build_table(). Adding function rtable layout add formatted rows containing statistics s_count_abnormal_by_worst_grade() table layout. s_count_abnormal_by_worst_grade() returns single statistic count_fraction grades 1 4 \"\" results. a_count_abnormal_by_worst_grade() returns corresponding list formatted rtables::CellValue().","code":""},{"path":"https://insightsengineering.github.io/tern/reference/abnormal_by_worst_grade.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Count patients by most extreme post-baseline toxicity grade per direction of abnormality — abnormal_by_worst_grade","text":"count_abnormal_by_worst_grade(): Layout-creating function can take statistics function arguments additional format arguments. function wrapper rtables::analyze(). s_count_abnormal_by_worst_grade(): Statistics function counts patients worst grade. a_count_abnormal_by_worst_grade(): Formatted analysis function used afun count_abnormal_by_worst_grade().","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/reference/abnormal_by_worst_grade.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Count patients by most extreme post-baseline toxicity grade per direction of abnormality — abnormal_by_worst_grade","text":"","code":"library(dplyr) library(forcats) adlb <- tern_ex_adlb  # Data is modified in order to have some parameters with grades only in one direction # and simulate the real data. adlb$ATOXGR[adlb$PARAMCD == \"ALT\" & adlb$ATOXGR %in% c(\"1\", \"2\", \"3\", \"4\")] <- \"-1\" adlb$ANRIND[adlb$PARAMCD == \"ALT\" & adlb$ANRIND == \"HIGH\"] <- \"LOW\" adlb$WGRHIFL[adlb$PARAMCD == \"ALT\"] <- \"\"  adlb$ATOXGR[adlb$PARAMCD == \"IGA\" & adlb$ATOXGR %in% c(\"-1\", \"-2\", \"-3\", \"-4\")] <- \"1\" adlb$ANRIND[adlb$PARAMCD == \"IGA\" & adlb$ANRIND == \"LOW\"] <- \"HIGH\" adlb$WGRLOFL[adlb$PARAMCD == \"IGA\"] <- \"\"  # Pre-processing adlb_f <- adlb %>% h_adlb_abnormal_by_worst_grade()  # Map excludes records without abnormal grade since they should not be displayed # in the table. map <- unique(adlb_f[adlb_f$GRADE_DIR != \"ZERO\", c(\"PARAM\", \"GRADE_DIR\", \"GRADE_ANL\")]) %>%   lapply(as.character) %>%   as.data.frame() %>%   arrange(PARAM, desc(GRADE_DIR), GRADE_ANL)  basic_table() %>%   split_cols_by(\"ARMCD\") %>%   split_rows_by(\"PARAM\") %>%   split_rows_by(\"GRADE_DIR\", split_fun = trim_levels_to_map(map)) %>%   count_abnormal_by_worst_grade(     var = \"GRADE_ANL\",     variables = list(id = \"USUBJID\", param = \"PARAM\", grade_dir = \"GRADE_DIR\")   ) %>%   build_table(df = adlb_f) #>                                          ARM A        ARM B        ARM C    #> ——————————————————————————————————————————————————————————————————————————— #> Alanine Aminotransferase Measurement                                        #>   LOW                                                                       #>     1                                  12 (17.4%)    5 (6.8%)    8 (13.8%)  #>     2                                   9 (13%)     13 (17.8%)   6 (10.3%)  #>     3                                   6 (8.7%)     4 (5.5%)    6 (10.3%)  #>     4                                  7 (10.1%)     7 (9.6%)    6 (10.3%)  #>     Any                                34 (49.3%)   29 (39.7%)   26 (44.8%) #> C-Reactive Protein Measurement                                              #>   LOW                                                                       #>     1                                  11 (15.9%)   12 (16.4%)   7 (12.1%)  #>     2                                  8 (11.6%)     2 (2.7%)    6 (10.3%)  #>     3                                   4 (5.8%)    9 (12.3%)    6 (10.3%)  #>     4                                  7 (10.1%)     6 (8.2%)     4 (6.9%)  #>     Any                                30 (43.5%)   29 (39.7%)   23 (39.7%) #>   HIGH                                                                      #>     1                                  8 (11.6%)    11 (15.1%)    2 (3.4%)  #>     2                                   9 (13%)     11 (15.1%)    11 (19%)  #>     3                                  14 (20.3%)   10 (13.7%)    5 (8.6%)  #>     4                                   2 (2.9%)     4 (5.5%)    6 (10.3%)  #>     Any                                33 (47.8%)   36 (49.3%)   24 (41.4%) #> Immunoglobulin A Measurement                                                #>   HIGH                                                                      #>     1                                  7 (10.1%)     7 (9.6%)    6 (10.3%)  #>     2                                  8 (11.6%)     6 (8.2%)    8 (13.8%)  #>     3                                  7 (10.1%)     5 (6.8%)    9 (15.5%)  #>     4                                   6 (8.7%)     2 (2.7%)     3 (5.2%)  #>     Any                                28 (40.6%)   20 (27.4%)   26 (44.8%)"},{"path":"https://insightsengineering.github.io/tern/reference/abnormal_by_worst_grade_worsen.html","id":null,"dir":"Reference","previous_headings":"","what":"Count patients with toxicity grades that have worsened from baseline by highest grade post-baseline — abnormal_by_worst_grade_worsen","title":"Count patients with toxicity grades that have worsened from baseline by highest grade post-baseline — abnormal_by_worst_grade_worsen","text":"analyze function count_abnormal_lab_worsen_by_baseline() creates layout element count patients analysis toxicity grades worsened baseline, categorized highest (worst) grade post-baseline. function analyzes primary analysis variable var indicates analysis toxicity grades. Additional analysis variables can supplied list via variables parameter id (defaults USUBJID), variable indicate unique subject identifiers, baseline_var (defaults BTOXGR), variable indicate baseline toxicity grades, direction_var (defaults GRADDIR), variable indicate toxicity grade directions interest include (e.g. \"H\" (high), \"L\" (low), \"B\" ()). direction(s) specified direction_var, patient counts worst grade patients worsened baseline calculated follows: 1 4: number patients worsened baseline grades worst grades 1-4, respectively. : total number patients worsened baseline grades. Fractions calculated dividing counts number patients analysis toxicity grades worsened baseline toxicity grades treatment. Prior using function table layout must use rtables::split_rows_by() create row split variable direction_var.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/abnormal_by_worst_grade_worsen.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Count patients with toxicity grades that have worsened from baseline by highest grade post-baseline — abnormal_by_worst_grade_worsen","text":"","code":"count_abnormal_lab_worsen_by_baseline(   lyt,   var,   variables = list(id = \"USUBJID\", baseline_var = \"BTOXGR\", direction_var = \"GRADDR\"),   na_str = default_na_str(),   nested = TRUE,   ...,   table_names = NULL,   .stats = NULL,   .formats = NULL,   .labels = NULL,   .indent_mods = NULL )  s_count_abnormal_lab_worsen_by_baseline(   df,   .var = \"ATOXGR\",   variables = list(id = \"USUBJID\", baseline_var = \"BTOXGR\", direction_var = \"GRADDR\") )  a_count_abnormal_lab_worsen_by_baseline(   df,   .var = \"ATOXGR\",   variables = list(id = \"USUBJID\", baseline_var = \"BTOXGR\", direction_var = \"GRADDR\") )"},{"path":"https://insightsengineering.github.io/tern/reference/abnormal_by_worst_grade_worsen.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Count patients with toxicity grades that have worsened from baseline by highest grade post-baseline — abnormal_by_worst_grade_worsen","text":"lyt (PreDataTableLayouts) layout analyses added . variables (named list string) list additional analysis variables including: id (string) subject variable name. baseline_var (string) name data column containing baseline toxicity variable. direction_var (string) see direction_var details. na_str (string) string used replace NA empty values output. nested (flag) whether layout instruction applied within existing layout structure _if possible (TRUE, default) new top-level element (FALSE). Ignored nest split. underneath analyses, allowed. ... additional arguments lower level functions. table_names (character) can customized case vars analyzed multiple times, avoid warnings rtables. .stats (character) statistics select table. Options : 'fraction' .formats (named character list) formats statistics. See Details analyze_vars information \"auto\" setting. .labels (named character) labels statistics (without indent). .indent_mods (named integer) indent modifiers labels. Defaults 0, corresponds unmodified default behavior. Can negative. df (data.frame) data set containing analysis variables. .var, var (string) single variable name passed rtables requested statistics function.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/abnormal_by_worst_grade_worsen.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Count patients with toxicity grades that have worsened from baseline by highest grade post-baseline — abnormal_by_worst_grade_worsen","text":"count_abnormal_lab_worsen_by_baseline() returns layout object suitable passing layouting functions, rtables::build_table(). Adding function rtable layout add formatted rows containing statistics s_count_abnormal_lab_worsen_by_baseline() table layout. s_count_abnormal_lab_worsen_by_baseline() returns counts fraction patients whose worst post-baseline lab grades worse baseline grades, post-baseline worst grades \"1\", \"2\", \"3\", \"4\" \"\". a_count_abnormal_lab_worsen_by_baseline() returns corresponding list formatted rtables::CellValue().","code":""},{"path":"https://insightsengineering.github.io/tern/reference/abnormal_by_worst_grade_worsen.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Count patients with toxicity grades that have worsened from baseline by highest grade post-baseline — abnormal_by_worst_grade_worsen","text":"count_abnormal_lab_worsen_by_baseline(): Layout-creating function can take statistics function arguments additional format arguments. function wrapper rtables::analyze(). s_count_abnormal_lab_worsen_by_baseline(): Statistics function patients whose worst post-baseline lab grades worse baseline grades. a_count_abnormal_lab_worsen_by_baseline(): Formatted analysis function used afun count_abnormal_lab_worsen_by_baseline().","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/reference/abnormal_by_worst_grade_worsen.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Count patients with toxicity grades that have worsened from baseline by highest grade post-baseline — abnormal_by_worst_grade_worsen","text":"","code":"library(dplyr)  # The direction variable, GRADDR, is based on metadata adlb <- tern_ex_adlb %>%   mutate(     GRADDR = case_when(       PARAMCD == \"ALT\" ~ \"B\",       PARAMCD == \"CRP\" ~ \"L\",       PARAMCD == \"IGA\" ~ \"H\"     )   ) %>%   filter(SAFFL == \"Y\" & ONTRTFL == \"Y\" & GRADDR != \"\")  df <- h_adlb_worsen(   adlb,   worst_flag_low = c(\"WGRLOFL\" = \"Y\"),   worst_flag_high = c(\"WGRHIFL\" = \"Y\"),   direction_var = \"GRADDR\" )  basic_table() %>%   split_cols_by(\"ARMCD\") %>%   add_colcounts() %>%   split_rows_by(\"PARAMCD\") %>%   split_rows_by(\"GRADDR\") %>%   count_abnormal_lab_worsen_by_baseline(     var = \"ATOXGR\",     variables = list(       id = \"USUBJID\",       baseline_var = \"BTOXGR\",       direction_var = \"GRADDR\"     )   ) %>%   append_topleft(\"Direction of Abnormality\") %>%   build_table(df = df, alt_counts_df = tern_ex_adsl) #>                                ARM A           ARM B           ARM C     #> Direction of Abnormality      (N=69)          (N=73)          (N=58)     #> ———————————————————————————————————————————————————————————————————————— #> IGA                                                                      #>   High                                                                   #>     1                       6/63 (9.5%)     6/64 (9.4%)      4/50 (8%)   #>     2                      8/64 (12.5%)     5/67 (7.5%)    8/53 (15.1%)  #>     3                      7/66 (10.6%)     5/68 (7.4%)    9/57 (15.8%)  #>     4                       6/68 (8.8%)     2/72 (2.8%)     3/58 (5.2%)  #>     Any                    27/68 (39.7%)    18/72 (25%)    24/58 (41.4%) #> ALT                                                                      #>   High                                                                   #>     1                      7/63 (11.1%)     6/62 (9.7%)     2/48 (4.2%)  #>     2                       12/63 (19%)      4/67 (6%)      11/50 (22%)  #>     3                       4/65 (6.2%)    11/71 (15.5%)   7/56 (12.5%)  #>     4                       1/67 (1.5%)    8/71 (11.3%)      4/57 (7%)   #>     Any                    24/67 (35.8%)   29/71 (40.8%)   24/57 (42.1%) #>   Low                                                                    #>     1                      12/67 (17.9%)    4/66 (6.1%)    7/52 (13.5%)  #>     2                      9/68 (13.2%)    12/69 (17.4%)   6/55 (10.9%)  #>     3                       6/69 (8.7%)     4/71 (5.6%)     5/56 (8.9%)  #>     4                      7/69 (10.1%)     7/73 (9.6%)    6/58 (10.3%)  #>     Any                    34/69 (49.3%)    27/73 (37%)    24/58 (41.4%) #> CRP                                                                      #>   Low                                                                    #>     1                      11/66 (16.7%)   10/67 (14.9%)    4/47 (8.5%)  #>     2                      8/66 (12.1%)     1/70 (1.4%)     6/50 (12%)   #>     3                       4/68 (5.9%)    9/70 (12.9%)     5/53 (9.4%)  #>     4                      7/69 (10.1%)     6/72 (8.3%)     4/55 (7.3%)  #>     Any                    30/69 (43.5%)   26/72 (36.1%)   19/55 (34.5%)"},{"path":"https://insightsengineering.github.io/tern/reference/add_riskdiff.html","id":null,"dir":"Reference","previous_headings":"","what":"Split function to configure risk difference column — add_riskdiff","title":"Split function to configure risk difference column — add_riskdiff","text":"Wrapper function rtables::add_combo_levels() configures settings risk difference column added rtables object. add risk difference column table, function used split_fun calls rtables::split_cols_by(), followed setting argument riskdiff TRUE following analyze function calls.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/add_riskdiff.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Split function to configure risk difference column — add_riskdiff","text":"","code":"add_riskdiff(   arm_x,   arm_y,   col_label = paste0(\"Risk Difference (%) (95% CI)\", if (length(arm_y) > 1)     paste0(\"\\n\", arm_x, \" vs. \", arm_y)),   pct = TRUE )"},{"path":"https://insightsengineering.github.io/tern/reference/add_riskdiff.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Split function to configure risk difference column — add_riskdiff","text":"arm_x (string) name reference arm use risk difference calculations. arm_y (character) names one arms compare reference arm risk difference calculations. new column added value arm_y. col_label (character) labels use rendering risk difference column within table. one comparison arm specified arm_y, default labels specify two arms compared (reference arm vs. comparison arm). pct (flag) whether output returned percentages. Defaults TRUE.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/add_riskdiff.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Split function to configure risk difference column — add_riskdiff","text":"closure suitable use split function (split_fun) within rtables::split_cols_by() creating table layout.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/reference/add_riskdiff.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Split function to configure risk difference column — add_riskdiff","text":"","code":"adae <- tern_ex_adae adae$AESEV <- factor(adae$AESEV)  lyt <- basic_table() %>%   split_cols_by(\"ARMCD\", split_fun = add_riskdiff(arm_x = \"ARM A\", arm_y = c(\"ARM B\", \"ARM C\"))) %>%   count_occurrences_by_grade(     var = \"AESEV\",     riskdiff = TRUE   )  tbl <- build_table(lyt, df = adae) tbl #>                                                   Risk Difference (%) (95% CI)   Risk Difference (%) (95% CI) #>              ARM A        ARM B        ARM C            ARM A vs. ARM B                ARM A vs. ARM C        #> ————————————————————————————————————————————————————————————————————————————————————————————————————————————— #> MILD        6 (3.0%)     4 (2.3%)     2 (1.2%)          0.7 (-2.5 - 3.9)               1.7 (-1.2 - 4.6)       #> MODERATE   19 (9.4%)    15 (8.5%)    14 (8.6%)          0.9 (-4.8 - 6.7)               0.8 (-5.1 - 6.7)       #> SEVERE     34 (16.8%)   38 (21.5%)   32 (19.8%)        -4.6 (-12.6 - 3.3)             -2.9 (-10.9 - 5.1)"},{"path":"https://insightsengineering.github.io/tern/reference/add_rowcounts.html","id":null,"dir":"Reference","previous_headings":"","what":"Layout-creating function to add row total counts — add_rowcounts","title":"Layout-creating function to add row total counts — add_rowcounts","text":"works analogously rtables::add_colcounts() rows. function wrapper rtables::summarize_row_groups().","code":""},{"path":"https://insightsengineering.github.io/tern/reference/add_rowcounts.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Layout-creating function to add row total counts — add_rowcounts","text":"","code":"add_rowcounts(lyt, alt_counts = FALSE)"},{"path":"https://insightsengineering.github.io/tern/reference/add_rowcounts.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Layout-creating function to add row total counts — add_rowcounts","text":"lyt (PreDataTableLayouts) layout analyses added . alt_counts (flag) whether row counts taken alt_counts_df (TRUE) df (FALSE). Defaults FALSE.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/add_rowcounts.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Layout-creating function to add row total counts — add_rowcounts","text":"modified layout latest row split labels now row-wise total counts (.e. without column-based subsetting) attached parentheses.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/add_rowcounts.html","id":"note","dir":"Reference","previous_headings":"","what":"Note","title":"Layout-creating function to add row total counts — add_rowcounts","text":"Row count values contained row count rows displayed considered zero rows default pruning.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/add_rowcounts.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Layout-creating function to add row total counts — add_rowcounts","text":"","code":"basic_table() %>%   split_cols_by(\"ARM\") %>%   add_colcounts() %>%   split_rows_by(\"RACE\", split_fun = drop_split_levels) %>%   add_rowcounts() %>%   analyze(\"AGE\", afun = list_wrap_x(summary), format = \"xx.xx\") %>%   build_table(DM) #>                                    A: Drug X   B: Placebo   C: Combination #>                                     (N=121)     (N=106)        (N=129)     #> —————————————————————————————————————————————————————————————————————————— #> ASIAN (N=231)                                                              #>   Min.                               20.00       21.00          22.00      #>   1st Qu.                            29.00       28.00          30.00      #>   Median                             33.00       32.50          33.50      #>   Mean                               34.20       32.68          34.63      #>   3rd Qu.                            38.50       36.00          38.00      #>   Max.                               58.00       55.00          53.00      #> BLACK OR AFRICAN AMERICAN (N=79)                                           #>   Min.                               23.00       21.00          24.00      #>   1st Qu.                            29.00       28.75          29.00      #>   Median                             33.00       30.00          32.00      #>   Mean                               34.68       31.71          34.00      #>   3rd Qu.                            37.25       36.25          39.00      #>   Max.                               60.00       42.00          51.00      #> WHITE (N=46)                                                               #>   Min.                               30.00       25.00          28.00      #>   1st Qu.                            38.00       31.00          30.25      #>   Median                             40.50       37.50          35.00      #>   Mean                               39.36       36.93          35.11      #>   3rd Qu.                            43.50       40.00          37.50      #>   Max.                               47.00       55.00          47.00"},{"path":[]},{"path":"https://insightsengineering.github.io/tern/reference/aesi_label.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Labels for adverse event baskets — aesi_label","text":"","code":"aesi_label(aesi, scope = NULL)"},{"path":"https://insightsengineering.github.io/tern/reference/aesi_label.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Labels for adverse event baskets — aesi_label","text":"aesi (character) vector standardized MedDRA query name (e.g. SMQxxNAM) customized query name (e.g. CQxxNAM). scope (character) vector scope query (e.g. SMQxxSC).","code":""},{"path":"https://insightsengineering.github.io/tern/reference/aesi_label.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Labels for adverse event baskets — aesi_label","text":"string standard label AE basket.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/aesi_label.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Labels for adverse event baskets — aesi_label","text":"","code":"adae <- tern_ex_adae  # Standardized query label includes scope. aesi_label(adae$SMQ01NAM, scope = adae$SMQ01SC) #> [1] \"C.1.1.1.3/B.2.2.3.1 aesi (BROAD)\"  # Customized query label. aesi_label(adae$CQ01NAM) #> [1] \"D.2.1.5.3/A.1.1.1.1 aesi\""},{"path":"https://insightsengineering.github.io/tern/reference/afun_riskdiff.html","id":null,"dir":"Reference","previous_headings":"","what":"Analysis function to calculate risk difference column values — afun_riskdiff","title":"Analysis function to calculate risk difference column values — afun_riskdiff","text":"risk difference column, function uses statistics function associated afun calculates risk difference values arm X (reference group) arm Y. arms specified configuring risk difference column done using add_riskdiff() split function previous call rtables::split_cols_by(). columns, applies afun usual. function utilizes stat_propdiff_ci() function perform risk difference calculations.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/afun_riskdiff.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Analysis function to calculate risk difference column values — afun_riskdiff","text":"","code":"afun_riskdiff(   df,   labelstr = \"\",   .var,   .N_col,   .N_row,   .df_row,   .spl_context,   .all_col_counts,   .stats,   .formats = NULL,   .labels = NULL,   .indent_mods = NULL,   na_str = default_na_str(),   afun,   s_args = list() )"},{"path":"https://insightsengineering.github.io/tern/reference/afun_riskdiff.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Analysis function to calculate risk difference column values — afun_riskdiff","text":"df (data.frame) data set containing analysis variables. labelstr (string) label level parent split currently summarized (must present second argument Content Row Functions). See rtables::summarize_row_groups() information. .var (string) single variable name passed rtables requested statistics function. .N_col (integer(1)) column-wise N (column count) full column analyzed typically passed rtables. .N_row (integer(1)) row-wise N (row group count) group observations analyzed (.e. column-based subsetting) typically passed rtables. .df_row (data.frame) data frame across columns given row split. .spl_context (data.frame) gives information ancestor split states passed rtables. .all_col_counts (integer) vector value represents global count column. Values taken alt_counts_df specified (see rtables::build_table()). .stats (character) statistics select table. .formats (named character list) formats statistics. See Details analyze_vars information \"auto\" setting. .labels (named character) labels statistics (without indent). .indent_mods (named integer) indent modifiers labels. Defaults 0, corresponds unmodified default behavior. Can negative. na_str (string) string used replace NA empty values output. afun (named list) named list containing one name-value pair name corresponds name statistics function used calculations value corresponding analysis function. s_args (named list) additional arguments passed statistics function analysis function supplied afun.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/afun_riskdiff.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Analysis function to calculate risk difference column values — afun_riskdiff","text":"list formatted rtables::CellValue().","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/reference/afun_selected_stats.html","id":null,"dir":"Reference","previous_headings":"","what":"Get selected statistics names — afun_selected_stats","title":"Get selected statistics names — afun_selected_stats","text":"Helper function used creating afun.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/afun_selected_stats.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get selected statistics names — afun_selected_stats","text":"","code":"afun_selected_stats(.stats, all_stats)"},{"path":"https://insightsengineering.github.io/tern/reference/afun_selected_stats.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get selected statistics names — afun_selected_stats","text":".stats (vector NULL) input layout creating function. Note NULL means context default statistics used. all_stats (character) statistics can selected potentially.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/afun_selected_stats.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get selected statistics names — afun_selected_stats","text":"character vector selected statistics.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/analyze_colvars_functions.html","id":null,"dir":"Reference","previous_headings":"","what":"Analyze functions in columns — analyze_colvars_functions","title":"Analyze functions in columns — analyze_colvars_functions","text":"functions wrappers rtables::analyze_colvars() apply corresponding tern statistics functions add analysis given table layout. particular, functions designed analysis methods split different columns. analyze_vars_in_cols(): fundamental tabulation analysis methods onto columns. words, analysis methods defined column space, .e. become column labels. changing variable vector, list functions can applied different variables, caveat number statistical functions. tabulate_rsp_subgroups(): similarly analyze_vars_in_cols, function combines analyze_colvars summarize_row_groups compact way produce standard tables show analysis methods columns. tabulate_survival_subgroups(): function similar , used tables. analyze_patients_exposure_in_cols(): based analyze_colvars. needs summarize_patients_exposure_in_cols() leverage nesting label rows analysis rtables::summarize_row_groups(). summarize_coxreg(): generally based rtables::summarize_row_groups(), behaves similarly tabulate_* functions described designed provide specific standard tables may contain nested structure combination summarize_row_groups() rtables::analyze_colvars().","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/reference/analyze_functions.html","id":null,"dir":"Reference","previous_headings":"","what":"Analyze functions — analyze_functions","title":"Analyze functions — analyze_functions","text":"functions wrappers rtables::analyze() apply corresponding tern statistics functions add analysis given table layout: analyze_num_patients() analyze_vars() compare_vars() count_abnormal() count_abnormal_by_baseline() count_abnormal_by_marked() count_abnormal_by_worst_grade() count_cumulative() count_missed_doses() count_occurrences() count_occurrences_by_grade() count_patients_events_in_cols() count_patients_with_event() count_patients_with_flags() count_values() coxph_pairwise() estimate_incidence_rate() estimate_multinomial_rsp() estimate_odds_ratio() estimate_proportion() estimate_proportion_diff() summarize_ancova() summarize_colvars(): even function uses rtables::analyze_colvars(), applies analysis methods different rows one variables split different columns. comparison, analyze_colvars_functions leverage analyze_colvars context split rows analysis methods columns. summarize_change() surv_time() surv_timepoint() test_proportion_diff()","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/reference/analyze_variables.html","id":null,"dir":"Reference","previous_headings":"","what":"Analyze variables — analyze_variables","title":"Analyze variables — analyze_variables","text":"analyze function analyze_vars() creates layout element summarize one variables, using S3 generic function s_summary() calculate list summary statistics. list available statistics numeric variables can viewed running get_stats(\"analyze_vars_numeric\") non-numeric variables running get_stats(\"analyze_vars_counts\"). Use .stats parameter specify statistics include output summary table.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/analyze_variables.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Analyze variables — analyze_variables","text":"","code":"analyze_vars(   lyt,   vars,   var_labels = vars,   na_str = default_na_str(),   nested = TRUE,   ...,   na.rm = TRUE,   show_labels = \"default\",   table_names = vars,   section_div = NA_character_,   .stats = c(\"n\", \"mean_sd\", \"median\", \"range\", \"count_fraction\"),   .formats = NULL,   .labels = NULL,   .indent_mods = NULL )  s_summary(x, na.rm = TRUE, denom, .N_row, .N_col, .var, ...)  # S3 method for class 'numeric' s_summary(   x,   na.rm = TRUE,   denom,   .N_row,   .N_col,   .var,   control = control_analyze_vars(),   ... )  # S3 method for class 'factor' s_summary(   x,   na.rm = TRUE,   denom = c(\"n\", \"N_col\", \"N_row\"),   .N_row,   .N_col,   ... )  # S3 method for class 'character' s_summary(   x,   na.rm = TRUE,   denom = c(\"n\", \"N_col\", \"N_row\"),   .N_row,   .N_col,   .var,   verbose = TRUE,   ... )  # S3 method for class 'logical' s_summary(   x,   na.rm = TRUE,   denom = c(\"n\", \"N_col\", \"N_row\"),   .N_row,   .N_col,   ... )  a_summary(   x,   .N_col,   .N_row,   .var = NULL,   .df_row = NULL,   .ref_group = NULL,   .in_ref_col = FALSE,   compare = FALSE,   .stats = NULL,   .formats = NULL,   .labels = NULL,   .indent_mods = NULL,   na.rm = TRUE,   na_str = default_na_str(),   ... )"},{"path":"https://insightsengineering.github.io/tern/reference/analyze_variables.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Analyze variables — analyze_variables","text":"lyt (PreDataTableLayouts) layout analyses added . vars (character) variable names primary analysis variable iterated . var_labels (character) variable labels. na_str (string) string used replace NA empty values output. nested (flag) whether layout instruction applied within existing layout structure _if possible (TRUE, default) new top-level element (FALSE). Ignored nest split. underneath analyses, allowed. ... arguments passed s_summary(). na.rm (flag) whether NA values removed x prior analysis. show_labels (string) label visibility: one \"default\", \"visible\" \"hidden\". table_names (character) can customized case vars analyzed multiple times, avoid warnings rtables. section_div (string) string repeated section divider group defined split instruction, NA_character_ (default) section divider. .stats (character) statistics select table. Options numeric variables : 'n', 'sum', 'mean', 'sd', 'se', 'mean_sd', 'mean_se', 'mean_ci', 'mean_sei', 'mean_sdi', 'mean_pval', 'median', 'mad', 'median_ci', 'quantiles', 'iqr', 'range', 'min', 'max', 'median_range', 'cv', 'geom_mean', 'geom_mean_ci', 'geom_cv', 'median_ci_3d', 'mean_ci_3d', 'geom_mean_ci_3d' Options non-numeric variables : 'n', 'count', 'count_fraction', 'count_fraction_fixed_dp', 'fraction', 'n_blq' .formats (named character list) formats statistics. See Details analyze_vars information \"auto\" setting. .labels (named character) labels statistics (without indent). .indent_mods (named integer) indent modifiers labels. element vector name-value pair name corresponding statistic specified .stats value indentation statistic's row label. x (numeric) vector numbers want analyze. denom (string) choice denominator proportion. Options : n: number values row column intersection. N_row: total number values row across columns. N_col: total number values column across rows. .N_row (integer(1)) row-wise N (row group count) group observations analyzed (.e. column-based subsetting) typically passed rtables. .N_col (integer(1)) column-wise N (column count) full column analyzed typically passed rtables. .var (string) single variable name passed rtables requested statistics function. control (list) parameters descriptive statistics details, specified using helper function control_analyze_vars(). possible parameter options : conf_level (proportion) confidence level interval mean median. quantiles (numeric(2)) vector length two specify quantiles. quantile_type (numeric(1)) 1 9 selecting quantile algorithms used. See type stats::quantile(). test_mean (numeric(1)) value test mean null hypothesis calculating p-value. verbose (flag) defaults TRUE, prints warnings messages. mainly used print information factor casting. .df_row (data.frame) data frame across columns given row split. .ref_group (data.frame vector) data corresponding reference group. .in_ref_col (flag)TRUE working reference level, FALSE otherwise. compare (flag) whether comparison statistics analyzed instead summary statistics (compare = TRUE adds pval statistic comparing reference group).","code":""},{"path":"https://insightsengineering.github.io/tern/reference/analyze_variables.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Analyze variables — analyze_variables","text":"analyze_vars() returns layout object suitable passing layouting functions, rtables::build_table(). Adding function rtable layout add formatted rows containing statistics s_summary() table layout. s_summary() returns different statistics depending class x. x class numeric, returns list following named numeric items: n: length() x. sum: sum() x. mean: mean() x. sd: stats::sd() x. se: standard error x mean, .e.: (sd(x) / sqrt(length(x))). mean_sd: mean() stats::sd() x. mean_se: mean() x standard error (see ). mean_ci: CI mean x (stat_mean_ci()). mean_sei: SE interval mean x, .e.: (mean() -/+ stats::sd() / sqrt()). mean_sdi: SD interval mean x, .e.: (mean() -/+ stats::sd()). mean_pval: two-sided p-value mean x (stat_mean_pval()). median: stats::median() x. mad: median absolute deviation x, .e.: (stats::median() xc, xc = x - stats::median()). median_ci: CI median x (stat_median_ci()). quantiles: Two sample quantiles x (stats::quantile()). iqr: stats::IQR() x. range: range_noinf() x. min: max() x. max: min() x. median_range: median() range_noinf() x. cv: coefficient variation x, .e.: (stats::sd() / mean() * 100). geom_mean: geometric mean x, .e.: (exp(mean(log(x)))). geom_cv: geometric coefficient variation x, .e.: (sqrt(exp(sd(log(x)) ^ 2) - 1) * 100). x class factor converted character, returns list named numeric items: n: length() x. count: list number cases level factor x. count_fraction: Similar count also includes proportion cases level factor x relative denominator, NA denominator zero. x class logical, returns list named numeric items: n: length() x (possibly removing NAs). count: Count TRUE x. count_fraction: Count proportion TRUE x relative denominator, NA denominator zero. Note NAs x never counted leading NA . a_summary() returns corresponding list formatted rtables::CellValue().","code":""},{"path":"https://insightsengineering.github.io/tern/reference/analyze_variables.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Analyze variables — analyze_variables","text":"Automatic digit formatting: number digits display can automatically determined analyzed variable(s) (vars) certain statistics setting statistic format \"auto\" .formats. utilizes format_auto() formatting function. Note data current row & variable (columns) considered (.df_row[[.var]], see rtables::additional_fun_params) whole dataset.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/analyze_variables.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Analyze variables — analyze_variables","text":"analyze_vars(): Layout-creating function can take statistics function arguments additional format arguments. function wrapper rtables::analyze(). s_summary(): S3 generic function produces variable summary. s_summary(numeric): Method numeric class. s_summary(factor): Method factor class. s_summary(character): Method character class. makes automatic conversion factor (warning) forwards method factors. s_summary(logical): Method logical class. a_summary(): Formatted analysis function used afun analyze_vars() compare_vars() cfun summarize_colvars().","code":""},{"path":"https://insightsengineering.github.io/tern/reference/analyze_variables.html","id":"note","dir":"Reference","previous_headings":"","what":"Note","title":"Analyze variables — analyze_variables","text":"x empty vector, NA returned. expected feature return rcell content rtables intersection column row delimits empty data selection. mean function applied empty vector, NA returned instead NaN, latter standard behavior R. x empty factor, list still returned counts one element per factor level. levels x, function fails. factor variables contain NA, NA values excluded default. include NA values set na.rm = FALSE missing values displayed NA level. Alternatively, explicit factor level can defined NA values pre-processing via df_explicit_na() - default na_level (\"<Missing>\") also excluded na.rm set TRUE. Automatic conversion character factor guarantee table can generated correctly. particular sparse tables likely can fail. therefore better always pre-process dataset factors manually created character variables passing dataset rtables::build_table(). use comparison (additional p-value statistic), parameter compare must set TRUE. Ensure either NA values converted explicit NA level NA values left .","code":""},{"path":"https://insightsengineering.github.io/tern/reference/analyze_variables.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Analyze variables — analyze_variables","text":"","code":"## Fabricated dataset. dta_test <- data.frame(   USUBJID = rep(1:6, each = 3),   PARAMCD = rep(\"lab\", 6 * 3),   AVISIT  = rep(paste0(\"V\", 1:3), 6),   ARM     = rep(LETTERS[1:3], rep(6, 3)),   AVAL    = c(9:1, rep(NA, 9)) )  # `analyze_vars()` in `rtables` pipelines ## Default output within a `rtables` pipeline. l <- basic_table() %>%   split_cols_by(var = \"ARM\") %>%   split_rows_by(var = \"AVISIT\") %>%   analyze_vars(vars = \"AVAL\")  build_table(l, df = dta_test) #>                   A           B       C  #> ———————————————————————————————————————— #> V1                                       #>   n               2           1       0  #>   Mean (SD)   7.5 (2.1)   3.0 (NA)    NA #>   Median         7.5         3.0      NA #>   Min - Max   6.0 - 9.0   3.0 - 3.0   NA #> V2                                       #>   n               2           1       0  #>   Mean (SD)   6.5 (2.1)   2.0 (NA)    NA #>   Median         6.5         2.0      NA #>   Min - Max   5.0 - 8.0   2.0 - 2.0   NA #> V3                                       #>   n               2           1       0  #>   Mean (SD)   5.5 (2.1)   1.0 (NA)    NA #>   Median         5.5         1.0      NA #>   Min - Max   4.0 - 7.0   1.0 - 1.0   NA  ## Select and format statistics output. l <- basic_table() %>%   split_cols_by(var = \"ARM\") %>%   split_rows_by(var = \"AVISIT\") %>%   analyze_vars(     vars = \"AVAL\",     .stats = c(\"n\", \"mean_sd\", \"quantiles\"),     .formats = c(\"mean_sd\" = \"xx.x, xx.x\"),     .labels = c(n = \"n\", mean_sd = \"Mean, SD\", quantiles = c(\"Q1 - Q3\"))   )  build_table(l, df = dta_test) #>                  A           B       C  #> ——————————————————————————————————————— #> V1                                      #>   n              2           1       0  #>   Mean, SD   7.5, 2.1     3.0, NA    NA #>   Q1 - Q3    6.0 - 9.0   3.0 - 3.0   NA #> V2                                      #>   n              2           1       0  #>   Mean, SD   6.5, 2.1     2.0, NA    NA #>   Q1 - Q3    5.0 - 8.0   2.0 - 2.0   NA #> V3                                      #>   n              2           1       0  #>   Mean, SD   5.5, 2.1     1.0, NA    NA #>   Q1 - Q3    4.0 - 7.0   1.0 - 1.0   NA  ## Use arguments interpreted by `s_summary`. l <- basic_table() %>%   split_cols_by(var = \"ARM\") %>%   split_rows_by(var = \"AVISIT\") %>%   analyze_vars(vars = \"AVAL\", na.rm = FALSE)  build_table(l, df = dta_test) #>                   A       B    C  #> ————————————————————————————————— #> V1                                #>   n               2       2    2  #>   Mean (SD)   7.5 (2.1)   NA   NA #>   Median         7.5      NA   NA #>   Min - Max   6.0 - 9.0   NA   NA #> V2                                #>   n               2       2    2  #>   Mean (SD)   6.5 (2.1)   NA   NA #>   Median         6.5      NA   NA #>   Min - Max   5.0 - 8.0   NA   NA #> V3                                #>   n               2       2    2  #>   Mean (SD)   5.5 (2.1)   NA   NA #>   Median         5.5      NA   NA #>   Min - Max   4.0 - 7.0   NA   NA  ## Handle `NA` levels first when summarizing factors. dta_test$AVISIT <- NA_character_ dta_test <- df_explicit_na(dta_test) l <- basic_table() %>%   split_cols_by(var = \"ARM\") %>%   analyze_vars(vars = \"AVISIT\", na.rm = FALSE)  build_table(l, df = dta_test) #>                A          B          C     #> —————————————————————————————————————————— #> n              6          6          6     #> <Missing>   6 (100%)   6 (100%)   6 (100%)  # auto format dt <- data.frame(\"VAR\" = c(0.001, 0.2, 0.0011000, 3, 4)) basic_table() %>%   analyze_vars(     vars = \"VAR\",     .stats = c(\"n\", \"mean\", \"mean_sd\", \"range\"),     .formats = c(\"mean_sd\" = \"auto\", \"range\" = \"auto\")   ) %>%   build_table(dt) #>                  all obs      #> ————————————————————————————— #> n                   5         #> Mean               1.4        #> Mean (SD)   1.44042 (1.91481) #> Min - Max    0.0010 - 4.0000   # `s_summary.numeric`  ## Basic usage: empty numeric returns NA-filled items. s_summary(numeric()) #> $n #> n  #> 0  #>  #> $sum #> sum  #>  NA  #>  #> $mean #> mean  #>   NA  #>  #> $sd #> sd  #> NA  #>  #> $se #> se  #> NA  #>  #> $mean_sd #> mean   sd  #>   NA   NA  #>  #> $mean_se #> mean   se  #>   NA   NA  #>  #> $mean_ci #> mean_ci_lwr mean_ci_upr  #>          NA          NA  #> attr(,\"label\") #> [1] \"Mean 95% CI\" #>  #> $mean_sei #> mean_sei_lwr mean_sei_upr  #>           NA           NA  #> attr(,\"label\") #> [1] \"Mean -/+ 1xSE\" #>  #> $mean_sdi #> mean_sdi_lwr mean_sdi_upr  #>           NA           NA  #> attr(,\"label\") #> [1] \"Mean -/+ 1xSD\" #>  #> $mean_ci_3d #>        mean mean_ci_lwr mean_ci_upr  #>          NA          NA          NA  #> attr(,\"label\") #> [1] \"Mean (95% CI)\" #>  #> $mean_pval #> p_value  #>      NA  #> attr(,\"label\") #> [1] \"Mean p-value (H0: mean = 0)\" #>  #> $median #> median  #>     NA  #>  #> $mad #> mad  #>  NA  #>  #> $median_ci #> median_ci_lwr median_ci_upr  #>            NA            NA  #> attr(,\"conf_level\") #> [1] NA #> attr(,\"label\") #> [1] \"Median 95% CI\" #>  #> $median_ci_3d #>        median median_ci_lwr median_ci_upr  #>            NA            NA            NA  #> attr(,\"label\") #> [1] \"Median (95% CI)\" #>  #> $quantiles #> quantile_0.25 quantile_0.75  #>            NA            NA  #> attr(,\"label\") #> [1] \"25% and 75%-ile\" #>  #> $iqr #> iqr  #>  NA  #>  #> $range #> min max  #>  NA  NA  #>  #> $min #> min  #>  NA  #>  #> $max #> max  #>  NA  #>  #> $median_range #> median    min    max  #>     NA     NA     NA  #> attr(,\"label\") #> [1] \"Median (Min - Max)\" #>  #> $cv #> cv  #> NA  #>  #> $geom_mean #> geom_mean  #>       NaN  #>  #> $geom_mean_ci #> mean_ci_lwr mean_ci_upr  #>          NA          NA  #> attr(,\"label\") #> [1] \"Geometric Mean 95% CI\" #>  #> $geom_cv #> geom_cv  #>      NA  #>  #> $geom_mean_ci_3d #>   geom_mean mean_ci_lwr mean_ci_upr  #>         NaN          NA          NA  #> attr(,\"label\") #> [1] \"Geometric Mean (95% CI)\" #>   ## Management of NA values. x <- c(NA_real_, 1) s_summary(x, na.rm = TRUE) #> $n #> n  #> 1  #>  #> $sum #> sum  #>   1  #>  #> $mean #> mean  #>    1  #>  #> $sd #> sd  #> NA  #>  #> $se #> se  #> NA  #>  #> $mean_sd #> mean   sd  #>    1   NA  #>  #> $mean_se #> mean   se  #>    1   NA  #>  #> $mean_ci #> mean_ci_lwr mean_ci_upr  #>          NA          NA  #> attr(,\"label\") #> [1] \"Mean 95% CI\" #>  #> $mean_sei #> mean_sei_lwr mean_sei_upr  #>           NA           NA  #> attr(,\"label\") #> [1] \"Mean -/+ 1xSE\" #>  #> $mean_sdi #> mean_sdi_lwr mean_sdi_upr  #>           NA           NA  #> attr(,\"label\") #> [1] \"Mean -/+ 1xSD\" #>  #> $mean_ci_3d #>        mean mean_ci_lwr mean_ci_upr  #>           1          NA          NA  #> attr(,\"label\") #> [1] \"Mean (95% CI)\" #>  #> $mean_pval #> p_value  #>      NA  #> attr(,\"label\") #> [1] \"Mean p-value (H0: mean = 0)\" #>  #> $median #> median  #>      1  #>  #> $mad #> mad  #>   0  #>  #> $median_ci #> median_ci_lwr median_ci_upr  #>            NA            NA  #> attr(,\"conf_level\") #> [1] NA #> attr(,\"label\") #> [1] \"Median 95% CI\" #>  #> $median_ci_3d #>        median median_ci_lwr median_ci_upr  #>             1            NA            NA  #> attr(,\"label\") #> [1] \"Median (95% CI)\" #>  #> $quantiles #> quantile_0.25 quantile_0.75  #>             1             1  #> attr(,\"label\") #> [1] \"25% and 75%-ile\" #>  #> $iqr #> iqr  #>   0  #>  #> $range #> min max  #>   1   1  #>  #> $min #> min  #>   1  #>  #> $max #> max  #>   1  #>  #> $median_range #> median    min    max  #>      1      1      1  #> attr(,\"label\") #> [1] \"Median (Min - Max)\" #>  #> $cv #> cv  #> NA  #>  #> $geom_mean #> geom_mean  #>         1  #>  #> $geom_mean_ci #> mean_ci_lwr mean_ci_upr  #>          NA          NA  #> attr(,\"label\") #> [1] \"Geometric Mean 95% CI\" #>  #> $geom_cv #> geom_cv  #>      NA  #>  #> $geom_mean_ci_3d #>   geom_mean mean_ci_lwr mean_ci_upr  #>           1          NA          NA  #> attr(,\"label\") #> [1] \"Geometric Mean (95% CI)\" #>  s_summary(x, na.rm = FALSE) #> $n #> n  #> 2  #>  #> $sum #> sum  #>  NA  #>  #> $mean #> mean  #>   NA  #>  #> $sd #> sd  #> NA  #>  #> $se #> se  #> NA  #>  #> $mean_sd #> mean   sd  #>   NA   NA  #>  #> $mean_se #> mean   se  #>   NA   NA  #>  #> $mean_ci #> mean_ci_lwr mean_ci_upr  #>          NA          NA  #> attr(,\"label\") #> [1] \"Mean 95% CI\" #>  #> $mean_sei #> mean_sei_lwr mean_sei_upr  #>           NA           NA  #> attr(,\"label\") #> [1] \"Mean -/+ 1xSE\" #>  #> $mean_sdi #> mean_sdi_lwr mean_sdi_upr  #>           NA           NA  #> attr(,\"label\") #> [1] \"Mean -/+ 1xSD\" #>  #> $mean_ci_3d #>        mean mean_ci_lwr mean_ci_upr  #>          NA          NA          NA  #> attr(,\"label\") #> [1] \"Mean (95% CI)\" #>  #> $mean_pval #> p_value  #>      NA  #> attr(,\"label\") #> [1] \"Mean p-value (H0: mean = 0)\" #>  #> $median #> median  #>     NA  #>  #> $mad #> mad  #>  NA  #>  #> $median_ci #> median_ci_lwr median_ci_upr  #>            NA            NA  #> attr(,\"conf_level\") #> [1] NA #> attr(,\"label\") #> [1] \"Median 95% CI\" #>  #> $median_ci_3d #>        median median_ci_lwr median_ci_upr  #>            NA            NA            NA  #> attr(,\"label\") #> [1] \"Median (95% CI)\" #>  #> $quantiles #> quantile_0.25 quantile_0.75  #>            NA            NA  #> attr(,\"label\") #> [1] \"25% and 75%-ile\" #>  #> $iqr #> iqr  #>  NA  #>  #> $range #> min max  #>  NA  NA  #>  #> $min #> min  #>  NA  #>  #> $max #> max  #>  NA  #>  #> $median_range #> median    min    max  #>     NA     NA     NA  #> attr(,\"label\") #> [1] \"Median (Min - Max)\" #>  #> $cv #> cv  #> NA  #>  #> $geom_mean #> geom_mean  #>        NA  #>  #> $geom_mean_ci #> mean_ci_lwr mean_ci_upr  #>          NA          NA  #> attr(,\"label\") #> [1] \"Geometric Mean 95% CI\" #>  #> $geom_cv #> geom_cv  #>      NA  #>  #> $geom_mean_ci_3d #>   geom_mean mean_ci_lwr mean_ci_upr  #>          NA          NA          NA  #> attr(,\"label\") #> [1] \"Geometric Mean (95% CI)\" #>   x <- c(NA_real_, 1, 2) s_summary(x, stats = NULL) #> $n #> n  #> 2  #>  #> $sum #> sum  #>   3  #>  #> $mean #> mean  #>  1.5  #>  #> $sd #>        sd  #> 0.7071068  #>  #> $se #>  se  #> 0.5  #>  #> $mean_sd #>      mean        sd  #> 1.5000000 0.7071068  #>  #> $mean_se #> mean   se  #>  1.5  0.5  #>  #> $mean_ci #> mean_ci_lwr mean_ci_upr  #>   -4.853102    7.853102  #> attr(,\"label\") #> [1] \"Mean 95% CI\" #>  #> $mean_sei #> mean_sei_lwr mean_sei_upr  #>            1            2  #> attr(,\"label\") #> [1] \"Mean -/+ 1xSE\" #>  #> $mean_sdi #> mean_sdi_lwr mean_sdi_upr  #>    0.7928932    2.2071068  #> attr(,\"label\") #> [1] \"Mean -/+ 1xSD\" #>  #> $mean_ci_3d #>        mean mean_ci_lwr mean_ci_upr  #>    1.500000   -4.853102    7.853102  #> attr(,\"label\") #> [1] \"Mean (95% CI)\" #>  #> $mean_pval #>   p_value  #> 0.2048328  #> attr(,\"label\") #> [1] \"Mean p-value (H0: mean = 0)\" #>  #> $median #> median  #>    1.5  #>  #> $mad #> mad  #>   0  #>  #> $median_ci #> median_ci_lwr median_ci_upr  #>            NA            NA  #> attr(,\"conf_level\") #> [1] NA #> attr(,\"label\") #> [1] \"Median 95% CI\" #>  #> $median_ci_3d #>        median median_ci_lwr median_ci_upr  #>           1.5            NA            NA  #> attr(,\"label\") #> [1] \"Median (95% CI)\" #>  #> $quantiles #> quantile_0.25 quantile_0.75  #>             1             2  #> attr(,\"label\") #> [1] \"25% and 75%-ile\" #>  #> $iqr #> iqr  #>   1  #>  #> $range #> min max  #>   1   2  #>  #> $min #> min  #>   1  #>  #> $max #> max  #>   2  #>  #> $median_range #> median    min    max  #>    1.5    1.0    2.0  #> attr(,\"label\") #> [1] \"Median (Min - Max)\" #>  #> $cv #>       cv  #> 47.14045  #>  #> $geom_mean #> geom_mean  #>  1.414214  #>  #> $geom_mean_ci #>  mean_ci_lwr  mean_ci_upr  #>   0.01729978 115.60839614  #> attr(,\"label\") #> [1] \"Geometric Mean 95% CI\" #>  #> $geom_cv #>  geom_cv  #> 52.10922  #>  #> $geom_mean_ci_3d #>    geom_mean  mean_ci_lwr  mean_ci_upr  #>   1.41421356   0.01729978 115.60839614  #> attr(,\"label\") #> [1] \"Geometric Mean (95% CI)\" #>   ## Benefits in `rtables` contructions: dta_test <- data.frame(   Group = rep(LETTERS[1:3], each = 2),   sub_group = rep(letters[1:2], each = 3),   x = 1:6 )  ## The summary obtained in with `rtables`: basic_table() %>%   split_cols_by(var = \"Group\") %>%   split_rows_by(var = \"sub_group\") %>%   analyze(vars = \"x\", afun = s_summary) %>%   build_table(df = dta_test) #>                                                           A                                  B                                C                           #> ————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————— #> a                                                                                                                                                         #>   n                                                       2                                  1                                0                           #>   sum                                                     3                                  3                                NA                          #>   mean                                                   1.5                                 3                                NA                          #>   sd                                              0.707106781186548                         NA                                NA                          #>   se                                                     0.5                                NA                                NA                          #>   mean_sd                                       1.5, 0.707106781186548                     3, NA                              NA                          #>   mean_se                                              1.5, 0.5                            3, NA                              NA                          #>   Mean 95% CI                            -4.85310236808735, 7.85310236808735                NA                                NA                          #>   Mean -/+ 1xSE                                          1, 2                               NA                                NA                          #>   Mean -/+ 1xSD                          0.792893218813452, 2.20710678118655                NA                                NA                          #>   Mean (95% CI)                        1.5, -4.85310236808735, 7.85310236808735          3, NA, NA                            NA                          #>   Mean p-value (H0: mean = 0)                     0.204832764699133                         NA                                NA                          #>   median                                                 1.5                                 3                                NA                          #>   mad                                                     0                                  0                                NA                          #>   Median 95% CI                                           NA                                NA                                NA                          #>   Median (95% CI)                                    1.5, NA, NA                         3, NA, NA                            NA                          #>   25% and 75%-ile                                        1, 2                              3, 3                               NA                          #>   iqr                                                     1                                  0                                NA                          #>   range                                                  1, 2                              3, 3                               NA                          #>   min                                                     1                                  3                                NA                          #>   max                                                     2                                  3                                NA                          #>   Median (Min - Max)                                  1.5, 1, 2                           3, 3, 3                             NA                          #>   cv                                               47.1404520791032                         NA                                NA                          #>   geom_mean                                        1.41421356237309                          3                                NA                          #>   Geometric Mean 95% CI                  0.0172997815631007, 115.608396135236               NA                                NA                          #>   geom_cv                                          52.1092246837487                         NA                                NA                          #>   Geometric Mean (95% CI)       1.41421356237309, 0.0172997815631007, 115.608396135236   3, NA, NA                            NA                          #> b                                                                                                                                                         #>   n                                                       0                                  1                                2                           #>   sum                                                     NA                                 4                                11                          #>   mean                                                    NA                                 4                               5.5                          #>   sd                                                      NA                                NA                        0.707106781186548                   #>   se                                                      NA                                NA                               0.5                          #>   mean_sd                                                 NA                               4, NA                    5.5, 0.707106781186548                #>   mean_se                                                 NA                               4, NA                           5.5, 0.5                       #>   Mean 95% CI                                             NA                                NA               -0.853102368087347, 11.8531023680873         #>   Mean -/+ 1xSE                                           NA                                NA                               5, 6                         #>   Mean -/+ 1xSD                                           NA                                NA                4.79289321881345, 6.20710678118655          #>   Mean (95% CI)                                           NA                             4, NA, NA        5.5, -0.853102368087347, 11.8531023680873       #>   Mean p-value (H0: mean = 0)                             NA                                NA                        0.0577158767526089                  #>   median                                                  NA                                 4                               5.5                          #>   mad                                                     NA                                 0                                0                           #>   Median 95% CI                                           NA                                NA                                NA                          #>   Median (95% CI)                                         NA                             4, NA, NA                       5.5, NA, NA                      #>   25% and 75%-ile                                         NA                               4, 4                              5, 6                         #>   iqr                                                     NA                                 0                                1                           #>   range                                                   NA                               4, 4                              5, 6                         #>   min                                                     NA                                 4                                5                           #>   max                                                     NA                                 4                                6                           #>   Median (Min - Max)                                      NA                              4, 4, 4                         5.5, 5, 6                       #>   cv                                                      NA                                NA                         12.8564869306645                   #>   geom_mean                                               NA                                 4                         5.47722557505166                   #>   Geometric Mean 95% CI                                   NA                                NA                1.71994304449266, 17.4424380482025          #>   geom_cv                                                 NA                                NA                         12.945835316564                    #>   Geometric Mean (95% CI)                                 NA                             4, NA, NA   5.47722557505166, 1.71994304449266, 17.4424380482025  ## By comparison with `lapply`: X <- split(dta_test, f = with(dta_test, interaction(Group, sub_group))) lapply(X, function(x) s_summary(x$x)) #> $A.a #> $A.a$n #> n  #> 2  #>  #> $A.a$sum #> sum  #>   3  #>  #> $A.a$mean #> mean  #>  1.5  #>  #> $A.a$sd #>        sd  #> 0.7071068  #>  #> $A.a$se #>  se  #> 0.5  #>  #> $A.a$mean_sd #>      mean        sd  #> 1.5000000 0.7071068  #>  #> $A.a$mean_se #> mean   se  #>  1.5  0.5  #>  #> $A.a$mean_ci #> mean_ci_lwr mean_ci_upr  #>   -4.853102    7.853102  #> attr(,\"label\") #> [1] \"Mean 95% CI\" #>  #> $A.a$mean_sei #> mean_sei_lwr mean_sei_upr  #>            1            2  #> attr(,\"label\") #> [1] \"Mean -/+ 1xSE\" #>  #> $A.a$mean_sdi #> mean_sdi_lwr mean_sdi_upr  #>    0.7928932    2.2071068  #> attr(,\"label\") #> [1] \"Mean -/+ 1xSD\" #>  #> $A.a$mean_ci_3d #>        mean mean_ci_lwr mean_ci_upr  #>    1.500000   -4.853102    7.853102  #> attr(,\"label\") #> [1] \"Mean (95% CI)\" #>  #> $A.a$mean_pval #>   p_value  #> 0.2048328  #> attr(,\"label\") #> [1] \"Mean p-value (H0: mean = 0)\" #>  #> $A.a$median #> median  #>    1.5  #>  #> $A.a$mad #> mad  #>   0  #>  #> $A.a$median_ci #> median_ci_lwr median_ci_upr  #>            NA            NA  #> attr(,\"conf_level\") #> [1] NA #> attr(,\"label\") #> [1] \"Median 95% CI\" #>  #> $A.a$median_ci_3d #>        median median_ci_lwr median_ci_upr  #>           1.5            NA            NA  #> attr(,\"label\") #> [1] \"Median (95% CI)\" #>  #> $A.a$quantiles #> quantile_0.25 quantile_0.75  #>             1             2  #> attr(,\"label\") #> [1] \"25% and 75%-ile\" #>  #> $A.a$iqr #> iqr  #>   1  #>  #> $A.a$range #> min max  #>   1   2  #>  #> $A.a$min #> min  #>   1  #>  #> $A.a$max #> max  #>   2  #>  #> $A.a$median_range #> median    min    max  #>    1.5    1.0    2.0  #> attr(,\"label\") #> [1] \"Median (Min - Max)\" #>  #> $A.a$cv #>       cv  #> 47.14045  #>  #> $A.a$geom_mean #> geom_mean  #>  1.414214  #>  #> $A.a$geom_mean_ci #>  mean_ci_lwr  mean_ci_upr  #>   0.01729978 115.60839614  #> attr(,\"label\") #> [1] \"Geometric Mean 95% CI\" #>  #> $A.a$geom_cv #>  geom_cv  #> 52.10922  #>  #> $A.a$geom_mean_ci_3d #>    geom_mean  mean_ci_lwr  mean_ci_upr  #>   1.41421356   0.01729978 115.60839614  #> attr(,\"label\") #> [1] \"Geometric Mean (95% CI)\" #>  #>  #> $B.a #> $B.a$n #> n  #> 1  #>  #> $B.a$sum #> sum  #>   3  #>  #> $B.a$mean #> mean  #>    3  #>  #> $B.a$sd #> sd  #> NA  #>  #> $B.a$se #> se  #> NA  #>  #> $B.a$mean_sd #> mean   sd  #>    3   NA  #>  #> $B.a$mean_se #> mean   se  #>    3   NA  #>  #> $B.a$mean_ci #> mean_ci_lwr mean_ci_upr  #>          NA          NA  #> attr(,\"label\") #> [1] \"Mean 95% CI\" #>  #> $B.a$mean_sei #> mean_sei_lwr mean_sei_upr  #>           NA           NA  #> attr(,\"label\") #> [1] \"Mean -/+ 1xSE\" #>  #> $B.a$mean_sdi #> mean_sdi_lwr mean_sdi_upr  #>           NA           NA  #> attr(,\"label\") #> [1] \"Mean -/+ 1xSD\" #>  #> $B.a$mean_ci_3d #>        mean mean_ci_lwr mean_ci_upr  #>           3          NA          NA  #> attr(,\"label\") #> [1] \"Mean (95% CI)\" #>  #> $B.a$mean_pval #> p_value  #>      NA  #> attr(,\"label\") #> [1] \"Mean p-value (H0: mean = 0)\" #>  #> $B.a$median #> median  #>      3  #>  #> $B.a$mad #> mad  #>   0  #>  #> $B.a$median_ci #> median_ci_lwr median_ci_upr  #>            NA            NA  #> attr(,\"conf_level\") #> [1] NA #> attr(,\"label\") #> [1] \"Median 95% CI\" #>  #> $B.a$median_ci_3d #>        median median_ci_lwr median_ci_upr  #>             3            NA            NA  #> attr(,\"label\") #> [1] \"Median (95% CI)\" #>  #> $B.a$quantiles #> quantile_0.25 quantile_0.75  #>             3             3  #> attr(,\"label\") #> [1] \"25% and 75%-ile\" #>  #> $B.a$iqr #> iqr  #>   0  #>  #> $B.a$range #> min max  #>   3   3  #>  #> $B.a$min #> min  #>   3  #>  #> $B.a$max #> max  #>   3  #>  #> $B.a$median_range #> median    min    max  #>      3      3      3  #> attr(,\"label\") #> [1] \"Median (Min - Max)\" #>  #> $B.a$cv #> cv  #> NA  #>  #> $B.a$geom_mean #> geom_mean  #>         3  #>  #> $B.a$geom_mean_ci #> mean_ci_lwr mean_ci_upr  #>          NA          NA  #> attr(,\"label\") #> [1] \"Geometric Mean 95% CI\" #>  #> $B.a$geom_cv #> geom_cv  #>      NA  #>  #> $B.a$geom_mean_ci_3d #>   geom_mean mean_ci_lwr mean_ci_upr  #>           3          NA          NA  #> attr(,\"label\") #> [1] \"Geometric Mean (95% CI)\" #>  #>  #> $C.a #> $C.a$n #> n  #> 0  #>  #> $C.a$sum #> sum  #>  NA  #>  #> $C.a$mean #> mean  #>   NA  #>  #> $C.a$sd #> sd  #> NA  #>  #> $C.a$se #> se  #> NA  #>  #> $C.a$mean_sd #> mean   sd  #>   NA   NA  #>  #> $C.a$mean_se #> mean   se  #>   NA   NA  #>  #> $C.a$mean_ci #> mean_ci_lwr mean_ci_upr  #>          NA          NA  #> attr(,\"label\") #> [1] \"Mean 95% CI\" #>  #> $C.a$mean_sei #> mean_sei_lwr mean_sei_upr  #>           NA           NA  #> attr(,\"label\") #> [1] \"Mean -/+ 1xSE\" #>  #> $C.a$mean_sdi #> mean_sdi_lwr mean_sdi_upr  #>           NA           NA  #> attr(,\"label\") #> [1] \"Mean -/+ 1xSD\" #>  #> $C.a$mean_ci_3d #>        mean mean_ci_lwr mean_ci_upr  #>          NA          NA          NA  #> attr(,\"label\") #> [1] \"Mean (95% CI)\" #>  #> $C.a$mean_pval #> p_value  #>      NA  #> attr(,\"label\") #> [1] \"Mean p-value (H0: mean = 0)\" #>  #> $C.a$median #> median  #>     NA  #>  #> $C.a$mad #> mad  #>  NA  #>  #> $C.a$median_ci #> median_ci_lwr median_ci_upr  #>            NA            NA  #> attr(,\"conf_level\") #> [1] NA #> attr(,\"label\") #> [1] \"Median 95% CI\" #>  #> $C.a$median_ci_3d #>        median median_ci_lwr median_ci_upr  #>            NA            NA            NA  #> attr(,\"label\") #> [1] \"Median (95% CI)\" #>  #> $C.a$quantiles #> quantile_0.25 quantile_0.75  #>            NA            NA  #> attr(,\"label\") #> [1] \"25% and 75%-ile\" #>  #> $C.a$iqr #> iqr  #>  NA  #>  #> $C.a$range #> min max  #>  NA  NA  #>  #> $C.a$min #> min  #>  NA  #>  #> $C.a$max #> max  #>  NA  #>  #> $C.a$median_range #> median    min    max  #>     NA     NA     NA  #> attr(,\"label\") #> [1] \"Median (Min - Max)\" #>  #> $C.a$cv #> cv  #> NA  #>  #> $C.a$geom_mean #> geom_mean  #>       NaN  #>  #> $C.a$geom_mean_ci #> mean_ci_lwr mean_ci_upr  #>          NA          NA  #> attr(,\"label\") #> [1] \"Geometric Mean 95% CI\" #>  #> $C.a$geom_cv #> geom_cv  #>      NA  #>  #> $C.a$geom_mean_ci_3d #>   geom_mean mean_ci_lwr mean_ci_upr  #>         NaN          NA          NA  #> attr(,\"label\") #> [1] \"Geometric Mean (95% CI)\" #>  #>  #> $A.b #> $A.b$n #> n  #> 0  #>  #> $A.b$sum #> sum  #>  NA  #>  #> $A.b$mean #> mean  #>   NA  #>  #> $A.b$sd #> sd  #> NA  #>  #> $A.b$se #> se  #> NA  #>  #> $A.b$mean_sd #> mean   sd  #>   NA   NA  #>  #> $A.b$mean_se #> mean   se  #>   NA   NA  #>  #> $A.b$mean_ci #> mean_ci_lwr mean_ci_upr  #>          NA          NA  #> attr(,\"label\") #> [1] \"Mean 95% CI\" #>  #> $A.b$mean_sei #> mean_sei_lwr mean_sei_upr  #>           NA           NA  #> attr(,\"label\") #> [1] \"Mean -/+ 1xSE\" #>  #> $A.b$mean_sdi #> mean_sdi_lwr mean_sdi_upr  #>           NA           NA  #> attr(,\"label\") #> [1] \"Mean -/+ 1xSD\" #>  #> $A.b$mean_ci_3d #>        mean mean_ci_lwr mean_ci_upr  #>          NA          NA          NA  #> attr(,\"label\") #> [1] \"Mean (95% CI)\" #>  #> $A.b$mean_pval #> p_value  #>      NA  #> attr(,\"label\") #> [1] \"Mean p-value (H0: mean = 0)\" #>  #> $A.b$median #> median  #>     NA  #>  #> $A.b$mad #> mad  #>  NA  #>  #> $A.b$median_ci #> median_ci_lwr median_ci_upr  #>            NA            NA  #> attr(,\"conf_level\") #> [1] NA #> attr(,\"label\") #> [1] \"Median 95% CI\" #>  #> $A.b$median_ci_3d #>        median median_ci_lwr median_ci_upr  #>            NA            NA            NA  #> attr(,\"label\") #> [1] \"Median (95% CI)\" #>  #> $A.b$quantiles #> quantile_0.25 quantile_0.75  #>            NA            NA  #> attr(,\"label\") #> [1] \"25% and 75%-ile\" #>  #> $A.b$iqr #> iqr  #>  NA  #>  #> $A.b$range #> min max  #>  NA  NA  #>  #> $A.b$min #> min  #>  NA  #>  #> $A.b$max #> max  #>  NA  #>  #> $A.b$median_range #> median    min    max  #>     NA     NA     NA  #> attr(,\"label\") #> [1] \"Median (Min - Max)\" #>  #> $A.b$cv #> cv  #> NA  #>  #> $A.b$geom_mean #> geom_mean  #>       NaN  #>  #> $A.b$geom_mean_ci #> mean_ci_lwr mean_ci_upr  #>          NA          NA  #> attr(,\"label\") #> [1] \"Geometric Mean 95% CI\" #>  #> $A.b$geom_cv #> geom_cv  #>      NA  #>  #> $A.b$geom_mean_ci_3d #>   geom_mean mean_ci_lwr mean_ci_upr  #>         NaN          NA          NA  #> attr(,\"label\") #> [1] \"Geometric Mean (95% CI)\" #>  #>  #> $B.b #> $B.b$n #> n  #> 1  #>  #> $B.b$sum #> sum  #>   4  #>  #> $B.b$mean #> mean  #>    4  #>  #> $B.b$sd #> sd  #> NA  #>  #> $B.b$se #> se  #> NA  #>  #> $B.b$mean_sd #> mean   sd  #>    4   NA  #>  #> $B.b$mean_se #> mean   se  #>    4   NA  #>  #> $B.b$mean_ci #> mean_ci_lwr mean_ci_upr  #>          NA          NA  #> attr(,\"label\") #> [1] \"Mean 95% CI\" #>  #> $B.b$mean_sei #> mean_sei_lwr mean_sei_upr  #>           NA           NA  #> attr(,\"label\") #> [1] \"Mean -/+ 1xSE\" #>  #> $B.b$mean_sdi #> mean_sdi_lwr mean_sdi_upr  #>           NA           NA  #> attr(,\"label\") #> [1] \"Mean -/+ 1xSD\" #>  #> $B.b$mean_ci_3d #>        mean mean_ci_lwr mean_ci_upr  #>           4          NA          NA  #> attr(,\"label\") #> [1] \"Mean (95% CI)\" #>  #> $B.b$mean_pval #> p_value  #>      NA  #> attr(,\"label\") #> [1] \"Mean p-value (H0: mean = 0)\" #>  #> $B.b$median #> median  #>      4  #>  #> $B.b$mad #> mad  #>   0  #>  #> $B.b$median_ci #> median_ci_lwr median_ci_upr  #>            NA            NA  #> attr(,\"conf_level\") #> [1] NA #> attr(,\"label\") #> [1] \"Median 95% CI\" #>  #> $B.b$median_ci_3d #>        median median_ci_lwr median_ci_upr  #>             4            NA            NA  #> attr(,\"label\") #> [1] \"Median (95% CI)\" #>  #> $B.b$quantiles #> quantile_0.25 quantile_0.75  #>             4             4  #> attr(,\"label\") #> [1] \"25% and 75%-ile\" #>  #> $B.b$iqr #> iqr  #>   0  #>  #> $B.b$range #> min max  #>   4   4  #>  #> $B.b$min #> min  #>   4  #>  #> $B.b$max #> max  #>   4  #>  #> $B.b$median_range #> median    min    max  #>      4      4      4  #> attr(,\"label\") #> [1] \"Median (Min - Max)\" #>  #> $B.b$cv #> cv  #> NA  #>  #> $B.b$geom_mean #> geom_mean  #>         4  #>  #> $B.b$geom_mean_ci #> mean_ci_lwr mean_ci_upr  #>          NA          NA  #> attr(,\"label\") #> [1] \"Geometric Mean 95% CI\" #>  #> $B.b$geom_cv #> geom_cv  #>      NA  #>  #> $B.b$geom_mean_ci_3d #>   geom_mean mean_ci_lwr mean_ci_upr  #>           4          NA          NA  #> attr(,\"label\") #> [1] \"Geometric Mean (95% CI)\" #>  #>  #> $C.b #> $C.b$n #> n  #> 2  #>  #> $C.b$sum #> sum  #>  11  #>  #> $C.b$mean #> mean  #>  5.5  #>  #> $C.b$sd #>        sd  #> 0.7071068  #>  #> $C.b$se #>  se  #> 0.5  #>  #> $C.b$mean_sd #>      mean        sd  #> 5.5000000 0.7071068  #>  #> $C.b$mean_se #> mean   se  #>  5.5  0.5  #>  #> $C.b$mean_ci #> mean_ci_lwr mean_ci_upr  #>  -0.8531024  11.8531024  #> attr(,\"label\") #> [1] \"Mean 95% CI\" #>  #> $C.b$mean_sei #> mean_sei_lwr mean_sei_upr  #>            5            6  #> attr(,\"label\") #> [1] \"Mean -/+ 1xSE\" #>  #> $C.b$mean_sdi #> mean_sdi_lwr mean_sdi_upr  #>     4.792893     6.207107  #> attr(,\"label\") #> [1] \"Mean -/+ 1xSD\" #>  #> $C.b$mean_ci_3d #>        mean mean_ci_lwr mean_ci_upr  #>   5.5000000  -0.8531024  11.8531024  #> attr(,\"label\") #> [1] \"Mean (95% CI)\" #>  #> $C.b$mean_pval #>    p_value  #> 0.05771588  #> attr(,\"label\") #> [1] \"Mean p-value (H0: mean = 0)\" #>  #> $C.b$median #> median  #>    5.5  #>  #> $C.b$mad #> mad  #>   0  #>  #> $C.b$median_ci #> median_ci_lwr median_ci_upr  #>            NA            NA  #> attr(,\"conf_level\") #> [1] NA #> attr(,\"label\") #> [1] \"Median 95% CI\" #>  #> $C.b$median_ci_3d #>        median median_ci_lwr median_ci_upr  #>           5.5            NA            NA  #> attr(,\"label\") #> [1] \"Median (95% CI)\" #>  #> $C.b$quantiles #> quantile_0.25 quantile_0.75  #>             5             6  #> attr(,\"label\") #> [1] \"25% and 75%-ile\" #>  #> $C.b$iqr #> iqr  #>   1  #>  #> $C.b$range #> min max  #>   5   6  #>  #> $C.b$min #> min  #>   5  #>  #> $C.b$max #> max  #>   6  #>  #> $C.b$median_range #> median    min    max  #>    5.5    5.0    6.0  #> attr(,\"label\") #> [1] \"Median (Min - Max)\" #>  #> $C.b$cv #>       cv  #> 12.85649  #>  #> $C.b$geom_mean #> geom_mean  #>  5.477226  #>  #> $C.b$geom_mean_ci #> mean_ci_lwr mean_ci_upr  #>    1.719943   17.442438  #> attr(,\"label\") #> [1] \"Geometric Mean 95% CI\" #>  #> $C.b$geom_cv #>  geom_cv  #> 12.94584  #>  #> $C.b$geom_mean_ci_3d #>   geom_mean mean_ci_lwr mean_ci_upr  #>    5.477226    1.719943   17.442438  #> attr(,\"label\") #> [1] \"Geometric Mean (95% CI)\" #>  #>   # `s_summary.factor`  ## Basic usage: s_summary(factor(c(\"a\", \"a\", \"b\", \"c\", \"a\"))) #> $n #> [1] 5 #>  #> $count #> $count$a #> [1] 3 #>  #> $count$b #> [1] 1 #>  #> $count$c #> [1] 1 #>  #>  #> $count_fraction #> $count_fraction$a #> [1] 3.0 0.6 #>  #> $count_fraction$b #> [1] 1.0 0.2 #>  #> $count_fraction$c #> [1] 1.0 0.2 #>  #>  #> $fraction #> $fraction$a #>   num denom  #>     3     5  #>  #> $fraction$b #>   num denom  #>     1     5  #>  #> $fraction$c #>   num denom  #>     1     5  #>  #>  #> $n_blq #> [1] 0 #>   # Empty factor returns zero-filled items. s_summary(factor(levels = c(\"a\", \"b\", \"c\"))) #> $n #> [1] 0 #>  #> $count #> $count$a #> [1] 0 #>  #> $count$b #> [1] 0 #>  #> $count$c #> [1] 0 #>  #>  #> $count_fraction #> $count_fraction$a #> [1] 0 0 #>  #> $count_fraction$b #> [1] 0 0 #>  #> $count_fraction$c #> [1] 0 0 #>  #>  #> $fraction #> $fraction$a #>   num denom  #>     0     0  #>  #> $fraction$b #>   num denom  #>     0     0  #>  #> $fraction$c #>   num denom  #>     0     0  #>  #>  #> $n_blq #> [1] 0 #>   ## Management of NA values. x <- factor(c(NA, \"Female\")) x <- explicit_na(x) s_summary(x, na.rm = TRUE) #> $n #> [1] 1 #>  #> $count #> $count$Female #> [1] 1 #>  #>  #> $count_fraction #> $count_fraction$Female #> [1] 1 1 #>  #>  #> $fraction #> $fraction$Female #>   num denom  #>     1     1  #>  #>  #> $n_blq #> [1] 0 #>  s_summary(x, na.rm = FALSE) #> $n #> [1] 2 #>  #> $count #> $count$Female #> [1] 1 #>  #> $count$`<Missing>` #> [1] 1 #>  #>  #> $count_fraction #> $count_fraction$Female #> [1] 1.0 0.5 #>  #> $count_fraction$`<Missing>` #> [1] 1.0 0.5 #>  #>  #> $fraction #> $fraction$Female #>   num denom  #>     1     2  #>  #> $fraction$`<Missing>` #>   num denom  #>     1     2  #>  #>  #> $n_blq #> [1] 0 #>   ## Different denominators. x <- factor(c(\"a\", \"a\", \"b\", \"c\", \"a\")) s_summary(x, denom = \"N_row\", .N_row = 10L) #> $n #> [1] 5 #>  #> $count #> $count$a #> [1] 3 #>  #> $count$b #> [1] 1 #>  #> $count$c #> [1] 1 #>  #>  #> $count_fraction #> $count_fraction$a #> [1] 3.0 0.3 #>  #> $count_fraction$b #> [1] 1.0 0.1 #>  #> $count_fraction$c #> [1] 1.0 0.1 #>  #>  #> $fraction #> $fraction$a #>   num denom  #>     3    10  #>  #> $fraction$b #>   num denom  #>     1    10  #>  #> $fraction$c #>   num denom  #>     1    10  #>  #>  #> $n_blq #> [1] 0 #>  s_summary(x, denom = \"N_col\", .N_col = 20L) #> $n #> [1] 5 #>  #> $count #> $count$a #> [1] 3 #>  #> $count$b #> [1] 1 #>  #> $count$c #> [1] 1 #>  #>  #> $count_fraction #> $count_fraction$a #> [1] 3.00 0.15 #>  #> $count_fraction$b #> [1] 1.00 0.05 #>  #> $count_fraction$c #> [1] 1.00 0.05 #>  #>  #> $fraction #> $fraction$a #>   num denom  #>     3    20  #>  #> $fraction$b #>   num denom  #>     1    20  #>  #> $fraction$c #>   num denom  #>     1    20  #>  #>  #> $n_blq #> [1] 0 #>   # `s_summary.character`  ## Basic usage: s_summary(c(\"a\", \"a\", \"b\", \"c\", \"a\"), .var = \"x\", verbose = FALSE) #> $n #> [1] 5 #>  #> $count #> $count$a #> [1] 3 #>  #> $count$b #> [1] 1 #>  #> $count$c #> [1] 1 #>  #>  #> $count_fraction #> $count_fraction$a #> [1] 3.0 0.6 #>  #> $count_fraction$b #> [1] 1.0 0.2 #>  #> $count_fraction$c #> [1] 1.0 0.2 #>  #>  #> $fraction #> $fraction$a #>   num denom  #>     3     5  #>  #> $fraction$b #>   num denom  #>     1     5  #>  #> $fraction$c #>   num denom  #>     1     5  #>  #>  #> $n_blq #> [1] 0 #>  s_summary(c(\"a\", \"a\", \"b\", \"c\", \"a\", \"\"), .var = \"x\", na.rm = FALSE, verbose = FALSE) #> $n #> [1] 6 #>  #> $count #> $count$a #> [1] 3 #>  #> $count$b #> [1] 1 #>  #> $count$c #> [1] 1 #>  #> $count$`NA` #> [1] 1 #>  #>  #> $count_fraction #> $count_fraction$a #> [1] 3.0 0.5 #>  #> $count_fraction$b #> [1] 1.0000000 0.1666667 #>  #> $count_fraction$c #> [1] 1.0000000 0.1666667 #>  #> $count_fraction$`NA` #> [1] 1.0000000 0.1666667 #>  #>  #> $fraction #> $fraction$a #>   num denom  #>     3     6  #>  #> $fraction$b #>   num denom  #>     1     6  #>  #> $fraction$c #>   num denom  #>     1     6  #>  #> $fraction$`NA` #>   num denom  #>     1     6  #>  #>  #> $n_blq #> [1] 0 #>   # `s_summary.logical`  ## Basic usage: s_summary(c(TRUE, FALSE, TRUE, TRUE)) #> $n #> [1] 4 #>  #> $count #> [1] 3 #>  #> $count_fraction #> [1] 3.00 0.75 #>  #> $n_blq #> [1] 0 #>   # Empty factor returns zero-filled items. s_summary(as.logical(c())) #> $n #> [1] 0 #>  #> $count #> [1] 0 #>  #> $count_fraction #> [1] 0 0 #>  #> $n_blq #> [1] 0 #>   ## Management of NA values. x <- c(NA, TRUE, FALSE) s_summary(x, na.rm = TRUE) #> $n #> [1] 2 #>  #> $count #> [1] 1 #>  #> $count_fraction #> [1] 1.0 0.5 #>  #> $n_blq #> [1] 0 #>  s_summary(x, na.rm = FALSE) #> $n #> [1] 3 #>  #> $count #> [1] 1 #>  #> $count_fraction #> [1] 1.0000000 0.3333333 #>  #> $n_blq #> [1] 0 #>   ## Different denominators. x <- c(TRUE, FALSE, TRUE, TRUE) s_summary(x, denom = \"N_row\", .N_row = 10L) #> $n #> [1] 4 #>  #> $count #> [1] 3 #>  #> $count_fraction #> [1] 3.0 0.3 #>  #> $n_blq #> [1] 0 #>  s_summary(x, denom = \"N_col\", .N_col = 20L) #> $n #> [1] 4 #>  #> $count #> [1] 3 #>  #> $count_fraction #> [1] 3.00 0.15 #>  #> $n_blq #> [1] 0 #>   a_summary(factor(c(\"a\", \"a\", \"b\", \"c\", \"a\")), .N_row = 10, .N_col = 10) #> RowsVerticalSection (in_rows) object print method: #> ---------------------------- #>                     row_name formatted_cell indent_mod row_label #> 1                          n              5          0         n #> 2                    count.a              3          0         a #> 3                    count.b              1          0         b #> 4                    count.c              1          0         c #> 5           count_fraction.a        3 (60%)          0         a #> 6           count_fraction.b        1 (20%)          0         b #> 7           count_fraction.c        1 (20%)          0         c #> 8  count_fraction_fixed_dp.a      3 (60.0%)          0         a #> 9  count_fraction_fixed_dp.b      1 (20.0%)          0         b #> 10 count_fraction_fixed_dp.c      1 (20.0%)          0         c #> 11                fraction.a    3/5 (60.0%)          0         a #> 12                fraction.b    1/5 (20.0%)          0         b #> 13                fraction.c    1/5 (20.0%)          0         c #> 14                     n_blq              0          0     n_blq a_summary(   factor(c(\"a\", \"a\", \"b\", \"c\", \"a\")),   .ref_group = factor(c(\"a\", \"a\", \"b\", \"c\")), compare = TRUE ) #> RowsVerticalSection (in_rows) object print method: #> ---------------------------- #>                     row_name formatted_cell indent_mod #> 1                          n              5          0 #> 2                    count.a              3          0 #> 3                    count.b              1          0 #> 4                    count.c              1          0 #> 5           count_fraction.a        3 (60%)          0 #> 6           count_fraction.b        1 (20%)          0 #> 7           count_fraction.c        1 (20%)          0 #> 8  count_fraction_fixed_dp.a      3 (60.0%)          0 #> 9  count_fraction_fixed_dp.b      1 (20.0%)          0 #> 10 count_fraction_fixed_dp.c      1 (20.0%)          0 #> 11                fraction.a    3/5 (60.0%)          0 #> 12                fraction.b    1/5 (20.0%)          0 #> 13                fraction.c    1/5 (20.0%)          0 #> 14                     n_blq              0          0 #> 15               pval_counts         0.9560          0 #>                     row_label #> 1                           n #> 2                           a #> 3                           b #> 4                           c #> 5                           a #> 6                           b #> 7                           c #> 8                           a #> 9                           b #> 10                          c #> 11                          a #> 12                          b #> 13                          c #> 14                      n_blq #> 15 p-value (chi-squared test)  a_summary(c(\"A\", \"B\", \"A\", \"C\"), .var = \"x\", .N_col = 10, .N_row = 10, verbose = FALSE) #> RowsVerticalSection (in_rows) object print method: #> ---------------------------- #>                     row_name formatted_cell indent_mod row_label #> 1                          n              4          0         n #> 2                    count.A              2          0         A #> 3                    count.B              1          0         B #> 4                    count.C              1          0         C #> 5           count_fraction.A        2 (50%)          0         A #> 6           count_fraction.B        1 (25%)          0         B #> 7           count_fraction.C        1 (25%)          0         C #> 8  count_fraction_fixed_dp.A      2 (50.0%)          0         A #> 9  count_fraction_fixed_dp.B      1 (25.0%)          0         B #> 10 count_fraction_fixed_dp.C      1 (25.0%)          0         C #> 11                fraction.A    2/4 (50.0%)          0         A #> 12                fraction.B    1/4 (25.0%)          0         B #> 13                fraction.C    1/4 (25.0%)          0         C #> 14                     n_blq              0          0     n_blq a_summary(   c(\"A\", \"B\", \"A\", \"C\"),   .ref_group = c(\"B\", \"A\", \"C\"), .var = \"x\", compare = TRUE, verbose = FALSE ) #> RowsVerticalSection (in_rows) object print method: #> ---------------------------- #>                     row_name formatted_cell indent_mod #> 1                          n              4          0 #> 2                    count.A              2          0 #> 3                    count.B              1          0 #> 4                    count.C              1          0 #> 5           count_fraction.A        2 (50%)          0 #> 6           count_fraction.B        1 (25%)          0 #> 7           count_fraction.C        1 (25%)          0 #> 8  count_fraction_fixed_dp.A      2 (50.0%)          0 #> 9  count_fraction_fixed_dp.B      1 (25.0%)          0 #> 10 count_fraction_fixed_dp.C      1 (25.0%)          0 #> 11                fraction.A    2/4 (50.0%)          0 #> 12                fraction.B    1/4 (25.0%)          0 #> 13                fraction.C    1/4 (25.0%)          0 #> 14                     n_blq              0          0 #> 15               pval_counts         0.9074          0 #>                     row_label #> 1                           n #> 2                           A #> 3                           B #> 4                           C #> 5                           A #> 6                           B #> 7                           C #> 8                           A #> 9                           B #> 10                          C #> 11                          A #> 12                          B #> 13                          C #> 14                      n_blq #> 15 p-value (chi-squared test)  a_summary(c(TRUE, FALSE, FALSE, TRUE, TRUE), .N_row = 10, .N_col = 10) #> RowsVerticalSection (in_rows) object print method: #> ---------------------------- #>                  row_name formatted_cell indent_mod      row_label #> 1                       n              5          0              n #> 2                   count              3          0          count #> 3          count_fraction        3 (60%)          0 count_fraction #> 4 count_fraction_fixed_dp      3 (60.0%)          0 count_fraction #> 5                fraction                         0       fraction #> 6                   n_blq              0          0          n_blq a_summary(   c(TRUE, FALSE, FALSE, TRUE, TRUE),   .ref_group = c(TRUE, FALSE), .in_ref_col = TRUE, compare = TRUE ) #> RowsVerticalSection (in_rows) object print method: #> ---------------------------- #>                  row_name formatted_cell indent_mod                  row_label #> 1                       n              5          0                          n #> 2                   count              3          0                      count #> 3          count_fraction        3 (60%)          0             count_fraction #> 4 count_fraction_fixed_dp      3 (60.0%)          0             count_fraction #> 5                fraction                         0                   fraction #> 6                   n_blq              0          0                      n_blq #> 7             pval_counts                         0 p-value (chi-squared test)  a_summary(rnorm(10), .N_col = 10, .N_row = 20, .var = \"bla\") #> RowsVerticalSection (in_rows) object print method: #> ---------------------------- #>           row_name       formatted_cell indent_mod                   row_label #> 1                n                   10          0                           n #> 2              sum                 -4.4          0                         Sum #> 3             mean                 -0.4          0                        Mean #> 4               sd                  1.1          0                          SD #> 5               se                  0.4          0                          SE #> 6          mean_sd           -0.4 (1.1)          0                   Mean (SD) #> 7          mean_se           -0.4 (0.4)          0                   Mean (SE) #> 8          mean_ci        (-1.24, 0.36)          0                 Mean 95% CI #> 9         mean_sei       (-0.79, -0.09)          0               Mean -/+ 1xSE #> 10        mean_sdi        (-1.56, 0.68)          0               Mean -/+ 1xSD #> 11       mean_pval               0.2432          0 Mean p-value (H0: mean = 0) #> 12          median                 -0.2          0                      Median #> 13             mad                  0.0          0   Median Absolute Deviation #> 14       median_ci        (-1.82, 0.62)          0               Median 95% CI #> 15       quantiles           -1.4 - 0.3          0             25% and 75%-ile #> 16             iqr                  1.7          0                         IQR #> 17           range           -2.4 - 1.1          0                   Min - Max #> 18             min                 -2.4          0                     Minimum #> 19             max                  1.1          0                     Maximum #> 20    median_range    -0.2 (-2.4 - 1.1)          0          Median (Min - Max) #> 21              cv               -253.2          0                      CV (%) #> 22       geom_mean                   NA          0              Geometric Mean #> 23    geom_mean_ci                   NA          0       Geometric Mean 95% CI #> 24         geom_cv                   NA          0         CV % Geometric Mean #> 25    median_ci_3d -0.25 (-1.82 - 0.62)          0             Median (95% CI) #> 26      mean_ci_3d -0.44 (-1.24 - 0.36)          0               Mean (95% CI) #> 27 geom_mean_ci_3d                   NA          0     Geometric Mean (95% CI) a_summary(rnorm(10, 5, 1), .ref_group = rnorm(20, -5, 1), .var = \"bla\", compare = TRUE) #> RowsVerticalSection (in_rows) object print method: #> ---------------------------- #>           row_name     formatted_cell indent_mod                   row_label #> 1                n                 10          0                           n #> 2              sum               48.2          0                         Sum #> 3             mean                4.8          0                        Mean #> 4               sd                1.2          0                          SD #> 5               se                0.4          0                          SE #> 6          mean_sd          4.8 (1.2)          0                   Mean (SD) #> 7          mean_se          4.8 (0.4)          0                   Mean (SE) #> 8          mean_ci       (3.98, 5.66)          0                 Mean 95% CI #> 9         mean_sei       (4.45, 5.19)          0               Mean -/+ 1xSE #> 10        mean_sdi       (3.65, 6.00)          0               Mean -/+ 1xSD #> 11       mean_pval            <0.0001          0 Mean p-value (H0: mean = 0) #> 12          median                4.7          0                      Median #> 13             mad                0.0          0   Median Absolute Deviation #> 14       median_ci       (3.37, 5.63)          0               Median 95% CI #> 15       quantiles          4.1 - 5.5          0             25% and 75%-ile #> 16             iqr                1.5          0                         IQR #> 17           range          3.1 - 7.1          0                   Min - Max #> 18             min                3.1          0                     Minimum #> 19             max                7.1          0                     Maximum #> 20    median_range    4.7 (3.1 - 7.1)          0          Median (Min - Max) #> 21              cv               24.4          0                      CV (%) #> 22       geom_mean                4.7          0              Geometric Mean #> 23    geom_mean_ci       (3.93, 5.60)          0       Geometric Mean 95% CI #> 24         geom_cv               25.2          0         CV % Geometric Mean #> 25    median_ci_3d 4.71 (3.37 - 5.63)          0             Median (95% CI) #> 26      mean_ci_3d 4.82 (3.98 - 5.66)          0               Mean (95% CI) #> 27 geom_mean_ci_3d 4.69 (3.93 - 5.60)          0     Geometric Mean (95% CI) #> 28            pval            <0.0001          0            p-value (t-test)"},{"path":"https://insightsengineering.github.io/tern/reference/analyze_vars_in_cols.html","id":null,"dir":"Reference","previous_headings":"","what":"Analyze numeric variables in columns — analyze_vars_in_cols","title":"Analyze numeric variables in columns — analyze_vars_in_cols","text":"layout-creating function analyze_vars_in_cols() creates layout element generate column-wise analysis table. function sets analysis methods column labels wrapper rtables::analyze_colvars(). designed principally PK tables.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/analyze_vars_in_cols.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Analyze numeric variables in columns — analyze_vars_in_cols","text":"","code":"analyze_vars_in_cols(   lyt,   vars,   ...,   .stats = c(\"n\", \"mean\", \"sd\", \"se\", \"cv\", \"geom_cv\"),   .labels = c(n = \"n\", mean = \"Mean\", sd = \"SD\", se = \"SE\", cv = \"CV (%)\", geom_cv =     \"CV % Geometric Mean\"),   row_labels = NULL,   do_summarize_row_groups = FALSE,   split_col_vars = TRUE,   imp_rule = NULL,   avalcat_var = \"AVALCAT1\",   cache = FALSE,   .indent_mods = NULL,   na_str = default_na_str(),   nested = TRUE,   .formats = NULL,   .aligns = NULL )"},{"path":"https://insightsengineering.github.io/tern/reference/analyze_vars_in_cols.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Analyze numeric variables in columns — analyze_vars_in_cols","text":"lyt (PreDataTableLayouts) layout analyses added . vars (character) variable names primary analysis variable iterated . ... additional arguments lower level functions. .stats (character) statistics select table. .labels (named character) labels statistics (without indent). row_labels (character) function works columns space, usually .labels character vector applies column space. can change row labels defining parameter named character vector names corresponding split values. defaults NULL contains one string, duplicate row label. do_summarize_row_groups (flag) defaults FALSE applies analysis current label rows. wrapper rtables::summarize_row_groups() can accept labelstr define row labels. behavior supported never need overload row labels. split_col_vars (flag) defaults TRUE puts analysis results onto columns. option allows add multiple instances functions, also nested fashion, without adding splits. split must happen one time single layout. imp_rule (string NULL) imputation rule setting. Defaults NULL imputation rule. Can also \"1/3\" implement 1/3 imputation rule \"1/2\" implement 1/2 imputation rule. order use imputation rule, avalcat_var argument must specified. See imputation_rule() details imputation. avalcat_var (string) imp_rule NULL, name variable indicates whether row data corresponds analysis value category \"BLQ\", \"LTR\", \"<PCLLOQ\", none (defaults \"AVALCAT1\"). Variable must present data match variable used calculate n_blq statistic (included .stats). cache (flag) whether store computed values temporary caching environment. speed calculations large tables, set FALSE rtable layout used multiple tables different data. Defaults FALSE. .indent_mods (named integer) indent modifiers labels. Defaults 0, corresponds unmodified default behavior. Can negative. na_str (string) string used replace NA empty values output. nested (flag) whether layout instruction applied within existing layout structure _if possible (TRUE, default) new top-level element (FALSE). Ignored nest split. underneath analyses, allowed. .formats (named character list) formats statistics. See Details analyze_vars information \"auto\" setting. .aligns (character NULL) alignment table contents (including labels). NULL, \"center\" applied. See formatters::list_valid_aligns() list currently supported alignments.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/analyze_vars_in_cols.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Analyze numeric variables in columns — analyze_vars_in_cols","text":"layout object suitable passing layouting functions, rtables::build_table(). Adding function rtable layout summarize given variables, arrange output columns, add table layout.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/analyze_vars_in_cols.html","id":"note","dir":"Reference","previous_headings":"","what":"Note","title":"Analyze numeric variables in columns — analyze_vars_in_cols","text":"experimental implementation rtables::summarize_row_groups() rtables::analyze_colvars() may subjected changes rtables extends support complex analysis pipelines column space. encourage users read examples carefully file issues different use cases. function, labelstr behaves atypically. labelstr = NULL (default), row labels assigned automatically split values do_summarize_row_groups = FALSE (default), group label do_summarize_row_groups = TRUE.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/reference/analyze_vars_in_cols.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Analyze numeric variables in columns — analyze_vars_in_cols","text":"","code":"library(dplyr)  # Data preparation adpp <- tern_ex_adpp %>% h_pkparam_sort()  lyt <- basic_table() %>%   split_rows_by(var = \"STRATA1\", label_pos = \"topleft\") %>%   split_rows_by(     var = \"SEX\",     label_pos = \"topleft\",     child_labels = \"hidden\"   ) %>% # Removes duplicated labels   analyze_vars_in_cols(vars = \"AGE\") result <- build_table(lyt = lyt, df = adpp) result #> STRATA1                                                          #>   SEX      n    Mean    SD    SE    CV (%)   CV % Geometric Mean #> ———————————————————————————————————————————————————————————————— #> A                                                                #>   F       81    38.8   5.4    0.6    13.8           14.3         #>   M       81    38.9   5.9    0.7    15.1           14.9         #> B                                                                #>   F       90    36.0   6.4    0.7    17.7           17.9         #>   M       81    36.4   6.5    0.7    17.9           17.8         #> C                                                                #>   F       117   34.1   6.2    0.6    18.2           18.3         #>   M       72    33.2   11.5   1.4    34.6           31.6          # By selecting just some statistics and ad-hoc labels lyt <- basic_table() %>%   split_rows_by(var = \"ARM\", label_pos = \"topleft\") %>%   split_rows_by(     var = \"SEX\",     label_pos = \"topleft\",     child_labels = \"hidden\",     split_fun = drop_split_levels   ) %>%   analyze_vars_in_cols(     vars = \"AGE\",     .stats = c(\"n\", \"cv\", \"geom_mean\"),     .labels = c(       n = \"aN\",       cv = \"aCV\",       geom_mean = \"aGeomMean\"     )   ) result <- build_table(lyt = lyt, df = adpp) result #> ARM                                     #>   SEX            aN    aCV    aGeomMean #> ——————————————————————————————————————— #> A: Drug X                               #> B: Placebo                              #> C: Combination                          #>   F              288   17.6     35.5    #>   M              234   23.4     35.3     # Changing row labels lyt <- basic_table() %>%   analyze_vars_in_cols(     vars = \"AGE\",     row_labels = \"some custom label\"   ) result <- build_table(lyt, df = adpp) result #>                      n    Mean   SD    SE    CV (%)   CV % Geometric Mean #> ————————————————————————————————————————————————————————————————————————— #> some custom label   522   36.1   7.4   0.3    20.4           20.6          # Pharmacokinetic parameters lyt <- basic_table() %>%   split_rows_by(     var = \"TLG_DISPLAY\",     split_label = \"PK Parameter\",     label_pos = \"topleft\",     child_labels = \"hidden\"   ) %>%   analyze_vars_in_cols(     vars = \"AVAL\"   ) result <- build_table(lyt, df = adpp) result #> PK Parameter   n    Mean     SD    SE    CV (%)   CV % Geometric Mean #> ————————————————————————————————————————————————————————————————————— #> Cmax           58   29.7    5.6    0.7    19.0           19.3         #> AUCinf obs     58   207.5   34.9   4.6    16.8           17.3         #> CL obs         58    5.1    1.0    0.1    20.6           22.7         #> Ae             58    1.5    0.3    0.0    21.3           24.1         #> Fe             58   15.7    3.6    0.5    22.7           24.0         #> CLR            58    0.0    0.0    0.0    19.9           22.2         #> Rmax           58    9.6    2.0    0.3    21.1           21.6         #> Tonset         58    3.0    0.7    0.1    22.4           23.3         #> RENALCLD       58    0.0    0.0    0.0    19.0           19.4          # Multiple calls (summarize label and analyze underneath) lyt <- basic_table() %>%   split_rows_by(     var = \"TLG_DISPLAY\",     split_label = \"PK Parameter\",     label_pos = \"topleft\"   ) %>%   analyze_vars_in_cols(     vars = \"AVAL\",     do_summarize_row_groups = TRUE # does a summarize level   ) %>%   split_rows_by(\"SEX\",     child_labels = \"hidden\",     label_pos = \"topleft\"   ) %>%   analyze_vars_in_cols(     vars = \"AVAL\",     split_col_vars = FALSE # avoids re-splitting the columns   ) result <- build_table(lyt, df = adpp) result #> PK Parameter                                                          #>   SEX          n    Mean     SD    SE    CV (%)   CV % Geometric Mean #> ————————————————————————————————————————————————————————————————————— #> Cmax           58   29.7    5.6    0.7    19.0           19.3         #>   F            32   30.1    6.1    1.1    20.4           21.0         #>   M            26   29.2    5.0    1.0    17.2           17.2         #> AUCinf obs     58   207.5   34.9   4.6    16.8           17.3         #>   F            32   209.5   43.3   7.7    20.7           21.6         #>   M            26   205.0   20.9   4.1    10.2           10.4         #> CL obs         58    5.1    1.0    0.1    20.6           22.7         #>   F            32    5.1    1.1    0.2    20.8           23.2         #>   M            26    5.1    1.1    0.2    20.7           22.5         #> Ae             58    1.5    0.3    0.0    21.3           24.1         #>   F            32    1.5    0.3    0.1    19.3           20.8         #>   M            26    1.5    0.4    0.1    23.9           27.9         #> Fe             58   15.7    3.6    0.5    22.7           24.0         #>   F            32   16.3    3.4    0.6    20.9           22.3         #>   M            26   15.0    3.7    0.7    24.7           25.6         #> CLR            58    0.0    0.0    0.0    19.9           22.2         #>   F            32    0.0    0.0    0.0    20.5           24.8         #>   M            26    0.0    0.0    0.0    19.5           18.9         #> Rmax           58    9.6    2.0    0.3    21.1           21.6         #>   F            32    9.6    2.2    0.4    22.4           23.5         #>   M            26    9.6    1.9    0.4    19.7           19.5         #> Tonset         58    3.0    0.7    0.1    22.4           23.3         #>   F            32    3.0    0.7    0.1    24.7           25.9         #>   M            26    3.0    0.6    0.1    19.8           20.0         #> RENALCLD       58    0.0    0.0    0.0    19.0           19.4         #>   F            32    0.0    0.0    0.0    19.6           20.4         #>   M            26    0.0    0.0    0.0    18.0           17.6"},{"path":"https://insightsengineering.github.io/tern/reference/append_varlabels.html","id":null,"dir":"Reference","previous_headings":"","what":"Add variable labels to top left corner in table — append_varlabels","title":"Add variable labels to top left corner in table — append_varlabels","text":"Helper layout-creating function append variable labels given variables vector given dataset top left corner. variable label found variable name used instead. Multiple variable labels concatenated slashes.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/append_varlabels.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Add variable labels to top left corner in table — append_varlabels","text":"","code":"append_varlabels(lyt, df, vars, indent = 0L)"},{"path":"https://insightsengineering.github.io/tern/reference/append_varlabels.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Add variable labels to top left corner in table — append_varlabels","text":"lyt (PreDataTableLayouts) layout analyses added . df (data.frame) data set containing analysis variables. vars (character) variable names labels looked df. indent (integer(1)) non-negative number nested indent space, default 0L means indent. 1L means two spaces indent, 2L means four spaces indent .","code":""},{"path":"https://insightsengineering.github.io/tern/reference/append_varlabels.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Add variable labels to top left corner in table — append_varlabels","text":"modified layout new variable label(s) added top-left material.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/append_varlabels.html","id":"note","dir":"Reference","previous_headings":"","what":"Note","title":"Add variable labels to top left corner in table — append_varlabels","text":"optimal implementation course, since using data set layout creation. mature rtables implementation also improved necessary anymore.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/append_varlabels.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Add variable labels to top left corner in table — append_varlabels","text":"","code":"lyt <- basic_table() %>%   split_cols_by(\"ARM\") %>%   add_colcounts() %>%   split_rows_by(\"SEX\") %>%   append_varlabels(DM, \"SEX\") %>%   analyze(\"AGE\", afun = mean) %>%   append_varlabels(DM, \"AGE\", indent = 1) build_table(lyt, DM) #> SEX                   A: Drug X          B: Placebo       C: Combination  #>   Age                  (N=121)            (N=106)            (N=129)      #> ————————————————————————————————————————————————————————————————————————— #> F                                                                         #>   mean             33.7142857142857   33.8392857142857   34.8852459016393 #> M                                                                         #>   mean             36.5490196078431         32.1         34.2794117647059 #> U                                                                         #>   mean                    NA                 NA                 NA        #> UNDIFFERENTIATED                                                          #>   mean                    NA                 NA                 NA         lyt <- basic_table() %>%   split_cols_by(\"ARM\") %>%   split_rows_by(\"SEX\") %>%   analyze(\"AGE\", afun = mean) %>%   append_varlabels(DM, c(\"SEX\", \"AGE\")) build_table(lyt, DM) #> SEX / Age             A: Drug X          B: Placebo       C: Combination  #> ————————————————————————————————————————————————————————————————————————— #> F                                                                         #>   mean             33.7142857142857   33.8392857142857   34.8852459016393 #> M                                                                         #>   mean             36.5490196078431         32.1         34.2794117647059 #> U                                                                         #>   mean                    NA                 NA                 NA        #> UNDIFFERENTIATED                                                          #>   mean                    NA                 NA                 NA"},{"path":"https://insightsengineering.github.io/tern/reference/apply_auto_formatting.html","id":null,"dir":"Reference","previous_headings":"","what":"Apply automatic formatting — apply_auto_formatting","title":"Apply automatic formatting — apply_auto_formatting","text":"Checks listed formats .formats \"auto\", replaces \"auto\" correct implementation format_auto given statistics, data, variable.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/apply_auto_formatting.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Apply automatic formatting — apply_auto_formatting","text":"","code":"apply_auto_formatting(.formats, x_stats, .df_row, .var)"},{"path":"https://insightsengineering.github.io/tern/reference/apply_auto_formatting.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Apply automatic formatting — apply_auto_formatting","text":".formats (named character list) formats statistics. See Details analyze_vars information \"auto\" setting. x_stats (named list) named list statistics element corresponds element .formats, matching names. .df_row (data.frame) data frame across columns given row split. .var (string) single variable name passed rtables requested statistics function.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/argument_convention.html","id":null,"dir":"Reference","previous_headings":"","what":"Standard arguments — argument_convention","title":"Standard arguments — argument_convention","text":"documentation function lists arguments tern used repeatedly express analysis.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/argument_convention.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Standard arguments — argument_convention","text":"... additional arguments lower level functions. .aligns (character NULL) alignment table contents (including labels). NULL, \"center\" applied. See formatters::list_valid_aligns() list currently supported alignments. .all_col_counts (integer) vector value represents global count column. Values taken alt_counts_df specified (see rtables::build_table()). .df_row (data.frame) data frame across columns given row split. .formats (named character list) formats statistics. See Details analyze_vars information \"auto\" setting. .in_ref_col (flag)TRUE working reference level, FALSE otherwise. .indent_mods (named integer) indent modifiers labels. Defaults 0, corresponds unmodified default behavior. Can negative. .labels (named character) labels statistics (without indent). .N_col (integer(1)) column-wise N (column count) full column analyzed typically passed rtables. .N_row (integer(1)) row-wise N (row group count) group observations analyzed (.e. column-based subsetting) typically passed rtables. .ref_group (data.frame vector) data corresponding reference group. .spl_context (data.frame) gives information ancestor split states passed rtables. .stats (character) statistics select table. .var (string) single variable name passed rtables requested statistics function. add_total_level (flag) adds \"total\" level others includes levels constitute split. custom label can set level via custom_label argument. col_by (factor) defining column groups. conf_level (proportion) confidence level interval. data (data.frame) dataset containing variables summarize. denom (string) choice denominator proportion. Options : n: number values row column intersection. N_row: total number values row across columns. N_col: total number values column across rows. df (data.frame) data set containing analysis variables. groups_lists (named list list) optionally contains subgroups variable list, specifies new group levels via names levels belong character vectors elements list. id (string) subject variable name. is_event (flag)TRUE event, FALSE time event censored. label_all (string) label total population analysis. labelstr (string) label level parent split currently summarized (must present second argument Content Row Functions). See rtables::summarize_row_groups() information. lyt (PreDataTableLayouts) layout analyses added . method (string NULL) specifies test used calculate p-value difference two proportions. options, see test_proportion_diff(). Default NULL test performed. na.rm (flag) whether NA values removed x prior analysis. na_str (string) string used replace NA empty values output. nested (flag) whether layout instruction applied within existing layout structure _if possible (TRUE, default) new top-level element (FALSE). Ignored nest split. underneath analyses, allowed. prune_zero_rows (flag) whether prune zero rows. riskdiff (flag) whether risk difference column present. set TRUE, add_riskdiff() must used split_fun prior column split table layout, specifying columns compared. See stat_propdiff_ci() details risk difference calculation. rsp (logical) vector indicating whether subject responder . show_labels (string) label visibility: one \"default\", \"visible\" \"hidden\". section_div (string) string repeated section divider group defined split instruction, NA_character_ (default) section divider. table_names (character) can customized case vars analyzed multiple times, avoid warnings rtables. tte (numeric) vector time--event duration values. var_labels (character) variable labels. variables (named list string) list additional analysis variables. vars (character) variable names primary analysis variable iterated . var (string) single variable name primary analysis variable. x (numeric) vector numbers want analyze. xlim (numeric(2)) vector containing lower upper limits x-axis, respectively. NULL (default), default scale range used. ylim (numeric(2)) vector containing lower upper limits y-axis, respectively. NULL (default), default scale range used.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/argument_convention.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Standard arguments — argument_convention","text":"Although function just returns NULL two uses, tern users provides documentation arguments commonly consistently used framework. developer adds single reference point import roxygen argument description : @inheritParams argument_convention","code":""},{"path":"https://insightsengineering.github.io/tern/reference/arrange_grobs.html","id":null,"dir":"Reference","previous_headings":"","what":"Arrange multiple grobs — arrange_grobs","title":"Arrange multiple grobs — arrange_grobs","text":"Arrange grobs new grob n * m (rows * cols) layout.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/arrange_grobs.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Arrange multiple grobs — arrange_grobs","text":"","code":"arrange_grobs(   ...,   grobs = list(...),   ncol = NULL,   nrow = NULL,   padding_ht = grid::unit(2, \"line\"),   padding_wt = grid::unit(2, \"line\"),   vp = NULL,   gp = NULL,   name = NULL )"},{"path":"https://insightsengineering.github.io/tern/reference/arrange_grobs.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Arrange multiple grobs — arrange_grobs","text":"... grobs. grobs (list grob) list grobs. ncol (integer(1)) number columns layout. nrow (integer(1)) number rows layout. padding_ht (grid::unit) unit length 1, vertical space grob. padding_wt (grid::unit) unit length 1, horizontal space grob. vp (viewport NULL) viewport() object (NULL). gp (gpar) gpar() object. name (string) character identifier grob.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/arrange_grobs.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Arrange multiple grobs — arrange_grobs","text":"grob.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/arrange_grobs.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Arrange multiple grobs — arrange_grobs","text":"","code":"library(grid)  # \\donttest{ num <- lapply(1:9, textGrob) grid::grid.newpage() grid.draw(arrange_grobs(grobs = num, ncol = 2)) #> Warning: `arrange_grobs()` was deprecated in tern 0.9.4. #> ℹ `tern` plotting functions no longer generate `grob` objects.  showViewport()   g1 <- circleGrob(gp = gpar(col = \"blue\")) g2 <- circleGrob(gp = gpar(col = \"red\")) g3 <- textGrob(\"TEST TEXT\") grid::grid.newpage() grid.draw(arrange_grobs(g1, g2, g3, nrow = 2))  showViewport()   grid::grid.newpage() grid.draw(arrange_grobs(g1, g2, g3, ncol = 3))   grid::grid.newpage() grid::pushViewport(grid::viewport(layout = grid::grid.layout(1, 2))) vp1 <- grid::viewport(layout.pos.row = 1, layout.pos.col = 2) grid.draw(arrange_grobs(g1, g2, g3, ncol = 2, vp = vp1))  showViewport()  # }"},{"path":"https://insightsengineering.github.io/tern/reference/as.rtable.html","id":null,"dir":"Reference","previous_headings":"","what":"Convert to rtable — as.rtable","title":"Convert to rtable — as.rtable","text":"new generic function convert objects rtable tables.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/as.rtable.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Convert to rtable — as.rtable","text":"","code":"as.rtable(x, ...)  # S3 method for class 'data.frame' as.rtable(x, format = \"xx.xx\", ...)"},{"path":"https://insightsengineering.github.io/tern/reference/as.rtable.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Convert to rtable — as.rtable","text":"x (data.frame) object converted rtable. ... additional arguments methods. format (string function) format used columns.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/as.rtable.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Convert to rtable — as.rtable","text":"rtables table object. Note concrete class depend method used.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/as.rtable.html","id":"methods-by-class-","dir":"Reference","previous_headings":"","what":"Methods (by class)","title":"Convert to rtable — as.rtable","text":".rtable(data.frame): Method converting data.frame contains numeric columns rtable.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/as.rtable.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Convert to rtable — as.rtable","text":"","code":"x <- data.frame(   a = 1:10,   b = rnorm(10) ) as.rtable(x) #>        a       b   #> —————————————————— #> 1    1.00    0.07  #> 2    2.00    -0.64 #> 3    3.00    -0.05 #> 4    4.00    -0.25 #> 5    5.00    0.44  #> 6    6.00    2.76  #> 7    7.00    0.05  #> 8    8.00    0.58  #> 9    9.00    0.12  #> 10   10.00   -1.91"},{"path":"https://insightsengineering.github.io/tern/reference/as_factor_keep_attributes.html","id":null,"dir":"Reference","previous_headings":"","what":"Conversion of a vector to a factor — as_factor_keep_attributes","title":"Conversion of a vector to a factor — as_factor_keep_attributes","text":"Converts x factor keeps attributes. Warns appropriately user can decide whether prefer converting factor manually (e.g. full control factor levels).","code":""},{"path":"https://insightsengineering.github.io/tern/reference/as_factor_keep_attributes.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Conversion of a vector to a factor — as_factor_keep_attributes","text":"","code":"as_factor_keep_attributes(   x,   x_name = deparse(substitute(x)),   na_level = \"<Missing>\",   verbose = TRUE )"},{"path":"https://insightsengineering.github.io/tern/reference/as_factor_keep_attributes.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Conversion of a vector to a factor — as_factor_keep_attributes","text":"x (vector) object convert. x_name (string) name x. na_level (string) explicit missing level used converting character vector. verbose (flag) defaults TRUE. prints warnings messages.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/as_factor_keep_attributes.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Conversion of a vector to a factor — as_factor_keep_attributes","text":"factor attributes (except class) x. modify x already factor.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/assertions.html","id":null,"dir":"Reference","previous_headings":"","what":"Additional assertions to use with checkmate — assertions","title":"Additional assertions to use with checkmate — assertions","text":"Additional assertion functions can used together checkmate package.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/assertions.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Additional assertions to use with checkmate — assertions","text":"","code":"assert_list_of_variables(x, .var.name = checkmate::vname(x), add = NULL)  assert_df_with_variables(   df,   variables,   na_level = NULL,   .var.name = checkmate::vname(df),   add = NULL )  assert_valid_factor(   x,   min.levels = 1,   max.levels = NULL,   null.ok = TRUE,   any.missing = TRUE,   n.levels = NULL,   len = NULL,   .var.name = checkmate::vname(x),   add = NULL )  assert_df_with_factors(   df,   variables,   min.levels = 1,   max.levels = NULL,   any.missing = TRUE,   na_level = NULL,   .var.name = checkmate::vname(df),   add = NULL )  assert_proportion_value(x, include_boundaries = FALSE)"},{"path":"https://insightsengineering.github.io/tern/reference/assertions.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Additional assertions to use with checkmate — assertions","text":"x () object test. .var.name [character(1)] Name checked object print assertions. Defaults heuristic implemented vname. add [AssertCollection] Collection store assertion messages. See AssertCollection. df (data.frame) data set test. variables (named list character) list variables test. na_level (string) string using represent NA missing data. NA values please consider using directly .na() similar approaches. min.levels [integer(1)] Minimum number factor levels. Default NULL (check). max.levels [integer(1)] Maximum number factor levels. Default NULL (check). null.ok [logical(1)] set TRUE, x may also NULL. case type check x performed, additional checks disabled. .missing [logical(1)] vectors missing values allowed? Default TRUE. n.levels [integer(1)] Exact number factor levels. Default NULL (check). len [integer(1)] Exact expected length x. include_boundaries (flag) whether include boundaries testing proportions.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/assertions.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Additional assertions to use with checkmate — assertions","text":"Nothing assertion passes, otherwise prints error message.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/assertions.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Additional assertions to use with checkmate — assertions","text":"assert_list_of_variables(): Checks whether x valid list variable names. NULL elements list x dropped Filter(Negate(.null), x). assert_df_with_variables(): Check whether df data frame analysis variables. Please notice produces error variables present data.frame opposite required. assert_valid_factor(): Check whether x valid factor (.e. levels empty string levels). Note NULL NA elements allowed. assert_df_with_factors(): Check whether df data frame analysis variables factors. Note creation NA direct call factor() trim NA levels vector list . assert_proportion_value(): Check whether x proportion: number 0 1.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/bins_percent_labels.html","id":null,"dir":"Reference","previous_headings":"","what":"Labels for bins in percent — bins_percent_labels","title":"Labels for bins in percent — bins_percent_labels","text":"creates labels quantile based bins percent. assumes right-closed intervals produced cut_quantile_bins().","code":""},{"path":"https://insightsengineering.github.io/tern/reference/bins_percent_labels.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Labels for bins in percent — bins_percent_labels","text":"","code":"bins_percent_labels(probs, digits = 0)"},{"path":"https://insightsengineering.github.io/tern/reference/bins_percent_labels.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Labels for bins in percent — bins_percent_labels","text":"probs (numeric) probabilities identifying quantiles. sorted vector unique proportion values, .e. 0 1, boundaries 0 1 must included. digits (integer(1)) number decimal places round percent numbers.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/bins_percent_labels.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Labels for bins in percent — bins_percent_labels","text":"character vector labels format [0%,20%], (20%,50%], etc.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/c_label_n.html","id":null,"dir":"Reference","previous_headings":"","what":"Content row function to add row total to labels — c_label_n","title":"Content row function to add row total to labels — c_label_n","text":"takes label latest row split level adds row total df parentheses. function differs c_label_n_alt() taking row counts df rather alt_counts_df, used add_rowcounts() alt_counts set FALSE.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/c_label_n.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Content row function to add row total to labels — c_label_n","text":"","code":"c_label_n(df, labelstr, .N_row)"},{"path":"https://insightsengineering.github.io/tern/reference/c_label_n.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Content row function to add row total to labels — c_label_n","text":"df (data.frame) data set containing analysis variables. labelstr (string) label level parent split currently summarized (must present second argument Content Row Functions). See rtables::summarize_row_groups() information. .N_row (integer(1)) row-wise N (row group count) group observations analyzed (.e. column-based subsetting) typically passed rtables.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/c_label_n.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Content row function to add row total to labels — c_label_n","text":"list formatted rtables::CellValue() row count value correct label.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/c_label_n.html","id":"note","dir":"Reference","previous_headings":"","what":"Note","title":"Content row function to add row total to labels — c_label_n","text":"important use df rather .N_row implementation, former already split columns refer first column data .","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/reference/c_label_n_alt.html","id":null,"dir":"Reference","previous_headings":"","what":"Content row function to add alt_counts_df row total to labels — c_label_n_alt","title":"Content row function to add alt_counts_df row total to labels — c_label_n_alt","text":"takes label latest row split level adds row total alt_counts_df parentheses. function differs c_label_n() taking row counts alt_counts_df rather df, used add_rowcounts() alt_counts set TRUE.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/c_label_n_alt.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Content row function to add alt_counts_df row total to labels — c_label_n_alt","text":"","code":"c_label_n_alt(df, labelstr, .alt_df_row)"},{"path":"https://insightsengineering.github.io/tern/reference/c_label_n_alt.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Content row function to add alt_counts_df row total to labels — c_label_n_alt","text":"df (data.frame) data set containing analysis variables. labelstr (string) label level parent split currently summarized (must present second argument Content Row Functions). See rtables::summarize_row_groups() information.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/c_label_n_alt.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Content row function to add alt_counts_df row total to labels — c_label_n_alt","text":"list formatted rtables::CellValue() row count value correct label.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/reference/cfun_by_flag.html","id":null,"dir":"Reference","previous_headings":"","what":"Constructor for content functions given a data frame with flag input — cfun_by_flag","title":"Constructor for content functions given a data frame with flag input — cfun_by_flag","text":"can useful tabulating model results.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/cfun_by_flag.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Constructor for content functions given a data frame with flag input — cfun_by_flag","text":"","code":"cfun_by_flag(analysis_var, flag_var, format = \"xx\", .indent_mods = NULL)"},{"path":"https://insightsengineering.github.io/tern/reference/cfun_by_flag.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Constructor for content functions given a data frame with flag input — cfun_by_flag","text":"analysis_var (string) variable name column containing values returned content function. flag_var (string) variable name logical column identifying row returned. format (string)rtables format use.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/cfun_by_flag.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Constructor for content functions given a data frame with flag input — cfun_by_flag","text":"content function gives df$analysis_var row identified .df_row$flag given format.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/check_diff_prop_ci.html","id":null,"dir":"Reference","previous_headings":"","what":"Check proportion difference arguments — check_diff_prop_ci","title":"Check proportion difference arguments — check_diff_prop_ci","text":"Verifies /convert arguments valid values used estimation difference responder proportions.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/check_diff_prop_ci.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Check proportion difference arguments — check_diff_prop_ci","text":"","code":"check_diff_prop_ci(rsp, grp, strata = NULL, conf_level, correct = NULL)"},{"path":"https://insightsengineering.github.io/tern/reference/check_diff_prop_ci.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Check proportion difference arguments — check_diff_prop_ci","text":"rsp (logical) vector indicating whether subject responder . grp (factor) vector assigning observations one two groups (e.g. reference treatment group). strata (factor) variable one level per stratum length rsp. conf_level (proportion) confidence level interval. correct (flag) whether include continuity correction. information, see stats::prop.test().","code":""},{"path":"https://insightsengineering.github.io/tern/reference/check_same_n.html","id":null,"dir":"Reference","previous_headings":"","what":"Check element dimension — check_same_n","title":"Check element dimension — check_same_n","text":"Checks elements ... dimension.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/check_same_n.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Check element dimension — check_same_n","text":"","code":"check_same_n(..., omit_null = TRUE)"},{"path":"https://insightsengineering.github.io/tern/reference/check_same_n.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Check element dimension — check_same_n","text":"... (data.frame vector) data frames vectors. omit_null (flag) whether NULL elements ... omitted check.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/check_same_n.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Check element dimension — check_same_n","text":"logical value.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/combination_function.html","id":null,"dir":"Reference","previous_headings":"","what":"Class for CombinationFunction — combination_function","title":"Class for CombinationFunction — combination_function","text":"CombinationFunction S4 class extends standard functions. special functions can combined negated logical operators.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/combination_function.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Class for CombinationFunction — combination_function","text":"","code":"# S4 method for class 'CombinationFunction,CombinationFunction' e1 & e2  # S4 method for class 'CombinationFunction,CombinationFunction' e1 | e2  # S4 method for class 'CombinationFunction' !x"},{"path":"https://insightsengineering.github.io/tern/reference/combination_function.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Class for CombinationFunction — combination_function","text":"e1 (CombinationFunction) left hand side logical operator. e2 (CombinationFunction) right hand side logical operator. x (CombinationFunction) function negated.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/combination_function.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Class for CombinationFunction — combination_function","text":"logical value indicating whether left hand side equation equals right hand side.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/combination_function.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Class for CombinationFunction — combination_function","text":"e1 & e2: Logical \"\" combination CombinationFunction functions. resulting object class, evaluates two argument functions. result \"\" two individual results. e1 | e2: Logical \"\" combination CombinationFunction functions. resulting object class, evaluates two argument functions. result \"\" two individual results. `!`(CombinationFunction): Logical negation CombinationFunction functions. resulting object class, evaluates original function. result opposite results.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/combination_function.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Class for CombinationFunction — combination_function","text":"","code":"higher <- function(a) {   force(a)   CombinationFunction(     function(x) {       x > a     }   ) }  lower <- function(b) {   force(b)   CombinationFunction(     function(x) {       x < b     }   ) }  c1 <- higher(5) c2 <- lower(10) c3 <- higher(5) & lower(10) c3(7) #> [1] TRUE"},{"path":"https://insightsengineering.github.io/tern/reference/combine_counts.html","id":null,"dir":"Reference","previous_headings":"","what":"Combine counts — combine_counts","title":"Combine counts — combine_counts","text":"Simplifies estimation column counts, especially group combination required.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/combine_counts.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Combine counts — combine_counts","text":"","code":"combine_counts(fct, groups_list = NULL)"},{"path":"https://insightsengineering.github.io/tern/reference/combine_counts.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Combine counts — combine_counts","text":"fct (factor) variable levels needs grouped. groups_list (named list character) specifies new group levels via names levels belong character vectors elements list.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/combine_counts.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Combine counts — combine_counts","text":"vector column counts.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/reference/combine_counts.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Combine counts — combine_counts","text":"","code":"ref <- c(\"A: Drug X\", \"B: Placebo\") groups <- combine_groups(fct = DM$ARM, ref = ref)  col_counts <- combine_counts(   fct = DM$ARM,   groups_list = groups )  basic_table() %>%   split_cols_by_groups(\"ARM\", groups) %>%   add_colcounts() %>%   analyze_vars(\"AGE\") %>%   build_table(DM, col_counts = col_counts) #>             A: Drug X/B: Placebo   C: Combination #>                   (N=227)             (N=129)     #> ————————————————————————————————————————————————— #> n                   227                 129       #> Mean (SD)        34.0 (7.2)          34.6 (6.5)   #> Median              33.0                33.0      #> Min - Max       20.0 - 60.0         22.0 - 53.0    ref <- \"A: Drug X\" groups <- combine_groups(fct = DM$ARM, ref = ref) col_counts <- combine_counts(   fct = DM$ARM,   groups_list = groups )  basic_table() %>%   split_cols_by_groups(\"ARM\", groups) %>%   add_colcounts() %>%   analyze_vars(\"AGE\") %>%   build_table(DM, col_counts = col_counts) #>              A: Drug X    B: Placebo/C: Combination #>               (N=121)              (N=235)          #> ——————————————————————————————————————————————————— #> n               121                  235            #> Mean (SD)   34.9 (7.8)           33.9 (6.5)         #> Median         33.0                 33.0            #> Min - Max   20.0 - 60.0          21.0 - 55.0"},{"path":"https://insightsengineering.github.io/tern/reference/combine_groups.html","id":null,"dir":"Reference","previous_headings":"","what":"Reference and treatment group combination — combine_groups","title":"Reference and treatment group combination — combine_groups","text":"Facilitate re-combination groups divided reference treatment groups; helps arranging groups columns rtables framework teal modules.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/combine_groups.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Reference and treatment group combination — combine_groups","text":"","code":"combine_groups(fct, ref = NULL, collapse = \"/\")"},{"path":"https://insightsengineering.github.io/tern/reference/combine_groups.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Reference and treatment group combination — combine_groups","text":"fct (factor) variable levels needs grouped. ref (character) reference level(s). collapse (string) character string separate fct ref.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/combine_groups.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Reference and treatment group combination — combine_groups","text":"list first item ref (reference) second item trt (treatment).","code":""},{"path":"https://insightsengineering.github.io/tern/reference/combine_groups.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Reference and treatment group combination — combine_groups","text":"","code":"groups <- combine_groups(   fct = DM$ARM,   ref = c(\"B: Placebo\") )  basic_table() %>%   split_cols_by_groups(\"ARM\", groups) %>%   add_colcounts() %>%   analyze_vars(\"AGE\") %>%   build_table(DM) #>             B: Placebo    A: Drug X/C: Combination #>               (N=106)             (N=250)          #> —————————————————————————————————————————————————— #> n               106                 250            #> Mean (SD)   33.0 (6.3)           34.7 (7.1)        #> Median         32.0                 33.0           #> Min - Max   21.0 - 55.0         20.0 - 60.0"},{"path":"https://insightsengineering.github.io/tern/reference/combine_levels.html","id":null,"dir":"Reference","previous_headings":"","what":"Combine factor levels — combine_levels","title":"Combine factor levels — combine_levels","text":"Combine specified old factor Levels single new level.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/combine_levels.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Combine factor levels — combine_levels","text":"","code":"combine_levels(x, levels, new_level = paste(levels, collapse = \"/\"))"},{"path":"https://insightsengineering.github.io/tern/reference/combine_levels.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Combine factor levels — combine_levels","text":"x (factor) factor variable. levels (character) level names combined. new_level (string) name new level.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/combine_levels.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Combine factor levels — combine_levels","text":"factor new levels.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/combine_levels.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Combine factor levels — combine_levels","text":"","code":"x <- factor(letters[1:5], levels = letters[5:1]) combine_levels(x, levels = c(\"a\", \"b\")) #> [1] a/b a/b c   d   e   #> Levels: e d c a/b  combine_levels(x, c(\"e\", \"b\")) #> [1] a   e/b c   d   e/b #> Levels: e/b d c a"},{"path":"https://insightsengineering.github.io/tern/reference/combine_vectors.html","id":null,"dir":"Reference","previous_headings":"","what":"Element-wise combination of two vectors — combine_vectors","title":"Element-wise combination of two vectors — combine_vectors","text":"Element-wise combination two vectors","code":""},{"path":"https://insightsengineering.github.io/tern/reference/combine_vectors.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Element-wise combination of two vectors — combine_vectors","text":"","code":"combine_vectors(x, y)"},{"path":"https://insightsengineering.github.io/tern/reference/combine_vectors.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Element-wise combination of two vectors — combine_vectors","text":"x (vector) first vector combine. y (vector) second vector combine.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/combine_vectors.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Element-wise combination of two vectors — combine_vectors","text":"list element combines corresponding elements x y.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/combine_vectors.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Element-wise combination of two vectors — combine_vectors","text":"","code":"combine_vectors(1:3, 4:6) #> [[1]] #> [1] 1 4 #>  #> [[2]] #> [1] 2 5 #>  #> [[3]] #> [1] 3 6 #>"},{"path":"https://insightsengineering.github.io/tern/reference/compare_variables.html","id":null,"dir":"Reference","previous_headings":"","what":"Compare variables between groups — compare_variables","title":"Compare variables between groups — compare_variables","text":"analyze function compare_vars() creates layout element summarize compare one variables, using S3 generic function s_summary() calculate list summary statistics. list available statistics numeric variables can viewed running get_stats(\"analyze_vars_numeric\", add_pval = TRUE) non-numeric variables running get_stats(\"analyze_vars_counts\", add_pval = TRUE). Use .stats parameter specify statistics include output summary table. Prior using function table layout must use rtables::split_cols_by() create column split variable used comparisons, specify reference group via ref_group parameter. Comparisons can performed group (column) specified reference group including p-value statistic.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/compare_variables.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Compare variables between groups — compare_variables","text":"","code":"compare_vars(   lyt,   vars,   var_labels = vars,   na_str = default_na_str(),   nested = TRUE,   ...,   na.rm = TRUE,   show_labels = \"default\",   table_names = vars,   section_div = NA_character_,   .stats = c(\"n\", \"mean_sd\", \"count_fraction\", \"pval\"),   .formats = NULL,   .labels = NULL,   .indent_mods = NULL )  s_compare(x, .ref_group, .in_ref_col, ...)  # S3 method for class 'numeric' s_compare(x, .ref_group, .in_ref_col, ...)  # S3 method for class 'factor' s_compare(x, .ref_group, .in_ref_col, denom = \"n\", na.rm = TRUE, ...)  # S3 method for class 'character' s_compare(   x,   .ref_group,   .in_ref_col,   denom = \"n\",   na.rm = TRUE,   .var,   verbose = TRUE,   ... )  # S3 method for class 'logical' s_compare(x, .ref_group, .in_ref_col, na.rm = TRUE, denom = \"n\", ...)"},{"path":"https://insightsengineering.github.io/tern/reference/compare_variables.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Compare variables between groups — compare_variables","text":"lyt (PreDataTableLayouts) layout analyses added . vars (character) variable names primary analysis variable iterated . var_labels (character) variable labels. na_str (string) string used replace NA empty values output. nested (flag) whether layout instruction applied within existing layout structure _if possible (TRUE, default) new top-level element (FALSE). Ignored nest split. underneath analyses, allowed. ... arguments passed s_compare(). na.rm (flag) whether NA values removed x prior analysis. show_labels (string) label visibility: one \"default\", \"visible\" \"hidden\". table_names (character) can customized case vars analyzed multiple times, avoid warnings rtables. section_div (string) string repeated section divider group defined split instruction, NA_character_ (default) section divider. .stats (character) statistics select table. Options numeric variables : 'n', 'sum', 'mean', 'sd', 'se', 'mean_sd', 'mean_se', 'mean_ci', 'mean_sei', 'mean_sdi', 'mean_pval', 'median', 'mad', 'median_ci', 'quantiles', 'iqr', 'range', 'min', 'max', 'median_range', 'cv', 'geom_mean', 'geom_mean_ci', 'geom_cv', 'median_ci_3d', 'mean_ci_3d', 'geom_mean_ci_3d', 'pval' Options non-numeric variables : 'n', 'count', 'count_fraction', 'count_fraction_fixed_dp', 'fraction', 'n_blq', 'pval_counts' .formats (named character list) formats statistics. See Details analyze_vars information \"auto\" setting. .labels (named character) labels statistics (without indent). .indent_mods (named integer) indent modifiers labels. element vector name-value pair name corresponding statistic specified .stats value indentation statistic's row label. x (numeric) vector numbers want analyze. .ref_group (data.frame vector) data corresponding reference group. .in_ref_col (flag)TRUE working reference level, FALSE otherwise. denom (string) choice denominator factor proportions, can n (number values row column intersection). .var (string) single variable name passed rtables requested statistics function. verbose (flag) whether warnings messages printed. Mainly used print information factor casting. Defaults TRUE.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/compare_variables.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Compare variables between groups — compare_variables","text":"compare_vars() returns layout object suitable passing layouting functions, rtables::build_table(). Adding function rtable layout add formatted rows containing statistics s_compare() table layout. s_compare() returns output s_summary() comparisons versus reference group form p-values.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/compare_variables.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Compare variables between groups — compare_variables","text":"compare_vars(): Layout-creating function can take statistics function arguments additional format arguments. function wrapper rtables::analyze(). s_compare(): S3 generic function produce comparison summary. s_compare(numeric): Method numeric class. uses standard t-test calculate p-value. s_compare(factor): Method factor class. uses chi-squared test calculate p-value. s_compare(character): Method character class. makes automatic conversion factor (warning) forwards method factors. s_compare(logical): Method logical class. chi-squared test used. missing values removed, counted FALSE.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/compare_variables.html","id":"note","dir":"Reference","previous_headings":"","what":"Note","title":"Compare variables between groups — compare_variables","text":"factor variables, denom factor proportions can n since purpose compare proportions columns, therefore row-based proportion make sense. Proportion based N_col difficult since use counts chi-squared test statistic, therefore missing values accounted explicit factor levels. factor variables contain NA, NA values excluded default. include NA values set na.rm = FALSE missing values displayed NA level. Alternatively, explicit factor level can defined NA values pre-processing via df_explicit_na() - default na_level (\"<Missing>\") also excluded na.rm set TRUE. character variables, automatic conversion factor guarantee table generated correctly. particular sparse tables likely can fail. Therefore always better manually convert character variables factors pre-processing. compare_vars(), column split must define reference group via ref_group comparison well defined.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/reference/compare_variables.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Compare variables between groups — compare_variables","text":"","code":"# `compare_vars()` in `rtables` pipelines  ## Default output within a `rtables` pipeline. lyt <- basic_table() %>%   split_cols_by(\"ARMCD\", ref_group = \"ARM B\") %>%   compare_vars(c(\"AGE\", \"SEX\")) build_table(lyt, tern_ex_adsl) #>                                  ARM A        ARM B        ARM C    #> ——————————————————————————————————————————————————————————————————— #> AGE                                                                 #>   n                                69           73           58     #>   Mean (SD)                    34.1 (6.8)   35.8 (7.1)   36.1 (7.4) #>   p-value (t-test)               0.1446                    0.8212   #> SEX                                                                 #>   n                                69           73           58     #>   F                            38 (55.1%)   40 (54.8%)   32 (55.2%) #>   M                            31 (44.9%)   33 (45.2%)   26 (44.8%) #>   p-value (chi-squared test)     1.0000                    1.0000    ## Select and format statistics output. lyt <- basic_table() %>%   split_cols_by(\"ARMCD\", ref_group = \"ARM C\") %>%   compare_vars(     vars = \"AGE\",     .stats = c(\"mean_sd\", \"pval\"),     .formats = c(mean_sd = \"xx.x, xx.x\"),     .labels = c(mean_sd = \"Mean, SD\")   ) build_table(lyt, df = tern_ex_adsl) #>                      ARM A       ARM B       ARM C   #> ———————————————————————————————————————————————————— #> Mean, SD           34.1, 6.8   35.8, 7.1   36.1, 7.4 #> p-value (t-test)    0.1176      0.8212                # `s_compare.numeric`  ## Usual case where both this and the reference group vector have more than 1 value. s_compare(rnorm(10, 5, 1), .ref_group = rnorm(5, -5, 1), .in_ref_col = FALSE) #> $n #>  n  #> 10  #>  #> $sum #>      sum  #> 51.27191  #>  #> $mean #>     mean  #> 5.127191  #>  #> $sd #>       sd  #> 1.226119  #>  #> $se #>       se  #> 0.387733  #>  #> $mean_sd #>     mean       sd  #> 5.127191 1.226119  #>  #> $mean_se #>     mean       se  #> 5.127191 0.387733  #>  #> $mean_ci #> mean_ci_lwr mean_ci_upr  #>    4.250078    6.004304  #> attr(,\"label\") #> [1] \"Mean 95% CI\" #>  #> $mean_sei #> mean_sei_lwr mean_sei_upr  #>     4.739458     5.514924  #> attr(,\"label\") #> [1] \"Mean -/+ 1xSE\" #>  #> $mean_sdi #> mean_sdi_lwr mean_sdi_upr  #>     3.901071     6.353310  #> attr(,\"label\") #> [1] \"Mean -/+ 1xSD\" #>  #> $mean_ci_3d #>        mean mean_ci_lwr mean_ci_upr  #>    5.127191    4.250078    6.004304  #> attr(,\"label\") #> [1] \"Mean (95% CI)\" #>  #> $mean_pval #>      p_value  #> 3.353908e-07  #> attr(,\"label\") #> [1] \"Mean p-value (H0: mean = 0)\" #>  #> $median #>   median  #> 5.024369  #>  #> $mad #>           mad  #> -4.440892e-16  #>  #> $median_ci #> median_ci_lwr median_ci_upr  #>      4.638779      5.862086  #> attr(,\"conf_level\") #> [1] 0.9785156 #> attr(,\"label\") #> [1] \"Median 95% CI\" #>  #> $median_ci_3d #>        median median_ci_lwr median_ci_upr  #>      5.024369      4.638779      5.862086  #> attr(,\"label\") #> [1] \"Median (95% CI)\" #>  #> $quantiles #> quantile_0.25 quantile_0.75  #>      4.756763      5.549828  #> attr(,\"label\") #> [1] \"25% and 75%-ile\" #>  #> $iqr #>       iqr  #> 0.7930643  #>  #> $range #>      min      max  #> 2.725885 7.682557  #>  #> $min #>      min  #> 2.725885  #>  #> $max #>      max  #> 7.682557  #>  #> $median_range #>   median      min      max  #> 5.024369 2.725885 7.682557  #> attr(,\"label\") #> [1] \"Median (Min - Max)\" #>  #> $cv #>       cv  #> 23.91406  #>  #> $geom_mean #> geom_mean  #>  4.985435  #>  #> $geom_mean_ci #> mean_ci_lwr mean_ci_upr  #>    4.144463    5.997052  #> attr(,\"label\") #> [1] \"Geometric Mean 95% CI\" #>  #> $geom_cv #>  geom_cv  #> 26.26258  #>  #> $geom_mean_ci_3d #>   geom_mean mean_ci_lwr mean_ci_upr  #>    4.985435    4.144463    5.997052  #> attr(,\"label\") #> [1] \"Geometric Mean (95% CI)\" #>  #> $pval #> [1] 2.25779e-08 #>   ## If one group has not more than 1 value, then p-value is not calculated. s_compare(rnorm(10, 5, 1), .ref_group = 1, .in_ref_col = FALSE) #> $n #>  n  #> 10  #>  #> $sum #>      sum  #> 50.71578  #>  #> $mean #>     mean  #> 5.071578  #>  #> $sd #>       sd  #> 1.105832  #>  #> $se #>        se  #> 0.3496948  #>  #> $mean_sd #>     mean       sd  #> 5.071578 1.105832  #>  #> $mean_se #>      mean        se  #> 5.0715780 0.3496948  #>  #> $mean_ci #> mean_ci_lwr mean_ci_upr  #>    4.280513    5.862643  #> attr(,\"label\") #> [1] \"Mean 95% CI\" #>  #> $mean_sei #> mean_sei_lwr mean_sei_upr  #>     4.721883     5.421273  #> attr(,\"label\") #> [1] \"Mean -/+ 1xSE\" #>  #> $mean_sdi #> mean_sdi_lwr mean_sdi_upr  #>     3.965746     6.177410  #> attr(,\"label\") #> [1] \"Mean -/+ 1xSD\" #>  #> $mean_ci_3d #>        mean mean_ci_lwr mean_ci_upr  #>    5.071578    4.280513    5.862643  #> attr(,\"label\") #> [1] \"Mean (95% CI)\" #>  #> $mean_pval #>      p_value  #> 1.511204e-07  #> attr(,\"label\") #> [1] \"Mean p-value (H0: mean = 0)\" #>  #> $median #>   median  #> 5.260423  #>  #> $mad #> mad  #>   0  #>  #> $median_ci #> median_ci_lwr median_ci_upr  #>      3.529264      6.318293  #> attr(,\"conf_level\") #> [1] 0.9785156 #> attr(,\"label\") #> [1] \"Median 95% CI\" #>  #> $median_ci_3d #>        median median_ci_lwr median_ci_upr  #>      5.260423      3.529264      6.318293  #> attr(,\"label\") #> [1] \"Median (95% CI)\" #>  #> $quantiles #> quantile_0.25 quantile_0.75  #>      4.024149      6.065057  #> attr(,\"label\") #> [1] \"25% and 75%-ile\" #>  #> $iqr #>      iqr  #> 2.040908  #>  #> $range #>      min      max  #> 3.300549 6.337320  #>  #> $min #>      min  #> 3.300549  #>  #> $max #>     max  #> 6.33732  #>  #> $median_range #>   median      min      max  #> 5.260423 3.300549 6.337320  #> attr(,\"label\") #> [1] \"Median (Min - Max)\" #>  #> $cv #>      cv  #> 21.8045  #>  #> $geom_mean #> geom_mean  #>  4.952266  #>  #> $geom_mean_ci #> mean_ci_lwr mean_ci_upr  #>    4.181833    5.864639  #> attr(,\"label\") #> [1] \"Geometric Mean 95% CI\" #>  #> $geom_cv #>  geom_cv  #> 23.97201  #>  #> $geom_mean_ci_3d #>   geom_mean mean_ci_lwr mean_ci_upr  #>    4.952266    4.181833    5.864639  #> attr(,\"label\") #> [1] \"Geometric Mean (95% CI)\" #>  #> $pval #> character(0) #>   ## Empty numeric does not fail, it returns NA-filled items and no p-value. s_compare(numeric(), .ref_group = numeric(), .in_ref_col = FALSE) #> $n #> n  #> 0  #>  #> $sum #> sum  #>  NA  #>  #> $mean #> mean  #>   NA  #>  #> $sd #> sd  #> NA  #>  #> $se #> se  #> NA  #>  #> $mean_sd #> mean   sd  #>   NA   NA  #>  #> $mean_se #> mean   se  #>   NA   NA  #>  #> $mean_ci #> mean_ci_lwr mean_ci_upr  #>          NA          NA  #> attr(,\"label\") #> [1] \"Mean 95% CI\" #>  #> $mean_sei #> mean_sei_lwr mean_sei_upr  #>           NA           NA  #> attr(,\"label\") #> [1] \"Mean -/+ 1xSE\" #>  #> $mean_sdi #> mean_sdi_lwr mean_sdi_upr  #>           NA           NA  #> attr(,\"label\") #> [1] \"Mean -/+ 1xSD\" #>  #> $mean_ci_3d #>        mean mean_ci_lwr mean_ci_upr  #>          NA          NA          NA  #> attr(,\"label\") #> [1] \"Mean (95% CI)\" #>  #> $mean_pval #> p_value  #>      NA  #> attr(,\"label\") #> [1] \"Mean p-value (H0: mean = 0)\" #>  #> $median #> median  #>     NA  #>  #> $mad #> mad  #>  NA  #>  #> $median_ci #> median_ci_lwr median_ci_upr  #>            NA            NA  #> attr(,\"conf_level\") #> [1] NA #> attr(,\"label\") #> [1] \"Median 95% CI\" #>  #> $median_ci_3d #>        median median_ci_lwr median_ci_upr  #>            NA            NA            NA  #> attr(,\"label\") #> [1] \"Median (95% CI)\" #>  #> $quantiles #> quantile_0.25 quantile_0.75  #>            NA            NA  #> attr(,\"label\") #> [1] \"25% and 75%-ile\" #>  #> $iqr #> iqr  #>  NA  #>  #> $range #> min max  #>  NA  NA  #>  #> $min #> min  #>  NA  #>  #> $max #> max  #>  NA  #>  #> $median_range #> median    min    max  #>     NA     NA     NA  #> attr(,\"label\") #> [1] \"Median (Min - Max)\" #>  #> $cv #> cv  #> NA  #>  #> $geom_mean #> geom_mean  #>       NaN  #>  #> $geom_mean_ci #> mean_ci_lwr mean_ci_upr  #>          NA          NA  #> attr(,\"label\") #> [1] \"Geometric Mean 95% CI\" #>  #> $geom_cv #> geom_cv  #>      NA  #>  #> $geom_mean_ci_3d #>   geom_mean mean_ci_lwr mean_ci_upr  #>         NaN          NA          NA  #> attr(,\"label\") #> [1] \"Geometric Mean (95% CI)\" #>  #> $pval #> character(0) #>   # `s_compare.factor`  ## Basic usage: x <- factor(c(\"a\", \"a\", \"b\", \"c\", \"a\")) y <- factor(c(\"a\", \"b\", \"c\")) s_compare(x = x, .ref_group = y, .in_ref_col = FALSE) #> $n #> [1] 5 #>  #> $count #> $count$a #> [1] 3 #>  #> $count$b #> [1] 1 #>  #> $count$c #> [1] 1 #>  #>  #> $count_fraction #> $count_fraction$a #> [1] 3.0 0.6 #>  #> $count_fraction$b #> [1] 1.0 0.2 #>  #> $count_fraction$c #> [1] 1.0 0.2 #>  #>  #> $fraction #> $fraction$a #>   num denom  #>     3     5  #>  #> $fraction$b #>   num denom  #>     1     5  #>  #> $fraction$c #>   num denom  #>     1     5  #>  #>  #> $n_blq #> [1] 0 #>  #> $pval_counts #> [1] 0.7659283 #>   ## Management of NA values. x <- explicit_na(factor(c(\"a\", \"a\", \"b\", \"c\", \"a\", NA, NA))) y <- explicit_na(factor(c(\"a\", \"b\", \"c\", NA))) s_compare(x = x, .ref_group = y, .in_ref_col = FALSE, na.rm = TRUE) #> $n #> [1] 5 #>  #> $count #> $count$a #> [1] 3 #>  #> $count$b #> [1] 1 #>  #> $count$c #> [1] 1 #>  #>  #> $count_fraction #> $count_fraction$a #> [1] 3.0 0.6 #>  #> $count_fraction$b #> [1] 1.0 0.2 #>  #> $count_fraction$c #> [1] 1.0 0.2 #>  #>  #> $fraction #> $fraction$a #>   num denom  #>     3     5  #>  #> $fraction$b #>   num denom  #>     1     5  #>  #> $fraction$c #>   num denom  #>     1     5  #>  #>  #> $n_blq #> [1] 0 #>  #> $pval_counts #> [1] 0.7659283 #>  s_compare(x = x, .ref_group = y, .in_ref_col = FALSE, na.rm = FALSE) #> $n #> [1] 7 #>  #> $count #> $count$a #> [1] 3 #>  #> $count$b #> [1] 1 #>  #> $count$c #> [1] 1 #>  #> $count$`<Missing>` #> [1] 2 #>  #>  #> $count_fraction #> $count_fraction$a #> [1] 3.0000000 0.4285714 #>  #> $count_fraction$b #> [1] 1.0000000 0.1428571 #>  #> $count_fraction$c #> [1] 1.0000000 0.1428571 #>  #> $count_fraction$`<Missing>` #> [1] 2.0000000 0.2857143 #>  #>  #> $fraction #> $fraction$a #>   num denom  #>     3     7  #>  #> $fraction$b #>   num denom  #>     1     7  #>  #> $fraction$c #>   num denom  #>     1     7  #>  #> $fraction$`<Missing>` #>   num denom  #>     2     7  #>  #>  #> $n_blq #> [1] 0 #>  #> $pval_counts #> [1] 0.9063036 #>   # `s_compare.character`  ## Basic usage: x <- c(\"a\", \"a\", \"b\", \"c\", \"a\") y <- c(\"a\", \"b\", \"c\") s_compare(x, .ref_group = y, .in_ref_col = FALSE, .var = \"x\", verbose = FALSE) #> $n #> [1] 5 #>  #> $count #> $count$a #> [1] 3 #>  #> $count$b #> [1] 1 #>  #> $count$c #> [1] 1 #>  #>  #> $count_fraction #> $count_fraction$a #> [1] 3.0 0.6 #>  #> $count_fraction$b #> [1] 1.0 0.2 #>  #> $count_fraction$c #> [1] 1.0 0.2 #>  #>  #> $fraction #> $fraction$a #>   num denom  #>     3     5  #>  #> $fraction$b #>   num denom  #>     1     5  #>  #> $fraction$c #>   num denom  #>     1     5  #>  #>  #> $n_blq #> [1] 0 #>  #> $pval_counts #> [1] 0.7659283 #>   ## Note that missing values handling can make a large difference: x <- c(\"a\", \"a\", \"b\", \"c\", \"a\", NA) y <- c(\"a\", \"b\", \"c\", rep(NA, 20)) s_compare(x,   .ref_group = y, .in_ref_col = FALSE,   .var = \"x\", verbose = FALSE ) #> $n #> [1] 5 #>  #> $count #> $count$a #> [1] 3 #>  #> $count$b #> [1] 1 #>  #> $count$c #> [1] 1 #>  #>  #> $count_fraction #> $count_fraction$a #> [1] 3.0 0.6 #>  #> $count_fraction$b #> [1] 1.0 0.2 #>  #> $count_fraction$c #> [1] 1.0 0.2 #>  #>  #> $fraction #> $fraction$a #>   num denom  #>     3     5  #>  #> $fraction$b #>   num denom  #>     1     5  #>  #> $fraction$c #>   num denom  #>     1     5  #>  #>  #> $n_blq #> [1] 0 #>  #> $pval_counts #> [1] 0.7659283 #>  s_compare(x,   .ref_group = y, .in_ref_col = FALSE, .var = \"x\",   na.rm = FALSE, verbose = FALSE ) #> $n #> [1] 6 #>  #> $count #> $count$a #> [1] 3 #>  #> $count$b #> [1] 1 #>  #> $count$c #> [1] 1 #>  #> $count$`<Missing>` #> [1] 1 #>  #>  #> $count_fraction #> $count_fraction$a #> [1] 3.0 0.5 #>  #> $count_fraction$b #> [1] 1.0000000 0.1666667 #>  #> $count_fraction$c #> [1] 1.0000000 0.1666667 #>  #> $count_fraction$`<Missing>` #> [1] 1.0000000 0.1666667 #>  #>  #> $fraction #> $fraction$a #>   num denom  #>     3     6  #>  #> $fraction$b #>   num denom  #>     1     6  #>  #> $fraction$c #>   num denom  #>     1     6  #>  #> $fraction$`<Missing>` #>   num denom  #>     1     6  #>  #>  #> $n_blq #> [1] 0 #>  #> $pval_counts #> [1] 0.005768471 #>   # `s_compare.logical`  ## Basic usage: x <- c(TRUE, FALSE, TRUE, TRUE) y <- c(FALSE, FALSE, TRUE) s_compare(x, .ref_group = y, .in_ref_col = FALSE) #> $n #> [1] 4 #>  #> $count #> [1] 3 #>  #> $count_fraction #> [1] 3.00 0.75 #>  #> $n_blq #> [1] 0 #>  #> $pval_counts #> [1] 0.2702894 #>   ## Management of NA values. x <- c(NA, TRUE, FALSE) y <- c(NA, NA, NA, NA, FALSE) s_compare(x, .ref_group = y, .in_ref_col = FALSE, na.rm = TRUE) #> $n #> [1] 2 #>  #> $count #> [1] 1 #>  #> $count_fraction #> [1] 1.0 0.5 #>  #> $n_blq #> [1] 0 #>  #> $pval_counts #> [1] 0.3864762 #>  s_compare(x, .ref_group = y, .in_ref_col = FALSE, na.rm = FALSE) #> $n #> [1] 3 #>  #> $count #> [1] 1 #>  #> $count_fraction #> [1] 1.0000000 0.3333333 #>  #> $n_blq #> [1] 0 #>  #> $pval_counts #> [1] 0.1675463 #>"},{"path":"https://insightsengineering.github.io/tern/reference/control_analyze_vars.html","id":null,"dir":"Reference","previous_headings":"","what":"Control function for descriptive statistics — control_analyze_vars","title":"Control function for descriptive statistics — control_analyze_vars","text":"Sets list parameters summaries descriptive statistics. Typically used internally specify details s_summary(). function family mainly used analyze_vars().","code":""},{"path":"https://insightsengineering.github.io/tern/reference/control_analyze_vars.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Control function for descriptive statistics — control_analyze_vars","text":"","code":"control_analyze_vars(   conf_level = 0.95,   quantiles = c(0.25, 0.75),   quantile_type = 2,   test_mean = 0 )"},{"path":"https://insightsengineering.github.io/tern/reference/control_analyze_vars.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Control function for descriptive statistics — control_analyze_vars","text":"conf_level (proportion) confidence level interval. quantiles (numeric(2)) vector length two specify quantiles calculate. quantile_type (numeric(1)) number 1 9 selecting quantile algorithms used. Default set 2 matches default quantile algorithm SAS proc univariate set QNTLDEF=5. differs R's default. See type stats::quantile(). test_mean (numeric(1)) number test mean null hypothesis calculating p-value.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/control_analyze_vars.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Control function for descriptive statistics — control_analyze_vars","text":"list components names arguments.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/control_annot.html","id":null,"dir":"Reference","previous_headings":"","what":"Control functions for Kaplan-Meier plot annotation tables — control_annot","title":"Control functions for Kaplan-Meier plot annotation tables — control_annot","text":"Auxiliary functions controlling arguments formatting annotation tables can added plots generated via g_km().","code":""},{"path":"https://insightsengineering.github.io/tern/reference/control_annot.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Control functions for Kaplan-Meier plot annotation tables — control_annot","text":"","code":"control_surv_med_annot(x = 0.8, y = 0.85, w = 0.32, h = 0.16, fill = TRUE)  control_coxph_annot(   x = 0.29,   y = 0.51,   w = 0.4,   h = 0.125,   fill = TRUE,   ref_lbls = FALSE )"},{"path":"https://insightsengineering.github.io/tern/reference/control_annot.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Control functions for Kaplan-Meier plot annotation tables — control_annot","text":"x (proportion) x-coordinate center annotation table. y (proportion) y-coordinate center annotation table. w (proportion) relative width annotation table. h (proportion) relative height annotation table. fill (flag character) whether annotation table background fill color. Can also color code use background fill color. TRUE, color code defaults \"#00000020\". ref_lbls (flag) whether reference group explicitly printed labels annotation table. FALSE (default), comparison groups printed table labels.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/control_annot.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Control functions for Kaplan-Meier plot annotation tables — control_annot","text":"list components names arguments.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/control_annot.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Control functions for Kaplan-Meier plot annotation tables — control_annot","text":"control_surv_med_annot(): Control function formatting median survival time annotation table. annotation table can added g_km() setting annot_surv_med=TRUE, can configured using control_surv_med_annot() function setting control_annot_surv_med argument. control_coxph_annot(): Control function formatting Cox-PH annotation table. annotation table can added g_km() setting annot_coxph=TRUE, can configured using control_coxph_annot() function setting control_annot_coxph argument.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/reference/control_annot.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Control functions for Kaplan-Meier plot annotation tables — control_annot","text":"","code":"control_surv_med_annot() #> $x #> [1] 0.8 #>  #> $y #> [1] 0.85 #>  #> $w #> [1] 0.32 #>  #> $h #> [1] 0.16 #>  #> $fill #> [1] TRUE #>   control_coxph_annot() #> $x #> [1] 0.29 #>  #> $y #> [1] 0.51 #>  #> $w #> [1] 0.4 #>  #> $h #> [1] 0.125 #>  #> $fill #> [1] TRUE #>  #> $ref_lbls #> [1] FALSE #>"},{"path":"https://insightsengineering.github.io/tern/reference/control_coxph.html","id":null,"dir":"Reference","previous_headings":"","what":"Control function for Cox-PH model — control_coxph","title":"Control function for Cox-PH model — control_coxph","text":"auxiliary function controlling arguments Cox-PH model, typically used internally specify details Cox-PH model s_coxph_pairwise(). conf_level refers Hazard Ratio estimation.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/control_coxph.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Control function for Cox-PH model — control_coxph","text":"","code":"control_coxph(   pval_method = c(\"log-rank\", \"wald\", \"likelihood\"),   ties = c(\"efron\", \"breslow\", \"exact\"),   conf_level = 0.95 )"},{"path":"https://insightsengineering.github.io/tern/reference/control_coxph.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Control function for Cox-PH model — control_coxph","text":"pval_method (string) p-value method testing hazard ratio = 1. Default method \"log-rank\", can also set \"wald\" \"likelihood\". ties (string) string specifying method tie handling. Default \"efron\", can also set \"breslow\" \"exact\". See survival::coxph(). conf_level (proportion) confidence level interval.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/control_coxph.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Control function for Cox-PH model — control_coxph","text":"list components names arguments.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/control_coxreg.html","id":null,"dir":"Reference","previous_headings":"","what":"Control function for Cox regression — control_coxreg","title":"Control function for Cox regression — control_coxreg","text":"Sets list parameters Cox regression fit. Used internally.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/control_coxreg.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Control function for Cox regression — control_coxreg","text":"","code":"control_coxreg(   pval_method = c(\"wald\", \"likelihood\"),   ties = c(\"exact\", \"efron\", \"breslow\"),   conf_level = 0.95,   interaction = FALSE )"},{"path":"https://insightsengineering.github.io/tern/reference/control_coxreg.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Control function for Cox regression — control_coxreg","text":"pval_method (string) method used estimation p.values; wald (default) likelihood. ties (string) among exact (equivalent DISCRETE SAS), efron breslow, see survival::coxph(). Note: equivalent SAS EXACT method R. conf_level (proportion) confidence level interval. interaction (flag) TRUE, model includes interaction studied treatment candidate covariate. Note univariate models without treatment arm, multivariate models, interaction can used needs FALSE.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/control_coxreg.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Control function for Cox regression — control_coxreg","text":"list items names corresponding arguments.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/reference/control_coxreg.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Control function for Cox regression — control_coxreg","text":"","code":"control_coxreg() #> $pval_method #> [1] \"wald\" #>  #> $ties #> [1] \"exact\" #>  #> $conf_level #> [1] 0.95 #>  #> $interaction #> [1] FALSE #>"},{"path":"https://insightsengineering.github.io/tern/reference/control_incidence_rate.html","id":null,"dir":"Reference","previous_headings":"","what":"Control function for incidence rate — control_incidence_rate","title":"Control function for incidence rate — control_incidence_rate","text":"auxiliary function controlling arguments incidence rate, used internally specify details s_incidence_rate().","code":""},{"path":"https://insightsengineering.github.io/tern/reference/control_incidence_rate.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Control function for incidence rate — control_incidence_rate","text":"","code":"control_incidence_rate(   conf_level = 0.95,   conf_type = c(\"normal\", \"normal_log\", \"exact\", \"byar\"),   input_time_unit = c(\"year\", \"day\", \"week\", \"month\"),   num_pt_year = 100 )"},{"path":"https://insightsengineering.github.io/tern/reference/control_incidence_rate.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Control function for incidence rate — control_incidence_rate","text":"conf_level (proportion) confidence level interval. conf_type (string)normal (default), normal_log, exact, byar confidence interval type. input_time_unit (string)day, week, month, year (default) indicating time unit data input. num_pt_year (numeric(1)) number patient-years use calculating adverse event rates.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/control_incidence_rate.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Control function for incidence rate — control_incidence_rate","text":"list components names arguments.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/reference/control_incidence_rate.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Control function for incidence rate — control_incidence_rate","text":"","code":"control_incidence_rate(0.9, \"exact\", \"month\", 100) #> $conf_level #> [1] 0.9 #>  #> $conf_type #> [1] \"exact\" #>  #> $input_time_unit #> [1] \"month\" #>  #> $num_pt_year #> [1] 100 #>"},{"path":"https://insightsengineering.github.io/tern/reference/control_lineplot_vars.html","id":null,"dir":"Reference","previous_headings":"","what":"Control function for g_lineplot() — control_lineplot_vars","title":"Control function for g_lineplot() — control_lineplot_vars","text":"Default values variables parameter g_lineplot function. variable's default value can overwritten variable.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/control_lineplot_vars.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Control function for g_lineplot() — control_lineplot_vars","text":"","code":"control_lineplot_vars(   x = \"AVISIT\",   y = \"AVAL\",   group_var = \"ARM\",   facet_var = NA,   paramcd = \"PARAMCD\",   y_unit = \"AVALU\",   subject_var = \"USUBJID\" )"},{"path":"https://insightsengineering.github.io/tern/reference/control_lineplot_vars.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Control function for g_lineplot() — control_lineplot_vars","text":"x (string) x-variable name. y (string) y-variable name. group_var (string NA) group variable name. facet_var (string NA) faceting variable name. paramcd (string NA) parameter code variable name. y_unit (string NA) y-axis unit variable name. subject_var (string NA) subject variable name.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/control_lineplot_vars.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Control function for g_lineplot() — control_lineplot_vars","text":"named character vector variable names.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/control_lineplot_vars.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Control function for g_lineplot() — control_lineplot_vars","text":"","code":"control_lineplot_vars() #>           x           y   group_var     paramcd      y_unit subject_var  #>    \"AVISIT\"      \"AVAL\"       \"ARM\"   \"PARAMCD\"     \"AVALU\"   \"USUBJID\"  #>   facet_var  #>          NA  control_lineplot_vars(group_var = NA) #>           x           y   group_var     paramcd      y_unit subject_var  #>    \"AVISIT\"      \"AVAL\"          NA   \"PARAMCD\"     \"AVALU\"   \"USUBJID\"  #>   facet_var  #>          NA"},{"path":"https://insightsengineering.github.io/tern/reference/control_logistic.html","id":null,"dir":"Reference","previous_headings":"","what":"Control function for logistic regression model fitting — control_logistic","title":"Control function for logistic regression model fitting — control_logistic","text":"auxiliary function controlling arguments logistic regression models. conf_level refers confidence level used Odds Ratio CIs.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/control_logistic.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Control function for logistic regression model fitting — control_logistic","text":"","code":"control_logistic(response_definition = \"response\", conf_level = 0.95)"},{"path":"https://insightsengineering.github.io/tern/reference/control_logistic.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Control function for logistic regression model fitting — control_logistic","text":"response_definition (string) definition event terms response. used fitting logistic regression model left hand side formula. Note evaluated expression result either logical vector factor 2 levels. default just \"response\" original response variable used modified . conf_level (proportion) confidence level interval.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/control_logistic.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Control function for logistic regression model fitting — control_logistic","text":"list components names arguments.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/control_logistic.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Control function for logistic regression model fitting — control_logistic","text":"","code":"# Standard options. control_logistic() #> $response_definition #> [1] \"response\" #>  #> $conf_level #> [1] 0.95 #>   # Modify confidence level. control_logistic(conf_level = 0.9) #> $response_definition #> [1] \"response\" #>  #> $conf_level #> [1] 0.9 #>   # Use a different response definition. control_logistic(response_definition = \"I(response %in% c('CR', 'PR'))\") #> $response_definition #> [1] \"I(response %in% c('CR', 'PR'))\" #>  #> $conf_level #> [1] 0.95 #>"},{"path":"https://insightsengineering.github.io/tern/reference/control_riskdiff.html","id":null,"dir":"Reference","previous_headings":"","what":"Control function for risk difference column — control_riskdiff","title":"Control function for risk difference column — control_riskdiff","text":"Sets list parameters use generating risk (proportion) difference column. Used input riskdiff parameter tabulate_rsp_subgroups() tabulate_survival_subgroups().","code":""},{"path":"https://insightsengineering.github.io/tern/reference/control_riskdiff.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Control function for risk difference column — control_riskdiff","text":"","code":"control_riskdiff(   arm_x = NULL,   arm_y = NULL,   format = \"xx.x (xx.x - xx.x)\",   col_label = \"Risk Difference (%) (95% CI)\",   pct = TRUE )"},{"path":"https://insightsengineering.github.io/tern/reference/control_riskdiff.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Control function for risk difference column — control_riskdiff","text":"arm_x (string) name reference arm use risk difference calculations. arm_y (character) names one arms compare reference arm risk difference calculations. new column added value arm_y. format (string function) format label (string) formatting function apply risk difference statistic. See 3d string options formatters::list_valid_format_labels() possible format strings. Defaults \"xx.x (xx.x - xx.x)\". col_label (character) labels use rendering risk difference column within table. one comparison arm specified arm_y, default labels specify two arms compared (reference arm vs. comparison arm). pct (flag) whether output returned percentages. Defaults TRUE.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/control_riskdiff.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Control function for risk difference column — control_riskdiff","text":"list items names corresponding arguments.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/reference/control_riskdiff.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Control function for risk difference column — control_riskdiff","text":"","code":"control_riskdiff() #> $arm_x #> NULL #>  #> $arm_y #> NULL #>  #> $format #> [1] \"xx.x (xx.x - xx.x)\" #>  #> $col_label #> [1] \"Risk Difference (%) (95% CI)\" #>  #> $pct #> [1] TRUE #>  control_riskdiff(arm_x = \"ARM A\", arm_y = \"ARM B\") #> $arm_x #> [1] \"ARM A\" #>  #> $arm_y #> [1] \"ARM B\" #>  #> $format #> [1] \"xx.x (xx.x - xx.x)\" #>  #> $col_label #> [1] \"Risk Difference (%) (95% CI)\" #>  #> $pct #> [1] TRUE #>"},{"path":"https://insightsengineering.github.io/tern/reference/control_step.html","id":null,"dir":"Reference","previous_headings":"","what":"Control function for subgroup treatment effect pattern (STEP) calculations — control_step","title":"Control function for subgroup treatment effect pattern (STEP) calculations — control_step","text":"auxiliary function controlling arguments STEP calculations.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/control_step.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Control function for subgroup treatment effect pattern (STEP) calculations — control_step","text":"","code":"control_step(   biomarker = NULL,   use_percentile = TRUE,   bandwidth,   degree = 0L,   num_points = 39L )"},{"path":"https://insightsengineering.github.io/tern/reference/control_step.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Control function for subgroup treatment effect pattern (STEP) calculations — control_step","text":"biomarker (numeric NULL) optional provision numeric biomarker variable, used infer bandwidth, see . use_percentile (flag) TRUE, running windows created according quantiles rather actual values, .e. bandwidth refers percentage data covered window. Suggest TRUE biomarker variable uniformly distributed. bandwidth (numeric(1) NULL) indicating bandwidth window. Depending argument use_percentile, can either length actual-value windows real biomarker scale, percentage windows. use_percentile = TRUE, number 0 1. NULL, treat bandwidth infinity, means one global model fitted. default, 0.25 used percentage windows one quarter range biomarker variable actual-value windows. degree (integer(1)) degree polynomial function biomarker interaction term treatment arm fitted window. 0 (default), biomarker variable included model fitted biomarker window. num_points (integer(1)) number points hazard ratios estimated. smallest number 2.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/control_step.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Control function for subgroup treatment effect pattern (STEP) calculations — control_step","text":"list components names arguments, except biomarker just used calculate bandwidth case actual biomarker windows requested.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/control_step.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Control function for subgroup treatment effect pattern (STEP) calculations — control_step","text":"","code":"# Provide biomarker values and request actual values to be used, # so that bandwidth is chosen from range. control_step(biomarker = 1:10, use_percentile = FALSE) #> $use_percentile #> [1] FALSE #>  #> $bandwidth #> [1] 2.25 #>  #> $degree #> [1] 0 #>  #> $num_points #> [1] 39 #>   # Use a global model with quadratic biomarker interaction term. control_step(bandwidth = NULL, degree = 2) #> $use_percentile #> [1] TRUE #>  #> $bandwidth #> NULL #>  #> $degree #> [1] 2 #>  #> $num_points #> [1] 39 #>   # Reduce number of points to be used. control_step(num_points = 10) #> $use_percentile #> [1] TRUE #>  #> $bandwidth #> [1] 0.25 #>  #> $degree #> [1] 0 #>  #> $num_points #> [1] 10 #>"},{"path":"https://insightsengineering.github.io/tern/reference/control_surv_time.html","id":null,"dir":"Reference","previous_headings":"","what":"Control function for survfit models for survival time — control_surv_time","title":"Control function for survfit models for survival time — control_surv_time","text":"auxiliary function controlling arguments survfit model, typically used internally specify details survfit model s_surv_time(). conf_level refers survival time estimation.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/control_surv_time.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Control function for survfit models for survival time — control_surv_time","text":"","code":"control_surv_time(   conf_level = 0.95,   conf_type = c(\"plain\", \"log\", \"log-log\"),   quantiles = c(0.25, 0.75) )"},{"path":"https://insightsengineering.github.io/tern/reference/control_surv_time.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Control function for survfit models for survival time — control_surv_time","text":"conf_level (proportion) confidence level interval. conf_type (string) confidence interval type. Options \"plain\" (default), \"log\", \"log-log\", see survival::survfit(). Note option \"none\" longer supported. quantiles (numeric(2)) vector length two specifying quantiles survival time.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/control_surv_time.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Control function for survfit models for survival time — control_surv_time","text":"list components names arguments.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/control_surv_timepoint.html","id":null,"dir":"Reference","previous_headings":"","what":"Control function for survfit models for patients' survival rate at time points — control_surv_timepoint","title":"Control function for survfit models for patients' survival rate at time points — control_surv_timepoint","text":"auxiliary function controlling arguments survfit model, typically used internally specify details survfit model s_surv_timepoint(). conf_level refers patient risk estimation time point.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/control_surv_timepoint.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Control function for survfit models for patients' survival rate at time points — control_surv_timepoint","text":"","code":"control_surv_timepoint(   conf_level = 0.95,   conf_type = c(\"plain\", \"log\", \"log-log\") )"},{"path":"https://insightsengineering.github.io/tern/reference/control_surv_timepoint.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Control function for survfit models for patients' survival rate at time points — control_surv_timepoint","text":"conf_level (proportion) confidence level interval. conf_type (string) confidence interval type. Options \"plain\" (default), \"log\", \"log-log\", see survival::survfit(). Note option \"none\" longer supported.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/control_surv_timepoint.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Control function for survfit models for patients' survival rate at time points — control_surv_timepoint","text":"list components names arguments.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/count_cumulative.html","id":null,"dir":"Reference","previous_headings":"","what":"Cumulative counts of numeric variable by thresholds — count_cumulative","title":"Cumulative counts of numeric variable by thresholds — count_cumulative","text":"analyze function count_cumulative() creates layout element calculate cumulative counts values numeric variable less , less equal , greater , greater equal user-specified threshold values. function analyzes numeric variable vars threshold values supplied thresholds argument numeric vector. Whether counts include threshold values, whether count values lower higher threshold values can set via include_eq lower_tail parameters, respectively.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/count_cumulative.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Cumulative counts of numeric variable by thresholds — count_cumulative","text":"","code":"count_cumulative(   lyt,   vars,   thresholds,   lower_tail = TRUE,   include_eq = TRUE,   var_labels = vars,   show_labels = \"visible\",   na_str = default_na_str(),   nested = TRUE,   ...,   table_names = vars,   .stats = NULL,   .formats = NULL,   .labels = NULL,   .indent_mods = NULL )  s_count_cumulative(   x,   thresholds,   lower_tail = TRUE,   include_eq = TRUE,   .N_col,   .N_row,   denom = c(\"N_col\", \"n\", \"N_row\"),   ... )  a_count_cumulative(   x,   thresholds,   lower_tail = TRUE,   include_eq = TRUE,   .N_col,   .N_row,   denom = c(\"N_col\", \"n\", \"N_row\"),   ... )"},{"path":"https://insightsengineering.github.io/tern/reference/count_cumulative.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Cumulative counts of numeric variable by thresholds — count_cumulative","text":"lyt (PreDataTableLayouts) layout analyses added . vars (character) variable names primary analysis variable iterated . thresholds (numeric) vector cutoff values counts. lower_tail (flag) whether count lower tail, default TRUE. include_eq (flag) whether include value equal threshold count, default TRUE. var_labels (character) variable labels. show_labels (string) label visibility: one \"default\", \"visible\" \"hidden\". na_str (string) string used replace NA empty values output. nested (flag) whether layout instruction applied within existing layout structure _if possible (TRUE, default) new top-level element (FALSE). Ignored nest split. underneath analyses, allowed. ... additional arguments lower level functions. table_names (character) can customized case vars analyzed multiple times, avoid warnings rtables. .stats (character) statistics select table. Options : 'count_fraction', 'count_fraction_fixed_dp' .formats (named character list) formats statistics. See Details analyze_vars information \"auto\" setting. .labels (named character) labels statistics (without indent). .indent_mods (named integer) indent modifiers labels. Defaults 0, corresponds unmodified default behavior. Can negative. x (numeric) vector numbers want analyze. .N_col (integer(1)) column-wise N (column count) full column analyzed typically passed rtables. .N_row (integer(1)) row-wise N (row group count) group observations analyzed (.e. column-based subsetting) typically passed rtables. denom (string) choice denominator proportion. Options : n: number values row column intersection. N_row: total number values row across columns. N_col: total number values column across rows.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/count_cumulative.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Cumulative counts of numeric variable by thresholds — count_cumulative","text":"count_cumulative() returns layout object suitable passing layouting functions, rtables::build_table(). Adding function rtable layout add formatted rows containing statistics s_count_cumulative() table layout. s_count_cumulative() returns named list count_fractions: list thresholds value component, component containing vector count fraction. a_count_cumulative() returns corresponding list formatted rtables::CellValue().","code":""},{"path":"https://insightsengineering.github.io/tern/reference/count_cumulative.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Cumulative counts of numeric variable by thresholds — count_cumulative","text":"count_cumulative(): Layout-creating function can take statistics function arguments additional format arguments. function wrapper rtables::analyze(). s_count_cumulative(): Statistics function produces named list given numeric vector thresholds. a_count_cumulative(): Formatted analysis function used afun count_cumulative().","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/reference/count_cumulative.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Cumulative counts of numeric variable by thresholds — count_cumulative","text":"","code":"basic_table() %>%   split_cols_by(\"ARM\") %>%   add_colcounts() %>%   count_cumulative(     vars = \"AGE\",     thresholds = c(40, 60)   ) %>%   build_table(tern_ex_adsl) #>           A: Drug X    B: Placebo   C: Combination #>             (N=69)       (N=73)         (N=58)     #> —————————————————————————————————————————————————— #> AGE                                                #>   <= 40   52 (75.4%)   58 (79.5%)     41 (70.7%)   #>   <= 60   69 (100%)    73 (100%)      58 (100%)"},{"path":"https://insightsengineering.github.io/tern/reference/count_missed_doses.html","id":null,"dir":"Reference","previous_headings":"","what":"Count number of patients with missed doses by thresholds — count_missed_doses","title":"Count number of patients with missed doses by thresholds — count_missed_doses","text":"analyze function creates layout element calculate cumulative counts patients number missed doses least equal user-specified threshold values. function analyzes numeric variable vars, variable numbers missed doses, threshold values supplied thresholds argument numeric vector. function assumes every row given data frame corresponds unique patient.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/count_missed_doses.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Count number of patients with missed doses by thresholds — count_missed_doses","text":"","code":"count_missed_doses(   lyt,   vars,   thresholds,   var_labels = vars,   show_labels = \"visible\",   na_str = default_na_str(),   nested = TRUE,   ...,   table_names = vars,   .stats = NULL,   .formats = NULL,   .labels = NULL,   .indent_mods = NULL )  s_count_nonmissing(x)  s_count_missed_doses(   x,   thresholds,   .N_col,   .N_row,   denom = c(\"N_col\", \"n\", \"N_row\") )  a_count_missed_doses(   x,   thresholds,   .N_col,   .N_row,   denom = c(\"N_col\", \"n\", \"N_row\") )"},{"path":"https://insightsengineering.github.io/tern/reference/count_missed_doses.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Count number of patients with missed doses by thresholds — count_missed_doses","text":"lyt (PreDataTableLayouts) layout analyses added . vars (character) variable names primary analysis variable iterated . thresholds (numeric) minimum number missed doses patients . var_labels (character) variable labels. show_labels (string) label visibility: one \"default\", \"visible\" \"hidden\". na_str (string) string used replace NA empty values output. nested (flag) whether layout instruction applied within existing layout structure _if possible (TRUE, default) new top-level element (FALSE). Ignored nest split. underneath analyses, allowed. ... additional arguments lower level functions. table_names (character) can customized case vars analyzed multiple times, avoid warnings rtables. .stats (character) statistics select table. Options : 'n', 'count_fraction', 'count_fraction_fixed_dp' .formats (named character list) formats statistics. See Details analyze_vars information \"auto\" setting. .labels (named character) labels statistics (without indent). .indent_mods (named integer) indent modifiers labels. Defaults 0, corresponds unmodified default behavior. Can negative. x (numeric) vector numbers want analyze. .N_col (integer(1)) column-wise N (column count) full column analyzed typically passed rtables. .N_row (integer(1)) row-wise N (row group count) group observations analyzed (.e. column-based subsetting) typically passed rtables. denom (string) choice denominator proportion. Options : n: number values row column intersection. N_row: total number values row across columns. N_col: total number values column across rows.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/count_missed_doses.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Count number of patients with missed doses by thresholds — count_missed_doses","text":"count_missed_doses() returns layout object suitable passing layouting functions, rtables::build_table(). Adding function rtable layout add formatted rows containing statistics s_count_missed_doses() table layout. s_count_nonmissing() returns statistic n count non-missing values x. s_count_missed_doses() returns statistics n count_fraction one element threshold. a_count_missed_doses() returns corresponding list formatted rtables::CellValue().","code":""},{"path":"https://insightsengineering.github.io/tern/reference/count_missed_doses.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Count number of patients with missed doses by thresholds — count_missed_doses","text":"count_missed_doses(): Layout-creating function can take statistics function arguments additional format arguments. function wrapper rtables::analyze(). s_count_nonmissing(): Statistics function count non-missing values. s_count_missed_doses(): Statistics function count patients missed doses. a_count_missed_doses(): Formatted analysis function used afun count_missed_doses().","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/reference/count_missed_doses.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Count number of patients with missed doses by thresholds — count_missed_doses","text":"","code":"library(dplyr)  anl <- tern_ex_adsl %>%   distinct(STUDYID, USUBJID, ARM) %>%   mutate(     PARAMCD = \"TNDOSMIS\",     PARAM = \"Total number of missed doses during study\",     AVAL = sample(0:20, size = nrow(tern_ex_adsl), replace = TRUE),     AVALC = \"\"   )  basic_table() %>%   split_cols_by(\"ARM\") %>%   add_colcounts() %>%   count_missed_doses(\"AVAL\", thresholds = c(1, 5, 10, 15), var_labels = \"Missed Doses\") %>%   build_table(anl, alt_counts_df = tern_ex_adsl) #>                              A: Drug X    B: Placebo   C: Combination #>                                (N=69)       (N=73)         (N=58)     #> ————————————————————————————————————————————————————————————————————— #> Missed Doses                                                          #>   n                              69           73             58       #>   At least 1 missed dose     69 (100%)    69 (94.5%)     55 (94.8%)   #>   At least 5 missed doses    57 (82.6%)   55 (75.3%)     50 (86.2%)   #>   At least 10 missed doses    40 (58%)    40 (54.8%)     32 (55.2%)   #>   At least 15 missed doses   26 (37.7%)   25 (34.2%)     13 (22.4%)"},{"path":"https://insightsengineering.github.io/tern/reference/count_occurrences.html","id":null,"dir":"Reference","previous_headings":"","what":"Count occurrences — count_occurrences","title":"Count occurrences — count_occurrences","text":"analyze function count_occurrences() creates layout element calculate occurrence counts patients. function analyzes variable(s) supplied vars returns table occurrence counts unique value (level) variable(s). variable (variables) must non-numeric. id variable used indicate unique subject identifiers (defaults USUBJID). multiple occurrences value recorded patient, value counted . summarize function summarize_occurrences() performs function count_occurrences() except creates content rows, data rows, summarize current table row/column context operates level latest row split root table row splits occurred.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/count_occurrences.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Count occurrences — count_occurrences","text":"","code":"count_occurrences(   lyt,   vars,   id = \"USUBJID\",   drop = TRUE,   var_labels = vars,   show_labels = \"hidden\",   riskdiff = FALSE,   na_str = default_na_str(),   nested = TRUE,   ...,   table_names = vars,   .stats = \"count_fraction_fixed_dp\",   .formats = NULL,   .labels = NULL,   .indent_mods = NULL )  summarize_occurrences(   lyt,   var,   id = \"USUBJID\",   drop = TRUE,   riskdiff = FALSE,   na_str = default_na_str(),   ...,   .stats = \"count_fraction_fixed_dp\",   .formats = NULL,   .indent_mods = NULL,   .labels = NULL )  s_count_occurrences(   df,   denom = c(\"N_col\", \"n\", \"N_row\"),   .N_col,   .N_row,   .df_row,   drop = TRUE,   .var = \"MHDECOD\",   id = \"USUBJID\" )  a_count_occurrences(   df,   labelstr = \"\",   id = \"USUBJID\",   denom = c(\"N_col\", \"n\", \"N_row\"),   drop = TRUE,   .N_col,   .N_row,   .var = NULL,   .df_row = NULL,   .stats = NULL,   .formats = NULL,   .labels = NULL,   .indent_mods = NULL,   na_str = default_na_str() )"},{"path":"https://insightsengineering.github.io/tern/reference/count_occurrences.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Count occurrences — count_occurrences","text":"lyt (PreDataTableLayouts) layout analyses added . vars (character) variable names primary analysis variable iterated . id (string) subject variable name. drop (flag) whether non-appearing occurrence levels dropped resulting table. Note case remaining occurrence levels table sorted alphabetically. var_labels (character) variable labels. show_labels (string) label visibility: one \"default\", \"visible\" \"hidden\". riskdiff (flag) whether risk difference column present. set TRUE, add_riskdiff() must used split_fun prior column split table layout, specifying columns compared. See stat_propdiff_ci() details risk difference calculation. na_str (string) string used replace NA empty values output. nested (flag) whether layout instruction applied within existing layout structure _if possible (TRUE, default) new top-level element (FALSE). Ignored nest split. underneath analyses, allowed. ... additional arguments lower level functions. table_names (character) can customized case vars analyzed multiple times, avoid warnings rtables. .stats (character) statistics select table. Options : 'count', 'count_fraction', 'count_fraction_fixed_dp', 'fraction' .formats (named character list) formats statistics. See Details analyze_vars information \"auto\" setting. .labels (named character) labels statistics (without indent). .indent_mods (named integer) indent modifiers labels. Defaults 0, corresponds unmodified default behavior. Can negative. df (data.frame) data set containing analysis variables. denom (string) choice denominator proportion. Options : N_col: total number patients column across rows. n: number patients occurrences. N_row: total number patients row across columns. .N_col (integer(1)) column-wise N (column count) full column analyzed typically passed rtables. .N_row (integer(1)) row-wise N (row group count) group observations analyzed (.e. column-based subsetting) typically passed rtables. .df_row (data.frame) data frame across columns given row split. .var, var (string) single variable name passed rtables requested statistics function. labelstr (string) label level parent split currently summarized (must present second argument Content Row Functions). See rtables::summarize_row_groups() information.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/count_occurrences.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Count occurrences — count_occurrences","text":"count_occurrences() returns layout object suitable passing layouting functions, rtables::build_table(). Adding function rtable layout add formatted rows containing statistics s_count_occurrences() table layout. summarize_occurrences() returns layout object suitable passing layouting functions, rtables::build_table(). Adding function rtable layout add formatted content rows containing statistics s_count_occurrences() table layout. s_count_occurrences() returns list : count: list counts one element per occurrence. count_fraction: list counts fractions one element per occurrence. fraction: list numerators denominators one element per occurrence. a_count_occurrences() returns corresponding list formatted rtables::CellValue().","code":""},{"path":"https://insightsengineering.github.io/tern/reference/count_occurrences.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Count occurrences — count_occurrences","text":"count_occurrences(): Layout-creating function can take statistics function arguments additional format arguments. function wrapper rtables::analyze(). summarize_occurrences(): Layout-creating function can take content function arguments additional format arguments. function wrapper rtables::summarize_row_groups(). s_count_occurrences(): Statistics function counts number patients report occurrence. a_count_occurrences(): Formatted analysis function used afun count_occurrences().","code":""},{"path":"https://insightsengineering.github.io/tern/reference/count_occurrences.html","id":"note","dir":"Reference","previous_headings":"","what":"Note","title":"Count occurrences — count_occurrences","text":"default, occurrences appear given row split dropped table occurrences table sorted alphabetically per row split. Therefore, corresponding layout needs use split_fun = drop_split_levels split_rows_by calls. Use drop = FALSE like show occurrences.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/count_occurrences.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Count occurrences — count_occurrences","text":"","code":"library(dplyr) df <- data.frame(   USUBJID = as.character(c(     1, 1, 2, 4, 4, 4,     6, 6, 6, 7, 7, 8   )),   MHDECOD = c(     \"MH1\", \"MH2\", \"MH1\", \"MH1\", \"MH1\", \"MH3\",     \"MH2\", \"MH2\", \"MH3\", \"MH1\", \"MH2\", \"MH4\"   ),   ARM = rep(c(\"A\", \"B\"), each = 6),   SEX = c(\"F\", \"F\", \"M\", \"M\", \"M\", \"M\", \"F\", \"F\", \"F\", \"M\", \"M\", \"F\") ) df_adsl <- df %>%   select(USUBJID, ARM) %>%   unique()  # Create table layout lyt <- basic_table() %>%   split_cols_by(\"ARM\") %>%   add_colcounts() %>%   count_occurrences(vars = \"MHDECOD\", .stats = c(\"count_fraction\"))  # Apply table layout to data and produce `rtable` object tbl <- lyt %>%   build_table(df, alt_counts_df = df_adsl) %>%   prune_table()  tbl #>           A           B     #>         (N=3)       (N=3)   #> ——————————————————————————— #> MH1   3 (100%)    1 (33.3%) #> MH2   1 (33.3%)   2 (66.7%) #> MH3   1 (33.3%)   1 (33.3%) #> MH4       0       1 (33.3%)  # Layout creating function with custom format. basic_table() %>%   add_colcounts() %>%   split_rows_by(\"SEX\", child_labels = \"visible\") %>%   summarize_occurrences(     var = \"MHDECOD\",     .formats = c(\"count_fraction\" = \"xx.xx (xx.xx%)\")   ) %>%   build_table(df, alt_counts_df = df_adsl) #>          all obs  #>           (N=6)   #> ————————————————— #> F                 #>   MH1   1 (16.7%) #>   MH2   2 (33.3%) #>   MH3   1 (16.7%) #>   MH4   1 (16.7%) #> M                 #>   MH1   3 (50.0%) #>   MH2   1 (16.7%) #>   MH3   1 (16.7%)  # Count unique occurrences per subject. s_count_occurrences(   df,   .N_col = 4L,   .N_row = 4L,   .df_row = df,   .var = \"MHDECOD\",   id = \"USUBJID\" ) #> $count #> $count$MH1 #> [1] 4 #>  #> $count$MH2 #> [1] 3 #>  #> $count$MH3 #> [1] 2 #>  #> $count$MH4 #> [1] 1 #>  #>  #> $count_fraction #> $count_fraction$MH1 #> [1] 4 1 #>  #> $count_fraction$MH2 #> [1] 3.00 0.75 #>  #> $count_fraction$MH3 #> [1] 2.0 0.5 #>  #> $count_fraction$MH4 #> [1] 1.00 0.25 #>  #>  #> $fraction #> $fraction$MH1 #>   num denom  #>     4     4  #>  #> $fraction$MH2 #>   num denom  #>     3     4  #>  #> $fraction$MH3 #>   num denom  #>     2     4  #>  #> $fraction$MH4 #>   num denom  #>     1     4  #>  #>   a_count_occurrences(   df,   .N_col = 4L,   .df_row = df,   .var = \"MHDECOD\",   id = \"USUBJID\" ) #> RowsVerticalSection (in_rows) object print method: #> ---------------------------- #>    row_name formatted_cell indent_mod row_label #> 1       MH1              4          0       MH1 #> 2       MH2              3          0       MH2 #> 3       MH3              2          0       MH3 #> 4       MH4              1          0       MH4 #> 5       MH1       4 (100%)          0       MH1 #> 6       MH2        3 (75%)          0       MH2 #> 7       MH3        2 (50%)          0       MH3 #> 8       MH4        1 (25%)          0       MH4 #> 9       MH1       4 (100%)          0       MH1 #> 10      MH2      3 (75.0%)          0       MH2 #> 11      MH3      2 (50.0%)          0       MH3 #> 12      MH4      1 (25.0%)          0       MH4 #> 13      MH1   4/4 (100.0%)          0       MH1 #> 14      MH2    3/4 (75.0%)          0       MH2 #> 15      MH3    2/4 (50.0%)          0       MH3 #> 16      MH4    1/4 (25.0%)          0       MH4"},{"path":"https://insightsengineering.github.io/tern/reference/count_occurrences_by_grade.html","id":null,"dir":"Reference","previous_headings":"","what":"Count occurrences by grade — count_occurrences_by_grade","title":"Count occurrences by grade — count_occurrences_by_grade","text":"analyze function count_occurrences_by_grade() creates layout element calculate occurrence counts grade. function analyzes primary analysis variable var indicates toxicity grades. id variable used indicate unique subject identifiers (defaults USUBJID). user can also supply list custom groups grades analyze via grade_groups parameter. remove_single  argument remove single grades analysis grade groups analyzed. multiple grades recorded one patient highest grade level counted. summarize function summarize_occurrences_by_grade() performs function count_occurrences_by_grade() except creates content rows, data rows, summarize current table row/column context operates level latest row split root table row splits occurred.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/count_occurrences_by_grade.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Count occurrences by grade — count_occurrences_by_grade","text":"","code":"count_occurrences_by_grade(   lyt,   var,   id = \"USUBJID\",   grade_groups = list(),   remove_single = TRUE,   only_grade_groups = FALSE,   var_labels = var,   show_labels = \"default\",   riskdiff = FALSE,   na_str = default_na_str(),   nested = TRUE,   ...,   table_names = var,   .stats = \"count_fraction\",   .formats = list(count_fraction = format_count_fraction_fixed_dp),   .indent_mods = NULL,   .labels = NULL )  summarize_occurrences_by_grade(   lyt,   var,   id = \"USUBJID\",   grade_groups = list(),   remove_single = TRUE,   only_grade_groups = FALSE,   riskdiff = FALSE,   na_str = default_na_str(),   ...,   .stats = \"count_fraction\",   .formats = list(count_fraction = format_count_fraction_fixed_dp),   .indent_mods = NULL,   .labels = NULL )  s_count_occurrences_by_grade(   df,   .var,   .N_row,   .N_col,   id = \"USUBJID\",   grade_groups = list(),   remove_single = TRUE,   only_grade_groups = FALSE,   denom = c(\"N_col\", \"n\", \"N_row\"),   labelstr = \"\" )  a_count_occurrences_by_grade(   df,   labelstr = \"\",   id = \"USUBJID\",   grade_groups = list(),   remove_single = TRUE,   only_grade_groups = FALSE,   denom = c(\"N_col\", \"n\", \"N_row\"),   .N_col,   .N_row,   .df_row,   .var = NULL,   .stats = NULL,   .formats = NULL,   .labels = NULL,   .indent_mods = NULL,   na_str = default_na_str() )"},{"path":"https://insightsengineering.github.io/tern/reference/count_occurrences_by_grade.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Count occurrences by grade — count_occurrences_by_grade","text":"lyt (PreDataTableLayouts) layout analyses added . id (string) subject variable name. grade_groups (named list character) list containing groupings grades. remove_single (flag)TRUE include elements one-element grade groups output list; case grade groups names included output. only_grade_groups set TRUE argument ignored. only_grade_groups (flag) whether specified grade groups included, individual grade rows removed (TRUE), grades grade groups displayed (FALSE). var_labels (character) variable labels. show_labels (string) label visibility: one \"default\", \"visible\" \"hidden\". riskdiff (flag) whether risk difference column present. set TRUE, add_riskdiff() must used split_fun prior column split table layout, specifying columns compared. See stat_propdiff_ci() details risk difference calculation. na_str (string) string used replace NA empty values output. nested (flag) whether layout instruction applied within existing layout structure _if possible (TRUE, default) new top-level element (FALSE). Ignored nest split. underneath analyses, allowed. ... additional arguments lower level functions. table_names (character) can customized case vars analyzed multiple times, avoid warnings rtables. .stats (character) statistics select table. Options : 'count_fraction', 'count_fraction_fixed_dp' .formats (named character list) formats statistics. See Details analyze_vars information \"auto\" setting. .indent_mods (named integer) indent modifiers labels. Defaults 0, corresponds unmodified default behavior. Can negative. .labels (named character) labels statistics (without indent). df (data.frame) data set containing analysis variables. .var, var (string) single variable name passed rtables requested statistics function. .N_row (integer(1)) row-wise N (row group count) group observations analyzed (.e. column-based subsetting) typically passed rtables. .N_col (integer(1)) column-wise N (column count) full column analyzed typically passed rtables. denom (string) choice denominator proportion. Options : N_col: total number patients column across rows. n: number patients occurrences. N_row: total number patients row across columns. labelstr (string) label level parent split currently summarized (must present second argument Content Row Functions). See rtables::summarize_row_groups() information. .df_row (data.frame) data frame across columns given row split.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/count_occurrences_by_grade.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Count occurrences by grade — count_occurrences_by_grade","text":"count_occurrences_by_grade() returns layout object suitable passing layouting functions, rtables::build_table(). Adding function rtable layout add formatted rows containing statistics s_count_occurrences_by_grade() table layout. summarize_occurrences_by_grade() returns layout object suitable passing layouting functions, rtables::build_table(). Adding function rtable layout add formatted content rows containing statistics s_count_occurrences_by_grade() table layout. s_count_occurrences_by_grade() returns list counts fractions one element per grade level grade level grouping. a_count_occurrences_by_grade() returns corresponding list formatted rtables::CellValue().","code":""},{"path":"https://insightsengineering.github.io/tern/reference/count_occurrences_by_grade.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Count occurrences by grade — count_occurrences_by_grade","text":"count_occurrences_by_grade(): Layout-creating function can take statistics function arguments additional format arguments. function wrapper rtables::analyze(). summarize_occurrences_by_grade(): Layout-creating function can take content function arguments additional format arguments. function wrapper rtables::summarize_row_groups(). s_count_occurrences_by_grade(): Statistics function counts number patients highest grade. a_count_occurrences_by_grade(): Formatted analysis function used afun count_occurrences_by_grade().","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/reference/count_occurrences_by_grade.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Count occurrences by grade — count_occurrences_by_grade","text":"","code":"library(dplyr)  df <- data.frame(   USUBJID = as.character(c(1:6, 1)),   ARM = factor(c(\"A\", \"A\", \"A\", \"B\", \"B\", \"B\", \"A\"), levels = c(\"A\", \"B\")),   AETOXGR = factor(c(1, 2, 3, 4, 1, 2, 3), levels = c(1:5)),   AESEV = factor(     x = c(\"MILD\", \"MODERATE\", \"SEVERE\", \"MILD\", \"MILD\", \"MODERATE\", \"SEVERE\"),     levels = c(\"MILD\", \"MODERATE\", \"SEVERE\")   ),   stringsAsFactors = FALSE )  df_adsl <- df %>%   select(USUBJID, ARM) %>%   unique()  # Layout creating function with custom format. basic_table() %>%   split_cols_by(\"ARM\") %>%   add_colcounts() %>%   count_occurrences_by_grade(     var = \"AESEV\",     .formats = c(\"count_fraction\" = \"xx.xx (xx.xx%)\")   ) %>%   build_table(df, alt_counts_df = df_adsl) #>                  A               B       #>                (N=3)           (N=3)     #> ———————————————————————————————————————— #> MILD       0.00 (0.00%)    2.00 (66.67%) #> MODERATE   1.00 (33.33%)   1.00 (33.33%) #> SEVERE     2.00 (66.67%)   0.00 (0.00%)   # Define additional grade groupings. grade_groups <- list(   \"-Any-\" = c(\"1\", \"2\", \"3\", \"4\", \"5\"),   \"Grade 1-2\" = c(\"1\", \"2\"),   \"Grade 3-5\" = c(\"3\", \"4\", \"5\") )  basic_table() %>%   split_cols_by(\"ARM\") %>%   add_colcounts() %>%   count_occurrences_by_grade(     var = \"AETOXGR\",     grade_groups = grade_groups,     only_grade_groups = TRUE   ) %>%   build_table(df, alt_counts_df = df_adsl) #>                 A           B     #>               (N=3)       (N=3)   #> ————————————————————————————————— #> -Any-       3 (100%)    3 (100%)  #> Grade 1-2   1 (33.3%)   2 (66.7%) #> Grade 3-5   2 (66.7%)   1 (33.3%)  # Layout creating function with custom format. basic_table() %>%   add_colcounts() %>%   split_rows_by(\"ARM\", child_labels = \"visible\", nested = TRUE) %>%   summarize_occurrences_by_grade(     var = \"AESEV\",     .formats = c(\"count_fraction\" = \"xx.xx (xx.xx%)\")   ) %>%   build_table(df, alt_counts_df = df_adsl) #>                 all obs    #>                  (N=6)     #> —————————————————————————— #> A                          #>   MILD       0.00 (0.00%)  #>   MODERATE   1.00 (16.67%) #>   SEVERE     2.00 (33.33%) #> B                          #>   MILD       2.00 (33.33%) #>   MODERATE   1.00 (16.67%) #>   SEVERE     0.00 (0.00%)   basic_table() %>%   add_colcounts() %>%   split_rows_by(\"ARM\", child_labels = \"visible\", nested = TRUE) %>%   summarize_occurrences_by_grade(     var = \"AETOXGR\",     grade_groups = grade_groups   ) %>%   build_table(df, alt_counts_df = df_adsl) #>                all obs  #>                 (N=6)   #> ——————————————————————— #> A                       #>   -Any-       3 (50.0%) #>   Grade 1-2   1 (16.7%) #>   1               0     #>   2           1 (16.7%) #>   Grade 3-5   2 (33.3%) #>   3           2 (33.3%) #>   4               0     #>   5               0     #> B                       #>   -Any-       3 (50.0%) #>   Grade 1-2   2 (33.3%) #>   1           1 (16.7%) #>   2           1 (16.7%) #>   Grade 3-5   1 (16.7%) #>   3               0     #>   4           1 (16.7%) #>   5               0      s_count_occurrences_by_grade(   df,   .N_col = 10L,   .var = \"AETOXGR\",   id = \"USUBJID\",   grade_groups = list(\"ANY\" = levels(df$AETOXGR)) ) #> $count_fraction #> $count_fraction$ANY #> [1] 6.0 0.6 #>  #> $count_fraction$`1` #> [1] 1.0 0.1 #>  #> $count_fraction$`2` #> [1] 2.0 0.2 #>  #> $count_fraction$`3` #> [1] 2.0 0.2 #>  #> $count_fraction$`4` #> [1] 1.0 0.1 #>  #> $count_fraction$`5` #> [1] 0 0 #>  #>   a_count_occurrences_by_grade(   df,   .N_col = 10L,   .N_row = 10L,   .var = \"AETOXGR\",   id = \"USUBJID\",   grade_groups = list(\"ANY\" = levels(df$AETOXGR)) ) #> RowsVerticalSection (in_rows) object print method: #> ---------------------------- #>    row_name formatted_cell indent_mod row_label #> 1       ANY        6 (60%)          0       ANY #> 2         1        1 (10%)          0         1 #> 3         2        2 (20%)          0         2 #> 4         3        2 (20%)          0         3 #> 5         4        1 (10%)          0         4 #> 6         5              0          0         5 #> 7       ANY      6 (60.0%)          0       ANY #> 8         1      1 (10.0%)          0         1 #> 9         2      2 (20.0%)          0         2 #> 10        3      2 (20.0%)          0         3 #> 11        4      1 (10.0%)          0         4 #> 12        5              0          0         5"},{"path":"https://insightsengineering.github.io/tern/reference/count_patients_events_in_cols.html","id":null,"dir":"Reference","previous_headings":"","what":"Count patient events in columns — count_patients_events_in_cols","title":"Count patient events in columns — count_patients_events_in_cols","text":"summarize function summarize_patients_events_in_cols() creates layout element summarize patient event counts columns. function analyzes elements (events) supplied via filters_list parameter returns row counts number patients event well total numbers patients events. id variable used indicate unique subject identifiers (defaults USUBJID). multiple occurrences event recorded patient, event counted .","code":""},{"path":"https://insightsengineering.github.io/tern/reference/count_patients_events_in_cols.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Count patient events in columns — count_patients_events_in_cols","text":"","code":"summarize_patients_events_in_cols(   lyt,   id = \"USUBJID\",   filters_list = list(),   empty_stats = character(),   na_str = default_na_str(),   ...,   .stats = c(\"unique\", \"all\", names(filters_list)),   .labels = c(unique = \"Patients (All)\", all = \"Events (All)\",     labels_or_names(filters_list)),   col_split = TRUE )  s_count_patients_and_multiple_events(   df,   id,   filters_list,   empty_stats = character(),   labelstr = \"\",   custom_label = NULL )"},{"path":"https://insightsengineering.github.io/tern/reference/count_patients_events_in_cols.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Count patient events in columns — count_patients_events_in_cols","text":"lyt (PreDataTableLayouts) layout analyses added . id (string) subject variable name. filters_list (named list character) list element list describes one type event describe filters, format s_count_patients_with_event(). label, used column title. empty_stats (character) optional names statistics returned empty corresponding table cells stay blank. na_str (string) string used replace NA empty values output. ... additional arguments lower level functions. .stats (character) statistics select table. addition statistics added using filters_list, statistic options : 'unique', '' .labels (named character) labels statistics (without indent). col_split (flag) whether columns split. Set FALSE required column split done already earlier layout pipe. df (data.frame) data set containing analysis variables. labelstr (string) label level parent split currently summarized (must present second argument Content Row Functions). See rtables::summarize_row_groups() information. custom_label (string NULL) provided labelstr empty used label.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/count_patients_events_in_cols.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Count patient events in columns — count_patients_events_in_cols","text":"summarize_patients_events_in_cols() returns layout object suitable passing layouting functions, rtables::build_table(). Adding function rtable layout add formatted content rows containing statistics s_count_patients_and_multiple_events() table layout. s_count_patients_and_multiple_events() returns list statistics: unique: number unique patients df. : number rows df. one element name filters_list: number rows df, .e. events, fulfilling filter condition.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/count_patients_events_in_cols.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Count patient events in columns — count_patients_events_in_cols","text":"summarize_patients_events_in_cols(): Layout-creating function can take statistics function arguments additional format arguments. function wrapper rtables::summarize_row_groups(). s_count_patients_and_multiple_events(): Statistics function counts numbers patients multiple events defined filters. Used analysis function afun summarize_patients_events_in_cols().","code":""},{"path":"https://insightsengineering.github.io/tern/reference/count_patients_events_in_cols.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Count patient events in columns — count_patients_events_in_cols","text":"","code":"df <- data.frame(   USUBJID = rep(c(\"id1\", \"id2\", \"id3\", \"id4\"), c(2, 3, 1, 1)),   ARM = c(\"A\", \"A\", \"B\", \"B\", \"B\", \"B\", \"A\"),   AESER = rep(\"Y\", 7),   AESDTH = c(\"Y\", \"Y\", \"N\", \"Y\", \"Y\", \"N\", \"N\"),   AEREL = c(\"Y\", \"Y\", \"N\", \"Y\", \"Y\", \"N\", \"Y\"),   AEDECOD = c(\"A\", \"A\", \"A\", \"B\", \"B\", \"C\", \"D\"),   AEBODSYS = rep(c(\"SOC1\", \"SOC2\", \"SOC3\"), c(3, 3, 1)) )  # `summarize_patients_events_in_cols()` basic_table() %>%   summarize_patients_events_in_cols(     filters_list = list(       related = formatters::with_label(c(AEREL = \"Y\"), \"Events (Related)\"),       fatal = c(AESDTH = \"Y\"),       fatal_related = c(AEREL = \"Y\", AESDTH = \"Y\")     ),     custom_label = \"%s Total number of patients and events\"   ) %>%   build_table(df) #>                                          Patients (All)   Events (All)   Events (Related)   fatal   fatal_related #> ————————————————————————————————————————————————————————————————————————————————————————————————————————————————— #> %s Total number of patients and events         4               7                5             4           4"},{"path":"https://insightsengineering.github.io/tern/reference/count_patients_with_event.html","id":null,"dir":"Reference","previous_headings":"","what":"Count the number of patients with a particular event — count_patients_with_event","title":"Count the number of patients with a particular event — count_patients_with_event","text":"analyze function count_patients_with_event() creates layout element calculate patient counts user-specified set events. function analyzes primary analysis variable vars indicates unique subject identifiers. Events defined user named vector via filters argument, name corresponds variable value value(s) variable takes event. multiple records event recorded patient, one occurrence counted.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/count_patients_with_event.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Count the number of patients with a particular event — count_patients_with_event","text":"","code":"count_patients_with_event(   lyt,   vars,   filters,   riskdiff = FALSE,   na_str = default_na_str(),   nested = TRUE,   ...,   table_names = vars,   .stats = \"count_fraction\",   .formats = list(count_fraction = format_count_fraction_fixed_dp),   .labels = NULL,   .indent_mods = NULL )  s_count_patients_with_event(   df,   .var,   filters,   .N_col,   .N_row,   denom = c(\"n\", \"N_col\", \"N_row\") )  a_count_patients_with_event(   df,   labelstr = \"\",   filters,   denom = c(\"n\", \"N_col\", \"N_row\"),   .N_col,   .N_row,   .df_row,   .var = NULL,   .stats = NULL,   .formats = NULL,   .labels = NULL,   .indent_mods = NULL,   na_str = default_na_str() )"},{"path":"https://insightsengineering.github.io/tern/reference/count_patients_with_event.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Count the number of patients with a particular event — count_patients_with_event","text":"lyt (PreDataTableLayouts) layout analyses added . vars (character) variable names primary analysis variable iterated . filters (character) character vector specifying column names flag variables used counting number unique identifiers satisfying conditions. Multiple column names flags accepted format c(\"column_name1\" = \"flag1\", \"column_name2\" = \"flag2\"). Note equality accepted condition. riskdiff (flag) whether risk difference column present. set TRUE, add_riskdiff() must used split_fun prior column split table layout, specifying columns compared. See stat_propdiff_ci() details risk difference calculation. na_str (string) string used replace NA empty values output. nested (flag) whether layout instruction applied within existing layout structure _if possible (TRUE, default) new top-level element (FALSE). Ignored nest split. underneath analyses, allowed. ... additional arguments lower level functions. table_names (character) can customized case vars analyzed multiple times, avoid warnings rtables. .stats (character) statistics select table. Options : 'n', 'count', 'count_fraction', 'count_fraction_fixed_dp', 'n_blq' .formats (named character list) formats statistics. See Details analyze_vars information \"auto\" setting. .labels (named character) labels statistics (without indent). .indent_mods (named integer) indent modifiers labels. Defaults 0, corresponds unmodified default behavior. Can negative. df (data.frame) data set containing analysis variables. .var (string) name column contains unique identifier. .N_col (integer(1)) column-wise N (column count) full column analyzed typically passed rtables. .N_row (integer(1)) row-wise N (row group count) group observations analyzed (.e. column-based subsetting) typically passed rtables. denom (string) choice denominator proportion. Options : n: number values row column intersection. N_row: total number values row across columns. N_col: total number values column across rows. labelstr (string) label level parent split currently summarized (must present second argument Content Row Functions). See rtables::summarize_row_groups() information. .df_row (data.frame) data frame across columns given row split.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/count_patients_with_event.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Count the number of patients with a particular event — count_patients_with_event","text":"count_patients_with_event() returns layout object suitable passing layouting functions, rtables::build_table(). Adding function rtable layout add formatted rows containing statistics s_count_patients_with_event() table layout. s_count_patients_with_event() returns count fraction unique identifiers defined event. a_count_patients_with_event() returns corresponding list formatted rtables::CellValue().","code":""},{"path":"https://insightsengineering.github.io/tern/reference/count_patients_with_event.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Count the number of patients with a particular event — count_patients_with_event","text":"count_patients_with_event(): Layout-creating function can take statistics function arguments additional format arguments. function wrapper rtables::analyze(). s_count_patients_with_event(): Statistics function counts number patients defined event occurred. a_count_patients_with_event(): Formatted analysis function used afun count_patients_with_event().","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/reference/count_patients_with_event.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Count the number of patients with a particular event — count_patients_with_event","text":"","code":"lyt <- basic_table() %>%   split_cols_by(\"ARM\") %>%   add_colcounts() %>%   count_values(     \"STUDYID\",     values = \"AB12345\",     .stats = \"count\",     .labels = c(count = \"Total AEs\")   ) %>%   count_patients_with_event(     \"SUBJID\",     filters = c(\"TRTEMFL\" = \"Y\"),     .labels = c(count_fraction = \"Total number of patients with at least one adverse event\"),     table_names = \"tbl_all\"   ) %>%   count_patients_with_event(     \"SUBJID\",     filters = c(\"TRTEMFL\" = \"Y\", \"AEOUT\" = \"FATAL\"),     .labels = c(count_fraction = \"Total number of patients with fatal AEs\"),     table_names = \"tbl_fatal\"   ) %>%   count_patients_with_event(     \"SUBJID\",     filters = c(\"TRTEMFL\" = \"Y\", \"AEOUT\" = \"FATAL\", \"AEREL\" = \"Y\"),     .labels = c(count_fraction = \"Total number of patients with related fatal AEs\"),     .indent_mods = c(count_fraction = 2L),     table_names = \"tbl_rel_fatal\"   )  build_table(lyt, tern_ex_adae, alt_counts_df = tern_ex_adsl) #>                                                            A: Drug X    B: Placebo   C: Combination #>                                                              (N=69)       (N=73)         (N=58)     #> ——————————————————————————————————————————————————————————————————————————————————————————————————— #> Total AEs                                                     202          177            162       #> Total number of patients with at least one adverse event   59 (100%)    57 (100%)      48 (100%)    #> Total number of patients with fatal AEs                    28 (47.5%)   31 (54.4%)     20 (41.7%)   #>     Total number of patients with related fatal AEs        28 (47.5%)   31 (54.4%)     20 (41.7%)    s_count_patients_with_event(   tern_ex_adae,   .var = \"SUBJID\",   filters = c(\"TRTEMFL\" = \"Y\") ) #> $n #> [1] 164 #>  #> $count #> [1] 164 #>  #> $count_fraction #> [1] 164   1 #>  #> $n_blq #> [1] 0 #>   s_count_patients_with_event(   tern_ex_adae,   .var = \"SUBJID\",   filters = c(\"TRTEMFL\" = \"Y\", \"AEOUT\" = \"FATAL\") ) #> $n #> [1] 164 #>  #> $count #> [1] 79 #>  #> $count_fraction #> [1] 79.0000000  0.4817073 #>  #> $n_blq #> [1] 0 #>   s_count_patients_with_event(   tern_ex_adae,   .var = \"SUBJID\",   filters = c(\"TRTEMFL\" = \"Y\", \"AEOUT\" = \"FATAL\"),   denom = \"N_col\",   .N_col = 456 ) #> $n #> [1] 164 #>  #> $count #> [1] 79 #>  #> $count_fraction #> [1] 79.0000000  0.1732456 #>  #> $n_blq #> [1] 0 #>   a_count_patients_with_event(   tern_ex_adae,   .var = \"SUBJID\",   filters = c(\"TRTEMFL\" = \"Y\"),   .N_col = 100,   .N_row = 100 ) #> RowsVerticalSection (in_rows) object print method: #> ---------------------------- #>                  row_name formatted_cell indent_mod      row_label #> 1                       n            164          0              n #> 2                   count            164          0          count #> 3          count_fraction     164 (100%)          0 count_fraction #> 4 count_fraction_fixed_dp     164 (100%)          0 count_fraction #> 5                   n_blq              0          0          n_blq"},{"path":"https://insightsengineering.github.io/tern/reference/count_patients_with_flags.html","id":null,"dir":"Reference","previous_headings":"","what":"Count the number of patients with particular flags — count_patients_with_flags","title":"Count the number of patients with particular flags — count_patients_with_flags","text":"analyze function count_patients_with_flags() creates layout element calculate counts patients user-specified flags present. function analyzes primary analysis variable var indicates unique subject identifiers. Flags variables analyze specified user via flag_variables argument, must either take value TRUE (flag present) FALSE (flag absent) record. multiple records flag present patient, one occurrence counted.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/count_patients_with_flags.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Count the number of patients with particular flags — count_patients_with_flags","text":"","code":"count_patients_with_flags(   lyt,   var,   flag_variables,   flag_labels = NULL,   var_labels = var,   show_labels = \"hidden\",   riskdiff = FALSE,   na_str = default_na_str(),   nested = TRUE,   ...,   table_names = paste0(\"tbl_flags_\", var),   .stats = \"count_fraction\",   .formats = list(count_fraction = format_count_fraction_fixed_dp),   .indent_mods = NULL,   .labels = NULL )  s_count_patients_with_flags(   df,   .var,   flag_variables,   flag_labels = NULL,   .N_col,   .N_row,   denom = c(\"n\", \"N_col\", \"N_row\") )  a_count_patients_with_flags(   df,   labelstr = \"\",   flag_variables,   flag_labels = NULL,   denom = c(\"n\", \"N_col\", \"N_row\"),   .N_col,   .N_row,   .df_row,   .var = NULL,   .stats = NULL,   .formats = NULL,   .labels = NULL,   .indent_mods = NULL,   na_str = default_na_str() )"},{"path":"https://insightsengineering.github.io/tern/reference/count_patients_with_flags.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Count the number of patients with particular flags — count_patients_with_flags","text":"lyt (PreDataTableLayouts) layout analyses added . var (string) single variable name passed rtables requested statistics function. flag_variables (character) vector specifying names logical variables analysis dataset used counting number unique identifiers. flag_labels (character) vector labels use flag variables. labels also specified via .labels parameter, .labels values take precedence replace labels. var_labels (character) variable labels. show_labels (string) label visibility: one \"default\", \"visible\" \"hidden\". riskdiff (flag) whether risk difference column present. set TRUE, add_riskdiff() must used split_fun prior column split table layout, specifying columns compared. See stat_propdiff_ci() details risk difference calculation. na_str (string) string used replace NA empty values output. nested (flag) whether layout instruction applied within existing layout structure _if possible (TRUE, default) new top-level element (FALSE). Ignored nest split. underneath analyses, allowed. ... additional arguments lower level functions. table_names (character) can customized case vars analyzed multiple times, avoid warnings rtables. .stats (character) statistics select table. Options : 'n', 'count', 'count_fraction', 'count_fraction_fixed_dp', 'n_blq' .formats (named character list) formats statistics. See Details analyze_vars information \"auto\" setting. .indent_mods (named integer) indent modifiers labels. Defaults 0, corresponds unmodified default behavior. Can negative. .labels (named character) labels statistics (without indent). df (data.frame) data set containing analysis variables. .var (string) name column contains unique identifier. .N_col (integer(1)) column-wise N (column count) full column analyzed typically passed rtables. .N_row (integer(1)) row-wise N (row group count) group observations analyzed (.e. column-based subsetting) typically passed rtables. denom (string) choice denominator proportion. Options : n: number values row column intersection. N_row: total number values row across columns. N_col: total number values column across rows. labelstr (string) label level parent split currently summarized (must present second argument Content Row Functions). See rtables::summarize_row_groups() information. .df_row (data.frame) data frame across columns given row split.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/count_patients_with_flags.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Count the number of patients with particular flags — count_patients_with_flags","text":"count_patients_with_flags() returns layout object suitable passing layouting functions, rtables::build_table(). Adding function rtable layout add formatted rows containing statistics s_count_patients_with_flags() table layout. s_count_patients_with_flags() returns count fraction unique identifiers particular flag list statistics n, count, count_fraction, n_blq, one element per flag. a_count_patients_with_flags() returns corresponding list formatted rtables::CellValue().","code":""},{"path":"https://insightsengineering.github.io/tern/reference/count_patients_with_flags.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Count the number of patients with particular flags — count_patients_with_flags","text":"count_patients_with_flags(): Layout-creating function can take statistics function arguments additional format arguments. function wrapper rtables::analyze(). s_count_patients_with_flags(): Statistics function counts number patients particular flag variable TRUE. a_count_patients_with_flags(): Formatted analysis function used afun count_patients_with_flags().","code":""},{"path":"https://insightsengineering.github.io/tern/reference/count_patients_with_flags.html","id":"note","dir":"Reference","previous_headings":"","what":"Note","title":"Count the number of patients with particular flags — count_patients_with_flags","text":"flag_labels specified, variables labels extracted df. variables labeled, variable names used instead. Alternatively, named vector can supplied flag_variables within name-value pair name corresponds variable name value label use variable.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/reference/count_patients_with_flags.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Count the number of patients with particular flags — count_patients_with_flags","text":"","code":"# Add labelled flag variables to analysis dataset. adae <- tern_ex_adae %>%   dplyr::mutate(     fl1 = TRUE %>% with_label(\"Total AEs\"),     fl2 = (TRTEMFL == \"Y\") %>%       with_label(\"Total number of patients with at least one adverse event\"),     fl3 = (TRTEMFL == \"Y\" & AEOUT == \"FATAL\") %>%       with_label(\"Total number of patients with fatal AEs\"),     fl4 = (TRTEMFL == \"Y\" & AEOUT == \"FATAL\" & AEREL == \"Y\") %>%       with_label(\"Total number of patients with related fatal AEs\")   )  lyt <- basic_table() %>%   split_cols_by(\"ARM\") %>%   add_colcounts() %>%   count_patients_with_flags(     \"SUBJID\",     flag_variables = c(\"fl1\", \"fl2\", \"fl3\", \"fl4\"),     denom = \"N_col\"   )  build_table(lyt, adae, alt_counts_df = tern_ex_adsl) #>                                                            A: Drug X    B: Placebo   C: Combination #>                                                              (N=69)       (N=73)         (N=58)     #> ——————————————————————————————————————————————————————————————————————————————————————————————————— #> Total AEs                                                  59 (85.5%)   57 (78.1%)     48 (82.8%)   #> Total number of patients with at least one adverse event   59 (85.5%)   57 (78.1%)     48 (82.8%)   #> Total number of patients with fatal AEs                    28 (40.6%)   31 (42.5%)     20 (34.5%)   #> Total number of patients with related fatal AEs            28 (40.6%)   31 (42.5%)     20 (34.5%)    # `s_count_patients_with_flags()`  s_count_patients_with_flags(   adae,   \"SUBJID\",   flag_variables = c(\"fl1\", \"fl2\", \"fl3\", \"fl4\"),   denom = \"N_col\",   .N_col = 1000 ) #> $n #> $n$`Total AEs` #> [1] 164 #>  #> $n$`Total number of patients with at least one adverse event` #> [1] 164 #>  #> $n$`Total number of patients with fatal AEs` #> [1] 164 #>  #> $n$`Total number of patients with related fatal AEs` #> [1] 164 #>  #>  #> $count #> $count$`Total AEs` #> [1] 164 #>  #> $count$`Total number of patients with at least one adverse event` #> [1] 164 #>  #> $count$`Total number of patients with fatal AEs` #> [1] 79 #>  #> $count$`Total number of patients with related fatal AEs` #> [1] 79 #>  #>  #> $count_fraction #> $count_fraction$`Total AEs` #> [1] 164.000   0.164 #>  #> $count_fraction$`Total number of patients with at least one adverse event` #> [1] 164.000   0.164 #>  #> $count_fraction$`Total number of patients with fatal AEs` #> [1] 79.000  0.079 #>  #> $count_fraction$`Total number of patients with related fatal AEs` #> [1] 79.000  0.079 #>  #>  #> $n_blq #> $n_blq$`Total AEs` #> [1] 0 #>  #> $n_blq$`Total number of patients with at least one adverse event` #> [1] 0 #>  #> $n_blq$`Total number of patients with fatal AEs` #> [1] 0 #>  #> $n_blq$`Total number of patients with related fatal AEs` #> [1] 0 #>  #>   a_count_patients_with_flags(   adae,   .N_col = 10L,   .N_row = 10L,   .var = \"USUBJID\",   flag_variables = c(\"fl1\", \"fl2\", \"fl3\", \"fl4\") ) #> RowsVerticalSection (in_rows) object print method: #> ---------------------------- #>                       row_name formatted_cell indent_mod #> 1                        n.fl1            164          0 #> 2                        n.fl2            164          0 #> 3                        n.fl3            164          0 #> 4                        n.fl4            164          0 #> 5                    count.fl1            164          0 #> 6                    count.fl2            164          0 #> 7                    count.fl3             79          0 #> 8                    count.fl4             79          0 #> 9           count_fraction.fl1     164 (100%)          0 #> 10          count_fraction.fl2     164 (100%)          0 #> 11          count_fraction.fl3     79 (48.2%)          0 #> 12          count_fraction.fl4     79 (48.2%)          0 #> 13 count_fraction_fixed_dp.fl1     164 (100%)          0 #> 14 count_fraction_fixed_dp.fl2     164 (100%)          0 #> 15 count_fraction_fixed_dp.fl3     79 (48.2%)          0 #> 16 count_fraction_fixed_dp.fl4     79 (48.2%)          0 #> 17                   n_blq.fl1              0          0 #> 18                   n_blq.fl2              0          0 #> 19                   n_blq.fl3              0          0 #> 20                   n_blq.fl4              0          0 #>                                                   row_label #> 1                                                 Total AEs #> 2  Total number of patients with at least one adverse event #> 3                   Total number of patients with fatal AEs #> 4           Total number of patients with related fatal AEs #> 5                                                 Total AEs #> 6  Total number of patients with at least one adverse event #> 7                   Total number of patients with fatal AEs #> 8           Total number of patients with related fatal AEs #> 9                                                 Total AEs #> 10 Total number of patients with at least one adverse event #> 11                  Total number of patients with fatal AEs #> 12          Total number of patients with related fatal AEs #> 13                                                Total AEs #> 14 Total number of patients with at least one adverse event #> 15                  Total number of patients with fatal AEs #> 16          Total number of patients with related fatal AEs #> 17                                                Total AEs #> 18 Total number of patients with at least one adverse event #> 19                  Total number of patients with fatal AEs #> 20          Total number of patients with related fatal AEs"},{"path":"https://insightsengineering.github.io/tern/reference/count_values.html","id":null,"dir":"Reference","previous_headings":"","what":"Count specific values — count_values","title":"Count specific values — count_values","text":"analyze function count_values() creates layout element calculate counts specific values within variable interest. function analyzes one variables interest supplied vector vars. Values count variable(s) vars can given vector via values argument. One row counts generated variable.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/count_values.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Count specific values — count_values","text":"","code":"count_values(   lyt,   vars,   values,   na_str = default_na_str(),   nested = TRUE,   ...,   table_names = vars,   .stats = \"count_fraction\",   .formats = NULL,   .labels = c(count_fraction = paste(values, collapse = \", \")),   .indent_mods = NULL )  s_count_values(   x,   values,   na.rm = TRUE,   .N_col,   .N_row,   denom = c(\"n\", \"N_col\", \"N_row\") )  # S3 method for class 'character' s_count_values(x, values = \"Y\", na.rm = TRUE, ...)  # S3 method for class 'factor' s_count_values(x, values = \"Y\", ...)  # S3 method for class 'logical' s_count_values(x, values = TRUE, ...)  a_count_values(   x,   values,   na.rm = TRUE,   .N_col,   .N_row,   denom = c(\"n\", \"N_col\", \"N_row\") )"},{"path":"https://insightsengineering.github.io/tern/reference/count_values.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Count specific values — count_values","text":"lyt (PreDataTableLayouts) layout analyses added . vars (character) variable names primary analysis variable iterated . values (character) specific values counted. na_str (string) string used replace NA empty values output. nested (flag) whether layout instruction applied within existing layout structure _if possible (TRUE, default) new top-level element (FALSE). Ignored nest split. underneath analyses, allowed. ... additional arguments lower level functions. table_names (character) can customized case vars analyzed multiple times, avoid warnings rtables. .stats (character) statistics select table. Options : 'n', 'count', 'count_fraction', 'count_fraction_fixed_dp', 'n_blq' .formats (named character list) formats statistics. See Details analyze_vars information \"auto\" setting. .labels (named character) labels statistics (without indent). .indent_mods (named integer) indent modifiers labels. Defaults 0, corresponds unmodified default behavior. Can negative. x (numeric) vector numbers want analyze. na.rm (flag) whether NA values removed x prior analysis. .N_col (integer(1)) column-wise N (column count) full column analyzed typically passed rtables. .N_row (integer(1)) row-wise N (row group count) group observations analyzed (.e. column-based subsetting) typically passed rtables. denom (string) choice denominator proportion. Options : n: number values row column intersection. N_row: total number values row across columns. N_col: total number values column across rows.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/count_values.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Count specific values — count_values","text":"count_values() returns layout object suitable passing layouting functions, rtables::build_table(). Adding function rtable layout add formatted rows containing statistics s_count_values() table layout. s_count_values() returns output s_summary() specified values non-numeric variable. a_count_values() returns corresponding list formatted rtables::CellValue().","code":""},{"path":"https://insightsengineering.github.io/tern/reference/count_values.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Count specific values — count_values","text":"count_values(): Layout-creating function can take statistics function arguments additional format arguments. function wrapper rtables::analyze(). s_count_values(): S3 generic function count values. s_count_values(character): Method character class. s_count_values(factor): Method factor class. makes automatic conversion character forwards method characters. s_count_values(logical): Method logical class. a_count_values(): Formatted analysis function used afun count_values().","code":""},{"path":"https://insightsengineering.github.io/tern/reference/count_values.html","id":"note","dir":"Reference","previous_headings":"","what":"Note","title":"Count specific values — count_values","text":"factor variables, s_count_values checks whether values included levels x fails otherwise. count_values(), variable labels shown one element vars, otherwise hidden.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/count_values.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Count specific values — count_values","text":"","code":"# `count_values` basic_table() %>%   count_values(\"Species\", values = \"setosa\") %>%   build_table(iris) #>            all obs   #> ———————————————————— #> setosa   50 (33.33%)  # `s_count_values.character` s_count_values(x = c(\"a\", \"b\", \"a\"), values = \"a\") #> $n #> [1] 3 #>  #> $count #> [1] 2 #>  #> $count_fraction #> [1] 2.0000000 0.6666667 #>  #> $n_blq #> [1] 0 #>  s_count_values(x = c(\"a\", \"b\", \"a\", NA, NA), values = \"b\", na.rm = FALSE) #> $n #> [1] 5 #>  #> $count #> [1] 1 #>  #> $count_fraction #> [1] 1.0 0.2 #>  #> $n_blq #> [1] 0 #>   # `s_count_values.factor` s_count_values(x = factor(c(\"a\", \"b\", \"a\")), values = \"a\") #> $n #> [1] 3 #>  #> $count #> [1] 2 #>  #> $count_fraction #> [1] 2.0000000 0.6666667 #>  #> $n_blq #> [1] 0 #>   # `s_count_values.logical` s_count_values(x = c(TRUE, FALSE, TRUE)) #> $n #> [1] 3 #>  #> $count #> [1] 2 #>  #> $count_fraction #> [1] 2.0000000 0.6666667 #>  #> $n_blq #> [1] 0 #>   # `a_count_values` a_count_values(x = factor(c(\"a\", \"b\", \"a\")), values = \"a\", .N_col = 10, .N_row = 10) #> RowsVerticalSection (in_rows) object print method: #> ---------------------------- #>         row_name formatted_cell indent_mod      row_label #> 1              n              3          0              n #> 2          count              2          0          count #> 3 count_fraction     2 (66.67%)          0 count_fraction #> 4          n_blq              0          0          n_blq"},{"path":"https://insightsengineering.github.io/tern/reference/cox_regression.html","id":null,"dir":"Reference","previous_headings":"","what":"Cox proportional hazards regression — cox_regression","title":"Cox proportional hazards regression — cox_regression","text":"Fits Cox regression model estimates hazard ratio describe effect size survival analysis.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/cox_regression.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Cox proportional hazards regression — cox_regression","text":"","code":"summarize_coxreg(   lyt,   variables,   control = control_coxreg(),   at = list(),   multivar = FALSE,   common_var = \"STUDYID\",   .stats = c(\"n\", \"hr\", \"ci\", \"pval\", \"pval_inter\"),   .formats = c(n = \"xx\", hr = \"xx.xx\", ci = \"(xx.xx, xx.xx)\", pval =     \"x.xxxx | (<0.0001)\", pval_inter = \"x.xxxx | (<0.0001)\"),   varlabels = NULL,   .indent_mods = NULL,   na_str = \"\",   .section_div = NA_character_ )  s_coxreg(model_df, .stats, .which_vars = \"all\", .var_nms = NULL)  a_coxreg(   df,   labelstr,   eff = FALSE,   var_main = FALSE,   multivar = FALSE,   variables,   at = list(),   control = control_coxreg(),   .spl_context,   .stats,   .formats,   .indent_mods = NULL,   na_str = \"\",   cache_env = NULL )"},{"path":"https://insightsengineering.github.io/tern/reference/cox_regression.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Cox proportional hazards regression — cox_regression","text":"lyt (PreDataTableLayouts) layout analyses added . variables (named list string) list additional analysis variables. control (list) list parameters returned helper function control_coxreg(). (list numeric) candidate covariate numeric, use specify value covariate effect estimated. multivar (flag) whether multivariate Cox regression run (defaults FALSE), otherwise univariate Cox regression run. common_var (string) name factor variable dataset takes value rows. created pre-processing variable currently exists. .stats (character) names statistics reported among: n: number observations (univariate ) hr: hazard ratio ci: confidence interval pval: p-value treatment effect pval_inter: p-value interaction effect treatment covariate (univariate ) .formats (named character list) formats statistics. See Details analyze_vars information \"auto\" setting. varlabels (list) named list corresponds names variables found data, passed named list corresponding time, event, arm, strata, covariates terms. arm missing variables, Cox model(s) including covariates fitted corresponding effect estimates tabulated later. .indent_mods (named integer) indent modifiers labels. Defaults 0, corresponds unmodified default behavior. Can negative. na_str (string) custom string replace NA values . Defaults \"\". .section_div (string NA) string repeated section divider sections. Defaults NA section divider. vector two strings given, first used treatment covariate sections second different covariates. model_df (data.frame) contains resulting model fit fit_coxreg function tidying applied via broom::tidy(). .which_vars (character) rows statistics returned given model. Defaults \"\". options include \"var_main\" main effects, \"inter\" interaction effects, \"multi_lvl\" multivariate model covariate level rows. .which_vars \"\", specific variables can selected specifying .var_nms. .var_nms (character) term value rows df .stats returned. Typically name variable. using variable labels, var vector desired variable name variable label order see .stats related variable. .which_vars \"var_main\", .var_nms variable name. df (data.frame) data set containing analysis variables. labelstr (string) label level parent split currently summarized (must present second argument Content Row Functions). See rtables::summarize_row_groups() information. eff (flag) whether treatment effect calculated. Defaults FALSE. var_main (flag) whether main effects calculated. Defaults FALSE. .spl_context (data.frame) gives information ancestor split states passed rtables. cache_env (environment) environment object used cache regression model order avoid repeatedly fitting model every row table. Defaults NULL (caching).","code":""},{"path":"https://insightsengineering.github.io/tern/reference/cox_regression.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Cox proportional hazards regression — cox_regression","text":"summarize_coxreg() returns layout object suitable passing layouting functions, rtables::build_table(). Adding function rtable layout add Cox regression table containing chosen statistics table layout. s_coxreg() returns selected statistic Cox regression model selected variable(s). a_coxreg() returns formatted rtables::CellValue().","code":""},{"path":"https://insightsengineering.github.io/tern/reference/cox_regression.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Cox proportional hazards regression — cox_regression","text":"Cox models commonly used methods estimate magnitude effect survival analysis. assumes proportional hazards: ratio hazards groups (e.g., two arms) constant time. ratio referred \"hazard ratio\" (HR) one commonly reported metrics describe effect size survival analysis (NEST Team, 2020).","code":""},{"path":"https://insightsengineering.github.io/tern/reference/cox_regression.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Cox proportional hazards regression — cox_regression","text":"summarize_coxreg(): Layout-creating function creates Cox regression summary table layout. function wrapper several rtables layouting functions. function wrapper rtables::analyze_colvars() rtables::summarize_row_groups(). s_coxreg(): Statistics function transforms results tabulated fit_coxreg_univar() fit_coxreg_multivar() list. a_coxreg(): Analysis function used afun rtables::analyze() cfun rtables::summarize_row_groups() within summarize_coxreg().","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/reference/cox_regression.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Cox proportional hazards regression — cox_regression","text":"","code":"library(survival)  # Testing dataset [survival::bladder]. set.seed(1, kind = \"Mersenne-Twister\") dta_bladder <- with(   data = bladder[bladder$enum < 5, ],   tibble::tibble(     TIME = stop,     STATUS = event,     ARM = as.factor(rx),     COVAR1 = as.factor(enum) %>% formatters::with_label(\"A Covariate Label\"),     COVAR2 = factor(       sample(as.factor(enum)),       levels = 1:4, labels = c(\"F\", \"F\", \"M\", \"M\")     ) %>% formatters::with_label(\"Sex (F/M)\")   ) ) dta_bladder$AGE <- sample(20:60, size = nrow(dta_bladder), replace = TRUE) dta_bladder$STUDYID <- factor(\"X\")  u1_variables <- list(   time = \"TIME\", event = \"STATUS\", arm = \"ARM\", covariates = c(\"COVAR1\", \"COVAR2\") )  u2_variables <- list(time = \"TIME\", event = \"STATUS\", covariates = c(\"COVAR1\", \"COVAR2\"))  m1_variables <- list(   time = \"TIME\", event = \"STATUS\", arm = \"ARM\", covariates = c(\"COVAR1\", \"COVAR2\") )  m2_variables <- list(time = \"TIME\", event = \"STATUS\", covariates = c(\"COVAR1\", \"COVAR2\"))  # summarize_coxreg  result_univar <- basic_table() %>%   summarize_coxreg(variables = u1_variables) %>%   build_table(dta_bladder) result_univar #>                        n    Hazard Ratio      95% CI      p-value #> ————————————————————————————————————————————————————————————————— #> Treatment:                                                        #>   2 vs control (1)    340       0.64       (0.43, 0.94)   0.0242  #> Covariate:                                                        #>   A Covariate Label   340       0.61       (0.41, 0.90)   0.0126  #>   Sex (F/M)           340       0.62       (0.42, 0.92)   0.0182   result_univar_covs <- basic_table() %>%   summarize_coxreg(     variables = u2_variables,   ) %>%   build_table(dta_bladder) result_univar_covs #>                                       Hazard Ratio      95% CI      p-value #> ——————————————————————————————————————————————————————————————————————————— #> Covariate:                                                                  #>   A Covariate Label (reference = 1)                                 <0.0001 #>     2                                     0.45       (0.28, 0.71)   0.0007  #>     3                                     0.31       (0.19, 0.52)   <0.0001 #>     4                                     0.18       (0.10, 0.33)   <0.0001 #>   Sex (F/M) (reference = F)                                                 #>     M                                     1.33       (0.91, 1.94)   0.1414   result_multivar <- basic_table() %>%   summarize_coxreg(     variables = m1_variables,     multivar = TRUE,   ) %>%   build_table(dta_bladder) result_multivar #>                                       Hazard Ratio      95% CI      p-value #> ——————————————————————————————————————————————————————————————————————————— #> Treatment:                                                                  #>   ARM (reference = 1)                                                       #>     2                                     0.61       (0.41, 0.90)   0.0123  #> Covariate:                                                                  #>   A Covariate Label (reference = 1)                                 <0.0001 #>     2                                     0.46       (0.28, 0.73)   0.0011  #>     3                                     0.31       (0.18, 0.51)   <0.0001 #>     4                                     0.18       (0.10, 0.33)   <0.0001 #>   Sex (F/M) (reference = F)                                                 #>     M                                     1.29       (0.88, 1.89)   0.1911   result_multivar_covs <- basic_table() %>%   summarize_coxreg(     variables = m2_variables,     multivar = TRUE,     varlabels = c(\"Covariate 1\", \"Covariate 2\") # custom labels   ) %>%   build_table(dta_bladder) result_multivar_covs #>                                 Hazard Ratio      95% CI      p-value #> ————————————————————————————————————————————————————————————————————— #> Covariate:                                                            #>   Covariate 1 (reference = 1)                                 <0.0001 #>     2                               0.46       (0.29, 0.74)   0.0012  #>     3                               0.31       (0.19, 0.52)   <0.0001 #>     4                               0.19       (0.10, 0.34)   <0.0001 #>   Covariate 2 (reference = F)                                         #>     M                               1.29       (0.88, 1.88)   0.1958   # s_coxreg  # Univariate univar_model <- fit_coxreg_univar(variables = u1_variables, data = dta_bladder) df1 <- broom::tidy(univar_model)  s_coxreg(model_df = df1, .stats = \"hr\") #> $hr #> $hr$`2 vs control (1)` #> [1] 0.6386426 #>  #>  #> $hr #> $hr$`A Covariate Label` #> [1] 0.607037 #>  #>  #> $hr #> $hr$`Sex (F/M)` #> [1] 0.6242738 #>  #>   # Univariate with interactions univar_model_inter <- fit_coxreg_univar(   variables = u1_variables, control = control_coxreg(interaction = TRUE), data = dta_bladder ) df1_inter <- broom::tidy(univar_model_inter)  s_coxreg(model_df = df1_inter, .stats = \"hr\", .which_vars = \"inter\", .var_nms = \"COVAR1\") #> $hr #> $hr$`  1` #> [1] 0.6284569 #>  #> $hr$`  2` #> [1] 0.5806499 #>  #> $hr$`  3` #> [1] 0.5486103 #>  #> $hr$`  4` #> [1] 0.6910725 #>  #>   # Univariate without treatment arm - only \"COVAR2\" covariate effects univar_covs_model <- fit_coxreg_univar(variables = u2_variables, data = dta_bladder) df1_covs <- broom::tidy(univar_covs_model)  s_coxreg(model_df = df1_covs, .stats = \"hr\", .var_nms = c(\"COVAR2\", \"Sex (F/M)\")) #> $hr #> $hr$`Sex (F/M) (reference = F)` #> numeric(0) #>  #>  #> $hr #> $hr$M #> [1] 1.3271 #>  #>   # Multivariate. multivar_model <- fit_coxreg_multivar(variables = m1_variables, data = dta_bladder) df2 <- broom::tidy(multivar_model)  s_coxreg(model_df = df2, .stats = \"pval\", .which_vars = \"var_main\", .var_nms = \"COVAR1\") #> $pval #> $pval$`A Covariate Label (reference = 1)` #> [1] 7.209956e-09 #>  #>  s_coxreg(   model_df = df2, .stats = \"pval\", .which_vars = \"multi_lvl\",   .var_nms = c(\"COVAR1\", \"A Covariate Label\") ) #> $pval #> $pval$`2` #> [1] 0.001120332 #>  #> $pval$`3` #> [1] 6.293725e-06 #>  #> $pval$`4` #> [1] 3.013875e-08 #>  #>   # Multivariate without treatment arm - only \"COVAR1\" main effect multivar_covs_model <- fit_coxreg_multivar(variables = m2_variables, data = dta_bladder) df2_covs <- broom::tidy(multivar_covs_model)  s_coxreg(model_df = df2_covs, .stats = \"hr\") #> $hr #> $hr$`2` #> [1] 0.4600728 #>  #> $hr$`3` #> [1] 0.3100455 #>  #> $hr$`4` #> [1] 0.1854177 #>  #>  #> $hr #> $hr$`A Covariate Label (reference = 1)` #> numeric(0) #>  #>  #> $hr #> $hr$`Sex (F/M) (reference = F)` #> numeric(0) #>  #>  #> $hr #> $hr$M #> [1] 1.285406 #>  #>   a_coxreg(   df = dta_bladder,   labelstr = \"Label 1\",   variables = u1_variables,   .spl_context = list(value = \"COVAR1\"),   .stats = \"n\",   .formats = \"xx\" ) #> RowsVerticalSection (in_rows) object print method: #> ---------------------------- #>   row_name formatted_cell indent_mod row_label #> 1  Label 1            340          0   Label 1  a_coxreg(   df = dta_bladder,   labelstr = \"\",   variables = u1_variables,   .spl_context = list(value = \"COVAR2\"),   .stats = \"pval\",   .formats = \"xx.xxxx\" ) #> RowsVerticalSection (in_rows) object print method: #> ---------------------------- #>    row_name formatted_cell indent_mod row_label #> 1 Sex (F/M)         0.0182          0 Sex (F/M)"},{"path":"https://insightsengineering.github.io/tern/reference/cox_regression_inter.html","id":null,"dir":"Reference","previous_headings":"","what":"Cox regression helper function for interactions — cox_regression_inter","title":"Cox regression helper function for interactions — cox_regression_inter","text":"Test estimate effect treatment interaction covariate. effect estimated HR tested treatment given level covariate, comparison treatment control.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/cox_regression_inter.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Cox regression helper function for interactions — cox_regression_inter","text":"","code":"h_coxreg_inter_effect(x, effect, covar, mod, label, control, ...)  # S3 method for class 'numeric' h_coxreg_inter_effect(x, effect, covar, mod, label, control, at, ...)  # S3 method for class 'factor' h_coxreg_inter_effect(x, effect, covar, mod, label, control, data, ...)  # S3 method for class 'character' h_coxreg_inter_effect(x, effect, covar, mod, label, control, data, ...)  h_coxreg_extract_interaction(effect, covar, mod, data, at, control)  h_coxreg_inter_estimations(   variable,   given,   lvl_var,   lvl_given,   mod,   conf_level = 0.95 )"},{"path":"https://insightsengineering.github.io/tern/reference/cox_regression_inter.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Cox regression helper function for interactions — cox_regression_inter","text":"x (numeric factor) values covariate tested. effect (string) name effect tested estimated. covar (string) name covariate model. mod (coxph) fitted Cox regression model (see survival::coxph()). label (string) label returned term_label. control (list) list controls returned control_coxreg(). ... see methods. (list) list items named covariate, every item vector levels interaction estimated. data (data.frame) data frame model fit. variable, given (string) name variables interaction. seek estimation levels variable given levels given. lvl_var, lvl_given (character) corresponding levels given levels(). conf_level (proportion) confidence level interval.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/cox_regression_inter.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Cox regression helper function for interactions — cox_regression_inter","text":"h_coxreg_inter_effect() returns data.frame covariate interaction effects consisting following variables: effect, term, term_label, level, n, hr, lcl, ucl, pval, pval_inter. h_coxreg_extract_interaction() returns result interaction test estimated values. interaction, h_coxreg_univar_extract() applied instead. h_coxreg_inter_estimations() returns list matrices (one per level variable) rows corresponding combinations variable given, columns: coef_hat: Estimation coefficient. coef_se: Standard error estimation. hr: Hazard ratio. lcl, ucl: Lower/upper confidence limit hazard ratio.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/cox_regression_inter.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Cox regression helper function for interactions — cox_regression_inter","text":"Given cox regression investigating effect Arm (, B, C; reference ) Sex (F, M; reference Female) model abbreviated: y ~ Arm + Sex + Arm:Sex. cox regression estimates coefficients along variance-covariance matrix : b1 (arm b), b2 (arm c) b3 (sex m) b4 (arm b: sex m), b5 (arm c: sex m) estimation Hazard Ratio arm C/sex M given reference arm /Sex M exp(b2 + b3 + b5)/ exp(b3) = exp(b2 + b5). interaction coefficient deduced b2 + b5 standard error obtained $sqrt(Var b2 + Var b5 + 2 * covariance (b2,b5))$.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/cox_regression_inter.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Cox regression helper function for interactions — cox_regression_inter","text":"h_coxreg_inter_effect(): S3 generic helper function determine interaction effect. h_coxreg_inter_effect(numeric): Method numeric class. Estimates interaction numeric covariate. h_coxreg_inter_effect(factor): Method factor class. Estimate interaction factor covariate. h_coxreg_inter_effect(character): Method character class. Estimate interaction character covariate. makes automatic conversion factor forwards method factors. h_coxreg_extract_interaction(): higher level function get results interaction test estimated values. h_coxreg_inter_estimations(): Hazard ratio estimation interactions.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/cox_regression_inter.html","id":"note","dir":"Reference","previous_headings":"","what":"Note","title":"Cox regression helper function for interactions — cox_regression_inter","text":"Automatic conversion character factor guarantee results can generated correctly. therefore better always pre-process dataset factors manually created character variables passing dataset rtables::build_table().","code":""},{"path":"https://insightsengineering.github.io/tern/reference/cox_regression_inter.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Cox regression helper function for interactions — cox_regression_inter","text":"","code":"library(survival)  set.seed(1, kind = \"Mersenne-Twister\")  # Testing dataset [survival::bladder]. dta_bladder <- with(   data = bladder[bladder$enum < 5, ],   data.frame(     time = stop,     status = event,     armcd = as.factor(rx),     covar1 = as.factor(enum),     covar2 = factor(       sample(as.factor(enum)),       levels = 1:4,       labels = c(\"F\", \"F\", \"M\", \"M\")     )   ) ) labels <- c(\"armcd\" = \"ARM\", \"covar1\" = \"A Covariate Label\", \"covar2\" = \"Sex (F/M)\") formatters::var_labels(dta_bladder)[names(labels)] <- labels dta_bladder$age <- sample(20:60, size = nrow(dta_bladder), replace = TRUE)  plot(   survfit(Surv(time, status) ~ armcd + covar1, data = dta_bladder),   lty = 2:4,   xlab = \"Months\",   col = c(\"blue1\", \"blue2\", \"blue3\", \"blue4\", \"red1\", \"red2\", \"red3\", \"red4\") )   mod <- coxph(Surv(time, status) ~ armcd * covar1, data = dta_bladder) h_coxreg_extract_interaction(   mod = mod, effect = \"armcd\", covar = \"covar1\", data = dta_bladder,   control = control_coxreg() ) #>                    effect   term        term_label level   n        hr #> 1              Covariate: covar1 A Covariate Label       340        NA #> armcd2/covar11 Covariate: covar1                 1     1  NA 0.6341111 #> armcd2/covar12 Covariate: covar1                 2     2  NA 0.5845305 #> armcd2/covar13 Covariate: covar1                 3     3  NA 0.5507703 #> armcd2/covar14 Covariate: covar1                 4     4  NA 0.6910643 #>                      lcl      ucl      pval pval_inter #> 1                     NA       NA 0.1302825   0.988245 #> armcd2/covar11 0.3514676 1.144051        NA         NA #> armcd2/covar12 0.2716689 1.257692        NA         NA #> armcd2/covar13 0.2244668 1.351415        NA         NA #> armcd2/covar14 0.2315248 2.062715        NA         NA  mod <- coxph(Surv(time, status) ~ armcd * covar1, data = dta_bladder) result <- h_coxreg_inter_estimations(   variable = \"armcd\", given = \"covar1\",   lvl_var = levels(dta_bladder$armcd),   lvl_given = levels(dta_bladder$covar1),   mod = mod, conf_level = .95 ) result #> $armcd2 #>                      coef  se(coef)        hr       lcl      ucl #> armcd2/covar11 -0.4555312 0.3010803 0.6341111 0.3514676 1.144051 #> armcd2/covar12 -0.5369464 0.3909383 0.5845305 0.2716689 1.257692 #> armcd2/covar13 -0.5964375 0.4579624 0.5507703 0.2244668 1.351415 #> armcd2/covar14 -0.3695225 0.5579418 0.6910643 0.2315248 2.062715 #>  #> attr(,\"details\") #> [1] \"Estimations of armcd hazard ratio given the level of covar1 compared to armcd level 1.\""},{"path":"https://insightsengineering.github.io/tern/reference/cut_quantile_bins.html","id":null,"dir":"Reference","previous_headings":"","what":"Cut numeric vector into empirical quantile bins — cut_quantile_bins","title":"Cut numeric vector into empirical quantile bins — cut_quantile_bins","text":"cuts numeric vector sample quantile bins.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/cut_quantile_bins.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Cut numeric vector into empirical quantile bins — cut_quantile_bins","text":"","code":"cut_quantile_bins(   x,   probs = c(0.25, 0.5, 0.75),   labels = NULL,   type = 7,   ordered = TRUE )"},{"path":"https://insightsengineering.github.io/tern/reference/cut_quantile_bins.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Cut numeric vector into empirical quantile bins — cut_quantile_bins","text":"x (numeric) continuous variable values cut quantile bins. may contain NA values, used quantile calculations, included return vector. probs (numeric) probabilities identifying quantiles. sorted vector unique proportion values, .e. 0 1, boundaries 0 1 must included. labels (character) unique labels quantile bins. n probabilities probs, must n + 1 long. type (integer(1)) type quantiles use, see stats::quantile() details. ordered (flag) result ordered factor.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/cut_quantile_bins.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Cut numeric vector into empirical quantile bins — cut_quantile_bins","text":"factor variable appropriately-labeled bins levels.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/cut_quantile_bins.html","id":"note","dir":"Reference","previous_headings":"","what":"Note","title":"Cut numeric vector into empirical quantile bins — cut_quantile_bins","text":"Intervals closed right side. , first bin interval [-Inf, q1] q1 first quantile, second bin (q1, q2], etc., last bin (qn, +Inf] qn last quantile.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/cut_quantile_bins.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Cut numeric vector into empirical quantile bins — cut_quantile_bins","text":"","code":"# Default is to cut into quartile bins. cut_quantile_bins(cars$speed) #>  [1] [0%,25%]   [0%,25%]   [0%,25%]   [0%,25%]   [0%,25%]   [0%,25%]   #>  [7] [0%,25%]   [0%,25%]   [0%,25%]   [0%,25%]   [0%,25%]   [0%,25%]   #> [13] [0%,25%]   [0%,25%]   [0%,25%]   (25%,50%]  (25%,50%]  (25%,50%]  #> [19] (25%,50%]  (25%,50%]  (25%,50%]  (25%,50%]  (25%,50%]  (25%,50%]  #> [25] (25%,50%]  (25%,50%]  (50%,75%]  (50%,75%]  (50%,75%]  (50%,75%]  #> [31] (50%,75%]  (50%,75%]  (50%,75%]  (50%,75%]  (50%,75%]  (50%,75%]  #> [37] (50%,75%]  (50%,75%]  (75%,100%] (75%,100%] (75%,100%] (75%,100%] #> [43] (75%,100%] (75%,100%] (75%,100%] (75%,100%] (75%,100%] (75%,100%] #> [49] (75%,100%] (75%,100%] #> Levels: [0%,25%] < (25%,50%] < (50%,75%] < (75%,100%]  # Use custom quantiles. cut_quantile_bins(cars$speed, probs = c(0.1, 0.2, 0.6, 0.88)) #>  [1] [0%,10%]   [0%,10%]   [0%,10%]   [0%,10%]   [0%,10%]   (10%,20%]  #>  [7] (10%,20%]  (10%,20%]  (10%,20%]  (10%,20%]  (10%,20%]  (20%,60%]  #> [13] (20%,60%]  (20%,60%]  (20%,60%]  (20%,60%]  (20%,60%]  (20%,60%]  #> [19] (20%,60%]  (20%,60%]  (20%,60%]  (20%,60%]  (20%,60%]  (20%,60%]  #> [25] (20%,60%]  (20%,60%]  (20%,60%]  (20%,60%]  (20%,60%]  (20%,60%]  #> [31] (20%,60%]  (60%,88%]  (60%,88%]  (60%,88%]  (60%,88%]  (60%,88%]  #> [37] (60%,88%]  (60%,88%]  (60%,88%]  (60%,88%]  (60%,88%]  (60%,88%]  #> [43] (60%,88%]  (60%,88%]  (88%,100%] (88%,100%] (88%,100%] (88%,100%] #> [49] (88%,100%] (88%,100%] #> Levels: [0%,10%] < (10%,20%] < (20%,60%] < (60%,88%] < (88%,100%]  # Use custom labels. cut_quantile_bins(cars$speed, labels = paste0(\"Q\", 1:4)) #>  [1] Q1 Q1 Q1 Q1 Q1 Q1 Q1 Q1 Q1 Q1 Q1 Q1 Q1 Q1 Q1 Q2 Q2 Q2 Q2 Q2 Q2 Q2 Q2 Q2 Q2 #> [26] Q2 Q3 Q3 Q3 Q3 Q3 Q3 Q3 Q3 Q3 Q3 Q3 Q3 Q4 Q4 Q4 Q4 Q4 Q4 Q4 Q4 Q4 Q4 Q4 Q4 #> Levels: Q1 < Q2 < Q3 < Q4  # NAs are preserved in result factor. ozone_binned <- cut_quantile_bins(airquality$Ozone) which(is.na(ozone_binned)) #>  [1]   5  10  25  26  27  32  33  34  35  36  37  39  42  43  45  46  52  53  54 #> [20]  55  56  57  58  59  60  61  65  72  75  83  84 102 103 107 115 119 150 # So you might want to make these explicit. explicit_na(ozone_binned) #>   [1] (50%,75%]  (50%,75%]  [0%,25%]   [0%,25%]   <Missing>  (25%,50%]  #>   [7] (25%,50%]  (25%,50%]  [0%,25%]   <Missing>  [0%,25%]   [0%,25%]   #>  [13] [0%,25%]   [0%,25%]   [0%,25%]   [0%,25%]   (50%,75%]  [0%,25%]   #>  [19] (25%,50%]  [0%,25%]   [0%,25%]   [0%,25%]   [0%,25%]   (50%,75%]  #>  [25] <Missing>  <Missing>  <Missing>  (25%,50%]  (50%,75%]  (75%,100%] #>  [31] (50%,75%]  <Missing>  <Missing>  <Missing>  <Missing>  <Missing>  #>  [37] <Missing>  (25%,50%]  <Missing>  (75%,100%] (50%,75%]  <Missing>  #>  [43] <Missing>  (25%,50%]  <Missing>  <Missing>  (25%,50%]  (50%,75%]  #>  [49] (25%,50%]  [0%,25%]   [0%,25%]   <Missing>  <Missing>  <Missing>  #>  [55] <Missing>  <Missing>  <Missing>  <Missing>  <Missing>  <Missing>  #>  [61] <Missing>  (75%,100%] (50%,75%]  (50%,75%]  <Missing>  (75%,100%] #>  [67] (50%,75%]  (75%,100%] (75%,100%] (75%,100%] (75%,100%] <Missing>  #>  [73] [0%,25%]   (25%,50%]  <Missing>  [0%,25%]   (50%,75%]  (50%,75%]  #>  [79] (50%,75%]  (75%,100%] (50%,75%]  [0%,25%]   <Missing>  <Missing>  #>  [85] (75%,100%] (75%,100%] (25%,50%]  (50%,75%]  (75%,100%] (50%,75%]  #>  [91] (75%,100%] (50%,75%]  (50%,75%]  [0%,25%]   [0%,25%]   (75%,100%] #>  [97] (50%,75%]  (75%,100%] (75%,100%] (75%,100%] (75%,100%] <Missing>  #> [103] <Missing>  (50%,75%]  (25%,50%]  (75%,100%] <Missing>  (25%,50%]  #> [109] (50%,75%]  (25%,50%]  (25%,50%]  (50%,75%]  (25%,50%]  [0%,25%]   #> [115] <Missing>  (50%,75%]  (75%,100%] (75%,100%] <Missing>  (75%,100%] #> [121] (75%,100%] (75%,100%] (75%,100%] (75%,100%] (75%,100%] (75%,100%] #> [127] (75%,100%] (50%,75%]  (50%,75%]  (25%,50%]  (25%,50%]  (25%,50%]  #> [133] (25%,50%]  (50%,75%]  (25%,50%]  (25%,50%]  [0%,25%]   [0%,25%]   #> [139] (50%,75%]  [0%,25%]   [0%,25%]   (25%,50%]  [0%,25%]   [0%,25%]   #> [145] (25%,50%]  (50%,75%]  [0%,25%]   [0%,25%]   (25%,50%]  <Missing>  #> [151] [0%,25%]   [0%,25%]   (25%,50%]  #> Levels: [0%,25%] < (25%,50%] < (50%,75%] < (75%,100%] < <Missing>"},{"path":"https://insightsengineering.github.io/tern/reference/d_count_abnormal_by_baseline.html","id":null,"dir":"Reference","previous_headings":"","what":"Description function for s_count_abnormal_by_baseline() — d_count_abnormal_by_baseline","title":"Description function for s_count_abnormal_by_baseline() — d_count_abnormal_by_baseline","text":"Description function produces labels s_count_abnormal_by_baseline().","code":""},{"path":"https://insightsengineering.github.io/tern/reference/d_count_abnormal_by_baseline.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Description function for s_count_abnormal_by_baseline() — d_count_abnormal_by_baseline","text":"","code":"d_count_abnormal_by_baseline(abnormal)"},{"path":"https://insightsengineering.github.io/tern/reference/d_count_abnormal_by_baseline.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Description function for s_count_abnormal_by_baseline() — d_count_abnormal_by_baseline","text":"abnormal (character) values identifying abnormal range level(s) .var.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/d_count_abnormal_by_baseline.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Description function for s_count_abnormal_by_baseline() — d_count_abnormal_by_baseline","text":"Abnormal category labels s_count_abnormal_by_baseline().","code":""},{"path":"https://insightsengineering.github.io/tern/reference/d_count_abnormal_by_baseline.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Description function for s_count_abnormal_by_baseline() — d_count_abnormal_by_baseline","text":"","code":"d_count_abnormal_by_baseline(\"LOW\") #> $not_abnormal #> [1] \"Not low\" #>  #> $abnormal #> [1] \"Low\" #>  #> $total #> [1] \"Total\" #>"},{"path":"https://insightsengineering.github.io/tern/reference/d_count_cumulative.html","id":null,"dir":"Reference","previous_headings":"","what":"Description of cumulative count — d_count_cumulative","title":"Description of cumulative count — d_count_cumulative","text":"helper function describes analysis s_count_cumulative().","code":""},{"path":"https://insightsengineering.github.io/tern/reference/d_count_cumulative.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Description of cumulative count — d_count_cumulative","text":"","code":"d_count_cumulative(threshold, lower_tail = TRUE, include_eq = TRUE)"},{"path":"https://insightsengineering.github.io/tern/reference/d_count_cumulative.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Description of cumulative count — d_count_cumulative","text":"threshold (numeric(1)) cutoff value threshold count values x. lower_tail (flag) whether count lower tail, default TRUE. include_eq (flag) whether include value equal threshold count, default TRUE.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/d_count_cumulative.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Description of cumulative count — d_count_cumulative","text":"Labels s_count_cumulative().","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/reference/d_count_missed_doses.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Description function that calculates labels for s_count_missed_doses() — d_count_missed_doses","text":"","code":"d_count_missed_doses(thresholds)"},{"path":"https://insightsengineering.github.io/tern/reference/d_count_missed_doses.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Description function that calculates labels for s_count_missed_doses() — d_count_missed_doses","text":"thresholds (numeric) minimum number missed doses patients .","code":""},{"path":"https://insightsengineering.github.io/tern/reference/d_count_missed_doses.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Description function that calculates labels for s_count_missed_doses() — d_count_missed_doses","text":"d_count_missed_doses() returns named character vector labels.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/reference/d_onco_rsp_label.html","id":null,"dir":"Reference","previous_headings":"","what":"Description of standard oncology response — d_onco_rsp_label","title":"Description of standard oncology response — d_onco_rsp_label","text":"Describe oncology response standard way.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/d_onco_rsp_label.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Description of standard oncology response — d_onco_rsp_label","text":"","code":"d_onco_rsp_label(x)"},{"path":"https://insightsengineering.github.io/tern/reference/d_onco_rsp_label.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Description of standard oncology response — d_onco_rsp_label","text":"x (character) standard oncology codes described.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/d_onco_rsp_label.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Description of standard oncology response — d_onco_rsp_label","text":"Response labels.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/reference/d_onco_rsp_label.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Description of standard oncology response — d_onco_rsp_label","text":"","code":"d_onco_rsp_label(   c(\"CR\", \"PR\", \"SD\", \"NON CR/PD\", \"PD\", \"NE\", \"Missing\", \"<Missing>\", \"NE/Missing\") ) #>                           CR                           PR  #>       Complete Response (CR)        Partial Response (PR)  #>                           SD                    NON CR/PD  #>          Stable Disease (SD) Non-CR or Non-PD (NON CR/PD)  #>                           PD                           NE  #>     Progressive Disease (PD)           Not Evaluable (NE)  #>                      Missing                    <Missing>  #>                      Missing                    <Missing>  #>                   NE/Missing  #>       Missing or unevaluable  #> 9 Levels: Complete Response (CR) Partial Response (PR) ... <Missing>  # Adding some values not considered in d_onco_rsp_label  d_onco_rsp_label(   c(\"CR\", \"PR\", \"hello\", \"hi\") ) #>                     CR                     PR                  hello  #> Complete Response (CR)  Partial Response (PR)                  hello  #>                     hi  #>                     hi  #> Levels: Complete Response (CR) Partial Response (PR) hello hi"},{"path":[]},{"path":"https://insightsengineering.github.io/tern/reference/d_pkparam.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Generate PK reference dataset — d_pkparam","text":"","code":"d_pkparam()"},{"path":"https://insightsengineering.github.io/tern/reference/d_pkparam.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Generate PK reference dataset — d_pkparam","text":"data.frame PK parameters.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/d_pkparam.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Generate PK reference dataset — d_pkparam","text":"","code":"pk_reference_dataset <- d_pkparam()"},{"path":"https://insightsengineering.github.io/tern/reference/d_proportion.html","id":null,"dir":"Reference","previous_headings":"","what":"Description of the proportion summary — d_proportion","title":"Description of the proportion summary — d_proportion","text":"helper function describes analysis s_proportion().","code":""},{"path":"https://insightsengineering.github.io/tern/reference/d_proportion.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Description of the proportion summary — d_proportion","text":"","code":"d_proportion(conf_level, method, long = FALSE)"},{"path":"https://insightsengineering.github.io/tern/reference/d_proportion.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Description of the proportion summary — d_proportion","text":"conf_level (proportion) confidence level interval. method (string) method used construct confidence interval proportion successful outcomes; one waldcc, wald, clopper-pearson, wilson, wilsonc, strat_wilson, strat_wilsonc, agresti-coull jeffreys. long (flag) whether long short (default) description required.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/d_proportion.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Description of the proportion summary — d_proportion","text":"String describing analysis.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/d_proportion_diff.html","id":null,"dir":"Reference","previous_headings":"","what":"Description of method used for proportion comparison — d_proportion_diff","title":"Description of method used for proportion comparison — d_proportion_diff","text":"auxiliary function describes analysis s_proportion_diff().","code":""},{"path":"https://insightsengineering.github.io/tern/reference/d_proportion_diff.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Description of method used for proportion comparison — d_proportion_diff","text":"","code":"d_proportion_diff(conf_level, method, long = FALSE)"},{"path":"https://insightsengineering.github.io/tern/reference/d_proportion_diff.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Description of method used for proportion comparison — d_proportion_diff","text":"conf_level (proportion) confidence level interval. method (string) method used confidence interval estimation. long (flag) whether long (TRUE) short (FALSE, default) description required.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/d_proportion_diff.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Description of method used for proportion comparison — d_proportion_diff","text":"string describing analysis.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/reference/d_rsp_subgroups_colvars.html","id":null,"dir":"Reference","previous_headings":"","what":"Labels for column variables in binary response by subgroup table — d_rsp_subgroups_colvars","title":"Labels for column variables in binary response by subgroup table — d_rsp_subgroups_colvars","text":"Internal function check variables included tabulate_rsp_subgroups() create column labels.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/d_rsp_subgroups_colvars.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Labels for column variables in binary response by subgroup table — d_rsp_subgroups_colvars","text":"","code":"d_rsp_subgroups_colvars(vars, conf_level = NULL, method = NULL)"},{"path":"https://insightsengineering.github.io/tern/reference/d_rsp_subgroups_colvars.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Labels for column variables in binary response by subgroup table — d_rsp_subgroups_colvars","text":"vars (character) variable names primary analysis variable iterated . conf_level (proportion) confidence level interval. method (string NULL) specifies test used calculate p-value difference two proportions. options, see test_proportion_diff(). Default NULL test performed.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/d_rsp_subgroups_colvars.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Labels for column variables in binary response by subgroup table — d_rsp_subgroups_colvars","text":"list variables tabulate labels.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/d_survival_subgroups_colvars.html","id":null,"dir":"Reference","previous_headings":"","what":"Labels for column variables in survival duration by subgroup table — d_survival_subgroups_colvars","title":"Labels for column variables in survival duration by subgroup table — d_survival_subgroups_colvars","text":"Internal function check variables included tabulate_survival_subgroups() create column labels.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/d_survival_subgroups_colvars.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Labels for column variables in survival duration by subgroup table — d_survival_subgroups_colvars","text":"","code":"d_survival_subgroups_colvars(vars, conf_level, method, time_unit = NULL)"},{"path":"https://insightsengineering.github.io/tern/reference/d_survival_subgroups_colvars.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Labels for column variables in survival duration by subgroup table — d_survival_subgroups_colvars","text":"vars (character) names statistics reported among: n_tot_events: Total number events per group. n_events: Number events per group. n_tot: Total number observations per group. n: Number observations per group. median: Median survival time. hr: Hazard ratio. ci: Confidence interval hazard ratio. pval: p-value effect. Note, one statistics n_tot n_tot_events, well hr ci required. conf_level (proportion) confidence level interval. method (string) p-value method testing hazard ratio = 1. time_unit (string) label unit median survival time. Default NULL skips displaying unit.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/d_survival_subgroups_colvars.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Labels for column variables in survival duration by subgroup table — d_survival_subgroups_colvars","text":"list variables labels tabulate.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/d_survival_subgroups_colvars.html","id":"note","dir":"Reference","previous_headings":"","what":"Note","title":"Labels for column variables in survival duration by subgroup table — d_survival_subgroups_colvars","text":"least one n_tot n_tot_events must provided vars.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/d_test_proportion_diff.html","id":null,"dir":"Reference","previous_headings":"","what":"Description of the difference test between two proportions — d_test_proportion_diff","title":"Description of the difference test between two proportions — d_test_proportion_diff","text":"auxiliary function describes analysis s_test_proportion_diff.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/d_test_proportion_diff.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Description of the difference test between two proportions — d_test_proportion_diff","text":"","code":"d_test_proportion_diff(method)"},{"path":"https://insightsengineering.github.io/tern/reference/d_test_proportion_diff.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Description of the difference test between two proportions — d_test_proportion_diff","text":"method (string) one chisq, cmh, fisher, schouten; specifies test used calculate p-value.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/d_test_proportion_diff.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Description of the difference test between two proportions — d_test_proportion_diff","text":"string describing test p-value derived.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/day2month.html","id":null,"dir":"Reference","previous_headings":"","what":"Conversion of days to months — day2month","title":"Conversion of days to months — day2month","text":"Conversion days months","code":""},{"path":"https://insightsengineering.github.io/tern/reference/day2month.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Conversion of days to months — day2month","text":"","code":"day2month(x)"},{"path":"https://insightsengineering.github.io/tern/reference/day2month.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Conversion of days to months — day2month","text":"x (numeric(1)) time days.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/day2month.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Conversion of days to months — day2month","text":"numeric vector time months.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/day2month.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Conversion of days to months — day2month","text":"","code":"x <- c(403, 248, 30, 86) day2month(x) #> [1] 13.2402464  8.1478439  0.9856263  2.8254620"},{"path":"https://insightsengineering.github.io/tern/reference/decorate_grob.html","id":null,"dir":"Reference","previous_headings":"","what":"Add titles, footnotes, page Number, and a bounding box to a grid grob — decorate_grob","title":"Add titles, footnotes, page Number, and a bounding box to a grid grob — decorate_grob","text":"function useful label grid grobs (also ggplot2, lattice plots) title, footnote, page numbers.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/decorate_grob.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Add titles, footnotes, page Number, and a bounding box to a grid grob — decorate_grob","text":"","code":"decorate_grob(   grob,   titles,   footnotes,   page = \"\",   width_titles = grid::unit(1, \"npc\"),   width_footnotes = grid::unit(1, \"npc\"),   border = TRUE,   padding = grid::unit(rep(1, 4), \"lines\"),   margins = grid::unit(c(1, 0, 1, 0), \"lines\"),   outer_margins = grid::unit(c(2, 1.5, 3, 1.5), \"cm\"),   gp_titles = grid::gpar(),   gp_footnotes = grid::gpar(fontsize = 8),   name = NULL,   gp = grid::gpar(),   vp = NULL )"},{"path":"https://insightsengineering.github.io/tern/reference/decorate_grob.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Add titles, footnotes, page Number, and a bounding box to a grid grob — decorate_grob","text":"grob (grob) grid grob object, optionally NULL grob decoration shown. titles (character) titles given vector strings separated newline wrapped according page width. footnotes (character) footnotes. Uses formatting rules titles. page (string NULL) page numeration. NULL page number displayed. width_titles (grid::unit) width titles. Usually defined available space grid::unit(1, \"npc\"), affected parameter outer_margins. Right margins (outer_margins[4]) need subtracted allowed width. width_footnotes (grid::unit) width footnotes. default margin correction width_titles. border (flag) whether border drawn around plot . padding (grid::unit) padding. unit object length 4. Innermost margin plot (grob) , possibly, border plot. Usually expressed 4 identical values (usually \"lines\"). defaults grid::unit(rep(1, 4), \"lines\"). margins (grid::unit) margins. unit object length 4. Margins plot elements list (e.g. titles, plot, footers). usually expressed 4 \"lines\", lateral ones 0s, top bottom 1s. defaults grid::unit(c(1, 0, 1, 0), \"lines\"). outer_margins (grid::unit) outer margins. unit object length 4. defines general margin plot, considering also decorations like titles, footnotes, page numbers. defaults grid::unit(c(2, 1.5, 3, 1.5), \"cm\"). gp_titles (gpar) gpar object. Mainly used set different \"fontsize\". gp_footnotes (gpar) gpar object. Mainly used set different \"fontsize\". name character identifier grob.  Used find     grob display list /child another grob. gp \"gpar\" object, typically output     call function gpar.  basically     list graphical parameter settings. vp viewport object (NULL).","code":""},{"path":"https://insightsengineering.github.io/tern/reference/decorate_grob.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Add titles, footnotes, page Number, and a bounding box to a grid grob — decorate_grob","text":"grid grob (gTree).","code":""},{"path":"https://insightsengineering.github.io/tern/reference/decorate_grob.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Add titles, footnotes, page Number, and a bounding box to a grid grob — decorate_grob","text":"titles footnotes ragged, .e. title wrapped individually.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/decorate_grob.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Add titles, footnotes, page Number, and a bounding box to a grid grob — decorate_grob","text":"","code":"library(grid)  titles <- c(   \"Edgar Anderson's Iris Data\",   paste(     \"This famous (Fisher's or Anderson's) iris data set gives the measurements\",     \"in centimeters of the variables sepal length and width and petal length\",     \"and width, respectively, for 50 flowers from each of 3 species of iris.\"   ) )  footnotes <- c(   \"The species are Iris setosa, versicolor, and virginica.\",   paste(     \"iris is a data frame with 150 cases (rows) and 5 variables (columns) named\",     \"Sepal.Length, Sepal.Width, Petal.Length, Petal.Width, and Species.\"   ) )  ## empty plot grid.newpage()  grid.draw(   decorate_grob(     NULL,     titles = titles,     footnotes = footnotes,     page = \"Page 4 of 10\"   ) )   # grid p <- gTree(   children = gList(     rectGrob(),     xaxisGrob(),     yaxisGrob(),     textGrob(\"Sepal.Length\", y = unit(-4, \"lines\")),     textGrob(\"Petal.Length\", x = unit(-3.5, \"lines\"), rot = 90),     pointsGrob(iris$Sepal.Length, iris$Petal.Length, gp = gpar(col = iris$Species), pch = 16)   ),   vp = vpStack(plotViewport(), dataViewport(xData = iris$Sepal.Length, yData = iris$Petal.Length)) ) grid.newpage() grid.draw(p)   grid.newpage() grid.draw(   decorate_grob(     grob = p,     titles = titles,     footnotes = footnotes,     page = \"Page 6 of 129\"   ) )   ## with ggplot2 library(ggplot2)  p_gg <- ggplot2::ggplot(iris, aes(Sepal.Length, Sepal.Width, col = Species)) +   ggplot2::geom_point() p_gg  p <- ggplotGrob(p_gg) grid.newpage() grid.draw(   decorate_grob(     grob = p,     titles = titles,     footnotes = footnotes,     page = \"Page 6 of 129\"   ) )   ## with lattice library(lattice)  xyplot(Sepal.Length ~ Petal.Length, data = iris, col = iris$Species)  p <- grid.grab()  grid.newpage() grid.draw(   decorate_grob(     grob = p,     titles = titles,     footnotes = footnotes,     page = \"Page 6 of 129\"   ) )   # with gridExtra - no borders library(gridExtra) #>  #> Attaching package: ‘gridExtra’ #> The following object is masked from ‘package:dplyr’: #>  #>     combine grid.newpage() grid.draw(   decorate_grob(     tableGrob(       head(mtcars)     ),     titles = \"title\",     footnotes = \"footnote\",     border = FALSE   ) )"},{"path":"https://insightsengineering.github.io/tern/reference/decorate_grob_factory.html","id":null,"dir":"Reference","previous_headings":"","what":"Update page number — decorate_grob_factory","title":"Update page number — decorate_grob_factory","text":"Automatically updates page number.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/decorate_grob_factory.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Update page number — decorate_grob_factory","text":"","code":"decorate_grob_factory(npages, ...)"},{"path":"https://insightsengineering.github.io/tern/reference/decorate_grob_factory.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Update page number — decorate_grob_factory","text":"npages (numeric(1)) total number pages. ... arguments passed decorate_grob().","code":""},{"path":"https://insightsengineering.github.io/tern/reference/decorate_grob_factory.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Update page number — decorate_grob_factory","text":"Closure increments page number.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/decorate_grob_set.html","id":null,"dir":"Reference","previous_headings":"","what":"Decorate set of grobs and add page numbering — decorate_grob_set","title":"Decorate set of grobs and add page numbering — decorate_grob_set","text":"Note uses decorate_grob_factory() function.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/decorate_grob_set.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Decorate set of grobs and add page numbering — decorate_grob_set","text":"","code":"decorate_grob_set(grobs, ...)"},{"path":"https://insightsengineering.github.io/tern/reference/decorate_grob_set.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Decorate set of grobs and add page numbering — decorate_grob_set","text":"grobs (list grob) list grid grobs. ... arguments passed decorate_grob().","code":""},{"path":"https://insightsengineering.github.io/tern/reference/decorate_grob_set.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Decorate set of grobs and add page numbering — decorate_grob_set","text":"decorated grob.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/decorate_grob_set.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Decorate set of grobs and add page numbering — decorate_grob_set","text":"","code":"library(ggplot2) library(grid) g <- with(data = iris, {   list(     ggplot2::ggplotGrob(       ggplot2::ggplot(mapping = aes(Sepal.Length, Sepal.Width, col = Species)) +         ggplot2::geom_point()     ),     ggplot2::ggplotGrob(       ggplot2::ggplot(mapping = aes(Sepal.Length, Petal.Length, col = Species)) +         ggplot2::geom_point()     ),     ggplot2::ggplotGrob(       ggplot2::ggplot(mapping = aes(Sepal.Length, Petal.Width, col = Species)) +         ggplot2::geom_point()     ),     ggplot2::ggplotGrob(       ggplot2::ggplot(mapping = aes(Sepal.Width, Petal.Length, col = Species)) +         ggplot2::geom_point()     ),     ggplot2::ggplotGrob(       ggplot2::ggplot(mapping = aes(Sepal.Width, Petal.Width, col = Species)) +         ggplot2::geom_point()     ),     ggplot2::ggplotGrob(       ggplot2::ggplot(mapping = aes(Petal.Length, Petal.Width, col = Species)) +         ggplot2::geom_point()     )   ) }) lg <- decorate_grob_set(grobs = g, titles = \"Hello\\nOne\\nTwo\\nThree\", footnotes = \"\")  draw_grob(lg[[1]]) #> Warning: `draw_grob()` was deprecated in tern 0.9.4. #> ℹ `tern` plotting functions no longer generate `grob` objects.  draw_grob(lg[[2]])  draw_grob(lg[[6]])"},{"path":"https://insightsengineering.github.io/tern/reference/default_na_str.html","id":null,"dir":"Reference","previous_headings":"","what":"Default string replacement for NA values — default_na_str","title":"Default string replacement for NA values — default_na_str","text":"default string used represent NA values. value used default value na_str argument throughout tern package, printed place NA values output tables. specified tern function user via na_str argument, R environment options via set_default_na_str(), NA used.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/default_na_str.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Default string replacement for NA values — default_na_str","text":"","code":"default_na_str()  set_default_na_str(na_str)"},{"path":"https://insightsengineering.github.io/tern/reference/default_na_str.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Default string replacement for NA values — default_na_str","text":"na_str (string) single string value set R environment options default value replace NAs. Use getOption(\"tern_default_na_str\") check current value set R environment (defaults NULL set).","code":""},{"path":"https://insightsengineering.github.io/tern/reference/default_na_str.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Default string replacement for NA values — default_na_str","text":"default_na_str returns current value R environment option set \"tern_default_na_str\", NA_character_ otherwise. set_default_na_str return value.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/default_na_str.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Default string replacement for NA values — default_na_str","text":"default_na_str(): Accessor default NA value replacement string. set_default_na_str(): Setter default NA value replacement string. Sets option \"tern_default_na_str\" within R environment.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/default_na_str.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Default string replacement for NA values — default_na_str","text":"","code":"# Default settings default_na_str() #> [1] NA getOption(\"tern_default_na_str\") #> NULL  # Set custom value set_default_na_str(\"<Missing>\")  # Settings after value has been set default_na_str() #> [1] \"<Missing>\" getOption(\"tern_default_na_str\") #> [1] \"<Missing>\""},{"path":"https://insightsengineering.github.io/tern/reference/default_stats_formats_labels.html","id":null,"dir":"Reference","previous_headings":"","what":"Get default statistical methods and their associated formats, labels, and indent modifiers — default_stats_formats_labels","title":"Get default statistical methods and their associated formats, labels, and indent modifiers — default_stats_formats_labels","text":"Utility functions get valid statistic methods different method groups (.stats) associated formats (.formats), labels (.labels), indent modifiers (.indent_mods). utility used across tern, working principles can seen analyze_vars(). See notes understand experimental.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/default_stats_formats_labels.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get default statistical methods and their associated formats, labels, and indent modifiers — default_stats_formats_labels","text":"","code":"get_stats(   method_groups = \"analyze_vars_numeric\",   stats_in = NULL,   add_pval = FALSE )  get_formats_from_stats(stats, formats_in = NULL)  get_labels_from_stats(stats, labels_in = NULL, row_nms = NULL)  get_indents_from_stats(stats, indents_in = NULL, row_nms = NULL)  tern_default_stats  tern_default_formats  tern_default_labels  summary_formats(type = \"numeric\", include_pval = FALSE)  summary_labels(type = \"numeric\", include_pval = FALSE)"},{"path":"https://insightsengineering.github.io/tern/reference/default_stats_formats_labels.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Get default statistical methods and their associated formats, labels, and indent modifiers — default_stats_formats_labels","text":"tern_default_stats named list available statistics, element named corresponding statistical method group. tern_default_formats named vector available default formats, element named corresponding statistic. tern_default_labels named character vector available default labels, element named corresponding statistic.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/default_stats_formats_labels.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get default statistical methods and their associated formats, labels, and indent modifiers — default_stats_formats_labels","text":"method_groups (character) indicates statistical method group (tern analyze function) retrieve default statistics . character vector can used specify one statistical method group. stats_in (character) statistics retrieve selected method group. add_pval (flag) \"pval\" (\"pval_counts\" method_groups contains \"analyze_vars_counts\") added statistical methods? stats (character) statistical methods get defaults . formats_in (named vector) inserted formats replace defaults. can character vector formatters::list_valid_format_labels() custom format function. labels_in (named character) inserted labels replace defaults. row_nms (character) row names. Levels factor character variable, statistics .stats calculated . parameter set, variable levels used defaults, names given custom values correspond levels (format statistic.level) instead statistics. Can also variable names rows correspond different variables instead levels. Defaults NULL. indents_in (named vector) inserted indent modifiers replace defaults (default 0L). type (string)\"numeric\" \"counts\". include_pval (flag) add_pval argument get_stats().","code":""},{"path":"https://insightsengineering.github.io/tern/reference/default_stats_formats_labels.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get default statistical methods and their associated formats, labels, and indent modifiers — default_stats_formats_labels","text":"get_stats() returns character vector statistical methods. get_formats_from_stats() returns named vector formats (present either tern_default_formats formats_in, otherwise NULL). Values can taken formatters::list_valid_format_labels() custom function (e.g. formatting_functions). get_labels_from_stats() returns named character vector labels (present either tern_default_labels labels_in, otherwise NULL). get_indents_from_stats() returns single indent modifier value apply rows named numeric vector indent modifiers (present, otherwise NULL). summary_formats() returns named vector default statistic formats given data type. summary_labels returns named vector default statistic labels given data type.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/default_stats_formats_labels.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Get default statistical methods and their associated formats, labels, and indent modifiers — default_stats_formats_labels","text":"Current choices type counts numeric analyze_vars() affect get_stats(). summary_* quick get functions labels formats uses get_stats get_labels_from_stats get_formats_from_stats respectively retrieve relevant information.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/default_stats_formats_labels.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Get default statistical methods and their associated formats, labels, and indent modifiers — default_stats_formats_labels","text":"get_stats(): Get statistics available given method group (analyze function). check available defaults see tern::tern_default_stats list. get_formats_from_stats(): Get formats corresponding list statistics. check available defaults see tern::tern_default_formats list. get_labels_from_stats(): Get labels corresponding list statistics. check available defaults see tern::tern_default_labels list. available , statistics name used label. get_indents_from_stats(): Format indent modifiers given vector/list statistics. defaults 0L values. tern_default_stats: Named list available statistics method group tern. tern_default_formats: Named vector default formats tern. tern_default_labels: Named character vector default labels tern. summary_formats():  Quick function retrieve default formats summary statistics: analyze_vars() analyze_vars_in_cols() principally. summary_labels():  Quick function retrieve default labels summary statistics. Returns labels descriptive statistics understood rtables. Similar summary_formats.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/default_stats_formats_labels.html","id":"note","dir":"Reference","previous_headings":"","what":"Note","title":"Get default statistical methods and their associated formats, labels, and indent modifiers — default_stats_formats_labels","text":"defaults experimental use names functions retrieve default statistics. generalized groups methods according reasonable groupings. Formats tern rtables can functions take table cell value return string. well documented vignette(\"custom_appearance\", package = \"rtables\").","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/reference/default_stats_formats_labels.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get default statistical methods and their associated formats, labels, and indent modifiers — default_stats_formats_labels","text":"","code":"# analyze_vars is numeric num_stats <- get_stats(\"analyze_vars_numeric\") # also the default  # Other type cnt_stats <- get_stats(\"analyze_vars_counts\")  # Weirdly taking the pval from count_occurrences only_pval <- get_stats(\"count_occurrences\", add_pval = TRUE, stats_in = \"pval\")  # All count_occurrences all_cnt_occ <- get_stats(\"count_occurrences\")  # Multiple get_stats(c(\"count_occurrences\", \"analyze_vars_counts\")) #> [1] \"count\"                   \"count_fraction\"          #> [3] \"count_fraction_fixed_dp\" \"fraction\"                #> [5] \"n\"                       \"n_blq\"                    # Defaults formats get_formats_from_stats(num_stats) #> $n #> [1] \"xx.\" #>  #> $sum #> [1] \"xx.x\" #>  #> $mean #> [1] \"xx.x\" #>  #> $sd #> [1] \"xx.x\" #>  #> $se #> [1] \"xx.x\" #>  #> $mean_sd #> [1] \"xx.x (xx.x)\" #>  #> $mean_se #> [1] \"xx.x (xx.x)\" #>  #> $mean_ci #> [1] \"(xx.xx, xx.xx)\" #>  #> $mean_sei #> [1] \"(xx.xx, xx.xx)\" #>  #> $mean_sdi #> [1] \"(xx.xx, xx.xx)\" #>  #> $mean_pval #> [1] \"x.xxxx | (<0.0001)\" #>  #> $median #> [1] \"xx.x\" #>  #> $mad #> [1] \"xx.x\" #>  #> $median_ci #> [1] \"(xx.xx, xx.xx)\" #>  #> $quantiles #> [1] \"xx.x - xx.x\" #>  #> $iqr #> [1] \"xx.x\" #>  #> $range #> [1] \"xx.x - xx.x\" #>  #> $min #> [1] \"xx.x\" #>  #> $max #> [1] \"xx.x\" #>  #> $median_range #> [1] \"xx.x (xx.x - xx.x)\" #>  #> $cv #> [1] \"xx.x\" #>  #> $geom_mean #> [1] \"xx.x\" #>  #> $geom_mean_ci #> [1] \"(xx.xx, xx.xx)\" #>  #> $geom_cv #> [1] \"xx.x\" #>  #> $median_ci_3d #> [1] \"xx.xx (xx.xx - xx.xx)\" #>  #> $mean_ci_3d #> [1] \"xx.xx (xx.xx - xx.xx)\" #>  #> $geom_mean_ci_3d #> [1] \"xx.xx (xx.xx - xx.xx)\" #>  get_formats_from_stats(cnt_stats) #> $n #> [1] \"xx.\" #>  #> $count #> [1] \"xx.\" #>  #> $count_fraction #> function(x, ...) { #>   attr(x, \"label\") <- NULL #>  #>   if (any(is.na(x))) { #>     return(\"NA\") #>   } #>  #>   checkmate::assert_vector(x) #>   checkmate::assert_integerish(x[1]) #>   assert_proportion_value(x[2], include_boundaries = TRUE) #>  #>   result <- if (x[1] == 0) { #>     \"0\" #>   } else { #>     paste0(x[1], \" (\", round(x[2] * 100, 1), \"%)\") #>   } #>  #>   return(result) #> } #> <environment: namespace:tern> #>  #> $count_fraction_fixed_dp #> function(x, ...) { #>   attr(x, \"label\") <- NULL #>  #>   if (any(is.na(x))) { #>     return(\"NA\") #>   } #>  #>   checkmate::assert_vector(x) #>   checkmate::assert_integerish(x[1]) #>   assert_proportion_value(x[2], include_boundaries = TRUE) #>  #>   result <- if (x[1] == 0) { #>     \"0\" #>   } else if (.is_equal_float(x[2], 1)) { #>     sprintf(\"%d (100%%)\", x[1]) #>   } else { #>     sprintf(\"%d (%.1f%%)\", x[1], x[2] * 100) #>   } #>  #>   return(result) #> } #> <environment: namespace:tern> #>  #> $fraction #> function(x, ...) { #>   attr(x, \"label\") <- NULL #>   checkmate::assert_vector(x) #>   checkmate::assert_count(x[\"num\"]) #>   checkmate::assert_count(x[\"denom\"]) #>  #>   result <- if (x[\"num\"] == 0) { #>     paste0(x[\"num\"], \"/\", x[\"denom\"]) #>   } else { #>     paste0( #>       x[\"num\"], \"/\", x[\"denom\"], #>       \" (\", sprintf(\"%.1f\", round(x[\"num\"] / x[\"denom\"] * 100, 1)), \"%)\" #>     ) #>   } #>   return(result) #> } #> <environment: namespace:tern> #>  #> $n_blq #> [1] \"xx.\" #>  get_formats_from_stats(only_pval) #> $pval #> [1] \"x.xxxx | (<0.0001)\" #>  get_formats_from_stats(all_cnt_occ) #> $count #> [1] \"xx.\" #>  #> $count_fraction #> function(x, ...) { #>   attr(x, \"label\") <- NULL #>  #>   if (any(is.na(x))) { #>     return(\"NA\") #>   } #>  #>   checkmate::assert_vector(x) #>   checkmate::assert_integerish(x[1]) #>   assert_proportion_value(x[2], include_boundaries = TRUE) #>  #>   result <- if (x[1] == 0) { #>     \"0\" #>   } else { #>     paste0(x[1], \" (\", round(x[2] * 100, 1), \"%)\") #>   } #>  #>   return(result) #> } #> <environment: namespace:tern> #>  #> $count_fraction_fixed_dp #> function(x, ...) { #>   attr(x, \"label\") <- NULL #>  #>   if (any(is.na(x))) { #>     return(\"NA\") #>   } #>  #>   checkmate::assert_vector(x) #>   checkmate::assert_integerish(x[1]) #>   assert_proportion_value(x[2], include_boundaries = TRUE) #>  #>   result <- if (x[1] == 0) { #>     \"0\" #>   } else if (.is_equal_float(x[2], 1)) { #>     sprintf(\"%d (100%%)\", x[1]) #>   } else { #>     sprintf(\"%d (%.1f%%)\", x[1], x[2] * 100) #>   } #>  #>   return(result) #> } #> <environment: namespace:tern> #>  #> $fraction #> function(x, ...) { #>   attr(x, \"label\") <- NULL #>   checkmate::assert_vector(x) #>   checkmate::assert_count(x[\"num\"]) #>   checkmate::assert_count(x[\"denom\"]) #>  #>   result <- if (x[\"num\"] == 0) { #>     paste0(x[\"num\"], \"/\", x[\"denom\"]) #>   } else { #>     paste0( #>       x[\"num\"], \"/\", x[\"denom\"], #>       \" (\", sprintf(\"%.1f\", round(x[\"num\"] / x[\"denom\"] * 100, 1)), \"%)\" #>     ) #>   } #>   return(result) #> } #> <environment: namespace:tern> #>   # Addition of customs get_formats_from_stats(all_cnt_occ, formats_in = c(\"fraction\" = c(\"xx\"))) #> $count #> [1] \"xx.\" #>  #> $count_fraction #> function(x, ...) { #>   attr(x, \"label\") <- NULL #>  #>   if (any(is.na(x))) { #>     return(\"NA\") #>   } #>  #>   checkmate::assert_vector(x) #>   checkmate::assert_integerish(x[1]) #>   assert_proportion_value(x[2], include_boundaries = TRUE) #>  #>   result <- if (x[1] == 0) { #>     \"0\" #>   } else { #>     paste0(x[1], \" (\", round(x[2] * 100, 1), \"%)\") #>   } #>  #>   return(result) #> } #> <environment: namespace:tern> #>  #> $count_fraction_fixed_dp #> function(x, ...) { #>   attr(x, \"label\") <- NULL #>  #>   if (any(is.na(x))) { #>     return(\"NA\") #>   } #>  #>   checkmate::assert_vector(x) #>   checkmate::assert_integerish(x[1]) #>   assert_proportion_value(x[2], include_boundaries = TRUE) #>  #>   result <- if (x[1] == 0) { #>     \"0\" #>   } else if (.is_equal_float(x[2], 1)) { #>     sprintf(\"%d (100%%)\", x[1]) #>   } else { #>     sprintf(\"%d (%.1f%%)\", x[1], x[2] * 100) #>   } #>  #>   return(result) #> } #> <environment: namespace:tern> #>  #> $fraction #> [1] \"xx\" #>  get_formats_from_stats(all_cnt_occ, formats_in = list(\"fraction\" = c(\"xx.xx\", \"xx\"))) #> $count #> [1] \"xx.\" #>  #> $count_fraction #> function(x, ...) { #>   attr(x, \"label\") <- NULL #>  #>   if (any(is.na(x))) { #>     return(\"NA\") #>   } #>  #>   checkmate::assert_vector(x) #>   checkmate::assert_integerish(x[1]) #>   assert_proportion_value(x[2], include_boundaries = TRUE) #>  #>   result <- if (x[1] == 0) { #>     \"0\" #>   } else { #>     paste0(x[1], \" (\", round(x[2] * 100, 1), \"%)\") #>   } #>  #>   return(result) #> } #> <environment: namespace:tern> #>  #> $count_fraction_fixed_dp #> function(x, ...) { #>   attr(x, \"label\") <- NULL #>  #>   if (any(is.na(x))) { #>     return(\"NA\") #>   } #>  #>   checkmate::assert_vector(x) #>   checkmate::assert_integerish(x[1]) #>   assert_proportion_value(x[2], include_boundaries = TRUE) #>  #>   result <- if (x[1] == 0) { #>     \"0\" #>   } else if (.is_equal_float(x[2], 1)) { #>     sprintf(\"%d (100%%)\", x[1]) #>   } else { #>     sprintf(\"%d (%.1f%%)\", x[1], x[2] * 100) #>   } #>  #>   return(result) #> } #> <environment: namespace:tern> #>  #> $fraction #> [1] \"xx.xx\" \"xx\"    #>   # Defaults labels get_labels_from_stats(num_stats) #>                             n                           sum  #>                           \"n\"                         \"Sum\"  #>                          mean                            sd  #>                        \"Mean\"                          \"SD\"  #>                            se                       mean_sd  #>                          \"SE\"                   \"Mean (SD)\"  #>                       mean_se                       mean_ci  #>                   \"Mean (SE)\"                 \"Mean 95% CI\"  #>                      mean_sei                      mean_sdi  #>               \"Mean -/+ 1xSE\"               \"Mean -/+ 1xSD\"  #>                     mean_pval                        median  #> \"Mean p-value (H0: mean = 0)\"                      \"Median\"  #>                           mad                     median_ci  #>   \"Median Absolute Deviation\"               \"Median 95% CI\"  #>                     quantiles                           iqr  #>             \"25% and 75%-ile\"                         \"IQR\"  #>                         range                           min  #>                   \"Min - Max\"                     \"Minimum\"  #>                           max                  median_range  #>                     \"Maximum\"          \"Median (Min - Max)\"  #>                            cv                     geom_mean  #>                      \"CV (%)\"              \"Geometric Mean\"  #>                  geom_mean_ci                       geom_cv  #>       \"Geometric Mean 95% CI\"         \"CV % Geometric Mean\"  #>                  median_ci_3d                    mean_ci_3d  #>             \"Median (95% CI)\"               \"Mean (95% CI)\"  #>               geom_mean_ci_3d  #>     \"Geometric Mean (95% CI)\"  get_labels_from_stats(cnt_stats) #>                       n                   count          count_fraction  #>                     \"n\"                 \"count\"        \"count_fraction\"  #> count_fraction_fixed_dp                fraction                   n_blq  #>        \"count_fraction\"              \"fraction\"                 \"n_blq\"  get_labels_from_stats(only_pval) #>               pval  #> \"p-value (t-test)\"  get_labels_from_stats(all_cnt_occ) #>                   count          count_fraction count_fraction_fixed_dp  #>                 \"count\"        \"count_fraction\"        \"count_fraction\"  #>                fraction  #>              \"fraction\"   # Addition of customs get_labels_from_stats(all_cnt_occ, labels_in = c(\"fraction\" = \"Fraction\")) #>                   count          count_fraction count_fraction_fixed_dp  #>                 \"count\"        \"count_fraction\"        \"count_fraction\"  #>                fraction  #>              \"Fraction\"  get_labels_from_stats(all_cnt_occ, labels_in = list(\"fraction\" = c(\"Some more fractions\"))) #> $count #> [1] \"count\" #>  #> $count_fraction #> [1] \"count_fraction\" #>  #> $count_fraction_fixed_dp #> [1] \"count_fraction\" #>  #> $fraction #> [1] \"Some more fractions\" #>   get_indents_from_stats(all_cnt_occ, indents_in = 3L) #> [1] 3 3 3 3 get_indents_from_stats(all_cnt_occ, indents_in = list(count = 2L, count_fraction = 5L)) #> $count #> [1] 2 #>  #> $count_fraction #> [1] 5 #>  #> $count_fraction_fixed_dp #> [1] 0 #>  #> $fraction #> [1] 0 #>  get_indents_from_stats(   all_cnt_occ,   indents_in = list(a = 2L, count.a = 1L, count.b = 5L), row_nms = c(\"a\", \"b\") ) #> $count.a #> [1] 1 #>  #> $count.b #> [1] 5 #>  #> $count_fraction.a #> [1] 2 #>  #> $count_fraction.b #> [1] 0 #>  #> $count_fraction_fixed_dp.a #> [1] 2 #>  #> $count_fraction_fixed_dp.b #> [1] 0 #>  #> $fraction.a #> [1] 2 #>  #> $fraction.b #> [1] 0 #>   summary_formats() #> $n #> [1] \"xx.\" #>  #> $sum #> [1] \"xx.x\" #>  #> $mean #> [1] \"xx.x\" #>  #> $sd #> [1] \"xx.x\" #>  #> $se #> [1] \"xx.x\" #>  #> $mean_sd #> [1] \"xx.x (xx.x)\" #>  #> $mean_se #> [1] \"xx.x (xx.x)\" #>  #> $mean_ci #> [1] \"(xx.xx, xx.xx)\" #>  #> $mean_sei #> [1] \"(xx.xx, xx.xx)\" #>  #> $mean_sdi #> [1] \"(xx.xx, xx.xx)\" #>  #> $mean_pval #> [1] \"x.xxxx | (<0.0001)\" #>  #> $median #> [1] \"xx.x\" #>  #> $mad #> [1] \"xx.x\" #>  #> $median_ci #> [1] \"(xx.xx, xx.xx)\" #>  #> $quantiles #> [1] \"xx.x - xx.x\" #>  #> $iqr #> [1] \"xx.x\" #>  #> $range #> [1] \"xx.x - xx.x\" #>  #> $min #> [1] \"xx.x\" #>  #> $max #> [1] \"xx.x\" #>  #> $median_range #> [1] \"xx.x (xx.x - xx.x)\" #>  #> $cv #> [1] \"xx.x\" #>  #> $geom_mean #> [1] \"xx.x\" #>  #> $geom_mean_ci #> [1] \"(xx.xx, xx.xx)\" #>  #> $geom_cv #> [1] \"xx.x\" #>  #> $median_ci_3d #> [1] \"xx.xx (xx.xx - xx.xx)\" #>  #> $mean_ci_3d #> [1] \"xx.xx (xx.xx - xx.xx)\" #>  #> $geom_mean_ci_3d #> [1] \"xx.xx (xx.xx - xx.xx)\" #>  summary_formats(type = \"counts\", include_pval = TRUE) #> $n #> [1] \"xx.\" #>  #> $count #> [1] \"xx.\" #>  #> $count_fraction #> function(x, ...) { #>   attr(x, \"label\") <- NULL #>  #>   if (any(is.na(x))) { #>     return(\"NA\") #>   } #>  #>   checkmate::assert_vector(x) #>   checkmate::assert_integerish(x[1]) #>   assert_proportion_value(x[2], include_boundaries = TRUE) #>  #>   result <- if (x[1] == 0) { #>     \"0\" #>   } else { #>     paste0(x[1], \" (\", round(x[2] * 100, 1), \"%)\") #>   } #>  #>   return(result) #> } #> <environment: namespace:tern> #>  #> $count_fraction_fixed_dp #> function(x, ...) { #>   attr(x, \"label\") <- NULL #>  #>   if (any(is.na(x))) { #>     return(\"NA\") #>   } #>  #>   checkmate::assert_vector(x) #>   checkmate::assert_integerish(x[1]) #>   assert_proportion_value(x[2], include_boundaries = TRUE) #>  #>   result <- if (x[1] == 0) { #>     \"0\" #>   } else if (.is_equal_float(x[2], 1)) { #>     sprintf(\"%d (100%%)\", x[1]) #>   } else { #>     sprintf(\"%d (%.1f%%)\", x[1], x[2] * 100) #>   } #>  #>   return(result) #> } #> <environment: namespace:tern> #>  #> $fraction #> function(x, ...) { #>   attr(x, \"label\") <- NULL #>   checkmate::assert_vector(x) #>   checkmate::assert_count(x[\"num\"]) #>   checkmate::assert_count(x[\"denom\"]) #>  #>   result <- if (x[\"num\"] == 0) { #>     paste0(x[\"num\"], \"/\", x[\"denom\"]) #>   } else { #>     paste0( #>       x[\"num\"], \"/\", x[\"denom\"], #>       \" (\", sprintf(\"%.1f\", round(x[\"num\"] / x[\"denom\"] * 100, 1)), \"%)\" #>     ) #>   } #>   return(result) #> } #> <environment: namespace:tern> #>  #> $n_blq #> [1] \"xx.\" #>  #> $pval_counts #> [1] \"x.xxxx | (<0.0001)\" #>   summary_labels() #>                             n                           sum  #>                           \"n\"                         \"Sum\"  #>                          mean                            sd  #>                        \"Mean\"                          \"SD\"  #>                            se                       mean_sd  #>                          \"SE\"                   \"Mean (SD)\"  #>                       mean_se                       mean_ci  #>                   \"Mean (SE)\"                 \"Mean 95% CI\"  #>                      mean_sei                      mean_sdi  #>               \"Mean -/+ 1xSE\"               \"Mean -/+ 1xSD\"  #>                     mean_pval                        median  #> \"Mean p-value (H0: mean = 0)\"                      \"Median\"  #>                           mad                     median_ci  #>   \"Median Absolute Deviation\"               \"Median 95% CI\"  #>                     quantiles                           iqr  #>             \"25% and 75%-ile\"                         \"IQR\"  #>                         range                           min  #>                   \"Min - Max\"                     \"Minimum\"  #>                           max                  median_range  #>                     \"Maximum\"          \"Median (Min - Max)\"  #>                            cv                     geom_mean  #>                      \"CV (%)\"              \"Geometric Mean\"  #>                  geom_mean_ci                       geom_cv  #>       \"Geometric Mean 95% CI\"         \"CV % Geometric Mean\"  #>                  median_ci_3d                    mean_ci_3d  #>             \"Median (95% CI)\"               \"Mean (95% CI)\"  #>               geom_mean_ci_3d  #>     \"Geometric Mean (95% CI)\"  summary_labels(type = \"counts\", include_pval = TRUE) #>                            n                        count  #>                          \"n\"                      \"count\"  #>               count_fraction      count_fraction_fixed_dp  #>             \"count_fraction\"             \"count_fraction\"  #>                     fraction                        n_blq  #>                   \"fraction\"                      \"n_blq\"  #>                  pval_counts  #> \"p-value (chi-squared test)\""},{"path":"https://insightsengineering.github.io/tern/reference/desctools_binom.html","id":null,"dir":"Reference","previous_headings":"","what":"Confidence intervals for a difference of binomials — desctools_binom","title":"Confidence intervals for a difference of binomials — desctools_binom","text":"Several confidence intervals difference proportions.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/desctools_binom.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Confidence intervals for a difference of binomials — desctools_binom","text":"","code":"desctools_binom(   x1,   n1,   x2,   n2,   conf.level = 0.95,   sides = c(\"two.sided\", \"left\", \"right\"),   method = c(\"ac\", \"wald\", \"waldcc\", \"score\", \"scorecc\", \"mn\", \"mee\", \"blj\", \"ha\", \"hal\",     \"jp\") )  desctools_binomci(   x,   n,   conf.level = 0.95,   sides = c(\"two.sided\", \"left\", \"right\"),   method = c(\"wilson\", \"wald\", \"waldcc\", \"agresti-coull\", \"jeffreys\", \"modified wilson\",     \"wilsoncc\", \"modified jeffreys\", \"clopper-pearson\", \"arcsine\", \"logit\", \"witting\",     \"pratt\", \"midp\", \"lik\", \"blaker\"),   rand = 123,   tol = 1e-05 )"},{"path":"https://insightsengineering.github.io/tern/reference/desctools_binom.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Confidence intervals for a difference of binomials — desctools_binom","text":"conf.level (proportion) confidence level, defaults 0.95. sides (string) side confidence interval compute. Must one \"two-sided\" (default), \"left\", \"right\". method (string) method use. Can one : \"wald\", \"wilson\", \"wilsoncc\", \"agresti-coull\", \"jeffreys\", \"modified wilson\", \"modified jeffreys\", \"clopper-pearson\", \"arcsine\", \"logit\", \"witting\", \"pratt\", \"midp\", \"lik\", \"blaker\". x (integer(1)) number successes. n (integer(1)) number trials.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/desctools_binom.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Confidence intervals for a difference of binomials — desctools_binom","text":"matrix 3 values: est: estimate proportion difference. lwr.ci: estimate lower end confidence interval. upr.ci: estimate upper end confidence interval. matrix 3 columns containing: est: estimate proportion difference. lwr.ci: lower end confidence interval. upr.ci: upper end confidence interval.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/desctools_binom.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Confidence intervals for a difference of binomials — desctools_binom","text":"desctools_binom(): Several confidence intervals difference proportions. desctools_binomci(): Compute confidence intervals binomial proportions.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/df2gg.html","id":null,"dir":"Reference","previous_headings":"","what":"Convert data.frame object to ggplot object — df2gg","title":"Convert data.frame object to ggplot object — df2gg","text":"Given data.frame object, performs basic conversion ggplot2::ggplot() object built using functions ggplot2 package.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/df2gg.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Convert data.frame object to ggplot object — df2gg","text":"","code":"df2gg(   df,   colwidths = NULL,   font_size = 10,   col_labels = TRUE,   col_lab_fontface = \"bold\",   hline = TRUE,   bg_fill = NULL )"},{"path":"https://insightsengineering.github.io/tern/reference/df2gg.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Convert data.frame object to ggplot object — df2gg","text":"df (data.frame) data frame. colwidths (numeric NULL) vector column widths. element's position colwidths corresponds column df position. NULL, column widths calculated according maximum number characters per column. font_size (numeric(1)) font size. col_labels (flag) whether column names (labels) df used first row output table. col_lab_fontface (string) font face apply first row (column labels col_labels = TRUE). Defaults \"bold\". hline (flag) whether horizontal line printed first row table. bg_fill (string) table background fill color.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/df2gg.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Convert data.frame object to ggplot object — df2gg","text":"ggplot object.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/df2gg.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Convert data.frame object to ggplot object — df2gg","text":"","code":"if (FALSE) { # \\dontrun{ df2gg(head(iris, 5))  df2gg(head(iris, 5), font_size = 15, colwidths = c(1, 1, 1, 1, 1)) } # }"},{"path":"https://insightsengineering.github.io/tern/reference/df_explicit_na.html","id":null,"dir":"Reference","previous_headings":"","what":"Encode categorical missing values in a data frame — df_explicit_na","title":"Encode categorical missing values in a data frame — df_explicit_na","text":"helper function encode missing entries across groups categorical variables data frame.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/df_explicit_na.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Encode categorical missing values in a data frame — df_explicit_na","text":"","code":"df_explicit_na(   data,   omit_columns = NULL,   char_as_factor = TRUE,   logical_as_factor = FALSE,   na_level = \"<Missing>\" )"},{"path":"https://insightsengineering.github.io/tern/reference/df_explicit_na.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Encode categorical missing values in a data frame — df_explicit_na","text":"data (data.frame) data set. omit_columns (character) names variables data modified function. char_as_factor (flag) whether convert character variables data factors. logical_as_factor (flag) whether convert logical variables data factors. na_level (string) string used replace NA empty values inside non-omit_columns columns.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/df_explicit_na.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Encode categorical missing values in a data frame — df_explicit_na","text":"data.frame chosen modifications applied.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/df_explicit_na.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Encode categorical missing values in a data frame — df_explicit_na","text":"Missing entries NA empty strings replaced specified value. factor variables include missing values, missing value inserted last level. Similarly, case character logical variables converted factors char_as_factor logical_as_factor options, missing values set last level.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/reference/df_explicit_na.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Encode categorical missing values in a data frame — df_explicit_na","text":"","code":"my_data <- data.frame(   u = c(TRUE, FALSE, NA, TRUE),   v = factor(c(\"A\", NA, NA, NA), levels = c(\"Z\", \"A\")),   w = c(\"A\", \"B\", NA, \"C\"),   x = c(\"D\", \"E\", \"F\", NA),   y = c(\"G\", \"H\", \"I\", \"\"),   z = c(1, 2, 3, 4),   stringsAsFactors = FALSE )  # Example 1 # Encode missing values in all character or factor columns. df_explicit_na(my_data) #>       u         v         w         x         y z #> 1  TRUE         A         A         D         G 1 #> 2 FALSE <Missing>         B         E         H 2 #> 3    NA <Missing> <Missing>         F         I 3 #> 4  TRUE <Missing>         C <Missing> <Missing> 4 # Also convert logical columns to factor columns. df_explicit_na(my_data, logical_as_factor = TRUE) #>           u         v         w         x         y z #> 1      TRUE         A         A         D         G 1 #> 2     FALSE <Missing>         B         E         H 2 #> 3 <Missing> <Missing> <Missing>         F         I 3 #> 4      TRUE <Missing>         C <Missing> <Missing> 4 # Encode missing values in a subset of columns. df_explicit_na(my_data, omit_columns = c(\"x\", \"y\")) #>       u         v         w    x y z #> 1  TRUE         A         A    D G 1 #> 2 FALSE <Missing>         B    E H 2 #> 3    NA <Missing> <Missing>    F I 3 #> 4  TRUE <Missing>         C <NA>   4  # Example 2 # Here we purposefully convert all `M` values to `NA` in the `SEX` variable. # After running `df_explicit_na` the `NA` values are encoded as `<Missing>` but they are not # included when generating `rtables`. adsl <- tern_ex_adsl adsl$SEX[adsl$SEX == \"M\"] <- NA adsl <- df_explicit_na(adsl)  # If you want the `Na` values to be displayed in the table use the `na_level` argument. adsl <- tern_ex_adsl adsl$SEX[adsl$SEX == \"M\"] <- NA adsl <- df_explicit_na(adsl, na_level = \"Missing Values\")  # Example 3 # Numeric variables that have missing values are not altered. This means that any `NA` value in # a numeric variable will not be included in the summary statistics, nor will they be included # in the denominator value for calculating the percent values. adsl <- tern_ex_adsl adsl$AGE[adsl$AGE < 30] <- NA adsl <- df_explicit_na(adsl)"},{"path":"https://insightsengineering.github.io/tern/reference/dot-is_equal_float.html","id":null,"dir":"Reference","previous_headings":"","what":"Utility function to check if a float value is equal to another float value — .is_equal_float","title":"Utility function to check if a float value is equal to another float value — .is_equal_float","text":"Uses .Machine$double.eps tolerance comparison.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/dot-is_equal_float.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Utility function to check if a float value is equal to another float value — .is_equal_float","text":"","code":".is_equal_float(x, y)"},{"path":"https://insightsengineering.github.io/tern/reference/dot-is_equal_float.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Utility function to check if a float value is equal to another float value — .is_equal_float","text":"x (numeric(1)) float number. y (numeric(1)) float number.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/dot-is_equal_float.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Utility function to check if a float value is equal to another float value — .is_equal_float","text":"TRUE identical, otherwise FALSE.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/draw_grob.html","id":null,"dir":"Reference","previous_headings":"","what":"Draw grob — draw_grob","title":"Draw grob — draw_grob","text":"Draw grob device page.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/draw_grob.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Draw grob — draw_grob","text":"","code":"draw_grob(grob, newpage = TRUE, vp = NULL)"},{"path":"https://insightsengineering.github.io/tern/reference/draw_grob.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Draw grob — draw_grob","text":"grob (grob) grid object. newpage (flag) draw new page. vp (viewport NULL) viewport() object (NULL).","code":""},{"path":"https://insightsengineering.github.io/tern/reference/draw_grob.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Draw grob — draw_grob","text":"grob.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/draw_grob.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Draw grob — draw_grob","text":"","code":"library(dplyr) library(grid)  # \\donttest{ rect <- rectGrob(width = grid::unit(0.5, \"npc\"), height = grid::unit(0.5, \"npc\")) rect %>% draw_grob(vp = grid::viewport(angle = 45))   num <- lapply(1:10, textGrob) num %>%   arrange_grobs(grobs = .) %>%   draw_grob() #> Warning: `stack_grobs()` was deprecated in tern 0.9.4. #> ℹ `tern` plotting functions no longer generate `grob` objects. #> ℹ The deprecated feature was likely used in the tern package. #>   Please report the issue at #>   <https://github.com/insightsengineering/tern/issues>. showViewport()  # }"},{"path":"https://insightsengineering.github.io/tern/reference/empty_vector_if_na.html","id":null,"dir":"Reference","previous_headings":"","what":"Return an empty numeric if all elements are NA. — empty_vector_if_na","title":"Return an empty numeric if all elements are NA. — empty_vector_if_na","text":"Return empty numeric elements NA.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/empty_vector_if_na.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Return an empty numeric if all elements are NA. — empty_vector_if_na","text":"","code":"empty_vector_if_na(x)"},{"path":"https://insightsengineering.github.io/tern/reference/empty_vector_if_na.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Return an empty numeric if all elements are NA. — empty_vector_if_na","text":"x (numeric) vector.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/empty_vector_if_na.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Return an empty numeric if all elements are NA. — empty_vector_if_na","text":"empty numeric elements x NA, otherwise x.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/empty_vector_if_na.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Return an empty numeric if all elements are NA. — empty_vector_if_na","text":"","code":"x <- c(NA, NA, NA) # Internal function - empty_vector_if_na"},{"path":"https://insightsengineering.github.io/tern/reference/estimate_coef.html","id":null,"dir":"Reference","previous_headings":"","what":"Hazard ratio estimation in interactions — estimate_coef","title":"Hazard ratio estimation in interactions — estimate_coef","text":"function estimates hazard ratios arms interaction variable given specific values.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/estimate_coef.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Hazard ratio estimation in interactions — estimate_coef","text":"","code":"estimate_coef(   variable,   given,   lvl_var,   lvl_given,   coef,   mmat,   vcov,   conf_level = 0.95 )"},{"path":"https://insightsengineering.github.io/tern/reference/estimate_coef.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Hazard ratio estimation in interactions — estimate_coef","text":"variable, given (character(2)) names two variables interaction. seek estimation levels variable given levels given. lvl_var, lvl_given (character) corresponding levels given levels(). coef (numeric) vector estimated coefficients. mmat (named numeric) vector filled 0s used template obtain design matrix. vcov (matrix) variance-covariance matrix underlying model. conf_level (proportion) confidence level estimate intervals.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/estimate_coef.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Hazard ratio estimation in interactions — estimate_coef","text":"list matrices (one per level variable) rows corresponding combinations variable given, columns: coef_hat: Estimation coefficient. coef_se: Standard error estimation. hr: Hazard ratio. lcl, ucl: Lower/upper confidence limit hazard ratio.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/estimate_coef.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Hazard ratio estimation in interactions — estimate_coef","text":"Given cox regression investigating effect Arm (, B, C; reference ) Sex (F, M; reference Female). model abbreviated: y ~ Arm + Sex + Arm x Sex. cox regression estimates coefficients along variance-covariance matrix : b1 (arm b), b2 (arm c) b3 (sex m) b4 (arm b: sex m), b5 (arm c: sex m) Given want estimation Hazard Ratio arm C/sex M, estimation given reference arm /Sex M exp(b2 + b3 + b5)/ exp(b3) = exp(b2 + b5), therefore interaction coefficient given b2 + b5 standard error obtained $1.96 * sqrt(Var b2 + Var b5 + 2 * covariance (b2,b5))$ confidence level 0.95.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/reference/estimate_coef.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Hazard ratio estimation in interactions — estimate_coef","text":"","code":"library(dplyr) library(survival)  ADSL <- tern_ex_adsl %>%   filter(SEX %in% c(\"F\", \"M\"))  adtte <- tern_ex_adtte %>% filter(PARAMCD == \"PFS\") adtte$ARMCD <- droplevels(adtte$ARMCD) adtte$SEX <- droplevels(adtte$SEX)  mod <- coxph(   formula = Surv(time = AVAL, event = 1 - CNSR) ~ (SEX + ARMCD)^2,   data = adtte )  mmat <- stats::model.matrix(mod)[1, ] mmat[!mmat == 0] <- 0"},{"path":"https://insightsengineering.github.io/tern/reference/estimate_multinomial_rsp.html","id":null,"dir":"Reference","previous_headings":"","what":"Estimate proportions of each level of a variable — estimate_multinomial_rsp","title":"Estimate proportions of each level of a variable — estimate_multinomial_rsp","text":"analyze & summarize function estimate_multinomial_response() creates layout element estimate proportion proportion confidence interval level factor variable. primary analysis variable, var, factor variable, values used labels within output table.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/estimate_multinomial_rsp.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Estimate proportions of each level of a variable — estimate_multinomial_rsp","text":"","code":"estimate_multinomial_response(   lyt,   var,   na_str = default_na_str(),   nested = TRUE,   ...,   show_labels = \"hidden\",   table_names = var,   .stats = \"prop_ci\",   .formats = NULL,   .labels = NULL,   .indent_mods = NULL )  s_length_proportion(x, .N_col, ...)  a_length_proportion(x, .N_col, ...)"},{"path":"https://insightsengineering.github.io/tern/reference/estimate_multinomial_rsp.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Estimate proportions of each level of a variable — estimate_multinomial_rsp","text":"lyt (PreDataTableLayouts) layout analyses added . var (string) single variable name passed rtables requested statistics function. na_str (string) string used replace NA empty values output. nested (flag) whether layout instruction applied within existing layout structure _if possible (TRUE, default) new top-level element (FALSE). Ignored nest split. underneath analyses, allowed. ... additional arguments lower level functions. show_labels (string) label visibility: one \"default\", \"visible\" \"hidden\". table_names (character) can customized case vars analyzed multiple times, avoid warnings rtables. .stats (character) statistics select table. Options : 'n_prop', 'prop_ci' .formats (named character list) formats statistics. See Details analyze_vars information \"auto\" setting. .labels (named character) labels statistics (without indent). .indent_mods (named integer) indent modifiers labels. Defaults 0, corresponds unmodified default behavior. Can negative. x (numeric) vector numbers want analyze. .N_col (integer(1)) column-wise N (column count) full column analyzed typically passed rtables.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/estimate_multinomial_rsp.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Estimate proportions of each level of a variable — estimate_multinomial_rsp","text":"estimate_multinomial_response() returns layout object suitable passing layouting functions, rtables::build_table(). Adding function rtable layout add formatted rows containing statistics s_length_proportion() table layout. s_length_proportion() returns statistics s_proportion(). a_length_proportion() returns corresponding list formatted rtables::CellValue().","code":""},{"path":"https://insightsengineering.github.io/tern/reference/estimate_multinomial_rsp.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Estimate proportions of each level of a variable — estimate_multinomial_rsp","text":"estimate_multinomial_response(): Layout-creating function can take statistics function arguments additional format arguments. function wrapper rtables::analyze() rtables::summarize_row_groups(). s_length_proportion(): Statistics function feeds length x number successes, .N_col total number successes failures s_proportion(). a_length_proportion(): Formatted analysis function used afun estimate_multinomial_response().","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/reference/estimate_multinomial_rsp.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Estimate proportions of each level of a variable — estimate_multinomial_rsp","text":"","code":"library(dplyr)  # Use of the layout creating function. dta_test <- data.frame(   USUBJID = paste0(\"S\", 1:12),   ARM     = factor(rep(LETTERS[1:3], each = 4)),   AVAL    = c(A = c(1, 1, 1, 1), B = c(0, 0, 1, 1), C = c(0, 0, 0, 0)) ) %>% mutate(   AVALC = factor(AVAL,     levels = c(0, 1),     labels = c(\"Complete Response (CR)\", \"Partial Response (PR)\")   ) )  lyt <- basic_table() %>%   split_cols_by(\"ARM\") %>%   estimate_multinomial_response(var = \"AVALC\")  tbl <- build_table(lyt, dta_test)  tbl #>                                           A                B                 C        #> ————————————————————————————————————————————————————————————————————————————————————— #> Complete Response (CR)                0 (0.0%)         2 (50.0%)        4 (100.0%)    #>   95% CI (Wald, with correction)    (0.00, 12.50)    (0.00, 100.00)   (87.50, 100.00) #> Partial Response (PR)                4 (100.0%)        2 (50.0%)         0 (0.0%)     #>   95% CI (Wald, with correction)   (87.50, 100.00)   (0.00, 100.00)    (0.00, 12.50)   s_length_proportion(rep(\"CR\", 10), .N_col = 100) #> $n_prop #> [1] 10.0  0.1 #> attr(,\"label\") #> [1] \"Responders\" #>  #> $prop_ci #> [1]  3.620108 16.379892 #> attr(,\"label\") #> [1] \"95% CI (Wald, with correction)\" #>  s_length_proportion(factor(character(0)), .N_col = 100) #> $n_prop #> [1] 0 0 #> attr(,\"label\") #> [1] \"Responders\" #>  #> $prop_ci #> [1] 0.0 0.5 #> attr(,\"label\") #> [1] \"95% CI (Wald, with correction)\" #>   a_length_proportion(rep(\"CR\", 10), .N_col = 100) #> RowsVerticalSection (in_rows) object print method: #> ---------------------------- #>   row_name formatted_cell indent_mod                      row_label #> 1   n_prop     10 (10.0%)          0                     Responders #> 2  prop_ci  (3.62, 16.38)          0 95% CI (Wald, with correction) a_length_proportion(factor(character(0)), .N_col = 100) #> RowsVerticalSection (in_rows) object print method: #> ---------------------------- #>   row_name formatted_cell indent_mod                      row_label #> 1   n_prop       0 (0.0%)          0                     Responders #> 2  prop_ci   (0.00, 0.50)          0 95% CI (Wald, with correction)"},{"path":"https://insightsengineering.github.io/tern/reference/estimate_proportion.html","id":null,"dir":"Reference","previous_headings":"","what":"Proportion estimation — estimate_proportion","title":"Proportion estimation — estimate_proportion","text":"analyze function estimate_proportion() creates layout element estimate proportion responders within studied population. primary analysis variable, vars, indicates whether response occurred record. See method parameter options methods use constructing confidence interval proportion. Additionally, stratification variable can supplied via strata element variables argument.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/estimate_proportion.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Proportion estimation — estimate_proportion","text":"","code":"estimate_proportion(   lyt,   vars,   conf_level = 0.95,   method = c(\"waldcc\", \"wald\", \"clopper-pearson\", \"wilson\", \"wilsonc\", \"strat_wilson\",     \"strat_wilsonc\", \"agresti-coull\", \"jeffreys\"),   weights = NULL,   max_iterations = 50,   variables = list(strata = NULL),   long = FALSE,   na_str = default_na_str(),   nested = TRUE,   ...,   show_labels = \"hidden\",   table_names = vars,   .stats = NULL,   .formats = NULL,   .labels = NULL,   .indent_mods = NULL )  s_proportion(   df,   .var,   conf_level = 0.95,   method = c(\"waldcc\", \"wald\", \"clopper-pearson\", \"wilson\", \"wilsonc\", \"strat_wilson\",     \"strat_wilsonc\", \"agresti-coull\", \"jeffreys\"),   weights = NULL,   max_iterations = 50,   variables = list(strata = NULL),   long = FALSE )  a_proportion(   df,   .var,   conf_level = 0.95,   method = c(\"waldcc\", \"wald\", \"clopper-pearson\", \"wilson\", \"wilsonc\", \"strat_wilson\",     \"strat_wilsonc\", \"agresti-coull\", \"jeffreys\"),   weights = NULL,   max_iterations = 50,   variables = list(strata = NULL),   long = FALSE )"},{"path":"https://insightsengineering.github.io/tern/reference/estimate_proportion.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Proportion estimation — estimate_proportion","text":"lyt (PreDataTableLayouts) layout analyses added . vars (character) variable names primary analysis variable iterated . conf_level (proportion) confidence level interval. method (string) method used construct confidence interval proportion successful outcomes; one waldcc, wald, clopper-pearson, wilson, wilsonc, strat_wilson, strat_wilsonc, agresti-coull jeffreys. weights (numeric NULL) weights level strata. NULL, estimated using iterative algorithm proposed Yan2010-jt;textualtern minimizes weighted squared length confidence interval. max_iterations (count) maximum number iterations iterative procedure used find estimates optimal weights. variables (named list string) list additional analysis variables. long (flag) whether long description required. na_str (string) string used replace NA empty values output. nested (flag) whether layout instruction applied within existing layout structure _if possible (TRUE, default) new top-level element (FALSE). Ignored nest split. underneath analyses, allowed. ... additional arguments lower level functions. show_labels (string) label visibility: one \"default\", \"visible\" \"hidden\". table_names (character) can customized case vars analyzed multiple times, avoid warnings rtables. .stats (character) statistics select table. Options : 'n_prop', 'prop_ci' .formats (named character list) formats statistics. See Details analyze_vars information \"auto\" setting. .labels (named character) labels statistics (without indent). .indent_mods (named integer) indent modifiers labels. Defaults 0, corresponds unmodified default behavior. Can negative. df (logical data.frame) logical vector used, indicates whether subject responder . TRUE represents successful outcome. data.frame provided, also strata variable names must provided variables list element strata strings. case data.frame, logical vector responses must indicated variable name .var. .var (string) single variable name passed rtables requested statistics function.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/estimate_proportion.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Proportion estimation — estimate_proportion","text":"estimate_proportion() returns layout object suitable passing layouting functions, rtables::build_table(). Adding function rtable layout add formatted rows containing statistics s_proportion() table layout. s_proportion() returns statistics n_prop (n proportion) prop_ci (proportion CI) given variable. a_proportion() returns corresponding list formatted rtables::CellValue().","code":""},{"path":"https://insightsengineering.github.io/tern/reference/estimate_proportion.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Proportion estimation — estimate_proportion","text":"estimate_proportion(): Layout-creating function can take statistics function arguments additional format arguments. function wrapper rtables::analyze(). s_proportion(): Statistics function estimating proportion along confidence interval. a_proportion(): Formatted analysis function used afun estimate_proportion().","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/reference/estimate_proportion.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Proportion estimation — estimate_proportion","text":"","code":"dta_test <- data.frame(   USUBJID = paste0(\"S\", 1:12),   ARM     = rep(LETTERS[1:3], each = 4),   AVAL    = rep(LETTERS[1:3], each = 4) )  basic_table() %>%   split_cols_by(\"ARM\") %>%   estimate_proportion(vars = \"AVAL\") %>%   build_table(df = dta_test) #>                                      A           B           C     #> —————————————————————————————————————————————————————————————————— #> Responders                       <Missing>   <Missing>   <Missing> #> 95% CI (Wald, with correction)   <Missing>   <Missing>   <Missing>  # Case with only logical vector. rsp_v <- c(1, 0, 1, 0, 1, 1, 0, 0) s_proportion(rsp_v) #> $n_prop #> [1] 4.0 0.5 #> attr(,\"label\") #> [1] \"Responders\" #>  #> $prop_ci #> [1]  9.102404 90.897596 #> attr(,\"label\") #> [1] \"95% CI (Wald, with correction)\" #>   # Example for Stratified Wilson CI nex <- 100 # Number of example rows dta <- data.frame(   \"rsp\" = sample(c(TRUE, FALSE), nex, TRUE),   \"grp\" = sample(c(\"A\", \"B\"), nex, TRUE),   \"f1\" = sample(c(\"a1\", \"a2\"), nex, TRUE),   \"f2\" = sample(c(\"x\", \"y\", \"z\"), nex, TRUE),   stringsAsFactors = TRUE )  s_proportion(   df = dta,   .var = \"rsp\",   variables = list(strata = c(\"f1\", \"f2\")),   conf_level = 0.90,   method = \"strat_wilson\" ) #> $n_prop #> [1] 49.00  0.49 #> attr(,\"label\") #> [1] \"Responders\" #>  #> $prop_ci #>    lower    upper  #> 40.80675 56.65017  #> attr(,\"label\") #> [1] \"90% CI (Stratified Wilson, without correction)\" #>"},{"path":"https://insightsengineering.github.io/tern/reference/ex_data.html","id":null,"dir":"Reference","previous_headings":"","what":"Simulated CDISC data for examples — ex_data","title":"Simulated CDISC data for examples — ex_data","text":"Simulated CDISC data examples","code":""},{"path":"https://insightsengineering.github.io/tern/reference/ex_data.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Simulated CDISC data for examples — ex_data","text":"","code":"tern_ex_adsl  tern_ex_adae  tern_ex_adlb  tern_ex_adpp  tern_ex_adrs  tern_ex_adtte"},{"path":"https://insightsengineering.github.io/tern/reference/ex_data.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Simulated CDISC data for examples — ex_data","text":"rds (data.frame) object class tbl_df (inherits tbl, data.frame) 200 rows 21 columns. object class tbl_df (inherits tbl, data.frame) 541 rows 42 columns. object class tbl_df (inherits tbl, data.frame) 4200 rows 50 columns. object class tbl_df (inherits tbl, data.frame) 522 rows 25 columns. object class tbl_df (inherits tbl, data.frame) 1600 rows 29 columns. object class tbl_df (inherits tbl, data.frame) 1000 rows 28 columns.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/ex_data.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Simulated CDISC data for examples — ex_data","text":"tern_ex_adsl: ADSL data tern_ex_adae: ADAE data tern_ex_adlb: ADLB data tern_ex_adpp: ADPP data tern_ex_adrs: ADRS data tern_ex_adtte: ADTTE data","code":""},{"path":"https://insightsengineering.github.io/tern/reference/explicit_na.html","id":null,"dir":"Reference","previous_headings":"","what":"Missing data — explicit_na","title":"Missing data — explicit_na","text":"Substitute missing data string factor level.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/explicit_na.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Missing data — explicit_na","text":"","code":"explicit_na(x, label = \"<Missing>\")"},{"path":"https://insightsengineering.github.io/tern/reference/explicit_na.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Missing data — explicit_na","text":"x (factor character) values missing values substituted. label (string) string missing data replaced .","code":""},{"path":"https://insightsengineering.github.io/tern/reference/explicit_na.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Missing data — explicit_na","text":"x NA values substituted label.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/explicit_na.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Missing data — explicit_na","text":"","code":"explicit_na(c(NA, \"a\", \"b\")) #> [1] \"<Missing>\" \"a\"         \"b\"         is.na(explicit_na(c(NA, \"a\", \"b\"))) #> [1] FALSE FALSE FALSE  explicit_na(factor(c(NA, \"a\", \"b\"))) #> [1] <Missing> a         b         #> Levels: a b <Missing> is.na(explicit_na(factor(c(NA, \"a\", \"b\")))) #> [1] FALSE FALSE FALSE  explicit_na(sas_na(c(\"a\", \"\"))) #> [1] \"a\"         \"<Missing>\""},{"path":"https://insightsengineering.github.io/tern/reference/extract_by_name.html","id":null,"dir":"Reference","previous_headings":"","what":"Extract elements by name — extract_by_name","title":"Extract elements by name — extract_by_name","text":"utility function extracts elements vector x names. Differences standard [ function :","code":""},{"path":"https://insightsengineering.github.io/tern/reference/extract_by_name.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Extract elements by name — extract_by_name","text":"","code":"extract_by_name(x, names)"},{"path":"https://insightsengineering.github.io/tern/reference/extract_by_name.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Extract elements by name — extract_by_name","text":"x (named vector) extract named elements . names (character) vector names extract.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/extract_by_name.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Extract elements by name — extract_by_name","text":"NULL x NULL, otherwise extracted elements x.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/extract_by_name.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Extract elements by name — extract_by_name","text":"x NULL, still always NULL returned (base function). x NULL, intersection names made names elements returned. , names appear x returned NAs.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/extract_rsp_biomarkers.html","id":null,"dir":"Reference","previous_headings":"","what":"Prepare response data estimates for multiple biomarkers in a single data frame — extract_rsp_biomarkers","title":"Prepare response data estimates for multiple biomarkers in a single data frame — extract_rsp_biomarkers","text":"Prepares estimates number responses, patients overall response rate, well odds ratio estimates, confidence intervals p-values, multiple biomarkers across population subgroups single data frame. variables corresponds names variables found data, passed named list requires elements rsp biomarkers (vector continuous biomarker variables) optionally covariates, subgroups strata. groups_lists optionally specifies groupings subgroups variables.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/extract_rsp_biomarkers.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Prepare response data estimates for multiple biomarkers in a single data frame — extract_rsp_biomarkers","text":"","code":"extract_rsp_biomarkers(   variables,   data,   groups_lists = list(),   control = control_logistic(),   label_all = \"All Patients\" )"},{"path":"https://insightsengineering.github.io/tern/reference/extract_rsp_biomarkers.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Prepare response data estimates for multiple biomarkers in a single data frame — extract_rsp_biomarkers","text":"variables (named list string) list additional analysis variables. data (data.frame) dataset containing variables summarize. groups_lists (named list list) optionally contains subgroups variable list, specifies new group levels via names levels belong character vectors elements list. control (named list) controls response definition confidence level produced control_logistic(). label_all (string) label total population analysis.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/extract_rsp_biomarkers.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Prepare response data estimates for multiple biomarkers in a single data frame — extract_rsp_biomarkers","text":"data.frame columns biomarker, biomarker_label, n_tot, n_rsp, prop, , lcl, ucl, conf_level, pval, pval_label, subgroup, var, var_label, row_type.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/extract_rsp_biomarkers.html","id":"note","dir":"Reference","previous_headings":"","what":"Note","title":"Prepare response data estimates for multiple biomarkers in a single data frame — extract_rsp_biomarkers","text":"can also specify continuous variable rsp use response_definition control convert internally logical variable reflecting binary response.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/reference/extract_rsp_biomarkers.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Prepare response data estimates for multiple biomarkers in a single data frame — extract_rsp_biomarkers","text":"","code":"library(dplyr) library(forcats)  adrs <- tern_ex_adrs adrs_labels <- formatters::var_labels(adrs)  adrs_f <- adrs %>%   filter(PARAMCD == \"BESRSPI\") %>%   mutate(rsp = AVALC == \"CR\")  # Typical analysis of two continuous biomarkers `BMRKR1` and `AGE`, # in logistic regression models with one covariate `RACE`. The subgroups # are defined by the levels of `BMRKR2`. df <- extract_rsp_biomarkers(   variables = list(     rsp = \"rsp\",     biomarkers = c(\"BMRKR1\", \"AGE\"),     covariates = \"SEX\",     subgroups = \"BMRKR2\"   ),   data = adrs_f ) df #>   biomarker              biomarker_label n_tot n_rsp      prop        or #> 1    BMRKR1 Continuous Level Biomarker 1   200   164 0.8200000 0.9755036 #> 2       AGE                          Age   200   164 0.8200000 0.9952416 #> 3    BMRKR1 Continuous Level Biomarker 1    70    53 0.7571429 1.1524547 #> 4       AGE                          Age    70    53 0.7571429 0.9261012 #> 5    BMRKR1 Continuous Level Biomarker 1    68    58 0.8529412 0.8773122 #> 6       AGE                          Age    68    58 0.8529412 0.9867104 #> 7    BMRKR1 Continuous Level Biomarker 1    62    53 0.8548387 0.8792921 #> 8       AGE                          Age    62    53 0.8548387 1.0630262 #>         lcl      ucl conf_level      pval     pval_label     subgroup    var #> 1 0.8804862 1.080775       0.95 0.6352602 p-value (Wald) All Patients    ALL #> 2 0.9462617 1.046757       0.95 0.8530389 p-value (Wald) All Patients    ALL #> 3 0.9462127 1.403650       0.95 0.1584187 p-value (Wald)          LOW BMRKR2 #> 4 0.8487519 1.010500       0.95 0.0844837 p-value (Wald)          LOW BMRKR2 #> 5 0.7277189 1.057657       0.95 0.1699778 p-value (Wald)       MEDIUM BMRKR2 #> 6 0.8798911 1.106498       0.95 0.8189816 p-value (Wald)       MEDIUM BMRKR2 #> 7 0.7189748 1.075357       0.95 0.2103709 p-value (Wald)         HIGH BMRKR2 #> 8 0.9595973 1.177603       0.95 0.2418840 p-value (Wald)         HIGH BMRKR2 #>                      var_label row_type #> 1                 All Patients  content #> 2                 All Patients  content #> 3 Continuous Level Biomarker 2 analysis #> 4 Continuous Level Biomarker 2 analysis #> 5 Continuous Level Biomarker 2 analysis #> 6 Continuous Level Biomarker 2 analysis #> 7 Continuous Level Biomarker 2 analysis #> 8 Continuous Level Biomarker 2 analysis  # Here we group the levels of `BMRKR2` manually, and we add a stratification # variable `STRATA1`. We also here use a continuous variable `EOSDY` # which is then binarized internally (response is defined as this variable # being larger than 750). df_grouped <- extract_rsp_biomarkers(   variables = list(     rsp = \"EOSDY\",     biomarkers = c(\"BMRKR1\", \"AGE\"),     covariates = \"SEX\",     subgroups = \"BMRKR2\",     strata = \"STRATA1\"   ),   data = adrs_f,   groups_lists = list(     BMRKR2 = list(       \"low\" = \"LOW\",       \"low/medium\" = c(\"LOW\", \"MEDIUM\"),       \"low/medium/high\" = c(\"LOW\", \"MEDIUM\", \"HIGH\")     )   ),   control = control_logistic(     response_definition = \"I(response > 750)\"   ) ) df_grouped #>   biomarker              biomarker_label n_tot n_rsp prop or lcl ucl conf_level #> 1    BMRKR1 Continuous Level Biomarker 1   200     0    0 NA  NA  NA       0.95 #> 2       AGE                          Age   200     0    0 NA  NA  NA       0.95 #> 3    BMRKR1 Continuous Level Biomarker 1    70     0    0 NA  NA  NA       0.95 #> 4       AGE                          Age    70     0    0 NA  NA  NA       0.95 #> 5    BMRKR1 Continuous Level Biomarker 1   138     0    0 NA  NA  NA       0.95 #> 6       AGE                          Age   138     0    0 NA  NA  NA       0.95 #> 7    BMRKR1 Continuous Level Biomarker 1   200     0    0 NA  NA  NA       0.95 #> 8       AGE                          Age   200     0    0 NA  NA  NA       0.95 #>   pval     pval_label        subgroup    var                    var_label #> 1   NA p-value (Wald)    All Patients    ALL                 All Patients #> 2   NA p-value (Wald)    All Patients    ALL                 All Patients #> 3   NA p-value (Wald)             low BMRKR2 Continuous Level Biomarker 2 #> 4   NA p-value (Wald)             low BMRKR2 Continuous Level Biomarker 2 #> 5   NA p-value (Wald)      low/medium BMRKR2 Continuous Level Biomarker 2 #> 6   NA p-value (Wald)      low/medium BMRKR2 Continuous Level Biomarker 2 #> 7   NA p-value (Wald) low/medium/high BMRKR2 Continuous Level Biomarker 2 #> 8   NA p-value (Wald) low/medium/high BMRKR2 Continuous Level Biomarker 2 #>   row_type #> 1  content #> 2  content #> 3 analysis #> 4 analysis #> 5 analysis #> 6 analysis #> 7 analysis #> 8 analysis"},{"path":"https://insightsengineering.github.io/tern/reference/extract_rsp_subgroups.html","id":null,"dir":"Reference","previous_headings":"","what":"Prepare response data for population subgroups in data frames — extract_rsp_subgroups","title":"Prepare response data for population subgroups in data frames — extract_rsp_subgroups","text":"Prepares response rates odds ratios population subgroups data frames. Simple wrapper h_odds_ratio_subgroups_df() h_proportion_subgroups_df(). Result list two data.frames: prop . variables corresponds names variables found data, passed named list requires elements rsp, arm optionally subgroups strata. groups_lists optionally specifies groupings subgroups variables.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/extract_rsp_subgroups.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Prepare response data for population subgroups in data frames — extract_rsp_subgroups","text":"","code":"extract_rsp_subgroups(   variables,   data,   groups_lists = list(),   conf_level = 0.95,   method = NULL,   label_all = \"All Patients\" )"},{"path":"https://insightsengineering.github.io/tern/reference/extract_rsp_subgroups.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Prepare response data for population subgroups in data frames — extract_rsp_subgroups","text":"variables (named list string) list additional analysis variables. data (data.frame) dataset containing variables summarize. groups_lists (named list list) optionally contains subgroups variable list, specifies new group levels via names levels belong character vectors elements list. conf_level (proportion) confidence level interval. method (string NULL) specifies test used calculate p-value difference two proportions. options, see test_proportion_diff(). Default NULL test performed. label_all (string) label total population analysis.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/extract_rsp_subgroups.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Prepare response data for population subgroups in data frames — extract_rsp_subgroups","text":"named list two elements: prop: data.frame containing columns arm, n, n_rsp, prop, subgroup, var, var_label, row_type. : data.frame containing columns arm, n_tot, , lcl, ucl, conf_level, subgroup, var, var_label, row_type.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/reference/extract_survival_biomarkers.html","id":null,"dir":"Reference","previous_headings":"","what":"Prepare survival data estimates for multiple biomarkers in a single data frame — extract_survival_biomarkers","title":"Prepare survival data estimates for multiple biomarkers in a single data frame — extract_survival_biomarkers","text":"Prepares estimates number events, patients median survival times, well hazard ratio estimates, confidence intervals p-values, multiple biomarkers across population subgroups single data frame. variables corresponds names variables found data, passed named list requires elements tte, is_event, biomarkers (vector continuous biomarker variables), optionally subgroups strata. groups_lists optionally specifies groupings subgroups variables.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/extract_survival_biomarkers.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Prepare survival data estimates for multiple biomarkers in a single data frame — extract_survival_biomarkers","text":"","code":"extract_survival_biomarkers(   variables,   data,   groups_lists = list(),   control = control_coxreg(),   label_all = \"All Patients\" )"},{"path":"https://insightsengineering.github.io/tern/reference/extract_survival_biomarkers.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Prepare survival data estimates for multiple biomarkers in a single data frame — extract_survival_biomarkers","text":"variables (named list string) list additional analysis variables. data (data.frame) dataset containing variables summarize. groups_lists (named list list) optionally contains subgroups variable list, specifies new group levels via names levels belong character vectors elements list. control (list) list parameters returned helper function control_coxreg(). label_all (string) label total population analysis.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/extract_survival_biomarkers.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Prepare survival data estimates for multiple biomarkers in a single data frame — extract_survival_biomarkers","text":"data.frame columns biomarker, biomarker_label, n_tot, n_tot_events, median, hr, lcl, ucl, conf_level, pval, pval_label, subgroup, var, var_label, row_type.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/reference/extract_survival_subgroups.html","id":null,"dir":"Reference","previous_headings":"","what":"Prepare survival data for population subgroups in data frames — extract_survival_subgroups","title":"Prepare survival data for population subgroups in data frames — extract_survival_subgroups","text":"Prepares estimates median survival times treatment hazard ratios population subgroups data frames. Simple wrapper h_survtime_subgroups_df() h_coxph_subgroups_df(). Result list two data.frames: survtime hr. variables corresponds names variables found data, passed named list requires elements tte, is_event, arm optionally subgroups strata. groups_lists optionally specifies groupings subgroups variables.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/extract_survival_subgroups.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Prepare survival data for population subgroups in data frames — extract_survival_subgroups","text":"","code":"extract_survival_subgroups(   variables,   data,   groups_lists = list(),   control = control_coxph(),   label_all = \"All Patients\" )"},{"path":"https://insightsengineering.github.io/tern/reference/extract_survival_subgroups.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Prepare survival data for population subgroups in data frames — extract_survival_subgroups","text":"variables (named list string) list additional analysis variables. data (data.frame) dataset containing variables summarize. groups_lists (named list list) optionally contains subgroups variable list, specifies new group levels via names levels belong character vectors elements list. control (list) parameters comparison details, specified using helper function control_coxph(). possible parameter options : pval_method (string) p-value method testing null hypothesis hazard ratio = 1. Default method \"log-rank\" comes survival::survdiff(), can also set \"wald\" \"likelihood\" (survival::coxph()). ties (string) specifying method tie handling. Default \"efron\", can also set \"breslow\" \"exact\". See survival::coxph(). conf_level (proportion) confidence level interval HR. label_all (string) label total population analysis.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/extract_survival_subgroups.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Prepare survival data for population subgroups in data frames — extract_survival_subgroups","text":"named list two elements: survtime: data.frame containing columns arm, n, n_events, median, subgroup, var, var_label, row_type. hr: data.frame containing columns arm, n_tot, n_tot_events, hr, lcl, ucl, conf_level, pval, pval_label, subgroup, var, var_label, row_type.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/reference/extreme_format.html","id":null,"dir":"Reference","previous_headings":"","what":"Format extreme values — extreme_format","title":"Format extreme values — extreme_format","text":"rtables formatting functions handle extreme values.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/extreme_format.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Format extreme values — extreme_format","text":"","code":"h_get_format_threshold(digits = 2L)  h_format_threshold(x, digits = 2L)"},{"path":"https://insightsengineering.github.io/tern/reference/extreme_format.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Format extreme values — extreme_format","text":"digits (integer(1)) number decimal places display. x (numeric(1)) value format.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/extreme_format.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Format extreme values — extreme_format","text":"h_get_format_threshold() returns list 2 elements: threshold, low high thresholds, format_string, thresholds formatted strings. h_format_threshold() returns given value, value within digit threshold relation given value digit threshold, formatted string.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/extreme_format.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Format extreme values — extreme_format","text":"input, apply format specified number digits. value threshold, returns \"<0.01\" e.g. number digits 2. value threshold, returns \">999.99\" e.g. number digits 2. zero, returns \"0.00\".","code":""},{"path":"https://insightsengineering.github.io/tern/reference/extreme_format.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Format extreme values — extreme_format","text":"h_get_format_threshold(): Internal helper function calculate threshold create formatted strings used Formatting Functions. Returns list elements threshold format_string. h_format_threshold(): Internal helper function apply threshold format value. Creates formatted string used Formatting Functions.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/reference/extreme_format.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Format extreme values — extreme_format","text":"","code":"h_get_format_threshold(2L) #> $threshold #>    low   high  #>   0.01 999.99  #>  #> $format_string #>       low      high  #>   \"<0.01\" \">999.99\"  #>   h_format_threshold(0.001) #> [1] \"<0.01\" h_format_threshold(1000) #> [1] \">999.99\""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/reference/f_conf_level.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Utility function to create label for confidence interval — f_conf_level","text":"","code":"f_conf_level(conf_level)"},{"path":"https://insightsengineering.github.io/tern/reference/f_conf_level.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Utility function to create label for confidence interval — f_conf_level","text":"conf_level (proportion) confidence level interval.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/f_conf_level.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Utility function to create label for confidence interval — f_conf_level","text":"string.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/reference/f_pval.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Utility function to create label for p-value — f_pval","text":"","code":"f_pval(test_mean)"},{"path":"https://insightsengineering.github.io/tern/reference/f_pval.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Utility function to create label for p-value — f_pval","text":"test_mean (numeric(1)) mean value test null hypothesis.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/f_pval.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Utility function to create label for p-value — f_pval","text":"string.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/fct_collapse_only.html","id":null,"dir":"Reference","previous_headings":"","what":"Collapse factor levels and keep only those new group levels — fct_collapse_only","title":"Collapse factor levels and keep only those new group levels — fct_collapse_only","text":"collapses levels keeps new group levels, order provided. returned factor levels order given, possible missing level last (included missing values).","code":""},{"path":"https://insightsengineering.github.io/tern/reference/fct_collapse_only.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Collapse factor levels and keep only those new group levels — fct_collapse_only","text":"","code":"fct_collapse_only(.f, ..., .na_level = \"<Missing>\")"},{"path":"https://insightsengineering.github.io/tern/reference/fct_collapse_only.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Collapse factor levels and keep only those new group levels — fct_collapse_only","text":".f (factor character) original vector. ... (named character) levels vector provided collapsed new level given respective name. .na_level (string) level use levels, missing new factor. Note level must contained new levels specified ....","code":""},{"path":"https://insightsengineering.github.io/tern/reference/fct_collapse_only.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Collapse factor levels and keep only those new group levels — fct_collapse_only","text":"modified factor collapsed levels. Values levels included given character vector input set missing level .na_level.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/fct_collapse_only.html","id":"note","dir":"Reference","previous_headings":"","what":"Note","title":"Collapse factor levels and keep only those new group levels — fct_collapse_only","text":"existing NAs input vector replaced missing level. needed, explicit_na() can called separately result.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/reference/fct_collapse_only.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Collapse factor levels and keep only those new group levels — fct_collapse_only","text":"","code":"fct_collapse_only(factor(c(\"a\", \"b\", \"c\", \"d\")), TRT = \"b\", CTRL = c(\"c\", \"d\")) #> [1] <Missing> TRT       CTRL      CTRL      #> Levels: TRT CTRL <Missing>"},{"path":"https://insightsengineering.github.io/tern/reference/fct_discard.html","id":null,"dir":"Reference","previous_headings":"","what":"Discard specified levels of a factor — fct_discard","title":"Discard specified levels of a factor — fct_discard","text":"discards observations well levels specified factor.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/fct_discard.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Discard specified levels of a factor — fct_discard","text":"","code":"fct_discard(x, discard)"},{"path":"https://insightsengineering.github.io/tern/reference/fct_discard.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Discard specified levels of a factor — fct_discard","text":"x (factor) original factor. discard (character) levels discard.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/fct_discard.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Discard specified levels of a factor — fct_discard","text":"modified factor observations well levels discard dropped.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/fct_discard.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Discard specified levels of a factor — fct_discard","text":"","code":"fct_discard(factor(c(\"a\", \"b\", \"c\")), \"c\") #> [1] a b #> Levels: a b"},{"path":"https://insightsengineering.github.io/tern/reference/fct_explicit_na_if.html","id":null,"dir":"Reference","previous_headings":"","what":"Insertion of explicit missing values in a factor — fct_explicit_na_if","title":"Insertion of explicit missing values in a factor — fct_explicit_na_if","text":"inserts explicit missing values factor based condition. Additionally, existing NA values explicitly converted given na_level.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/fct_explicit_na_if.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Insertion of explicit missing values in a factor — fct_explicit_na_if","text":"","code":"fct_explicit_na_if(x, condition, na_level = \"<Missing>\")"},{"path":"https://insightsengineering.github.io/tern/reference/fct_explicit_na_if.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Insertion of explicit missing values in a factor — fct_explicit_na_if","text":"x (factor) original factor. condition (logical) positions insert missing values. na_level (string) level use missing values.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/fct_explicit_na_if.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Insertion of explicit missing values in a factor — fct_explicit_na_if","text":"modified factor inserted existing NA converted na_level.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/reference/fct_explicit_na_if.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Insertion of explicit missing values in a factor — fct_explicit_na_if","text":"","code":"fct_explicit_na_if(factor(c(\"a\", \"b\", NA)), c(TRUE, FALSE, FALSE)) #> [1] <Missing> b         <Missing> #> Levels: a b <Missing>"},{"path":"https://insightsengineering.github.io/tern/reference/fit_coxreg.html","id":null,"dir":"Reference","previous_headings":"","what":"Fitting functions for Cox proportional hazards regression — fit_coxreg","title":"Fitting functions for Cox proportional hazards regression — fit_coxreg","text":"Fitting functions univariate multivariate Cox regression models.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/fit_coxreg.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Fitting functions for Cox proportional hazards regression — fit_coxreg","text":"","code":"fit_coxreg_univar(variables, data, at = list(), control = control_coxreg())  fit_coxreg_multivar(variables, data, control = control_coxreg())"},{"path":"https://insightsengineering.github.io/tern/reference/fit_coxreg.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Fitting functions for Cox proportional hazards regression — fit_coxreg","text":"variables (named list) names variables found data, passed named list corresponding time, event, arm, strata, covariates terms. arm missing variables, Cox model(s) including covariates fitted corresponding effect estimates tabulated later. data (data.frame) dataset containing variables fit models. (list numeric) candidate covariate numeric, use specify value covariate effect estimated. control (list) list parameters returned helper function control_coxreg().","code":""},{"path":"https://insightsengineering.github.io/tern/reference/fit_coxreg.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Fitting functions for Cox proportional hazards regression — fit_coxreg","text":"fit_coxreg_univar() returns coxreg.univar class object named list 5 elements: mod: Cox regression models fitted survival::coxph(). data: original data frame input. control: original control input. vars: variables used model. : Value covariate effect estimated. fit_coxreg_multivar() returns coxreg.multivar class object named list 4 elements: mod: Cox regression model fitted survival::coxph(). data: original data frame input. control: original control input. vars: variables used model.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/fit_coxreg.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Fitting functions for Cox proportional hazards regression — fit_coxreg","text":"fit_coxreg_univar(): Fit series univariate Cox regression models given inputs. fit_coxreg_multivar(): Fit multivariate Cox regression model.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/fit_coxreg.html","id":"note","dir":"Reference","previous_headings":"","what":"Note","title":"Fitting functions for Cox proportional hazards regression — fit_coxreg","text":"using fit_coxreg_univar two study arms.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/reference/fit_coxreg.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Fitting functions for Cox proportional hazards regression — fit_coxreg","text":"","code":"library(survival)  set.seed(1, kind = \"Mersenne-Twister\")  # Testing dataset [survival::bladder]. dta_bladder <- with(   data = bladder[bladder$enum < 5, ],   data.frame(     time = stop,     status = event,     armcd = as.factor(rx),     covar1 = as.factor(enum),     covar2 = factor(       sample(as.factor(enum)),       levels = 1:4, labels = c(\"F\", \"F\", \"M\", \"M\")     )   ) ) labels <- c(\"armcd\" = \"ARM\", \"covar1\" = \"A Covariate Label\", \"covar2\" = \"Sex (F/M)\") formatters::var_labels(dta_bladder)[names(labels)] <- labels dta_bladder$age <- sample(20:60, size = nrow(dta_bladder), replace = TRUE)  plot(   survfit(Surv(time, status) ~ armcd + covar1, data = dta_bladder),   lty = 2:4,   xlab = \"Months\",   col = c(\"blue1\", \"blue2\", \"blue3\", \"blue4\", \"red1\", \"red2\", \"red3\", \"red4\") )   # fit_coxreg_univar  ## Cox regression: arm + 1 covariate. mod1 <- fit_coxreg_univar(   variables = list(     time = \"time\", event = \"status\", arm = \"armcd\",     covariates = \"covar1\"   ),   data = dta_bladder,   control = control_coxreg(conf_level = 0.91) )  ## Cox regression: arm + 1 covariate + interaction, 2 candidate covariates. mod2 <- fit_coxreg_univar(   variables = list(     time = \"time\", event = \"status\", arm = \"armcd\",     covariates = c(\"covar1\", \"covar2\")   ),   data = dta_bladder,   control = control_coxreg(conf_level = 0.91, interaction = TRUE) )  ## Cox regression: arm + 1 covariate, stratified analysis. mod3 <- fit_coxreg_univar(   variables = list(     time = \"time\", event = \"status\", arm = \"armcd\", strata = \"covar2\",     covariates = c(\"covar1\")   ),   data = dta_bladder,   control = control_coxreg(conf_level = 0.91) )  ## Cox regression: no arm, only covariates. mod4 <- fit_coxreg_univar(   variables = list(     time = \"time\", event = \"status\",     covariates = c(\"covar1\", \"covar2\")   ),   data = dta_bladder )  # fit_coxreg_multivar  ## Cox regression: multivariate Cox regression. multivar_model <- fit_coxreg_multivar(   variables = list(     time = \"time\", event = \"status\", arm = \"armcd\",     covariates = c(\"covar1\", \"covar2\")   ),   data = dta_bladder )  # Example without treatment arm. multivar_covs_model <- fit_coxreg_multivar(   variables = list(     time = \"time\", event = \"status\",     covariates = c(\"covar1\", \"covar2\")   ),   data = dta_bladder )"},{"path":"https://insightsengineering.github.io/tern/reference/fit_logistic.html","id":null,"dir":"Reference","previous_headings":"","what":"Fit for logistic regression — fit_logistic","title":"Fit for logistic regression — fit_logistic","text":"Fit (conditional) logistic regression model.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/fit_logistic.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Fit for logistic regression — fit_logistic","text":"","code":"fit_logistic(   data,   variables = list(response = \"Response\", arm = \"ARMCD\", covariates = NULL, interaction =     NULL, strata = NULL),   response_definition = \"response\" )"},{"path":"https://insightsengineering.github.io/tern/reference/fit_logistic.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Fit for logistic regression — fit_logistic","text":"data (data.frame) data frame model fit. variables (named list string) list additional analysis variables. response_definition (string) definition event terms response. used fitting (conditional) logistic regression model left hand side formula.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/fit_logistic.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Fit for logistic regression — fit_logistic","text":"fitted logistic regression model.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/fit_logistic.html","id":"model-specification","dir":"Reference","previous_headings":"","what":"Model Specification","title":"Fit for logistic regression — fit_logistic","text":"variables list needs include following elements: arm: Treatment arm variable name. response: response arm variable name. Usually 0/1 variable. covariates: either NULL (covariates) character vector covariate variable names. interaction: either NULL (interaction) string single covariate variable name already included covariates. interaction treatment arm included model.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/fit_logistic.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Fit for logistic regression — fit_logistic","text":"","code":"library(dplyr)  adrs_f <- tern_ex_adrs %>%   filter(PARAMCD == \"BESRSPI\") %>%   filter(RACE %in% c(\"ASIAN\", \"WHITE\", \"BLACK OR AFRICAN AMERICAN\")) %>%   mutate(     Response = case_when(AVALC %in% c(\"PR\", \"CR\") ~ 1, TRUE ~ 0),     RACE = factor(RACE),     SEX = factor(SEX)   ) formatters::var_labels(adrs_f) <- c(formatters::var_labels(tern_ex_adrs), Response = \"Response\") mod1 <- fit_logistic(   data = adrs_f,   variables = list(     response = \"Response\",     arm = \"ARMCD\",     covariates = c(\"AGE\", \"RACE\")   ) ) #> Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred mod2 <- fit_logistic(   data = adrs_f,   variables = list(     response = \"Response\",     arm = \"ARMCD\",     covariates = c(\"AGE\", \"RACE\"),     interaction = \"AGE\"   ) ) #> Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred"},{"path":"https://insightsengineering.github.io/tern/reference/fit_rsp_step.html","id":null,"dir":"Reference","previous_headings":"","what":"Subgroup treatment effect pattern (STEP) fit for binary (response) outcome — fit_rsp_step","title":"Subgroup treatment effect pattern (STEP) fit for binary (response) outcome — fit_rsp_step","text":"fits Subgroup Treatment Effect Pattern logistic regression models binary (response) outcome. treatment arm variable must exactly 2 levels, first one taken reference estimated odds ratios comparison second level vs. first one. (conditional) logistic regression model fit : response ~ arm * poly(biomarker, degree) + covariates + strata(strata) degree specified control_step().","code":""},{"path":"https://insightsengineering.github.io/tern/reference/fit_rsp_step.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Subgroup treatment effect pattern (STEP) fit for binary (response) outcome — fit_rsp_step","text":"","code":"fit_rsp_step(variables, data, control = c(control_step(), control_logistic()))"},{"path":"https://insightsengineering.github.io/tern/reference/fit_rsp_step.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Subgroup treatment effect pattern (STEP) fit for binary (response) outcome — fit_rsp_step","text":"variables (named list character) list analysis variables: needs response, arm, biomarker, optional covariates strata. data (data.frame) dataset containing variables summarize. control (named list) combined control list control_step() control_logistic().","code":""},{"path":"https://insightsengineering.github.io/tern/reference/fit_rsp_step.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Subgroup treatment effect pattern (STEP) fit for binary (response) outcome — fit_rsp_step","text":"matrix class step. first part columns describe subgroup intervals used biomarker variable, including center intervals bounds. second part columns contain estimates treatment arm comparison.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/fit_rsp_step.html","id":"note","dir":"Reference","previous_headings":"","what":"Note","title":"Subgroup treatment effect pattern (STEP) fit for binary (response) outcome — fit_rsp_step","text":"default degree 0 biomarker variable included model.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/reference/fit_rsp_step.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Subgroup treatment effect pattern (STEP) fit for binary (response) outcome — fit_rsp_step","text":"","code":"# Testing dataset with just two treatment arms. library(survival) library(dplyr)  adrs_f <- tern_ex_adrs %>%   filter(     PARAMCD == \"BESRSPI\",     ARM %in% c(\"B: Placebo\", \"A: Drug X\")   ) %>%   mutate(     # Reorder levels of ARM to have Placebo as reference arm for Odds Ratio calculations.     ARM = droplevels(forcats::fct_relevel(ARM, \"B: Placebo\")),     RSP = case_when(AVALC %in% c(\"PR\", \"CR\") ~ 1, TRUE ~ 0),     SEX = factor(SEX)   )  variables <- list(   arm = \"ARM\",   biomarker = \"BMRKR1\",   covariates = \"AGE\",   response = \"RSP\" )  # Fit default STEP models: Here a constant treatment effect is estimated in each subgroup. # We use a large enough bandwidth to avoid too small subgroups and linear separation in those. step_matrix <- fit_rsp_step(   variables = variables,   data = adrs_f,   control = c(control_logistic(), control_step(bandwidth = 0.9)) ) dim(step_matrix) #> [1] 39 11 head(step_matrix) #>      Percentile Center Percentile Lower Percentile Upper Interval Center #> [1,]             0.025                0            0.925        1.472755 #> [2,]             0.050                0            0.950        2.028546 #> [3,]             0.075                0            0.975        2.204086 #> [4,]             0.100                0            1.000        2.799776 #> [5,]             0.125                0            1.000        2.969998 #> [6,]             0.150                0            1.000        3.149068 #>      Interval Lower Interval Upper   n    logor       se   ci_lower ci_upper #> [1,]      0.4459546       11.74529 131 1.835008 1.134560 -0.3886885 4.058703 #> [2,]      0.4459546       12.73387 134 1.895158 1.136248 -0.3318481 4.122163 #> [3,]      0.4459546       14.75099 138 1.947699 1.136969 -0.2807193 4.176116 #> [4,]      0.4459546       18.49236 142 1.931001 1.135866 -0.2952561 4.157258 #> [5,]      0.4459546       18.49236 142 1.931001 1.135866 -0.2952561 4.157258 #> [6,]      0.4459546       18.49236 142 1.931001 1.135866 -0.2952561 4.157258  # Specify different polynomial degree for the biomarker interaction to use more flexible local # models. Or specify different logistic regression options, including confidence level. step_matrix2 <- fit_rsp_step(   variables = variables,   data = adrs_f,   control = c(control_logistic(conf_level = 0.9), control_step(bandwidth = NULL, degree = 1)) )  # Use a global constant model. This is helpful as a reference for the subgroup models. step_matrix3 <- fit_rsp_step(   variables = variables,   data = adrs_f,   control = c(control_logistic(), control_step(bandwidth = NULL, num_points = 2L)) )  # It is also possible to use strata, i.e. use conditional logistic regression models. variables2 <- list(   arm = \"ARM\",   biomarker = \"BMRKR1\",   covariates = \"AGE\",   response = \"RSP\",   strata = c(\"STRATA1\", \"STRATA2\") )  step_matrix4 <- fit_rsp_step(   variables = variables2,   data = adrs_f,   control = c(control_logistic(), control_step(bandwidth = NULL)) )"},{"path":"https://insightsengineering.github.io/tern/reference/fit_survival_step.html","id":null,"dir":"Reference","previous_headings":"","what":"Subgroup treatment effect pattern (STEP) fit for survival outcome — fit_survival_step","title":"Subgroup treatment effect pattern (STEP) fit for survival outcome — fit_survival_step","text":"fits subgroup treatment effect pattern (STEP) models survival outcome. treatment arm variable must exactly 2 levels, first one taken reference estimated hazard ratios comparison second level vs. first one. model fit : Surv(time, event) ~ arm * poly(biomarker, degree) + covariates + strata(strata) degree specified control_step().","code":""},{"path":"https://insightsengineering.github.io/tern/reference/fit_survival_step.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Subgroup treatment effect pattern (STEP) fit for survival outcome — fit_survival_step","text":"","code":"fit_survival_step(   variables,   data,   control = c(control_step(), control_coxph()) )"},{"path":"https://insightsengineering.github.io/tern/reference/fit_survival_step.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Subgroup treatment effect pattern (STEP) fit for survival outcome — fit_survival_step","text":"variables (named list character) list analysis variables: needs time, event, arm, biomarker, optional covariates strata. data (data.frame) dataset containing variables summarize. control (named list) combined control list control_step() control_coxph().","code":""},{"path":"https://insightsengineering.github.io/tern/reference/fit_survival_step.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Subgroup treatment effect pattern (STEP) fit for survival outcome — fit_survival_step","text":"matrix class step. first part columns describe subgroup intervals used biomarker variable, including center intervals bounds. second part columns contain estimates treatment arm comparison.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/fit_survival_step.html","id":"note","dir":"Reference","previous_headings":"","what":"Note","title":"Subgroup treatment effect pattern (STEP) fit for survival outcome — fit_survival_step","text":"default degree 0 biomarker variable included model.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/reference/fit_survival_step.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Subgroup treatment effect pattern (STEP) fit for survival outcome — fit_survival_step","text":"","code":"# Testing dataset with just two treatment arms. library(dplyr)  adtte_f <- tern_ex_adtte %>%   filter(     PARAMCD == \"OS\",     ARM %in% c(\"B: Placebo\", \"A: Drug X\")   ) %>%   mutate(     # Reorder levels of ARM to display reference arm before treatment arm.     ARM = droplevels(forcats::fct_relevel(ARM, \"B: Placebo\")),     is_event = CNSR == 0   ) labels <- c(\"ARM\" = \"Treatment Arm\", \"is_event\" = \"Event Flag\") formatters::var_labels(adtte_f)[names(labels)] <- labels  variables <- list(   arm = \"ARM\",   biomarker = \"BMRKR1\",   covariates = c(\"AGE\", \"BMRKR2\"),   event = \"is_event\",   time = \"AVAL\" )  # Fit default STEP models: Here a constant treatment effect is estimated in each subgroup. step_matrix <- fit_survival_step(   variables = variables,   data = adtte_f ) dim(step_matrix) #> [1] 39 12 head(step_matrix) #>      Percentile Center Percentile Lower Percentile Upper Interval Center #> [1,]             0.025                0            0.275        1.472755 #> [2,]             0.050                0            0.300        2.028546 #> [3,]             0.075                0            0.325        2.204086 #> [4,]             0.100                0            0.350        2.799776 #> [5,]             0.125                0            0.375        2.969998 #> [6,]             0.150                0            0.400        3.149068 #>      Interval Lower Interval Upper  n events      loghr        se   ci_lower #> [1,]      0.4459546       4.182444 39     29 0.03729601 0.4243013 -0.7943192 #> [2,]      0.4459546       4.349471 43     31 0.23246622 0.3881347 -0.5282639 #> [3,]      0.4459546       4.626913 46     32 0.07952492 0.3813113 -0.6678314 #> [4,]      0.4459546       4.805767 50     35 0.09020455 0.3638368 -0.6229026 #> [5,]      0.4459546       4.929816 53     37 0.15522702 0.3477999 -0.5264483 #> [6,]      0.4459546       5.020539 57     41 0.11135760 0.3332843 -0.5418676 #>       ci_upper #> [1,] 0.8689112 #> [2,] 0.9931963 #> [3,] 0.8268813 #> [4,] 0.8033117 #> [5,] 0.8369023 #> [6,] 0.7645828  # Specify different polynomial degree for the biomarker interaction to use more flexible local # models. Or specify different Cox regression options. step_matrix2 <- fit_survival_step(   variables = variables,   data = adtte_f,   control = c(control_coxph(conf_level = 0.9), control_step(degree = 2)) )  # Use a global model with cubic interaction and only 5 points. step_matrix3 <- fit_survival_step(   variables = variables,   data = adtte_f,   control = c(control_coxph(), control_step(bandwidth = NULL, degree = 3, num_points = 5L)) )"},{"path":[]},{"path":"https://insightsengineering.github.io/tern/reference/forest_viewport.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create a viewport tree for the forest plot — forest_viewport","text":"","code":"forest_viewport(   tbl,   width_row_names = NULL,   width_columns = NULL,   width_forest = grid::unit(1, \"null\"),   gap_column = grid::unit(1, \"lines\"),   gap_header = grid::unit(1, \"lines\"),   mat_form = NULL )"},{"path":"https://insightsengineering.github.io/tern/reference/forest_viewport.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create a viewport tree for the forest plot — forest_viewport","text":"tbl (VTableTree)rtables table object. width_row_names (grid::unit) width row names. width_columns (grid::unit) width column spans. width_forest (grid::unit) width forest plot. gap_column (grid::unit) gap width columns. gap_header (grid::unit) gap width header. mat_form (MatrixPrintForm) matrix print form table.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/forest_viewport.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Create a viewport tree for the forest plot — forest_viewport","text":"viewport tree.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/forest_viewport.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Create a viewport tree for the forest plot — forest_viewport","text":"","code":"library(grid)  tbl <- rtable(   header = rheader(     rrow(\"\", \"E\", rcell(\"CI\", colspan = 2)),     rrow(\"\", \"A\", \"B\", \"C\")   ),   rrow(\"row 1\", 1, 0.8, 1.1),   rrow(\"row 2\", 1.4, 0.8, 1.6),   rrow(\"row 3\", 1.2, 0.8, 1.2) )  # \\donttest{ v <- forest_viewport(tbl) #> Warning: `forest_viewport()` was deprecated in tern 0.9.4. #> ℹ `g_forest` now generates `ggplot` objects. This function is no longer used #>   within `tern`. #> Warning: `vp_forest_table_part()` was deprecated in tern 0.9.4. #> ℹ `g_forest` now generates `ggplot` objects. This function is no longer used #>   within `tern`. #> ℹ The deprecated feature was likely used in the tern package. #>   Please report the issue at #>   <https://github.com/insightsengineering/tern/issues>.  grid::grid.newpage() showViewport(v)  # }"},{"path":"https://insightsengineering.github.io/tern/reference/format_auto.html","id":null,"dir":"Reference","previous_headings":"","what":"Format automatically using data significant digits — format_auto","title":"Format automatically using data significant digits — format_auto","text":"Formatting function majority default methods used analyze_vars(). non-derived values, significant digits data used (e.g. range), derived values one digits (measure location dispersion like mean, standard deviation). function can called internally \"auto\" like, example, .formats = c(\"mean\" = \"auto\"). See details see works inner function.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/format_auto.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Format automatically using data significant digits — format_auto","text":"","code":"format_auto(dt_var, x_stat)"},{"path":"https://insightsengineering.github.io/tern/reference/format_auto.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Format automatically using data significant digits — format_auto","text":"dt_var (numeric) variable data statistics calculated . Used find significant digits. analyze_vars comes .df_row (see rtables::additional_fun_params), row data row splits. column split considered. x_stat (string) string indicating current statistical method used.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/format_auto.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Format automatically using data significant digits — format_auto","text":"string rtables prints table cell.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/format_auto.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Format automatically using data significant digits — format_auto","text":"internal function needed work rtables default structure format functions, .e. function(x, ...), x results statistical evaluation. can one element (e.g. .stats = \"mean_sd\").","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/reference/format_auto.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Format automatically using data significant digits — format_auto","text":"","code":"x_todo <- c(0.001, 0.2, 0.0011000, 3, 4) res <- c(mean(x_todo[1:3]), sd(x_todo[1:3]))  # x is the result coming into the formatting function -> res!! format_auto(dt_var = x_todo, x_stat = \"mean_sd\")(x = res) #> [1] \"0.06737 (0.11486)\" format_auto(x_todo, \"range\")(x = range(x_todo)) #> [1] \"0.0010 - 4.0000\" no_sc_x <- c(0.0000001, 1) format_auto(no_sc_x, \"range\")(x = no_sc_x) #> [1] \"0.0000001 - 1.0000000\""},{"path":"https://insightsengineering.github.io/tern/reference/format_count_fraction.html","id":null,"dir":"Reference","previous_headings":"","what":"Format count and fraction — format_count_fraction","title":"Format count and fraction — format_count_fraction","text":"Formats count together fraction special consideration count 0.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/format_count_fraction.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Format count and fraction — format_count_fraction","text":"","code":"format_count_fraction(x, ...)"},{"path":"https://insightsengineering.github.io/tern/reference/format_count_fraction.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Format count and fraction — format_count_fraction","text":"x (numeric(2)) vector length 2 count fraction, respectively. ... used. Required rtables interface.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/format_count_fraction.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Format count and fraction — format_count_fraction","text":"string format count (fraction %). count 0, format 0.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/reference/format_count_fraction.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Format count and fraction — format_count_fraction","text":"","code":"format_count_fraction(x = c(2, 0.6667)) #> [1] \"2 (66.7%)\" format_count_fraction(x = c(0, 0)) #> [1] \"0\""},{"path":"https://insightsengineering.github.io/tern/reference/format_count_fraction_fixed_dp.html","id":null,"dir":"Reference","previous_headings":"","what":"Format count and percentage with fixed single decimal place — format_count_fraction_fixed_dp","title":"Format count and percentage with fixed single decimal place — format_count_fraction_fixed_dp","text":"Formats count together fraction special consideration count 0.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/format_count_fraction_fixed_dp.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Format count and percentage with fixed single decimal place — format_count_fraction_fixed_dp","text":"","code":"format_count_fraction_fixed_dp(x, ...)"},{"path":"https://insightsengineering.github.io/tern/reference/format_count_fraction_fixed_dp.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Format count and percentage with fixed single decimal place — format_count_fraction_fixed_dp","text":"x (numeric(2)) vector length 2 count fraction, respectively. ... used. Required rtables interface.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/format_count_fraction_fixed_dp.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Format count and percentage with fixed single decimal place — format_count_fraction_fixed_dp","text":"string format count (fraction %). count 0, format 0.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/reference/format_count_fraction_fixed_dp.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Format count and percentage with fixed single decimal place — format_count_fraction_fixed_dp","text":"","code":"format_count_fraction_fixed_dp(x = c(2, 0.6667)) #> [1] \"2 (66.7%)\" format_count_fraction_fixed_dp(x = c(2, 0.5)) #> [1] \"2 (50.0%)\" format_count_fraction_fixed_dp(x = c(0, 0)) #> [1] \"0\""},{"path":"https://insightsengineering.github.io/tern/reference/format_count_fraction_lt10.html","id":null,"dir":"Reference","previous_headings":"","what":"Format count and fraction with special case for count < 10 — format_count_fraction_lt10","title":"Format count and fraction with special case for count < 10 — format_count_fraction_lt10","text":"Formats count together fraction special consideration count less 10.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/format_count_fraction_lt10.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Format count and fraction with special case for count < 10 — format_count_fraction_lt10","text":"","code":"format_count_fraction_lt10(x, ...)"},{"path":"https://insightsengineering.github.io/tern/reference/format_count_fraction_lt10.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Format count and fraction with special case for count < 10 — format_count_fraction_lt10","text":"x (numeric(2)) vector length 2 count fraction, respectively. ... used. Required rtables interface.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/format_count_fraction_lt10.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Format count and fraction with special case for count < 10 — format_count_fraction_lt10","text":"string format count (fraction %). count less 10, count printed.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/reference/format_count_fraction_lt10.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Format count and fraction with special case for count < 10 — format_count_fraction_lt10","text":"","code":"format_count_fraction_lt10(x = c(275, 0.9673)) #> [1] \"275 (96.7%)\" format_count_fraction_lt10(x = c(2, 0.6667)) #> [1] \"2\" format_count_fraction_lt10(x = c(9, 1)) #> [1] \"9\""},{"path":"https://insightsengineering.github.io/tern/reference/format_extreme_values.html","id":null,"dir":"Reference","previous_headings":"","what":"Format a single extreme value — format_extreme_values","title":"Format a single extreme value — format_extreme_values","text":"Create formatting function single extreme value.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/format_extreme_values.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Format a single extreme value — format_extreme_values","text":"","code":"format_extreme_values(digits = 2L)"},{"path":"https://insightsengineering.github.io/tern/reference/format_extreme_values.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Format a single extreme value — format_extreme_values","text":"digits (integer(1)) number decimal places display.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/format_extreme_values.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Format a single extreme value — format_extreme_values","text":"rtables formatting function uses threshold digits return formatted extreme value.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/reference/format_extreme_values.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Format a single extreme value — format_extreme_values","text":"","code":"format_fun <- format_extreme_values(2L) format_fun(x = 0.127) #> [1] \"0.13\" format_fun(x = Inf) #> [1] \">999.99\" format_fun(x = 0) #> [1] \"0.00\" format_fun(x = 0.009) #> [1] \"<0.01\""},{"path":"https://insightsengineering.github.io/tern/reference/format_extreme_values_ci.html","id":null,"dir":"Reference","previous_headings":"","what":"Format extreme values part of a confidence interval — format_extreme_values_ci","title":"Format extreme values part of a confidence interval — format_extreme_values_ci","text":"Formatting Function extreme values part confidence interval. Values formatted e.g. \"(xx.xx, xx.xx)\" number digits 2.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/format_extreme_values_ci.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Format extreme values part of a confidence interval — format_extreme_values_ci","text":"","code":"format_extreme_values_ci(digits = 2L)"},{"path":"https://insightsengineering.github.io/tern/reference/format_extreme_values_ci.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Format extreme values part of a confidence interval — format_extreme_values_ci","text":"digits (integer(1)) number decimal places display.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/format_extreme_values_ci.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Format extreme values part of a confidence interval — format_extreme_values_ci","text":"rtables formatting function uses threshold digits return formatted extreme values confidence interval.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/reference/format_extreme_values_ci.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Format extreme values part of a confidence interval — format_extreme_values_ci","text":"","code":"format_fun <- format_extreme_values_ci(2L) format_fun(x = c(0.127, Inf)) #> [1] \"(0.13, >999.99)\" format_fun(x = c(0, 0.009)) #> [1] \"(0.00, <0.01)\""},{"path":"https://insightsengineering.github.io/tern/reference/format_fraction.html","id":null,"dir":"Reference","previous_headings":"","what":"Format fraction and percentage — format_fraction","title":"Format fraction and percentage — format_fraction","text":"Formats fraction together ratio percent.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/format_fraction.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Format fraction and percentage — format_fraction","text":"","code":"format_fraction(x, ...)"},{"path":"https://insightsengineering.github.io/tern/reference/format_fraction.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Format fraction and percentage — format_fraction","text":"x (named integer) vector elements num denom. ... used. Required rtables interface.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/format_fraction.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Format fraction and percentage — format_fraction","text":"string format num / denom (ratio %). num 0, format num / denom.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/reference/format_fraction.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Format fraction and percentage — format_fraction","text":"","code":"format_fraction(x = c(num = 2L, denom = 3L)) #> [1] \"2/3 (66.7%)\" format_fraction(x = c(num = 0L, denom = 3L)) #> [1] \"0/3\""},{"path":"https://insightsengineering.github.io/tern/reference/format_fraction_fixed_dp.html","id":null,"dir":"Reference","previous_headings":"","what":"Format fraction and percentage with fixed single decimal place — format_fraction_fixed_dp","title":"Format fraction and percentage with fixed single decimal place — format_fraction_fixed_dp","text":"Formats fraction together ratio percent fixed single decimal place. Includes trailing zero case whole number percentages always keep one decimal place.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/format_fraction_fixed_dp.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Format fraction and percentage with fixed single decimal place — format_fraction_fixed_dp","text":"","code":"format_fraction_fixed_dp(x, ...)"},{"path":"https://insightsengineering.github.io/tern/reference/format_fraction_fixed_dp.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Format fraction and percentage with fixed single decimal place — format_fraction_fixed_dp","text":"x (named integer) vector elements num denom. ... used. Required rtables interface.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/format_fraction_fixed_dp.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Format fraction and percentage with fixed single decimal place — format_fraction_fixed_dp","text":"string format num / denom (ratio %). num 0, format num / denom.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/reference/format_fraction_fixed_dp.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Format fraction and percentage with fixed single decimal place — format_fraction_fixed_dp","text":"","code":"format_fraction_fixed_dp(x = c(num = 1L, denom = 2L)) #> [1] \"1/2 (50.0%)\" format_fraction_fixed_dp(x = c(num = 1L, denom = 4L)) #> [1] \"1/4 (25.0%)\" format_fraction_fixed_dp(x = c(num = 0L, denom = 3L)) #> [1] \"0/3\""},{"path":"https://insightsengineering.github.io/tern/reference/format_fraction_threshold.html","id":null,"dir":"Reference","previous_headings":"","what":"Format fraction with lower threshold — format_fraction_threshold","title":"Format fraction with lower threshold — format_fraction_threshold","text":"Formats fraction second element input x fraction. applies lower threshold, just stated fraction smaller .","code":""},{"path":"https://insightsengineering.github.io/tern/reference/format_fraction_threshold.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Format fraction with lower threshold — format_fraction_threshold","text":"","code":"format_fraction_threshold(threshold)"},{"path":"https://insightsengineering.github.io/tern/reference/format_fraction_threshold.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Format fraction with lower threshold — format_fraction_threshold","text":"threshold (proportion) lower threshold.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/format_fraction_threshold.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Format fraction with lower threshold — format_fraction_threshold","text":"rtables formatting function takes numeric input x second element fraction formatted. fraction equal threshold, displayed percentage. positive threshold, returns, e.g. \"<1\" threshold 0.01. zero, just \"0\" returned.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/reference/format_fraction_threshold.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Format fraction with lower threshold — format_fraction_threshold","text":"","code":"format_fun <- format_fraction_threshold(0.05) format_fun(x = c(20, 0.1)) #> [1] 10 format_fun(x = c(2, 0.01)) #> [1] \"<5\" format_fun(x = c(0, 0)) #> [1] \"0\""},{"path":"https://insightsengineering.github.io/tern/reference/format_sigfig.html","id":null,"dir":"Reference","previous_headings":"","what":"Format numeric values by significant figures — format_sigfig","title":"Format numeric values by significant figures — format_sigfig","text":"Format numeric values print specified number significant figures.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/format_sigfig.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Format numeric values by significant figures — format_sigfig","text":"","code":"format_sigfig(sigfig, format = \"xx\", num_fmt = \"fg\")"},{"path":"https://insightsengineering.github.io/tern/reference/format_sigfig.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Format numeric values by significant figures — format_sigfig","text":"sigfig (integer(1)) number significant figures display. format (string) format label (string) apply printing value. Decimal places string ignored favor formatting significant figures. Formats options : \"xx\", \"xx / xx\", \"(xx, xx)\", \"xx - xx\", \"xx (xx)\". num_fmt (string) numeric format modifiers apply value. Defaults \"fg\" standard significant figures formatting - fixed (non-scientific notation) format (\"f\") sigfig equal number significant figures instead decimal places (\"g\"). See formatC() format argument options.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/format_sigfig.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Format numeric values by significant figures — format_sigfig","text":"rtables formatting function.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/reference/format_sigfig.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Format numeric values by significant figures — format_sigfig","text":"","code":"fmt_3sf <- format_sigfig(3) fmt_3sf(1.658) #> [1] \"1.66\" fmt_3sf(1e1) #> [1] \"10.0\"  fmt_5sf <- format_sigfig(5) fmt_5sf(0.57) #> [1] \"0.57000\" fmt_5sf(0.000025645) #> [1] \"0.000025645\""},{"path":"https://insightsengineering.github.io/tern/reference/format_xx.html","id":null,"dir":"Reference","previous_headings":"","what":"Format XX as a formatting function — format_xx","title":"Format XX as a formatting function — format_xx","text":"Translate string x dots interpreted number place holders, others formatting elements.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/format_xx.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Format XX as a formatting function — format_xx","text":"","code":"format_xx(str)"},{"path":"https://insightsengineering.github.io/tern/reference/format_xx.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Format XX as a formatting function — format_xx","text":"str (string) template.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/format_xx.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Format XX as a formatting function — format_xx","text":"rtables formatting function.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/reference/format_xx.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Format XX as a formatting function — format_xx","text":"","code":"test <- list(c(1.658, 0.5761), c(1e1, 785.6))  z <- format_xx(\"xx (xx.x)\") sapply(test, z) #> [1] \"2 (0.6)\"    \"10 (785.6)\"  z <- format_xx(\"xx.x - xx.x\") sapply(test, z) #> [1] \"1.7 - 0.6\"  \"10 - 785.6\"  z <- format_xx(\"xx.x, incl. xx.x% NE\") sapply(test, z) #> [1] \"1.7, incl. 0.6% NE\"  \"10, incl. 785.6% NE\""},{"path":"https://insightsengineering.github.io/tern/reference/formatting_functions.html","id":null,"dir":"Reference","previous_headings":"","what":"Formatting functions — formatting_functions","title":"Formatting functions — formatting_functions","text":"See list formatting functions created tern work rtables.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/formatting_functions.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Formatting functions — formatting_functions","text":"available formats can listed via formatters::list_valid_format_labels(). Additional custom formats can created via formatters::sprintf_format() function.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/reference/g_bland_altman.html","id":null,"dir":"Reference","previous_headings":"","what":"Bland-Altman plot — g_bland_altman","title":"Bland-Altman plot — g_bland_altman","text":"Graphing function produces Bland-Altman plot.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/g_bland_altman.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Bland-Altman plot — g_bland_altman","text":"","code":"g_bland_altman(x, y, conf_level = 0.95)"},{"path":"https://insightsengineering.github.io/tern/reference/g_bland_altman.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Bland-Altman plot — g_bland_altman","text":"x (numeric) vector numbers want analyze. y (numeric) vector numbers want analyze, compared x. conf_level (proportion) confidence level interval.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/g_bland_altman.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Bland-Altman plot — g_bland_altman","text":"ggplot Bland-Altman plot.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/g_bland_altman.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Bland-Altman plot — g_bland_altman","text":"","code":"x <- seq(1, 60, 5) y <- seq(5, 50, 4)  g_bland_altman(x = x, y = y, conf_level = 0.9)"},{"path":[]},{"path":"https://insightsengineering.github.io/tern/reference/g_forest.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create a forest plot from an rtable — g_forest","text":"","code":"g_forest(   tbl,   col_x = attr(tbl, \"col_x\"),   col_ci = attr(tbl, \"col_ci\"),   vline = 1,   forest_header = attr(tbl, \"forest_header\"),   xlim = c(0.1, 10),   logx = TRUE,   x_at = c(0.1, 1, 10),   width_row_names = lifecycle::deprecated(),   width_columns = NULL,   width_forest = lifecycle::deprecated(),   lbl_col_padding = 0,   rel_width_forest = 0.25,   font_size = 12,   col_symbol_size = attr(tbl, \"col_symbol_size\"),   col = getOption(\"ggplot2.discrete.colour\")[1],   ggtheme = NULL,   as_list = FALSE,   gp = lifecycle::deprecated(),   draw = lifecycle::deprecated(),   newpage = lifecycle::deprecated() )"},{"path":"https://insightsengineering.github.io/tern/reference/g_forest.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create a forest plot from an rtable — g_forest","text":"tbl (VTableTree)rtables table least one column single value one column 2 values. col_x (integer(1) NULL) column index estimator. default tries get tbl attribute col_x, otherwise needs manually specified. NULL, points excluded forest plot. col_ci (integer(1) NULL) column index confidence intervals. default tries get tbl attribute col_ci, otherwise needs manually specified. NULL, lines excluded forest plot. vline (numeric(1) NULL) x coordinate vertical line, NULL line omitted. forest_header (character(2)) text displayed left right vline, respectively. vline = NULL forest_header printed. default tries get tbl attribute forest_header. NULL, defaults extracted table possible, set \"Comparison\\nBetter\" \"Treatment\\nBetter\" . xlim (numeric(2)) limits x axis. logx (flag) show x-values logarithm scale. x_at (numeric) x-tick locations, NULL, x_at set vline xlim values. width_row_names Please use lbl_col_padding argument instead. width_columns (numeric) vector column widths. element's position colwidths corresponds column tbl position. NULL, column widths calculated according maximum number characters per column. width_forest Please use rel_width_forest argument instead. lbl_col_padding (numeric) additional padding use calculating spacing first (label) column second column tbl. colwidths specified, width first column becomes colwidths[1] + lbl_col_padding. Defaults 0. rel_width_forest (proportion) proportion total width allocate forest plot. Relative width table 1 - rel_width_forest. as_list = TRUE, parameter ignored. font_size (numeric(1)) font size. col_symbol_size (numeric NULL) column index tbl containing data used determine relative size estimator plot symbol. Typically, symbol size proportional sample size used calculate estimator. NULL, symbol size used subgroups. default tries get tbl attribute col_symbol_size, otherwise needs manually specified. col (character) color(s). ggtheme (theme) graphical theme provided ggplot2 control styling plot. as_list (flag) whether two ggplot objects returned list. TRUE, named list two elements, table plot, returned. FALSE (default) table forest plot printed side--side via cowplot::plot_grid(). gp g_forest now generated ggplot object. argument longer used. draw g_forest now generated ggplot object. argument longer used. newpage g_forest now generated ggplot object. argument longer used.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/g_forest.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Create a forest plot from an rtable — g_forest","text":"ggplot forest plot table.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/g_forest.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Create a forest plot from an rtable — g_forest","text":"Given rtables::rtable() object least one column single value one column 2 values, converts table ggplot2::ggplot() object generates accompanying forest plot. table forest plot printed side--side.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/g_forest.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Create a forest plot from an rtable — g_forest","text":"","code":"library(dplyr) library(forcats)  adrs <- tern_ex_adrs n_records <- 20 adrs_labels <- formatters::var_labels(adrs, fill = TRUE) adrs <- adrs %>%   filter(PARAMCD == \"BESRSPI\") %>%   filter(ARM %in% c(\"A: Drug X\", \"B: Placebo\")) %>%   slice(seq_len(n_records)) %>%   droplevels() %>%   mutate(     # Reorder levels of factor to make the placebo group the reference arm.     ARM = fct_relevel(ARM, \"B: Placebo\"),     rsp = AVALC == \"CR\"   ) formatters::var_labels(adrs) <- c(adrs_labels, \"Response\") df <- extract_rsp_subgroups(   variables = list(rsp = \"rsp\", arm = \"ARM\", subgroups = c(\"SEX\", \"STRATA2\")),   data = adrs ) # Full commonly used response table.  tbl <- basic_table() %>%   tabulate_rsp_subgroups(df) g_forest(tbl)   # Odds ratio only table.  tbl_or <- basic_table() %>%   tabulate_rsp_subgroups(df, vars = c(\"n_tot\", \"or\", \"ci\")) g_forest(   tbl_or,   forest_header = c(\"Comparison\\nBetter\", \"Treatment\\nBetter\") )   # Survival forest plot example. adtte <- tern_ex_adtte # Save variable labels before data processing steps. adtte_labels <- formatters::var_labels(adtte, fill = TRUE) adtte_f <- adtte %>%   filter(     PARAMCD == \"OS\",     ARM %in% c(\"B: Placebo\", \"A: Drug X\"),     SEX %in% c(\"M\", \"F\")   ) %>%   mutate(     # Reorder levels of ARM to display reference arm before treatment arm.     ARM = droplevels(fct_relevel(ARM, \"B: Placebo\")),     SEX = droplevels(SEX),     AVALU = as.character(AVALU),     is_event = CNSR == 0   ) labels <- list(   \"ARM\" = adtte_labels[\"ARM\"],   \"SEX\" = adtte_labels[\"SEX\"],   \"AVALU\" = adtte_labels[\"AVALU\"],   \"is_event\" = \"Event Flag\" ) formatters::var_labels(adtte_f)[names(labels)] <- as.character(labels) df <- extract_survival_subgroups(   variables = list(     tte = \"AVAL\",     is_event = \"is_event\",     arm = \"ARM\", subgroups = c(\"SEX\", \"BMRKR2\")   ),   data = adtte_f ) table_hr <- basic_table() %>%   tabulate_survival_subgroups(df, time_unit = adtte_f$AVALU[1]) g_forest(table_hr)   # Works with any `rtable`. tbl <- rtable(   header = c(\"E\", \"CI\", \"N\"),   rrow(\"\", 1, c(.8, 1.2), 200),   rrow(\"\", 1.2, c(1.1, 1.4), 50) ) g_forest(   tbl = tbl,   col_x = 1,   col_ci = 2,   xlim = c(0.5, 2),   x_at = c(0.5, 1, 2),   col_symbol_size = 3 )   tbl <- rtable(   header = rheader(     rrow(\"\", rcell(\"A\", colspan = 2)),     rrow(\"\", \"c1\", \"c2\")   ),   rrow(\"row 1\", 1, c(.8, 1.2)),   rrow(\"row 2\", 1.2, c(1.1, 1.4)) ) g_forest(   tbl = tbl,   col_x = 1,   col_ci = 2,   xlim = c(0.5, 2),   x_at = c(0.5, 1, 2),   vline = 1,   forest_header = c(\"Hello\", \"World\") )"},{"path":"https://insightsengineering.github.io/tern/reference/g_ipp.html","id":null,"dir":"Reference","previous_headings":"","what":"Individual patient plots — g_ipp","title":"Individual patient plots — g_ipp","text":"Line plot(s) displaying trend patients' parameter values time rendered. Patients' individual baseline values can added plot(s) reference.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/g_ipp.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Individual patient plots — g_ipp","text":"","code":"g_ipp(   df,   xvar,   yvar,   xlab,   ylab,   id_var = \"USUBJID\",   title = \"Individual Patient Plots\",   subtitle = \"\",   caption = NULL,   add_baseline_hline = FALSE,   yvar_baseline = \"BASE\",   ggtheme = nestcolor::theme_nest(),   plotting_choices = c(\"all_in_one\", \"split_by_max_obs\", \"separate_by_obs\"),   max_obs_per_plot = 4,   col = NULL )"},{"path":"https://insightsengineering.github.io/tern/reference/g_ipp.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Individual patient plots — g_ipp","text":"df (data.frame) data set containing analysis variables. xvar (string) time point variable plotted x-axis. yvar (string) continuous analysis variable plotted y-axis. xlab (string) plot label x-axis. ylab (string) plot label y-axis. id_var (string) variable used patient identifier. title (string) title plot. subtitle (string) subtitle plot. caption (string) optional caption plot. add_baseline_hline (flag) adds horizontal line baseline y-value plot TRUE. yvar_baseline (string) variable baseline values . Ignored add_baseline_hline FALSE. ggtheme (theme) optional graphical theme function provided ggplot2 control outlook plot. Use ggplot2::theme() tweak display. plotting_choices (string) specifies options displaying plots. Must one \"all_in_one\", \"split_by_max_obs\", \"separate_by_obs\". max_obs_per_plot (integer(1)) number observations plotted one plot. Ignored plotting_choices \"separate_by_obs\". col (character) line colors.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/g_ipp.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Individual patient plots — g_ipp","text":"ggplot object list ggplot objects.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/g_ipp.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Individual patient plots — g_ipp","text":"g_ipp(): Plotting function individual patient plots , depending user preference, renders single graphic compiles list graphics show trends individual's parameter values time.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/reference/g_ipp.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Individual patient plots — g_ipp","text":"","code":"library(dplyr)  # Select a small sample of data to plot. adlb <- tern_ex_adlb %>%   filter(PARAMCD == \"ALT\", !(AVISIT %in% c(\"SCREENING\", \"BASELINE\"))) %>%   slice(1:36)  plot_list <- g_ipp(   df = adlb,   xvar = \"AVISIT\",   yvar = \"AVAL\",   xlab = \"Visit\",   ylab = \"SGOT/ALT (U/L)\",   title = \"Individual Patient Plots\",   add_baseline_hline = TRUE,   plotting_choices = \"split_by_max_obs\",   max_obs_per_plot = 5 ) plot_list #> [[1]]  #>  #> [[2]]  #>"},{"path":"https://insightsengineering.github.io/tern/reference/g_km.html","id":null,"dir":"Reference","previous_headings":"","what":"Kaplan-Meier plot — g_km","title":"Kaplan-Meier plot — g_km","text":"survival model, graphic rendered along tabulated annotation including number patient risk given time median survival per group.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/g_km.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Kaplan-Meier plot — g_km","text":"","code":"g_km(   df,   variables,   control_surv = control_surv_timepoint(),   col = NULL,   lty = NULL,   lwd = 0.5,   censor_show = TRUE,   pch = 3,   size = 2,   max_time = NULL,   xticks = NULL,   xlab = \"Days\",   yval = c(\"Survival\", \"Failure\"),   ylab = paste(yval, \"Probability\"),   ylim = NULL,   title = NULL,   footnotes = NULL,   font_size = 10,   ci_ribbon = FALSE,   annot_at_risk = TRUE,   annot_at_risk_title = TRUE,   annot_surv_med = TRUE,   annot_coxph = FALSE,   annot_stats = NULL,   annot_stats_vlines = FALSE,   control_coxph_pw = control_coxph(),   ref_group_coxph = NULL,   control_annot_surv_med = control_surv_med_annot(),   control_annot_coxph = control_coxph_annot(),   legend_pos = NULL,   rel_height_plot = 0.75,   ggtheme = NULL,   as_list = FALSE,   draw = lifecycle::deprecated(),   newpage = lifecycle::deprecated(),   gp = lifecycle::deprecated(),   vp = lifecycle::deprecated(),   name = lifecycle::deprecated(),   annot_coxph_ref_lbls = lifecycle::deprecated(),   position_coxph = lifecycle::deprecated(),   position_surv_med = lifecycle::deprecated(),   width_annots = lifecycle::deprecated() )"},{"path":"https://insightsengineering.github.io/tern/reference/g_km.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Kaplan-Meier plot — g_km","text":"df (data.frame) data set containing analysis variables. variables (named list) variable names. Details : tte (numeric) variable indicating time--event duration values. is_event (logical) event variable. TRUE event, FALSE time event censored. arm (factor) treatment group variable. strata (character NULL) variable names indicating stratification factors. control_surv (list) parameters comparison details, specified using helper function control_surv_timepoint(). possible parameter options : conf_level (proportion) confidence level interval survival rate. conf_type (string)\"plain\" (default), \"log\", \"log-log\" confidence interval type, see survival::survfit(). Note option \"none\" longer supported. col (character) lines colors. Length vector equal number strata survival::survfit(). lty (numeric) line type. vector given, length equal number strata survival::survfit(). lwd (numeric) line width. vector given, length equal number strata survival::survfit(). censor_show (flag) whether show censored observations. pch (string) name symbol character use point symbol indicate censored cases. size (numeric(1)) size censored point symbols. max_time (numeric(1)) maximum value show x-axis. data values less threshold value plotted (defaults NULL). xticks (numeric NULL) numeric vector tick positions single number spacing ticks x-axis. NULL (default), labeling::extended() used determine optimal tick positions x-axis. xlab (string) x-axis label. yval (string) type plot, plotted y-axis. Options Survival (default) Failure probability. ylab (string) y-axis label. ylim (numeric(2)) vector containing lower upper limits y-axis, respectively. NULL (default), default scale range used. title (string) plot title. footnotes (string) plot footnotes. font_size (numeric(1)) font size use text. ci_ribbon (flag) whether confidence interval drawn around Kaplan-Meier curve. annot_at_risk (flag) compute add annotation table reporting number patient risk matching main grid Kaplan-Meier curve. annot_at_risk_title (flag) whether \"Patients Risk\" title added annot_at_risk table. effect annot_at_risk FALSE. Defaults TRUE. annot_surv_med (flag) compute add annotation table Kaplan-Meier curve estimating median survival time per group. annot_coxph (flag) whether add annotation table survival::coxph() model. annot_stats (string NULL) statistics annotations add plot. Options median (median survival follow-time) min (minimum survival follow-time). annot_stats_vlines (flag) add vertical lines corresponding statistics specified annot_stats. annot_stats NULL lines added. control_coxph_pw (list) parameters comparison details, specified using helper function control_coxph(). possible parameter options : pval_method (string) p-value method testing hazard ratio = 1. Default method \"log-rank\", can also set \"wald\" \"likelihood\". ties (string) method tie handling. Default \"efron\", can also set \"breslow\" \"exact\". See survival::coxph() conf_level (proportion) confidence level interval HR. ref_group_coxph (string NULL) level arm variable use reference group calculations annot_coxph table. NULL (default), uses first level arm variable. control_annot_surv_med (list) parameters control position size annotation table added plot annot_surv_med = TRUE, specified using control_surv_med_annot() function. Parameter options : x, y, w, h, fill. See control_surv_med_annot() details. control_annot_coxph (list) parameters control position size annotation table added plot annot_coxph = TRUE, specified using control_coxph_annot() function. Parameter options : x, y, w, h, fill, ref_lbls. See control_coxph_annot() details. legend_pos (numeric(2) NULL) vector containing x- y-coordinates, respectively, legend position relative KM plot area. NULL (default), legend positioned bottom right corner plot, middle right plot needed prevent overlapping. rel_height_plot (proportion) proportion total figure height allocate Kaplan-Meier plot. Relative height patients risk table 1 - rel_height_plot. annot_at_risk = FALSE as_list = TRUE, parameter ignored. ggtheme (theme) graphical theme provided ggplot2 format Kaplan-Meier plot. as_list (flag) whether two ggplot objects returned list annot_at_risk = TRUE. TRUE, named list two elements, plot table, returned. FALSE (default) patients risk table printed plot via cowplot::plot_grid(). draw function longer generates grob objects. newpage function longer generates grob objects. gp function longer generates grob objects. vp function longer generates grob objects. name function longer generates grob objects. annot_coxph_ref_lbls Please use ref_lbls element control_annot_coxph instead. position_coxph Please use x y elements control_annot_coxph instead. position_surv_med Please use x y elements control_annot_surv_med instead. width_annots Please use w element control_annot_surv_med (surv_med) control_annot_coxph (coxph).\"","code":""},{"path":"https://insightsengineering.github.io/tern/reference/g_km.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Kaplan-Meier plot — g_km","text":"ggplot Kaplan-Meier plot (optionally) summary table.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/g_km.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Kaplan-Meier plot — g_km","text":"","code":"library(dplyr)  df <- tern_ex_adtte %>%   filter(PARAMCD == \"OS\") %>%   mutate(is_event = CNSR == 0) variables <- list(tte = \"AVAL\", is_event = \"is_event\", arm = \"ARMCD\")  # Basic examples g_km(df = df, variables = variables)  g_km(df = df, variables = variables, yval = \"Failure\")   # Examples with customization parameters applied g_km(   df = df,   variables = variables,   control_surv = control_surv_timepoint(conf_level = 0.9),   col = c(\"grey25\", \"grey50\", \"grey75\"),   annot_at_risk_title = FALSE,   lty = 1:3,   font_size = 8 )  g_km(   df = df,   variables = variables,   annot_stats = c(\"min\", \"median\"),   annot_stats_vlines = TRUE,   max_time = 3000,   ggtheme = ggplot2::theme_minimal() )   # Example with pairwise Cox-PH analysis annotation table, adjusted annotation tables g_km(   df = df, variables = variables,   annot_coxph = TRUE,   control_coxph = control_coxph(pval_method = \"wald\", ties = \"exact\", conf_level = 0.99),   control_annot_coxph = control_coxph_annot(x = 0.26, w = 0.35),   control_annot_surv_med = control_surv_med_annot(x = 0.8, y = 0.9, w = 0.35) )"},{"path":"https://insightsengineering.github.io/tern/reference/g_lineplot.html","id":null,"dir":"Reference","previous_headings":"","what":"Line plot with optional table — g_lineplot","title":"Line plot with optional table — g_lineplot","text":"Line plot optional table.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/g_lineplot.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Line plot with optional table — g_lineplot","text":"","code":"g_lineplot(   df,   alt_counts_df = NULL,   variables = control_lineplot_vars(),   mid = \"mean\",   interval = \"mean_ci\",   whiskers = c(\"mean_ci_lwr\", \"mean_ci_upr\"),   table = NULL,   sfun = s_summary,   ...,   mid_type = \"pl\",   mid_point_size = 2,   position = ggplot2::position_dodge(width = 0.4),   legend_title = NULL,   legend_position = \"bottom\",   ggtheme = nestcolor::theme_nest(),   xticks = NULL,   xlim = NULL,   ylim = NULL,   x_lab = obj_label(df[[variables[[\"x\"]]]]),   y_lab = NULL,   y_lab_add_paramcd = TRUE,   y_lab_add_unit = TRUE,   title = \"Plot of Mean and 95% Confidence Limits by Visit\",   subtitle = \"\",   subtitle_add_paramcd = TRUE,   subtitle_add_unit = TRUE,   caption = NULL,   table_format = NULL,   table_labels = NULL,   table_font_size = 3,   errorbar_width = 0.45,   newpage = lifecycle::deprecated(),   col = NULL,   linetype = NULL,   rel_height_plot = 0.5,   as_list = FALSE )"},{"path":"https://insightsengineering.github.io/tern/reference/g_lineplot.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Line plot with optional table — g_lineplot","text":"df (data.frame) data set containing analysis variables. alt_counts_df (data.frame NULL) data set used () counts objects groups stratification. variables (named character) vector variable names df include: x (string) name x-axis variable. y (string) name y-axis variable. group_var (string NULL) name grouping variable (strata), .e. treatment arm. Can NA indicate lack groups. subject_var (string NULL) name subject variable. applies group_var NULL. paramcd (string NA) name variable parameter's code. Used y-axis label plot's subtitle. Can NA paramcd added y-axis label subtitle. y_unit (string NA) name variable units y. Used y-axis label plot's subtitle. Can NA y unit added y-axis label subtitle. facet_var (string NA) name secondary grouping variable used plot faceting, .e. treatment arm. Can NA indicate lack groups. mid (character NULL) names statistics plotted midpoints. statistics indicated mid variable must present object returned sfun, double numeric type vector length one. interval (character NULL) names statistics plotted intervals. statistics indicated interval variable must present object returned sfun, double numeric type vector length two. Set interval = NULL intervals added plot. whiskers (character) names interval whiskers plotted. Names must match names list element interval returned sfun (e.g. mean_ci_lwr element sfun(x)[[\"mean_ci\"]]). possible specify one whisker , suppress whiskers setting interval = NULL. table (character NULL) names statistics displayed table plot. statistics indicated table variable must present object returned sfun. sfun (function) function compute values required statistics. must return named list atomic vectors. names list elements refer names statistics used mid, interval, table. must able accept input vector data statistics computed. ... optional arguments sfun. mid_type (string) controls type mid plot, can point (\"p\"), line (\"l\"), point line (\"pl\"). mid_point_size (numeric(1)) font size mid plot points. position (character call) geom element position adjustment, either string, result call position adjustment function. legend_title (string) legend title. legend_position (string) position plot legend (\"none\", \"left\", \"right\", \"bottom\", \"top\", two-element numeric vector). ggtheme (theme) graphical theme provided ggplot2 control styling plot. xticks (numeric NULL) numeric vector tick positions single number spacing ticks x-axis, use variables$x numeric. NULL (default), labeling::extended() used determine optimal tick positions x-axis. variables$x numeric, argument ignored. xlim (numeric(2)) vector containing lower upper limits x-axis, respectively. NULL (default), default scale range used. ylim (numeric(2)) vector containing lower upper limits y-axis, respectively. NULL (default), default scale range used. x_lab (string NULL) x-axis label. NULL label added. y_lab (string NULL) y-axis label. NULL label added. y_lab_add_paramcd (flag) whether paramcd, .e. unique(df[[variables[\"paramcd\"]]]) added y-axis label (y_lab). y_lab_add_unit (flag) whether y-axis unit, .e. unique(df[[variables[\"y_unit\"]]]) added y-axis label (y_lab). title (string) plot title. subtitle (string) plot subtitle. subtitle_add_paramcd (flag) whether paramcd, .e. unique(df[[variables[\"paramcd\"]]]) added plot's subtitle (subtitle). subtitle_add_unit (flag) whether y-axis unit, .e. unique(df[[variables[\"y_unit\"]]]) added plot's subtitle (subtitle). caption (string) optional caption plot. table_format (named character NULL) format patterns descriptive statistics used (optional) table appended plot. passed directly h_format_row function format parameter. Names table_format must match names statistics returned sfun function. table_labels (named character NULL) labels descriptive statistics used (optional) table appended plot. Names table_labels must match names statistics returned sfun function. table_font_size (numeric(1)) font size text table. errorbar_width (numeric(1)) width error bars. newpage used. col (character) color(s). See ?ggplot2::aes_colour_fill_alpha example values. linetype (character) line type(s). See ?ggplot2::aes_linetype_size_shape example values. rel_height_plot (proportion) proportion total figure height allocate line plot. Relative height annotation table 1 - rel_height_plot. table = NULL, parameter ignored. as_list (flag) whether two ggplot objects returned list table NULL. TRUE, named list two elements, plot table, returned. FALSE (default) annotation table printed plot via cowplot::plot_grid().","code":""},{"path":"https://insightsengineering.github.io/tern/reference/g_lineplot.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Line plot with optional table — g_lineplot","text":"ggplot line plot (statistics table applicable).","code":""},{"path":"https://insightsengineering.github.io/tern/reference/g_lineplot.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Line plot with optional table — g_lineplot","text":"","code":"adsl <- tern_ex_adsl adlb <- tern_ex_adlb %>% dplyr::filter(ANL01FL == \"Y\", PARAMCD == \"ALT\", AVISIT != \"SCREENING\") adlb$AVISIT <- droplevels(adlb$AVISIT) adlb <- dplyr::mutate(adlb, AVISIT = forcats::fct_reorder(AVISIT, AVISITN, min))  # Mean with CI g_lineplot(adlb, adsl, subtitle = \"Laboratory Test:\")   # Mean with CI, no stratification with group_var g_lineplot(adlb, variables = control_lineplot_vars(group_var = NA))   # Mean, upper whisker of CI, no group_var(strata) counts N g_lineplot(   adlb,   whiskers = \"mean_ci_upr\",   title = \"Plot of Mean and Upper 95% Confidence Limit by Visit\" )   # Median with CI g_lineplot(   adlb,   adsl,   mid = \"median\",   interval = \"median_ci\",   whiskers = c(\"median_ci_lwr\", \"median_ci_upr\"),   title = \"Plot of Median and 95% Confidence Limits by Visit\" )   # Mean, +/- SD g_lineplot(adlb, adsl,   interval = \"mean_sdi\",   whiskers = c(\"mean_sdi_lwr\", \"mean_sdi_upr\"),   title = \"Plot of Median +/- SD by Visit\" )   # Mean with CI plot with stats table g_lineplot(adlb, adsl, table = c(\"n\", \"mean\", \"mean_ci\"))   # Mean with CI, table and customized confidence level g_lineplot(   adlb,   adsl,   table = c(\"n\", \"mean\", \"mean_ci\"),   control = control_analyze_vars(conf_level = 0.80),   title = \"Plot of Mean and 80% Confidence Limits by Visit\" )   # Mean with CI, table, filtered data adlb_f <- dplyr::filter(adlb, ARMCD != \"ARM A\" | AVISIT == \"BASELINE\") g_lineplot(adlb_f, table = c(\"n\", \"mean\"))"},{"path":"https://insightsengineering.github.io/tern/reference/g_step.html","id":null,"dir":"Reference","previous_headings":"","what":"Create a STEP graph — g_step","title":"Create a STEP graph — g_step","text":"Based STEP results, creates ggplot graph showing estimated HR along continuous biomarker value subgroups.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/g_step.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create a STEP graph — g_step","text":"","code":"g_step(   df,   use_percentile = \"Percentile Center\" %in% names(df),   est = list(col = \"blue\", lty = 1),   ci_ribbon = list(fill = getOption(\"ggplot2.discrete.colour\")[1], alpha = 0.5),   col = getOption(\"ggplot2.discrete.colour\") )"},{"path":"https://insightsengineering.github.io/tern/reference/g_step.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create a STEP graph — g_step","text":"df (tibble) result tidy.step(). use_percentile (flag) whether use percentiles x axis actual biomarker values. est (named list)col lty settings estimate line. ci_ribbon (named list NULL)fill alpha settings confidence interval ribbon area, NULL plot CI ribbon. col (character) color(s).","code":""},{"path":"https://insightsengineering.github.io/tern/reference/g_step.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Create a STEP graph — g_step","text":"ggplot STEP graph.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/reference/g_step.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Create a STEP graph — g_step","text":"","code":"library(survival) lung$sex <- factor(lung$sex)  # Survival example. vars <- list(   time = \"time\",   event = \"status\",   arm = \"sex\",   biomarker = \"age\" )  step_matrix <- fit_survival_step(   variables = vars,   data = lung,   control = c(control_coxph(), control_step(num_points = 10, degree = 2)) ) step_data <- broom::tidy(step_matrix)  # Default plot. g_step(step_data)   # Add the reference 1 horizontal line. library(ggplot2) g_step(step_data) +   ggplot2::geom_hline(ggplot2::aes(yintercept = 1), linetype = 2)   # Use actual values instead of percentiles, different color for estimate and no CI, # use log scale for y axis. g_step(   step_data,   use_percentile = FALSE,   est = list(col = \"blue\", lty = 1),   ci_ribbon = NULL ) + scale_y_log10()   # Adding another curve based on additional column. step_data$extra <- exp(step_data$`Percentile Center`) g_step(step_data) +   ggplot2::geom_line(ggplot2::aes(y = extra), linetype = 2, color = \"green\")   # Response example. vars <- list(   response = \"status\",   arm = \"sex\",   biomarker = \"age\" )  step_matrix <- fit_rsp_step(   variables = vars,   data = lung,   control = c(     control_logistic(response_definition = \"I(response == 2)\"),     control_step()   ) ) step_data <- broom::tidy(step_matrix) g_step(step_data)"},{"path":"https://insightsengineering.github.io/tern/reference/g_waterfall.html","id":null,"dir":"Reference","previous_headings":"","what":"Horizontal waterfall plot — g_waterfall","title":"Horizontal waterfall plot — g_waterfall","text":"basic waterfall plot visualizes quantity height ordered value markup.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/g_waterfall.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Horizontal waterfall plot — g_waterfall","text":"","code":"g_waterfall(   height,   id,   col_var = NULL,   col = getOption(\"ggplot2.discrete.colour\"),   xlab = NULL,   ylab = NULL,   col_legend_title = NULL,   title = NULL )"},{"path":"https://insightsengineering.github.io/tern/reference/g_waterfall.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Horizontal waterfall plot — g_waterfall","text":"height (numeric) vector containing values plotted waterfall bars. id (character) vector containing identifiers use x-axis label waterfall bars. col_var (factor, character, NULL) categorical variable bar coloring. NULL default. col (character) color(s). xlab (string) x label. Default \"ID\". ylab (string) y label. Default \"Value\". col_legend_title (string) text displayed legend title. title (string) text displayed plot title.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/g_waterfall.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Horizontal waterfall plot — g_waterfall","text":"ggplot waterfall plot.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/g_waterfall.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Horizontal waterfall plot — g_waterfall","text":"","code":"library(dplyr)  g_waterfall(height = c(3, 5, -1), id = letters[1:3])   g_waterfall(   height = c(3, 5, -1),   id = letters[1:3],   col_var = letters[1:3] )   adsl_f <- tern_ex_adsl %>%   select(USUBJID, STUDYID, ARM, ARMCD, SEX)  adrs_f <- tern_ex_adrs %>%   filter(PARAMCD == \"OVRINV\") %>%   mutate(pchg = rnorm(n(), 10, 50))  adrs_f <- head(adrs_f, 30) adrs_f <- adrs_f[!duplicated(adrs_f$USUBJID), ] head(adrs_f) #> # A tibble: 5 × 30 #>   STUDYID COUNTRY SITEID SUBJID   AGE SEX   ARMCD ARM      ACTARMCD ACTARM RACE  #>   <chr>   <fct>   <chr>  <chr>  <dbl> <fct> <fct> <fct>    <fct>    <fct>  <fct> #> 1 AB12345 BRA     BRA-1  id-105  37.8 F     ARM A A: Drug… ARM A    A: Dr… ASIAN #> 2 AB12345 BRA     BRA-1  id-171  29.8 F     ARM B B: Plac… ARM B    B: Pl… ASIAN #> 3 AB12345 BRA     BRA-1  id-177  38.9 F     ARM B B: Plac… ARM B    B: Pl… ASIAN #> 4 AB12345 BRA     BRA-1  id-23   41.3 F     ARM A A: Drug… ARM A    A: Dr… AMER… #> 5 AB12345 BRA     BRA-1  id-59   26.7 F     ARM A A: Drug… ARM A    A: Dr… ASIAN #> # ℹ 19 more variables: TRTSDTM <dttm>, TRTEDTM <dttm>, EOSDY <dbl>, #> #   STRATA1 <fct>, STRATA2 <fct>, BMRKR1 <dbl>, BMRKR2 <fct>, REGION1 <fct>, #> #   SAFFL <fct>, USUBJID <chr>, AVISIT <fct>, PARAMCD <fct>, PARAM <fct>, #> #   AVALC <fct>, AVAL <int>, ADTM <date>, AVISITN <dbl>, DTHFL <fct>, #> #   pchg <dbl>  g_waterfall(   height = adrs_f$pchg,   id = adrs_f$USUBJID,   col_var = adrs_f$AVALC )   g_waterfall(   height = adrs_f$pchg,   id = paste(\"asdfdsfdsfsd\", adrs_f$USUBJID),   col_var = adrs_f$SEX )   g_waterfall(   height = adrs_f$pchg,   id = paste(\"asdfdsfdsfsd\", adrs_f$USUBJID),   xlab = \"ID\",   ylab = \"Percentage Change\",   title = \"Waterfall plot\" )"},{"path":"https://insightsengineering.github.io/tern/reference/get_covariates.html","id":null,"dir":"Reference","previous_headings":"","what":"Utility function to return a named list of covariate names — get_covariates","title":"Utility function to return a named list of covariate names — get_covariates","text":"Utility function return named list covariate names","code":""},{"path":"https://insightsengineering.github.io/tern/reference/get_covariates.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Utility function to return a named list of covariate names — get_covariates","text":"","code":"get_covariates(covariates)"},{"path":"https://insightsengineering.github.io/tern/reference/get_covariates.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Utility function to return a named list of covariate names — get_covariates","text":"covariates (character) vector can contain single variable names (\"X1\"), /interaction terms indicated \"X1 * X2\".","code":""},{"path":"https://insightsengineering.github.io/tern/reference/get_covariates.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Utility function to return a named list of covariate names — get_covariates","text":"named list character vector.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/get_smooths.html","id":null,"dir":"Reference","previous_headings":"","what":"Smooth function with optional grouping — get_smooths","title":"Smooth function with optional grouping — get_smooths","text":"produces loess smoothed estimates y Student confidence intervals.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/get_smooths.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Smooth function with optional grouping — get_smooths","text":"","code":"get_smooths(df, x, y, groups = NULL, level = 0.95)"},{"path":"https://insightsengineering.github.io/tern/reference/get_smooths.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Smooth function with optional grouping — get_smooths","text":"df (data.frame) data set containing analysis variables. x (string) x column name. y (string) y column name. groups (character NULL) vector optional grouping variables names. level (proportion) level confidence interval use (0.95 default).","code":""},{"path":"https://insightsengineering.github.io/tern/reference/get_smooths.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Smooth function with optional grouping — get_smooths","text":"data.frame original x, smoothed y, ylow, yhigh, optional groups variables formatted factor type.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/groups_list_to_df.html","id":null,"dir":"Reference","previous_headings":"","what":"Convert list of groups to a data frame — groups_list_to_df","title":"Convert list of groups to a data frame — groups_list_to_df","text":"converts list group levels data frame format expected rtables::add_combo_levels().","code":""},{"path":"https://insightsengineering.github.io/tern/reference/groups_list_to_df.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Convert list of groups to a data frame — groups_list_to_df","text":"","code":"groups_list_to_df(groups_list)"},{"path":"https://insightsengineering.github.io/tern/reference/groups_list_to_df.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Convert list of groups to a data frame — groups_list_to_df","text":"groups_list (named list character) specifies new group levels via names levels belong character vectors elements list.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/groups_list_to_df.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Convert list of groups to a data frame — groups_list_to_df","text":"tibble required format.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/groups_list_to_df.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Convert list of groups to a data frame — groups_list_to_df","text":"","code":"grade_groups <- list(   \"Any Grade (%)\" = c(\"1\", \"2\", \"3\", \"4\", \"5\"),   \"Grade 3-4 (%)\" = c(\"3\", \"4\"),   \"Grade 5 (%)\" = \"5\" ) groups_list_to_df(grade_groups) #> # A tibble: 3 × 4 #>   valname  label         levelcombo exargs     #>   <chr>    <chr>         <list>     <list>     #> 1 AnyGrade Any Grade (%) <chr [5]>  <list [0]> #> 2 Grade34  Grade 3-4 (%) <chr [2]>  <list [0]> #> 3 Grade5   Grade 5 (%)   <chr [1]>  <list [0]>"},{"path":"https://insightsengineering.github.io/tern/reference/h_adlb_abnormal_by_worst_grade.html","id":null,"dir":"Reference","previous_headings":"","what":"Helper function to prepare ADLB for count_abnormal_by_worst_grade() — h_adlb_abnormal_by_worst_grade","title":"Helper function to prepare ADLB for count_abnormal_by_worst_grade() — h_adlb_abnormal_by_worst_grade","text":"Helper function prepare ADLB data frame used input count_abnormal_by_worst_grade(). following pre-processing steps applied: adlb filtered variable avisit include post-baseline visits. adlb filtered variables worst_flag_low worst_flag_high worst grades (either direction) included. standard lab grade variable atoxgr, following two variables derived added adlb: grade direction variable (e.g. GRADE_DIR). variable takes value \"HIGH\" atoxgr > 0, \"LOW\" atoxgr < 0, \"ZERO\" otherwise. toxicity grade variable (e.g. GRADE_ANL) negative values atoxgr replaced absolute values. Unused factor levels dropped adlb via droplevels().","code":""},{"path":"https://insightsengineering.github.io/tern/reference/h_adlb_abnormal_by_worst_grade.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Helper function to prepare ADLB for count_abnormal_by_worst_grade() — h_adlb_abnormal_by_worst_grade","text":"","code":"h_adlb_abnormal_by_worst_grade(   adlb,   atoxgr = \"ATOXGR\",   avisit = \"AVISIT\",   worst_flag_low = \"WGRLOFL\",   worst_flag_high = \"WGRHIFL\" )"},{"path":"https://insightsengineering.github.io/tern/reference/h_adlb_abnormal_by_worst_grade.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Helper function to prepare ADLB for count_abnormal_by_worst_grade() — h_adlb_abnormal_by_worst_grade","text":"adlb (data.frame) ADLB data frame. atoxgr (string) name analysis toxicity grade variable. must factor variable. avisit (string) name analysis visit variable. worst_flag_low (string) name worst low lab grade flag variable. variable set \"Y\" indicating records worst low lab grades. worst_flag_high (string) name worst high lab grade flag variable. variable set \"Y\" indicating records worst high lab grades.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/h_adlb_abnormal_by_worst_grade.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Helper function to prepare ADLB for count_abnormal_by_worst_grade() — h_adlb_abnormal_by_worst_grade","text":"h_adlb_abnormal_by_worst_grade() returns adlb data frame two new variables: GRADE_DIR GRADE_ANL.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/reference/h_adlb_abnormal_by_worst_grade.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Helper function to prepare ADLB for count_abnormal_by_worst_grade() — h_adlb_abnormal_by_worst_grade","text":"","code":"h_adlb_abnormal_by_worst_grade(tern_ex_adlb) %>%   dplyr::select(ATOXGR, GRADE_DIR, GRADE_ANL) %>%   head(10) #> # A tibble: 10 × 3 #>    ATOXGR GRADE_DIR GRADE_ANL #>    <fct>  <fct>     <fct>     #>  1 -3     LOW       3         #>  2 0      ZERO      0         #>  3 0      ZERO      0         #>  4 2      HIGH      2         #>  5 0      ZERO      0         #>  6 0      ZERO      0         #>  7 -4     LOW       4         #>  8 1      HIGH      1         #>  9 -1     LOW       1         #> 10 0      ZERO      0"},{"path":"https://insightsengineering.github.io/tern/reference/h_adlb_worsen.html","id":null,"dir":"Reference","previous_headings":"","what":"Helper function to prepare ADLB with worst labs — h_adlb_worsen","title":"Helper function to prepare ADLB with worst labs — h_adlb_worsen","text":"Helper function prepare df generate patient count shift table.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/h_adlb_worsen.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Helper function to prepare ADLB with worst labs — h_adlb_worsen","text":"","code":"h_adlb_worsen(   adlb,   worst_flag_low = NULL,   worst_flag_high = NULL,   direction_var )"},{"path":"https://insightsengineering.github.io/tern/reference/h_adlb_worsen.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Helper function to prepare ADLB with worst labs — h_adlb_worsen","text":"adlb (data.frame) ADLB data frame. worst_flag_low (named vector) worst low post-baseline lab grade flag variable. See implemented following examples. worst_flag_high (named vector) worst high post-baseline lab grade flag variable. See implemented following examples. direction_var (string) name direction variable specifying direction shift table interest. lab records flagged L, H B included shift table. L: low direction H: high direction B: low high directions","code":""},{"path":"https://insightsengineering.github.io/tern/reference/h_adlb_worsen.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Helper function to prepare ADLB with worst labs — h_adlb_worsen","text":"h_adlb_worsen() returns adlb data.frame containing worst labs specified according worst_flag_low worst_flag_high direction specified according direction_var. instance, lab needed low direction , records flagged worst_flag_low selected. lab needed low high directions, worst low records selected low direction, worst high record selected high direction.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/reference/h_adlb_worsen.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Helper function to prepare ADLB with worst labs — h_adlb_worsen","text":"","code":"library(dplyr)  # The direction variable, GRADDR, is based on metadata adlb <- tern_ex_adlb %>%   mutate(     GRADDR = case_when(       PARAMCD == \"ALT\" ~ \"B\",       PARAMCD == \"CRP\" ~ \"L\",       PARAMCD == \"IGA\" ~ \"H\"     )   ) %>%   filter(SAFFL == \"Y\" & ONTRTFL == \"Y\" & GRADDR != \"\")  df <- h_adlb_worsen(   adlb,   worst_flag_low = c(\"WGRLOFL\" = \"Y\"),   worst_flag_high = c(\"WGRHIFL\" = \"Y\"),   direction_var = \"GRADDR\" )"},{"path":"https://insightsengineering.github.io/tern/reference/h_adsl_adlb_merge_using_worst_flag.html","id":null,"dir":"Reference","previous_headings":"","what":"Helper function for deriving analysis datasets for select laboratory tables — h_adsl_adlb_merge_using_worst_flag","title":"Helper function for deriving analysis datasets for select laboratory tables — h_adsl_adlb_merge_using_worst_flag","text":"Helper function merges ADSL ADLB datasets missing lab test records inserted output dataset. Remember na_level must match needed pre-processing done df_explicit_na() desired output.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/h_adsl_adlb_merge_using_worst_flag.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Helper function for deriving analysis datasets for select laboratory tables — h_adsl_adlb_merge_using_worst_flag","text":"","code":"h_adsl_adlb_merge_using_worst_flag(   adsl,   adlb,   worst_flag = c(WGRHIFL = \"Y\"),   by_visit = FALSE,   no_fillin_visits = c(\"SCREENING\", \"BASELINE\") )"},{"path":"https://insightsengineering.github.io/tern/reference/h_adsl_adlb_merge_using_worst_flag.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Helper function for deriving analysis datasets for select laboratory tables — h_adsl_adlb_merge_using_worst_flag","text":"adsl (data.frame) ADSL data frame. adlb (data.frame) ADLB data frame. worst_flag (named character) worst post-baseline lab flag variable. See implemented following examples. by_visit (flag) defaults FALSE generate worst grade per patient. worst grade per patient per visit specified worst_flag, by_visit TRUE generate worst grade patient per visit. no_fillin_visits (named character) visits considered post-baseline worst toxicity grade. Defaults c(\"SCREENING\", \"BASELINE\").","code":""},{"path":"https://insightsengineering.github.io/tern/reference/h_adsl_adlb_merge_using_worst_flag.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Helper function for deriving analysis datasets for select laboratory tables — h_adsl_adlb_merge_using_worst_flag","text":"df containing variables shared adlb adsl along variables PARAM, PARAMCD, ATOXGR, BTOXGR relevant analysis. Optionally, AVISIT AVISITN included by_visit = TRUE no_fillin_visits = c(\"SCREENING\", \"BASELINE\").","code":""},{"path":"https://insightsengineering.github.io/tern/reference/h_adsl_adlb_merge_using_worst_flag.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Helper function for deriving analysis datasets for select laboratory tables — h_adsl_adlb_merge_using_worst_flag","text":"result data missing records created following situations: Patients present adsl lab data adlb (baseline post-baseline). Patients post-baseline lab values. Patients without post-baseline values flagged worst.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/h_adsl_adlb_merge_using_worst_flag.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Helper function for deriving analysis datasets for select laboratory tables — h_adsl_adlb_merge_using_worst_flag","text":"","code":"# `h_adsl_adlb_merge_using_worst_flag` adlb_out <- h_adsl_adlb_merge_using_worst_flag(   tern_ex_adsl,   tern_ex_adlb,   worst_flag = c(\"WGRHIFL\" = \"Y\") )  # `h_adsl_adlb_merge_using_worst_flag` by visit example adlb_out_by_visit <- h_adsl_adlb_merge_using_worst_flag(   tern_ex_adsl,   tern_ex_adlb,   worst_flag = c(\"WGRLOVFL\" = \"Y\"),   by_visit = TRUE )"},{"path":[]},{"path":"https://insightsengineering.github.io/tern/reference/h_ancova.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Helper function to return results of a linear model — h_ancova","text":"","code":"h_ancova(.var, .df_row, variables, interaction_item = NULL)"},{"path":"https://insightsengineering.github.io/tern/reference/h_ancova.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Helper function to return results of a linear model — h_ancova","text":".var (string) single variable name passed rtables requested statistics function. .df_row (data.frame) data set includes variables called .var variables. variables (named list string) list additional analysis variables, expected elements: arm (string) group variable, covariate adjusted means multiple groups summarized. Specifically, first level arm variable taken reference group. covariates (character) vector can contain single variable names (\"X1\"), /interaction terms indicated \"X1 * X2\". interaction_item (string NULL) name variable interactions arm. interaction needed, default option NULL.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/h_ancova.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Helper function to return results of a linear model — h_ancova","text":"summary linear model.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/h_ancova.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Helper function to return results of a linear model — h_ancova","text":"","code":"h_ancova(   .var = \"Sepal.Length\",   .df_row = iris,   variables = list(arm = \"Species\", covariates = c(\"Petal.Length * Petal.Width\", \"Sepal.Width\")) ) #>  Species    emmean     SE  df lower.CL upper.CL #>  setosa       6.15 0.3370 143     5.49     6.82 #>  versicolor   5.72 0.0668 143     5.59     5.85 #>  virginica    5.41 0.1490 143     5.11     5.70 #>  #> Confidence level used: 0.95"},{"path":"https://insightsengineering.github.io/tern/reference/h_append_grade_groups.html","id":null,"dir":"Reference","previous_headings":"","what":"Helper function for s_count_occurrences_by_grade() — h_append_grade_groups","title":"Helper function for s_count_occurrences_by_grade() — h_append_grade_groups","text":"Helper function s_count_occurrences_by_grade() insert grade groupings list individual grade frequencies. order final result follows order grade_groups. elements -grade group (), .e. grade group equal refs moved end. Grade groups names must unique.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/h_append_grade_groups.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Helper function for s_count_occurrences_by_grade() — h_append_grade_groups","text":"","code":"h_append_grade_groups(   grade_groups,   refs,   remove_single = TRUE,   only_grade_groups = FALSE )"},{"path":"https://insightsengineering.github.io/tern/reference/h_append_grade_groups.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Helper function for s_count_occurrences_by_grade() — h_append_grade_groups","text":"grade_groups (named list character) list containing groupings grades. refs (named list numeric) named list name corresponds reference grade level entry represents count. remove_single (flag)TRUE include elements one-element grade groups output list; case grade groups names included output. only_grade_groups set TRUE argument ignored. only_grade_groups (flag) whether specified grade groups included, individual grade rows removed (TRUE), grades grade groups displayed (FALSE).","code":""},{"path":"https://insightsengineering.github.io/tern/reference/h_append_grade_groups.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Helper function for s_count_occurrences_by_grade() — h_append_grade_groups","text":"Formatted list grade groupings.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/h_append_grade_groups.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Helper function for s_count_occurrences_by_grade() — h_append_grade_groups","text":"","code":"h_append_grade_groups(   list(     \"Any Grade\" = as.character(1:5),     \"Grade 1-2\" = c(\"1\", \"2\"),     \"Grade 3-4\" = c(\"3\", \"4\")   ),   list(\"1\" = 10, \"2\" = 20, \"3\" = 30, \"4\" = 40, \"5\" = 50) ) #> $`Any Grade` #> [1] 150 #>  #> $`Grade 1-2` #> [1] 30 #>  #> $`1` #> [1] 10 #>  #> $`2` #> [1] 20 #>  #> $`Grade 3-4` #> [1] 70 #>  #> $`3` #> [1] 30 #>  #> $`4` #> [1] 40 #>  #> $`5` #> [1] 50 #>   h_append_grade_groups(   list(     \"Any Grade\" = as.character(5:1),     \"Grade A\" = \"5\",     \"Grade B\" = c(\"4\", \"3\")   ),   list(\"1\" = 10, \"2\" = 20, \"3\" = 30, \"4\" = 40, \"5\" = 50) ) #> $`Any Grade` #> [1] 150 #>  #> $`Grade A` #> [1] 50 #>  #> $`Grade B` #> [1] 70 #>  #> $`4` #> [1] 40 #>  #> $`3` #> [1] 30 #>  #> $`2` #> [1] 20 #>  #> $`1` #> [1] 10 #>   h_append_grade_groups(   list(     \"Any Grade\" = as.character(1:5),     \"Grade 1-2\" = c(\"1\", \"2\"),     \"Grade 3-4\" = c(\"3\", \"4\")   ),   list(\"1\" = 10, \"2\" = 5, \"3\" = 0) ) #> $`Any Grade` #> [1] 15 #>  #> $`Grade 1-2` #> [1] 15 #>  #> $`1` #> [1] 10 #>  #> $`2` #> [1] 5 #>  #> $`Grade 3-4` #> [1] 0 #>  #> $`3` #> [1] 0 #>"},{"path":"https://insightsengineering.github.io/tern/reference/h_col_indices.html","id":null,"dir":"Reference","previous_headings":"","what":"Obtain column indices — h_col_indices","title":"Obtain column indices — h_col_indices","text":"Helper function extract column indices VTableTree given vector column names.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/h_col_indices.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Obtain column indices — h_col_indices","text":"","code":"h_col_indices(table_tree, col_names)"},{"path":"https://insightsengineering.github.io/tern/reference/h_col_indices.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Obtain column indices — h_col_indices","text":"table_tree (VTableTree)rtables table object extract indices . col_names (character) vector column names.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/h_col_indices.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Obtain column indices — h_col_indices","text":"vector column indices.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/h_count_cumulative.html","id":null,"dir":"Reference","previous_headings":"","what":"Helper function for s_count_cumulative() — h_count_cumulative","title":"Helper function for s_count_cumulative() — h_count_cumulative","text":"Helper function calculate count fraction x values lower upper tail given threshold.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/h_count_cumulative.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Helper function for s_count_cumulative() — h_count_cumulative","text":"","code":"h_count_cumulative(   x,   threshold,   lower_tail = TRUE,   include_eq = TRUE,   na.rm = TRUE,   .N_col )"},{"path":"https://insightsengineering.github.io/tern/reference/h_count_cumulative.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Helper function for s_count_cumulative() — h_count_cumulative","text":"x (numeric) vector numbers want analyze. threshold (numeric(1)) cutoff value threshold count values x. lower_tail (flag) whether count lower tail, default TRUE. include_eq (flag) whether include value equal threshold count, default TRUE. na.rm (flag) whether NA values removed x prior analysis. .N_col (integer(1)) column-wise N (column count) full column analyzed typically passed rtables.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/h_count_cumulative.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Helper function for s_count_cumulative() — h_count_cumulative","text":"named vector items: count: count values less , less equal , greater , greater equal threshold user specification. fraction: fraction count.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/reference/h_count_cumulative.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Helper function for s_count_cumulative() — h_count_cumulative","text":"","code":"set.seed(1, kind = \"Mersenne-Twister\") x <- c(sample(1:10, 10), NA) .N_col <- length(x)  h_count_cumulative(x, 5, .N_col = .N_col) #>     count  fraction  #> 5.0000000 0.4545455  h_count_cumulative(x, 5, lower_tail = FALSE, include_eq = FALSE, na.rm = FALSE, .N_col = .N_col) #>     count  fraction  #> 6.0000000 0.5454545  h_count_cumulative(x, 0, lower_tail = FALSE, .N_col = .N_col) #>      count   fraction  #> 10.0000000  0.9090909  h_count_cumulative(x, 100, lower_tail = FALSE, .N_col = .N_col) #>    count fraction  #>        0        0"},{"path":"https://insightsengineering.github.io/tern/reference/h_cox_regression.html","id":null,"dir":"Reference","previous_headings":"","what":"Helper functions for Cox proportional hazards regression — h_cox_regression","title":"Helper functions for Cox proportional hazards regression — h_cox_regression","text":"Helper functions used fit_coxreg_univar() fit_coxreg_multivar().","code":""},{"path":"https://insightsengineering.github.io/tern/reference/h_cox_regression.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Helper functions for Cox proportional hazards regression — h_cox_regression","text":"","code":"h_coxreg_univar_formulas(variables, interaction = FALSE)  h_coxreg_multivar_formula(variables)  h_coxreg_univar_extract(effect, covar, data, mod, control = control_coxreg())  h_coxreg_multivar_extract(var, data, mod, control = control_coxreg())"},{"path":"https://insightsengineering.github.io/tern/reference/h_cox_regression.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Helper functions for Cox proportional hazards regression — h_cox_regression","text":"variables (named list string) list additional analysis variables. interaction (flag) TRUE, model includes interaction studied treatment candidate covariate. Note univariate models without treatment arm, multivariate models, interaction can used needs FALSE. effect (string) treatment variable. covar (string) name covariate model. data (data.frame) dataset containing variables summarize. mod (coxph) Cox regression model fitted survival::coxph(). control (list) list controls returned control_coxreg(). var (string) single variable name passed rtables requested statistics function.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/h_cox_regression.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Helper functions for Cox proportional hazards regression — h_cox_regression","text":"h_coxreg_univar_formulas() returns character vector coercible formulas (e.g stats::.formula()). h_coxreg_multivar_formula() returns string coercible formula (e.g stats::.formula()). h_coxreg_univar_extract() returns data.frame variables effect, term, term_label, level, n, hr, lcl, ucl, pval. h_coxreg_multivar_extract() returns data.frame variables pval, hr, lcl, ucl, level, n, term, term_label.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/h_cox_regression.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Helper functions for Cox proportional hazards regression — h_cox_regression","text":"h_coxreg_univar_formulas(): Helper Cox regression formula. Creates list formulas. used internally fit_coxreg_univar() comparison univariate Cox regression models. h_coxreg_multivar_formula(): Helper multivariate Cox regression formula. Creates formulas string. used internally fit_coxreg_multivar() comparison multivariate Cox regression models. Interactions included multivariate Cox regression model. h_coxreg_univar_extract(): Utility function help tabulate result univariate Cox regression model. h_coxreg_multivar_extract(): Tabulation multivariate Cox regressions. Utility function help tabulate result multivariate Cox regression model treatment/covariate variable.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/reference/h_cox_regression.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Helper functions for Cox proportional hazards regression — h_cox_regression","text":"","code":"# `h_coxreg_univar_formulas`  ## Simple formulas. h_coxreg_univar_formulas(   variables = list(     time = \"time\", event = \"status\", arm = \"armcd\", covariates = c(\"X\", \"y\")   ) ) #>                                        ref  #>     \"survival::Surv(time, status) ~ armcd\"  #>                                          X  #> \"survival::Surv(time, status) ~ armcd + X\"  #>                                          y  #> \"survival::Surv(time, status) ~ armcd + y\"   ## Addition of an optional strata. h_coxreg_univar_formulas(   variables = list(     time = \"time\", event = \"status\", arm = \"armcd\", covariates = c(\"X\", \"y\"),     strata = \"SITE\"   ) ) #>                                                       ref  #>     \"survival::Surv(time, status) ~ armcd + strata(SITE)\"  #>                                                         X  #> \"survival::Surv(time, status) ~ armcd + X + strata(SITE)\"  #>                                                         y  #> \"survival::Surv(time, status) ~ armcd + y + strata(SITE)\"   ## Inclusion of the interaction term. h_coxreg_univar_formulas(   variables = list(     time = \"time\", event = \"status\", arm = \"armcd\", covariates = c(\"X\", \"y\"),     strata = \"SITE\"   ),   interaction = TRUE ) #>                                                       ref  #>     \"survival::Surv(time, status) ~ armcd + strata(SITE)\"  #>                                                         X  #> \"survival::Surv(time, status) ~ armcd * X + strata(SITE)\"  #>                                                         y  #> \"survival::Surv(time, status) ~ armcd * y + strata(SITE)\"   ## Only covariates fitted in separate models. h_coxreg_univar_formulas(   variables = list(     time = \"time\", event = \"status\", covariates = c(\"X\", \"y\")   ) ) #>                                      X                                      y  #> \"survival::Surv(time, status) ~ 1 + X\" \"survival::Surv(time, status) ~ 1 + y\"   # `h_coxreg_multivar_formula`  h_coxreg_multivar_formula(   variables = list(     time = \"AVAL\", event = \"event\", arm = \"ARMCD\", covariates = c(\"RACE\", \"AGE\")   ) ) #> [1] \"survival::Surv(AVAL, event) ~ ARMCD + RACE + AGE\"  # Addition of an optional strata. h_coxreg_multivar_formula(   variables = list(     time = \"AVAL\", event = \"event\", arm = \"ARMCD\", covariates = c(\"RACE\", \"AGE\"),     strata = \"SITE\"   ) ) #> [1] \"survival::Surv(AVAL, event) ~ ARMCD + RACE + AGE + strata(SITE)\"  # Example without treatment arm. h_coxreg_multivar_formula(   variables = list(     time = \"AVAL\", event = \"event\", covariates = c(\"RACE\", \"AGE\"),     strata = \"SITE\"   ) ) #> [1] \"survival::Surv(AVAL, event) ~ 1 + RACE + AGE + strata(SITE)\"  library(survival)  dta_simple <- data.frame(   time = c(5, 5, 10, 10, 5, 5, 10, 10),   status = c(0, 0, 1, 0, 0, 1, 1, 1),   armcd = factor(LETTERS[c(1, 1, 1, 1, 2, 2, 2, 2)], levels = c(\"A\", \"B\")),   var1 = c(45, 55, 65, 75, 55, 65, 85, 75),   var2 = c(\"F\", \"M\", \"F\", \"M\", \"F\", \"M\", \"F\", \"U\") ) mod <- coxph(Surv(time, status) ~ armcd + var1, data = dta_simple) result <- h_coxreg_univar_extract(   effect = \"armcd\", covar = \"armcd\", mod = mod, data = dta_simple ) result #>       effect  term       term_label level n       hr       lcl      ucl #> 1 Treatment: armcd B vs control (A)     B 8 6.551448 0.4606904 93.16769 #>       pval #> 1 0.165209  mod <- coxph(Surv(time, status) ~ armcd + var1, data = dta_simple) result <- h_coxreg_multivar_extract(   var = \"var1\", mod = mod, data = dta_simple ) result #>        pval        hr      lcl      ucl level n term term_label #> 2 0.4456195 0.9423284 0.808931 1.097724  var1 8 var1       var1"},{"path":"https://insightsengineering.github.io/tern/reference/h_data_plot.html","id":null,"dir":"Reference","previous_headings":"","what":"Helper function to tidy survival fit data — h_data_plot","title":"Helper function to tidy survival fit data — h_data_plot","text":"Convert survival fit data data frame designed plotting within g_km. starts broom::tidy() result, : Post-processes strata column factor. Extends stratum additional first row time 0 probability 1 downstream plot lines start coordinates. Adds censor column. Filters rows max_time.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/h_data_plot.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Helper function to tidy survival fit data — h_data_plot","text":"","code":"h_data_plot(fit_km, armval = \"All\", max_time = NULL)"},{"path":"https://insightsengineering.github.io/tern/reference/h_data_plot.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Helper function to tidy survival fit data — h_data_plot","text":"fit_km (survfit) result survival::survfit(). armval (string) used strata name treatment arm variable one level. Default \"\". max_time (numeric(1)) maximum value show x-axis. data values less threshold value plotted (defaults NULL).","code":""},{"path":"https://insightsengineering.github.io/tern/reference/h_data_plot.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Helper function to tidy survival fit data — h_data_plot","text":"tibble columns time, n.risk, n.event, n.censor, estimate, std.error, conf.high, conf.low, strata, censor.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/h_data_plot.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Helper function to tidy survival fit data — h_data_plot","text":"","code":"library(dplyr) library(survival)  # Test with multiple arms tern_ex_adtte %>%   filter(PARAMCD == \"OS\") %>%   survfit(formula = Surv(AVAL, 1 - CNSR) ~ ARMCD, data = .) %>%   h_data_plot() #> # A tibble: 203 × 10 #>     time n.risk n.event n.censor estimate std.error conf.high conf.low strata #>    <dbl>  <dbl>   <dbl>    <dbl>    <dbl>     <dbl>     <dbl>    <dbl> <fct>  #>  1   0       70       0        0    1        0          1        1     ARM A  #>  2  10.4     69       1        0    0.986    0.0146     1        0.958 ARM A  #>  3  20.5     68       1        0    0.971    0.0208     1        0.932 ARM A  #>  4  21.5     67       1        0    0.957    0.0257     1        0.910 ARM A  #>  5  25.3     66       0        1    0.957    0.0257     1        0.910 ARM A  #>  6  48.1     65       1        0    0.942    0.0300     0.999    0.888 ARM A  #>  7  66.6     64       0        1    0.942    0.0300     0.999    0.888 ARM A  #>  8  73.9     63       0        1    0.942    0.0300     0.999    0.888 ARM A  #>  9  78.9     62       0        1    0.942    0.0300     0.999    0.888 ARM A  #> 10  90.3     61       1        0    0.926    0.0342     0.991    0.866 ARM A  #> # ℹ 193 more rows #> # ℹ 1 more variable: censor <dbl>  # Test with single arm tern_ex_adtte %>%   filter(PARAMCD == \"OS\", ARMCD == \"ARM B\") %>%   survfit(formula = Surv(AVAL, 1 - CNSR) ~ ARMCD, data = .) %>%   h_data_plot(armval = \"ARM B\") #> # A tibble: 74 × 10 #>      time n.risk n.event n.censor estimate std.error conf.high conf.low strata #>     <dbl>  <dbl>   <dbl>    <dbl>    <dbl>     <dbl>     <dbl>    <dbl> <chr>  #>  1   0        74       0        0    1        0          1        1     ARM B  #>  2   2.17     73       1        0    0.986    0.0138     1        0.960 ARM B  #>  3  16.9      72       1        0    0.973    0.0196     1        0.936 ARM B  #>  4  22.6      71       1        0    0.959    0.0242     1        0.914 ARM B  #>  5  26.3      70       1        0    0.945    0.0282     0.999    0.894 ARM B  #>  6  57.5      69       1        0    0.932    0.0317     0.991    0.875 ARM B  #>  7  80.0      68       1        0    0.918    0.0350     0.983    0.857 ARM B  #>  8  81.6      67       1        0    0.904    0.0381     0.974    0.839 ARM B  #>  9  88.6      66       1        0    0.890    0.0411     0.965    0.822 ARM B  #> 10 102.       65       1        0    0.877    0.0439     0.955    0.804 ARM B  #> # ℹ 64 more rows #> # ℹ 1 more variable: censor <dbl>"},{"path":"https://insightsengineering.github.io/tern/reference/h_decompose_gg.html","id":null,"dir":"Reference","previous_headings":"","what":"ggplot decomposition — h_decompose_gg","title":"ggplot decomposition — h_decompose_gg","text":"elements composing ggplot extracted organized list.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/h_decompose_gg.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"ggplot decomposition — h_decompose_gg","text":"","code":"h_decompose_gg(gg)"},{"path":"https://insightsengineering.github.io/tern/reference/h_decompose_gg.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"ggplot decomposition — h_decompose_gg","text":"gg (ggplot) graphic decompose.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/h_decompose_gg.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"ggplot decomposition — h_decompose_gg","text":"named list elements: panel: panel. yaxis: y-axis. xaxis: x-axis. xlab: x-axis label. ylab: y-axis label. guide: legend.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/h_decompose_gg.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"ggplot decomposition — h_decompose_gg","text":"","code":"# \\donttest{ library(dplyr) library(survival) library(grid)  fit_km <- tern_ex_adtte %>%   filter(PARAMCD == \"OS\") %>%   survfit(formula = Surv(AVAL, 1 - CNSR) ~ ARMCD, data = .) data_plot <- h_data_plot(fit_km = fit_km) xticks <- h_xticks(data = data_plot) gg <- h_ggkm(   data = data_plot,   yval = \"Survival\",   censor_show = TRUE,   xticks = xticks, xlab = \"Days\", ylab = \"Survival Probability\",   title = \"tt\",   footnotes = \"ff\" ) #> Warning: `h_ggkm()` was deprecated in tern 0.9.4. #> ℹ `g_km` now generates `ggplot` objects. This function is no longer used within #>   `tern`.  g_el <- h_decompose_gg(gg) #> Warning: `h_decompose_gg()` was deprecated in tern 0.9.4. #> ℹ `g_km` now generates `ggplot` objects. This function is no longer used within #>   `tern`. grid::grid.newpage() grid.rect(gp = grid::gpar(lty = 1, col = \"red\", fill = \"gray85\", lwd = 5)) grid::grid.draw(g_el$panel)   grid::grid.newpage() grid.rect(gp = grid::gpar(lty = 1, col = \"royalblue\", fill = \"gray85\", lwd = 5)) grid::grid.draw(with(g_el, cbind(ylab, yaxis)))  # }"},{"path":[]},{"path":"https://insightsengineering.github.io/tern/reference/h_format_row.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Helper function to format the optional g_lineplot table — h_format_row","text":"","code":"h_format_row(x, format, labels = NULL)"},{"path":"https://insightsengineering.github.io/tern/reference/h_format_row.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Helper function to format the optional g_lineplot table — h_format_row","text":"x (named list) list numerical values formatted optionally labeled. Elements x must numeric vectors. format (named character NULL) format patterns x. Names format must match names x. parameter passed directly rtables::format_rcell function format parameter. labels (named character NULL) optional labels x. Names labels must match names x. label specified element x, function tries use label names (order) attribute element (depending one exists NULL NA NaN). none attributes attached given element x, label automatically generated.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/h_format_row.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Helper function to format the optional g_lineplot table — h_format_row","text":"single row data.frame object.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/h_format_row.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Helper function to format the optional g_lineplot table — h_format_row","text":"","code":"mean_ci <- c(48, 51) x <- list(mean = 50, mean_ci = mean_ci) format <- c(mean = \"xx.x\", mean_ci = \"(xx.xx, xx.xx)\") labels <- c(mean = \"My Mean\") h_format_row(x, format, labels) #>   My Mean             V1 #> 1    50.0 (48.00, 51.00)  attr(mean_ci, \"label\") <- \"Mean 95% CI\" x <- list(mean = 50, mean_ci = mean_ci) h_format_row(x, format, labels) #>   My Mean    Mean 95% CI #> 1    50.0 (48.00, 51.00)"},{"path":"https://insightsengineering.github.io/tern/reference/h_g_ipp.html","id":null,"dir":"Reference","previous_headings":"","what":"Helper function to create simple line plot over time — h_g_ipp","title":"Helper function to create simple line plot over time — h_g_ipp","text":"Function generates simple line plot displaying parameter trends time.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/h_g_ipp.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Helper function to create simple line plot over time — h_g_ipp","text":"","code":"h_g_ipp(   df,   xvar,   yvar,   xlab,   ylab,   id_var,   title = \"Individual Patient Plots\",   subtitle = \"\",   caption = NULL,   add_baseline_hline = FALSE,   yvar_baseline = \"BASE\",   ggtheme = nestcolor::theme_nest(),   col = NULL )"},{"path":"https://insightsengineering.github.io/tern/reference/h_g_ipp.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Helper function to create simple line plot over time — h_g_ipp","text":"df (data.frame) data set containing analysis variables. xvar (string) time point variable plotted x-axis. yvar (string) continuous analysis variable plotted y-axis. xlab (string) plot label x-axis. ylab (string) plot label y-axis. id_var (string) variable used patient identifier. title (string) title plot. subtitle (string) subtitle plot. caption (string) optional caption plot. add_baseline_hline (flag) adds horizontal line baseline y-value plot TRUE. yvar_baseline (string) variable baseline values . Ignored add_baseline_hline FALSE. ggtheme (theme) optional graphical theme function provided ggplot2 control outlook plot. Use ggplot2::theme() tweak display. col (character) line colors.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/h_g_ipp.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Helper function to create simple line plot over time — h_g_ipp","text":"ggplot line plot.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/reference/h_g_ipp.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Helper function to create simple line plot over time — h_g_ipp","text":"","code":"library(dplyr)  # Select a small sample of data to plot. adlb <- tern_ex_adlb %>%   filter(PARAMCD == \"ALT\", !(AVISIT %in% c(\"SCREENING\", \"BASELINE\"))) %>%   slice(1:36)  p <- h_g_ipp(   df = adlb,   xvar = \"AVISIT\",   yvar = \"AVAL\",   xlab = \"Visit\",   id_var = \"USUBJID\",   ylab = \"SGOT/ALT (U/L)\",   add_baseline_hline = TRUE ) p"},{"path":"https://insightsengineering.github.io/tern/reference/h_ggkm.html","id":null,"dir":"Reference","previous_headings":"","what":"Helper function to create a KM plot — h_ggkm","title":"Helper function to create a KM plot — h_ggkm","text":"Draw Kaplan-Meier plot using ggplot2.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/h_ggkm.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Helper function to create a KM plot — h_ggkm","text":"","code":"h_ggkm(   data,   xticks = NULL,   yval = \"Survival\",   censor_show,   xlab,   ylab,   ylim = NULL,   title,   footnotes = NULL,   max_time = NULL,   lwd = 1,   lty = NULL,   pch = 3,   size = 2,   col = NULL,   ci_ribbon = FALSE,   ggtheme = nestcolor::theme_nest() )"},{"path":"https://insightsengineering.github.io/tern/reference/h_ggkm.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Helper function to create a KM plot — h_ggkm","text":"data (data.frame) survival data pre-processed h_data_plot. xticks (numeric NULL) numeric vector tick positions single number spacing ticks x-axis. NULL (default), labeling::extended() used determine optimal tick positions x-axis. yval (string) type plot, plotted y-axis. Options Survival (default) Failure probability. censor_show (flag) whether show censored observations. xlab (string) x-axis label. ylab (string) y-axis label. ylim (numeric(2)) vector containing lower upper limits y-axis, respectively. NULL (default), default scale range used. title (string) plot title. footnotes (string) plot footnotes. max_time (numeric(1)) maximum value show x-axis. data values less threshold value plotted (defaults NULL). lwd (numeric) line width. vector given, length equal number strata survival::survfit(). lty (numeric) line type. vector given, length equal number strata survival::survfit(). pch (string) name symbol character use point symbol indicate censored cases. size (numeric(1)) size censored point symbols. col (character) lines colors. Length vector equal number strata survival::survfit(). ci_ribbon (flag) whether confidence interval drawn around Kaplan-Meier curve. ggtheme (theme) graphical theme provided ggplot2 format Kaplan-Meier plot.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/h_ggkm.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Helper function to create a KM plot — h_ggkm","text":"ggplot object.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/h_ggkm.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Helper function to create a KM plot — h_ggkm","text":"","code":"# \\donttest{ library(dplyr) library(survival)  fit_km <- tern_ex_adtte %>%   filter(PARAMCD == \"OS\") %>%   survfit(formula = Surv(AVAL, 1 - CNSR) ~ ARMCD, data = .) data_plot <- h_data_plot(fit_km = fit_km) xticks <- h_xticks(data = data_plot) gg <- h_ggkm(   data = data_plot,   censor_show = TRUE,   xticks = xticks,   xlab = \"Days\",   yval = \"Survival\",   ylab = \"Survival Probability\",   title = \"Survival\" ) gg  # }"},{"path":"https://insightsengineering.github.io/tern/reference/h_glm_count.html","id":null,"dir":"Reference","previous_headings":"","what":"Helper functions for Poisson models — h_glm_count","title":"Helper functions for Poisson models — h_glm_count","text":"Helper functions returns results stats::glm() Poisson Quasi-Poisson distributions needed (see family parameter), MASS::glm.nb() Negative Binomial distributions. Link function GLM log.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/h_glm_count.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Helper functions for Poisson models — h_glm_count","text":"","code":"h_glm_count(.var, .df_row, variables, distribution, weights)  h_glm_poisson(.var, .df_row, variables, weights)  h_glm_quasipoisson(.var, .df_row, variables, weights)  h_glm_negbin(.var, .df_row, variables, weights)"},{"path":"https://insightsengineering.github.io/tern/reference/h_glm_count.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Helper functions for Poisson models — h_glm_count","text":".var (string) single variable name passed rtables requested statistics function. .df_row (data.frame) dataset includes variables called .var variables. variables (named list string) list additional analysis variables, expected elements: arm (string) group variable, covariate adjusted means multiple groups summarized. Specifically, first level arm variable taken reference group. covariates (character) vector can contain single variable names (\"X1\"), /interaction terms indicated \"X1 * X2\". offset (numeric) numeric vector scalar adding offset. distribution (character) character value specifying distribution used regression (Poisson, Quasi-Poisson, negative binomial). weights (character) character vector specifying weights used averaging predictions. Number weights must equal number levels included covariates. Weights option passed emmeans::emmeans().","code":""},{"path":"https://insightsengineering.github.io/tern/reference/h_glm_count.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Helper functions for Poisson models — h_glm_count","text":"h_glm_count() returns results selected model. h_glm_poisson() returns results Poisson model. h_glm_quasipoisson() returns results Quasi-Poisson model. h_glm_negbin() returns results negative binomial model.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/h_glm_count.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Helper functions for Poisson models — h_glm_count","text":"h_glm_count(): Helper function return results selected model (Poisson, Quasi-Poisson, negative binomial). h_glm_poisson(): Helper function return results Poisson model. h_glm_quasipoisson(): Helper function return results Quasi-Poisson model. h_glm_negbin(): Helper function return results negative binomial model.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/reference/h_grob_coxph.html","id":null,"dir":"Reference","previous_headings":"","what":"Helper function to create Cox-PH grobs — h_grob_coxph","title":"Helper function to create Cox-PH grobs — h_grob_coxph","text":"Grob rtable output h_tbl_coxph_pairwise()","code":""},{"path":"https://insightsengineering.github.io/tern/reference/h_grob_coxph.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Helper function to create Cox-PH grobs — h_grob_coxph","text":"","code":"h_grob_coxph(   ...,   x = 0,   y = 0,   width = grid::unit(0.4, \"npc\"),   ttheme = gridExtra::ttheme_default(padding = grid::unit(c(1, 0.5), \"lines\"), core =     list(bg_params = list(fill = c(\"grey95\", \"grey90\"), alpha = 0.5))) )"},{"path":"https://insightsengineering.github.io/tern/reference/h_grob_coxph.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Helper function to create Cox-PH grobs — h_grob_coxph","text":"... arguments pass h_tbl_coxph_pairwise(). x (proportion) value 0 1 specifying x-location. y (proportion) value 0 1 specifying y-location. width (grid::unit) width (unit) use printing grob. ttheme (list) see gridExtra::ttheme_default().","code":""},{"path":"https://insightsengineering.github.io/tern/reference/h_grob_coxph.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Helper function to create Cox-PH grobs — h_grob_coxph","text":"grob table containing statistics HR, XX% CI (XX taken control_coxph_pw), p-value (log-rank).","code":""},{"path":"https://insightsengineering.github.io/tern/reference/h_grob_coxph.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Helper function to create Cox-PH grobs — h_grob_coxph","text":"","code":"# \\donttest{ library(dplyr) library(survival) library(grid)  grid::grid.newpage() grid.rect(gp = grid::gpar(lty = 1, col = \"pink\", fill = \"gray85\", lwd = 1)) data <- tern_ex_adtte %>%   filter(PARAMCD == \"OS\") %>%   mutate(is_event = CNSR == 0) tbl_grob <- h_grob_coxph(   df = data,   variables = list(tte = \"AVAL\", is_event = \"is_event\", arm = \"ARMCD\"),   control_coxph_pw = control_coxph(conf_level = 0.9), x = 0.5, y = 0.5 ) #> Warning: `h_grob_coxph()` was deprecated in tern 0.9.4. #> ℹ `g_km` now generates `ggplot` objects. This function is no longer used within #>   `tern`. grid::grid.draw(tbl_grob)  # }"},{"path":"https://insightsengineering.github.io/tern/reference/h_grob_median_surv.html","id":null,"dir":"Reference","previous_headings":"","what":"Helper function to create survival estimation grobs — h_grob_median_surv","title":"Helper function to create survival estimation grobs — h_grob_median_surv","text":"survival fit transformed grob containing table groups rows characterized N, median 95% confidence interval.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/h_grob_median_surv.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Helper function to create survival estimation grobs — h_grob_median_surv","text":"","code":"h_grob_median_surv(   fit_km,   armval = \"All\",   x = 0.9,   y = 0.9,   width = grid::unit(0.3, \"npc\"),   ttheme = gridExtra::ttheme_default() )"},{"path":"https://insightsengineering.github.io/tern/reference/h_grob_median_surv.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Helper function to create survival estimation grobs — h_grob_median_surv","text":"fit_km (survfit) result survival::survfit(). armval (string) used strata name treatment arm variable one level. Default \"\". x (proportion) value 0 1 specifying x-location. y (proportion) value 0 1 specifying y-location. width (grid::unit) width (unit) use printing grob. ttheme (list) see gridExtra::ttheme_default().","code":""},{"path":"https://insightsengineering.github.io/tern/reference/h_grob_median_surv.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Helper function to create survival estimation grobs — h_grob_median_surv","text":"grob table containing statistics N, Median, XX% CI (XX taken fit_km).","code":""},{"path":"https://insightsengineering.github.io/tern/reference/h_grob_median_surv.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Helper function to create survival estimation grobs — h_grob_median_surv","text":"","code":"# \\donttest{ library(dplyr) library(survival) library(grid)  grid::grid.newpage() grid.rect(gp = grid::gpar(lty = 1, col = \"pink\", fill = \"gray85\", lwd = 1)) tern_ex_adtte %>%   filter(PARAMCD == \"OS\") %>%   survfit(formula = Surv(AVAL, 1 - CNSR) ~ ARMCD, data = .) %>%   h_grob_median_surv() %>%   grid::grid.draw() #> Warning: `h_grob_median_surv()` was deprecated in tern 0.9.4. #> ℹ `g_km` now generates `ggplot` objects. This function is no longer used within #>   `tern`.  # }"},{"path":"https://insightsengineering.github.io/tern/reference/h_grob_tbl_at_risk.html","id":null,"dir":"Reference","previous_headings":"","what":"Helper function to create patient-at-risk grobs — h_grob_tbl_at_risk","title":"Helper function to create patient-at-risk grobs — h_grob_tbl_at_risk","text":"Two graphical objects obtained, one corresponding row labeling second table numbers patients risk. title = TRUE, third object corresponding table title also obtained.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/h_grob_tbl_at_risk.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Helper function to create patient-at-risk grobs — h_grob_tbl_at_risk","text":"","code":"h_grob_tbl_at_risk(data, annot_tbl, xlim, title = TRUE)"},{"path":"https://insightsengineering.github.io/tern/reference/h_grob_tbl_at_risk.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Helper function to create patient-at-risk grobs — h_grob_tbl_at_risk","text":"data (data.frame) survival data pre-processed h_data_plot. annot_tbl (data.frame) annotation prepared survival::summary.survfit() includes number patients risk given time points. xlim (numeric(1)) maximum value x-axis (used ensure risk table aligns KM graph). title (flag) whether \"Patients Risk\" title added annot_at_risk table. effect annot_at_risk FALSE. Defaults TRUE.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/h_grob_tbl_at_risk.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Helper function to create patient-at-risk grobs — h_grob_tbl_at_risk","text":"named list two gTree objects title = FALSE: at_risk label, three gTree objects title = TRUE: at_risk, label, title.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/h_grob_tbl_at_risk.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Helper function to create patient-at-risk grobs — h_grob_tbl_at_risk","text":"","code":"# \\donttest{ library(dplyr) library(survival) library(grid)  fit_km <- tern_ex_adtte %>%   filter(PARAMCD == \"OS\") %>%   survfit(formula = Surv(AVAL, 1 - CNSR) ~ ARMCD, data = .)  data_plot <- h_data_plot(fit_km = fit_km)  xticks <- h_xticks(data = data_plot)  gg <- h_ggkm(   data = data_plot,   censor_show = TRUE,   xticks = xticks, xlab = \"Days\", ylab = \"Survival Probability\",   title = \"tt\", footnotes = \"ff\", yval = \"Survival\" )  # The annotation table reports the patient at risk for a given strata and # times (`xticks`). annot_tbl <- summary(fit_km, times = xticks) if (is.null(fit_km$strata)) {   annot_tbl <- with(annot_tbl, data.frame(n.risk = n.risk, time = time, strata = \"All\")) } else {   strata_lst <- strsplit(sub(\"=\", \"equals\", levels(annot_tbl$strata)), \"equals\")   levels(annot_tbl$strata) <- matrix(unlist(strata_lst), ncol = 2, byrow = TRUE)[, 2]   annot_tbl <- data.frame(     n.risk = annot_tbl$n.risk,     time = annot_tbl$time,     strata = annot_tbl$strata   ) }  # The annotation table is transformed into a grob. tbl <- h_grob_tbl_at_risk(data = data_plot, annot_tbl = annot_tbl, xlim = max(xticks)) #> Warning: `h_grob_tbl_at_risk()` was deprecated in tern 0.9.4. #> ℹ `g_km` now generates `ggplot` objects. This function is no longer used within #>   `tern`.  # For the representation, the layout is estimated for which the decomposition # of the graphic element is necessary. g_el <- h_decompose_gg(gg) lyt <- h_km_layout(data = data_plot, g_el = g_el, title = \"t\", footnotes = \"f\") #> Warning: `h_km_layout()` was deprecated in tern 0.9.4. #> ℹ `g_km` now generates `ggplot` objects. This function is no longer used within #>   `tern`.  grid::grid.newpage() pushViewport(viewport(layout = lyt, height = .95, width = .95)) grid.rect(gp = grid::gpar(lty = 1, col = \"purple\", fill = \"gray85\", lwd = 1)) pushViewport(viewport(layout.pos.row = 3:4, layout.pos.col = 2)) grid.rect(gp = grid::gpar(lty = 1, col = \"orange\", fill = \"gray85\", lwd = 1)) grid::grid.draw(tbl$at_risk) popViewport() pushViewport(viewport(layout.pos.row = 3:4, layout.pos.col = 1)) grid.rect(gp = grid::gpar(lty = 1, col = \"green3\", fill = \"gray85\", lwd = 1)) grid::grid.draw(tbl$label)  # }"},{"path":"https://insightsengineering.github.io/tern/reference/h_grob_y_annot.html","id":null,"dir":"Reference","previous_headings":"","what":"Helper function to create grid object with y-axis annotation — h_grob_y_annot","title":"Helper function to create grid object with y-axis annotation — h_grob_y_annot","text":"Build y-axis annotation decomposed ggplot.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/h_grob_y_annot.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Helper function to create grid object with y-axis annotation — h_grob_y_annot","text":"","code":"h_grob_y_annot(ylab, yaxis)"},{"path":"https://insightsengineering.github.io/tern/reference/h_grob_y_annot.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Helper function to create grid object with y-axis annotation — h_grob_y_annot","text":"ylab (gtable) y-lab graphical object derived ggplot. yaxis (gtable) y-axis graphical object derived ggplot.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/h_grob_y_annot.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Helper function to create grid object with y-axis annotation — h_grob_y_annot","text":"gTree object containing y-axis annotation ggplot.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/h_grob_y_annot.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Helper function to create grid object with y-axis annotation — h_grob_y_annot","text":"","code":"# \\donttest{ library(dplyr) library(survival) library(grid)  fit_km <- tern_ex_adtte %>%   filter(PARAMCD == \"OS\") %>%   survfit(formula = Surv(AVAL, 1 - CNSR) ~ ARMCD, data = .) data_plot <- h_data_plot(fit_km = fit_km) xticks <- h_xticks(data = data_plot) gg <- h_ggkm(   data = data_plot,   censor_show = TRUE,   xticks = xticks, xlab = \"Days\", ylab = \"Survival Probability\",   title = \"title\", footnotes = \"footnotes\", yval = \"Survival\" )  g_el <- h_decompose_gg(gg)  grid::grid.newpage() pvp <- grid::plotViewport(margins = c(5, 4, 2, 20)) pushViewport(pvp) grid::grid.draw(h_grob_y_annot(ylab = g_el$ylab, yaxis = g_el$yaxis)) #> Warning: `h_grob_y_annot()` was deprecated in tern 0.9.4. #> ℹ `g_km` now generates `ggplot` objects. This function is no longer used within #>   `tern`. grid.rect(gp = grid::gpar(lty = 1, col = \"gray35\", fill = NA))  # }"},{"path":[]},{"path":"https://insightsengineering.github.io/tern/reference/h_incidence_rate.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Helper functions for incidence rate — h_incidence_rate","text":"","code":"h_incidence_rate(person_years, n_events, control = control_incidence_rate())  h_incidence_rate_normal(person_years, n_events, alpha = 0.05)  h_incidence_rate_normal_log(person_years, n_events, alpha = 0.05)  h_incidence_rate_exact(person_years, n_events, alpha = 0.05)  h_incidence_rate_byar(person_years, n_events, alpha = 0.05)"},{"path":"https://insightsengineering.github.io/tern/reference/h_incidence_rate.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Helper functions for incidence rate — h_incidence_rate","text":"person_years (numeric(1)) total person-years risk. n_events (integer(1)) number events observed. control (list) parameters estimation details, specified using helper function control_incidence_rate(). Possible parameter options : conf_level: (proportion) confidence level estimated incidence rate. conf_type: (string)normal (default), normal_log, exact, byar confidence interval type. input_time_unit: (string)day, week, month, year (default) indicating time unit data input. num_pt_year: (numeric) time unit desired output (person-years). alpha (numeric(1)) two-sided alpha-level confidence interval.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/h_incidence_rate.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Helper functions for incidence rate — h_incidence_rate","text":"Estimated incidence rate, rate, associated confidence interval, rate_ci.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/h_incidence_rate.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Helper functions for incidence rate — h_incidence_rate","text":"h_incidence_rate(): Helper function estimate incidence rate associated confidence interval. h_incidence_rate_normal(): Helper function estimate incidence rate associated confidence interval based normal approximation incidence rate. Unit one person-year. h_incidence_rate_normal_log(): Helper function estimate incidence rate associated confidence interval based normal approximation logarithm incidence rate. Unit one person-year. h_incidence_rate_exact(): Helper function estimate incidence rate associated exact confidence interval. Unit one person-year. h_incidence_rate_byar(): Helper function estimate incidence rate associated Byar's confidence interval. Unit one person-year.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/reference/h_incidence_rate.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Helper functions for incidence rate — h_incidence_rate","text":"","code":"h_incidence_rate_normal(200, 2) #> $rate #> [1] 0.01 #>  #> $rate_ci #> [1] -0.003859038  0.023859038 #>   h_incidence_rate_normal_log(200, 2) #> $rate #> [1] 0.01 #>  #> $rate_ci #> [1] 0.002500977 0.039984382 #>   h_incidence_rate_exact(200, 2) #> $rate #> [1] 0.01 #>  #> $rate_ci #> [1] 0.001211046 0.036123438 #>   h_incidence_rate_byar(200, 2) #> $rate #> [1] 0.01 #>  #> $rate_ci #> [1] 0.001994207 0.032054171 #>"},{"path":"https://insightsengineering.github.io/tern/reference/h_km_layout.html","id":null,"dir":"Reference","previous_headings":"","what":"Helper function to prepare a KM layout — h_km_layout","title":"Helper function to prepare a KM layout — h_km_layout","text":"Prepares (5 rows) x (2 cols) layout Kaplan-Meier curve.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/h_km_layout.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Helper function to prepare a KM layout — h_km_layout","text":"","code":"h_km_layout(   data,   g_el,   title,   footnotes,   annot_at_risk = TRUE,   annot_at_risk_title = TRUE )"},{"path":"https://insightsengineering.github.io/tern/reference/h_km_layout.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Helper function to prepare a KM layout — h_km_layout","text":"data (data.frame) survival data pre-processed h_data_plot. g_el (list gtable) list obtained h_decompose_gg(). title (string) plot title. footnotes (string) plot footnotes. annot_at_risk (flag) compute add annotation table reporting number patient risk matching main grid Kaplan-Meier curve. annot_at_risk_title (flag) whether \"Patients Risk\" title added annot_at_risk table. effect annot_at_risk FALSE. Defaults TRUE.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/h_km_layout.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Helper function to prepare a KM layout — h_km_layout","text":"grid layout.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/h_km_layout.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Helper function to prepare a KM layout — h_km_layout","text":"layout corresponds grid two columns five rows unequal dimensions. dimension fixed, curve flexible accommodate remaining free space. left column gets annotation ggplot (y-axis) names strata patient risk tabulation. main constraint width columns must allow writing strata name. right column receive ggplot, legend, x-axis patient risk table.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/h_km_layout.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Helper function to prepare a KM layout — h_km_layout","text":"","code":"# \\donttest{ library(dplyr) library(survival) library(grid)  fit_km <- tern_ex_adtte %>%   filter(PARAMCD == \"OS\") %>%   survfit(formula = Surv(AVAL, 1 - CNSR) ~ ARMCD, data = .) data_plot <- h_data_plot(fit_km = fit_km) xticks <- h_xticks(data = data_plot) gg <- h_ggkm(   data = data_plot,   censor_show = TRUE,   xticks = xticks, xlab = \"Days\", ylab = \"Survival Probability\",   title = \"tt\", footnotes = \"ff\", yval = \"Survival\" ) g_el <- h_decompose_gg(gg) lyt <- h_km_layout(data = data_plot, g_el = g_el, title = \"t\", footnotes = \"f\") grid.show.layout(lyt)  # }"},{"path":"https://insightsengineering.github.io/tern/reference/h_logistic_regression.html","id":null,"dir":"Reference","previous_headings":"","what":"Helper functions for multivariate logistic regression — h_logistic_regression","title":"Helper functions for multivariate logistic regression — h_logistic_regression","text":"Helper functions used calculations logistic regression.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/h_logistic_regression.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Helper functions for multivariate logistic regression — h_logistic_regression","text":"","code":"h_get_interaction_vars(fit_glm)  h_interaction_coef_name(   interaction_vars,   first_var_with_level,   second_var_with_level )  h_or_cat_interaction(   odds_ratio_var,   interaction_var,   fit_glm,   conf_level = 0.95 )  h_or_cont_interaction(   odds_ratio_var,   interaction_var,   fit_glm,   at = NULL,   conf_level = 0.95 )  h_or_interaction(   odds_ratio_var,   interaction_var,   fit_glm,   at = NULL,   conf_level = 0.95 )  h_simple_term_labels(terms, table)  h_interaction_term_labels(terms1, terms2, table, any = FALSE)  h_glm_simple_term_extract(x, fit_glm)  h_glm_interaction_extract(x, fit_glm)  h_glm_inter_term_extract(odds_ratio_var, interaction_var, fit_glm, ...)  h_logistic_simple_terms(x, fit_glm, conf_level = 0.95)  h_logistic_inter_terms(x, fit_glm, conf_level = 0.95, at = NULL)"},{"path":"https://insightsengineering.github.io/tern/reference/h_logistic_regression.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Helper functions for multivariate logistic regression — h_logistic_regression","text":"fit_glm (glm) logistic regression model fitted stats::glm() \"binomial\" family. Limited functionality also available conditional logistic regression models fitted survival::clogit(), currently used extract_rsp_biomarkers(). interaction_vars (character(2)) interaction variable names. first_var_with_level (character(2)) first variable name interaction level. second_var_with_level (character(2)) second variable name interaction level. odds_ratio_var (string) odds ratio variable. interaction_var (string) interaction variable. conf_level (proportion) confidence level interval. (numeric NULL) optional values interaction variable. Otherwise median used. terms (character) simple terms. table (table) table containing numbers terms. terms1 (character) terms first dimension (rows). terms2 (character) terms second dimension (rows). (flag) whether term1 term2 can fulfilled count number patients. case can scalar (strings). x (character) variable interaction term fit_glm (depending helper function used). ... additional arguments lower level functions.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/h_logistic_regression.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Helper functions for multivariate logistic regression — h_logistic_regression","text":"Vector names interaction variables. Name coefficient. Odds ratio. Odds ratio. Odds ratio. Term labels containing numbers patients. Term labels containing numbers patients. Tabulated main effect results logistic regression model. Tabulated interaction term results logistic regression model. data.frame tabulated interaction term results logistic regression model. Tabulated statistics given variable(s) logistic regression model. Tabulated statistics given variable(s) logistic regression model.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/h_logistic_regression.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Helper functions for multivariate logistic regression — h_logistic_regression","text":"h_get_interaction_vars(): Helper function extract interaction variable names fitted model assuming one interaction term. h_interaction_coef_name(): Helper function get right coefficient name interaction variable names given levels. main value order first second variable checked interaction_vars input. h_or_cat_interaction(): Helper function calculate odds ratio estimates case odds ratio interaction variable categorical. h_or_cont_interaction(): Helper function calculate odds ratio estimates case either odds ratio interaction variable continuous. h_or_interaction(): Helper function calculate odds ratio estimates case interaction. wrapper h_or_cont_interaction() h_or_cat_interaction(). h_simple_term_labels(): Helper function construct term labels simple terms table numbers patients. h_interaction_term_labels(): Helper function construct term labels interaction terms table numbers patients. h_glm_simple_term_extract(): Helper function tabulate main effect results (conditional) logistic regression model. h_glm_interaction_extract(): Helper function tabulate interaction term results logistic regression model. h_glm_inter_term_extract(): Helper function tabulate interaction results logistic regression model. basically wrapper h_or_interaction() h_glm_simple_term_extract() puts results right data frame format. h_logistic_simple_terms(): Helper function tabulate results including odds ratios confidence intervals simple terms. h_logistic_inter_terms(): Helper function tabulate results including odds ratios confidence intervals interaction terms.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/h_logistic_regression.html","id":"note","dir":"Reference","previous_headings":"","what":"Note","title":"Helper functions for multivariate logistic regression — h_logistic_regression","text":"provide function case variables continuous arise table, treatment arm variable always involved categorical.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/h_logistic_regression.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Helper functions for multivariate logistic regression — h_logistic_regression","text":"","code":"library(dplyr) library(broom)  adrs_f <- tern_ex_adrs %>%   filter(PARAMCD == \"BESRSPI\") %>%   filter(RACE %in% c(\"ASIAN\", \"WHITE\", \"BLACK OR AFRICAN AMERICAN\")) %>%   mutate(     Response = case_when(AVALC %in% c(\"PR\", \"CR\") ~ 1, TRUE ~ 0),     RACE = factor(RACE),     SEX = factor(SEX)   ) formatters::var_labels(adrs_f) <- c(formatters::var_labels(tern_ex_adrs), Response = \"Response\") mod1 <- fit_logistic(   data = adrs_f,   variables = list(     response = \"Response\",     arm = \"ARMCD\",     covariates = c(\"AGE\", \"RACE\")   ) ) #> Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred mod2 <- fit_logistic(   data = adrs_f,   variables = list(     response = \"Response\",     arm = \"ARMCD\",     covariates = c(\"AGE\", \"RACE\"),     interaction = \"AGE\"   ) ) #> Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred  h_glm_simple_term_extract(\"AGE\", mod1) #>   variable variable_label term term_label interaction interaction_label #> 1      AGE            Age  AGE        Age                               #>   reference reference_label  estimate  std_error df     pvalue #> 1                           0.1698216 0.09524116  1 0.07457501 #>   is_variable_summary is_term_summary #> 1               FALSE            TRUE h_glm_simple_term_extract(\"ARMCD\", mod1) #>   variable   variable_label  term              term_label interaction #> 1    ARMCD Planned Arm Code ARM A Reference ARM A, n = 64             #> 2    ARMCD Planned Arm Code ARM B           ARM B, n = 68             #> 3    ARMCD Planned Arm Code ARM C           ARM C, n = 52             #>   interaction_label reference reference_label  estimate std_error df    pvalue #> 1                                                                  2 0.3004308 #> 2                                             -1.774769  1.144405  1 0.1209443 #> 3                                               17.1922  3626.588  1 0.9962176 #>   is_variable_summary is_term_summary #> 1                TRUE           FALSE #> 2               FALSE            TRUE #> 3               FALSE            TRUE  h_glm_interaction_extract(\"ARMCD:AGE\", mod2) #>    variable                        variable_label  term              term_label #> 1 ARMCD:AGE Interaction of Planned Arm Code * Age ARM A Reference ARM A, n = 64 #> 2 ARMCD:AGE Interaction of Planned Arm Code * Age ARM B           ARM B, n = 68 #> 3 ARMCD:AGE Interaction of Planned Arm Code * Age ARM C           ARM C, n = 52 #>   interaction interaction_label reference reference_label   estimate std_error #> 1                                                                              #> 2                                                          0.3081205 0.2062392 #> 3                                                         0.02948826  548.5923 #>   df    pvalue is_variable_summary is_term_summary #> 1  2 0.3275837                TRUE           FALSE #> 2  1 0.1351767               FALSE            TRUE #> 3  1 0.9999571               FALSE            TRUE  h_glm_inter_term_extract(\"AGE\", \"ARMCD\", mod2) #>   variable variable_label term term_label interaction interaction_label #> 1      AGE            Age  AGE        Age                               #> 2      AGE            Age  AGE        Age       ARMCD  Planned Arm Code #> 3      AGE            Age  AGE        Age       ARMCD  Planned Arm Code #> 4      AGE            Age  AGE        Age       ARMCD  Planned Arm Code #>   reference reference_label    estimate std_error odds_ratio       lcl      ucl #> 1                           -0.03873898 0.1514322         NA        NA       NA #> 2     ARM A           ARM A          NA        NA  0.9620018 0.7149514 1.294420 #> 3     ARM B           ARM B          NA        NA  1.3091545 1.0021802 1.710157 #> 4     ARM C           ARM C          NA        NA  0.9907919 0.0000000      Inf #>   df   pvalue is_variable_summary is_term_summary is_reference_summary #> 1  1 0.798092               FALSE            TRUE                FALSE #> 2 NA       NA               FALSE           FALSE                 TRUE #> 3 NA       NA               FALSE           FALSE                 TRUE #> 4 NA       NA               FALSE           FALSE                 TRUE  h_logistic_simple_terms(\"AGE\", mod1) #>   variable variable_label term term_label interaction interaction_label #> 1      AGE            Age  AGE        Age                               #>   reference reference_label  estimate  std_error df     pvalue #> 1                           0.1698216 0.09524116  1 0.07457501 #>   is_variable_summary is_term_summary odds_ratio       lcl      ucl #> 1               FALSE            TRUE   1.185093 0.9832935 1.428308 #>                     ci #> 1 0.9832935, 1.4283084  h_logistic_inter_terms(c(\"RACE\", \"AGE\", \"ARMCD\", \"AGE:ARMCD\"), mod2) #>        variable                        variable_label                      term #> 1          RACE                                  Race                     ASIAN #> 2          RACE                                  Race BLACK OR AFRICAN AMERICAN #> 3          RACE                                  Race                     WHITE #> 13        ARMCD                      Planned Arm Code                     ARM A #> 23        ARMCD                      Planned Arm Code                     ARM B #> ARM B     ARMCD                      Planned Arm Code                     ARM B #> 33        ARMCD                      Planned Arm Code                     ARM C #> ARM C     ARMCD                      Planned Arm Code                     ARM C #> 11          AGE                                   Age                       AGE #> 21          AGE                                   Age                       AGE #> 31          AGE                                   Age                       AGE #> 4           AGE                                   Age                       AGE #> 12    AGE:ARMCD Interaction of Planned Arm Code * Age                     ARM A #> 22    AGE:ARMCD Interaction of Planned Arm Code * Age                     ARM B #> 32    AGE:ARMCD Interaction of Planned Arm Code * Age                     ARM C #>                              term_label interaction interaction_label reference #> 1              Reference ASIAN, n = 110                                         #> 2     BLACK OR AFRICAN AMERICAN, n = 40                                         #> 3                         WHITE, n = 34                                         #> 13              Reference ARM A, n = 64                                         #> 23                        ARM B, n = 68                                         #> ARM B                     ARM B, n = 68         AGE               Age        35 #> 33                        ARM C, n = 52                                         #> ARM C                     ARM C, n = 52         AGE               Age        35 #> 11                                  Age                                         #> 21                                  Age       ARMCD  Planned Arm Code     ARM A #> 31                                  Age       ARMCD  Planned Arm Code     ARM B #> 4                                   Age       ARMCD  Planned Arm Code     ARM C #> 12              Reference ARM A, n = 64                                         #> 22                        ARM B, n = 68                                         #> 32                        ARM C, n = 52                                         #>       reference_label    estimate std_error df     pvalue odds_ratio        lcl #> 1                                            2  0.9361139                       #> 2                        18.15018  3944.701  1  0.9963288   76299564          0 #> 3                      -0.3727152  1.025808  1  0.7163522  0.6888614 0.09224926 #> 13                                           2   0.253914         NA         NA #> 23                      -11.52715   6.96188  1 0.09777185         NA         NA #> ARM B              35          NA        NA NA         NA  0.4757148 0.03361147 #> 33                       16.33327  20278.39  1  0.9993573         NA         NA #> ARM C              35          NA        NA NA         NA   34808099          0 #> 11                    -0.03873898 0.1514322  1   0.798092         NA         NA #> 21              ARM A          NA        NA NA         NA  0.9620018  0.7149514 #> 31              ARM B          NA        NA NA         NA   1.309155    1.00218 #> 4               ARM C          NA        NA NA         NA  0.9907919          0 #> 12                                          NA         NA         NA         NA #> 22                      0.3081205 0.2062392  1  0.1351767         NA         NA #> 32                     0.02948826  548.5923  1  0.9999571         NA         NA #>            ucl is_variable_summary is_term_summary is_reference_summary #> 1                             TRUE           FALSE                FALSE #> 2          Inf               FALSE            TRUE                FALSE #> 3     5.143998               FALSE            TRUE                FALSE #> 13          NA                TRUE           FALSE                FALSE #> 23          NA               FALSE            TRUE                FALSE #> ARM B 6.732956               FALSE           FALSE                 TRUE #> 33          NA               FALSE            TRUE                FALSE #> ARM C      Inf               FALSE           FALSE                 TRUE #> 11          NA               FALSE            TRUE                FALSE #> 21     1.29442               FALSE           FALSE                 TRUE #> 31    1.710157               FALSE           FALSE                 TRUE #> 4          Inf               FALSE           FALSE                 TRUE #> 12          NA                TRUE           FALSE                FALSE #> 22          NA               FALSE            TRUE                FALSE #> 32          NA               FALSE            TRUE                FALSE #>                           ci #> 1                            #> 2                     0, Inf #> 3     0.09224926, 5.14399810 #> 13                    NA, NA #> 23                    NA, NA #> ARM B 0.03361147, 6.73295611 #> 33                    NA, NA #> ARM C                 0, Inf #> 11                    NA, NA #> 21      0.7149514, 1.2944200 #> 31        1.002180, 1.710157 #> 4                     0, Inf #> 12                    NA, NA #> 22                    NA, NA #> 32                    NA, NA"},{"path":"https://insightsengineering.github.io/tern/reference/h_map_for_count_abnormal.html","id":null,"dir":"Reference","previous_headings":"","what":"Helper function to create a map data frame for trim_levels_to_map() — h_map_for_count_abnormal","title":"Helper function to create a map data frame for trim_levels_to_map() — h_map_for_count_abnormal","text":"Helper function create map data frame input dataset, can used argument trim_levels_to_map split function. Based different method, map constructed differently.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/h_map_for_count_abnormal.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Helper function to create a map data frame for trim_levels_to_map() — h_map_for_count_abnormal","text":"","code":"h_map_for_count_abnormal(   df,   variables = list(anl = \"ANRIND\", split_rows = c(\"PARAM\"), range_low = \"ANRLO\",     range_high = \"ANRHI\"),   abnormal = list(low = c(\"LOW\", \"LOW LOW\"), high = c(\"HIGH\", \"HIGH HIGH\")),   method = c(\"default\", \"range\"),   na_str = \"<Missing>\" )"},{"path":"https://insightsengineering.github.io/tern/reference/h_map_for_count_abnormal.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Helper function to create a map data frame for trim_levels_to_map() — h_map_for_count_abnormal","text":"df (data.frame) data set containing analysis variables. variables (named list string) list additional analysis variables. abnormal (named list) identifying abnormal range level(s) df. Based levels abnormality input dataset, can something like list(Low = \"LOW LOW\", High = \"HIGH HIGH\") abnormal = list(Low = \"LOW\", High = \"HIGH\")) method (string) indicates returned map constructed. Can \"default\" \"range\". na_str (string) string used replace NA empty values output.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/h_map_for_count_abnormal.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Helper function to create a map data frame for trim_levels_to_map() — h_map_for_count_abnormal","text":"map data.frame.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/h_map_for_count_abnormal.html","id":"note","dir":"Reference","previous_headings":"","what":"Note","title":"Helper function to create a map data frame for trim_levels_to_map() — h_map_for_count_abnormal","text":"method \"default\", returned map abnormal directions observed df, records normal values excluded avoid error creating layout. method \"range\", returned map based rule least one observation low range > 0 low direction least one observation high range missing high direction.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/h_map_for_count_abnormal.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Helper function to create a map data frame for trim_levels_to_map() — h_map_for_count_abnormal","text":"","code":"adlb <- df_explicit_na(tern_ex_adlb)  h_map_for_count_abnormal(   df = adlb,   variables = list(anl = \"ANRIND\", split_rows = c(\"LBCAT\", \"PARAM\")),   abnormal = list(low = c(\"LOW\"), high = c(\"HIGH\")),   method = \"default\",   na_str = \"<Missing>\" ) #>        LBCAT                                PARAM ANRIND #> 1  CHEMISTRY Alanine Aminotransferase Measurement    LOW #> 4  CHEMISTRY Alanine Aminotransferase Measurement   HIGH #> 7  CHEMISTRY Alanine Aminotransferase Measurement NORMAL #> 2  CHEMISTRY       C-Reactive Protein Measurement    LOW #> 3  CHEMISTRY       C-Reactive Protein Measurement   HIGH #> 8  CHEMISTRY       C-Reactive Protein Measurement NORMAL #> 5 IMMUNOLOGY         Immunoglobulin A Measurement    LOW #> 6 IMMUNOLOGY         Immunoglobulin A Measurement   HIGH #> 9 IMMUNOLOGY         Immunoglobulin A Measurement NORMAL  df <- data.frame(   USUBJID = c(rep(\"1\", 4), rep(\"2\", 4), rep(\"3\", 4)),   AVISIT = c(     rep(\"WEEK 1\", 2),     rep(\"WEEK 2\", 2),     rep(\"WEEK 1\", 2),     rep(\"WEEK 2\", 2),     rep(\"WEEK 1\", 2),     rep(\"WEEK 2\", 2)   ),   PARAM = rep(c(\"ALT\", \"CPR\"), 6),   ANRIND = c(     \"NORMAL\", \"NORMAL\", \"LOW\",     \"HIGH\", \"LOW\", \"LOW\", \"HIGH\", \"HIGH\", rep(\"NORMAL\", 4)   ),   ANRLO = rep(5, 12),   ANRHI = rep(20, 12) ) df$ANRIND <- factor(df$ANRIND, levels = c(\"LOW\", \"HIGH\", \"NORMAL\")) h_map_for_count_abnormal(   df = df,   variables = list(     anl = \"ANRIND\",     split_rows = c(\"PARAM\"),     range_low = \"ANRLO\",     range_high = \"ANRHI\"   ),   abnormal = list(low = c(\"LOW\"), high = c(\"HIGH\")),   method = \"range\",   na_str = \"<Missing>\" ) #>   PARAM ANRIND #> 1   ALT    LOW #> 3   ALT   HIGH #> 5   ALT NORMAL #> 2   CPR    LOW #> 4   CPR   HIGH #> 6   CPR NORMAL"},{"path":"https://insightsengineering.github.io/tern/reference/h_odds_ratio.html","id":null,"dir":"Reference","previous_headings":"","what":"Helper functions for odds ratio estimation — h_odds_ratio","title":"Helper functions for odds ratio estimation — h_odds_ratio","text":"Functions calculate odds ratios estimate_odds_ratio().","code":""},{"path":"https://insightsengineering.github.io/tern/reference/h_odds_ratio.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Helper functions for odds ratio estimation — h_odds_ratio","text":"","code":"or_glm(data, conf_level)  or_clogit(data, conf_level, method = \"exact\")"},{"path":"https://insightsengineering.github.io/tern/reference/h_odds_ratio.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Helper functions for odds ratio estimation — h_odds_ratio","text":"data (data.frame) data frame containing least variables rsp grp, optionally strata or_clogit(). conf_level (proportion) confidence level interval. method (string) whether use correct (\"exact\") calculation conditional likelihood one approximations. See survival::clogit() details.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/h_odds_ratio.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Helper functions for odds ratio estimation — h_odds_ratio","text":"named list elements or_ci n_tot.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/h_odds_ratio.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Helper functions for odds ratio estimation — h_odds_ratio","text":"or_glm(): Estimates odds ratio based stats::glm(). Note must exactly 2 groups data specified grp variable. or_clogit(): Estimates odds ratio based survival::clogit(). done whole data set including groups, since results pairwise comparisons groups.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/reference/h_odds_ratio.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Helper functions for odds ratio estimation — h_odds_ratio","text":"","code":"# Data with 2 groups. data <- data.frame(   rsp = as.logical(c(1, 1, 0, 1, 0, 0, 1, 1)),   grp = letters[c(1, 1, 1, 2, 2, 2, 1, 2)],   strata = letters[c(1, 2, 1, 2, 2, 2, 1, 2)],   stringsAsFactors = TRUE )  # Odds ratio based on glm. or_glm(data, conf_level = 0.95) #> $or_ci #>        est        lcl        ucl  #> 0.33333333 0.01669735 6.65441589  #>  #> $n_tot #> n_tot  #>     8  #>   # Data with 3 groups. data <- data.frame(   rsp = as.logical(c(1, 1, 0, 1, 0, 0, 1, 1, 0, 0, 1, 1, 0, 1, 0, 0, 1, 1, 0, 0)),   grp = letters[c(1, 1, 1, 2, 2, 2, 3, 3, 3, 3, 1, 1, 1, 2, 2, 2, 3, 3, 3, 3)],   strata = LETTERS[c(1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2)],   stringsAsFactors = TRUE )  # Odds ratio based on stratified estimation by conditional logistic regression. or_clogit(data, conf_level = 0.95) #> $or_ci #> $or_ci$b #>        est        lcl        ucl  #> 0.28814553 0.02981009 2.78522598  #>  #> $or_ci$c #>       est       lcl       ucl  #> 0.5367919 0.0673365 4.2791881  #>  #>  #> $n_tot #> n_tot  #>    20  #>"},{"path":[]},{"path":"https://insightsengineering.github.io/tern/reference/h_pkparam_sort.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Sort pharmacokinetic data by PARAM variable — h_pkparam_sort","text":"","code":"h_pkparam_sort(pk_data, key_var = \"PARAMCD\")"},{"path":"https://insightsengineering.github.io/tern/reference/h_pkparam_sort.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Sort pharmacokinetic data by PARAM variable — h_pkparam_sort","text":"pk_data (data.frame) pharmacokinetic data frame. key_var (string) key variable used merge pk_data metadata created d_pkparam().","code":""},{"path":"https://insightsengineering.github.io/tern/reference/h_pkparam_sort.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Sort pharmacokinetic data by PARAM variable — h_pkparam_sort","text":"pharmacokinetic data.frame sorted PARAM variable.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/h_pkparam_sort.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Sort pharmacokinetic data by PARAM variable — h_pkparam_sort","text":"","code":"library(dplyr)  adpp <- tern_ex_adpp %>% mutate(PKPARAM = factor(paste0(PARAM, \" (\", AVALU, \")\"))) pk_ordered_data <- h_pkparam_sort(adpp)"},{"path":"https://insightsengineering.github.io/tern/reference/h_ppmeans.html","id":null,"dir":"Reference","previous_headings":"","what":"Function to return the estimated means using predicted probabilities — h_ppmeans","title":"Function to return the estimated means using predicted probabilities — h_ppmeans","text":"arm level, predicted mean rate calculated using fitted model object, newdata set result stats::model.frame, reconstructed data original data, depending object formula (coming fit). confidence interval derived using conf_level parameter.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/h_ppmeans.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Function to return the estimated means using predicted probabilities — h_ppmeans","text":"","code":"h_ppmeans(obj, .df_row, arm, conf_level)"},{"path":"https://insightsengineering.github.io/tern/reference/h_ppmeans.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Function to return the estimated means using predicted probabilities — h_ppmeans","text":"obj (glm.fit) fitted model object used derive mean rate estimates treatment arm. .df_row (data.frame) dataset includes variables called .var variables. arm (string) group variable, covariate adjusted means multiple groups summarized. Specifically, first level arm variable taken reference group. conf_level (proportion) value used derive confidence interval rate.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/h_ppmeans.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Function to return the estimated means using predicted probabilities — h_ppmeans","text":"h_ppmeans() returns estimated means.","code":""},{"path":[]},{"path":[]},{"path":"https://insightsengineering.github.io/tern/reference/h_prop_diff.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Helper functions to calculate proportion difference — h_prop_diff","text":"","code":"prop_diff_wald(rsp, grp, conf_level = 0.95, correct = FALSE)  prop_diff_ha(rsp, grp, conf_level)  prop_diff_nc(rsp, grp, conf_level, correct = FALSE)  prop_diff_cmh(rsp, grp, strata, conf_level = 0.95)  prop_diff_strat_nc(   rsp,   grp,   strata,   weights_method = c(\"cmh\", \"wilson_h\"),   conf_level = 0.95,   correct = FALSE )"},{"path":"https://insightsengineering.github.io/tern/reference/h_prop_diff.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Helper functions to calculate proportion difference — h_prop_diff","text":"rsp (logical) vector indicating whether subject responder . grp (factor) vector assigning observations one two groups (e.g. reference treatment group). conf_level (proportion) confidence level interval. correct (flag) whether include continuity correction. information, see stats::prop.test(). strata (factor) variable one level per stratum length rsp. weights_method (string) weights method. Can either \"cmh\" \"heuristic\" directs way weights estimated.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/h_prop_diff.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Helper functions to calculate proportion difference — h_prop_diff","text":"named list elements diff (proportion difference) diff_ci (proportion difference confidence interval).","code":""},{"path":"https://insightsengineering.github.io/tern/reference/h_prop_diff.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Helper functions to calculate proportion difference — h_prop_diff","text":"prop_diff_wald(): Wald interval follows usual textbook definition single proportion confidence interval using normal approximation. possible include continuity correction Wald's interval. prop_diff_ha(): Anderson-Hauck confidence interval. prop_diff_nc(): Newcombe confidence interval. based Wilson score confidence interval single binomial proportion. prop_diff_cmh(): Calculates weighted difference. defined difference response rates experimental treatment group control treatment group, adjusted stratification factors applying Cochran-Mantel-Haenszel (CMH) weights. CMH chi-squared test, use stats::mantelhaen.test(). prop_diff_strat_nc(): Calculates stratified Newcombe confidence interval difference response rates experimental treatment group control treatment group, adjusted stratification factors. implementation follows closely one proposed Yan2010-jt;textualtern. Weights can estimated heuristic proposed prop_strat_wilson() CMH-derived weights (see prop_diff_cmh()).","code":""},{"path":"https://insightsengineering.github.io/tern/reference/h_prop_diff.html","id":"references","dir":"Reference","previous_headings":"","what":"References","title":"Helper functions to calculate proportion difference — h_prop_diff","text":"Yan2010-jttern","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/reference/h_prop_diff.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Helper functions to calculate proportion difference — h_prop_diff","text":"","code":"# Wald confidence interval set.seed(2) rsp <- sample(c(TRUE, FALSE), replace = TRUE, size = 20) grp <- factor(c(rep(\"A\", 10), rep(\"B\", 10)))  prop_diff_wald(rsp = rsp, grp = grp, conf_level = 0.95, correct = FALSE) #> $diff #> [1] 0 #>  #> $diff_ci #> [1] -0.4382613  0.4382613 #>   # Anderson-Hauck confidence interval ## \"Mid\" case: 3/4 respond in group A, 1/2 respond in group B. rsp <- c(TRUE, FALSE, FALSE, TRUE, TRUE, TRUE) grp <- factor(c(\"A\", \"B\", \"A\", \"B\", \"A\", \"A\"), levels = c(\"B\", \"A\"))  prop_diff_ha(rsp = rsp, grp = grp, conf_level = 0.90) #> $diff #> [1] 0.25 #>  #> $diff_ci #> [1] -0.9195011  1.0000000 #>   ## Edge case: Same proportion of response in A and B. rsp <- c(TRUE, FALSE, TRUE, FALSE) grp <- factor(c(\"A\", \"A\", \"B\", \"B\"), levels = c(\"A\", \"B\"))  prop_diff_ha(rsp = rsp, grp = grp, conf_level = 0.6) #> $diff #> [1] 0 #>  #> $diff_ci #> [1] -0.8451161  0.8451161 #>   # Newcombe confidence interval  set.seed(1) rsp <- c(   sample(c(TRUE, FALSE), size = 40, prob = c(3 / 4, 1 / 4), replace = TRUE),   sample(c(TRUE, FALSE), size = 40, prob = c(1 / 2, 1 / 2), replace = TRUE) ) grp <- factor(rep(c(\"A\", \"B\"), each = 40), levels = c(\"B\", \"A\")) table(rsp, grp) #>        grp #> rsp      B  A #>   FALSE 20 10 #>   TRUE  20 30  prop_diff_nc(rsp = rsp, grp = grp, conf_level = 0.9) #> $diff #> [1] 0.25 #>  #> $diff_ci #> [1] 0.07193388 0.40725819 #>   # Cochran-Mantel-Haenszel confidence interval  set.seed(2) rsp <- sample(c(TRUE, FALSE), 100, TRUE) grp <- sample(c(\"Placebo\", \"Treatment\"), 100, TRUE) grp <- factor(grp, levels = c(\"Placebo\", \"Treatment\")) strata_data <- data.frame(   \"f1\" = sample(c(\"a\", \"b\"), 100, TRUE),   \"f2\" = sample(c(\"x\", \"y\", \"z\"), 100, TRUE),   stringsAsFactors = TRUE )  prop_diff_cmh(   rsp = rsp, grp = grp, strata = interaction(strata_data),   conf_level = 0.90 ) #> $prop #>   Placebo Treatment  #> 0.5331117 0.3954251  #>  #> $prop_ci #> $prop_ci$Placebo #> [1] 0.4306536 0.6355698 #>  #> $prop_ci$Treatment #> [1] 0.2890735 0.5017768 #>  #>  #> $diff #> [1] -0.1376866 #>  #> $diff_ci #> [1] -0.285363076  0.009989872 #>  #> $weights #>       a.x       b.x       a.y       b.y       a.z       b.z  #> 0.1148388 0.2131696 0.1148388 0.2131696 0.1767914 0.1671918  #>  #> $n1 #> a.x b.x a.y b.y a.z b.z  #>   4  11   8  11  13  11  #>  #> $n2 #> a.x b.x a.y b.y a.z b.z  #>   8   9   4   9   6   6  #>   # Stratified Newcombe confidence interval  set.seed(2) data_set <- data.frame(   \"rsp\" = sample(c(TRUE, FALSE), 100, TRUE),   \"f1\" = sample(c(\"a\", \"b\"), 100, TRUE),   \"f2\" = sample(c(\"x\", \"y\", \"z\"), 100, TRUE),   \"grp\" = sample(c(\"Placebo\", \"Treatment\"), 100, TRUE),   stringsAsFactors = TRUE )  prop_diff_strat_nc(   rsp = data_set$rsp, grp = data_set$grp, strata = interaction(data_set[2:3]),   weights_method = \"cmh\",   conf_level = 0.90 ) #> $diff #> [1] -0.05777672 #>  #> $diff_ci #>      lower      upper  #> -0.2236537  0.1119331  #>   prop_diff_strat_nc(   rsp = data_set$rsp, grp = data_set$grp, strata = interaction(data_set[2:3]),   weights_method = \"wilson_h\",   conf_level = 0.90 ) #> $diff #> [1] -0.07771884 #>  #> $diff_ci #>      lower      upper  #> -0.2540844  0.1027720  #>"},{"path":"https://insightsengineering.github.io/tern/reference/h_prop_diff_test.html","id":null,"dir":"Reference","previous_headings":"","what":"Helper functions to test proportion differences — h_prop_diff_test","title":"Helper functions to test proportion differences — h_prop_diff_test","text":"Helper functions implement various tests difference two proportions.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/h_prop_diff_test.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Helper functions to test proportion differences — h_prop_diff_test","text":"","code":"prop_chisq(tbl)  prop_cmh(ary)  prop_schouten(tbl)  prop_fisher(tbl)"},{"path":"https://insightsengineering.github.io/tern/reference/h_prop_diff_test.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Helper functions to test proportion differences — h_prop_diff_test","text":"tbl (matrix) matrix two groups rows binary response (TRUE/FALSE) columns. ary (array, 3 dimensions) array two groups rows, binary response (TRUE/FALSE) columns, strata third dimension.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/h_prop_diff_test.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Helper functions to test proportion differences — h_prop_diff_test","text":"p-value.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/h_prop_diff_test.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Helper functions to test proportion differences — h_prop_diff_test","text":"prop_chisq(): Performs Chi-Squared test. Internally calls stats::prop.test(). prop_cmh(): Performs stratified Cochran-Mantel-Haenszel test. Internally calls stats::mantelhaen.test(). Note strata less two observations automatically discarded. prop_schouten(): Performs Chi-Squared test Schouten correction. prop_fisher(): Performs Fisher's exact test. Internally calls stats::fisher.test().","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/reference/h_proportions.html","id":null,"dir":"Reference","previous_headings":"","what":"Helper functions for calculating proportion confidence intervals — h_proportions","title":"Helper functions for calculating proportion confidence intervals — h_proportions","text":"Functions calculate different proportion confidence intervals use estimate_proportion().","code":""},{"path":"https://insightsengineering.github.io/tern/reference/h_proportions.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Helper functions for calculating proportion confidence intervals — h_proportions","text":"","code":"prop_wilson(rsp, conf_level, correct = FALSE)  prop_strat_wilson(   rsp,   strata,   weights = NULL,   conf_level = 0.95,   max_iterations = NULL,   correct = FALSE )  prop_clopper_pearson(rsp, conf_level)  prop_wald(rsp, conf_level, correct = FALSE)  prop_agresti_coull(rsp, conf_level)  prop_jeffreys(rsp, conf_level)"},{"path":"https://insightsengineering.github.io/tern/reference/h_proportions.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Helper functions for calculating proportion confidence intervals — h_proportions","text":"rsp (logical) vector indicating whether subject responder . conf_level (proportion) confidence level interval. correct (flag) whether apply continuity correction. strata (factor) variable one level per stratum length rsp. weights (numeric NULL) weights level strata. NULL, estimated using iterative algorithm proposed Yan2010-jt;textualtern minimizes weighted squared length confidence interval. max_iterations (count) maximum number iterations iterative procedure used find estimates optimal weights.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/h_proportions.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Helper functions for calculating proportion confidence intervals — h_proportions","text":"Confidence interval proportion.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/h_proportions.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Helper functions for calculating proportion confidence intervals — h_proportions","text":"prop_wilson(): Calculates Wilson interval calling stats::prop.test(). Also referred Wilson score interval. prop_strat_wilson(): Calculates stratified Wilson confidence interval unequal proportions described Yan2010-jt;textualtern prop_clopper_pearson(): Calculates Clopper-Pearson interval calling stats::binom.test(). Also referred exact method. prop_wald(): Calculates Wald interval following usual textbook definition single proportion confidence interval using normal approximation. prop_agresti_coull(): Calculates Agresti-Coull interval. Constructed (95% CI) adding two successes two failures data using Wald formula construct CI. prop_jeffreys(): Calculates Jeffreys interval, equal-tailed interval based non-informative Jeffreys prior binomial proportion.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/h_proportions.html","id":"references","dir":"Reference","previous_headings":"","what":"References","title":"Helper functions for calculating proportion confidence intervals — h_proportions","text":"Yan2010-jttern","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/reference/h_proportions.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Helper functions for calculating proportion confidence intervals — h_proportions","text":"","code":"rsp <- c(   TRUE, TRUE, TRUE, TRUE, TRUE,   FALSE, FALSE, FALSE, FALSE, FALSE ) prop_wilson(rsp, conf_level = 0.9) #> [1] 0.2692718 0.7307282  # Stratified Wilson confidence interval with unequal probabilities  set.seed(1) rsp <- sample(c(TRUE, FALSE), 100, TRUE) strata_data <- data.frame(   \"f1\" = sample(c(\"a\", \"b\"), 100, TRUE),   \"f2\" = sample(c(\"x\", \"y\", \"z\"), 100, TRUE),   stringsAsFactors = TRUE ) strata <- interaction(strata_data) n_strata <- ncol(table(rsp, strata)) # Number of strata  prop_strat_wilson(   rsp = rsp, strata = strata,   conf_level = 0.90 ) #> $conf_int #>     lower     upper  #> 0.4072891 0.5647887  #>  #> $weights #>       a.x       b.x       a.y       b.y       a.z       b.z  #> 0.2074199 0.1776464 0.1915610 0.1604678 0.1351096 0.1277952  #>   # Not automatic setting of weights prop_strat_wilson(   rsp = rsp, strata = strata,   weights = rep(1 / n_strata, n_strata),   conf_level = 0.90 ) #> $conf_int #>     lower     upper  #> 0.4190436 0.5789733  #>   prop_clopper_pearson(rsp, conf_level = .95) #> [1] 0.3886442 0.5919637  prop_wald(rsp, conf_level = 0.95) #> [1] 0.3920214 0.5879786 prop_wald(rsp, conf_level = 0.95, correct = TRUE) #> [1] 0.3870214 0.5929786  prop_agresti_coull(rsp, conf_level = 0.95) #> [1] 0.3942193 0.5865206  prop_jeffreys(rsp, conf_level = 0.95) #> [1] 0.3934779 0.5870917"},{"path":"https://insightsengineering.github.io/tern/reference/h_response_biomarkers_subgroups.html","id":null,"dir":"Reference","previous_headings":"","what":"Helper functions for tabulating biomarker effects on binary response by subgroup — h_response_biomarkers_subgroups","title":"Helper functions for tabulating biomarker effects on binary response by subgroup — h_response_biomarkers_subgroups","text":"Helper functions documented separately confuse user reading user-facing functions.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/h_response_biomarkers_subgroups.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Helper functions for tabulating biomarker effects on binary response by subgroup — h_response_biomarkers_subgroups","text":"","code":"h_rsp_to_logistic_variables(variables, biomarker)  h_logistic_mult_cont_df(variables, data, control = control_logistic())  h_tab_rsp_one_biomarker(df, vars, na_str = default_na_str(), .indent_mods = 0L)"},{"path":"https://insightsengineering.github.io/tern/reference/h_response_biomarkers_subgroups.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Helper functions for tabulating biomarker effects on binary response by subgroup — h_response_biomarkers_subgroups","text":"variables (named list string) list additional analysis variables. biomarker (string) name biomarker variable. data (data.frame) dataset containing variables summarize. control (named list) controls response definition confidence level produced control_logistic(). df (data.frame) results single biomarker, part returned extract_rsp_biomarkers() (needs couple columns added high-level function relative returned h_logistic_mult_cont_df(), see example). vars (character) names statistics reported among: n_tot: Total number patients per group. n_rsp: Total number responses per group. prop: Total response proportion per group. : Odds ratio. ci: Confidence interval odds ratio. pval: p-value effect. Note, statistics n_tot, ci required. na_str (string) string used replace NA empty values output. .indent_mods (named integer) indent modifiers labels. Defaults 0, corresponds unmodified default behavior. Can negative.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/h_response_biomarkers_subgroups.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Helper functions for tabulating biomarker effects on binary response by subgroup — h_response_biomarkers_subgroups","text":"h_rsp_to_logistic_variables() returns named list elements response, arm, covariates, strata. h_logistic_mult_cont_df() returns data.frame containing estimates statistics selected biomarkers. h_tab_rsp_one_biomarker() returns rtables table object given statistics arranged columns.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/h_response_biomarkers_subgroups.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Helper functions for tabulating biomarker effects on binary response by subgroup — h_response_biomarkers_subgroups","text":"h_rsp_to_logistic_variables(): helps converting \"response\" function variable list \"logistic regression\" variable list. reason currently inconsistency variable names accepted extract_rsp_subgroups() fit_logistic(). h_logistic_mult_cont_df(): prepares estimates number responses, patients overall response rate, well odds ratio estimates, confidence intervals p-values, multiple biomarkers given single data set. variables corresponds names variables found data, passed named list requires elements rsp biomarkers (vector continuous biomarker variables) optionally covariates strata. h_tab_rsp_one_biomarker(): Prepares single sub-table given df_sub containing results single biomarker.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/h_response_biomarkers_subgroups.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Helper functions for tabulating biomarker effects on binary response by subgroup — h_response_biomarkers_subgroups","text":"","code":"library(dplyr) library(forcats)  adrs <- tern_ex_adrs adrs_labels <- formatters::var_labels(adrs)  adrs_f <- adrs %>%   filter(PARAMCD == \"BESRSPI\") %>%   mutate(rsp = AVALC == \"CR\") formatters::var_labels(adrs_f) <- c(adrs_labels, \"Response\")  # This is how the variable list is converted internally. h_rsp_to_logistic_variables(   variables = list(     rsp = \"RSP\",     covariates = c(\"A\", \"B\"),     strata = \"D\"   ),   biomarker = \"AGE\" ) #> $response #> [1] \"RSP\" #>  #> $arm #> [1] \"AGE\" #>  #> $covariates #> [1] \"A\" \"B\" #>  #> $strata #> [1] \"D\" #>   # For a single population, estimate separately the effects # of two biomarkers. df <- h_logistic_mult_cont_df(   variables = list(     rsp = \"rsp\",     biomarkers = c(\"BMRKR1\", \"AGE\"),     covariates = \"SEX\"   ),   data = adrs_f ) df #>   biomarker              biomarker_label n_tot n_rsp prop        or       lcl #> 1    BMRKR1 Continuous Level Biomarker 1   200   164 0.82 0.9755036 0.8804862 #> 2       AGE                          Age   200   164 0.82 0.9952416 0.9462617 #>        ucl conf_level      pval     pval_label #> 1 1.080775       0.95 0.6352602 p-value (Wald) #> 2 1.046757       0.95 0.8530389 p-value (Wald)  # If the data set is empty, still the corresponding rows with missings are returned. h_coxreg_mult_cont_df(   variables = list(     rsp = \"rsp\",     biomarkers = c(\"BMRKR1\", \"AGE\"),     covariates = \"SEX\",     strata = \"STRATA1\"   ),   data = adrs_f[NULL, ] ) #>   biomarker              biomarker_label n_tot n_tot_events median hr lcl ucl #> 1    BMRKR1 Continuous Level Biomarker 1     0            0     NA NA  NA  NA #> 2       AGE                          Age     0            0     NA NA  NA  NA #>   conf_level pval     pval_label #> 1       0.95   NA p-value (Wald) #> 2       0.95   NA p-value (Wald)  # Starting from above `df`, zoom in on one biomarker and add required columns. df1 <- df[1, ] df1$subgroup <- \"All patients\" df1$row_type <- \"content\" df1$var <- \"ALL\" df1$var_label <- \"All patients\"  h_tab_rsp_one_biomarker(   df1,   vars = c(\"n_tot\", \"n_rsp\", \"prop\", \"or\", \"ci\", \"pval\") ) #>                Total n   Responders   Response (%)   Odds Ratio      95% CI      p-value (Wald) #> ——————————————————————————————————————————————————————————————————————————————————————————————— #> All patients     200        164          82.0%          0.98      (0.88, 1.08)       0.6353"},{"path":"https://insightsengineering.github.io/tern/reference/h_response_subgroups.html","id":null,"dir":"Reference","previous_headings":"","what":"Helper functions for tabulating binary response by subgroup — h_response_subgroups","title":"Helper functions for tabulating binary response by subgroup — h_response_subgroups","text":"Helper functions tabulate data frame statistics response rate odds ratio population subgroups.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/h_response_subgroups.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Helper functions for tabulating binary response by subgroup — h_response_subgroups","text":"","code":"h_proportion_df(rsp, arm)  h_proportion_subgroups_df(   variables,   data,   groups_lists = list(),   label_all = \"All Patients\" )  h_odds_ratio_df(rsp, arm, strata_data = NULL, conf_level = 0.95, method = NULL)  h_odds_ratio_subgroups_df(   variables,   data,   groups_lists = list(),   conf_level = 0.95,   method = NULL,   label_all = \"All Patients\" )"},{"path":"https://insightsengineering.github.io/tern/reference/h_response_subgroups.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Helper functions for tabulating binary response by subgroup — h_response_subgroups","text":"rsp (logical) vector indicating whether subject responder . arm (factor) treatment group variable. variables (named list string) list additional analysis variables. data (data.frame) dataset containing variables summarize. groups_lists (named list list) optionally contains subgroups variable list, specifies new group levels via names levels belong character vectors elements list. label_all (string) label total population analysis. strata_data (factor, data.frame, NULL) required stratified analysis performed. conf_level (proportion) confidence level interval. method (string NULL) specifies test used calculate p-value difference two proportions. options, see test_proportion_diff(). Default NULL test performed.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/h_response_subgroups.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Helper functions for tabulating binary response by subgroup — h_response_subgroups","text":"h_proportion_df() returns data.frame columns arm, n, n_rsp, prop. h_proportion_subgroups_df() returns data.frame columns arm, n, n_rsp, prop, subgroup, var, var_label, row_type. h_odds_ratio_df() returns data.frame columns arm, n_tot, , lcl, ucl, conf_level, optionally pval pval_label. h_odds_ratio_subgroups_df() returns data.frame columns arm, n_tot, , lcl, ucl, conf_level, subgroup, var, var_label, row_type.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/h_response_subgroups.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Helper functions for tabulating binary response by subgroup — h_response_subgroups","text":"Main functionality prepare data use layout-creating function.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/h_response_subgroups.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Helper functions for tabulating binary response by subgroup — h_response_subgroups","text":"h_proportion_df(): Helper prepare data frame binary responses arm. h_proportion_subgroups_df(): Summarizes proportion binary responses arm across subgroups data frame. variables corresponds names variables found data, passed named list requires elements rsp, arm optionally subgroups. groups_lists optionally specifies groupings subgroups variables. h_odds_ratio_df(): Helper prepare data frame estimates odds ratio treatment control arm. h_odds_ratio_subgroups_df(): Summarizes estimates odds ratio treatment control arm across subgroups data frame. variables corresponds names variables found data, passed named list requires elements rsp, arm optionally subgroups strata. groups_lists optionally specifies groupings subgroups variables.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/h_response_subgroups.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Helper functions for tabulating binary response by subgroup — h_response_subgroups","text":"","code":"library(dplyr) library(forcats)  adrs <- tern_ex_adrs adrs_labels <- formatters::var_labels(adrs)  adrs_f <- adrs %>%   filter(PARAMCD == \"BESRSPI\") %>%   filter(ARM %in% c(\"A: Drug X\", \"B: Placebo\")) %>%   droplevels() %>%   mutate(     # Reorder levels of factor to make the placebo group the reference arm.     ARM = fct_relevel(ARM, \"B: Placebo\"),     rsp = AVALC == \"CR\"   ) formatters::var_labels(adrs_f) <- c(adrs_labels, \"Response\")  h_proportion_df(   c(TRUE, FALSE, FALSE),   arm = factor(c(\"A\", \"A\", \"B\"), levels = c(\"A\", \"B\")) ) #>   arm n n_rsp prop #> 1   A 2     1  0.5 #> 2   B 1     0  0.0  h_proportion_subgroups_df(   variables = list(rsp = \"rsp\", arm = \"ARM\", subgroups = c(\"SEX\", \"BMRKR2\")),   data = adrs_f ) #>           arm  n n_rsp      prop     subgroup    var #> 1  B: Placebo 73    50 0.6849315 All Patients    ALL #> 2   A: Drug X 69    59 0.8550725 All Patients    ALL #> 3  B: Placebo 40    25 0.6250000            F    SEX #> 4   A: Drug X 38    36 0.9473684            F    SEX #> 5  B: Placebo 33    25 0.7575758            M    SEX #> 6   A: Drug X 31    23 0.7419355            M    SEX #> 7  B: Placebo 24    13 0.5416667          LOW BMRKR2 #> 8   A: Drug X 26    21 0.8076923          LOW BMRKR2 #> 9  B: Placebo 23    17 0.7391304       MEDIUM BMRKR2 #> 10  A: Drug X 26    23 0.8846154       MEDIUM BMRKR2 #> 11 B: Placebo 26    20 0.7692308         HIGH BMRKR2 #> 12  A: Drug X 17    15 0.8823529         HIGH BMRKR2 #>                       var_label row_type #> 1                  All Patients  content #> 2                  All Patients  content #> 3                           Sex analysis #> 4                           Sex analysis #> 5                           Sex analysis #> 6                           Sex analysis #> 7  Continuous Level Biomarker 2 analysis #> 8  Continuous Level Biomarker 2 analysis #> 9  Continuous Level Biomarker 2 analysis #> 10 Continuous Level Biomarker 2 analysis #> 11 Continuous Level Biomarker 2 analysis #> 12 Continuous Level Biomarker 2 analysis  # Define groupings for BMRKR2 levels. h_proportion_subgroups_df(   variables = list(rsp = \"rsp\", arm = \"ARM\", subgroups = c(\"SEX\", \"BMRKR2\")),   data = adrs_f,   groups_lists = list(     BMRKR2 = list(       \"low\" = \"LOW\",       \"low/medium\" = c(\"LOW\", \"MEDIUM\"),       \"low/medium/high\" = c(\"LOW\", \"MEDIUM\", \"HIGH\")     )   ) ) #>           arm  n n_rsp      prop        subgroup    var #> 1  B: Placebo 73    50 0.6849315    All Patients    ALL #> 2   A: Drug X 69    59 0.8550725    All Patients    ALL #> 3  B: Placebo 40    25 0.6250000               F    SEX #> 4   A: Drug X 38    36 0.9473684               F    SEX #> 5  B: Placebo 33    25 0.7575758               M    SEX #> 6   A: Drug X 31    23 0.7419355               M    SEX #> 7  B: Placebo 24    13 0.5416667             low BMRKR2 #> 8   A: Drug X 26    21 0.8076923             low BMRKR2 #> 9  B: Placebo 47    30 0.6382979      low/medium BMRKR2 #> 10  A: Drug X 52    44 0.8461538      low/medium BMRKR2 #> 11 B: Placebo 73    50 0.6849315 low/medium/high BMRKR2 #> 12  A: Drug X 69    59 0.8550725 low/medium/high BMRKR2 #>                       var_label row_type #> 1                  All Patients  content #> 2                  All Patients  content #> 3                           Sex analysis #> 4                           Sex analysis #> 5                           Sex analysis #> 6                           Sex analysis #> 7  Continuous Level Biomarker 2 analysis #> 8  Continuous Level Biomarker 2 analysis #> 9  Continuous Level Biomarker 2 analysis #> 10 Continuous Level Biomarker 2 analysis #> 11 Continuous Level Biomarker 2 analysis #> 12 Continuous Level Biomarker 2 analysis  # Unstratatified analysis. h_odds_ratio_df(   c(TRUE, FALSE, FALSE, TRUE),   arm = factor(c(\"A\", \"A\", \"B\", \"B\"), levels = c(\"A\", \"B\")) ) #>   arm n_tot or        lcl      ucl conf_level #> 1         4  1 0.01984252 50.39681       0.95  # Include p-value. h_odds_ratio_df(adrs_f$rsp, adrs_f$ARM, method = \"chisq\") #>   arm n_tot    or      lcl      ucl conf_level       pval #> 1       142 2.714 1.180449 6.239827       0.95 0.01643036 #>                   pval_label #> 1 p-value (Chi-Squared Test)  # Stratatified analysis. h_odds_ratio_df(   rsp = adrs_f$rsp,   arm = adrs_f$ARM,   strata_data = adrs_f[, c(\"STRATA1\", \"STRATA2\")],   method = \"cmh\" ) #>   arm n_tot       or      lcl      ucl conf_level       pval #> 1       142 2.665586 1.146149 6.199324       0.95 0.02019665 #>                               pval_label #> 1 p-value (Cochran-Mantel-Haenszel Test)  # Unstratified analysis. h_odds_ratio_subgroups_df(   variables = list(rsp = \"rsp\", arm = \"ARM\", subgroups = c(\"SEX\", \"BMRKR2\")),   data = adrs_f ) #>   arm n_tot        or       lcl       ucl conf_level     subgroup    var #> 1       142  2.714000 1.1804488  6.239827       0.95 All Patients    ALL #> 2        78 10.800000 2.2669576 51.452218       0.95            F    SEX #> 3        64  0.920000 0.2966470  2.853223       0.95            M    SEX #> 4        50  3.553846 1.0047370 12.570277       0.95          LOW BMRKR2 #> 5        49  2.705882 0.5911718 12.385232       0.95       MEDIUM BMRKR2 #> 6        43  2.250000 0.3970298 12.750933       0.95         HIGH BMRKR2 #>                      var_label row_type #> 1                 All Patients  content #> 2                          Sex analysis #> 3                          Sex analysis #> 4 Continuous Level Biomarker 2 analysis #> 5 Continuous Level Biomarker 2 analysis #> 6 Continuous Level Biomarker 2 analysis  # Stratified analysis. h_odds_ratio_subgroups_df(   variables = list(     rsp = \"rsp\",     arm = \"ARM\",     subgroups = c(\"SEX\", \"BMRKR2\"),     strata = c(\"STRATA1\", \"STRATA2\")   ),   data = adrs_f ) #>   arm n_tot        or       lcl       ucl conf_level     subgroup    var #> 1       142 2.6655860 1.1461490  6.199324       0.95 All Patients    ALL #> 2        78 7.7065093 1.5817529 37.547132       0.95            F    SEX #> 3        64 0.9572284 0.2990954  3.063525       0.95            M    SEX #> 4        50 3.0323726 0.8833232 10.409875       0.95          LOW BMRKR2 #> 5        49 2.1264996 0.4312008 10.486995       0.95       MEDIUM BMRKR2 #> 6        43 2.5134820 0.4351747 14.517370       0.95         HIGH BMRKR2 #>                      var_label row_type #> 1                 All Patients  content #> 2                          Sex analysis #> 3                          Sex analysis #> 4 Continuous Level Biomarker 2 analysis #> 5 Continuous Level Biomarker 2 analysis #> 6 Continuous Level Biomarker 2 analysis  # Define groupings of BMRKR2 levels. h_odds_ratio_subgroups_df(   variables = list(     rsp = \"rsp\",     arm = \"ARM\",     subgroups = c(\"SEX\", \"BMRKR2\")   ),   data = adrs_f,   groups_lists = list(     BMRKR2 = list(       \"low\" = \"LOW\",       \"low/medium\" = c(\"LOW\", \"MEDIUM\"),       \"low/medium/high\" = c(\"LOW\", \"MEDIUM\", \"HIGH\")     )   ) ) #>   arm n_tot        or      lcl       ucl conf_level        subgroup    var #> 1       142  2.714000 1.180449  6.239827       0.95    All Patients    ALL #> 2        78 10.800000 2.266958 51.452218       0.95               F    SEX #> 3        64  0.920000 0.296647  2.853223       0.95               M    SEX #> 4        50  3.553846 1.004737 12.570277       0.95             low BMRKR2 #> 5        99  3.116667 1.193409  8.139385       0.95      low/medium BMRKR2 #> 6       142  2.714000 1.180449  6.239827       0.95 low/medium/high BMRKR2 #>                      var_label row_type #> 1                 All Patients  content #> 2                          Sex analysis #> 3                          Sex analysis #> 4 Continuous Level Biomarker 2 analysis #> 5 Continuous Level Biomarker 2 analysis #> 6 Continuous Level Biomarker 2 analysis"},{"path":"https://insightsengineering.github.io/tern/reference/h_split_by_subgroups.html","id":null,"dir":"Reference","previous_headings":"","what":"Split data frame by subgroups — h_split_by_subgroups","title":"Split data frame by subgroups — h_split_by_subgroups","text":"Split data frame non-nested list subsets.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/h_split_by_subgroups.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Split data frame by subgroups — h_split_by_subgroups","text":"","code":"h_split_by_subgroups(data, subgroups, groups_lists = list())"},{"path":"https://insightsengineering.github.io/tern/reference/h_split_by_subgroups.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Split data frame by subgroups — h_split_by_subgroups","text":"data (data.frame) dataset split. subgroups (character) names factor variables data used create subsets. Unused levels present data dropped. Note order vector determines order downstream table. groups_lists (named list list) optionally contains subgroups variable list, specifies new group levels via names levels belong character vectors elements list.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/h_split_by_subgroups.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Split data frame by subgroups — h_split_by_subgroups","text":"list subset data (df) metadata subset (df_labels).","code":""},{"path":"https://insightsengineering.github.io/tern/reference/h_split_by_subgroups.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Split data frame by subgroups — h_split_by_subgroups","text":"Main functionality prepare data use forest plot layouts.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/h_split_by_subgroups.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Split data frame by subgroups — h_split_by_subgroups","text":"","code":"df <- data.frame(   x = c(1:5),   y = factor(c(\"A\", \"B\", \"A\", \"B\", \"A\"), levels = c(\"A\", \"B\", \"C\")),   z = factor(c(\"C\", \"C\", \"D\", \"D\", \"D\"), levels = c(\"D\", \"C\")) ) formatters::var_labels(df) <- paste(\"label for\", names(df))  h_split_by_subgroups(   data = df,   subgroups = c(\"y\", \"z\") ) #> $y.A #> $y.A$df #>   x y z #> 1 1 A C #> 2 3 A D #> 3 5 A D #>  #> $y.A$df_labels #>   subgroup var   var_label #> 1        A   y label for y #>  #>  #> $y.B #> $y.B$df #>   x y z #> 1 2 B C #> 2 4 B D #>  #> $y.B$df_labels #>   subgroup var   var_label #> 1        B   y label for y #>  #>  #> $z.D #> $z.D$df #>   x y z #> 1 3 A D #> 2 4 B D #> 3 5 A D #>  #> $z.D$df_labels #>   subgroup var   var_label #> 1        D   z label for z #>  #>  #> $z.C #> $z.C$df #>   x y z #> 1 1 A C #> 2 2 B C #>  #> $z.C$df_labels #>   subgroup var   var_label #> 1        C   z label for z #>  #>   h_split_by_subgroups(   data = df,   subgroups = c(\"y\", \"z\"),   groups_lists = list(     y = list(\"AB\" = c(\"A\", \"B\"), \"C\" = \"C\")   ) ) #> $y.AB #> $y.AB$df #>   x y z #> 1 1 A C #> 2 2 B C #> 3 3 A D #> 4 4 B D #> 5 5 A D #>  #> $y.AB$df_labels #>   subgroup var   var_label #> 1       AB   y label for y #>  #>  #> $z.D #> $z.D$df #>   x y z #> 1 3 A D #> 2 4 B D #> 3 5 A D #>  #> $z.D$df_labels #>   subgroup var   var_label #> 1        D   z label for z #>  #>  #> $z.C #> $z.C$df #>   x y z #> 1 1 A C #> 2 2 B C #>  #> $z.C$df_labels #>   subgroup var   var_label #> 1        C   z label for z #>  #>"},{"path":"https://insightsengineering.github.io/tern/reference/h_split_param.html","id":null,"dir":"Reference","previous_headings":"","what":"Split parameters — h_split_param","title":"Split parameters — h_split_param","text":"divides data vector param groups defined f based specified values. relevant rtables layers distribute parameters .stats ' .formats lists items corresponding specific analysis function.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/h_split_param.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Split parameters — h_split_param","text":"","code":"h_split_param(param, value, f)"},{"path":"https://insightsengineering.github.io/tern/reference/h_split_param.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Split parameters — h_split_param","text":"param (vector) parameter split. value (vector) value used split. f (list) reference make split.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/h_split_param.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Split parameters — h_split_param","text":"named list element names f, containing elements specified .stats.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/h_split_param.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Split parameters — h_split_param","text":"","code":"f <- list(   surv = c(\"pt_at_risk\", \"event_free_rate\", \"rate_se\", \"rate_ci\"),   surv_diff = c(\"rate_diff\", \"rate_diff_ci\", \"ztest_pval\") )  .stats <- c(\"pt_at_risk\", \"rate_diff\") h_split_param(.stats, .stats, f = f) #> $surv #> [1] \"pt_at_risk\" #>  #> $surv_diff #> [1] \"rate_diff\" #>   # $surv # [1] \"pt_at_risk\" # # $surv_diff # [1] \"rate_diff\"  .formats <- c(\"pt_at_risk\" = \"xx\", \"event_free_rate\" = \"xxx\") h_split_param(.formats, names(.formats), f = f) #> $surv #>      pt_at_risk event_free_rate  #>            \"xx\"           \"xxx\"  #>  #> $surv_diff #> NULL #>   # $surv # pt_at_risk event_free_rate # \"xx\"           \"xxx\" # # $surv_diff # NULL"},{"path":"https://insightsengineering.github.io/tern/reference/h_stack_by_baskets.html","id":null,"dir":"Reference","previous_headings":"","what":"Helper function to create a new SMQ variable in ADAE by stacking SMQ and/or CQ records. — h_stack_by_baskets","title":"Helper function to create a new SMQ variable in ADAE by stacking SMQ and/or CQ records. — h_stack_by_baskets","text":"Helper function create new SMQ variable ADAE consists adverse events belonging selected Standardized/Customized queries. new dataset contain records adverse events belonging selected baskets. Remember na_str must match needed pre-processing done df_explicit_na() desired output.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/h_stack_by_baskets.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Helper function to create a new SMQ variable in ADAE by stacking SMQ and/or CQ records. — h_stack_by_baskets","text":"","code":"h_stack_by_baskets(   df,   baskets = grep(\"^(SMQ|CQ).+NAM$\", names(df), value = TRUE),   smq_varlabel = \"Standardized MedDRA Query\",   keys = c(\"STUDYID\", \"USUBJID\", \"ASTDTM\", \"AEDECOD\", \"AESEQ\"),   aag_summary = NULL,   na_str = \"<Missing>\" )"},{"path":"https://insightsengineering.github.io/tern/reference/h_stack_by_baskets.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Helper function to create a new SMQ variable in ADAE by stacking SMQ and/or CQ records. — h_stack_by_baskets","text":"df (data.frame) data set containing analysis variables. baskets (character) variable names selected Standardized/Customized queries. smq_varlabel (string) label new variable created. keys (character) names key variables returned along new variable created. aag_summary (data.frame) containing SMQ baskets levels interest final SMQ variable. useful levels interest observed df dataset. two columns dataset named basket basket_name. na_str (string) string used replace NA empty values output.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/h_stack_by_baskets.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Helper function to create a new SMQ variable in ADAE by stacking SMQ and/or CQ records. — h_stack_by_baskets","text":"data.frame variables keys taken df new variable SMQ containing records belonging baskets selected via baskets argument.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/h_stack_by_baskets.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Helper function to create a new SMQ variable in ADAE by stacking SMQ and/or CQ records. — h_stack_by_baskets","text":"","code":"adae <- tern_ex_adae[1:20, ] %>% df_explicit_na() h_stack_by_baskets(df = adae) #> # A tibble: 8 × 6 #>   STUDYID USUBJID               ASTDTM              AEDECOD       AESEQ SMQ      #>   <fct>   <fct>                 <dttm>              <fct>         <int> <fct>    #> 1 AB12345 AB12345-BRA-11-id-8   2021-12-05 02:02:07 dcd D.2.1.5.3     2 D.2.1.5… #> 2 AB12345 AB12345-BRA-12-id-120 2020-02-05 01:42:29 dcd D.2.1.5.3     2 D.2.1.5… #> 3 AB12345 AB12345-BRA-1-id-171  2022-11-29 12:18:31 dcd C.1.1.1.3     2 C.1.1.1… #> 4 AB12345 AB12345-BRA-1-id-23   2020-07-10 07:32:49 dcd B.2.2.3.1     3 C.1.1.1… #> 5 AB12345 AB12345-BRA-1-id-59   2021-10-10 23:54:46 dcd C.1.1.1.3     4 C.1.1.1… #> 6 AB12345 AB12345-BRA-1-id-9    2021-06-01 14:39:09 dcd C.1.1.1.3     1 C.1.1.1… #> 7 AB12345 AB12345-BRA-11-id-8   2021-12-21 02:02:07 dcd C.1.1.1.3     3 C.1.1.1… #> 8 AB12345 AB12345-BRA-12-id-120 2020-10-01 01:42:29 dcd C.1.1.1.3     3 C.1.1.1…  aag <- data.frame(   NAMVAR = c(\"CQ01NAM\", \"CQ02NAM\", \"SMQ01NAM\", \"SMQ02NAM\"),   REFNAME = c(     \"D.2.1.5.3/A.1.1.1.1 aesi\", \"X.9.9.9.9/Y.8.8.8.8 aesi\",     \"C.1.1.1.3/B.2.2.3.1 aesi\", \"C.1.1.1.3/B.3.3.3.3 aesi\"   ),   SCOPE = c(\"\", \"\", \"BROAD\", \"BROAD\"),   stringsAsFactors = FALSE )  basket_name <- character(nrow(aag)) cq_pos <- grep(\"^(CQ).+NAM$\", aag$NAMVAR) smq_pos <- grep(\"^(SMQ).+NAM$\", aag$NAMVAR) basket_name[cq_pos] <- aag$REFNAME[cq_pos] basket_name[smq_pos] <- paste0(   aag$REFNAME[smq_pos], \"(\", aag$SCOPE[smq_pos], \")\" )  aag_summary <- data.frame(   basket = aag$NAMVAR,   basket_name = basket_name,   stringsAsFactors = TRUE )  result <- h_stack_by_baskets(df = adae, aag_summary = aag_summary) all(levels(aag_summary$basket_name) %in% levels(result$SMQ)) #> [1] TRUE  h_stack_by_baskets(   df = adae,   aag_summary = NULL,   keys = c(\"STUDYID\", \"USUBJID\", \"AEDECOD\", \"ARM\"),   baskets = \"SMQ01NAM\" ) #> # A tibble: 6 × 5 #>   STUDYID USUBJID               AEDECOD       ARM            SMQ                 #>   <fct>   <fct>                 <fct>         <fct>          <fct>               #> 1 AB12345 AB12345-BRA-1-id-171  dcd C.1.1.1.3 B: Placebo     C.1.1.1.3/B.2.2.3.… #> 2 AB12345 AB12345-BRA-1-id-23   dcd B.2.2.3.1 A: Drug X      C.1.1.1.3/B.2.2.3.… #> 3 AB12345 AB12345-BRA-1-id-59   dcd C.1.1.1.3 A: Drug X      C.1.1.1.3/B.2.2.3.… #> 4 AB12345 AB12345-BRA-1-id-9    dcd C.1.1.1.3 C: Combination C.1.1.1.3/B.2.2.3.… #> 5 AB12345 AB12345-BRA-11-id-8   dcd C.1.1.1.3 A: Drug X      C.1.1.1.3/B.2.2.3.… #> 6 AB12345 AB12345-BRA-12-id-120 dcd C.1.1.1.3 A: Drug X      C.1.1.1.3/B.2.2.3.…"},{"path":"https://insightsengineering.github.io/tern/reference/h_step.html","id":null,"dir":"Reference","previous_headings":"","what":"Helper functions for subgroup treatment effect pattern (STEP) calculations — h_step","title":"Helper functions for subgroup treatment effect pattern (STEP) calculations — h_step","text":"Helper functions used internally STEP calculations.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/h_step.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Helper functions for subgroup treatment effect pattern (STEP) calculations — h_step","text":"","code":"h_step_window(x, control = control_step())  h_step_trt_effect(data, model, variables, x)  h_step_survival_formula(variables, control = control_step())  h_step_survival_est(   formula,   data,   variables,   x,   subset = rep(TRUE, nrow(data)),   control = control_coxph() )  h_step_rsp_formula(variables, control = c(control_step(), control_logistic()))  h_step_rsp_est(   formula,   data,   variables,   x,   subset = rep(TRUE, nrow(data)),   control = control_logistic() )"},{"path":"https://insightsengineering.github.io/tern/reference/h_step.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Helper functions for subgroup treatment effect pattern (STEP) calculations — h_step","text":"x (numeric) biomarker value(s) use (without NA). control (named list) output control_step(). data (data.frame) dataset containing variables summarize. model (coxph glm) regression model object. variables (named list string) list additional analysis variables. formula (formula) regression model formula. subset (logical) subset vector.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/h_step.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Helper functions for subgroup treatment effect pattern (STEP) calculations — h_step","text":"h_step_window() returns list containing window-selection matrix sel interval information matrix interval. h_step_trt_effect() returns vector elements est se. h_step_survival_formula() returns model formula. h_step_survival_est() returns matrix number observations n, events, log hazard ratio estimates loghr, standard error se, Wald confidence interval bounds ci_lower ci_upper. One row included biomarker value x. h_step_rsp_formula() returns model formula. h_step_rsp_est() returns matrix number observations n, log odds ratio estimates logor, standard error se, Wald confidence interval bounds ci_lower ci_upper. One row included biomarker value x.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/h_step.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Helper functions for subgroup treatment effect pattern (STEP) calculations — h_step","text":"h_step_window(): Creates windows STEP, based control settings provided. h_step_trt_effect(): Calculates estimated treatment effect estimate linear predictor scale corresponding standard error STEP model fitted data given variables specification, single biomarker value x. works coxph glm models, .e. calculating log hazard ratio log odds ratio estimates. h_step_survival_formula(): Builds model formula used survival STEP calculations. h_step_survival_est(): Estimates model formula built based variables data given subset control parameters Cox regression. h_step_rsp_formula(): Builds model formula used response STEP calculations. h_step_rsp_est(): Estimates model formula built based variables data given subset control parameters logistic regression.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/h_survival_biomarkers_subgroups.html","id":null,"dir":"Reference","previous_headings":"","what":"Helper functions for tabulating biomarker effects on survival by subgroup — h_survival_biomarkers_subgroups","title":"Helper functions for tabulating biomarker effects on survival by subgroup — h_survival_biomarkers_subgroups","text":"Helper functions documented separately confuse user reading user-facing functions.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/h_survival_biomarkers_subgroups.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Helper functions for tabulating biomarker effects on survival by subgroup — h_survival_biomarkers_subgroups","text":"","code":"h_surv_to_coxreg_variables(variables, biomarker)  h_coxreg_mult_cont_df(variables, data, control = control_coxreg())  h_tab_surv_one_biomarker(   df,   vars,   time_unit,   na_str = default_na_str(),   .indent_mods = 0L,   ... )"},{"path":"https://insightsengineering.github.io/tern/reference/h_survival_biomarkers_subgroups.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Helper functions for tabulating biomarker effects on survival by subgroup — h_survival_biomarkers_subgroups","text":"variables (named list string) list additional analysis variables. biomarker (string) name biomarker variable. data (data.frame) dataset containing variables summarize. control (list) list parameters returned helper function control_coxreg(). df (data.frame) results single biomarker, part returned extract_survival_biomarkers() (needs couple columns added high-level function relative returned h_coxreg_mult_cont_df(), see example). vars (character) names statistics reported among: n_tot_events: Total number events per group. n_tot: Total number observations per group. median: Median survival time. hr: Hazard ratio. ci: Confidence interval hazard ratio. pval: p-value effect. Note, one statistics n_tot n_tot_events, well hr ci required. time_unit (string) label unit median survival time. Default NULL skips displaying unit. na_str (string) string used replace NA empty values output. .indent_mods (named integer) indent modifiers labels. Defaults 0, corresponds unmodified default behavior. Can negative. ... additional arguments lower level functions.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/h_survival_biomarkers_subgroups.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Helper functions for tabulating biomarker effects on survival by subgroup — h_survival_biomarkers_subgroups","text":"h_surv_to_coxreg_variables() returns named list elements time, event, arm, covariates, strata. h_coxreg_mult_cont_df() returns data.frame containing estimates statistics selected biomarkers. h_tab_surv_one_biomarker() returns rtables table object given statistics arranged columns.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/h_survival_biomarkers_subgroups.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Helper functions for tabulating biomarker effects on survival by subgroup — h_survival_biomarkers_subgroups","text":"h_surv_to_coxreg_variables(): Helps converting \"survival\" function variable list \"Cox regression\" variable list. reason currently inconsistency variable names accepted extract_survival_subgroups() fit_coxreg_multivar(). h_coxreg_mult_cont_df(): Prepares estimates number events, patients median survival times, well hazard ratio estimates, confidence intervals p-values, multiple biomarkers given single data set. variables corresponds names variables found data, passed named list requires elements tte, is_event, biomarkers (vector continuous biomarker variables) optionally subgroups strata. h_tab_surv_one_biomarker(): Prepares single sub-table given df_sub containing results single biomarker.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/h_survival_biomarkers_subgroups.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Helper functions for tabulating biomarker effects on survival by subgroup — h_survival_biomarkers_subgroups","text":"","code":"library(dplyr) library(forcats)  adtte <- tern_ex_adtte  # Save variable labels before data processing steps. adtte_labels <- formatters::var_labels(adtte, fill = FALSE)  adtte_f <- adtte %>%   filter(PARAMCD == \"OS\") %>%   mutate(     AVALU = as.character(AVALU),     is_event = CNSR == 0   ) labels <- c(\"AVALU\" = adtte_labels[[\"AVALU\"]], \"is_event\" = \"Event Flag\") formatters::var_labels(adtte_f)[names(labels)] <- labels  # This is how the variable list is converted internally. h_surv_to_coxreg_variables(   variables = list(     tte = \"AVAL\",     is_event = \"EVNT\",     covariates = c(\"A\", \"B\"),     strata = \"D\"   ),   biomarker = \"AGE\" ) #> $time #> [1] \"AVAL\" #>  #> $event #> [1] \"EVNT\" #>  #> $arm #> [1] \"AGE\" #>  #> $covariates #> [1] \"A\" \"B\" #>  #> $strata #> [1] \"D\" #>   # For a single population, estimate separately the effects # of two biomarkers. df <- h_coxreg_mult_cont_df(   variables = list(     tte = \"AVAL\",     is_event = \"is_event\",     biomarkers = c(\"BMRKR1\", \"AGE\"),     covariates = \"SEX\",     strata = c(\"STRATA1\", \"STRATA2\")   ),   data = adtte_f ) df #>   biomarker              biomarker_label n_tot n_tot_events   median       hr #> 1    BMRKR1 Continuous Level Biomarker 1   200          141 753.5176 1.000189 #> 2       AGE                          Age   200          141 753.5176 1.008267 #>         lcl      ucl conf_level      pval     pval_label #> 1 0.9511092 1.051802       0.95 0.9941244 p-value (Wald) #> 2 0.9845155 1.032591       0.95 0.4984743 p-value (Wald)  # If the data set is empty, still the corresponding rows with missings are returned. h_coxreg_mult_cont_df(   variables = list(     tte = \"AVAL\",     is_event = \"is_event\",     biomarkers = c(\"BMRKR1\", \"AGE\"),     covariates = \"REGION1\",     strata = c(\"STRATA1\", \"STRATA2\")   ),   data = adtte_f[NULL, ] ) #>   biomarker              biomarker_label n_tot n_tot_events median hr lcl ucl #> 1    BMRKR1 Continuous Level Biomarker 1     0            0     NA NA  NA  NA #> 2       AGE                          Age     0            0     NA NA  NA  NA #>   conf_level pval     pval_label #> 1       0.95   NA p-value (Wald) #> 2       0.95   NA p-value (Wald)  # Starting from above `df`, zoom in on one biomarker and add required columns. df1 <- df[1, ] df1$subgroup <- \"All patients\" df1$row_type <- \"content\" df1$var <- \"ALL\" df1$var_label <- \"All patients\" h_tab_surv_one_biomarker(   df1,   vars = c(\"n_tot\", \"n_tot_events\", \"median\", \"hr\", \"ci\", \"pval\"),   time_unit = \"days\" ) #>                Total n   Total Events   Median (days)   Hazard Ratio   95% Wald CI    p-value (Wald) #> ———————————————————————————————————————————————————————————————————————————————————————————————————— #> All patients     200         141            753.5           1.00       (0.95, 1.05)       0.9941"},{"path":"https://insightsengineering.github.io/tern/reference/h_survival_duration_subgroups.html","id":null,"dir":"Reference","previous_headings":"","what":"Helper functions for tabulating survival duration by subgroup — h_survival_duration_subgroups","title":"Helper functions for tabulating survival duration by subgroup — h_survival_duration_subgroups","text":"Helper functions tabulate data frame statistics median survival time hazard ratio population subgroups.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/h_survival_duration_subgroups.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Helper functions for tabulating survival duration by subgroup — h_survival_duration_subgroups","text":"","code":"h_survtime_df(tte, is_event, arm)  h_survtime_subgroups_df(   variables,   data,   groups_lists = list(),   label_all = \"All Patients\" )  h_coxph_df(tte, is_event, arm, strata_data = NULL, control = control_coxph())  h_coxph_subgroups_df(   variables,   data,   groups_lists = list(),   control = control_coxph(),   label_all = \"All Patients\" )"},{"path":"https://insightsengineering.github.io/tern/reference/h_survival_duration_subgroups.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Helper functions for tabulating survival duration by subgroup — h_survival_duration_subgroups","text":"tte (numeric) vector time--event duration values. is_event (flag)TRUE event, FALSE time event censored. arm (factor) treatment group variable. variables (named list string) list additional analysis variables. data (data.frame) dataset containing variables summarize. groups_lists (named list list) optionally contains subgroups variable list, specifies new group levels via names levels belong character vectors elements list. label_all (string) label total population analysis. strata_data (factor, data.frame, NULL) required stratified analysis performed. control (list) parameters comparison details, specified using helper function control_coxph(). possible parameter options : pval_method (string) p-value method testing null hypothesis hazard ratio = 1. Default method \"log-rank\" comes survival::survdiff(), can also set \"wald\" \"likelihood\" (survival::coxph()). ties (string) specifying method tie handling. Default \"efron\", can also set \"breslow\" \"exact\". See survival::coxph(). conf_level (proportion) confidence level interval HR.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/h_survival_duration_subgroups.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Helper functions for tabulating survival duration by subgroup — h_survival_duration_subgroups","text":"h_survtime_df() returns data.frame columns arm, n, n_events, median. h_survtime_subgroups_df() returns data.frame columns arm, n, n_events, median, subgroup, var, var_label, row_type. h_coxph_df() returns data.frame columns arm, n_tot, n_tot_events, hr, lcl, ucl, conf_level, pval pval_label. h_coxph_subgroups_df() returns data.frame columns arm, n_tot, n_tot_events, hr, lcl, ucl, conf_level, pval, pval_label, subgroup, var, var_label, row_type.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/h_survival_duration_subgroups.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Helper functions for tabulating survival duration by subgroup — h_survival_duration_subgroups","text":"Main functionality prepare data use layout-creating function.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/h_survival_duration_subgroups.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Helper functions for tabulating survival duration by subgroup — h_survival_duration_subgroups","text":"h_survtime_df(): Helper prepare data frame median survival times arm. h_survtime_subgroups_df(): Summarizes median survival times arm across subgroups data frame. variables corresponds names variables found data, passed named list requires elements tte, is_event, arm optionally subgroups. groups_lists optionally specifies groupings subgroups variables. h_coxph_df(): Helper prepare data frame estimates treatment hazard ratio. h_coxph_subgroups_df(): Summarizes estimates treatment hazard ratio across subgroups data frame. variables corresponds names variables found data, passed named list requires elements tte, is_event, arm optionally subgroups strata. groups_lists optionally specifies groupings subgroups variables.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/h_survival_duration_subgroups.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Helper functions for tabulating survival duration by subgroup — h_survival_duration_subgroups","text":"","code":"library(dplyr) library(forcats)  adtte <- tern_ex_adtte  # Save variable labels before data processing steps. adtte_labels <- formatters::var_labels(adtte)  adtte_f <- adtte %>%   filter(     PARAMCD == \"OS\",     ARM %in% c(\"B: Placebo\", \"A: Drug X\"),     SEX %in% c(\"M\", \"F\")   ) %>%   mutate(     # Reorder levels of ARM to display reference arm before treatment arm.     ARM = droplevels(fct_relevel(ARM, \"B: Placebo\")),     SEX = droplevels(SEX),     is_event = CNSR == 0   ) labels <- c(\"ARM\" = adtte_labels[[\"ARM\"]], \"SEX\" = adtte_labels[[\"SEX\"]], \"is_event\" = \"Event Flag\") formatters::var_labels(adtte_f)[names(labels)] <- labels  # Extract median survival time for one group. h_survtime_df(   tte = adtte_f$AVAL,   is_event = adtte_f$is_event,   arm = adtte_f$ARM ) #>          arm  n n_events   median #> 1 B: Placebo 73       57 727.8043 #> 2  A: Drug X 69       44 974.6402  # Extract median survival time for multiple groups. h_survtime_subgroups_df(   variables = list(     tte = \"AVAL\",     is_event = \"is_event\",     arm = \"ARM\",     subgroups = c(\"SEX\", \"BMRKR2\")   ),   data = adtte_f ) #>           arm  n n_events    median     subgroup    var #> 1  B: Placebo 73       57  727.8043 All Patients    ALL #> 2   A: Drug X 69       44  974.6402 All Patients    ALL #> 3  B: Placebo 40       31  599.1772            F    SEX #> 4   A: Drug X 38       24 1016.2982            F    SEX #> 5  B: Placebo 33       26  888.4916            M    SEX #> 6   A: Drug X 31       20  974.6402            M    SEX #> 7  B: Placebo 24       21  735.4722          LOW BMRKR2 #> 8   A: Drug X 26       15  974.6402          LOW BMRKR2 #> 9  B: Placebo 23       14  731.8352       MEDIUM BMRKR2 #> 10  A: Drug X 26       17  964.2197       MEDIUM BMRKR2 #> 11 B: Placebo 26       22  654.8245         HIGH BMRKR2 #> 12  A: Drug X 17       12 1016.2982         HIGH BMRKR2 #>                       var_label row_type #> 1                  All Patients  content #> 2                  All Patients  content #> 3                           Sex analysis #> 4                           Sex analysis #> 5                           Sex analysis #> 6                           Sex analysis #> 7  Continuous Level Biomarker 2 analysis #> 8  Continuous Level Biomarker 2 analysis #> 9  Continuous Level Biomarker 2 analysis #> 10 Continuous Level Biomarker 2 analysis #> 11 Continuous Level Biomarker 2 analysis #> 12 Continuous Level Biomarker 2 analysis  # Define groupings for BMRKR2 levels. h_survtime_subgroups_df(   variables = list(     tte = \"AVAL\",     is_event = \"is_event\",     arm = \"ARM\",     subgroups = c(\"SEX\", \"BMRKR2\")   ),   data = adtte_f,   groups_lists = list(     BMRKR2 = list(       \"low\" = \"LOW\",       \"low/medium\" = c(\"LOW\", \"MEDIUM\"),       \"low/medium/high\" = c(\"LOW\", \"MEDIUM\", \"HIGH\")     )   ) ) #>           arm  n n_events    median        subgroup    var #> 1  B: Placebo 73       57  727.8043    All Patients    ALL #> 2   A: Drug X 69       44  974.6402    All Patients    ALL #> 3  B: Placebo 40       31  599.1772               F    SEX #> 4   A: Drug X 38       24 1016.2982               F    SEX #> 5  B: Placebo 33       26  888.4916               M    SEX #> 6   A: Drug X 31       20  974.6402               M    SEX #> 7  B: Placebo 24       21  735.4722             low BMRKR2 #> 8   A: Drug X 26       15  974.6402             low BMRKR2 #> 9  B: Placebo 47       35  735.4722      low/medium BMRKR2 #> 10  A: Drug X 52       32  964.2197      low/medium BMRKR2 #> 11 B: Placebo 73       57  727.8043 low/medium/high BMRKR2 #> 12  A: Drug X 69       44  974.6402 low/medium/high BMRKR2 #>                       var_label row_type #> 1                  All Patients  content #> 2                  All Patients  content #> 3                           Sex analysis #> 4                           Sex analysis #> 5                           Sex analysis #> 6                           Sex analysis #> 7  Continuous Level Biomarker 2 analysis #> 8  Continuous Level Biomarker 2 analysis #> 9  Continuous Level Biomarker 2 analysis #> 10 Continuous Level Biomarker 2 analysis #> 11 Continuous Level Biomarker 2 analysis #> 12 Continuous Level Biomarker 2 analysis  # Extract hazard ratio for one group. h_coxph_df(adtte_f$AVAL, adtte_f$is_event, adtte_f$ARM) #>   arm n_tot n_tot_events        hr       lcl      ucl conf_level       pval #> 1       142          101 0.7108557 0.4779138 1.057337       0.95 0.09049511 #>           pval_label #> 1 p-value (log-rank)  # Extract hazard ratio for one group with stratification factor. h_coxph_df(adtte_f$AVAL, adtte_f$is_event, adtte_f$ARM, strata_data = adtte_f$STRATA1) #>   arm n_tot n_tot_events        hr       lcl     ucl conf_level       pval #> 1       142          101 0.6646586 0.4399495 1.00414       0.95 0.05089188 #>           pval_label #> 1 p-value (log-rank)  # Extract hazard ratio for multiple groups. h_coxph_subgroups_df(   variables = list(     tte = \"AVAL\",     is_event = \"is_event\",     arm = \"ARM\",     subgroups = c(\"SEX\", \"BMRKR2\")   ),   data = adtte_f ) #>   arm n_tot n_tot_events        hr       lcl       ucl conf_level       pval #> 1       142          101 0.7108557 0.4779138 1.0573368       0.95 0.09049511 #> 2        78           55 0.5595391 0.3246658 0.9643271       0.95 0.03411759 #> 3        64           46 0.9102874 0.5032732 1.6464678       0.95 0.75582028 #> 4        50           36 0.7617717 0.3854349 1.5055617       0.95 0.43236030 #> 5        49           31 0.7651261 0.3641277 1.6077269       0.95 0.47860004 #> 6        43           34 0.6662356 0.3257413 1.3626456       0.95 0.26285846 #>           pval_label     subgroup    var                    var_label row_type #> 1 p-value (log-rank) All Patients    ALL                 All Patients  content #> 2 p-value (log-rank)            F    SEX                          Sex analysis #> 3 p-value (log-rank)            M    SEX                          Sex analysis #> 4 p-value (log-rank)          LOW BMRKR2 Continuous Level Biomarker 2 analysis #> 5 p-value (log-rank)       MEDIUM BMRKR2 Continuous Level Biomarker 2 analysis #> 6 p-value (log-rank)         HIGH BMRKR2 Continuous Level Biomarker 2 analysis  # Define groupings of BMRKR2 levels. h_coxph_subgroups_df(   variables = list(     tte = \"AVAL\",     is_event = \"is_event\",     arm = \"ARM\",     subgroups = c(\"SEX\", \"BMRKR2\")   ),   data = adtte_f,   groups_lists = list(     BMRKR2 = list(       \"low\" = \"LOW\",       \"low/medium\" = c(\"LOW\", \"MEDIUM\"),       \"low/medium/high\" = c(\"LOW\", \"MEDIUM\", \"HIGH\")     )   ) ) #>   arm n_tot n_tot_events        hr       lcl       ucl conf_level       pval #> 1       142          101 0.7108557 0.4779138 1.0573368       0.95 0.09049511 #> 2        78           55 0.5595391 0.3246658 0.9643271       0.95 0.03411759 #> 3        64           46 0.9102874 0.5032732 1.6464678       0.95 0.75582028 #> 4        50           36 0.7617717 0.3854349 1.5055617       0.95 0.43236030 #> 5        99           67 0.7472958 0.4600419 1.2139136       0.95 0.23764314 #> 6       142          101 0.7108557 0.4779138 1.0573368       0.95 0.09049511 #>           pval_label        subgroup    var                    var_label #> 1 p-value (log-rank)    All Patients    ALL                 All Patients #> 2 p-value (log-rank)               F    SEX                          Sex #> 3 p-value (log-rank)               M    SEX                          Sex #> 4 p-value (log-rank)             low BMRKR2 Continuous Level Biomarker 2 #> 5 p-value (log-rank)      low/medium BMRKR2 Continuous Level Biomarker 2 #> 6 p-value (log-rank) low/medium/high BMRKR2 Continuous Level Biomarker 2 #>   row_type #> 1  content #> 2 analysis #> 3 analysis #> 4 analysis #> 5 analysis #> 6 analysis  # Extract hazard ratio for multiple groups with stratification factors. h_coxph_subgroups_df(   variables = list(     tte = \"AVAL\",     is_event = \"is_event\",     arm = \"ARM\",     subgroups = c(\"SEX\", \"BMRKR2\"),     strata = c(\"STRATA1\", \"STRATA2\")   ),   data = adtte_f ) #>   arm n_tot n_tot_events        hr       lcl       ucl conf_level       pval #> 1       142          101 0.6126133 0.3913507 0.9589739       0.95 0.03086774 #> 2        78           55 0.3934024 0.2027682 0.7632630       0.95 0.00469167 #> 3        64           46 0.9501768 0.4730073 1.9087145       0.95 0.88580522 #> 4        50           36 0.7378635 0.3140465 1.7336363       0.95 0.48408079 #> 5        49           31 0.9408062 0.4172095 2.1215148       0.95 0.88305965 #> 6        43           34 0.5125617 0.2125140 1.2362459       0.95 0.13124382 #>           pval_label     subgroup    var                    var_label row_type #> 1 p-value (log-rank) All Patients    ALL                 All Patients  content #> 2 p-value (log-rank)            F    SEX                          Sex analysis #> 3 p-value (log-rank)            M    SEX                          Sex analysis #> 4 p-value (log-rank)          LOW BMRKR2 Continuous Level Biomarker 2 analysis #> 5 p-value (log-rank)       MEDIUM BMRKR2 Continuous Level Biomarker 2 analysis #> 6 p-value (log-rank)         HIGH BMRKR2 Continuous Level Biomarker 2 analysis"},{"path":"https://insightsengineering.github.io/tern/reference/h_tab_one_biomarker.html","id":null,"dir":"Reference","previous_headings":"","what":"Helper function for tabulation of a single biomarker result — h_tab_one_biomarker","title":"Helper function for tabulation of a single biomarker result — h_tab_one_biomarker","text":"Please see h_tab_surv_one_biomarker() h_tab_rsp_one_biomarker(), use function examples. function wrapper rtables::summarize_row_groups().","code":""},{"path":"https://insightsengineering.github.io/tern/reference/h_tab_one_biomarker.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Helper function for tabulation of a single biomarker result — h_tab_one_biomarker","text":"","code":"h_tab_one_biomarker(   df,   afuns,   colvars,   na_str = default_na_str(),   .indent_mods = 0L,   ... )"},{"path":"https://insightsengineering.github.io/tern/reference/h_tab_one_biomarker.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Helper function for tabulation of a single biomarker result — h_tab_one_biomarker","text":"df (data.frame) results single biomarker. afuns (named list function) analysis functions. colvars (named list) named list elements vars (variables tabulate) labels (labels). na_str (string) string used replace NA empty values output. .indent_mods (named integer) indent modifiers labels. Defaults 0, corresponds unmodified default behavior. Can negative. ... additional arguments lower level functions.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/h_tab_one_biomarker.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Helper function for tabulation of a single biomarker result — h_tab_one_biomarker","text":"rtables table object statistics columns.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/h_tbl_coxph_pairwise.html","id":null,"dir":"Reference","previous_headings":"","what":"Helper function for generating a pairwise Cox-PH table — h_tbl_coxph_pairwise","title":"Helper function for generating a pairwise Cox-PH table — h_tbl_coxph_pairwise","text":"Create data.frame pairwise stratified unstratified Cox-PH analysis results.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/h_tbl_coxph_pairwise.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Helper function for generating a pairwise Cox-PH table — h_tbl_coxph_pairwise","text":"","code":"h_tbl_coxph_pairwise(   df,   variables,   ref_group_coxph = NULL,   control_coxph_pw = control_coxph(),   annot_coxph_ref_lbls = FALSE )"},{"path":"https://insightsengineering.github.io/tern/reference/h_tbl_coxph_pairwise.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Helper function for generating a pairwise Cox-PH table — h_tbl_coxph_pairwise","text":"df (data.frame) data set containing analysis variables. variables (named list) variable names. Details : tte (numeric) variable indicating time--event duration values. is_event (logical) event variable. TRUE event, FALSE time event censored. arm (factor) treatment group variable. strata (character NULL) variable names indicating stratification factors. ref_group_coxph (string NULL) level arm variable use reference group calculations annot_coxph table. NULL (default), uses first level arm variable. control_coxph_pw (list) parameters comparison details, specified using helper function control_coxph(). possible parameter options : pval_method (string) p-value method testing hazard ratio = 1. Default method \"log-rank\", can also set \"wald\" \"likelihood\". ties (string) method tie handling. Default \"efron\", can also set \"breslow\" \"exact\". See survival::coxph() conf_level (proportion) confidence level interval HR. annot_coxph_ref_lbls (flag) whether reference group explicitly printed labels annot_coxph table. FALSE (default), comparison groups printed annot_coxph table labels.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/h_tbl_coxph_pairwise.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Helper function for generating a pairwise Cox-PH table — h_tbl_coxph_pairwise","text":"data.frame containing statistics HR, XX% CI (XX taken control_coxph_pw), p-value (log-rank).","code":""},{"path":"https://insightsengineering.github.io/tern/reference/h_tbl_coxph_pairwise.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Helper function for generating a pairwise Cox-PH table — h_tbl_coxph_pairwise","text":"","code":"library(dplyr)  adtte <- tern_ex_adtte %>%   filter(PARAMCD == \"OS\") %>%   mutate(is_event = CNSR == 0)  h_tbl_coxph_pairwise(   df = adtte,   variables = list(tte = \"AVAL\", is_event = \"is_event\", arm = \"ARM\"),   control_coxph_pw = control_coxph(conf_level = 0.9) ) #>                  HR       90% CI p-value (log-rank) #> B: Placebo     1.41 (1.01, 1.96)             0.0905 #> C: Combination 1.81 (1.24, 2.64)             0.0086"},{"path":"https://insightsengineering.github.io/tern/reference/h_tbl_median_surv.html","id":null,"dir":"Reference","previous_headings":"","what":"Helper function for survival estimations — h_tbl_median_surv","title":"Helper function for survival estimations — h_tbl_median_surv","text":"Transform survival fit table groups rows characterized N, median confidence interval.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/h_tbl_median_surv.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Helper function for survival estimations — h_tbl_median_surv","text":"","code":"h_tbl_median_surv(fit_km, armval = \"All\")"},{"path":"https://insightsengineering.github.io/tern/reference/h_tbl_median_surv.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Helper function for survival estimations — h_tbl_median_surv","text":"fit_km (survfit) result survival::survfit(). armval (string) used strata name treatment arm variable one level. Default \"\".","code":""},{"path":"https://insightsengineering.github.io/tern/reference/h_tbl_median_surv.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Helper function for survival estimations — h_tbl_median_surv","text":"summary table statistics N, Median, XX% CI (XX taken fit_km).","code":""},{"path":"https://insightsengineering.github.io/tern/reference/h_tbl_median_surv.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Helper function for survival estimations — h_tbl_median_surv","text":"","code":"library(dplyr) library(survival)  adtte <- tern_ex_adtte %>% filter(PARAMCD == \"OS\") fit <- survfit(   formula = Surv(AVAL, 1 - CNSR) ~ ARMCD,   data = adtte ) h_tbl_median_surv(fit_km = fit) #>        N Median        95% CI #> ARM A 69  974.6   (687, 1625) #> ARM B 73  727.8 (555.8, 1156) #> ARM C 58  632.3   (393, 1001)"},{"path":"https://insightsengineering.github.io/tern/reference/h_worsen_counter.html","id":null,"dir":"Reference","previous_headings":"","what":"Helper function to analyze patients for s_count_abnormal_lab_worsen_by_baseline() — h_worsen_counter","title":"Helper function to analyze patients for s_count_abnormal_lab_worsen_by_baseline() — h_worsen_counter","text":"Helper function count number patients fraction patients according highest post-baseline lab grade variable .var, baseline lab grade variable baseline_var, direction interest specified direction_var.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/h_worsen_counter.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Helper function to analyze patients for s_count_abnormal_lab_worsen_by_baseline() — h_worsen_counter","text":"","code":"h_worsen_counter(df, id, .var, baseline_var, direction_var)"},{"path":"https://insightsengineering.github.io/tern/reference/h_worsen_counter.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Helper function to analyze patients for s_count_abnormal_lab_worsen_by_baseline() — h_worsen_counter","text":"df (data.frame) data set containing analysis variables. id (string) subject variable name. .var (string) single variable name passed rtables requested statistics function. baseline_var (string) name baseline lab grade variable. direction_var (string) name direction variable specifying direction shift table interest. lab records flagged L, H B included shift table. L: low direction H: high direction B: low high directions","code":""},{"path":"https://insightsengineering.github.io/tern/reference/h_worsen_counter.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Helper function to analyze patients for s_count_abnormal_lab_worsen_by_baseline() — h_worsen_counter","text":"counts fraction patients whose worst post-baseline lab grades worse baseline grades, post-baseline worst grades \"1\", \"2\", \"3\", \"4\" \"\".","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/reference/h_worsen_counter.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Helper function to analyze patients for s_count_abnormal_lab_worsen_by_baseline() — h_worsen_counter","text":"","code":"library(dplyr)  # The direction variable, GRADDR, is based on metadata adlb <- tern_ex_adlb %>%   mutate(     GRADDR = case_when(       PARAMCD == \"ALT\" ~ \"B\",       PARAMCD == \"CRP\" ~ \"L\",       PARAMCD == \"IGA\" ~ \"H\"     )   ) %>%   filter(SAFFL == \"Y\" & ONTRTFL == \"Y\" & GRADDR != \"\")  df <- h_adlb_worsen(   adlb,   worst_flag_low = c(\"WGRLOFL\" = \"Y\"),   worst_flag_high = c(\"WGRHIFL\" = \"Y\"),   direction_var = \"GRADDR\" )  # `h_worsen_counter` h_worsen_counter(   df %>% filter(PARAMCD == \"CRP\" & GRADDR == \"Low\"),   id = \"USUBJID\",   .var = \"ATOXGR\",   baseline_var = \"BTOXGR\",   direction_var = \"GRADDR\" ) #> $fraction #> $fraction$`1` #>   num denom  #>    25   180  #>  #> $fraction$`2` #>   num denom  #>    15   186  #>  #> $fraction$`3` #>   num denom  #>    18   191  #>  #> $fraction$`4` #>   num denom  #>    17   196  #>  #> $fraction$Any #>   num denom  #>    75   196  #>  #>"},{"path":"https://insightsengineering.github.io/tern/reference/h_xticks.html","id":null,"dir":"Reference","previous_headings":"","what":"Helper function to calculate x-tick positions — h_xticks","title":"Helper function to calculate x-tick positions — h_xticks","text":"Calculate positions ticks x-axis. However, xticks already exists kept . based function ggplot2 relies , required graphic patient--risk annotation table.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/h_xticks.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Helper function to calculate x-tick positions — h_xticks","text":"","code":"h_xticks(data, xticks = NULL, max_time = NULL)"},{"path":"https://insightsengineering.github.io/tern/reference/h_xticks.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Helper function to calculate x-tick positions — h_xticks","text":"data (data.frame) survival data pre-processed h_data_plot. xticks (numeric NULL) numeric vector tick positions single number spacing ticks x-axis. NULL (default), labeling::extended() used determine optimal tick positions x-axis. max_time (numeric(1)) maximum value show x-axis. data values less threshold value plotted (defaults NULL).","code":""},{"path":"https://insightsengineering.github.io/tern/reference/h_xticks.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Helper function to calculate x-tick positions — h_xticks","text":"vector positions use x-axis ticks ggplot object.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/h_xticks.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Helper function to calculate x-tick positions — h_xticks","text":"","code":"library(dplyr) library(survival)  data <- tern_ex_adtte %>%   filter(PARAMCD == \"OS\") %>%   survfit(formula = Surv(AVAL, 1 - CNSR) ~ ARMCD, data = .) %>%   h_data_plot()  h_xticks(data) #> [1]    0 1000 2000 3000 4000 5000 h_xticks(data, xticks = seq(0, 3000, 500)) #> [1]    0  500 1000 1500 2000 2500 3000 h_xticks(data, xticks = 500) #>  [1]    0  500 1000 1500 2000 2500 3000 3500 4000 4500 h_xticks(data, xticks = 500, max_time = 6000) #>  [1]    0  500 1000 1500 2000 2500 3000 3500 4000 4500 5000 5500 6000 h_xticks(data, xticks = c(0, 500), max_time = 300) #> [1]   0 500 h_xticks(data, xticks = 500, max_time = 300) #>  [1]    0  500 1000 1500 2000 2500 3000 3500 4000 4500"},{"path":[]},{"path":"https://insightsengineering.github.io/tern/reference/imputation_rule.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Apply 1/3 or 1/2 imputation rule to data — imputation_rule","text":"","code":"imputation_rule(   df,   x_stats,   stat,   imp_rule,   post = FALSE,   avalcat_var = \"AVALCAT1\" )"},{"path":"https://insightsengineering.github.io/tern/reference/imputation_rule.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Apply 1/3 or 1/2 imputation rule to data — imputation_rule","text":"df (data.frame) data set containing analysis variables. x_stats (named list) named list statistics, typically results s_summary(). stat (string) statistic return value/NA level according imputation rule applied. imp_rule (string) imputation rule setting. Set \"1/3\" implement 1/3 imputation rule \"1/2\" implement 1/2 imputation rule. post (flag) whether data corresponds post-dose time-point (defaults FALSE). parameter used imp_rule set \"1/3\". avalcat_var (string) name variable indicates whether row df corresponds analysis value category \"BLQ\", \"LTR\", \"<PCLLOQ\", none (defaults \"AVALCAT1\"). Variable avalcat_var must present df.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/imputation_rule.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Apply 1/3 or 1/2 imputation rule to data — imputation_rule","text":"list containing statistic value (val) NA level (na_str) displayed according specified imputation rule.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/reference/imputation_rule.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Apply 1/3 or 1/2 imputation rule to data — imputation_rule","text":"","code":"set.seed(1) df <- data.frame(   AVAL = runif(50, 0, 1),   AVALCAT1 = sample(c(1, \"BLQ\"), 50, replace = TRUE) ) x_stats <- s_summary(df$AVAL) imputation_rule(df, x_stats, \"max\", \"1/3\") #> $val #>       max  #> 0.9919061  #>  #> $na_str #> [1] \"ND\" #>  imputation_rule(df, x_stats, \"geom_mean\", \"1/3\") #> $val #> [1] NA #>  #> $na_str #> [1] \"NE\" #>  imputation_rule(df, x_stats, \"mean\", \"1/2\") #> $val #> [1] NA #>  #> $na_str #> [1] \"ND\" #>"},{"path":"https://insightsengineering.github.io/tern/reference/incidence_rate.html","id":null,"dir":"Reference","previous_headings":"","what":"Incidence rate estimation — incidence_rate","title":"Incidence rate estimation — incidence_rate","text":"analyze function estimate_incidence_rate() creates layout element estimate event rate adjusted person-years risk, otherwise known incidence rate. primary analysis variable specified via vars person-years risk. addition variable, n_events variable number events observed (value 1 means event observed 0 means event observed) must also specified.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/incidence_rate.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Incidence rate estimation — incidence_rate","text":"","code":"estimate_incidence_rate(   lyt,   vars,   n_events,   id_var = \"USUBJID\",   control = control_incidence_rate(),   na_str = default_na_str(),   nested = TRUE,   summarize = FALSE,   label_fmt = \"%s - %.labels\",   ...,   show_labels = \"hidden\",   table_names = vars,   .stats = c(\"person_years\", \"n_events\", \"rate\", \"rate_ci\"),   .formats = NULL,   .labels = NULL,   .indent_mods = NULL )  s_incidence_rate(   df,   .var,   n_events,   is_event = lifecycle::deprecated(),   id_var = \"USUBJID\",   control = control_incidence_rate() )  a_incidence_rate(   df,   labelstr = \"\",   .var,   .df_row,   n_events,   id_var = \"USUBJID\",   control = control_incidence_rate(),   .stats = NULL,   .formats = c(person_years = \"xx.x\", n_events = \"xx\", rate = \"xx.xx\", rate_ci =     \"(xx.xx, xx.xx)\", n_unique = \"xx\", n_rate = \"xx (xx.x)\"),   .labels = NULL,   .indent_mods = NULL,   na_str = default_na_str(),   label_fmt = \"%s - %.labels\" )"},{"path":"https://insightsengineering.github.io/tern/reference/incidence_rate.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Incidence rate estimation — incidence_rate","text":"lyt (PreDataTableLayouts) layout analyses added . vars (character) variable names primary analysis variable iterated . n_events (string) name integer variable indicating whether event observed (1) (0). id_var (string) name variable used patient identifier \"n_unique\" included .stats. Defaults \"USUBJID\". control (list) parameters estimation details, specified using helper function control_incidence_rate(). Possible parameter options : conf_level (proportion) confidence level estimated incidence rate. conf_type (string)normal (default), normal_log, exact, byar confidence interval type. input_time_unit (string)day, week, month, year (default) indicating time unit data input. num_pt_year (numeric) time unit desired output (person-years). na_str (string) string used replace NA empty values output. nested (flag) whether layout instruction applied within existing layout structure _if possible (TRUE, default) new top-level element (FALSE). Ignored nest split. underneath analyses, allowed. summarize (flag) whether function act analyze function (summarize = FALSE), summarize function (summarize = TRUE). Defaults FALSE. label_fmt (string) labels formatted row split occurs summarize = TRUE. string use \"%s\" represent row split levels, \"%.labels\" represent labels supplied .labels argument. Defaults \"%s - %.labels\". ... additional arguments lower level functions. show_labels (string) label visibility: one \"default\", \"visible\" \"hidden\". table_names (character) can customized case vars analyzed multiple times, avoid warnings rtables. .stats (character) statistics select table. Options : 'person_years', 'n_events', 'rate', 'rate_ci', 'n_unique', 'n_rate' .formats (named character list) formats statistics. See Details analyze_vars information \"auto\" setting. .labels (named character) labels statistics (without indent). .indent_mods (named integer) indent modifiers labels. Defaults 0, corresponds unmodified default behavior. Can negative. df (data.frame) data set containing analysis variables. .var (string) single variable name passed rtables requested statistics function. is_event (flag)TRUE event, FALSE time event censored. labelstr (string) label level parent split currently summarized (must present second argument Content Row Functions). See rtables::summarize_row_groups() information. .df_row (data.frame) data frame across columns given row split.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/incidence_rate.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Incidence rate estimation — incidence_rate","text":"estimate_incidence_rate() returns layout object suitable passing layouting functions, rtables::build_table(). Adding function rtable layout add formatted rows containing statistics s_incidence_rate() table layout. s_incidence_rate() returns following statistics: person_years: Total person-years risk. n_events: Total number events observed. rate: Estimated incidence rate. rate_ci: Confidence interval incidence rate. n_unique: Total number patients least one event observed. n_rate: Total number events observed & estimated incidence rate. a_incidence_rate() returns corresponding list formatted rtables::CellValue().","code":""},{"path":"https://insightsengineering.github.io/tern/reference/incidence_rate.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Incidence rate estimation — incidence_rate","text":"estimate_incidence_rate(): Layout-creating function can take statistics function arguments additional format arguments. function wrapper rtables::analyze(). s_incidence_rate(): Statistics function estimates incidence rate associated confidence interval. a_incidence_rate(): Formatted analysis function used afun estimate_incidence_rate().","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/reference/incidence_rate.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Incidence rate estimation — incidence_rate","text":"","code":"df <- data.frame(   USUBJID = as.character(seq(6)),   CNSR = c(0, 1, 1, 0, 0, 0),   AVAL = c(10.1, 20.4, 15.3, 20.8, 18.7, 23.4),   ARM = factor(c(\"A\", \"A\", \"A\", \"B\", \"B\", \"B\")),   STRATA1 = factor(c(\"X\", \"Y\", \"Y\", \"X\", \"X\", \"Y\")) ) df$n_events <- 1 - df$CNSR  basic_table(show_colcounts = TRUE) %>%   split_cols_by(\"ARM\") %>%   estimate_incidence_rate(     vars = \"AVAL\",     n_events = \"n_events\",     control = control_incidence_rate(       input_time_unit = \"month\",       num_pt_year = 100     )   ) %>%   build_table(df) #>                                            A                 B        #>                                          (N=3)             (N=3)      #> ————————————————————————————————————————————————————————————————————— #> Total patient-years at risk               3.8               5.2       #> Number of adverse events observed          1                 3        #> AE rate per 100 patient-years            26.20             57.23      #> 95% CI                              (-25.15, 77.55)   (-7.53, 122.00)  # summarize = TRUE basic_table(show_colcounts = TRUE) %>%   split_cols_by(\"ARM\") %>%   split_rows_by(\"STRATA1\", child_labels = \"visible\") %>%   estimate_incidence_rate(     vars = \"AVAL\",     n_events = \"n_events\",     .stats = c(\"n_unique\", \"n_rate\"),     summarize = TRUE,     label_fmt = \"%.labels\"   ) %>%   build_table(df) #>                                                                          A         B    #>                                                                        (N=3)     (N=3)  #> ——————————————————————————————————————————————————————————————————————————————————————— #> X                                                                                       #>   Total number of patients with at least one adverse event               1         2    #>   Number of adverse events observed (AE rate per 100 patient-years)   1 (9.9)   2 (5.1) #> Y                                                                                       #>   Total number of patients with at least one adverse event               0         1    #>   Number of adverse events observed (AE rate per 100 patient-years)   0 (0.0)   1 (4.3)  a_incidence_rate(   df,   .var = \"AVAL\",   .df_row = df,   n_events = \"n_events\" ) #> RowsVerticalSection (in_rows) object print method: #> ---------------------------- #>       row_name formatted_cell indent_mod #> 1 person_years          108.7          0 #> 2     n_events              4          0 #> 3         rate           3.68          0 #> 4      rate_ci   (0.07, 7.29)          0 #> 5     n_unique              4          0 #> 6       n_rate        4 (3.7)          0 #>                                                           row_label #> 1                                       Total patient-years at risk #> 2                                 Number of adverse events observed #> 3                                     AE rate per 100 patient-years #> 4                                                            95% CI #> 5          Total number of patients with at least one adverse event #> 6 Number of adverse events observed (AE rate per 100 patient-years)"},{"path":"https://insightsengineering.github.io/tern/reference/labels_or_names.html","id":null,"dir":"Reference","previous_headings":"","what":"Labels or names of list elements — labels_or_names","title":"Labels or names of list elements — labels_or_names","text":"Internal helper function working nested statistic function results typically labels names can use.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/labels_or_names.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Labels or names of list elements — labels_or_names","text":"","code":"labels_or_names(x)"},{"path":"https://insightsengineering.github.io/tern/reference/labels_or_names.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Labels or names of list elements — labels_or_names","text":"x (list) list.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/labels_or_names.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Labels or names of list elements — labels_or_names","text":"character vector labels names list elements.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/labels_use_control.html","id":null,"dir":"Reference","previous_headings":"","what":"Update labels according to control specifications — labels_use_control","title":"Update labels according to control specifications — labels_use_control","text":"Given list statistic labels list control parameters, updates labels relevant control specification. example, control element conf_level set 0.9, default label statistic mean_ci updated \"Mean 90% CI\". labels supplied via labels_custom updated regardless control.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/labels_use_control.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Update labels according to control specifications — labels_use_control","text":"","code":"labels_use_control(labels_default, control, labels_custom = NULL)"},{"path":"https://insightsengineering.github.io/tern/reference/labels_use_control.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Update labels according to control specifications — labels_use_control","text":"labels_default (named character) named vector statistic labels modify according control specifications. Labels explicitly defined labels_custom affected. control (named list) list control parameters apply adjust default labels. labels_custom (named character) named vector labels customized user affected control.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/labels_use_control.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Update labels according to control specifications — labels_use_control","text":"named character vector labels control specifications applied relevant labels.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/labels_use_control.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Update labels according to control specifications — labels_use_control","text":"","code":"control <- list(conf_level = 0.80, quantiles = c(0.1, 0.83), test_mean = 0.57) get_labels_from_stats(c(\"mean_ci\", \"quantiles\", \"mean_pval\")) %>%   labels_use_control(control = control) #>                          mean_ci                        quantiles  #>                    \"Mean 80% CI\"                \"10% and 83%-ile\"  #>                        mean_pval  #> \"Mean p-value (H0: mean = 0.57)\""},{"path":"https://insightsengineering.github.io/tern/reference/logistic_regression_cols.html","id":null,"dir":"Reference","previous_headings":"","what":"Logistic regression multivariate column layout function — logistic_regression_cols","title":"Logistic regression multivariate column layout function — logistic_regression_cols","text":"Layout-creating function creates multivariate column layout summarizing logistic regression results. function wrapper rtables::split_cols_by_multivar().","code":""},{"path":"https://insightsengineering.github.io/tern/reference/logistic_regression_cols.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Logistic regression multivariate column layout function — logistic_regression_cols","text":"","code":"logistic_regression_cols(lyt, conf_level = 0.95)"},{"path":"https://insightsengineering.github.io/tern/reference/logistic_regression_cols.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Logistic regression multivariate column layout function — logistic_regression_cols","text":"lyt (PreDataTableLayouts) layout analyses added . conf_level (proportion) confidence level interval.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/logistic_regression_cols.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Logistic regression multivariate column layout function — logistic_regression_cols","text":"layout object suitable passing layouting functions. Adding function rtable layout split table columns corresponding statistics df, estimate, std_error, odds_ratio, ci, pvalue.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/logistic_summary_by_flag.html","id":null,"dir":"Reference","previous_headings":"","what":"Logistic regression summary table — logistic_summary_by_flag","title":"Logistic regression summary table — logistic_summary_by_flag","text":"Constructor content functions used summarize_logistic() summarize logistic regression results. function wrapper rtables::summarize_row_groups().","code":""},{"path":"https://insightsengineering.github.io/tern/reference/logistic_summary_by_flag.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Logistic regression summary table — logistic_summary_by_flag","text":"","code":"logistic_summary_by_flag(   flag_var,   na_str = default_na_str(),   .indent_mods = NULL )"},{"path":"https://insightsengineering.github.io/tern/reference/logistic_summary_by_flag.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Logistic regression summary table — logistic_summary_by_flag","text":"flag_var (string) variable name identifying row used content function. na_str (string) string used replace NA empty values output. .indent_mods (named integer) indent modifiers labels. Defaults 0, corresponds unmodified default behavior. Can negative.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/logistic_summary_by_flag.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Logistic regression summary table — logistic_summary_by_flag","text":"content function.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/make_names.html","id":null,"dir":"Reference","previous_headings":"","what":"Make names without dots — make_names","title":"Make names without dots — make_names","text":"Make names without dots","code":""},{"path":"https://insightsengineering.github.io/tern/reference/make_names.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Make names without dots — make_names","text":"","code":"make_names(nams)"},{"path":"https://insightsengineering.github.io/tern/reference/make_names.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Make names without dots — make_names","text":"nams (character) vector original names.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/make_names.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Make names without dots — make_names","text":"character vector proper names, use dots contrast make.names().","code":""},{"path":"https://insightsengineering.github.io/tern/reference/month2day.html","id":null,"dir":"Reference","previous_headings":"","what":"Conversion of months to days — month2day","title":"Conversion of months to days — month2day","text":"Conversion months days. approximative calculation considers month average 30.4375 days.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/month2day.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Conversion of months to days — month2day","text":"","code":"month2day(x)"},{"path":"https://insightsengineering.github.io/tern/reference/month2day.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Conversion of months to days — month2day","text":"x (numeric(1)) time months.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/month2day.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Conversion of months to days — month2day","text":"numeric vector time days.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/month2day.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Conversion of months to days — month2day","text":"","code":"x <- c(13.25, 8.15, 1, 2.834) month2day(x) #> [1] 403.29688 248.06563  30.43750  86.25988"},{"path":"https://insightsengineering.github.io/tern/reference/muffled_car_anova.html","id":null,"dir":"Reference","previous_headings":"","what":"Muffled car::Anova — muffled_car_anova","title":"Muffled car::Anova — muffled_car_anova","text":"Applied survival models, car::Anova() signal strata terms dropped model formula present, function deliberately muffles message.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/muffled_car_anova.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Muffled car::Anova — muffled_car_anova","text":"","code":"muffled_car_anova(mod, test_statistic)"},{"path":"https://insightsengineering.github.io/tern/reference/muffled_car_anova.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Muffled car::Anova — muffled_car_anova","text":"mod (coxph) Cox regression model fitted survival::coxph(). test_statistic (string) method used estimation p.values; wald (default) likelihood.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/muffled_car_anova.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Muffled car::Anova — muffled_car_anova","text":"output car::Anova(), convergence message muffled.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/n_available.html","id":null,"dir":"Reference","previous_headings":"","what":"Number of available (non-missing entries) in a vector — n_available","title":"Number of available (non-missing entries) in a vector — n_available","text":"Small utility function better readability.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/n_available.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Number of available (non-missing entries) in a vector — n_available","text":"","code":"n_available(x)"},{"path":"https://insightsengineering.github.io/tern/reference/n_available.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Number of available (non-missing entries) in a vector — n_available","text":"x (vector) vector count non-missing values.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/n_available.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Number of available (non-missing entries) in a vector — n_available","text":"Number non-missing values.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/odds_ratio.html","id":null,"dir":"Reference","previous_headings":"","what":"Odds ratio estimation — odds_ratio","title":"Odds ratio estimation — odds_ratio","text":"analyze function estimate_odds_ratio() creates layout element compare bivariate responses two groups estimating odds ratio confidence interval. primary analysis variable specified vars group variable. Additional variables can included analysis via variables argument, accepts arm, arm variable, strata, stratification variable. two arm levels present, can combined two groups using groups_list argument.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/odds_ratio.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Odds ratio estimation — odds_ratio","text":"","code":"estimate_odds_ratio(   lyt,   vars,   variables = list(arm = NULL, strata = NULL),   conf_level = 0.95,   groups_list = NULL,   na_str = default_na_str(),   nested = TRUE,   method = \"exact\",   show_labels = \"hidden\",   table_names = vars,   var_labels = vars,   .stats = \"or_ci\",   .formats = NULL,   .labels = NULL,   .indent_mods = NULL )  s_odds_ratio(   df,   .var,   .ref_group,   .in_ref_col,   .df_row,   variables = list(arm = NULL, strata = NULL),   conf_level = 0.95,   groups_list = NULL,   method = \"exact\" )  a_odds_ratio(   df,   .var,   .ref_group,   .in_ref_col,   .df_row,   variables = list(arm = NULL, strata = NULL),   conf_level = 0.95,   groups_list = NULL,   method = \"exact\" )"},{"path":"https://insightsengineering.github.io/tern/reference/odds_ratio.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Odds ratio estimation — odds_ratio","text":"lyt (PreDataTableLayouts) layout analyses added . vars (character) variable names primary analysis variable iterated . variables (named list string) list additional analysis variables. conf_level (proportion) confidence level interval. groups_list (named list character) specifies new group levels via names levels belong character vectors elements list. na_str (string) string used replace NA empty values output. nested (flag) whether layout instruction applied within existing layout structure _if possible (TRUE, default) new top-level element (FALSE). Ignored nest split. underneath analyses, allowed. method (string) whether use correct (\"exact\") calculation conditional likelihood one approximations. See survival::clogit() details. show_labels (string) label visibility: one \"default\", \"visible\" \"hidden\". table_names (character) can customized case vars analyzed multiple times, avoid warnings rtables. var_labels (character) variable labels. .stats (character) statistics select table. Options : 'or_ci', 'n_tot' .formats (named character list) formats statistics. See Details analyze_vars information \"auto\" setting. .labels (named character) labels statistics (without indent). .indent_mods (named integer) indent modifiers labels. Defaults 0, corresponds unmodified default behavior. Can negative. df (data.frame) data set containing analysis variables. .var (string) single variable name passed rtables requested statistics function. .ref_group (data.frame vector) data corresponding reference group. .in_ref_col (flag)TRUE working reference level, FALSE otherwise. .df_row (data.frame) data frame across columns given row split.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/odds_ratio.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Odds ratio estimation — odds_ratio","text":"estimate_odds_ratio() returns layout object suitable passing layouting functions, rtables::build_table(). Adding function rtable layout add formatted rows containing statistics s_odds_ratio() table layout. s_odds_ratio() returns named list statistics or_ci (containing est, lcl, ucl) n_tot. a_odds_ratio() returns corresponding list formatted rtables::CellValue().","code":""},{"path":"https://insightsengineering.github.io/tern/reference/odds_ratio.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Odds ratio estimation — odds_ratio","text":"estimate_odds_ratio(): Layout-creating function can take statistics function arguments additional format arguments. function wrapper rtables::analyze(). s_odds_ratio(): Statistics function estimates odds ratio treatment control. variables list arm strata variable names must passed stratified analysis required. a_odds_ratio(): Formatted analysis function used afun estimate_odds_ratio().","code":""},{"path":"https://insightsengineering.github.io/tern/reference/odds_ratio.html","id":"note","dir":"Reference","previous_headings":"","what":"Note","title":"Odds ratio estimation — odds_ratio","text":"function uses logistic regression unstratified analyses, conditional logistic regression stratified analyses. Wald confidence interval calculated specified confidence level. stratified analyses, currently implementation conditional likelihood confidence intervals, therefore likelihood confidence interval available option. vars contains responders non-responders odds ratio estimation possible returned values NA.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/reference/odds_ratio.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Odds ratio estimation — odds_ratio","text":"","code":"set.seed(12) dta <- data.frame(   rsp = sample(c(TRUE, FALSE), 100, TRUE),   grp = factor(rep(c(\"A\", \"B\"), each = 50), levels = c(\"A\", \"B\")),   strata = factor(sample(c(\"C\", \"D\"), 100, TRUE)) )  l <- basic_table() %>%   split_cols_by(var = \"grp\", ref_group = \"B\") %>%   estimate_odds_ratio(vars = \"rsp\")  build_table(l, df = dta) #>                               A            B #> ———————————————————————————————————————————— #> Odds Ratio (95% CI)   0.85 (0.38 - 1.88)      # Unstratified analysis. s_odds_ratio(   df = subset(dta, grp == \"A\"),   .var = \"rsp\",   .ref_group = subset(dta, grp == \"B\"),   .in_ref_col = FALSE,   .df_row = dta ) #> $or_ci #>       est       lcl       ucl  #> 0.8484848 0.3831831 1.8788053  #> attr(,\"label\") #> [1] \"Odds Ratio (95% CI)\" #>  #> $n_tot #> n_tot  #>   100  #> attr(,\"label\") #> [1] \"Total n\" #>   # Stratified analysis. s_odds_ratio(   df = subset(dta, grp == \"A\"),   .var = \"rsp\",   .ref_group = subset(dta, grp == \"B\"),   .in_ref_col = FALSE,   .df_row = dta,   variables = list(arm = \"grp\", strata = \"strata\") ) #> $or_ci #>       est       lcl       ucl  #> 0.7689750 0.3424155 1.7269154  #> attr(,\"label\") #> [1] \"Odds Ratio (95% CI)\" #>  #> $n_tot #> n_tot  #>   100  #> attr(,\"label\") #> [1] \"Total n\" #>   a_odds_ratio(   df = subset(dta, grp == \"A\"),   .var = \"rsp\",   .ref_group = subset(dta, grp == \"B\"),   .in_ref_col = FALSE,   .df_row = dta ) #> RowsVerticalSection (in_rows) object print method: #> ---------------------------- #>   row_name     formatted_cell indent_mod           row_label #> 1    or_ci 0.85 (0.38 - 1.88)          1 Odds Ratio (95% CI) #> 2    n_tot                100          0             Total n"},{"path":"https://insightsengineering.github.io/tern/reference/prop_diff.html","id":null,"dir":"Reference","previous_headings":"","what":"Proportion difference estimation — prop_diff","title":"Proportion difference estimation — prop_diff","text":"analysis function estimate_proportion_diff() creates layout element estimate difference proportion responders within studied population. primary analysis variable, vars, logical variable indicating whether response occurred record. See method parameter options methods use constructing confidence interval proportion difference. stratification variable can supplied via strata element variables argument.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/prop_diff.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Proportion difference estimation — prop_diff","text":"","code":"estimate_proportion_diff(   lyt,   vars,   variables = list(strata = NULL),   conf_level = 0.95,   method = c(\"waldcc\", \"wald\", \"cmh\", \"ha\", \"newcombe\", \"newcombecc\", \"strat_newcombe\",     \"strat_newcombecc\"),   weights_method = \"cmh\",   na_str = default_na_str(),   nested = TRUE,   ...,   var_labels = vars,   show_labels = \"hidden\",   table_names = vars,   .stats = NULL,   .formats = NULL,   .labels = NULL,   .indent_mods = NULL )  s_proportion_diff(   df,   .var,   .ref_group,   .in_ref_col,   variables = list(strata = NULL),   conf_level = 0.95,   method = c(\"waldcc\", \"wald\", \"cmh\", \"ha\", \"newcombe\", \"newcombecc\", \"strat_newcombe\",     \"strat_newcombecc\"),   weights_method = \"cmh\" )  a_proportion_diff(   df,   .var,   .ref_group,   .in_ref_col,   variables = list(strata = NULL),   conf_level = 0.95,   method = c(\"waldcc\", \"wald\", \"cmh\", \"ha\", \"newcombe\", \"newcombecc\", \"strat_newcombe\",     \"strat_newcombecc\"),   weights_method = \"cmh\" )"},{"path":"https://insightsengineering.github.io/tern/reference/prop_diff.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Proportion difference estimation — prop_diff","text":"lyt (PreDataTableLayouts) layout analyses added . vars (character) variable names primary analysis variable iterated . variables (named list string) list additional analysis variables. conf_level (proportion) confidence level interval. method (string) method used confidence interval estimation. weights_method (string) weights method. Can either \"cmh\" \"heuristic\" directs way weights estimated. na_str (string) string used replace NA empty values output. nested (flag) whether layout instruction applied within existing layout structure _if possible (TRUE, default) new top-level element (FALSE). Ignored nest split. underneath analyses, allowed. ... additional arguments lower level functions. var_labels (character) variable labels. show_labels (string) label visibility: one \"default\", \"visible\" \"hidden\". table_names (character) can customized case vars analyzed multiple times, avoid warnings rtables. .stats (character) statistics select table. Options : 'diff', 'diff_ci' .formats (named character list) formats statistics. See Details analyze_vars information \"auto\" setting. .labels (named character) labels statistics (without indent). .indent_mods (named integer) indent modifiers labels. Defaults 0, corresponds unmodified default behavior. Can negative. df (data.frame) data set containing analysis variables. .var (string) single variable name passed rtables requested statistics function. .ref_group (data.frame vector) data corresponding reference group. .in_ref_col (flag)TRUE working reference level, FALSE otherwise.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/prop_diff.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Proportion difference estimation — prop_diff","text":"estimate_proportion_diff() returns layout object suitable passing layouting functions, rtables::build_table(). Adding function rtable layout add formatted rows containing statistics s_proportion_diff() table layout. s_proportion_diff() returns named list elements diff diff_ci. a_proportion_diff() returns corresponding list formatted rtables::CellValue().","code":""},{"path":"https://insightsengineering.github.io/tern/reference/prop_diff.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Proportion difference estimation — prop_diff","text":"estimate_proportion_diff(): Layout-creating function can take statistics function arguments additional format arguments. function wrapper rtables::analyze(). s_proportion_diff(): Statistics function estimating difference terms responder proportion. a_proportion_diff(): Formatted analysis function used afun estimate_proportion_diff().","code":""},{"path":"https://insightsengineering.github.io/tern/reference/prop_diff.html","id":"note","dir":"Reference","previous_headings":"","what":"Note","title":"Proportion difference estimation — prop_diff","text":"performing unstratified analysis, methods \"cmh\", \"strat_newcombe\", \"strat_newcombecc\" permitted.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/reference/prop_diff.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Proportion difference estimation — prop_diff","text":"","code":"## \"Mid\" case: 4/4 respond in group A, 1/2 respond in group B. nex <- 100 # Number of example rows dta <- data.frame(   \"rsp\" = sample(c(TRUE, FALSE), nex, TRUE),   \"grp\" = sample(c(\"A\", \"B\"), nex, TRUE),   \"f1\" = sample(c(\"a1\", \"a2\"), nex, TRUE),   \"f2\" = sample(c(\"x\", \"y\", \"z\"), nex, TRUE),   stringsAsFactors = TRUE )  l <- basic_table() %>%   split_cols_by(var = \"grp\", ref_group = \"B\") %>%   estimate_proportion_diff(     vars = \"rsp\",     conf_level = 0.90,     method = \"ha\"   )  build_table(l, df = dta) #>                                        A         B #> —————————————————————————————————————————————————— #> Difference in Response rate (%)       12.0         #>   90% CI (Anderson-Hauck)         (-5.4, 29.4)      s_proportion_diff(   df = subset(dta, grp == \"A\"),   .var = \"rsp\",   .ref_group = subset(dta, grp == \"B\"),   .in_ref_col = FALSE,   conf_level = 0.90,   method = \"ha\" ) #> $diff #> [1] 12 #> attr(,\"label\") #> [1] \"Difference in Response rate (%)\" #>  #> $diff_ci #> [1] -5.374519 29.374519 #> attr(,\"label\") #> [1] \"90% CI (Anderson-Hauck)\" #>   # CMH example with strata s_proportion_diff(   df = subset(dta, grp == \"A\"),   .var = \"rsp\",   .ref_group = subset(dta, grp == \"B\"),   .in_ref_col = FALSE,   variables = list(strata = c(\"f1\", \"f2\")),   conf_level = 0.90,   method = \"cmh\" ) #> $diff #> [1] 12.05847 #> attr(,\"label\") #> [1] \"Difference in Response rate (%)\" #>  #> $diff_ci #> [1] -2.67057 26.78750 #> attr(,\"label\") #> [1] \"90% CI (CMH, without correction)\" #>   a_proportion_diff(   df = subset(dta, grp == \"A\"),   .var = \"rsp\",   .ref_group = subset(dta, grp == \"B\"),   .in_ref_col = FALSE,   conf_level = 0.90,   method = \"ha\" ) #> RowsVerticalSection (in_rows) object print method: #> ---------------------------- #>   row_name formatted_cell indent_mod                       row_label #> 1     diff           12.0          0 Difference in Response rate (%) #> 2  diff_ci   (-5.4, 29.4)          1         90% CI (Anderson-Hauck)"},{"path":"https://insightsengineering.github.io/tern/reference/prop_diff_test.html","id":null,"dir":"Reference","previous_headings":"","what":"Difference test for two proportions — prop_diff_test","title":"Difference test for two proportions — prop_diff_test","text":"analyze function test_proportion_diff() creates layout element test difference two proportions. primary analysis variable, vars, indicates whether response occurred record. See method parameter options methods use calculate p-value. Additionally, stratification variable can supplied via strata element variables argument.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/prop_diff_test.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Difference test for two proportions — prop_diff_test","text":"","code":"test_proportion_diff(   lyt,   vars,   variables = list(strata = NULL),   method = c(\"chisq\", \"schouten\", \"fisher\", \"cmh\"),   na_str = default_na_str(),   nested = TRUE,   ...,   var_labels = vars,   show_labels = \"hidden\",   table_names = vars,   .stats = NULL,   .formats = NULL,   .labels = NULL,   .indent_mods = NULL )  s_test_proportion_diff(   df,   .var,   .ref_group,   .in_ref_col,   variables = list(strata = NULL),   method = c(\"chisq\", \"schouten\", \"fisher\", \"cmh\") )  a_test_proportion_diff(   df,   .var,   .ref_group,   .in_ref_col,   variables = list(strata = NULL),   method = c(\"chisq\", \"schouten\", \"fisher\", \"cmh\") )"},{"path":"https://insightsengineering.github.io/tern/reference/prop_diff_test.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Difference test for two proportions — prop_diff_test","text":"lyt (PreDataTableLayouts) layout analyses added . vars (character) variable names primary analysis variable iterated . variables (named list string) list additional analysis variables. method (string) one chisq, cmh, fisher, schouten; specifies test used calculate p-value. na_str (string) string used replace NA empty values output. nested (flag) whether layout instruction applied within existing layout structure _if possible (TRUE, default) new top-level element (FALSE). Ignored nest split. underneath analyses, allowed. ... additional arguments lower level functions. var_labels (character) variable labels. show_labels (string) label visibility: one \"default\", \"visible\" \"hidden\". table_names (character) can customized case vars analyzed multiple times, avoid warnings rtables. .stats (character) statistics select table. Options : 'pval' .formats (named character list) formats statistics. See Details analyze_vars information \"auto\" setting. .labels (named character) labels statistics (without indent). .indent_mods (named integer) indent modifiers labels. Defaults 0, corresponds unmodified default behavior. Can negative. df (data.frame) data set containing analysis variables. .var (string) single variable name passed rtables requested statistics function. .ref_group (data.frame vector) data corresponding reference group. .in_ref_col (flag)TRUE working reference level, FALSE otherwise.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/prop_diff_test.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Difference test for two proportions — prop_diff_test","text":"test_proportion_diff() returns layout object suitable passing layouting functions, rtables::build_table(). Adding function rtable layout add formatted rows containing statistics s_test_proportion_diff() table layout. s_test_proportion_diff() returns named list single item pval attribute label describing method used. p-value tests null hypothesis proportions two groups . a_test_proportion_diff() returns corresponding list formatted rtables::CellValue().","code":""},{"path":"https://insightsengineering.github.io/tern/reference/prop_diff_test.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Difference test for two proportions — prop_diff_test","text":"test_proportion_diff(): Layout-creating function can take statistics function arguments additional format arguments. function wrapper rtables::analyze(). s_test_proportion_diff(): Statistics function tests difference two proportions. a_test_proportion_diff(): Formatted analysis function used afun test_proportion_diff().","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/reference/prop_diff_test.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Difference test for two proportions — prop_diff_test","text":"","code":"dta <- data.frame(   rsp = sample(c(TRUE, FALSE), 100, TRUE),   grp = factor(rep(c(\"A\", \"B\"), each = 50)),   strata = factor(rep(c(\"V\", \"W\", \"X\", \"Y\", \"Z\"), each = 20)) )  # With `rtables` pipelines. l <- basic_table() %>%   split_cols_by(var = \"grp\", ref_group = \"B\") %>%   test_proportion_diff(     vars = \"rsp\",     method = \"cmh\", variables = list(strata = \"strata\")   )  build_table(l, df = dta) #>                                              A      B #> ————————————————————————————————————————————————————— #>   p-value (Cochran-Mantel-Haenszel Test)   1.0000"},{"path":"https://insightsengineering.github.io/tern/reference/prune_occurrences.html","id":null,"dir":"Reference","previous_headings":"","what":"Occurrence table pruning — prune_occurrences","title":"Occurrence table pruning — prune_occurrences","text":"Family constructor condition functions flexibly prune occurrence tables. condition functions always return whether row result higher threshold. Since class CombinationFunction() can logically combined condition functions.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/prune_occurrences.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Occurrence table pruning — prune_occurrences","text":"","code":"keep_rows(row_condition)  keep_content_rows(content_row_condition)  has_count_in_cols(atleast, ...)  has_count_in_any_col(atleast, ...)  has_fraction_in_cols(atleast, ...)  has_fraction_in_any_col(atleast, ...)  has_fractions_difference(atleast, ...)  has_counts_difference(atleast, ...)"},{"path":"https://insightsengineering.github.io/tern/reference/prune_occurrences.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Occurrence table pruning — prune_occurrences","text":"row_condition (CombinationFunction) condition function works individual analysis rows flags whether kept pruned table. content_row_condition (CombinationFunction) condition function works individual first content rows leaf tables flags whether leaf tables kept pruned table. atleast (numeric(1)) threshold met order keep row. ... arguments row column access, see rtables_access: either col_names (character) including names columns used, alternatively col_indices (integer) giving indices directly instead.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/prune_occurrences.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Occurrence table pruning — prune_occurrences","text":"keep_rows() returns pruning function can used rtables::prune_table() prune rtables table. keep_content_rows() returns pruning function checks condition first content row leaf tables table. has_count_in_cols() returns condition function sums counts specified column. has_count_in_any_col() returns condition function compares counts specified columns threshold. has_fraction_in_cols() returns condition function sums counts specified column, computes fraction dividing total column counts. has_fraction_in_any_col() returns condition function looks fractions specified columns checks whether fulfill threshold. has_fractions_difference() returns condition function extracts fractions specified column, computes difference minimum maximum. has_counts_difference() returns condition function extracts counts specified column, computes difference minimum maximum.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/prune_occurrences.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Occurrence table pruning — prune_occurrences","text":"keep_rows(): Constructor creating pruning functions based row condition function. removes analysis rows (TableRow) pruned, .e., fulfill row condition. removes sub-tree children left. keep_content_rows(): Constructor creating pruning functions based condition (first) content row leaf tables. removes leaf tables first content row fulfill condition. check individual rows. proceeds recursively removing sub tree children left. has_count_in_cols(): Constructor creating condition functions total counts specified columns. has_count_in_any_col(): Constructor creating condition functions counts specified columns satisfying threshold. has_fraction_in_cols(): Constructor creating condition functions total fraction specified columns. has_fraction_in_any_col(): Constructor creating condition functions fraction specified columns. has_fractions_difference(): Constructor creating condition function checks difference fractions reported specified column. has_counts_difference(): Constructor creating condition function checks difference counts reported specified column.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/prune_occurrences.html","id":"note","dir":"Reference","previous_headings":"","what":"Note","title":"Occurrence table pruning — prune_occurrences","text":"Since table specifications worded positively, name constructor condition functions positively, . However, note result keep_rows() says pruned, conform rtables::prune_table() interface.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/prune_occurrences.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Occurrence table pruning — prune_occurrences","text":"","code":"# \\donttest{ tab <- basic_table() %>%   split_cols_by(\"ARM\") %>%   split_rows_by(\"RACE\") %>%   split_rows_by(\"STRATA1\") %>%   summarize_row_groups() %>%   analyze_vars(\"COUNTRY\", .stats = \"count_fraction\") %>%   build_table(DM) # }  # \\donttest{ # `keep_rows` is_non_empty <- !CombinationFunction(all_zero_or_na) prune_table(tab, keep_rows(is_non_empty)) #>                             A: Drug X    B: Placebo   C: Combination #> ———————————————————————————————————————————————————————————————————— #> ASIAN                                                                #>   A                         27 (22.3%)   20 (18.9%)     31 (24.0%)   #>     CHN                     14 (51.9%)    9 (45%)       12 (38.7%)   #>     USA                      2 (7.4%)      1 (5%)       8 (25.8%)    #>     BRA                      1 (3.7%)     4 (20%)        1 (3.2%)    #>     PAK                     3 (11.1%)     2 (10%)        2 (6.5%)    #>     NGA                     3 (11.1%)      1 (5%)        3 (9.7%)    #>     RUS                      2 (7.4%)      1 (5%)        1 (3.2%)    #>     JPN                         0          1 (5%)        2 (6.5%)    #>     GBR                         0          1 (5%)        1 (3.2%)    #>     CAN                      2 (7.4%)        0           1 (3.2%)    #>   B                         24 (19.8%)   29 (27.4%)     22 (17.1%)   #>     CHN                      12 (50%)    13 (44.8%)      11 (50%)    #>     USA                      2 (8.3%)    5 (17.2%)       1 (4.5%)    #>     BRA                     4 (16.7%)    3 (10.3%)       1 (4.5%)    #>     PAK                      2 (8.3%)     2 (6.9%)      4 (18.2%)    #>     NGA                      2 (8.3%)     1 (3.4%)      3 (13.6%)    #>     RUS                      1 (4.2%)     1 (3.4%)       2 (9.1%)    #>     JPN                         0        4 (13.8%)          0        #>     GBR                      1 (4.2%)        0              0        #>   C                         28 (23.1%)   19 (17.9%)     31 (24.0%)   #>     CHN                     13 (46.4%)   10 (52.6%)     16 (51.6%)   #>     USA                     3 (10.7%)    3 (15.8%)      4 (12.9%)    #>     BRA                      1 (3.6%)     1 (5.3%)      4 (12.9%)    #>     PAK                      1 (3.6%)     1 (5.3%)       3 (9.7%)    #>     NGA                     4 (14.3%)     1 (5.3%)       2 (6.5%)    #>     RUS                     4 (14.3%)    2 (10.5%)       1 (3.2%)    #>     JPN                      2 (7.1%)     1 (5.3%)       1 (3.2%)    #> BLACK OR AFRICAN AMERICAN                                            #>   A                          6 (5.0%)     7 (6.6%)       8 (6.2%)    #>     CHN                      3 (50%)     3 (42.9%)      5 (62.5%)    #>     USA                     2 (33.3%)    1 (14.3%)      1 (12.5%)    #>     BRA                         0        1 (14.3%)          0        #>     PAK                         0            0          1 (12.5%)    #>     NGA                         0            0          1 (12.5%)    #>     JPN                     1 (16.7%)        0              0        #>     GBR                         0        2 (28.6%)          0        #>   B                         10 (8.3%)     6 (5.7%)      12 (9.3%)    #>     CHN                      3 (30%)     2 (33.3%)      8 (66.7%)    #>     USA                      1 (10%)         0           1 (8.3%)    #>     BRA                      2 (20%)     1 (16.7%)       1 (8.3%)    #>     PAK                         0        1 (16.7%)          0        #>     RUS                         0        1 (16.7%)          0        #>     JPN                      2 (20%)         0           1 (8.3%)    #>     GBR                      1 (10%)         0           1 (8.3%)    #>     CAN                      1 (10%)     1 (16.7%)          0        #>   C                         12 (9.9%)    11 (10.4%)      7 (5.4%)    #>     CHN                     8 (66.7%)    5 (45.5%)      5 (71.4%)    #>     USA                      1 (8.3%)    2 (18.2%)      1 (14.3%)    #>     BRA                      1 (8.3%)    2 (18.2%)          0        #>     PAK                      1 (8.3%)     1 (9.1%)      1 (14.3%)    #>     NGA                         0         1 (9.1%)          0        #>     RUS                      1 (8.3%)        0              0        #> WHITE                                                                #>   A                          3 (2.5%)     6 (5.7%)       6 (4.7%)    #>     CHN                     2 (66.7%)    2 (33.3%)       3 (50%)     #>     USA                     1 (33.3%)    1 (16.7%)          0        #>     PAK                         0        1 (16.7%)      1 (16.7%)    #>     NGA                         0        1 (16.7%)          0        #>     RUS                         0            0          1 (16.7%)    #>     JPN                         0        1 (16.7%)          0        #>     CAN                         0            0          1 (16.7%)    #>   B                          7 (5.8%)     5 (4.7%)       4 (3.1%)    #>     CHN                     4 (57.1%)     1 (20%)        3 (75%)     #>     USA                         0         1 (20%)           0        #>     BRA                         0         1 (20%)           0        #>     PAK                     1 (14.3%)        0              0        #>     NGA                     1 (14.3%)        0              0        #>     RUS                     1 (14.3%)        0           1 (25%)     #>     JPN                         0         1 (20%)           0        #>     CAN                         0         1 (20%)           0        #>   C                          4 (3.3%)     3 (2.8%)       8 (6.2%)    #>     CHN                      3 (75%)      3 (100%)       6 (75%)     #>     USA                      1 (25%)         0          1 (12.5%)    #>     JPN                         0            0          1 (12.5%)    # }  # `keep_content_rows` # \\donttest{ more_than_twenty <- has_count_in_cols(atleast = 20L, col_names = names(tab)) prune_table(tab, keep_content_rows(more_than_twenty)) #>                             A: Drug X    B: Placebo   C: Combination #> ———————————————————————————————————————————————————————————————————— #> ASIAN                                                                #>   A                         27 (22.3%)   20 (18.9%)     31 (24.0%)   #>     CHN                     14 (51.9%)    9 (45%)       12 (38.7%)   #>     USA                      2 (7.4%)      1 (5%)       8 (25.8%)    #>     BRA                      1 (3.7%)     4 (20%)        1 (3.2%)    #>     PAK                     3 (11.1%)     2 (10%)        2 (6.5%)    #>     NGA                     3 (11.1%)      1 (5%)        3 (9.7%)    #>     RUS                      2 (7.4%)      1 (5%)        1 (3.2%)    #>     JPN                         0          1 (5%)        2 (6.5%)    #>     GBR                         0          1 (5%)        1 (3.2%)    #>     CAN                      2 (7.4%)        0           1 (3.2%)    #>     CHE                         0            0              0        #>   B                         24 (19.8%)   29 (27.4%)     22 (17.1%)   #>     CHN                      12 (50%)    13 (44.8%)      11 (50%)    #>     USA                      2 (8.3%)    5 (17.2%)       1 (4.5%)    #>     BRA                     4 (16.7%)    3 (10.3%)       1 (4.5%)    #>     PAK                      2 (8.3%)     2 (6.9%)      4 (18.2%)    #>     NGA                      2 (8.3%)     1 (3.4%)      3 (13.6%)    #>     RUS                      1 (4.2%)     1 (3.4%)       2 (9.1%)    #>     JPN                         0        4 (13.8%)          0        #>     GBR                      1 (4.2%)        0              0        #>     CAN                         0            0              0        #>     CHE                         0            0              0        #>   C                         28 (23.1%)   19 (17.9%)     31 (24.0%)   #>     CHN                     13 (46.4%)   10 (52.6%)     16 (51.6%)   #>     USA                     3 (10.7%)    3 (15.8%)      4 (12.9%)    #>     BRA                      1 (3.6%)     1 (5.3%)      4 (12.9%)    #>     PAK                      1 (3.6%)     1 (5.3%)       3 (9.7%)    #>     NGA                     4 (14.3%)     1 (5.3%)       2 (6.5%)    #>     RUS                     4 (14.3%)    2 (10.5%)       1 (3.2%)    #>     JPN                      2 (7.1%)     1 (5.3%)       1 (3.2%)    #>     GBR                         0            0              0        #>     CAN                         0            0              0        #>     CHE                         0            0              0        #> BLACK OR AFRICAN AMERICAN                                            #>   A                          6 (5.0%)     7 (6.6%)       8 (6.2%)    #>     CHN                      3 (50%)     3 (42.9%)      5 (62.5%)    #>     USA                     2 (33.3%)    1 (14.3%)      1 (12.5%)    #>     BRA                         0        1 (14.3%)          0        #>     PAK                         0            0          1 (12.5%)    #>     NGA                         0            0          1 (12.5%)    #>     RUS                         0            0              0        #>     JPN                     1 (16.7%)        0              0        #>     GBR                         0        2 (28.6%)          0        #>     CAN                         0            0              0        #>     CHE                         0            0              0        #>   B                         10 (8.3%)     6 (5.7%)      12 (9.3%)    #>     CHN                      3 (30%)     2 (33.3%)      8 (66.7%)    #>     USA                      1 (10%)         0           1 (8.3%)    #>     BRA                      2 (20%)     1 (16.7%)       1 (8.3%)    #>     PAK                         0        1 (16.7%)          0        #>     NGA                         0            0              0        #>     RUS                         0        1 (16.7%)          0        #>     JPN                      2 (20%)         0           1 (8.3%)    #>     GBR                      1 (10%)         0           1 (8.3%)    #>     CAN                      1 (10%)     1 (16.7%)          0        #>     CHE                         0            0              0        #>   C                         12 (9.9%)    11 (10.4%)      7 (5.4%)    #>     CHN                     8 (66.7%)    5 (45.5%)      5 (71.4%)    #>     USA                      1 (8.3%)    2 (18.2%)      1 (14.3%)    #>     BRA                      1 (8.3%)    2 (18.2%)          0        #>     PAK                      1 (8.3%)     1 (9.1%)      1 (14.3%)    #>     NGA                         0         1 (9.1%)          0        #>     RUS                      1 (8.3%)        0              0        #>     JPN                         0            0              0        #>     GBR                         0            0              0        #>     CAN                         0            0              0        #>     CHE                         0            0              0        # }  # \\donttest{ more_than_one <- has_count_in_cols(atleast = 1L, col_names = names(tab)) prune_table(tab, keep_rows(more_than_one)) #>                             A: Drug X    B: Placebo   C: Combination #> ———————————————————————————————————————————————————————————————————— #> ASIAN                                                                #>   A                         27 (22.3%)   20 (18.9%)     31 (24.0%)   #>     CHN                     14 (51.9%)    9 (45%)       12 (38.7%)   #>     USA                      2 (7.4%)      1 (5%)       8 (25.8%)    #>     BRA                      1 (3.7%)     4 (20%)        1 (3.2%)    #>     PAK                     3 (11.1%)     2 (10%)        2 (6.5%)    #>     NGA                     3 (11.1%)      1 (5%)        3 (9.7%)    #>     RUS                      2 (7.4%)      1 (5%)        1 (3.2%)    #>     JPN                         0          1 (5%)        2 (6.5%)    #>     GBR                         0          1 (5%)        1 (3.2%)    #>     CAN                      2 (7.4%)        0           1 (3.2%)    #>   B                         24 (19.8%)   29 (27.4%)     22 (17.1%)   #>     CHN                      12 (50%)    13 (44.8%)      11 (50%)    #>     USA                      2 (8.3%)    5 (17.2%)       1 (4.5%)    #>     BRA                     4 (16.7%)    3 (10.3%)       1 (4.5%)    #>     PAK                      2 (8.3%)     2 (6.9%)      4 (18.2%)    #>     NGA                      2 (8.3%)     1 (3.4%)      3 (13.6%)    #>     RUS                      1 (4.2%)     1 (3.4%)       2 (9.1%)    #>     JPN                         0        4 (13.8%)          0        #>     GBR                      1 (4.2%)        0              0        #>   C                         28 (23.1%)   19 (17.9%)     31 (24.0%)   #>     CHN                     13 (46.4%)   10 (52.6%)     16 (51.6%)   #>     USA                     3 (10.7%)    3 (15.8%)      4 (12.9%)    #>     BRA                      1 (3.6%)     1 (5.3%)      4 (12.9%)    #>     PAK                      1 (3.6%)     1 (5.3%)       3 (9.7%)    #>     NGA                     4 (14.3%)     1 (5.3%)       2 (6.5%)    #>     RUS                     4 (14.3%)    2 (10.5%)       1 (3.2%)    #>     JPN                      2 (7.1%)     1 (5.3%)       1 (3.2%)    #> BLACK OR AFRICAN AMERICAN                                            #>   A                          6 (5.0%)     7 (6.6%)       8 (6.2%)    #>     CHN                      3 (50%)     3 (42.9%)      5 (62.5%)    #>     USA                     2 (33.3%)    1 (14.3%)      1 (12.5%)    #>     BRA                         0        1 (14.3%)          0        #>     PAK                         0            0          1 (12.5%)    #>     NGA                         0            0          1 (12.5%)    #>     JPN                     1 (16.7%)        0              0        #>     GBR                         0        2 (28.6%)          0        #>   B                         10 (8.3%)     6 (5.7%)      12 (9.3%)    #>     CHN                      3 (30%)     2 (33.3%)      8 (66.7%)    #>     USA                      1 (10%)         0           1 (8.3%)    #>     BRA                      2 (20%)     1 (16.7%)       1 (8.3%)    #>     PAK                         0        1 (16.7%)          0        #>     RUS                         0        1 (16.7%)          0        #>     JPN                      2 (20%)         0           1 (8.3%)    #>     GBR                      1 (10%)         0           1 (8.3%)    #>     CAN                      1 (10%)     1 (16.7%)          0        #>   C                         12 (9.9%)    11 (10.4%)      7 (5.4%)    #>     CHN                     8 (66.7%)    5 (45.5%)      5 (71.4%)    #>     USA                      1 (8.3%)    2 (18.2%)      1 (14.3%)    #>     BRA                      1 (8.3%)    2 (18.2%)          0        #>     PAK                      1 (8.3%)     1 (9.1%)      1 (14.3%)    #>     NGA                         0         1 (9.1%)          0        #>     RUS                      1 (8.3%)        0              0        #> WHITE                                                                #>   A                          3 (2.5%)     6 (5.7%)       6 (4.7%)    #>     CHN                     2 (66.7%)    2 (33.3%)       3 (50%)     #>     USA                     1 (33.3%)    1 (16.7%)          0        #>     PAK                         0        1 (16.7%)      1 (16.7%)    #>     NGA                         0        1 (16.7%)          0        #>     RUS                         0            0          1 (16.7%)    #>     JPN                         0        1 (16.7%)          0        #>     CAN                         0            0          1 (16.7%)    #>   B                          7 (5.8%)     5 (4.7%)       4 (3.1%)    #>     CHN                     4 (57.1%)     1 (20%)        3 (75%)     #>     USA                         0         1 (20%)           0        #>     BRA                         0         1 (20%)           0        #>     PAK                     1 (14.3%)        0              0        #>     NGA                     1 (14.3%)        0              0        #>     RUS                     1 (14.3%)        0           1 (25%)     #>     JPN                         0         1 (20%)           0        #>     CAN                         0         1 (20%)           0        #>   C                          4 (3.3%)     3 (2.8%)       8 (6.2%)    #>     CHN                      3 (75%)      3 (100%)       6 (75%)     #>     USA                      1 (25%)         0          1 (12.5%)    #>     JPN                         0            0          1 (12.5%)    # }  # \\donttest{ # `has_count_in_any_col` any_more_than_one <- has_count_in_any_col(atleast = 1L, col_names = names(tab)) prune_table(tab, keep_rows(any_more_than_one)) #>                             A: Drug X    B: Placebo   C: Combination #> ———————————————————————————————————————————————————————————————————— #> ASIAN                                                                #>   A                         27 (22.3%)   20 (18.9%)     31 (24.0%)   #>     CHN                     14 (51.9%)    9 (45%)       12 (38.7%)   #>     USA                      2 (7.4%)      1 (5%)       8 (25.8%)    #>     BRA                      1 (3.7%)     4 (20%)        1 (3.2%)    #>     PAK                     3 (11.1%)     2 (10%)        2 (6.5%)    #>     NGA                     3 (11.1%)      1 (5%)        3 (9.7%)    #>     RUS                      2 (7.4%)      1 (5%)        1 (3.2%)    #>     JPN                         0          1 (5%)        2 (6.5%)    #>     GBR                         0          1 (5%)        1 (3.2%)    #>     CAN                      2 (7.4%)        0           1 (3.2%)    #>   B                         24 (19.8%)   29 (27.4%)     22 (17.1%)   #>     CHN                      12 (50%)    13 (44.8%)      11 (50%)    #>     USA                      2 (8.3%)    5 (17.2%)       1 (4.5%)    #>     BRA                     4 (16.7%)    3 (10.3%)       1 (4.5%)    #>     PAK                      2 (8.3%)     2 (6.9%)      4 (18.2%)    #>     NGA                      2 (8.3%)     1 (3.4%)      3 (13.6%)    #>     RUS                      1 (4.2%)     1 (3.4%)       2 (9.1%)    #>     JPN                         0        4 (13.8%)          0        #>     GBR                      1 (4.2%)        0              0        #>   C                         28 (23.1%)   19 (17.9%)     31 (24.0%)   #>     CHN                     13 (46.4%)   10 (52.6%)     16 (51.6%)   #>     USA                     3 (10.7%)    3 (15.8%)      4 (12.9%)    #>     BRA                      1 (3.6%)     1 (5.3%)      4 (12.9%)    #>     PAK                      1 (3.6%)     1 (5.3%)       3 (9.7%)    #>     NGA                     4 (14.3%)     1 (5.3%)       2 (6.5%)    #>     RUS                     4 (14.3%)    2 (10.5%)       1 (3.2%)    #>     JPN                      2 (7.1%)     1 (5.3%)       1 (3.2%)    #> BLACK OR AFRICAN AMERICAN                                            #>   A                          6 (5.0%)     7 (6.6%)       8 (6.2%)    #>     CHN                      3 (50%)     3 (42.9%)      5 (62.5%)    #>     USA                     2 (33.3%)    1 (14.3%)      1 (12.5%)    #>     BRA                         0        1 (14.3%)          0        #>     PAK                         0            0          1 (12.5%)    #>     NGA                         0            0          1 (12.5%)    #>     JPN                     1 (16.7%)        0              0        #>     GBR                         0        2 (28.6%)          0        #>   B                         10 (8.3%)     6 (5.7%)      12 (9.3%)    #>     CHN                      3 (30%)     2 (33.3%)      8 (66.7%)    #>     USA                      1 (10%)         0           1 (8.3%)    #>     BRA                      2 (20%)     1 (16.7%)       1 (8.3%)    #>     PAK                         0        1 (16.7%)          0        #>     RUS                         0        1 (16.7%)          0        #>     JPN                      2 (20%)         0           1 (8.3%)    #>     GBR                      1 (10%)         0           1 (8.3%)    #>     CAN                      1 (10%)     1 (16.7%)          0        #>   C                         12 (9.9%)    11 (10.4%)      7 (5.4%)    #>     CHN                     8 (66.7%)    5 (45.5%)      5 (71.4%)    #>     USA                      1 (8.3%)    2 (18.2%)      1 (14.3%)    #>     BRA                      1 (8.3%)    2 (18.2%)          0        #>     PAK                      1 (8.3%)     1 (9.1%)      1 (14.3%)    #>     NGA                         0         1 (9.1%)          0        #>     RUS                      1 (8.3%)        0              0        #> WHITE                                                                #>   A                          3 (2.5%)     6 (5.7%)       6 (4.7%)    #>     CHN                     2 (66.7%)    2 (33.3%)       3 (50%)     #>     USA                     1 (33.3%)    1 (16.7%)          0        #>     PAK                         0        1 (16.7%)      1 (16.7%)    #>     NGA                         0        1 (16.7%)          0        #>     RUS                         0            0          1 (16.7%)    #>     JPN                         0        1 (16.7%)          0        #>     CAN                         0            0          1 (16.7%)    #>   B                          7 (5.8%)     5 (4.7%)       4 (3.1%)    #>     CHN                     4 (57.1%)     1 (20%)        3 (75%)     #>     USA                         0         1 (20%)           0        #>     BRA                         0         1 (20%)           0        #>     PAK                     1 (14.3%)        0              0        #>     NGA                     1 (14.3%)        0              0        #>     RUS                     1 (14.3%)        0           1 (25%)     #>     JPN                         0         1 (20%)           0        #>     CAN                         0         1 (20%)           0        #>   C                          4 (3.3%)     3 (2.8%)       8 (6.2%)    #>     CHN                      3 (75%)      3 (100%)       6 (75%)     #>     USA                      1 (25%)         0          1 (12.5%)    #>     JPN                         0            0          1 (12.5%)    # }  # \\donttest{ # `has_fraction_in_cols` more_than_five_percent <- has_fraction_in_cols(atleast = 0.05, col_names = names(tab)) prune_table(tab, keep_rows(more_than_five_percent)) #>                             A: Drug X    B: Placebo   C: Combination #> ———————————————————————————————————————————————————————————————————— #> ASIAN                                                                #>   A                         27 (22.3%)   20 (18.9%)     31 (24.0%)   #>     CHN                     14 (51.9%)    9 (45%)       12 (38.7%)   #>   B                         24 (19.8%)   29 (27.4%)     22 (17.1%)   #>     CHN                      12 (50%)    13 (44.8%)      11 (50%)    #>   C                         28 (23.1%)   19 (17.9%)     31 (24.0%)   #>     CHN                     13 (46.4%)   10 (52.6%)     16 (51.6%)   #> BLACK OR AFRICAN AMERICAN                                            #>   C                         12 (9.9%)    11 (10.4%)      7 (5.4%)    #>     CHN                     8 (66.7%)    5 (45.5%)      5 (71.4%)    # }  # \\donttest{ # `has_fraction_in_any_col` any_atleast_five_percent <- has_fraction_in_any_col(atleast = 0.05, col_names = names(tab)) prune_table(tab, keep_rows(any_atleast_five_percent)) #>                             A: Drug X    B: Placebo   C: Combination #> ———————————————————————————————————————————————————————————————————— #> ASIAN                                                                #>   A                         27 (22.3%)   20 (18.9%)     31 (24.0%)   #>     CHN                     14 (51.9%)    9 (45%)       12 (38.7%)   #>     USA                      2 (7.4%)      1 (5%)       8 (25.8%)    #>     BRA                      1 (3.7%)     4 (20%)        1 (3.2%)    #>     PAK                     3 (11.1%)     2 (10%)        2 (6.5%)    #>     NGA                     3 (11.1%)      1 (5%)        3 (9.7%)    #>     RUS                      2 (7.4%)      1 (5%)        1 (3.2%)    #>     JPN                         0          1 (5%)        2 (6.5%)    #>     GBR                         0          1 (5%)        1 (3.2%)    #>     CAN                      2 (7.4%)        0           1 (3.2%)    #>   B                         24 (19.8%)   29 (27.4%)     22 (17.1%)   #>     CHN                      12 (50%)    13 (44.8%)      11 (50%)    #>     USA                      2 (8.3%)    5 (17.2%)       1 (4.5%)    #>     BRA                     4 (16.7%)    3 (10.3%)       1 (4.5%)    #>     PAK                      2 (8.3%)     2 (6.9%)      4 (18.2%)    #>     NGA                      2 (8.3%)     1 (3.4%)      3 (13.6%)    #>     RUS                      1 (4.2%)     1 (3.4%)       2 (9.1%)    #>     JPN                         0        4 (13.8%)          0        #>   C                         28 (23.1%)   19 (17.9%)     31 (24.0%)   #>     CHN                     13 (46.4%)   10 (52.6%)     16 (51.6%)   #>     USA                     3 (10.7%)    3 (15.8%)      4 (12.9%)    #>     BRA                      1 (3.6%)     1 (5.3%)      4 (12.9%)    #>     PAK                      1 (3.6%)     1 (5.3%)       3 (9.7%)    #>     NGA                     4 (14.3%)     1 (5.3%)       2 (6.5%)    #>     RUS                     4 (14.3%)    2 (10.5%)       1 (3.2%)    #>     JPN                      2 (7.1%)     1 (5.3%)       1 (3.2%)    #> BLACK OR AFRICAN AMERICAN                                            #>   A                          6 (5.0%)     7 (6.6%)       8 (6.2%)    #>     CHN                      3 (50%)     3 (42.9%)      5 (62.5%)    #>     USA                     2 (33.3%)    1 (14.3%)      1 (12.5%)    #>     BRA                         0        1 (14.3%)          0        #>     PAK                         0            0          1 (12.5%)    #>     NGA                         0            0          1 (12.5%)    #>     JPN                     1 (16.7%)        0              0        #>     GBR                         0        2 (28.6%)          0        #>   B                         10 (8.3%)     6 (5.7%)      12 (9.3%)    #>     CHN                      3 (30%)     2 (33.3%)      8 (66.7%)    #>     USA                      1 (10%)         0           1 (8.3%)    #>     BRA                      2 (20%)     1 (16.7%)       1 (8.3%)    #>     PAK                         0        1 (16.7%)          0        #>     RUS                         0        1 (16.7%)          0        #>     JPN                      2 (20%)         0           1 (8.3%)    #>     GBR                      1 (10%)         0           1 (8.3%)    #>     CAN                      1 (10%)     1 (16.7%)          0        #>   C                         12 (9.9%)    11 (10.4%)      7 (5.4%)    #>     CHN                     8 (66.7%)    5 (45.5%)      5 (71.4%)    #>     USA                      1 (8.3%)    2 (18.2%)      1 (14.3%)    #>     BRA                      1 (8.3%)    2 (18.2%)          0        #>     PAK                      1 (8.3%)     1 (9.1%)      1 (14.3%)    #>     NGA                         0         1 (9.1%)          0        #>     RUS                      1 (8.3%)        0              0        #> WHITE                                                                #>   A                          3 (2.5%)     6 (5.7%)       6 (4.7%)    #>     CHN                     2 (66.7%)    2 (33.3%)       3 (50%)     #>     USA                     1 (33.3%)    1 (16.7%)          0        #>     PAK                         0        1 (16.7%)      1 (16.7%)    #>     NGA                         0        1 (16.7%)          0        #>     RUS                         0            0          1 (16.7%)    #>     JPN                         0        1 (16.7%)          0        #>     CAN                         0            0          1 (16.7%)    #>   B                          7 (5.8%)     5 (4.7%)       4 (3.1%)    #>     CHN                     4 (57.1%)     1 (20%)        3 (75%)     #>     USA                         0         1 (20%)           0        #>     BRA                         0         1 (20%)           0        #>     PAK                     1 (14.3%)        0              0        #>     NGA                     1 (14.3%)        0              0        #>     RUS                     1 (14.3%)        0           1 (25%)     #>     JPN                         0         1 (20%)           0        #>     CAN                         0         1 (20%)           0        #>   C                          4 (3.3%)     3 (2.8%)       8 (6.2%)    #>     CHN                      3 (75%)      3 (100%)       6 (75%)     #>     USA                      1 (25%)         0          1 (12.5%)    #>     JPN                         0            0          1 (12.5%)    # }  # \\donttest{ # `has_fractions_difference` more_than_five_percent_diff <- has_fractions_difference(atleast = 0.05, col_names = names(tab)) prune_table(tab, keep_rows(more_than_five_percent_diff)) #>                             A: Drug X    B: Placebo   C: Combination #> ———————————————————————————————————————————————————————————————————— #> ASIAN                                                                #>   A                         27 (22.3%)   20 (18.9%)     31 (24.0%)   #>     CHN                     14 (51.9%)    9 (45%)       12 (38.7%)   #>     USA                      2 (7.4%)      1 (5%)       8 (25.8%)    #>     BRA                      1 (3.7%)     4 (20%)        1 (3.2%)    #>     NGA                     3 (11.1%)      1 (5%)        3 (9.7%)    #>     JPN                         0          1 (5%)        2 (6.5%)    #>     GBR                         0          1 (5%)        1 (3.2%)    #>     CAN                      2 (7.4%)        0           1 (3.2%)    #>   B                         24 (19.8%)   29 (27.4%)     22 (17.1%)   #>     CHN                      12 (50%)    13 (44.8%)      11 (50%)    #>     USA                      2 (8.3%)    5 (17.2%)       1 (4.5%)    #>     BRA                     4 (16.7%)    3 (10.3%)       1 (4.5%)    #>     PAK                      2 (8.3%)     2 (6.9%)      4 (18.2%)    #>     NGA                      2 (8.3%)     1 (3.4%)      3 (13.6%)    #>     RUS                      1 (4.2%)     1 (3.4%)       2 (9.1%)    #>     JPN                         0        4 (13.8%)          0        #>   C                         28 (23.1%)   19 (17.9%)     31 (24.0%)   #>     CHN                     13 (46.4%)   10 (52.6%)     16 (51.6%)   #>     USA                     3 (10.7%)    3 (15.8%)      4 (12.9%)    #>     BRA                      1 (3.6%)     1 (5.3%)      4 (12.9%)    #>     PAK                      1 (3.6%)     1 (5.3%)       3 (9.7%)    #>     NGA                     4 (14.3%)     1 (5.3%)       2 (6.5%)    #>     RUS                     4 (14.3%)    2 (10.5%)       1 (3.2%)    #> BLACK OR AFRICAN AMERICAN                                            #>   A                          6 (5.0%)     7 (6.6%)       8 (6.2%)    #>     CHN                      3 (50%)     3 (42.9%)      5 (62.5%)    #>     USA                     2 (33.3%)    1 (14.3%)      1 (12.5%)    #>     BRA                         0        1 (14.3%)          0        #>     PAK                         0            0          1 (12.5%)    #>     NGA                         0            0          1 (12.5%)    #>     JPN                     1 (16.7%)        0              0        #>     GBR                         0        2 (28.6%)          0        #>   B                         10 (8.3%)     6 (5.7%)      12 (9.3%)    #>     CHN                      3 (30%)     2 (33.3%)      8 (66.7%)    #>     USA                      1 (10%)         0           1 (8.3%)    #>     BRA                      2 (20%)     1 (16.7%)       1 (8.3%)    #>     PAK                         0        1 (16.7%)          0        #>     RUS                         0        1 (16.7%)          0        #>     JPN                      2 (20%)         0           1 (8.3%)    #>     GBR                      1 (10%)         0           1 (8.3%)    #>     CAN                      1 (10%)     1 (16.7%)          0        #>   C                         12 (9.9%)    11 (10.4%)      7 (5.4%)    #>     CHN                     8 (66.7%)    5 (45.5%)      5 (71.4%)    #>     USA                      1 (8.3%)    2 (18.2%)      1 (14.3%)    #>     BRA                      1 (8.3%)    2 (18.2%)          0        #>     PAK                      1 (8.3%)     1 (9.1%)      1 (14.3%)    #>     NGA                         0         1 (9.1%)          0        #>     RUS                      1 (8.3%)        0              0        #> WHITE                                                                #>   A                          3 (2.5%)     6 (5.7%)       6 (4.7%)    #>     CHN                     2 (66.7%)    2 (33.3%)       3 (50%)     #>     USA                     1 (33.3%)    1 (16.7%)          0        #>     PAK                         0        1 (16.7%)      1 (16.7%)    #>     NGA                         0        1 (16.7%)          0        #>     RUS                         0            0          1 (16.7%)    #>     JPN                         0        1 (16.7%)          0        #>     CAN                         0            0          1 (16.7%)    #>   B                          7 (5.8%)     5 (4.7%)       4 (3.1%)    #>     CHN                     4 (57.1%)     1 (20%)        3 (75%)     #>     USA                         0         1 (20%)           0        #>     BRA                         0         1 (20%)           0        #>     PAK                     1 (14.3%)        0              0        #>     NGA                     1 (14.3%)        0              0        #>     RUS                     1 (14.3%)        0           1 (25%)     #>     JPN                         0         1 (20%)           0        #>     CAN                         0         1 (20%)           0        #>   C                          4 (3.3%)     3 (2.8%)       8 (6.2%)    #>     CHN                      3 (75%)      3 (100%)       6 (75%)     #>     USA                      1 (25%)         0          1 (12.5%)    #>     JPN                         0            0          1 (12.5%)    # }  # \\donttest{ more_than_one_diff <- has_counts_difference(atleast = 1L, col_names = names(tab)) prune_table(tab, keep_rows(more_than_one_diff)) #>                             A: Drug X    B: Placebo   C: Combination #> ———————————————————————————————————————————————————————————————————— #> ASIAN                                                                #>   A                         27 (22.3%)   20 (18.9%)     31 (24.0%)   #>     CHN                     14 (51.9%)    9 (45%)       12 (38.7%)   #>     USA                      2 (7.4%)      1 (5%)       8 (25.8%)    #>     BRA                      1 (3.7%)     4 (20%)        1 (3.2%)    #>     PAK                     3 (11.1%)     2 (10%)        2 (6.5%)    #>     NGA                     3 (11.1%)      1 (5%)        3 (9.7%)    #>     RUS                      2 (7.4%)      1 (5%)        1 (3.2%)    #>     JPN                         0          1 (5%)        2 (6.5%)    #>     GBR                         0          1 (5%)        1 (3.2%)    #>     CAN                      2 (7.4%)        0           1 (3.2%)    #>   B                         24 (19.8%)   29 (27.4%)     22 (17.1%)   #>     CHN                      12 (50%)    13 (44.8%)      11 (50%)    #>     USA                      2 (8.3%)    5 (17.2%)       1 (4.5%)    #>     BRA                     4 (16.7%)    3 (10.3%)       1 (4.5%)    #>     PAK                      2 (8.3%)     2 (6.9%)      4 (18.2%)    #>     NGA                      2 (8.3%)     1 (3.4%)      3 (13.6%)    #>     RUS                      1 (4.2%)     1 (3.4%)       2 (9.1%)    #>     JPN                         0        4 (13.8%)          0        #>     GBR                      1 (4.2%)        0              0        #>   C                         28 (23.1%)   19 (17.9%)     31 (24.0%)   #>     CHN                     13 (46.4%)   10 (52.6%)     16 (51.6%)   #>     USA                     3 (10.7%)    3 (15.8%)      4 (12.9%)    #>     BRA                      1 (3.6%)     1 (5.3%)      4 (12.9%)    #>     PAK                      1 (3.6%)     1 (5.3%)       3 (9.7%)    #>     NGA                     4 (14.3%)     1 (5.3%)       2 (6.5%)    #>     RUS                     4 (14.3%)    2 (10.5%)       1 (3.2%)    #>     JPN                      2 (7.1%)     1 (5.3%)       1 (3.2%)    #> BLACK OR AFRICAN AMERICAN                                            #>   A                          6 (5.0%)     7 (6.6%)       8 (6.2%)    #>     CHN                      3 (50%)     3 (42.9%)      5 (62.5%)    #>     USA                     2 (33.3%)    1 (14.3%)      1 (12.5%)    #>     BRA                         0        1 (14.3%)          0        #>     PAK                         0            0          1 (12.5%)    #>     NGA                         0            0          1 (12.5%)    #>     JPN                     1 (16.7%)        0              0        #>     GBR                         0        2 (28.6%)          0        #>   B                         10 (8.3%)     6 (5.7%)      12 (9.3%)    #>     CHN                      3 (30%)     2 (33.3%)      8 (66.7%)    #>     USA                      1 (10%)         0           1 (8.3%)    #>     BRA                      2 (20%)     1 (16.7%)       1 (8.3%)    #>     PAK                         0        1 (16.7%)          0        #>     RUS                         0        1 (16.7%)          0        #>     JPN                      2 (20%)         0           1 (8.3%)    #>     GBR                      1 (10%)         0           1 (8.3%)    #>     CAN                      1 (10%)     1 (16.7%)          0        #>   C                         12 (9.9%)    11 (10.4%)      7 (5.4%)    #>     CHN                     8 (66.7%)    5 (45.5%)      5 (71.4%)    #>     USA                      1 (8.3%)    2 (18.2%)      1 (14.3%)    #>     BRA                      1 (8.3%)    2 (18.2%)          0        #>     NGA                         0         1 (9.1%)          0        #>     RUS                      1 (8.3%)        0              0        #> WHITE                                                                #>   A                          3 (2.5%)     6 (5.7%)       6 (4.7%)    #>     CHN                     2 (66.7%)    2 (33.3%)       3 (50%)     #>     USA                     1 (33.3%)    1 (16.7%)          0        #>     PAK                         0        1 (16.7%)      1 (16.7%)    #>     NGA                         0        1 (16.7%)          0        #>     RUS                         0            0          1 (16.7%)    #>     JPN                         0        1 (16.7%)          0        #>     CAN                         0            0          1 (16.7%)    #>   B                          7 (5.8%)     5 (4.7%)       4 (3.1%)    #>     CHN                     4 (57.1%)     1 (20%)        3 (75%)     #>     USA                         0         1 (20%)           0        #>     BRA                         0         1 (20%)           0        #>     PAK                     1 (14.3%)        0              0        #>     NGA                     1 (14.3%)        0              0        #>     RUS                     1 (14.3%)        0           1 (25%)     #>     JPN                         0         1 (20%)           0        #>     CAN                         0         1 (20%)           0        #>   C                          4 (3.3%)     3 (2.8%)       8 (6.2%)    #>     CHN                      3 (75%)      3 (100%)       6 (75%)     #>     USA                      1 (25%)         0          1 (12.5%)    #>     JPN                         0            0          1 (12.5%)    # }"},{"path":"https://insightsengineering.github.io/tern/reference/range_noinf.html","id":null,"dir":"Reference","previous_headings":"","what":"Re-implemented range() default S3 method for numerical objects — range_noinf","title":"Re-implemented range() default S3 method for numerical objects — range_noinf","text":"function returns c(NA, NA) instead c(-Inf, Inf) zero-length data without warnings.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/range_noinf.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Re-implemented range() default S3 method for numerical objects — range_noinf","text":"","code":"range_noinf(x, na.rm = FALSE, finite = FALSE)"},{"path":"https://insightsengineering.github.io/tern/reference/range_noinf.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Re-implemented range() default S3 method for numerical objects — range_noinf","text":"x (numeric) sequence numbers range computed. na.rm (flag) flag indicating NA omitted. finite (flag) flag indicating non-finite elements removed.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/range_noinf.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Re-implemented range() default S3 method for numerical objects — range_noinf","text":"2-element vector class numeric.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/reapply_varlabels.html","id":null,"dir":"Reference","previous_headings":"","what":"Reapply variable labels — reapply_varlabels","title":"Reapply variable labels — reapply_varlabels","text":"helper function used tests.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/reapply_varlabels.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Reapply variable labels — reapply_varlabels","text":"","code":"reapply_varlabels(x, varlabels, ...)"},{"path":"https://insightsengineering.github.io/tern/reference/reapply_varlabels.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Reapply variable labels — reapply_varlabels","text":"x (vector) vector elements needs new labels. varlabels (character) vector labels x. ... parameters added list.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/reapply_varlabels.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Reapply variable labels — reapply_varlabels","text":"x variable labels reapplied.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/response_biomarkers_subgroups.html","id":null,"dir":"Reference","previous_headings":"","what":"Tabulate biomarker effects on binary response by subgroup — response_biomarkers_subgroups","title":"Tabulate biomarker effects on binary response by subgroup — response_biomarkers_subgroups","text":"tabulate_rsp_biomarkers() function creates layout element tabulate estimated biomarker effects binary response endpoint across subgroups, returning statistics including response rate odds ratio population subgroup. table created df, list data frames returned extract_rsp_biomarkers(), statistics include specified via vars parameter. forest plot can created resulting table using g_forest() function.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/response_biomarkers_subgroups.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Tabulate biomarker effects on binary response by subgroup — response_biomarkers_subgroups","text":"","code":"tabulate_rsp_biomarkers(   df,   vars = c(\"n_tot\", \"n_rsp\", \"prop\", \"or\", \"ci\", \"pval\"),   na_str = default_na_str(),   .indent_mods = 0L )"},{"path":"https://insightsengineering.github.io/tern/reference/response_biomarkers_subgroups.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Tabulate biomarker effects on binary response by subgroup — response_biomarkers_subgroups","text":"df (data.frame) containing analysis variables, returned extract_rsp_biomarkers(). vars (character) names statistics reported among: n_tot: Total number patients per group. n_rsp: Total number responses per group. prop: Total response proportion per group. : Odds ratio. ci: Confidence interval odds ratio. pval: p-value effect. Note, statistics n_tot, ci required. na_str (string) string used replace NA empty values output. .indent_mods (named integer) indent modifiers labels. Defaults 0, corresponds unmodified default behavior. Can negative.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/response_biomarkers_subgroups.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Tabulate biomarker effects on binary response by subgroup — response_biomarkers_subgroups","text":"rtables table summarizing biomarker effects binary response subgroup.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/response_biomarkers_subgroups.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Tabulate biomarker effects on binary response by subgroup — response_biomarkers_subgroups","text":"functions create layout starting data frame contains required statistics. tables typically used input forest plots.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/response_biomarkers_subgroups.html","id":"note","dir":"Reference","previous_headings":"","what":"Note","title":"Tabulate biomarker effects on binary response by subgroup — response_biomarkers_subgroups","text":"contrast tabulate_rsp_subgroups() tabulation function start input layout lyt. internally table created combining multiple subtables.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/reference/response_biomarkers_subgroups.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Tabulate biomarker effects on binary response by subgroup — response_biomarkers_subgroups","text":"","code":"library(dplyr) library(forcats)  adrs <- tern_ex_adrs adrs_labels <- formatters::var_labels(adrs)  adrs_f <- adrs %>%   filter(PARAMCD == \"BESRSPI\") %>%   mutate(rsp = AVALC == \"CR\") formatters::var_labels(adrs_f) <- c(adrs_labels, \"Response\")  df <- extract_rsp_biomarkers(   variables = list(     rsp = \"rsp\",     biomarkers = c(\"BMRKR1\", \"AGE\"),     covariates = \"SEX\",     subgroups = \"BMRKR2\"   ),   data = adrs_f )  # \\donttest{ ## Table with default columns. tabulate_rsp_biomarkers(df) #>                                  Total n   Responders   Response (%)   Odds Ratio      95% CI      p-value (Wald) #> ————————————————————————————————————————————————————————————————————————————————————————————————————————————————— #> Age                                                                                                               #>   All Patients                     200        164          82.0%          1.00      (0.95, 1.05)       0.8530     #>   Continuous Level Biomarker 2                                                                                    #>     LOW                            70          53          75.7%          0.93      (0.85, 1.01)       0.0845     #>     MEDIUM                         68          58          85.3%          0.99      (0.88, 1.11)       0.8190     #>     HIGH                           62          53          85.5%          1.06      (0.96, 1.18)       0.2419     #> Continuous Level Biomarker 1                                                                                      #>   All Patients                     200        164          82.0%          0.98      (0.88, 1.08)       0.6353     #>   Continuous Level Biomarker 2                                                                                    #>     LOW                            70          53          75.7%          1.15      (0.95, 1.40)       0.1584     #>     MEDIUM                         68          58          85.3%          0.88      (0.73, 1.06)       0.1700     #>     HIGH                           62          53          85.5%          0.88      (0.72, 1.08)       0.2104      ## Table with a manually chosen set of columns: leave out \"pval\", reorder. tab <- tabulate_rsp_biomarkers(   df = df,   vars = c(\"n_rsp\", \"ci\", \"n_tot\", \"prop\", \"or\") )  ## Finally produce the forest plot. g_forest(tab, xlim = c(0.7, 1.4))  # }"},{"path":"https://insightsengineering.github.io/tern/reference/response_subgroups.html","id":null,"dir":"Reference","previous_headings":"","what":"Tabulate binary response by subgroup — response_subgroups","title":"Tabulate binary response by subgroup — response_subgroups","text":"tabulate_rsp_subgroups() function creates layout element tabulate binary response subgroup, returning statistics including response rate odds ratio population subgroup. table created df, list data frames returned extract_rsp_subgroups(), statistics include specified via vars parameter. forest plot can created resulting table using g_forest() function.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/response_subgroups.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Tabulate binary response by subgroup — response_subgroups","text":"","code":"tabulate_rsp_subgroups(   lyt,   df,   vars = c(\"n_tot\", \"n\", \"prop\", \"or\", \"ci\"),   groups_lists = list(),   label_all = \"All Patients\",   riskdiff = NULL,   na_str = default_na_str(),   .formats = c(n = \"xx\", n_rsp = \"xx\", prop = \"xx.x%\", n_tot = \"xx\", or =     list(format_extreme_values(2L)), ci = list(format_extreme_values_ci(2L)), pval =     \"x.xxxx | (<0.0001)\") )  a_response_subgroups(   .formats = list(n = \"xx\", n_rsp = \"xx\", prop = \"xx.x%\", n_tot = \"xx\", or =     list(format_extreme_values(2L)), ci = list(format_extreme_values_ci(2L)), pval =     \"x.xxxx | (<0.0001)\", riskdiff = \"xx.x (xx.x - xx.x)\"),   na_str = default_na_str() )"},{"path":"https://insightsengineering.github.io/tern/reference/response_subgroups.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Tabulate binary response by subgroup — response_subgroups","text":"lyt (PreDataTableLayouts) layout analyses added . df (list) list data frames containing analysis variables. List created using extract_rsp_subgroups(). vars (character) names statistics reported among: n: Total number observations per group. n_rsp: Number responders per group. prop: Proportion responders. n_tot: Total number observations. : Odds ratio. ci : Confidence interval odds ratio. pval: p-value effect. Note, statistics n_tot, , ci required. groups_lists (named list list) optionally contains subgroups variable list, specifies new group levels via names levels belong character vectors elements list. label_all (string) label total population analysis. riskdiff (list) risk (proportion) difference column added, list settings apply within column. See control_riskdiff() details. NULL, risk difference column added. riskdiff$arm_x riskdiff$arm_y NULL, first level df$prop$arm used arm_x second level arm_y. na_str (string) string used replace NA empty values output. .formats (named character list) formats statistics. See Details analyze_vars information \"auto\" setting.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/response_subgroups.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Tabulate binary response by subgroup — response_subgroups","text":"rtables table summarizing binary response subgroup. a_response_subgroups() returns corresponding list formatted rtables::CellValue().","code":""},{"path":"https://insightsengineering.github.io/tern/reference/response_subgroups.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Tabulate binary response by subgroup — response_subgroups","text":"functions create layout starting data frame contains required statistics. Tables typically used part forest plot.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/response_subgroups.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Tabulate binary response by subgroup — response_subgroups","text":"tabulate_rsp_subgroups(): Table-creating function creates table summarizing binary response subgroup. function wrapper rtables::analyze_colvars() rtables::summarize_row_groups(). a_response_subgroups(): Formatted analysis function used afun tabulate_rsp_subgroups().","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/reference/response_subgroups.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Tabulate binary response by subgroup — response_subgroups","text":"","code":"library(dplyr) library(forcats)  adrs <- tern_ex_adrs adrs_labels <- formatters::var_labels(adrs)  adrs_f <- adrs %>%   filter(PARAMCD == \"BESRSPI\") %>%   filter(ARM %in% c(\"A: Drug X\", \"B: Placebo\")) %>%   droplevels() %>%   mutate(     # Reorder levels of factor to make the placebo group the reference arm.     ARM = fct_relevel(ARM, \"B: Placebo\"),     rsp = AVALC == \"CR\"   ) formatters::var_labels(adrs_f) <- c(adrs_labels, \"Response\")  # Unstratified analysis. df <- extract_rsp_subgroups(   variables = list(rsp = \"rsp\", arm = \"ARM\", subgroups = c(\"SEX\", \"BMRKR2\")),   data = adrs_f ) df #> $prop #>           arm  n n_rsp      prop     subgroup    var #> 1  B: Placebo 73    50 0.6849315 All Patients    ALL #> 2   A: Drug X 69    59 0.8550725 All Patients    ALL #> 3  B: Placebo 40    25 0.6250000            F    SEX #> 4   A: Drug X 38    36 0.9473684            F    SEX #> 5  B: Placebo 33    25 0.7575758            M    SEX #> 6   A: Drug X 31    23 0.7419355            M    SEX #> 7  B: Placebo 24    13 0.5416667          LOW BMRKR2 #> 8   A: Drug X 26    21 0.8076923          LOW BMRKR2 #> 9  B: Placebo 23    17 0.7391304       MEDIUM BMRKR2 #> 10  A: Drug X 26    23 0.8846154       MEDIUM BMRKR2 #> 11 B: Placebo 26    20 0.7692308         HIGH BMRKR2 #> 12  A: Drug X 17    15 0.8823529         HIGH BMRKR2 #>                       var_label row_type #> 1                  All Patients  content #> 2                  All Patients  content #> 3                           Sex analysis #> 4                           Sex analysis #> 5                           Sex analysis #> 6                           Sex analysis #> 7  Continuous Level Biomarker 2 analysis #> 8  Continuous Level Biomarker 2 analysis #> 9  Continuous Level Biomarker 2 analysis #> 10 Continuous Level Biomarker 2 analysis #> 11 Continuous Level Biomarker 2 analysis #> 12 Continuous Level Biomarker 2 analysis #>  #> $or #>   arm n_tot        or       lcl       ucl conf_level     subgroup    var #> 1       142  2.714000 1.1804488  6.239827       0.95 All Patients    ALL #> 2        78 10.800000 2.2669576 51.452218       0.95            F    SEX #> 3        64  0.920000 0.2966470  2.853223       0.95            M    SEX #> 4        50  3.553846 1.0047370 12.570277       0.95          LOW BMRKR2 #> 5        49  2.705882 0.5911718 12.385232       0.95       MEDIUM BMRKR2 #> 6        43  2.250000 0.3970298 12.750933       0.95         HIGH BMRKR2 #>                      var_label row_type #> 1                 All Patients  content #> 2                          Sex analysis #> 3                          Sex analysis #> 4 Continuous Level Biomarker 2 analysis #> 5 Continuous Level Biomarker 2 analysis #> 6 Continuous Level Biomarker 2 analysis #>   # Stratified analysis. df_strat <- extract_rsp_subgroups(   variables = list(rsp = \"rsp\", arm = \"ARM\", subgroups = c(\"SEX\", \"BMRKR2\"), strata = \"STRATA1\"),   data = adrs_f ) df_strat #> $prop #>           arm  n n_rsp      prop     subgroup    var #> 1  B: Placebo 73    50 0.6849315 All Patients    ALL #> 2   A: Drug X 69    59 0.8550725 All Patients    ALL #> 3  B: Placebo 40    25 0.6250000            F    SEX #> 4   A: Drug X 38    36 0.9473684            F    SEX #> 5  B: Placebo 33    25 0.7575758            M    SEX #> 6   A: Drug X 31    23 0.7419355            M    SEX #> 7  B: Placebo 24    13 0.5416667          LOW BMRKR2 #> 8   A: Drug X 26    21 0.8076923          LOW BMRKR2 #> 9  B: Placebo 23    17 0.7391304       MEDIUM BMRKR2 #> 10  A: Drug X 26    23 0.8846154       MEDIUM BMRKR2 #> 11 B: Placebo 26    20 0.7692308         HIGH BMRKR2 #> 12  A: Drug X 17    15 0.8823529         HIGH BMRKR2 #>                       var_label row_type #> 1                  All Patients  content #> 2                  All Patients  content #> 3                           Sex analysis #> 4                           Sex analysis #> 5                           Sex analysis #> 6                           Sex analysis #> 7  Continuous Level Biomarker 2 analysis #> 8  Continuous Level Biomarker 2 analysis #> 9  Continuous Level Biomarker 2 analysis #> 10 Continuous Level Biomarker 2 analysis #> 11 Continuous Level Biomarker 2 analysis #> 12 Continuous Level Biomarker 2 analysis #>  #> $or #>   arm n_tot        or       lcl       ucl conf_level     subgroup    var #> 1       142 2.6343899 1.1537821  6.015009       0.95 All Patients    ALL #> 2        78 9.5946605 2.0379337 45.171985       0.95            F    SEX #> 3        64 0.8947158 0.2936803  2.725809       0.95            M    SEX #> 4        50 3.5976656 1.0101319 12.813374       0.95          LOW BMRKR2 #> 5        49 2.6242168 0.5162572 13.339308       0.95       MEDIUM BMRKR2 #> 6        43 2.2816865 0.4116391 12.647228       0.95         HIGH BMRKR2 #>                      var_label row_type #> 1                 All Patients  content #> 2                          Sex analysis #> 3                          Sex analysis #> 4 Continuous Level Biomarker 2 analysis #> 5 Continuous Level Biomarker 2 analysis #> 6 Continuous Level Biomarker 2 analysis #>   # Grouping of the BMRKR2 levels. df_grouped <- extract_rsp_subgroups(   variables = list(rsp = \"rsp\", arm = \"ARM\", subgroups = c(\"SEX\", \"BMRKR2\")),   data = adrs_f,   groups_lists = list(     BMRKR2 = list(       \"low\" = \"LOW\",       \"low/medium\" = c(\"LOW\", \"MEDIUM\"),       \"low/medium/high\" = c(\"LOW\", \"MEDIUM\", \"HIGH\")     )   ) ) df_grouped #> $prop #>           arm  n n_rsp      prop        subgroup    var #> 1  B: Placebo 73    50 0.6849315    All Patients    ALL #> 2   A: Drug X 69    59 0.8550725    All Patients    ALL #> 3  B: Placebo 40    25 0.6250000               F    SEX #> 4   A: Drug X 38    36 0.9473684               F    SEX #> 5  B: Placebo 33    25 0.7575758               M    SEX #> 6   A: Drug X 31    23 0.7419355               M    SEX #> 7  B: Placebo 24    13 0.5416667             low BMRKR2 #> 8   A: Drug X 26    21 0.8076923             low BMRKR2 #> 9  B: Placebo 47    30 0.6382979      low/medium BMRKR2 #> 10  A: Drug X 52    44 0.8461538      low/medium BMRKR2 #> 11 B: Placebo 73    50 0.6849315 low/medium/high BMRKR2 #> 12  A: Drug X 69    59 0.8550725 low/medium/high BMRKR2 #>                       var_label row_type #> 1                  All Patients  content #> 2                  All Patients  content #> 3                           Sex analysis #> 4                           Sex analysis #> 5                           Sex analysis #> 6                           Sex analysis #> 7  Continuous Level Biomarker 2 analysis #> 8  Continuous Level Biomarker 2 analysis #> 9  Continuous Level Biomarker 2 analysis #> 10 Continuous Level Biomarker 2 analysis #> 11 Continuous Level Biomarker 2 analysis #> 12 Continuous Level Biomarker 2 analysis #>  #> $or #>   arm n_tot        or      lcl       ucl conf_level        subgroup    var #> 1       142  2.714000 1.180449  6.239827       0.95    All Patients    ALL #> 2        78 10.800000 2.266958 51.452218       0.95               F    SEX #> 3        64  0.920000 0.296647  2.853223       0.95               M    SEX #> 4        50  3.553846 1.004737 12.570277       0.95             low BMRKR2 #> 5        99  3.116667 1.193409  8.139385       0.95      low/medium BMRKR2 #> 6       142  2.714000 1.180449  6.239827       0.95 low/medium/high BMRKR2 #>                      var_label row_type #> 1                 All Patients  content #> 2                          Sex analysis #> 3                          Sex analysis #> 4 Continuous Level Biomarker 2 analysis #> 5 Continuous Level Biomarker 2 analysis #> 6 Continuous Level Biomarker 2 analysis #>   # Table with default columns basic_table() %>%   tabulate_rsp_subgroups(df) #>                                             B: Placebo           A: Drug X                                  #> Baseline Risk Factors          Total n   n    Response (%)   n    Response (%)   Odds Ratio      95% CI     #> ——————————————————————————————————————————————————————————————————————————————————————————————————————————— #> All Patients                     142     73      68.5%       69      85.5%          2.71      (1.18, 6.24)  #> Sex                                                                                                         #>   F                              78      40      62.5%       38      94.7%         10.80      (2.27, 51.45) #>   M                              64      33      75.8%       31      74.2%          0.92      (0.30, 2.85)  #> Continuous Level Biomarker 2                                                                                #>   LOW                            50      24      54.2%       26      80.8%          3.55      (1.00, 12.57) #>   MEDIUM                         49      23      73.9%       26      88.5%          2.71      (0.59, 12.39) #>   HIGH                           43      26      76.9%       17      88.2%          2.25      (0.40, 12.75)  # Table with selected columns basic_table() %>%   tabulate_rsp_subgroups(     df = df,     vars = c(\"n_tot\", \"n\", \"n_rsp\", \"prop\", \"or\", \"ci\")   ) #>                                                    B: Placebo                       A: Drug X                                         #> Baseline Risk Factors          Total n   n    Responders   Response (%)   n    Responders   Response (%)   Odds Ratio      95% CI     #> ————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————— #> All Patients                     142     73       50          68.5%       69       59          85.5%          2.71      (1.18, 6.24)  #> Sex                                                                                                                                   #>   F                              78      40       25          62.5%       38       36          94.7%         10.80      (2.27, 51.45) #>   M                              64      33       25          75.8%       31       23          74.2%          0.92      (0.30, 2.85)  #> Continuous Level Biomarker 2                                                                                                          #>   LOW                            50      24       13          54.2%       26       21          80.8%          3.55      (1.00, 12.57) #>   MEDIUM                         49      23       17          73.9%       26       23          88.5%          2.71      (0.59, 12.39) #>   HIGH                           43      26       20          76.9%       17       15          88.2%          2.25      (0.40, 12.75)  # Table with risk difference column added basic_table() %>%   tabulate_rsp_subgroups(     df,     riskdiff = control_riskdiff(       arm_x = levels(df$prop$arm)[1],       arm_y = levels(df$prop$arm)[2]     )   ) #>                                             B: Placebo           A: Drug X                                                                 #> Baseline Risk Factors          Total n   n    Response (%)   n    Response (%)   Odds Ratio      95% CI       Risk Difference (%) (95% CI) #> —————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————— #> All Patients                     142     73      68.5%       69      85.5%          2.71      (1.18, 6.24)        -17.0 (-30.5 - -3.5)     #> Sex                                                                                                                                        #>   F                              78      40      62.5%       38      94.7%         10.80      (2.27, 51.45)      -32.2 (-48.8 - -15.6)     #>   M                              64      33      75.8%       31      74.2%          0.92      (0.30, 2.85)         1.6 (-19.7 - 22.8)      #> Continuous Level Biomarker 2                                                                                                               #>   LOW                            50      24      54.2%       26      80.8%          3.55      (1.00, 12.57)       -26.6 (-51.6 - -1.6)     #>   MEDIUM                         49      23      73.9%       26      88.5%          2.71      (0.59, 12.39)       -14.5 (-36.3 - 7.2)      #>   HIGH                           43      26      76.9%       17      88.2%          2.25      (0.40, 12.75)       -11.3 (-33.6 - 11.0)"},{"path":"https://insightsengineering.github.io/tern/reference/rtable2gg.html","id":null,"dir":"Reference","previous_headings":"","what":"Convert rtable objects to ggplot objects — rtable2gg","title":"Convert rtable objects to ggplot objects — rtable2gg","text":"Given rtables::rtable() object, performs basic conversion ggplot2::ggplot() object built using functions ggplot2 package. table titles /footnotes ignored.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/rtable2gg.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Convert rtable objects to ggplot objects — rtable2gg","text":"","code":"rtable2gg(tbl, fontsize = 12, colwidths = NULL, lbl_col_padding = 0)"},{"path":"https://insightsengineering.github.io/tern/reference/rtable2gg.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Convert rtable objects to ggplot objects — rtable2gg","text":"tbl (VTableTree)rtables table object. fontsize (numeric(1)) font size. colwidths (numeric NULL) vector column widths. element's position colwidths corresponds column tbl position. NULL, column widths calculated according maximum number characters per column. lbl_col_padding (numeric) additional padding use calculating spacing first (label) column second column tbl. colwidths specified, width first column becomes colwidths[1] + lbl_col_padding. Defaults 0.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/rtable2gg.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Convert rtable objects to ggplot objects — rtable2gg","text":"ggplot object.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/rtable2gg.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Convert rtable objects to ggplot objects — rtable2gg","text":"","code":"dta <- data.frame(   ARM     = rep(LETTERS[1:3], rep(6, 3)),   AVISIT  = rep(paste0(\"V\", 1:3), 6),   AVAL    = c(9:1, rep(NA, 9)) )  lyt <- basic_table() %>%   split_cols_by(var = \"ARM\") %>%   split_rows_by(var = \"AVISIT\") %>%   analyze_vars(vars = \"AVAL\")  tbl <- build_table(lyt, df = dta)  rtable2gg(tbl)   rtable2gg(tbl, fontsize = 15, colwidths = c(2, 1, 1, 1))"},{"path":"https://insightsengineering.github.io/tern/reference/rtables_access.html","id":null,"dir":"Reference","previous_headings":"","what":"Helper functions for accessing information from rtables — rtables_access","title":"Helper functions for accessing information from rtables — rtables_access","text":"couple functions help accessing data rtables objects. Currently work occurrence tables, defined count first element fraction second element cell.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/rtables_access.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Helper functions for accessing information from rtables — rtables_access","text":"","code":"h_row_first_values(table_row, col_names = NULL, col_indices = NULL)  h_row_counts(table_row, col_names = NULL, col_indices = NULL)  h_row_fractions(table_row, col_names = NULL, col_indices = NULL)  h_col_counts(table, col_names = NULL, col_indices = NULL)  h_content_first_row(table)  is_leaf_table(table)  check_names_indices(table_row, col_names = NULL, col_indices = NULL)"},{"path":"https://insightsengineering.github.io/tern/reference/rtables_access.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Helper functions for accessing information from rtables — rtables_access","text":"table_row (TableRow) analysis row occurrence table. col_names (character) names columns extract . col_indices (integer) indices columns extract . col_names provided, inferred names table_row. Note currently works well single column split. table (VTableNodeInfo) occurrence table row.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/rtables_access.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Helper functions for accessing information from rtables — rtables_access","text":"h_row_first_values() returns vector numeric values. h_row_counts() returns vector numeric values. h_row_fractions() returns vector proportions. h_col_counts() returns vector column counts. h_content_first_row() returns row rtables table. is_leaf_table() returns logical value indicating whether current table leaf. check_names_indices returns column indices.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/rtables_access.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Helper functions for accessing information from rtables — rtables_access","text":"h_row_first_values(): Helper function extract first values content cell specified columns TableRow. Defaults columns. h_row_counts(): Helper function extracts row values checks convertible integers (integerish values). h_row_fractions(): Helper function extract fractions specified columns TableRow. specifically extracts second values content cell checks fraction. h_col_counts(): Helper function extract column counts specified columns table. h_content_first_row(): Helper function get first row content table current table. is_leaf_table(): Helper function says whether current table leaf tree. check_names_indices(): Internal helper function tests standard inputs column indices.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/reference/rtables_access.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Helper functions for accessing information from rtables — rtables_access","text":"","code":"tbl <- basic_table() %>%   split_cols_by(\"ARM\") %>%   split_rows_by(\"RACE\") %>%   analyze(\"AGE\", function(x) {     list(       \"mean (sd)\" = rcell(c(mean(x), sd(x)), format = \"xx.x (xx.x)\"),       \"n\" = length(x),       \"frac\" = rcell(c(0.1, 0.1), format = \"xx (xx)\")     )   }) %>%   build_table(tern_ex_adsl) %>%   prune_table() tree_row_elem <- collect_leaves(tbl[2, ])[[1]] result <- max(h_row_first_values(tree_row_elem)) result #> [1] 35.31214  # Row counts (integer values) # h_row_counts(tree_row_elem) # Fails because there are no integers # Using values with integers tree_row_elem <- collect_leaves(tbl[3, ])[[1]] result <- h_row_counts(tree_row_elem) # result  # Row fractions tree_row_elem <- collect_leaves(tbl[4, ])[[1]] h_row_fractions(tree_row_elem) #>      A: Drug X     B: Placebo C: Combination  #>            0.1            0.1            0.1"},{"path":"https://insightsengineering.github.io/tern/reference/s_bland_altman.html","id":null,"dir":"Reference","previous_headings":"","what":"Bland-Altman analysis — s_bland_altman","title":"Bland-Altman analysis — s_bland_altman","text":"Statistics function uses Bland-Altman method assess agreement two numerical vectors calculates variety statistics.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/s_bland_altman.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Bland-Altman analysis — s_bland_altman","text":"","code":"s_bland_altman(x, y, conf_level = 0.95)"},{"path":"https://insightsengineering.github.io/tern/reference/s_bland_altman.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Bland-Altman analysis — s_bland_altman","text":"x (numeric) vector numbers want analyze. y (numeric) vector numbers want analyze, compared x. conf_level (proportion) confidence level interval.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/s_bland_altman.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Bland-Altman analysis — s_bland_altman","text":"named list following elements: df difference_mean ci_mean difference_sd difference_se upper_agreement_limit lower_agreement_limit agreement_limit_se upper_agreement_limit_ci lower_agreement_limit_ci t_value n","code":""},{"path":"https://insightsengineering.github.io/tern/reference/s_bland_altman.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Bland-Altman analysis — s_bland_altman","text":"","code":"x <- seq(1, 60, 5) y <- seq(5, 50, 4)  s_bland_altman(x, y, conf_level = 0.9) #> $df #>    average difference #> 1      3.0         -4 #> 2      7.5         -3 #> 3     12.0         -2 #> 4     16.5         -1 #> 5     21.0          0 #> 6     25.5          1 #> 7     30.0          2 #> 8     34.5          3 #> 9     39.0          4 #> 10    43.5          5 #> 11    48.0          6 #> 12    52.5          7 #>  #> $difference_mean #> [1] 1.5 #>  #> $ci_mean #> [1] -0.3692162  3.3692162 #>  #> $difference_sd #> [1] 3.605551 #>  #> $difference_se #> [1] 1.040833 #>  #> $upper_agreement_limit #> [1] 7.430604 #>  #> $lower_agreement_limit #> [1] -4.430604 #>  #> $agreement_limit_se #> [1] 1.802776 #>  #> $upper_agreement_limit_ci #> [1]  4.193027 10.668181 #>  #> $lower_agreement_limit_ci #> [1] -7.668181 -1.193027 #>  #> $t_value #> [1] 1.795885 #>  #> $n #> [1] 12 #>"},{"path":"https://insightsengineering.github.io/tern/reference/s_cox_multivariate.html","id":null,"dir":"Reference","previous_headings":"","what":"Multivariate Cox model - summarized results — s_cox_multivariate","title":"Multivariate Cox model - summarized results — s_cox_multivariate","text":"Analyses based multivariate Cox model usually performed Controlled Substance Reporting regulatory documents serve exploratory purposes (e.g., publication). practice, model usually includes main effects (without interaction terms). produces hazard ratio estimates covariates included model. analysis follows principles (e.g., stratified vs. unstratified analysis tie handling) usual Cox model analysis. Since usually pre-specified hypothesis testing analysis, p.values need interpreted caution. (Statistical Analysis Clinical Trials Data R, NEST's bookdown)","code":""},{"path":"https://insightsengineering.github.io/tern/reference/s_cox_multivariate.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Multivariate Cox model - summarized results — s_cox_multivariate","text":"","code":"s_cox_multivariate(   formula,   data,   conf_level = 0.95,   pval_method = c(\"wald\", \"likelihood\"),   ... )"},{"path":"https://insightsengineering.github.io/tern/reference/s_cox_multivariate.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Multivariate Cox model - summarized results — s_cox_multivariate","text":"formula (formula) formula corresponding investigated survival::Surv() survival model including covariates. data (data.frame) data frame includes variable formula covariates. conf_level (proportion) confidence level hazard ratio interval estimations. Default 0.95. pval_method (string) method used estimation p-values, one \"wald\" (default) \"likelihood\". ... optional parameters passed survival::coxph(). Can include ties, character string specifying method tie handling, one exact (default), efron, breslow.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/s_cox_multivariate.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Multivariate Cox model - summarized results — s_cox_multivariate","text":"list elements mod, msum, aov, coef_inter.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/s_cox_multivariate.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Multivariate Cox model - summarized results — s_cox_multivariate","text":"output limited single effect terms. Work ongoing estimation interaction terms scope defined  Global Data Standards Repository (GDS_Standard_TLG_Specs_Tables_2.doc).","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/reference/s_cox_multivariate.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Multivariate Cox model - summarized results — s_cox_multivariate","text":"","code":"library(dplyr)  adtte <- tern_ex_adtte adtte_f <- subset(adtte, PARAMCD == \"OS\") # _f: filtered adtte_f <- filter(   adtte_f,   PARAMCD == \"OS\" &     SEX %in% c(\"F\", \"M\") &     RACE %in% c(\"ASIAN\", \"BLACK OR AFRICAN AMERICAN\", \"WHITE\") ) adtte_f$SEX <- droplevels(adtte_f$SEX) adtte_f$RACE <- droplevels(adtte_f$RACE)"},{"path":"https://insightsengineering.github.io/tern/reference/sas_na.html","id":null,"dir":"Reference","previous_headings":"","what":"Convert strings to NA — sas_na","title":"Convert strings to NA — sas_na","text":"SAS imports missing data empty strings strings whitespaces . helper function can used convert values NAs.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/sas_na.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Convert strings to NA — sas_na","text":"","code":"sas_na(x, empty = TRUE, whitespaces = TRUE)"},{"path":"https://insightsengineering.github.io/tern/reference/sas_na.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Convert strings to NA — sas_na","text":"x (factor character) values missing values substituted. empty (flag) TRUE, empty strings get replaced NA. whitespaces (flag) TRUE, strings made whitespaces get replaced NA.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/sas_na.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Convert strings to NA — sas_na","text":"x \"\" /whitespace-values substituted NA, depending values empty whitespaces.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/sas_na.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Convert strings to NA — sas_na","text":"","code":"sas_na(c(\"1\", \"\", \" \", \"   \", \"b\")) #> [1] \"1\" NA  NA  NA  \"b\" sas_na(factor(c(\"\", \" \", \"b\"))) #> [1] <NA> <NA> b    #> Levels: b  is.na(sas_na(c(\"1\", \"\", \" \", \"   \", \"b\"))) #> [1] FALSE  TRUE  TRUE  TRUE FALSE"},{"path":"https://insightsengineering.github.io/tern/reference/score_occurrences.html","id":null,"dir":"Reference","previous_headings":"","what":"Occurrence table sorting — score_occurrences","title":"Occurrence table sorting — score_occurrences","text":"Functions score occurrence table subtables rows can used sorting occurrence tables.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/score_occurrences.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Occurrence table sorting — score_occurrences","text":"","code":"score_occurrences(table_row)  score_occurrences_cols(...)  score_occurrences_subtable(...)  score_occurrences_cont_cols(...)"},{"path":"https://insightsengineering.github.io/tern/reference/score_occurrences.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Occurrence table sorting — score_occurrences","text":"table_row (TableRow) analysis row occurrence table. ... arguments row column access, see rtables_access: either col_names (character) including names columns used, alternatively col_indices (integer) giving indices directly instead.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/score_occurrences.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Occurrence table sorting — score_occurrences","text":"score_occurrences() returns sum counts across columns table row. score_occurrences_cols() returns function sums counts across specified columns table row. score_occurrences_subtable() returns function sums counts subtable across specified columns. score_occurrences_cont_cols() returns function sums counts first content row specified columns.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/score_occurrences.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Occurrence table sorting — score_occurrences","text":"score_occurrences(): Scoring function sums counts across columns. fail anything else counts used. score_occurrences_cols(): Scoring functions can produced constructor include specific columns scoring. See h_row_counts() information. score_occurrences_subtable(): Scoring functions produced constructor can used subtables: sum specified column counts subtable. useful available content row summing counts. score_occurrences_cont_cols(): Produces score function sorting table summing first content row specified columns. Note extending rtables::cont_n_onecol() rtables::cont_n_allcols().","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/reference/score_occurrences.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Occurrence table sorting — score_occurrences","text":"","code":"lyt <- basic_table() %>%   split_cols_by(\"ARM\") %>%   add_colcounts() %>%   analyze_num_patients(     vars = \"USUBJID\",     .stats = c(\"unique\"),     .labels = c(\"Total number of patients with at least one event\")   ) %>%   split_rows_by(\"AEBODSYS\", child_labels = \"visible\", nested = FALSE) %>%   summarize_num_patients(     var = \"USUBJID\",     .stats = c(\"unique\", \"nonunique\"),     .labels = c(       \"Total number of patients with at least one event\",       \"Total number of events\"     )   ) %>%   count_occurrences(vars = \"AEDECOD\")  tbl <- build_table(lyt, tern_ex_adae, alt_counts_df = tern_ex_adsl) %>%   prune_table()  tbl_sorted <- tbl %>%   sort_at_path(path = c(\"AEBODSYS\", \"*\", \"AEDECOD\"), scorefun = score_occurrences)  tbl_sorted #>                                                      A: Drug X    B: Placebo   C: Combination #>                                                        (N=69)       (N=73)         (N=58)     #> ————————————————————————————————————————————————————————————————————————————————————————————— #> Total number of patients with at least one event     59 (85.5%)   57 (78.1%)     48 (82.8%)   #> cl D.1                                                                                        #>   Total number of patients with at least one event   29 (42.0%)   27 (37.0%)     20 (34.5%)   #>   Total number of events                                 39           35             28       #>     dcd D.1.1.4.2                                    16 (23.2%)   13 (17.8%)     16 (27.6%)   #>     dcd D.1.1.1.1                                    17 (24.6%)   18 (24.7%)     7 (12.1%)    #> cl C.1                                                                                        #>   Total number of patients with at least one event   15 (21.7%)   13 (17.8%)     18 (31.0%)   #>   Total number of events                                 17           15             19       #>     dcd C.1.1.1.3                                    15 (21.7%)   13 (17.8%)     18 (31.0%)   #> cl C.2                                                                                        #>   Total number of patients with at least one event   20 (29.0%)   14 (19.2%)     10 (17.2%)   #>   Total number of events                                 21           15             14       #>     dcd C.2.1.2.1                                    20 (29.0%)   14 (19.2%)     10 (17.2%)   #> cl B.2                                                                                        #>   Total number of patients with at least one event   29 (42.0%)   27 (37.0%)     24 (41.4%)   #>   Total number of events                                 40           38             33       #>     dcd B.2.2.3.1                                    17 (24.6%)   15 (20.5%)     16 (27.6%)   #>     dcd B.2.1.2.1                                    17 (24.6%)   16 (21.9%)     13 (22.4%)   #> cl B.1                                                                                        #>   Total number of patients with at least one event   15 (21.7%)   19 (26.0%)     15 (25.9%)   #>   Total number of events                                 19           19             18       #>     dcd B.1.1.1.1                                    15 (21.7%)   19 (26.0%)     15 (25.9%)   #> cl D.2                                                                                        #>   Total number of patients with at least one event   21 (30.4%)   20 (27.4%)     12 (20.7%)   #>   Total number of events                                 27           22             15       #>     dcd D.2.1.5.3                                    21 (30.4%)   20 (27.4%)     12 (20.7%)   #> cl A.1                                                                                        #>   Total number of patients with at least one event   31 (44.9%)   24 (32.9%)     27 (46.6%)   #>   Total number of events                                 39           33             35       #>     dcd A.1.1.1.1                                    17 (24.6%)   17 (23.3%)     14 (24.1%)   #>     dcd A.1.1.1.2                                    17 (24.6%)   14 (19.2%)     17 (29.3%)    score_cols_a_and_b <- score_occurrences_cols(col_names = c(\"A: Drug X\", \"B: Placebo\"))  # Note that this here just sorts the AEDECOD inside the AEBODSYS. The AEBODSYS are not sorted. # That would require a second pass of `sort_at_path`. tbl_sorted <- tbl %>%   sort_at_path(path = c(\"AEBODSYS\", \"*\", \"AEDECOD\"), scorefun = score_cols_a_and_b)  tbl_sorted #>                                                      A: Drug X    B: Placebo   C: Combination #>                                                        (N=69)       (N=73)         (N=58)     #> ————————————————————————————————————————————————————————————————————————————————————————————— #> Total number of patients with at least one event     59 (85.5%)   57 (78.1%)     48 (82.8%)   #> cl D.1                                                                                        #>   Total number of patients with at least one event   29 (42.0%)   27 (37.0%)     20 (34.5%)   #>   Total number of events                                 39           35             28       #>     dcd D.1.1.1.1                                    17 (24.6%)   18 (24.7%)     7 (12.1%)    #>     dcd D.1.1.4.2                                    16 (23.2%)   13 (17.8%)     16 (27.6%)   #> cl C.1                                                                                        #>   Total number of patients with at least one event   15 (21.7%)   13 (17.8%)     18 (31.0%)   #>   Total number of events                                 17           15             19       #>     dcd C.1.1.1.3                                    15 (21.7%)   13 (17.8%)     18 (31.0%)   #> cl C.2                                                                                        #>   Total number of patients with at least one event   20 (29.0%)   14 (19.2%)     10 (17.2%)   #>   Total number of events                                 21           15             14       #>     dcd C.2.1.2.1                                    20 (29.0%)   14 (19.2%)     10 (17.2%)   #> cl B.2                                                                                        #>   Total number of patients with at least one event   29 (42.0%)   27 (37.0%)     24 (41.4%)   #>   Total number of events                                 40           38             33       #>     dcd B.2.1.2.1                                    17 (24.6%)   16 (21.9%)     13 (22.4%)   #>     dcd B.2.2.3.1                                    17 (24.6%)   15 (20.5%)     16 (27.6%)   #> cl B.1                                                                                        #>   Total number of patients with at least one event   15 (21.7%)   19 (26.0%)     15 (25.9%)   #>   Total number of events                                 19           19             18       #>     dcd B.1.1.1.1                                    15 (21.7%)   19 (26.0%)     15 (25.9%)   #> cl D.2                                                                                        #>   Total number of patients with at least one event   21 (30.4%)   20 (27.4%)     12 (20.7%)   #>   Total number of events                                 27           22             15       #>     dcd D.2.1.5.3                                    21 (30.4%)   20 (27.4%)     12 (20.7%)   #> cl A.1                                                                                        #>   Total number of patients with at least one event   31 (44.9%)   24 (32.9%)     27 (46.6%)   #>   Total number of events                                 39           33             35       #>     dcd A.1.1.1.1                                    17 (24.6%)   17 (23.3%)     14 (24.1%)   #>     dcd A.1.1.1.2                                    17 (24.6%)   14 (19.2%)     17 (29.3%)    score_subtable_all <- score_occurrences_subtable(col_names = names(tbl))  # Note that this code just sorts the AEBODSYS, not the AEDECOD within AEBODSYS. That # would require a second pass of `sort_at_path`. tbl_sorted <- tbl %>%   sort_at_path(path = c(\"AEBODSYS\"), scorefun = score_subtable_all, decreasing = FALSE)  tbl_sorted #>                                                      A: Drug X    B: Placebo   C: Combination #>                                                        (N=69)       (N=73)         (N=58)     #> ————————————————————————————————————————————————————————————————————————————————————————————— #> Total number of patients with at least one event     59 (85.5%)   57 (78.1%)     48 (82.8%)   #> cl C.2                                                                                        #>   Total number of patients with at least one event   20 (29.0%)   14 (19.2%)     10 (17.2%)   #>   Total number of events                                 21           15             14       #>     dcd C.2.1.2.1                                    20 (29.0%)   14 (19.2%)     10 (17.2%)   #> cl C.1                                                                                        #>   Total number of patients with at least one event   15 (21.7%)   13 (17.8%)     18 (31.0%)   #>   Total number of events                                 17           15             19       #>     dcd C.1.1.1.3                                    15 (21.7%)   13 (17.8%)     18 (31.0%)   #> cl B.1                                                                                        #>   Total number of patients with at least one event   15 (21.7%)   19 (26.0%)     15 (25.9%)   #>   Total number of events                                 19           19             18       #>     dcd B.1.1.1.1                                    15 (21.7%)   19 (26.0%)     15 (25.9%)   #> cl D.2                                                                                        #>   Total number of patients with at least one event   21 (30.4%)   20 (27.4%)     12 (20.7%)   #>   Total number of events                                 27           22             15       #>     dcd D.2.1.5.3                                    21 (30.4%)   20 (27.4%)     12 (20.7%)   #> cl D.1                                                                                        #>   Total number of patients with at least one event   29 (42.0%)   27 (37.0%)     20 (34.5%)   #>   Total number of events                                 39           35             28       #>     dcd D.1.1.1.1                                    17 (24.6%)   18 (24.7%)     7 (12.1%)    #>     dcd D.1.1.4.2                                    16 (23.2%)   13 (17.8%)     16 (27.6%)   #> cl B.2                                                                                        #>   Total number of patients with at least one event   29 (42.0%)   27 (37.0%)     24 (41.4%)   #>   Total number of events                                 40           38             33       #>     dcd B.2.1.2.1                                    17 (24.6%)   16 (21.9%)     13 (22.4%)   #>     dcd B.2.2.3.1                                    17 (24.6%)   15 (20.5%)     16 (27.6%)   #> cl A.1                                                                                        #>   Total number of patients with at least one event   31 (44.9%)   24 (32.9%)     27 (46.6%)   #>   Total number of events                                 39           33             35       #>     dcd A.1.1.1.1                                    17 (24.6%)   17 (23.3%)     14 (24.1%)   #>     dcd A.1.1.1.2                                    17 (24.6%)   14 (19.2%)     17 (29.3%)"},{"path":[]},{"path":"https://insightsengineering.github.io/tern/reference/split_cols_by_groups.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Split columns by groups of levels — split_cols_by_groups","text":"","code":"split_cols_by_groups(lyt, var, groups_list = NULL, ref_group = NULL, ...)"},{"path":"https://insightsengineering.github.io/tern/reference/split_cols_by_groups.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Split columns by groups of levels — split_cols_by_groups","text":"lyt (PreDataTableLayouts) layout analyses added . var (string) single variable name passed rtables requested statistics function. groups_list (named list character) specifies new group levels via names levels belong character vectors elements list. ref_group (data.frame vector) data corresponding reference group. ... additional arguments rtables::split_cols_by() order. instance, control formats (format), add joint column groups (incl_all).","code":""},{"path":"https://insightsengineering.github.io/tern/reference/split_cols_by_groups.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Split columns by groups of levels — split_cols_by_groups","text":"layout object suitable passing layouting functions. Adding function rtable layout add column split including given groups table layout.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/reference/split_cols_by_groups.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Split columns by groups of levels — split_cols_by_groups","text":"","code":"# 1 - Basic use  # Without group combination `split_cols_by_groups` is # equivalent to [rtables::split_cols_by()]. basic_table() %>%   split_cols_by_groups(\"ARM\") %>%   add_colcounts() %>%   analyze(\"AGE\") %>%   build_table(DM) #>        A: Drug X   B: Placebo   C: Combination #>         (N=121)     (N=106)        (N=129)     #> —————————————————————————————————————————————— #> Mean     34.91       33.02          34.57       # Add a reference column. basic_table() %>%   split_cols_by_groups(\"ARM\", ref_group = \"B: Placebo\") %>%   add_colcounts() %>%   analyze(     \"AGE\",     afun = function(x, .ref_group, .in_ref_col) {       if (.in_ref_col) {         in_rows(\"Diff Mean\" = rcell(NULL))       } else {         in_rows(\"Diff Mean\" = rcell(mean(x) - mean(.ref_group), format = \"xx.xx\"))       }     }   ) %>%   build_table(DM) #>             A: Drug X   B: Placebo   C: Combination #>              (N=121)     (N=106)        (N=129)     #> ——————————————————————————————————————————————————— #> Diff Mean     1.89                        1.55       # 2 - Adding group specification  # Manual preparation of the groups. groups <- list(   \"Arms A+B\" = c(\"A: Drug X\", \"B: Placebo\"),   \"Arms A+C\" = c(\"A: Drug X\", \"C: Combination\") )  # Use of split_cols_by_groups without reference column. basic_table() %>%   split_cols_by_groups(\"ARM\", groups) %>%   add_colcounts() %>%   analyze(\"AGE\") %>%   build_table(DM) #>        Arms A+B   Arms A+C #>        (N=227)    (N=250)  #> —————————————————————————— #> Mean    34.03      34.73    # Including differentiated output in the reference column. basic_table() %>%   split_cols_by_groups(\"ARM\", groups_list = groups, ref_group = \"Arms A+B\") %>%   analyze(     \"AGE\",     afun = function(x, .ref_group, .in_ref_col) {       if (.in_ref_col) {         in_rows(\"Diff. of Averages\" = rcell(NULL))       } else {         in_rows(\"Diff. of Averages\" = rcell(mean(x) - mean(.ref_group), format = \"xx.xx\"))       }     }   ) %>%   build_table(DM) #>                     Arms A+B   Arms A+C #> ——————————————————————————————————————— #> Diff. of Averages                0.71    # 3 - Binary list dividing factor levels into reference and treatment  # `combine_groups` defines reference and treatment. groups <- combine_groups(   fct = DM$ARM,   ref = c(\"A: Drug X\", \"B: Placebo\") ) groups #> $`A: Drug X/B: Placebo` #> [1] \"A: Drug X\"  \"B: Placebo\" #>  #> $`C: Combination` #> [1] \"C: Combination\" #>   # Use group definition without reference column. basic_table() %>%   split_cols_by_groups(\"ARM\", groups_list = groups) %>%   add_colcounts() %>%   analyze(\"AGE\") %>%   build_table(DM) #>        A: Drug X/B: Placebo   C: Combination #>              (N=227)             (N=129)     #> ———————————————————————————————————————————— #> Mean          34.03               34.57       # Use group definition with reference column (first item of groups). basic_table() %>%   split_cols_by_groups(\"ARM\", groups, ref_group = names(groups)[1]) %>%   add_colcounts() %>%   analyze(     \"AGE\",     afun = function(x, .ref_group, .in_ref_col) {       if (.in_ref_col) {         in_rows(\"Diff Mean\" = rcell(NULL))       } else {         in_rows(\"Diff Mean\" = rcell(mean(x) - mean(.ref_group), format = \"xx.xx\"))       }     }   ) %>%   build_table(DM) #>             A: Drug X/B: Placebo   C: Combination #>                   (N=227)             (N=129)     #> ————————————————————————————————————————————————— #> Diff Mean                               0.54"},{"path":"https://insightsengineering.github.io/tern/reference/split_text_grob.html","id":null,"dir":"Reference","previous_headings":"","what":"Split text according to available text width — split_text_grob","title":"Split text according to available text width — split_text_grob","text":"Dynamically wrap text.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/split_text_grob.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Split text according to available text width — split_text_grob","text":"","code":"split_text_grob(   text,   x = grid::unit(0.5, \"npc\"),   y = grid::unit(0.5, \"npc\"),   width = grid::unit(1, \"npc\"),   just = \"centre\",   hjust = NULL,   vjust = NULL,   default.units = \"npc\",   name = NULL,   gp = grid::gpar(),   vp = NULL )"},{"path":"https://insightsengineering.github.io/tern/reference/split_text_grob.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Split text according to available text width — split_text_grob","text":"text (string) text wrap. x numeric vector unit object specifying x-values. y numeric vector unit object specifying y-values. width (grid::unit) unit object specifying maximum width text. just justification text     relative (x, y) location.  two values, first     value specifies horizontal justification second value specifies     vertical justification.  Possible string values : \"left\",     \"right\", \"centre\", \"center\", \"bottom\",     \"top\".  numeric values, 0 means left (bottom) alignment     1 means right (top) alignment. hjust numeric vector specifying horizontal justification.     specified, overrides just setting. vjust numeric vector specifying vertical justification.     specified, overrides just setting. default.units string indicating default units use     x y     given numeric vectors. name character identifier. gp object class \"gpar\", typically output     call function gpar.  basically     list graphical parameter settings. vp Grid viewport object (NULL).","code":""},{"path":"https://insightsengineering.github.io/tern/reference/split_text_grob.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Split text according to available text width — split_text_grob","text":"text grob.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/split_text_grob.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Split text according to available text width — split_text_grob","text":"code taken R Graphics Paul Murell, 2nd edition","code":""},{"path":"https://insightsengineering.github.io/tern/reference/stack_grobs.html","id":null,"dir":"Reference","previous_headings":"","what":"Stack multiple grobs — stack_grobs","title":"Stack multiple grobs — stack_grobs","text":"Stack grobs new grob 1 column multiple rows layout.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/stack_grobs.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Stack multiple grobs — stack_grobs","text":"","code":"stack_grobs(   ...,   grobs = list(...),   padding = grid::unit(2, \"line\"),   vp = NULL,   gp = NULL,   name = NULL )"},{"path":"https://insightsengineering.github.io/tern/reference/stack_grobs.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Stack multiple grobs — stack_grobs","text":"... grobs. grobs (list grob) list grobs. padding (grid::unit) unit length 1, space grob. vp (viewport NULL) viewport() object (NULL). gp (gpar) gpar() object. name (string) character identifier grob.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/stack_grobs.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Stack multiple grobs — stack_grobs","text":"grob.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/stack_grobs.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Stack multiple grobs — stack_grobs","text":"","code":"library(grid)  g1 <- circleGrob(gp = gpar(col = \"blue\")) g2 <- circleGrob(gp = gpar(col = \"red\")) g3 <- textGrob(\"TEST TEXT\") grid.newpage() grid.draw(stack_grobs(g1, g2, g3))  showViewport()   grid.newpage() pushViewport(viewport(layout = grid.layout(1, 2))) vp1 <- viewport(layout.pos.row = 1, layout.pos.col = 2) grid.draw(stack_grobs(g1, g2, g3, vp = vp1, name = \"test\"))  showViewport()  grid.ls(grobs = TRUE, viewports = TRUE, print = FALSE)"},{"path":"https://insightsengineering.github.io/tern/reference/stat_mean_ci.html","id":null,"dir":"Reference","previous_headings":"","what":"Confidence interval for mean — stat_mean_ci","title":"Confidence interval for mean — stat_mean_ci","text":"Convenient function calculating mean confidence interval. calculates arithmetic well geometric mean. can used ggplot helper function plotting.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/stat_mean_ci.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Confidence interval for mean — stat_mean_ci","text":"","code":"stat_mean_ci(   x,   conf_level = 0.95,   na.rm = TRUE,   n_min = 2,   gg_helper = TRUE,   geom_mean = FALSE )"},{"path":"https://insightsengineering.github.io/tern/reference/stat_mean_ci.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Confidence interval for mean — stat_mean_ci","text":"x (numeric) vector numbers want analyze. conf_level (proportion) confidence level interval. na.rm (flag) whether NA values removed x prior analysis. n_min (numeric(1)) minimum number non-missing x estimate confidence interval mean. gg_helper (flag) whether output aligned use ggplots. geom_mean (flag) whether geometric mean calculated.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/stat_mean_ci.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Confidence interval for mean — stat_mean_ci","text":"named vector values mean_ci_lwr mean_ci_upr.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/stat_mean_ci.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Confidence interval for mean — stat_mean_ci","text":"","code":"stat_mean_ci(sample(10), gg_helper = FALSE) #> mean_ci_lwr mean_ci_upr  #>    3.334149    7.665851   p <- ggplot2::ggplot(mtcars, ggplot2::aes(cyl, mpg)) +   ggplot2::geom_point()  p + ggplot2::stat_summary(   fun.data = stat_mean_ci,   geom = \"errorbar\" )   p + ggplot2::stat_summary(   fun.data = stat_mean_ci,   fun.args = list(conf_level = 0.5),   geom = \"errorbar\" )   p + ggplot2::stat_summary(   fun.data = stat_mean_ci,   fun.args = list(conf_level = 0.5, geom_mean = TRUE),   geom = \"errorbar\" )"},{"path":"https://insightsengineering.github.io/tern/reference/stat_mean_pval.html","id":null,"dir":"Reference","previous_headings":"","what":"p-Value of the mean — stat_mean_pval","title":"p-Value of the mean — stat_mean_pval","text":"Convenient function calculating two-sided p-value mean.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/stat_mean_pval.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"p-Value of the mean — stat_mean_pval","text":"","code":"stat_mean_pval(x, na.rm = TRUE, n_min = 2, test_mean = 0)"},{"path":"https://insightsengineering.github.io/tern/reference/stat_mean_pval.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"p-Value of the mean — stat_mean_pval","text":"x (numeric) vector numbers want analyze. na.rm (flag) whether NA values removed x prior analysis. n_min (numeric(1)) minimum number non-missing x estimate p-value mean. test_mean (numeric(1)) mean value test null hypothesis.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/stat_mean_pval.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"p-Value of the mean — stat_mean_pval","text":"p-value.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/stat_mean_pval.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"p-Value of the mean — stat_mean_pval","text":"","code":"stat_mean_pval(sample(10)) #>     p_value  #> 0.000278196   stat_mean_pval(rnorm(10), test_mean = 0.5) #>    p_value  #> 0.04235675"},{"path":"https://insightsengineering.github.io/tern/reference/stat_median_ci.html","id":null,"dir":"Reference","previous_headings":"","what":"Confidence interval for median — stat_median_ci","title":"Confidence interval for median — stat_median_ci","text":"Convenient function calculating median confidence interval. can used ggplot helper function plotting.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/stat_median_ci.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Confidence interval for median — stat_median_ci","text":"","code":"stat_median_ci(x, conf_level = 0.95, na.rm = TRUE, gg_helper = TRUE)"},{"path":"https://insightsengineering.github.io/tern/reference/stat_median_ci.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Confidence interval for median — stat_median_ci","text":"x (numeric) vector numbers want analyze. conf_level (proportion) confidence level interval. na.rm (flag) whether NA values removed x prior analysis. gg_helper (flag) whether output aligned use ggplots.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/stat_median_ci.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Confidence interval for median — stat_median_ci","text":"named vector values median_ci_lwr median_ci_upr.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/stat_median_ci.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Confidence interval for median — stat_median_ci","text":"function adapted DescTools/versions/0.99.35/source","code":""},{"path":"https://insightsengineering.github.io/tern/reference/stat_median_ci.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Confidence interval for median — stat_median_ci","text":"","code":"stat_median_ci(sample(10), gg_helper = FALSE) #> median_ci_lwr median_ci_upr  #>             2             9  #> attr(,\"conf_level\") #> [1] 0.9785156  p <- ggplot2::ggplot(mtcars, ggplot2::aes(cyl, mpg)) +   ggplot2::geom_point() p + ggplot2::stat_summary(   fun.data = stat_median_ci,   geom = \"errorbar\" )"},{"path":"https://insightsengineering.github.io/tern/reference/stat_propdiff_ci.html","id":null,"dir":"Reference","previous_headings":"","what":"Proportion difference and confidence interval — stat_propdiff_ci","title":"Proportion difference and confidence interval — stat_propdiff_ci","text":"Function calculating proportion (risk) difference confidence interval arm X (reference group) arm Y. Risk difference calculated subtracting cumulative incidence arm Y cumulative incidence arm X.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/stat_propdiff_ci.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Proportion difference and confidence interval — stat_propdiff_ci","text":"","code":"stat_propdiff_ci(   x,   y,   N_x,   N_y,   list_names = NULL,   conf_level = 0.95,   pct = TRUE )"},{"path":"https://insightsengineering.github.io/tern/reference/stat_propdiff_ci.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Proportion difference and confidence interval — stat_propdiff_ci","text":"x (list integer) list number occurrences arm X (reference group). y (list integer) list number occurrences arm Y. Must equal length x. N_x (numeric(1)) total number records arm X. N_y (numeric(1)) total number records arm Y. list_names (character) names variable/level corresponding pair proportions x y. Must equal length x y. conf_level (proportion) confidence level interval. pct (flag) whether output returned percentages. Defaults TRUE.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/stat_propdiff_ci.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Proportion difference and confidence interval — stat_propdiff_ci","text":"List proportion differences CIs corresponding pair number occurrences x y. list element consists 3 statistics: proportion difference, CI lower bound, CI upper bound.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/reference/stat_propdiff_ci.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Proportion difference and confidence interval — stat_propdiff_ci","text":"","code":"stat_propdiff_ci(   x = list(0.375), y = list(0.01), N_x = 5, N_y = 5, list_names = \"x\", conf_level = 0.9 ) #> $x #> [1]   7.30000 -12.35184  26.95184 #>   stat_propdiff_ci(   x = list(0.5, 0.75, 1), y = list(0.25, 0.05, 0.5), N_x = 10, N_y = 20, pct = FALSE ) #> [[1]] #> [1]  0.0375000 -0.1060891  0.1810891 #>  #> [[2]] #> [1]  0.07250000 -0.09220915  0.23720915 #>  #> [[3]] #> [1]  0.0750000 -0.1231285  0.2731285 #>"},{"path":"https://insightsengineering.github.io/tern/reference/strata_normal_quantile.html","id":null,"dir":"Reference","previous_headings":"","what":"Helper function for the estimation of stratified quantiles — strata_normal_quantile","title":"Helper function for the estimation of stratified quantiles — strata_normal_quantile","text":"function wraps estimation stratified percentiles assume approximation large numbers. necessary case proportions strata unequal.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/strata_normal_quantile.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Helper function for the estimation of stratified quantiles — strata_normal_quantile","text":"","code":"strata_normal_quantile(vars, weights, conf_level)"},{"path":"https://insightsengineering.github.io/tern/reference/strata_normal_quantile.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Helper function for the estimation of stratified quantiles — strata_normal_quantile","text":"vars (character) variable names primary analysis variable iterated . weights (numeric NULL) weights level strata. NULL, estimated using iterative algorithm proposed Yan2010-jt;textualtern minimizes weighted squared length confidence interval. conf_level (proportion) confidence level interval.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/strata_normal_quantile.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Helper function for the estimation of stratified quantiles — strata_normal_quantile","text":"Stratified quantile.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/reference/strata_normal_quantile.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Helper function for the estimation of stratified quantiles — strata_normal_quantile","text":"","code":"strata_data <- table(data.frame(   \"f1\" = sample(c(TRUE, FALSE), 100, TRUE),   \"f2\" = sample(c(\"x\", \"y\", \"z\"), 100, TRUE),   stringsAsFactors = TRUE )) ns <- colSums(strata_data) ests <- strata_data[\"TRUE\", ] / ns vars <- ests * (1 - ests) / ns weights <- rep(1 / length(ns), length(ns))  strata_normal_quantile(vars, weights, 0.95) #> [1] 1.14181"},{"path":"https://insightsengineering.github.io/tern/reference/study_arm.html","id":null,"dir":"Reference","previous_headings":"","what":"Indicate study arm variable in formula — study_arm","title":"Indicate study arm variable in formula — study_arm","text":"use study_arm indicate study arm variable tern formulas.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/study_arm.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Indicate study arm variable in formula — study_arm","text":"","code":"study_arm(x)"},{"path":"https://insightsengineering.github.io/tern/reference/study_arm.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Indicate study arm variable in formula — study_arm","text":"x arm information","code":""},{"path":"https://insightsengineering.github.io/tern/reference/study_arm.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Indicate study arm variable in formula — study_arm","text":"x","code":""},{"path":"https://insightsengineering.github.io/tern/reference/summarize_ancova.html","id":null,"dir":"Reference","previous_headings":"","what":"Summarize analysis of covariance (ANCOVA) results — summarize_ancova","title":"Summarize analysis of covariance (ANCOVA) results — summarize_ancova","text":"analyze function summarize_ancova() creates layout element summarize ANCOVA results. function can used analyze multiple endpoints /multiple timepoints within response variable(s) specified vars. Additional variables analysis, namely arm (grouping) variable covariate variables, can defined via variables argument. See details specify variables. interaction term can implemented model needed. interaction variable interact arm variable specified via interaction_term parameter, specific value interaction_term extract ANCOVA results via interaction_y parameter.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/summarize_ancova.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Summarize analysis of covariance (ANCOVA) results — summarize_ancova","text":"","code":"summarize_ancova(   lyt,   vars,   variables,   conf_level,   interaction_y = FALSE,   interaction_item = NULL,   var_labels,   na_str = default_na_str(),   nested = TRUE,   ...,   show_labels = \"visible\",   table_names = vars,   .stats = NULL,   .formats = NULL,   .labels = NULL,   .indent_mods = NULL )  s_ancova(   df,   .var,   .df_row,   variables,   .ref_group,   .in_ref_col,   conf_level,   interaction_y = FALSE,   interaction_item = NULL )  a_ancova(   df,   .var,   .df_row,   variables,   .ref_group,   .in_ref_col,   conf_level,   interaction_y = FALSE,   interaction_item = NULL )"},{"path":"https://insightsengineering.github.io/tern/reference/summarize_ancova.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Summarize analysis of covariance (ANCOVA) results — summarize_ancova","text":"lyt (PreDataTableLayouts) layout analyses added . vars (character) variable names primary analysis variable iterated . variables (named list string) list additional analysis variables, expected elements: arm (string) group variable, covariate adjusted means multiple groups summarized. Specifically, first level arm variable taken reference group. covariates (character) vector can contain single variable names (\"X1\"), /interaction terms indicated \"X1 * X2\". conf_level (proportion) confidence level interval. interaction_y (string flag) selected item inside interaction_item variable used select specific ANCOVA results. interaction needed, default option FALSE. interaction_item (string NULL) name variable interactions arm. interaction needed, default option NULL. var_labels (character) variable labels. na_str (string) string used replace NA empty values output. nested (flag) whether layout instruction applied within existing layout structure _if possible (TRUE, default) new top-level element (FALSE). Ignored nest split. underneath analyses, allowed. ... additional arguments lower level functions. show_labels (string) label visibility: one \"default\", \"visible\" \"hidden\". table_names (character) can customized case vars analyzed multiple times, avoid warnings rtables. .stats (character) statistics select table. Options : 'n', 'lsmean', 'lsmean_diff', 'lsmean_diff_ci', 'pval' .formats (named character list) formats statistics. See Details analyze_vars information \"auto\" setting. .labels (named character) labels statistics (without indent). .indent_mods (named integer) indent modifiers labels. Defaults 0, corresponds unmodified default behavior. Can negative. df (data.frame) data set containing analysis variables. .var (string) single variable name passed rtables requested statistics function. .df_row (data.frame) data set includes variables called .var variables. .ref_group (data.frame vector) data corresponding reference group. .in_ref_col (flag)TRUE working reference level, FALSE otherwise.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/summarize_ancova.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Summarize analysis of covariance (ANCOVA) results — summarize_ancova","text":"summarize_ancova() returns layout object suitable passing layouting functions, rtables::build_table(). Adding function rtable layout add formatted rows containing statistics s_ancova() table layout. s_ancova() returns named list 5 statistics: n: Count complete sample size group. lsmean: Estimated marginal means group. lsmean_diff: Difference estimated marginal means comparison reference group. working reference group, empty. lsmean_diff_ci: Confidence level difference estimated marginal means comparison reference group. pval: p-value (adjusted multiple comparisons). a_ancova() returns corresponding list formatted rtables::CellValue().","code":""},{"path":"https://insightsengineering.github.io/tern/reference/summarize_ancova.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Summarize analysis of covariance (ANCOVA) results — summarize_ancova","text":"summarize_ancova(): Layout-creating function can take statistics function arguments additional format arguments. function wrapper rtables::analyze(). s_ancova(): Statistics function produces named list results investigated linear model. a_ancova(): Formatted analysis function used afun summarize_ancova().","code":""},{"path":"https://insightsengineering.github.io/tern/reference/summarize_ancova.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Summarize analysis of covariance (ANCOVA) results — summarize_ancova","text":"","code":"basic_table() %>%   split_cols_by(\"Species\", ref_group = \"setosa\") %>%   add_colcounts() %>%   summarize_ancova(     vars = \"Petal.Length\",     variables = list(arm = \"Species\", covariates = NULL),     table_names = \"unadj\",     conf_level = 0.95, var_labels = \"Unadjusted comparison\",     .labels = c(lsmean = \"Mean\", lsmean_diff = \"Difference in Means\")   ) %>%   summarize_ancova(     vars = \"Petal.Length\",     variables = list(arm = \"Species\", covariates = c(\"Sepal.Length\", \"Sepal.Width\")),     table_names = \"adj\",     conf_level = 0.95, var_labels = \"Adjusted comparison (covariates: Sepal.Length and Sepal.Width)\"   ) %>%   build_table(iris) #>                                                                  setosa    versicolor     virginica   #>                                                                  (N=50)      (N=50)         (N=50)    #> ————————————————————————————————————————————————————————————————————————————————————————————————————— #> Unadjusted comparison                                                                                 #>   n                                                                50          50             50      #>   Mean                                                            1.46        4.26           5.55     #>   Difference in Means                                                         2.80           4.09     #>     95% CI                                                                (2.63, 2.97)   (3.92, 4.26) #>     p-value                                                                 <0.0001        <0.0001    #> Adjusted comparison (covariates: Sepal.Length and Sepal.Width)                                        #>   n                                                                50          50             50      #>   Adjusted Mean                                                   2.02        4.19           5.07     #>   Difference in Adjusted Means                                                2.17           3.05     #>     95% CI                                                                (1.96, 2.38)   (2.81, 3.29) #>     p-value                                                                 <0.0001        <0.0001"},{"path":"https://insightsengineering.github.io/tern/reference/summarize_change.html","id":null,"dir":"Reference","previous_headings":"","what":"Summarize change from baseline values or absolute baseline values — summarize_change","title":"Summarize change from baseline values or absolute baseline values — summarize_change","text":"analyze function summarize_change() creates layout element summarize change baseline absolute baseline values. primary analysis variable vars indicates numerical change baseline results. Required secondary analysis variables value baseline_flag can supplied function via variables argument. value element name analysis value variable, baseline_flag element name flag variable indicates whether records contain baseline values. Depending baseline flag given, either absolute baseline values (baseline) change baseline values (post-baseline) summarized.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/summarize_change.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Summarize change from baseline values or absolute baseline values — summarize_change","text":"","code":"summarize_change(   lyt,   vars,   variables,   var_labels = vars,   na_str = default_na_str(),   na_rm = TRUE,   nested = TRUE,   show_labels = \"default\",   table_names = vars,   section_div = NA_character_,   ...,   .stats = c(\"n\", \"mean_sd\", \"median\", \"range\"),   .formats = c(n = \"xx\", mean_sd = \"xx.xx (xx.xx)\", mean_se = \"xx.xx (xx.xx)\", median =     \"xx.xx\", range = \"xx.xx - xx.xx\", mean_ci = \"(xx.xx, xx.xx)\", median_ci =     \"(xx.xx, xx.xx)\", mean_pval = \"xx.xx\"),   .labels = c(mean_sd = \"Mean (SD)\", mean_se = \"Mean (SE)\", median = \"Median\", range =     \"Min - Max\"),   .indent_mods = NULL )  s_change_from_baseline(df, ...)  a_change_from_baseline(   df,   ...,   .stats = NULL,   .formats = NULL,   .labels = NULL,   .indent_mods = NULL )"},{"path":"https://insightsengineering.github.io/tern/reference/summarize_change.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Summarize change from baseline values or absolute baseline values — summarize_change","text":"lyt (PreDataTableLayouts) layout analyses added . vars (character) variable names primary analysis variable iterated . variables (named list string) list additional analysis variables. var_labels (character) variable labels. na_str (string) string used replace NA empty values output. nested (flag) whether layout instruction applied within existing layout structure _if possible (TRUE, default) new top-level element (FALSE). Ignored nest split. underneath analyses, allowed. show_labels (string) label visibility: one \"default\", \"visible\" \"hidden\". table_names (character) can customized case vars analyzed multiple times, avoid warnings rtables. section_div (string) string repeated section divider group defined split instruction, NA_character_ (default) section divider. ... additional arguments lower level functions. .stats (character) statistics select table. Options : 'n', 'sum', 'mean', 'sd', 'se', 'mean_sd', 'mean_se', 'mean_ci', 'mean_sei', 'mean_sdi', 'mean_pval', 'median', 'mad', 'median_ci', 'quantiles', 'iqr', 'range', 'min', 'max', 'median_range', 'cv', 'geom_mean', 'geom_mean_ci', 'geom_cv', 'median_ci_3d', 'mean_ci_3d', 'geom_mean_ci_3d' .formats (named character list) formats statistics. See Details analyze_vars information \"auto\" setting. .labels (named character) labels statistics (without indent). .indent_mods (named integer) indent modifiers labels. Defaults 0, corresponds unmodified default behavior. Can negative. df (data.frame) data set containing analysis variables.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/summarize_change.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Summarize change from baseline values or absolute baseline values — summarize_change","text":"summarize_change() returns layout object suitable passing layouting functions, rtables::build_table(). Adding function rtable layout add formatted rows containing statistics s_change_from_baseline() table layout. s_change_from_baseline() returns values returned s_summary.numeric(). a_change_from_baseline() returns corresponding list formatted rtables::CellValue().","code":""},{"path":"https://insightsengineering.github.io/tern/reference/summarize_change.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Summarize change from baseline values or absolute baseline values — summarize_change","text":"summarize_change(): Layout-creating function can take statistics function arguments additional format arguments. function wrapper rtables::analyze(). s_change_from_baseline(): Statistics function summarizes baseline post-baseline visits. a_change_from_baseline(): Formatted analysis function used afun summarize_change().","code":""},{"path":"https://insightsengineering.github.io/tern/reference/summarize_change.html","id":"note","dir":"Reference","previous_headings":"","what":"Note","title":"Summarize change from baseline values or absolute baseline values — summarize_change","text":"used split visits layout, data subset contains either baseline post-baseline data. data df must either baseline post-baseline visits. Otherwise error thrown.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/summarize_change.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Summarize change from baseline values or absolute baseline values — summarize_change","text":"","code":"library(dplyr)  # Fabricate dataset dta_test <- data.frame(   USUBJID = rep(1:6, each = 3),   AVISIT = rep(paste0(\"V\", 1:3), 6),   ARM = rep(LETTERS[1:3], rep(6, 3)),   AVAL = c(9:1, rep(NA, 9)) ) %>%   mutate(ABLFLL = AVISIT == \"V1\") %>%   group_by(USUBJID) %>%   mutate(     BLVAL = AVAL[ABLFLL],     CHG = AVAL - BLVAL   ) %>%   ungroup()  results <- basic_table() %>%   split_cols_by(\"ARM\") %>%   split_rows_by(\"AVISIT\") %>%   summarize_change(\"CHG\", variables = list(value = \"AVAL\", baseline_flag = \"ABLFLL\")) %>%   build_table(dta_test)  results #>                     A                 B               C     #> ——————————————————————————————————————————————————————————— #> V1                                                          #>   n                 2                 1               0     #>   Mean (SD)    7.50 (2.12)    3.00 (<Missing>)    <Missing> #>   Median          7.50              3.00          <Missing> #>   Min - Max    6.00 - 9.00       3.00 - 3.00      <Missing> #> V2                                                          #>   n                 2                 1               0     #>   Mean (SD)   -1.00 (0.00)    -1.00 (<Missing>)   <Missing> #>   Median          -1.00             -1.00         <Missing> #>   Min - Max   -1.00 - -1.00     -1.00 - -1.00     <Missing> #> V3                                                          #>   n                 2                 1               0     #>   Mean (SD)   -2.00 (0.00)    -2.00 (<Missing>)   <Missing> #>   Median          -2.00             -2.00         <Missing> #>   Min - Max   -2.00 - -2.00     -2.00 - -2.00     <Missing>"},{"path":"https://insightsengineering.github.io/tern/reference/summarize_colvars.html","id":null,"dir":"Reference","previous_headings":"","what":"Summarize variables in columns — summarize_colvars","title":"Summarize variables in columns — summarize_colvars","text":"analyze function summarize_colvars() uses statistics function s_summary() analyze variables arranged columns. variables analyze specified table layout via column splits (see rtables::split_cols_by() rtables::split_cols_by_multivar()) prior using summarize_colvars(). function minimal wrapper rtables::analyze_colvars(), function typically used apply different analysis methods rows column variable. use analysis methods column labels, please refer analyze_vars_in_cols() function.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/summarize_colvars.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Summarize variables in columns — summarize_colvars","text":"","code":"summarize_colvars(   lyt,   ...,   na_str = default_na_str(),   .stats = c(\"n\", \"mean_sd\", \"median\", \"range\", \"count_fraction\"),   .formats = NULL,   .labels = NULL,   .indent_mods = NULL )"},{"path":"https://insightsengineering.github.io/tern/reference/summarize_colvars.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Summarize variables in columns — summarize_colvars","text":"lyt (PreDataTableLayouts) layout analyses added . ... arguments passed s_summary(). na_str (string) string used replace NA empty values output. .stats (character) statistics select table. .formats (named character list) formats statistics. See Details analyze_vars information \"auto\" setting. .labels (named character) labels statistics (without indent). .indent_mods (named vector integer) indent modifiers labels. element vector name-value pair name corresponding statistic specified .stats value indentation statistic's row label.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/summarize_colvars.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Summarize variables in columns — summarize_colvars","text":"layout object suitable passing layouting functions, rtables::build_table(). Adding function rtable layout summarize given variables, arrange output columns, add table layout.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/reference/summarize_colvars.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Summarize variables in columns — summarize_colvars","text":"","code":"dta_test <- data.frame(   USUBJID = rep(1:6, each = 3),   PARAMCD = rep(\"lab\", 6 * 3),   AVISIT = rep(paste0(\"V\", 1:3), 6),   ARM = rep(LETTERS[1:3], rep(6, 3)),   AVAL = c(9:1, rep(NA, 9)),   CHG = c(1:9, rep(NA, 9)) )  ## Default output within a `rtables` pipeline. basic_table() %>%   split_cols_by(\"ARM\") %>%   split_rows_by(\"AVISIT\") %>%   split_cols_by_multivar(vars = c(\"AVAL\", \"CHG\")) %>%   summarize_colvars() %>%   build_table(dta_test) #>                         A                             B                             C           #>                 AVAL         CHG           AVAL               CHG           AVAL         CHG    #> ——————————————————————————————————————————————————————————————————————————————————————————————— #> V1                                                                                              #>   n               2           2              1                 1              0           0     #>   Mean (SD)   7.5 (2.1)   2.5 (2.1)   3.0 (<Missing>)   7.0 (<Missing>)   <Missing>   <Missing> #>   Median         7.5         2.5            3.0               7.0         <Missing>   <Missing> #>   Min - Max   6.0 - 9.0   1.0 - 4.0      3.0 - 3.0         7.0 - 7.0      <Missing>   <Missing> #> V2                                                                                              #>   n               2           2              1                 1              0           0     #>   Mean (SD)   6.5 (2.1)   3.5 (2.1)   2.0 (<Missing>)   8.0 (<Missing>)   <Missing>   <Missing> #>   Median         6.5         3.5            2.0               8.0         <Missing>   <Missing> #>   Min - Max   5.0 - 8.0   2.0 - 5.0      2.0 - 2.0         8.0 - 8.0      <Missing>   <Missing> #> V3                                                                                              #>   n               2           2              1                 1              0           0     #>   Mean (SD)   5.5 (2.1)   4.5 (2.1)   1.0 (<Missing>)   9.0 (<Missing>)   <Missing>   <Missing> #>   Median         5.5         4.5            1.0               9.0         <Missing>   <Missing> #>   Min - Max   4.0 - 7.0   3.0 - 6.0      1.0 - 1.0         9.0 - 9.0      <Missing>   <Missing>  ## Selection of statistics, formats and labels also work. basic_table() %>%   split_cols_by(\"ARM\") %>%   split_rows_by(\"AVISIT\") %>%   split_cols_by_multivar(vars = c(\"AVAL\", \"CHG\")) %>%   summarize_colvars(     .stats = c(\"n\", \"mean_sd\"),     .formats = c(\"mean_sd\" = \"xx.x, xx.x\"),     .labels = c(n = \"n\", mean_sd = \"Mean, SD\")   ) %>%   build_table(dta_test) #>                       A                           B                            C           #>                AVAL       CHG           AVAL             CHG           AVAL         CHG    #> —————————————————————————————————————————————————————————————————————————————————————————— #> V1                                                                                         #>   n             2          2             1                1              0           0     #>   Mean, SD   7.5, 2.1   2.5, 2.1   3.0, <Missing>   7.0, <Missing>   <Missing>   <Missing> #> V2                                                                                         #>   n             2          2             1                1              0           0     #>   Mean, SD   6.5, 2.1   3.5, 2.1   2.0, <Missing>   8.0, <Missing>   <Missing>   <Missing> #> V3                                                                                         #>   n             2          2             1                1              0           0     #>   Mean, SD   5.5, 2.1   4.5, 2.1   1.0, <Missing>   9.0, <Missing>   <Missing>   <Missing>  ## Use arguments interpreted by `s_summary`. basic_table() %>%   split_cols_by(\"ARM\") %>%   split_rows_by(\"AVISIT\") %>%   split_cols_by_multivar(vars = c(\"AVAL\", \"CHG\")) %>%   summarize_colvars(na.rm = FALSE) %>%   build_table(dta_test) #>                         A                             B                             C           #>                 AVAL         CHG           AVAL               CHG           AVAL         CHG    #> ——————————————————————————————————————————————————————————————————————————————————————————————— #> V1                                                                                              #>   n               2           2              1                 1              0           0     #>   Mean (SD)   7.5 (2.1)   2.5 (2.1)   3.0 (<Missing>)   7.0 (<Missing>)   <Missing>   <Missing> #>   Median         7.5         2.5            3.0               7.0         <Missing>   <Missing> #>   Min - Max   6.0 - 9.0   1.0 - 4.0      3.0 - 3.0         7.0 - 7.0      <Missing>   <Missing> #> V2                                                                                              #>   n               2           2              1                 1              0           0     #>   Mean (SD)   6.5 (2.1)   3.5 (2.1)   2.0 (<Missing>)   8.0 (<Missing>)   <Missing>   <Missing> #>   Median         6.5         3.5            2.0               8.0         <Missing>   <Missing> #>   Min - Max   5.0 - 8.0   2.0 - 5.0      2.0 - 2.0         8.0 - 8.0      <Missing>   <Missing> #> V3                                                                                              #>   n               2           2              1                 1              0           0     #>   Mean (SD)   5.5 (2.1)   4.5 (2.1)   1.0 (<Missing>)   9.0 (<Missing>)   <Missing>   <Missing> #>   Median         5.5         4.5            1.0               9.0         <Missing>   <Missing> #>   Min - Max   4.0 - 7.0   3.0 - 6.0      1.0 - 1.0         9.0 - 9.0      <Missing>   <Missing>"},{"path":"https://insightsengineering.github.io/tern/reference/summarize_functions.html","id":null,"dir":"Reference","previous_headings":"","what":"Summarize functions — summarize_functions","title":"Summarize functions — summarize_functions","text":"functions wrappers rtables::summarize_row_groups(), applying corresponding tern content functions add summary rows given table layout:","code":""},{"path":"https://insightsengineering.github.io/tern/reference/summarize_functions.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Summarize functions — summarize_functions","text":"add_rowcounts() estimate_multinomial_response() (rtables::analyze()) h_tab_one_biomarker() (probably deprecate) logistic_summary_by_flag() summarize_num_patients() summarize_occurrences() summarize_occurrences_by_grade() summarize_patients_events_in_cols() summarize_patients_exposure_in_cols() Additionally, summarize_coxreg() function utilizes rtables::summarize_row_groups() (combination several rtables functions like rtables::analyze_colvars()) output Cox regression summary table.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/reference/summarize_glm_count.html","id":null,"dir":"Reference","previous_headings":"","what":"Summarize Poisson negative binomial regression — summarize_glm_count","title":"Summarize Poisson negative binomial regression — summarize_glm_count","text":"Summarize results Poisson negative binomial regression. can used analyze count /frequency data using linear model. specifically useful analyzing count data (using Poisson Negative Binomial distribution) result generalized linear model one (e.g. arm) covariates.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/summarize_glm_count.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Summarize Poisson negative binomial regression — summarize_glm_count","text":"","code":"summarize_glm_count(   lyt,   vars,   variables,   distribution,   conf_level,   rate_mean_method = c(\"emmeans\", \"ppmeans\")[1],   weights = stats::weights,   scale = 1,   var_labels,   na_str = default_na_str(),   nested = TRUE,   ...,   show_labels = \"visible\",   table_names = vars,   .stats = get_stats(\"summarize_glm_count\"),   .formats = NULL,   .labels = NULL,   .indent_mods = c(n = 0L, rate = 0L, rate_ci = 1L, rate_ratio = 0L, rate_ratio_ci = 1L,     pval = 1L) )  s_glm_count(   df,   .var,   .df_row,   variables,   .ref_group,   .in_ref_col,   distribution,   conf_level,   rate_mean_method,   weights,   scale = 1 )"},{"path":"https://insightsengineering.github.io/tern/reference/summarize_glm_count.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Summarize Poisson negative binomial regression — summarize_glm_count","text":"lyt (PreDataTableLayouts) layout analyses added . vars (character) variable names primary analysis variable iterated . variables (named list string) list additional analysis variables, expected elements: arm (string) group variable, covariate adjusted means multiple groups summarized. Specifically, first level arm variable taken reference group. covariates (character) vector can contain single variable names (\"X1\"), /interaction terms indicated \"X1 * X2\". offset (numeric) numeric vector scalar adding offset. distribution (character) character value specifying distribution used regression (Poisson, Quasi-Poisson, negative binomial). conf_level (proportion) confidence level interval. rate_mean_method (character(1)) method used estimate mean odds ratio. Defaults emmeans. see details information. weights (character) character vector specifying weights used averaging predictions. Number weights must equal number levels included covariates. Weights option passed emmeans::emmeans(). scale (numeric(1)) linear scaling factor rate confidence intervals. Defaults 1. var_labels (character) variable labels. na_str (string) string used replace NA empty values output. nested (flag) whether layout instruction applied within existing layout structure _if possible (TRUE, default) new top-level element (FALSE). Ignored nest split. underneath analyses, allowed. ... additional arguments lower level functions. show_labels (string) label visibility: one \"default\", \"visible\" \"hidden\". table_names (character) can customized case vars analyzed multiple times, avoid warnings rtables. .stats (character) statistics select table. Options : 'n', 'rate', 'rate_ci', 'rate_ratio', 'rate_ratio_ci', 'pval' .formats (named character list) formats statistics. See Details analyze_vars information \"auto\" setting. .labels (named character) labels statistics (without indent). .indent_mods (named integer) indent modifiers labels. Defaults 0, corresponds unmodified default behavior. Can negative. df (data.frame) data set containing analysis variables. .var (string) single variable name passed rtables requested statistics function. .df_row (data.frame) dataset includes variables called .var variables. .ref_group (data.frame vector) data corresponding reference group. .in_ref_col (flag)TRUE working reference level, FALSE otherwise.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/summarize_glm_count.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Summarize Poisson negative binomial regression — summarize_glm_count","text":"summarize_glm_count() returns layout object suitable passing layouting functions, rtables::build_table(). Adding function rtable layout add formatted rows containing statistics s_glm_count() table layout. s_glm_count() returns named list 5 statistics: n: Count complete sample size group. rate: Estimated event rate per follow-time. rate_ci: Confidence level estimated rate per follow-time. rate_ratio: Ratio event rates treatment arm reference arm. rate_ratio_ci: Confidence level rate ratio. pval: p-value.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/summarize_glm_count.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Summarize Poisson negative binomial regression — summarize_glm_count","text":"summarize_glm_count() uses s_glm_count() calculate statistics table. analysis function uses h_glm_count() estimate GLM stats::glm() Poisson Quasi-Poisson distributions MASS::glm.nb() Negative Binomial distribution. methods assume logarithmic link function. point, rates confidence intervals estimated model using either emmeans::emmeans() rate_mean_method = \"emmeans\" h_ppmeans() rate_mean_method = \"ppmeans\". reference group specified building table split_cols_by(ref_group), rate ratio p-value calculated. Otherwise, use emmeans::contrast() calculate rate ratio p-value reference group. Values always estimated method = \"trt.vs.ctrl\" ref equal first arm value.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/summarize_glm_count.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Summarize Poisson negative binomial regression — summarize_glm_count","text":"summarize_glm_count(): Layout-creating function can take statistics function arguments additional format arguments. function wrapper rtables::analyze(). s_glm_count(): Statistics function produces named list results investigated Poisson model.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/summarize_glm_count.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Summarize Poisson negative binomial regression — summarize_glm_count","text":"","code":"library(dplyr)  anl <- tern_ex_adtte %>% filter(PARAMCD == \"TNE\") anl$AVAL_f <- as.factor(anl$AVAL)  lyt <- basic_table() %>%   split_cols_by(\"ARM\", ref_group = \"B: Placebo\") %>%   add_colcounts() %>%   analyze_vars(     \"AVAL_f\",     var_labels = \"Number of exacerbations per patient\",     .stats = c(\"count_fraction\"),     .formats = c(\"count_fraction\" = \"xx (xx.xx%)\"),     .labels = c(\"Number of exacerbations per patient\")   ) %>%   summarize_glm_count(     vars = \"AVAL\",     variables = list(arm = \"ARM\", offset = \"lgTMATRSK\", covariates = NULL),     conf_level = 0.95,     distribution = \"poisson\",     rate_mean_method = \"emmeans\",     var_labels = \"Adjusted (P) exacerbation rate (per year)\",     table_names = \"adjP\",     .stats = c(\"rate\"),     .labels = c(rate = \"Rate\")   ) %>%   summarize_glm_count(     vars = \"AVAL\",     variables = list(arm = \"ARM\", offset = \"lgTMATRSK\", covariates = c(\"REGION1\")),     conf_level = 0.95,     distribution = \"quasipoisson\",     rate_mean_method = \"ppmeans\",     var_labels = \"Adjusted (QP) exacerbation rate (per year)\",     table_names = \"adjQP\",     .stats = c(\"rate\", \"rate_ci\", \"rate_ratio\", \"rate_ratio_ci\", \"pval\"),     .labels = c(       rate = \"Rate\", rate_ci = \"Rate CI\", rate_ratio = \"Rate Ratio\",       rate_ratio_ci = \"Rate Ratio CI\", pval = \"p value\"     )   ) %>%   summarize_glm_count(     vars = \"AVAL\",     variables = list(arm = \"ARM\", offset = \"lgTMATRSK\", covariates = c(\"REGION1\")),     conf_level = 0.95,     distribution = \"negbin\",     rate_mean_method = \"emmeans\",     var_labels = \"Adjusted (NB) exacerbation rate (per year)\",     table_names = \"adjNB\",     .stats = c(\"rate\", \"rate_ci\", \"rate_ratio\", \"rate_ratio_ci\", \"pval\"),     .labels = c(       rate = \"Rate\", rate_ci = \"Rate CI\", rate_ratio = \"Rate Ratio\",       rate_ratio_ci = \"Rate Ratio CI\", pval = \"p value\"     )   )  build_table(lyt = lyt, df = anl) #>                                                  A: Drug X            B: Placebo         C: Combination   #>                                                    (N=69)               (N=73)               (N=58)       #> ————————————————————————————————————————————————————————————————————————————————————————————————————————— #> Number of exacerbations per patient                                                                       #>   0                                              3 (4.35%)            8 (10.96%)           6 (10.34%)     #>   1                                             11 (15.94%)           9 (12.33%)           6 (10.34%)     #>   2                                             18 (26.09%)          15 (20.55%)           9 (15.52%)     #>   3                                             14 (20.29%)          11 (15.07%)          15 (25.86%)     #>   4                                             10 (14.49%)           9 (12.33%)           9 (15.52%)     #>   5                                              7 (10.14%)           9 (12.33%)           8 (13.79%)     #>   6                                              4 (5.80%)            4 (5.48%)            4 (6.90%)      #>   7                                              2 (2.90%)            8 (10.96%)           0 (0.00%)      #>   10                                             0 (0.00%)            0 (0.00%)            1 (1.72%)      #> Adjusted (P) exacerbation rate (per year)                                                                 #>   Rate                                             8.2061               9.1554               7.8551       #> Adjusted (QP) exacerbation rate (per year)                                                                #>   Rate                                             3.1214               3.4860               2.6152       #>     Rate CI                                   (1.7307, 5.6294)     (1.9833, 6.1272)     (1.3661, 5.0065)  #>   Rate Ratio                                       0.8954                                    0.7502       #>     Rate Ratio CI                             (0.3975, 2.0170)                          (0.3067, 1.8348)  #>     p value                                        0.7897                                    0.5288       #> Adjusted (NB) exacerbation rate (per year)                                                                #>   Rate                                            33.0138              37.3569              34.9046       #>     Rate CI                                  (21.6999, 50.2266)   (24.5906, 56.7507)   (23.0925, 52.7587) #>   Rate Ratio                                       0.8837                                    0.9344       #>     Rate Ratio CI                             (0.5872, 1.3300)                          (0.6063, 1.4400)  #>     p value                                        0.5534                                    0.7583"},{"path":"https://insightsengineering.github.io/tern/reference/summarize_logistic.html","id":null,"dir":"Reference","previous_headings":"","what":"Multivariate logistic regression table — summarize_logistic","title":"Multivariate logistic regression table — summarize_logistic","text":"Layout-creating function summarizes logistic variable regression binary outcome categorical/continuous covariates model statement. covariate category (categorical) specified values (continuous), present degrees freedom, regression parameter estimate standard error (SE) relative reference group category. Report odds ratios covariate category specified values corresponding Wald confidence intervals default allow user specify confidence levels. Report p-value Wald chi-square test null hypothesis covariate effect response model containing specified covariates. Allow option include one two-way interaction present similar output interaction degree freedom.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/summarize_logistic.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Multivariate logistic regression table — summarize_logistic","text":"","code":"summarize_logistic(   lyt,   conf_level,   drop_and_remove_str = \"\",   .indent_mods = NULL )"},{"path":"https://insightsengineering.github.io/tern/reference/summarize_logistic.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Multivariate logistic regression table — summarize_logistic","text":"lyt (PreDataTableLayouts) layout analyses added . conf_level (proportion) confidence level interval. drop_and_remove_str (string) string dropped removed. .indent_mods (named integer) indent modifiers labels. Defaults 0, corresponds unmodified default behavior. Can negative.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/summarize_logistic.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Multivariate logistic regression table — summarize_logistic","text":"layout object suitable passing layouting functions, rtables::build_table(). Adding function rtable layout add logistic regression variable summary table layout.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/summarize_logistic.html","id":"note","dir":"Reference","previous_headings":"","what":"Note","title":"Multivariate logistic regression table — summarize_logistic","text":"formula, variable names need standard data.frame column names without special characters.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/summarize_logistic.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Multivariate logistic regression table — summarize_logistic","text":"","code":"library(dplyr) library(broom)  adrs_f <- tern_ex_adrs %>%   filter(PARAMCD == \"BESRSPI\") %>%   filter(RACE %in% c(\"ASIAN\", \"WHITE\", \"BLACK OR AFRICAN AMERICAN\")) %>%   mutate(     Response = case_when(AVALC %in% c(\"PR\", \"CR\") ~ 1, TRUE ~ 0),     RACE = factor(RACE),     SEX = factor(SEX)   ) formatters::var_labels(adrs_f) <- c(formatters::var_labels(tern_ex_adrs), Response = \"Response\") mod1 <- fit_logistic(   data = adrs_f,   variables = list(     response = \"Response\",     arm = \"ARMCD\",     covariates = c(\"AGE\", \"RACE\")   ) ) #> Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred mod2 <- fit_logistic(   data = adrs_f,   variables = list(     response = \"Response\",     arm = \"ARMCD\",     covariates = c(\"AGE\", \"RACE\"),     interaction = \"AGE\"   ) ) #> Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred  df <- tidy(mod1, conf_level = 0.99) df2 <- tidy(mod2, conf_level = 0.99)  # flagging empty strings with \"_\" df <- df_explicit_na(df, na_level = \"_\") df2 <- df_explicit_na(df2, na_level = \"_\")  result1 <- basic_table() %>%   summarize_logistic(     conf_level = 0.95,     drop_and_remove_str = \"_\"   ) %>%   build_table(df = df) result1 #>                                       Degrees of Freedom   Parameter Estimate   Standard Error   Odds Ratio     Wald 95% CI     p-value #> ——————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————— #> Planned Arm Code                              2                                                                                 0.3004  #>   Reference ARM A, n = 64                                                                                                               #>   ARM B, n = 68                               1                  -1.775             1.144           0.17       (<0.01, 3.23)    0.1209  #>   ARM C, n = 52                               1                  17.192            3626.588       >999.99     (0.00, >999.99)   0.9962  #> Age                                                                                                                                     #>   Age                                         1                  0.170              0.095           1.19       (0.93, 1.51)     0.0746  #> Race                                          2                                                                                 0.7967  #>   Reference ASIAN, n = 110                                                                                                              #>   BLACK OR AFRICAN AMERICAN, n = 40           1                  17.923            4001.705       >999.99     (0.00, >999.99)   0.9964  #>   WHITE, n = 34                               1                  -0.656             0.974           0.52       (0.04, 6.37)     0.5002   result2 <- basic_table() %>%   summarize_logistic(     conf_level = 0.95,     drop_and_remove_str = \"_\"   ) %>%   build_table(df = df2) result2 #>                                         Degrees of Freedom   Parameter Estimate   Standard Error   Odds Ratio     Wald 95% CI     p-value #> ————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————— #> Race                                            2                                                                                 0.9361  #>   Reference ASIAN, n = 110                                                                                                                #>   BLACK OR AFRICAN AMERICAN, n = 40             1                  18.150            3944.701       >999.99     (0.00, >999.99)   0.9963  #>   WHITE, n = 34                                 1                  -0.373             1.026           0.69       (0.05, 9.68)     0.7164  #> Planned Arm Code                                2                                                                                 0.2539  #>   Reference ARM A, n = 64                                                                                                                 #>   ARM B, n = 68                                 1                 -11.527             6.962                                       0.0978  #>     Age                                                                                                                                   #>       35                                                                                              0.48       (0.01, 15.48)            #>   ARM C, n = 52                                 1                  16.333           20278.387                                     0.9994  #>     Age                                                                                                                                   #>       35                                                                                            >999.99     (0.00, >999.99)           #> Age                                                                                                                                       #>   Age                                           1                  -0.039             0.151                                       0.7981  #>     Planned Arm Code                                                                                                                      #>       ARM A                                                                                           0.96       (0.65, 1.42)             #>       ARM B                                                                                           1.31       (0.92, 1.86)             #>       ARM C                                                                                           0.99      (0.00, >999.99)           #> Interaction of Planned Arm Code * Age           2                                                                                 0.3276  #>   Reference ARM A, n = 64                                                                                                                 #>   ARM B, n = 68                                 1                  0.308              0.206                                       0.1352  #>   ARM C, n = 52                                 1                  0.029             548.592                                      1.0000"},{"path":"https://insightsengineering.github.io/tern/reference/summarize_num_patients.html","id":null,"dir":"Reference","previous_headings":"","what":"Count number of patients — summarize_num_patients","title":"Count number of patients — summarize_num_patients","text":"analyze function analyze_num_patients() creates layout element count total numbers unique non-unique patients. primary analysis variable vars used uniquely identify patients. count_by variable can used identify non-unique patients number patients unique combination values vars count_by returned instead nonunique statistic. required variable can used specify variable required non-missing record included counts. summarize function summarize_num_patients() performs function analyze_num_patients() except creates content rows, data rows, summarize current table row/column context operates level latest row split root table row splits occurred.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/summarize_num_patients.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Count number of patients — summarize_num_patients","text":"","code":"analyze_num_patients(   lyt,   vars,   required = NULL,   count_by = NULL,   unique_count_suffix = TRUE,   na_str = default_na_str(),   nested = TRUE,   .stats = NULL,   .formats = NULL,   .labels = c(unique = \"Number of patients with at least one event\", nonunique =     \"Number of events\"),   show_labels = c(\"default\", \"visible\", \"hidden\"),   .indent_mods = 0L,   riskdiff = FALSE,   ... )  summarize_num_patients(   lyt,   var,   required = NULL,   count_by = NULL,   unique_count_suffix = TRUE,   na_str = default_na_str(),   .stats = NULL,   .formats = NULL,   .labels = c(unique = \"Number of patients with at least one event\", nonunique =     \"Number of events\"),   .indent_mods = 0L,   riskdiff = FALSE,   ... )  s_num_patients(   x,   labelstr,   .N_col,   count_by = NULL,   unique_count_suffix = TRUE )  s_num_patients_content(   df,   labelstr = \"\",   .N_col,   .var,   required = NULL,   count_by = NULL,   unique_count_suffix = TRUE )"},{"path":"https://insightsengineering.github.io/tern/reference/summarize_num_patients.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Count number of patients — summarize_num_patients","text":"lyt (PreDataTableLayouts) layout analyses added . vars (character) variable names primary analysis variable iterated . required (character NULL) name variable required non-missing. count_by (character NULL) name variable combined vars counting nonunique records. unique_count_suffix (flag) whether \"(n)\" suffix added unique_count labels. Defaults TRUE. na_str (string) string used replace NA empty values output. nested (flag) whether layout instruction applied within existing layout structure _if possible (TRUE, default) new top-level element (FALSE). Ignored nest split. underneath analyses, allowed. .stats (character) statistics select table. Options : 'unique', 'nonunique', 'unique_count' .formats (named character list) formats statistics. See Details analyze_vars information \"auto\" setting. .labels (named character) labels statistics (without indent). show_labels (string) label visibility: one \"default\", \"visible\" \"hidden\". .indent_mods (named integer) indent modifiers labels. Defaults 0, corresponds unmodified default behavior. Can negative. riskdiff (flag) whether risk difference column present. set TRUE, add_riskdiff() must used split_fun prior column split table layout, specifying columns compared. See stat_propdiff_ci() details risk difference calculation. ... additional arguments lower level functions. x (character factor) vector patient IDs. labelstr (string) label level parent split currently summarized (must present second argument Content Row Functions). See rtables::summarize_row_groups() information. .N_col (integer(1)) column-wise N (column count) full column analyzed typically passed rtables. df (data.frame) data set containing analysis variables. .var, var (string) single variable name passed rtables requested statistics function.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/summarize_num_patients.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Count number of patients — summarize_num_patients","text":"analyze_num_patients() returns layout object suitable passing layouting functions, rtables::build_table(). Adding function rtable layout add formatted rows containing statistics s_num_patients_content() table layout. summarize_num_patients() returns layout object suitable passing layouting functions, rtables::build_table(). Adding function rtable layout add formatted rows containing statistics s_num_patients_content() table layout. s_num_patients() returns named list 3 statistics: unique: Vector counts percentages. nonunique: Vector counts. unique_count: Counts. s_num_patients_content() returns values s_num_patients().","code":""},{"path":"https://insightsengineering.github.io/tern/reference/summarize_num_patients.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Count number of patients — summarize_num_patients","text":"general, functions starts analyze* expected work like rtables::analyze(), functions starts summarize* based upon rtables::summarize_row_groups(). latter provides value dividing split row column space, , bound fundamental splits, repeated design every page pagination involved.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/summarize_num_patients.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Count number of patients — summarize_num_patients","text":"analyze_num_patients(): Layout-creating function can take statistics function arguments additional format arguments. function wrapper rtables::analyze(). summarize_num_patients(): Layout-creating function can take statistics function arguments additional format arguments. function wrapper rtables::summarize_row_groups(). s_num_patients(): Statistics function counts number unique patients, corresponding percentage taken respect total number patients, number non-unique patients. s_num_patients_content(): Statistics function counts number unique patients column (variable), corresponding percentage taken respect total number patients, number non-unique patients column.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/summarize_num_patients.html","id":"note","dir":"Reference","previous_headings":"","what":"Note","title":"Count number of patients — summarize_num_patients","text":"opposed summarize_num_patients(), function repeat produced rows.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/summarize_num_patients.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Count number of patients — summarize_num_patients","text":"","code":"df <- data.frame(   USUBJID = as.character(c(1, 2, 1, 4, NA, 6, 6, 8, 9)),   ARM = c(\"A\", \"A\", \"A\", \"A\", \"A\", \"B\", \"B\", \"B\", \"B\"),   AGE = c(10, 15, 10, 17, 8, 11, 11, 19, 17),   SEX = c(\"M\", \"M\", \"M\", \"F\", \"F\", \"F\", \"M\", \"F\", \"M\") )  # analyze_num_patients tbl <- basic_table() %>%   split_cols_by(\"ARM\") %>%   add_colcounts() %>%   analyze_num_patients(\"USUBJID\", .stats = c(\"unique\")) %>%   build_table(df)  tbl #>                                                  A           B     #>                                                (N=5)       (N=4)   #> —————————————————————————————————————————————————————————————————— #> Number of patients with at least one event   3 (60.0%)   3 (75.0%)  # summarize_num_patients tbl <- basic_table() %>%   split_cols_by(\"ARM\") %>%   split_rows_by(\"SEX\") %>%   summarize_num_patients(\"USUBJID\", .stats = \"unique_count\") %>%   build_table(df)  tbl #>         A   B #> ————————————— #> M (n)   2   2 #> F (n)   1   2  # Use the statistics function to count number of unique and nonunique patients. s_num_patients(x = as.character(c(1, 1, 1, 2, 4, NA)), labelstr = \"\", .N_col = 6L) #> $unique #> [1] 3.0 0.5 #> attr(,\"label\") #> [1] \"\" #>  #> $nonunique #> [1] 5 #> attr(,\"label\") #> [1] \"\" #>  #> $unique_count #> [1] 3 #> attr(,\"label\") #> [1] \"(n)\" #>  s_num_patients(   x = as.character(c(1, 1, 1, 2, 4, NA)),   labelstr = \"\",   .N_col = 6L,   count_by = c(1, 1, 2, 1, 1, 1) ) #> $unique #> [1] 3.0 0.5 #> attr(,\"label\") #> [1] \"\" #>  #> $nonunique #> [1] 4 #> attr(,\"label\") #> [1] \"\" #>  #> $unique_count #> [1] 3 #> attr(,\"label\") #> [1] \"(n)\" #>   # Count number of unique and non-unique patients.  df <- data.frame(   USUBJID = as.character(c(1, 2, 1, 4, NA)),   EVENT = as.character(c(10, 15, 10, 17, 8)) ) s_num_patients_content(df, .N_col = 5, .var = \"USUBJID\") #> $unique #> [1] 3.0 0.6 #> attr(,\"label\") #> [1] \"\" #>  #> $nonunique #> [1] 4 #> attr(,\"label\") #> [1] \"\" #>  #> $unique_count #> [1] 3 #> attr(,\"label\") #> [1] \"(n)\" #>   df_by_event <- data.frame(   USUBJID = as.character(c(1, 2, 1, 4, NA)),   EVENT = c(10, 15, 10, 17, 8) ) s_num_patients_content(df_by_event, .N_col = 5, .var = \"USUBJID\", count_by = \"EVENT\") #> $unique #> [1] 3.0 0.6 #> attr(,\"label\") #> [1] \"\" #>  #> $nonunique #> [1] 3 #> attr(,\"label\") #> [1] \"\" #>  #> $unique_count #> [1] 3 #> attr(,\"label\") #> [1] \"(n)\" #>"},{"path":"https://insightsengineering.github.io/tern/reference/summarize_patients_exposure_in_cols.html","id":null,"dir":"Reference","previous_headings":"","what":"Count number of patients and sum exposure across all patients in columns — summarize_patients_exposure_in_cols","title":"Count number of patients and sum exposure across all patients in columns — summarize_patients_exposure_in_cols","text":"analyze function analyze_patients_exposure_in_cols() creates layout element count total numbers patients sum analysis value (.e. exposure) across patients columns. primary analysis variable ex_var exposure variable used calculate sum_exposure statistic. id variable used uniquely identify patients data unique patients counted n_patients statistic, var variable used create row split needed. percentage returned part n_patients statistic proportion records correspond unique patient. summarize function summarize_patients_exposure_in_cols() performs function analyze_patients_exposure_in_cols() except creates content rows, data rows, summarize current table row/column context operates level latest row split root table row splits occurred. column split yet performed table, col_split must set TRUE first call analyze_patients_exposure_in_cols() summarize_patients_exposure_in_cols().","code":""},{"path":"https://insightsengineering.github.io/tern/reference/summarize_patients_exposure_in_cols.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Count number of patients and sum exposure across all patients in columns — summarize_patients_exposure_in_cols","text":"","code":"analyze_patients_exposure_in_cols(   lyt,   var = NULL,   ex_var = \"AVAL\",   id = \"USUBJID\",   add_total_level = FALSE,   custom_label = NULL,   col_split = TRUE,   na_str = default_na_str(),   .stats = c(\"n_patients\", \"sum_exposure\"),   .labels = c(n_patients = \"Patients\", sum_exposure = \"Person time\"),   .indent_mods = 0L,   ... )  summarize_patients_exposure_in_cols(   lyt,   var,   ex_var = \"AVAL\",   id = \"USUBJID\",   add_total_level = FALSE,   custom_label = NULL,   col_split = TRUE,   na_str = default_na_str(),   ...,   .stats = c(\"n_patients\", \"sum_exposure\"),   .labels = c(n_patients = \"Patients\", sum_exposure = \"Person time\"),   .indent_mods = NULL )  s_count_patients_sum_exposure(   df,   ex_var = \"AVAL\",   id = \"USUBJID\",   labelstr = \"\",   .stats = c(\"n_patients\", \"sum_exposure\"),   .N_col,   custom_label = NULL )  a_count_patients_sum_exposure(   df,   var = NULL,   ex_var = \"AVAL\",   id = \"USUBJID\",   add_total_level = FALSE,   custom_label = NULL,   labelstr = \"\",   .N_col,   .stats,   .formats = list(n_patients = \"xx (xx.x%)\", sum_exposure = \"xx\") )"},{"path":"https://insightsengineering.github.io/tern/reference/summarize_patients_exposure_in_cols.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Count number of patients and sum exposure across all patients in columns — summarize_patients_exposure_in_cols","text":"lyt (PreDataTableLayouts) layout analyses added . var (string) single variable name passed rtables requested statistics function. ex_var (string) name variable df containing exposure values. id (string) subject variable name. add_total_level (flag) adds \"total\" level others includes levels constitute split. custom label can set level via custom_label argument. custom_label (string NULL) provided labelstr empty, used label. col_split (flag) whether columns split. Set FALSE required column split done already earlier layout pipe. na_str (string) string used replace NA empty values output. .stats (character) statistics select table. Options : 'n_patients', 'sum_exposure' .labels (named character) labels statistics (without indent). .indent_mods (named integer) indent modifiers labels. Defaults 0, corresponds unmodified default behavior. Can negative. ... additional arguments lower level functions. df (data.frame) data set containing analysis variables. labelstr (string) label level parent split currently summarized (must present second argument Content Row Functions). See rtables::summarize_row_groups() information. .N_col (integer(1)) column-wise N (column count) full column analyzed typically passed rtables. .formats (named character list) formats statistics. See Details analyze_vars information \"auto\" setting.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/summarize_patients_exposure_in_cols.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Count number of patients and sum exposure across all patients in columns — summarize_patients_exposure_in_cols","text":"analyze_patients_exposure_in_cols() returns layout object suitable passing layouting functions, rtables::build_table(). Adding function rtable layout add formatted data rows, statistics s_count_patients_sum_exposure() arranged columns, table layout. summarize_patients_exposure_in_cols() returns layout object suitable passing layouting functions, rtables::build_table(). Adding function rtable layout add formatted content rows, statistics s_count_patients_sum_exposure() arranged columns, table layout. s_count_patients_sum_exposure() returns named list statistics: n_patients: Number unique patients df. sum_exposure: Sum ex_var across patients df. a_count_patients_sum_exposure() returns formatted rtables::CellValue().","code":""},{"path":"https://insightsengineering.github.io/tern/reference/summarize_patients_exposure_in_cols.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Count number of patients and sum exposure across all patients in columns — summarize_patients_exposure_in_cols","text":"analyze_patients_exposure_in_cols(): Layout-creating function can take statistics function arguments additional format arguments. function wrapper rtables::split_cols_by_multivar() rtables::analyze_colvars(). summarize_patients_exposure_in_cols(): Layout-creating function can take statistics function arguments additional format arguments. function wrapper rtables::split_cols_by_multivar() rtables::summarize_row_groups(). s_count_patients_sum_exposure(): Statistics function counts numbers patients sum exposure across patients. a_count_patients_sum_exposure(): Analysis function used afun rtables::analyze_colvars() within analyze_patients_exposure_in_cols() cfun rtables::summarize_row_groups() within summarize_patients_exposure_in_cols().","code":""},{"path":"https://insightsengineering.github.io/tern/reference/summarize_patients_exposure_in_cols.html","id":"note","dir":"Reference","previous_headings":"","what":"Note","title":"Count number of patients and sum exposure across all patients in columns — summarize_patients_exposure_in_cols","text":"opposed summarize_patients_exposure_in_cols() generates content rows, analyze_patients_exposure_in_cols() generates data rows repeated multiple pages pagination used.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/summarize_patients_exposure_in_cols.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Count number of patients and sum exposure across all patients in columns — summarize_patients_exposure_in_cols","text":"","code":"set.seed(1) df <- data.frame(   USUBJID = c(paste(\"id\", seq(1, 12), sep = \"\")),   ARMCD = c(rep(\"ARM A\", 6), rep(\"ARM B\", 6)),   SEX = c(rep(\"Female\", 6), rep(\"Male\", 6)),   AVAL = as.numeric(sample(seq(1, 20), 12)),   stringsAsFactors = TRUE ) adsl <- data.frame(   USUBJID = c(paste(\"id\", seq(1, 12), sep = \"\")),   ARMCD = c(rep(\"ARM A\", 2), rep(\"ARM B\", 2)),   SEX = c(rep(\"Female\", 2), rep(\"Male\", 2)),   stringsAsFactors = TRUE )  lyt <- basic_table() %>%   split_cols_by(\"ARMCD\", split_fun = add_overall_level(\"Total\", first = FALSE)) %>%   summarize_patients_exposure_in_cols(var = \"AVAL\", col_split = TRUE) %>%   analyze_patients_exposure_in_cols(var = \"SEX\", col_split = FALSE) result <- build_table(lyt, df = df, alt_counts_df = adsl) result #>                                               ARM A                      ARM B                       Total           #>                                       Patients    Person time    Patients    Person time    Patients     Person time #> ———————————————————————————————————————————————————————————————————————————————————————————————————————————————————— #> Total patients numbers/person time   6 (100.0%)       46        6 (100.0%)       68        12 (100.0%)       114     #>   Female                             6 (100.0%)       46         0 (0.0%)         0         6 (50.0%)        46      #>   Male                                0 (0.0%)         0        6 (100.0%)       68         6 (50.0%)        68       lyt2 <- basic_table() %>%   split_cols_by(\"ARMCD\", split_fun = add_overall_level(\"Total\", first = FALSE)) %>%   summarize_patients_exposure_in_cols(     var = \"AVAL\", col_split = TRUE,     .stats = \"n_patients\", custom_label = \"some custom label\"   ) %>%   analyze_patients_exposure_in_cols(var = \"SEX\", col_split = FALSE, ex_var = \"AVAL\") result2 <- build_table(lyt2, df = df, alt_counts_df = adsl) result2 #>                       ARM A        ARM B         Total    #>                      Patients     Patients     Patients   #> ————————————————————————————————————————————————————————— #> some custom label   6 (100.0%)   6 (100.0%)   12 (100.0%) #>   Female            6 (100.0%)    0 (0.0%)     6 (50.0%)  #>   Male               0 (0.0%)    6 (100.0%)    6 (50.0%)   lyt3 <- basic_table() %>%   analyze_patients_exposure_in_cols(var = \"SEX\", col_split = TRUE, ex_var = \"AVAL\") result3 <- build_table(lyt3, df = df, alt_counts_df = adsl) result3 #>          Patients    Person time #> ———————————————————————————————— #> Female   6 (50.0%)       46      #> Male     6 (50.0%)       68       # Adding total levels and custom label lyt4 <- basic_table(   show_colcounts = TRUE ) %>%   analyze_patients_exposure_in_cols(     var = \"ARMCD\",     col_split = TRUE,     add_total_level = TRUE,     custom_label = \"TOTAL\"   ) %>%   append_topleft(c(\"\", \"Sex\"))  result4 <- build_table(lyt4, df = df, alt_counts_df = adsl) result4 #>          Patients     Person time #> Sex       (N=12)        (N=12)    #> ————————————————————————————————— #> ARM A    6 (50.0%)        46      #> ARM B    6 (50.0%)        68      #> TOTAL   12 (100.0%)       114      lyt5 <- basic_table() %>%   summarize_patients_exposure_in_cols(var = \"AVAL\", col_split = TRUE)  result5 <- build_table(lyt5, df = df, alt_counts_df = adsl) result5 #>                                       Patients     Person time #> —————————————————————————————————————————————————————————————— #> Total patients numbers/person time   12 (100.0%)       114      lyt6 <- basic_table() %>%   summarize_patients_exposure_in_cols(var = \"AVAL\", col_split = TRUE, .stats = \"sum_exposure\")  result6 <- build_table(lyt6, df = df, alt_counts_df = adsl) result6 #>                                      Person time #> ———————————————————————————————————————————————— #> Total patients numbers/person time       114      a_count_patients_sum_exposure(   df = df,   var = \"SEX\",   .N_col = nrow(df),   .stats = \"n_patients\" ) #> RowsVerticalSection (in_rows) object print method: #> ---------------------------- #>   row_name formatted_cell indent_mod row_label #> 1   Female      6 (50.0%)          0    Female #> 2     Male      6 (50.0%)          0      Male"},{"path":"https://insightsengineering.github.io/tern/reference/survival_biomarkers_subgroups.html","id":null,"dir":"Reference","previous_headings":"","what":"Tabulate biomarker effects on survival by subgroup — survival_biomarkers_subgroups","title":"Tabulate biomarker effects on survival by subgroup — survival_biomarkers_subgroups","text":"tabulate_survival_biomarkers() function creates layout element tabulate estimated effects multiple continuous biomarker variables survival across subgroups, returning statistics including median survival time hazard ratio population subgroup. table created df, list data frames returned extract_survival_biomarkers(), statistics include specified via vars parameter. forest plot can created resulting table using g_forest() function.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/survival_biomarkers_subgroups.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Tabulate biomarker effects on survival by subgroup — survival_biomarkers_subgroups","text":"","code":"tabulate_survival_biomarkers(   df,   vars = c(\"n_tot\", \"n_tot_events\", \"median\", \"hr\", \"ci\", \"pval\"),   groups_lists = list(),   control = control_coxreg(),   label_all = lifecycle::deprecated(),   time_unit = NULL,   na_str = default_na_str(),   .indent_mods = 0L )"},{"path":"https://insightsengineering.github.io/tern/reference/survival_biomarkers_subgroups.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Tabulate biomarker effects on survival by subgroup — survival_biomarkers_subgroups","text":"df (data.frame) containing analysis variables, returned extract_survival_biomarkers(). vars (character) names statistics reported among: n_tot_events: Total number events per group. n_tot: Total number observations per group. median: Median survival time. hr: Hazard ratio. ci: Confidence interval hazard ratio. pval: p-value effect. Note, one statistics n_tot n_tot_events, well hr ci required. groups_lists (named list list) optionally contains subgroups variable list, specifies new group levels via names levels belong character vectors elements list. control (list) list parameters returned helper function control_coxreg(). label_all please assign label_all parameter within extract_survival_biomarkers() function creating df. time_unit (string) label unit median survival time. Default NULL skips displaying unit. na_str (string) string used replace NA empty values output. .indent_mods (named integer) indent modifiers labels. Defaults 0, corresponds unmodified default behavior. Can negative.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/survival_biomarkers_subgroups.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Tabulate biomarker effects on survival by subgroup — survival_biomarkers_subgroups","text":"rtables table summarizing biomarker effects survival subgroup.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/survival_biomarkers_subgroups.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Tabulate biomarker effects on survival by subgroup — survival_biomarkers_subgroups","text":"functions create layout starting data frame contains required statistics. tables typically used input forest plots.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/survival_biomarkers_subgroups.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Tabulate biomarker effects on survival by subgroup — survival_biomarkers_subgroups","text":"tabulate_survival_biomarkers(): Table-creating function creates table summarizing biomarker effects survival subgroup.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/survival_biomarkers_subgroups.html","id":"note","dir":"Reference","previous_headings":"","what":"Note","title":"Tabulate biomarker effects on survival by subgroup — survival_biomarkers_subgroups","text":"contrast tabulate_survival_subgroups() tabulation function start input layout lyt. internally table created combining multiple subtables.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/reference/survival_biomarkers_subgroups.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Tabulate biomarker effects on survival by subgroup — survival_biomarkers_subgroups","text":"","code":"library(dplyr)  adtte <- tern_ex_adtte  # Save variable labels before data processing steps. adtte_labels <- formatters::var_labels(adtte)  adtte_f <- adtte %>%   filter(PARAMCD == \"OS\") %>%   mutate(     AVALU = as.character(AVALU),     is_event = CNSR == 0   ) labels <- c(\"AVALU\" = adtte_labels[[\"AVALU\"]], \"is_event\" = \"Event Flag\") formatters::var_labels(adtte_f)[names(labels)] <- labels  # Typical analysis of two continuous biomarkers `BMRKR1` and `AGE`, # in multiple regression models containing one covariate `RACE`, # as well as one stratification variable `STRATA1`. The subgroups # are defined by the levels of `BMRKR2`.  df <- extract_survival_biomarkers(   variables = list(     tte = \"AVAL\",     is_event = \"is_event\",     biomarkers = c(\"BMRKR1\", \"AGE\"),     strata = \"STRATA1\",     covariates = \"SEX\",     subgroups = \"BMRKR2\"   ),   label_all = \"Total Patients\",   data = adtte_f ) df #>   biomarker              biomarker_label n_tot n_tot_events   median        hr #> 1    BMRKR1 Continuous Level Biomarker 1   200          141 753.5176 1.0010939 #> 2       AGE                          Age   200          141 753.5176 1.0106406 #> 3    BMRKR1 Continuous Level Biomarker 1    70           52 735.4722 0.9905065 #> 4       AGE                          Age    70           52 735.4722 1.0106279 #> 5    BMRKR1 Continuous Level Biomarker 1    68           42 858.9952 0.9623210 #> 6       AGE                          Age    68           42 858.9952 1.0360765 #> 7    BMRKR1 Continuous Level Biomarker 1    62           47 727.8043 1.0770946 #> 8       AGE                          Age    62           47 727.8043 1.0009890 #>         lcl      ucl conf_level      pval     pval_label       subgroup    var #> 1 0.9538978 1.050625       0.95 0.9646086 p-value (Wald) Total Patients    ALL #> 2 0.9871004 1.034742       0.95 0.3787395 p-value (Wald) Total Patients    ALL #> 3 0.9142220 1.073156       0.95 0.8155443 p-value (Wald)            LOW BMRKR2 #> 4 0.9621192 1.061582       0.95 0.6735773 p-value (Wald)            LOW BMRKR2 #> 5 0.8708694 1.063376       0.95 0.4509368 p-value (Wald)         MEDIUM BMRKR2 #> 6 0.9727439 1.103532       0.95 0.2707796 p-value (Wald)         MEDIUM BMRKR2 #> 7 0.9756250 1.189118       0.95 0.1412524 p-value (Wald)           HIGH BMRKR2 #> 8 0.9678535 1.035259       0.95 0.9541048 p-value (Wald)           HIGH BMRKR2 #>                      var_label row_type #> 1               Total Patients  content #> 2               Total Patients  content #> 3 Continuous Level Biomarker 2 analysis #> 4 Continuous Level Biomarker 2 analysis #> 5 Continuous Level Biomarker 2 analysis #> 6 Continuous Level Biomarker 2 analysis #> 7 Continuous Level Biomarker 2 analysis #> 8 Continuous Level Biomarker 2 analysis  # Here we group the levels of `BMRKR2` manually. df_grouped <- extract_survival_biomarkers(   variables = list(     tte = \"AVAL\",     is_event = \"is_event\",     biomarkers = c(\"BMRKR1\", \"AGE\"),     strata = \"STRATA1\",     covariates = \"SEX\",     subgroups = \"BMRKR2\"   ),   data = adtte_f,   groups_lists = list(     BMRKR2 = list(       \"low\" = \"LOW\",       \"low/medium\" = c(\"LOW\", \"MEDIUM\"),       \"low/medium/high\" = c(\"LOW\", \"MEDIUM\", \"HIGH\")     )   ) ) df_grouped #>   biomarker              biomarker_label n_tot n_tot_events   median        hr #> 1    BMRKR1 Continuous Level Biomarker 1   200          141 753.5176 1.0010939 #> 2       AGE                          Age   200          141 753.5176 1.0106406 #> 3    BMRKR1 Continuous Level Biomarker 1    70           52 735.4722 0.9905065 #> 4       AGE                          Age    70           52 735.4722 1.0106279 #> 5    BMRKR1 Continuous Level Biomarker 1   138           94 777.8929 0.9801709 #> 6       AGE                          Age   138           94 777.8929 1.0236283 #> 7    BMRKR1 Continuous Level Biomarker 1   200          141 753.5176 1.0010939 #> 8       AGE                          Age   200          141 753.5176 1.0106406 #>         lcl      ucl conf_level      pval     pval_label        subgroup    var #> 1 0.9538978 1.050625       0.95 0.9646086 p-value (Wald)    All Patients    ALL #> 2 0.9871004 1.034742       0.95 0.3787395 p-value (Wald)    All Patients    ALL #> 3 0.9142220 1.073156       0.95 0.8155443 p-value (Wald)             low BMRKR2 #> 4 0.9621192 1.061582       0.95 0.6735773 p-value (Wald)             low BMRKR2 #> 5 0.9235465 1.040267       0.95 0.5094582 p-value (Wald)      low/medium BMRKR2 #> 6 0.9859367 1.062761       0.95 0.2224475 p-value (Wald)      low/medium BMRKR2 #> 7 0.9538978 1.050625       0.95 0.9646086 p-value (Wald) low/medium/high BMRKR2 #> 8 0.9871004 1.034742       0.95 0.3787395 p-value (Wald) low/medium/high BMRKR2 #>                      var_label row_type #> 1                 All Patients  content #> 2                 All Patients  content #> 3 Continuous Level Biomarker 2 analysis #> 4 Continuous Level Biomarker 2 analysis #> 5 Continuous Level Biomarker 2 analysis #> 6 Continuous Level Biomarker 2 analysis #> 7 Continuous Level Biomarker 2 analysis #> 8 Continuous Level Biomarker 2 analysis  ## Table with default columns. tabulate_survival_biomarkers(df) #>                                  Total n   Total Events   Median   Hazard Ratio   95% Wald CI    p-value (Wald) #> ——————————————————————————————————————————————————————————————————————————————————————————————————————————————— #> Age                                                                                                             #>   Total Patients                   200         141        753.5        1.01       (0.99, 1.03)       0.3787     #>   Continuous Level Biomarker 2                                                                                  #>     LOW                            70           52        735.5        1.01       (0.96, 1.06)       0.6736     #>     MEDIUM                         68           42        859.0        1.04       (0.97, 1.10)       0.2708     #>     HIGH                           62           47        727.8        1.00       (0.97, 1.04)       0.9541     #> Continuous Level Biomarker 1                                                                                    #>   Total Patients                   200         141        753.5        1.00       (0.95, 1.05)       0.9646     #>   Continuous Level Biomarker 2                                                                                  #>     LOW                            70           52        735.5        0.99       (0.91, 1.07)       0.8155     #>     MEDIUM                         68           42        859.0        0.96       (0.87, 1.06)       0.4509     #>     HIGH                           62           47        727.8        1.08       (0.98, 1.19)       0.1413      ## Table with a manually chosen set of columns: leave out \"pval\", reorder. tab <- tabulate_survival_biomarkers(   df = df,   vars = c(\"n_tot_events\", \"ci\", \"n_tot\", \"median\", \"hr\"),   time_unit = as.character(adtte_f$AVALU[1]) )  ## Finally produce the forest plot. # \\donttest{ g_forest(tab, xlim = c(0.8, 1.2))  # }"},{"path":"https://insightsengineering.github.io/tern/reference/survival_coxph_pairwise.html","id":null,"dir":"Reference","previous_headings":"","what":"Analyze a pairwise Cox-PH model — survival_coxph_pairwise","title":"Analyze a pairwise Cox-PH model — survival_coxph_pairwise","text":"analyze function coxph_pairwise() creates layout element analyze pairwise Cox-PH model. function can return statistics including p-value, hazard ratio (HR), HR confidence intervals stratified unstratified Cox-PH models. variable(s) analyzed specified via vars argument stratification factors via strata argument.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/survival_coxph_pairwise.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Analyze a pairwise Cox-PH model — survival_coxph_pairwise","text":"","code":"coxph_pairwise(   lyt,   vars,   strata = NULL,   control = control_coxph(),   na_str = default_na_str(),   nested = TRUE,   ...,   var_labels = \"CoxPH\",   show_labels = \"visible\",   table_names = vars,   .stats = c(\"pvalue\", \"hr\", \"hr_ci\"),   .formats = NULL,   .labels = NULL,   .indent_mods = NULL )  s_coxph_pairwise(   df,   .ref_group,   .in_ref_col,   .var,   is_event,   strata = NULL,   strat = lifecycle::deprecated(),   control = control_coxph() )  a_coxph_pairwise(   df,   .ref_group,   .in_ref_col,   .var,   is_event,   strata = NULL,   strat = lifecycle::deprecated(),   control = control_coxph() )"},{"path":"https://insightsengineering.github.io/tern/reference/survival_coxph_pairwise.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Analyze a pairwise Cox-PH model — survival_coxph_pairwise","text":"lyt (PreDataTableLayouts) layout analyses added . vars (character) variable names primary analysis variable iterated . strata (character NULL) variable names indicating stratification factors. control (list) parameters comparison details, specified using helper function control_coxph(). possible parameter options : pval_method (string) p-value method testing null hypothesis hazard ratio = 1. Default method \"log-rank\" comes survival::survdiff(), can also set \"wald\" \"likelihood\" (survival::coxph()). ties (string) specifying method tie handling. Default \"efron\", can also set \"breslow\" \"exact\". See survival::coxph(). conf_level (proportion) confidence level interval HR. na_str (string) string used replace NA empty values output. nested (flag) whether layout instruction applied within existing layout structure _if possible (TRUE, default) new top-level element (FALSE). Ignored nest split. underneath analyses, allowed. ... additional arguments lower level functions. var_labels (character) variable labels. show_labels (string) label visibility: one \"default\", \"visible\" \"hidden\". table_names (character) can customized case vars analyzed multiple times, avoid warnings rtables. .stats (character) statistics select table. Options : 'pvalue', 'hr', 'hr_ci', 'n_tot', 'n_tot_events' .formats (named character list) formats statistics. See Details analyze_vars information \"auto\" setting. .labels (named character) labels statistics (without indent). .indent_mods (named integer) indent modifiers labels. Defaults 0, corresponds unmodified default behavior. Can negative. df (data.frame) data set containing analysis variables. .ref_group (data.frame vector) data corresponding reference group. .in_ref_col (flag)TRUE working reference level, FALSE otherwise. .var (string) single variable name passed rtables requested statistics function. is_event (flag)TRUE event, FALSE time event censored. strat Please use strata argument instead.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/survival_coxph_pairwise.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Analyze a pairwise Cox-PH model — survival_coxph_pairwise","text":"coxph_pairwise() returns layout object suitable passing layouting functions, rtables::build_table(). Adding function rtable layout add formatted rows containing statistics s_coxph_pairwise() table layout. s_coxph_pairwise() returns statistics: pvalue: p-value test null hypothesis hazard ratio = 1. hr: Hazard ratio. hr_ci: Confidence interval hazard ratio. n_tot: Total number observations. n_tot_events: Total number events. a_coxph_pairwise() returns corresponding list formatted rtables::CellValue().","code":""},{"path":"https://insightsengineering.github.io/tern/reference/survival_coxph_pairwise.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Analyze a pairwise Cox-PH model — survival_coxph_pairwise","text":"coxph_pairwise(): Layout-creating function can take statistics function arguments additional format arguments. function wrapper rtables::analyze(). s_coxph_pairwise(): Statistics function analyzes HR, CIs HR, p-value Cox-PH model. a_coxph_pairwise(): Formatted analysis function used afun coxph_pairwise().","code":""},{"path":"https://insightsengineering.github.io/tern/reference/survival_coxph_pairwise.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Analyze a pairwise Cox-PH model — survival_coxph_pairwise","text":"","code":"library(dplyr)  adtte_f <- tern_ex_adtte %>%   filter(PARAMCD == \"OS\") %>%   mutate(is_event = CNSR == 0)  df <- adtte_f %>% filter(ARMCD == \"ARM A\") df_ref_group <- adtte_f %>% filter(ARMCD == \"ARM B\")  basic_table() %>%   split_cols_by(var = \"ARMCD\", ref_group = \"ARM A\") %>%   add_colcounts() %>%   coxph_pairwise(     vars = \"AVAL\",     is_event = \"is_event\",     var_labels = \"Unstratified Analysis\"   ) %>%   build_table(df = adtte_f) #>                         ARM A       ARM B          ARM C     #>                         (N=69)      (N=73)         (N=58)    #> ———————————————————————————————————————————————————————————— #> Unstratified Analysis                                        #>   p-value (log-rank)                0.0905         0.0086    #>   Hazard Ratio                       1.41           1.81     #>   95% CI                         (0.95, 2.09)   (1.16, 2.84)  basic_table() %>%   split_cols_by(var = \"ARMCD\", ref_group = \"ARM A\") %>%   add_colcounts() %>%   coxph_pairwise(     vars = \"AVAL\",     is_event = \"is_event\",     var_labels = \"Stratified Analysis\",     strata = \"SEX\",     control = control_coxph(pval_method = \"wald\")   ) %>%   build_table(df = adtte_f) #>                       ARM A       ARM B          ARM C     #>                       (N=69)      (N=73)         (N=58)    #> —————————————————————————————————————————————————————————— #> Stratified Analysis                                        #>   p-value (wald)                  0.0784         0.0066    #>   Hazard Ratio                     1.44           1.89     #>   95% CI                       (0.96, 2.15)   (1.19, 2.98)"},{"path":"https://insightsengineering.github.io/tern/reference/survival_duration_subgroups.html","id":null,"dir":"Reference","previous_headings":"","what":"Tabulate survival duration by subgroup — survival_duration_subgroups","title":"Tabulate survival duration by subgroup — survival_duration_subgroups","text":"tabulate_survival_subgroups() function creates layout element tabulate survival duration subgroup, returning statistics including median survival time hazard ratio population subgroup. table created df, list data frames returned extract_survival_subgroups(), statistics include specified via vars parameter. forest plot can created resulting table using g_forest() function.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/survival_duration_subgroups.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Tabulate survival duration by subgroup — survival_duration_subgroups","text":"","code":"tabulate_survival_subgroups(   lyt,   df,   vars = c(\"n_tot_events\", \"n_events\", \"median\", \"hr\", \"ci\"),   groups_lists = list(),   label_all = lifecycle::deprecated(),   time_unit = NULL,   riskdiff = NULL,   na_str = default_na_str(),   .formats = c(n = \"xx\", n_events = \"xx\", n_tot_events = \"xx\", median = \"xx.x\", n_tot =     \"xx\", hr = list(format_extreme_values(2L)), ci = list(format_extreme_values_ci(2L)),     pval = \"x.xxxx | (<0.0001)\") )  a_survival_subgroups(   .formats = list(n = \"xx\", n_events = \"xx\", n_tot_events = \"xx\", median = \"xx.x\", n_tot     = \"xx\", hr = list(format_extreme_values(2L)), ci =     list(format_extreme_values_ci(2L)), pval = \"x.xxxx | (<0.0001)\"),   na_str = default_na_str() )"},{"path":"https://insightsengineering.github.io/tern/reference/survival_duration_subgroups.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Tabulate survival duration by subgroup — survival_duration_subgroups","text":"lyt (PreDataTableLayouts) layout analyses added . df (list) list data frames containing analysis variables. List created using extract_survival_subgroups(). vars (character) names statistics reported among: n_tot_events: Total number events per group. n_events: Number events per group. n_tot: Total number observations per group. n: Number observations per group. median: Median survival time. hr: Hazard ratio. ci: Confidence interval hazard ratio. pval: p-value effect. Note, one statistics n_tot n_tot_events, well hr ci required. groups_lists (named list list) optionally contains subgroups variable list, specifies new group levels via names levels belong character vectors elements list. label_all please assign label_all parameter within extract_survival_subgroups() function creating df. time_unit (string) label unit median survival time. Default NULL skips displaying unit. riskdiff (list) risk (proportion) difference column added, list settings apply within column. See control_riskdiff() details. NULL, risk difference column added. riskdiff$arm_x riskdiff$arm_y NULL, first level df$survtime$arm used arm_x second level arm_y. na_str (string) string used replace NA empty values output. .formats (named character list) formats statistics. See Details analyze_vars information \"auto\" setting.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/survival_duration_subgroups.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Tabulate survival duration by subgroup — survival_duration_subgroups","text":"rtables table summarizing survival subgroup. a_survival_subgroups() returns corresponding list formatted rtables::CellValue().","code":""},{"path":"https://insightsengineering.github.io/tern/reference/survival_duration_subgroups.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Tabulate survival duration by subgroup — survival_duration_subgroups","text":"functions create layout starting data frame contains required statistics. Tables typically used part forest plot.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/survival_duration_subgroups.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Tabulate survival duration by subgroup — survival_duration_subgroups","text":"tabulate_survival_subgroups(): Table-creating function creates table summarizing survival subgroup. function wrapper rtables::analyze_colvars() rtables::summarize_row_groups(). a_survival_subgroups(): Formatted analysis function used afun tabulate_survival_subgroups().","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/reference/survival_duration_subgroups.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Tabulate survival duration by subgroup — survival_duration_subgroups","text":"","code":"library(dplyr)  adtte <- tern_ex_adtte  # Save variable labels before data processing steps. adtte_labels <- formatters::var_labels(adtte)  adtte_f <- adtte %>%   filter(     PARAMCD == \"OS\",     ARM %in% c(\"B: Placebo\", \"A: Drug X\"),     SEX %in% c(\"M\", \"F\")   ) %>%   mutate(     # Reorder levels of ARM to display reference arm before treatment arm.     ARM = droplevels(forcats::fct_relevel(ARM, \"B: Placebo\")),     SEX = droplevels(SEX),     AVALU = as.character(AVALU),     is_event = CNSR == 0   ) labels <- c(   \"ARM\" = adtte_labels[[\"ARM\"]],   \"SEX\" = adtte_labels[[\"SEX\"]],   \"AVALU\" = adtte_labels[[\"AVALU\"]],   \"is_event\" = \"Event Flag\" ) formatters::var_labels(adtte_f)[names(labels)] <- labels  df <- extract_survival_subgroups(   variables = list(     tte = \"AVAL\",     is_event = \"is_event\",     arm = \"ARM\", subgroups = c(\"SEX\", \"BMRKR2\")   ),   label_all = \"Total Patients\",   data = adtte_f ) df #> $survtime #>           arm  n n_events    median       subgroup    var #> 1  B: Placebo 73       57  727.8043 Total Patients    ALL #> 2   A: Drug X 69       44  974.6402 Total Patients    ALL #> 3  B: Placebo 40       31  599.1772              F    SEX #> 4   A: Drug X 38       24 1016.2982              F    SEX #> 5  B: Placebo 33       26  888.4916              M    SEX #> 6   A: Drug X 31       20  974.6402              M    SEX #> 7  B: Placebo 24       21  735.4722            LOW BMRKR2 #> 8   A: Drug X 26       15  974.6402            LOW BMRKR2 #> 9  B: Placebo 23       14  731.8352         MEDIUM BMRKR2 #> 10  A: Drug X 26       17  964.2197         MEDIUM BMRKR2 #> 11 B: Placebo 26       22  654.8245           HIGH BMRKR2 #> 12  A: Drug X 17       12 1016.2982           HIGH BMRKR2 #>                       var_label row_type #> 1                Total Patients  content #> 2                Total Patients  content #> 3                           Sex analysis #> 4                           Sex analysis #> 5                           Sex analysis #> 6                           Sex analysis #> 7  Continuous Level Biomarker 2 analysis #> 8  Continuous Level Biomarker 2 analysis #> 9  Continuous Level Biomarker 2 analysis #> 10 Continuous Level Biomarker 2 analysis #> 11 Continuous Level Biomarker 2 analysis #> 12 Continuous Level Biomarker 2 analysis #>  #> $hr #>   arm n_tot n_tot_events        hr       lcl       ucl conf_level       pval #> 1       142          101 0.7108557 0.4779138 1.0573368       0.95 0.09049511 #> 2        78           55 0.5595391 0.3246658 0.9643271       0.95 0.03411759 #> 3        64           46 0.9102874 0.5032732 1.6464678       0.95 0.75582028 #> 4        50           36 0.7617717 0.3854349 1.5055617       0.95 0.43236030 #> 5        49           31 0.7651261 0.3641277 1.6077269       0.95 0.47860004 #> 6        43           34 0.6662356 0.3257413 1.3626456       0.95 0.26285846 #>           pval_label       subgroup    var                    var_label #> 1 p-value (log-rank) Total Patients    ALL               Total Patients #> 2 p-value (log-rank)              F    SEX                          Sex #> 3 p-value (log-rank)              M    SEX                          Sex #> 4 p-value (log-rank)            LOW BMRKR2 Continuous Level Biomarker 2 #> 5 p-value (log-rank)         MEDIUM BMRKR2 Continuous Level Biomarker 2 #> 6 p-value (log-rank)           HIGH BMRKR2 Continuous Level Biomarker 2 #>   row_type #> 1  content #> 2 analysis #> 3 analysis #> 4 analysis #> 5 analysis #> 6 analysis #>   df_grouped <- extract_survival_subgroups(   variables = list(     tte = \"AVAL\",     is_event = \"is_event\",     arm = \"ARM\", subgroups = c(\"SEX\", \"BMRKR2\")   ),   data = adtte_f,   groups_lists = list(     BMRKR2 = list(       \"low\" = \"LOW\",       \"low/medium\" = c(\"LOW\", \"MEDIUM\"),       \"low/medium/high\" = c(\"LOW\", \"MEDIUM\", \"HIGH\")     )   ) ) df_grouped #> $survtime #>           arm  n n_events    median        subgroup    var #> 1  B: Placebo 73       57  727.8043    All Patients    ALL #> 2   A: Drug X 69       44  974.6402    All Patients    ALL #> 3  B: Placebo 40       31  599.1772               F    SEX #> 4   A: Drug X 38       24 1016.2982               F    SEX #> 5  B: Placebo 33       26  888.4916               M    SEX #> 6   A: Drug X 31       20  974.6402               M    SEX #> 7  B: Placebo 24       21  735.4722             low BMRKR2 #> 8   A: Drug X 26       15  974.6402             low BMRKR2 #> 9  B: Placebo 47       35  735.4722      low/medium BMRKR2 #> 10  A: Drug X 52       32  964.2197      low/medium BMRKR2 #> 11 B: Placebo 73       57  727.8043 low/medium/high BMRKR2 #> 12  A: Drug X 69       44  974.6402 low/medium/high BMRKR2 #>                       var_label row_type #> 1                  All Patients  content #> 2                  All Patients  content #> 3                           Sex analysis #> 4                           Sex analysis #> 5                           Sex analysis #> 6                           Sex analysis #> 7  Continuous Level Biomarker 2 analysis #> 8  Continuous Level Biomarker 2 analysis #> 9  Continuous Level Biomarker 2 analysis #> 10 Continuous Level Biomarker 2 analysis #> 11 Continuous Level Biomarker 2 analysis #> 12 Continuous Level Biomarker 2 analysis #>  #> $hr #>   arm n_tot n_tot_events        hr       lcl       ucl conf_level       pval #> 1       142          101 0.7108557 0.4779138 1.0573368       0.95 0.09049511 #> 2        78           55 0.5595391 0.3246658 0.9643271       0.95 0.03411759 #> 3        64           46 0.9102874 0.5032732 1.6464678       0.95 0.75582028 #> 4        50           36 0.7617717 0.3854349 1.5055617       0.95 0.43236030 #> 5        99           67 0.7472958 0.4600419 1.2139136       0.95 0.23764314 #> 6       142          101 0.7108557 0.4779138 1.0573368       0.95 0.09049511 #>           pval_label        subgroup    var                    var_label #> 1 p-value (log-rank)    All Patients    ALL                 All Patients #> 2 p-value (log-rank)               F    SEX                          Sex #> 3 p-value (log-rank)               M    SEX                          Sex #> 4 p-value (log-rank)             low BMRKR2 Continuous Level Biomarker 2 #> 5 p-value (log-rank)      low/medium BMRKR2 Continuous Level Biomarker 2 #> 6 p-value (log-rank) low/medium/high BMRKR2 Continuous Level Biomarker 2 #>   row_type #> 1  content #> 2 analysis #> 3 analysis #> 4 analysis #> 5 analysis #> 6 analysis #>   ## Table with default columns. basic_table() %>%   tabulate_survival_subgroups(df, time_unit = adtte_f$AVALU[1]) #>                                                     B: Placebo               A: Drug X                                      #> Baseline Risk Factors          Total Events   Events   Median (DAYS)   Events   Median (DAYS)   Hazard Ratio   95% Wald CI  #> ——————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————— #> Total Patients                     101          57         727.8         44         974.6           0.71       (0.48, 1.06) #> Sex                                                                                                                         #>   F                                 55          31         599.2         24        1016.3           0.56       (0.32, 0.96) #>   M                                 46          26         888.5         20         974.6           0.91       (0.50, 1.65) #> Continuous Level Biomarker 2                                                                                                #>   LOW                               36          21         735.5         15         974.6           0.76       (0.39, 1.51) #>   MEDIUM                            31          14         731.8         17         964.2           0.77       (0.36, 1.61) #>   HIGH                              34          22         654.8         12        1016.3           0.67       (0.33, 1.36)  ## Table with a manually chosen set of columns: adding \"pval\". basic_table() %>%   tabulate_survival_subgroups(     df = df,     vars = c(\"n_tot_events\", \"n_events\", \"median\", \"hr\", \"ci\", \"pval\"),     time_unit = adtte_f$AVALU[1]   ) #>                                                     B: Placebo               A: Drug X                                                           #> Baseline Risk Factors          Total Events   Events   Median (DAYS)   Events   Median (DAYS)   Hazard Ratio   95% Wald CI    p-value (log-rank) #> ———————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————— #> Total Patients                     101          57         727.8         44         974.6           0.71       (0.48, 1.06)         0.0905       #> Sex                                                                                                                                              #>   F                                 55          31         599.2         24        1016.3           0.56       (0.32, 0.96)         0.0341       #>   M                                 46          26         888.5         20         974.6           0.91       (0.50, 1.65)         0.7558       #> Continuous Level Biomarker 2                                                                                                                     #>   LOW                               36          21         735.5         15         974.6           0.76       (0.39, 1.51)         0.4324       #>   MEDIUM                            31          14         731.8         17         964.2           0.77       (0.36, 1.61)         0.4786       #>   HIGH                              34          22         654.8         12        1016.3           0.67       (0.33, 1.36)         0.2629"},{"path":"https://insightsengineering.github.io/tern/reference/survival_time.html","id":null,"dir":"Reference","previous_headings":"","what":"Survival time analysis — survival_time","title":"Survival time analysis — survival_time","text":"analyze function surv_time() creates layout element analyze survival time calculating survival time median, median confidence interval, quantiles, range (, censored, event patients). primary analysis variable vars time variable secondary analysis variable is_event indicates whether event occurred.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/survival_time.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Survival time analysis — survival_time","text":"","code":"surv_time(   lyt,   vars,   is_event,   control = control_surv_time(),   ref_fn_censor = TRUE,   na_str = default_na_str(),   nested = TRUE,   ...,   var_labels = \"Time to Event\",   show_labels = \"visible\",   table_names = vars,   .stats = c(\"median\", \"median_ci\", \"quantiles\", \"range\"),   .formats = NULL,   .labels = NULL,   .indent_mods = c(median_ci = 1L) )  s_surv_time(df, .var, is_event, control = control_surv_time())  a_surv_time(   df,   labelstr = \"\",   .var = NULL,   .df_row = NULL,   is_event,   control = control_surv_time(),   ref_fn_censor = TRUE,   .stats = NULL,   .formats = NULL,   .labels = NULL,   .indent_mods = NULL,   na_str = default_na_str() )"},{"path":"https://insightsengineering.github.io/tern/reference/survival_time.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Survival time analysis — survival_time","text":"lyt (PreDataTableLayouts) layout analyses added . vars (character) variable names primary analysis variable iterated . is_event (flag)TRUE event, FALSE time event censored. control (list) parameters comparison details, specified using helper function control_surv_time(). possible parameter options : conf_level (proportion) confidence level interval survival time. conf_type (string) confidence interval type. Options \"plain\" (default), \"log\", \"log-log\", see survival::survfit(). Note option \"none\" supported. quantiles (numeric) vector length two specify quantiles survival time. ref_fn_censor (flag) whether referential footnotes indicating censored observations printed range statistic included. na_str (string) string used replace NA empty values output. nested (flag) whether layout instruction applied within existing layout structure _if possible (TRUE, default) new top-level element (FALSE). Ignored nest split. underneath analyses, allowed. ... additional arguments lower level functions. var_labels (character) variable labels. show_labels (string) label visibility: one \"default\", \"visible\" \"hidden\". table_names (character) can customized case vars analyzed multiple times, avoid warnings rtables. .stats (character) statistics select table. Options : 'median', 'median_ci', 'median_ci_3d', 'quantiles', 'quantiles_lower', 'quantiles_upper', 'range_censor', 'range_event', 'range' .formats (named character list) formats statistics. See Details analyze_vars information \"auto\" setting. .labels (named character) labels statistics (without indent). .indent_mods (named integer) indent modifiers labels. element vector name-value pair name corresponding statistic specified .stats value indentation statistic's row label. df (data.frame) data set containing analysis variables. .var (string) single variable name passed rtables requested statistics function. labelstr (string) label level parent split currently summarized (must present second argument Content Row Functions). See rtables::summarize_row_groups() information. .df_row (data.frame) data frame across columns given row split.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/survival_time.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Survival time analysis — survival_time","text":"surv_time() returns layout object suitable passing layouting functions, rtables::build_table(). Adding function rtable layout add formatted rows containing statistics s_surv_time() table layout. s_surv_time() returns statistics: median: Median survival time. median_ci: Confidence interval median time. median_ci_3d: Median confidence interval median time. quantiles: Survival time two specified quantiles. quantiles_lower: quantile confidence interval first specified quantile. quantiles_upper: quantile confidence interval second specified quantile. range_censor: Survival time range censored observations. range_event: Survival time range observations events. range: Survival time range observations. a_surv_time() returns corresponding list formatted rtables::CellValue().","code":""},{"path":"https://insightsengineering.github.io/tern/reference/survival_time.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Survival time analysis — survival_time","text":"surv_time(): Layout-creating function can take statistics function arguments additional format arguments. function wrapper rtables::analyze(). s_surv_time(): Statistics function analyzes survival times. a_surv_time(): Formatted analysis function used afun surv_time().","code":""},{"path":"https://insightsengineering.github.io/tern/reference/survival_time.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Survival time analysis — survival_time","text":"","code":"library(dplyr)  adtte_f <- tern_ex_adtte %>%   filter(PARAMCD == \"OS\") %>%   mutate(     AVAL = day2month(AVAL),     is_event = CNSR == 0   ) df <- adtte_f %>% filter(ARMCD == \"ARM A\")  basic_table() %>%   split_cols_by(var = \"ARMCD\") %>%   add_colcounts() %>%   surv_time(     vars = \"AVAL\",     var_labels = \"Survival Time (Months)\",     is_event = \"is_event\",     control = control_surv_time(conf_level = 0.9, conf_type = \"log-log\")   ) %>%   build_table(df = adtte_f) #>                             ARM A          ARM B          ARM C     #>                             (N=69)         (N=73)         (N=58)    #> ——————————————————————————————————————————————————————————————————— #> Survival Time (Months)                                              #>   Median                     32.0           23.9           20.8     #>     90% CI               (22.6, 46.5)   (18.3, 29.2)   (12.9, 25.9) #>   25% and 75%-ile         17.4, 65.3     9.8, 42.0      7.3, 37.1   #>   Range                  0.3 to 155.5   0.1 to 154.1   0.6 to 80.7   a_surv_time(   df,   .df_row = df,   .var = \"AVAL\",   is_event = \"is_event\" ) #> RowsVerticalSection (in_rows) object print method: #> ---------------------------- #>           row_name     formatted_cell indent_mod        row_label #> 1           Median               32.0          0           Median #> 2           95% CI       (22.5, 49.3)          0           95% CI #> 3  Median (95% CI) 32.0 (22.5 - 49.3)          0  Median (95% CI) #> 4  25% and 75%-ile         17.4, 65.3          0  25% and 75%-ile #> 5 25%-ile (95% CI) 17.4 (10.1 - 22.5)          0 25%-ile (95% CI) #> 6 75%-ile (95% CI) 65.3 (49.3 - 87.2)          0 75%-ile (95% CI) #> 7 Range (censored)        0.8 to 63.5          0 Range (censored) #> 8    Range (event)       0.3 to 155.5          0    Range (event) #> 9            Range       0.3 to 155.5          0            Range"},{"path":"https://insightsengineering.github.io/tern/reference/survival_timepoint.html","id":null,"dir":"Reference","previous_headings":"","what":"Survival time point analysis — survival_timepoint","title":"Survival time point analysis — survival_timepoint","text":"analyze function surv_timepoint() creates layout element analyze patient survival rates difference survival rates groups given time point. primary analysis variable vars time variable. required inputs time_point, numeric time point interest, is_event, variable indicates whether event occurred. method argument used specify whether want analyze survival estimations (\"surv\"), difference survival control (\"surv_diff\"), (\"\").","code":""},{"path":"https://insightsengineering.github.io/tern/reference/survival_timepoint.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Survival time point analysis — survival_timepoint","text":"","code":"surv_timepoint(   lyt,   vars,   time_point,   is_event,   control = control_surv_timepoint(),   method = c(\"surv\", \"surv_diff\", \"both\"),   na_str = default_na_str(),   nested = TRUE,   ...,   table_names_suffix = \"\",   var_labels = \"Time\",   show_labels = \"visible\",   .stats = c(\"pt_at_risk\", \"event_free_rate\", \"rate_ci\", \"rate_diff\", \"rate_diff_ci\",     \"ztest_pval\"),   .formats = NULL,   .labels = NULL,   .indent_mods = if (method == \"both\") {      c(rate_diff = 1L, rate_diff_ci = 2L,     ztest_pval = 2L)  } else {      c(rate_diff_ci = 1L, ztest_pval = 1L)  } )  s_surv_timepoint(   df,   .var,   time_point,   is_event,   control = control_surv_timepoint() )  a_surv_timepoint(   df,   .var,   time_point,   is_event,   control = control_surv_timepoint() )  s_surv_timepoint_diff(   df,   .var,   .ref_group,   .in_ref_col,   time_point,   control = control_surv_timepoint(),   ... )  a_surv_timepoint_diff(   df,   .var,   .ref_group,   .in_ref_col,   time_point,   control = control_surv_timepoint(),   ... )"},{"path":"https://insightsengineering.github.io/tern/reference/survival_timepoint.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Survival time point analysis — survival_timepoint","text":"lyt (PreDataTableLayouts) layout analyses added . vars (character) variable names primary analysis variable iterated . time_point (numeric(1)) survival time point interest. is_event (flag)TRUE event, FALSE time event censored. control (list) parameters comparison details, specified using helper function control_surv_timepoint(). possible parameter options : conf_level (proportion) confidence level interval survival rate. conf_type (string) confidence interval type. Options \"plain\" (default), \"log\", \"log-log\", see survival::survfit(). Note option \"none\" longer supported. method (string)\"surv\" (survival estimations), \"surv_diff\" (difference survival control), \"\". na_str (string) string used replace NA empty values output. nested (flag) whether layout instruction applied within existing layout structure _if possible (TRUE, default) new top-level element (FALSE). Ignored nest split. underneath analyses, allowed. ... additional arguments lower level functions. table_names_suffix (string) optional suffix table_names used rtables avoid warnings duplicate table names. var_labels (character) variable labels. show_labels (string) label visibility: one \"default\", \"visible\" \"hidden\". .stats (character) statistics select table. Options : 'pt_at_risk', 'event_free_rate', 'rate_se', 'rate_ci', 'rate_diff', 'rate_diff_ci', 'ztest_pval', 'event_free_rate_3d' .formats (named character list) formats statistics. See Details analyze_vars information \"auto\" setting. .labels (named character) labels statistics (without indent). .indent_mods (named integer) indent modifiers labels. element vector name-value pair name corresponding statistic specified .stats value indentation statistic's row label. df (data.frame) data set containing analysis variables. .var (string) single variable name passed rtables requested statistics function. .ref_group (data.frame vector) data corresponding reference group. .in_ref_col (flag)TRUE working reference level, FALSE otherwise.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/survival_timepoint.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Survival time point analysis — survival_timepoint","text":"surv_timepoint() returns layout object suitable passing layouting functions, rtables::build_table(). Adding function rtable layout add formatted rows containing statistics s_surv_timepoint() /s_surv_timepoint_diff() table layout depending value method. s_surv_timepoint() returns statistics: pt_at_risk: Patients remaining risk. event_free_rate: Event-free rate (%). rate_se: Standard error event free rate. rate_ci: Confidence interval event free rate. event_free_rate_3d: Event-free rate (%) Confidence interval. a_surv_timepoint() returns corresponding list formatted rtables::CellValue(). s_surv_timepoint_diff() returns statistics: rate_diff: Event-free rate difference two groups. rate_diff_ci: Confidence interval difference. rate_diff_ci_3d: Event-free rate difference confidence interval two groups. ztest_pval: p-value test difference 0. a_surv_timepoint_diff() returns corresponding list formatted rtables::CellValue().","code":""},{"path":"https://insightsengineering.github.io/tern/reference/survival_timepoint.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Survival time point analysis — survival_timepoint","text":"surv_timepoint(): Layout-creating function can take statistics function arguments additional format arguments. function wrapper rtables::analyze(). s_surv_timepoint(): Statistics function analyzes survival rate. a_surv_timepoint(): Formatted analysis function used afun surv_timepoint() method = \"surv\". s_surv_timepoint_diff(): Statistics function analyzes difference two survival rates. a_surv_timepoint_diff(): Formatted analysis function used afun surv_timepoint() method = \"surv_diff\".","code":""},{"path":"https://insightsengineering.github.io/tern/reference/survival_timepoint.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Survival time point analysis — survival_timepoint","text":"","code":"library(dplyr)  adtte_f <- tern_ex_adtte %>%   filter(PARAMCD == \"OS\") %>%   mutate(     AVAL = day2month(AVAL),     is_event = CNSR == 0   )  # Survival at given time points. basic_table() %>%   split_cols_by(var = \"ARMCD\", ref_group = \"ARM A\") %>%   add_colcounts() %>%   surv_timepoint(     vars = \"AVAL\",     var_labels = \"Months\",     is_event = \"is_event\",     time_point = 7   ) %>%   build_table(df = adtte_f) #>                                    ARM A            ARM B            ARM C      #>                                    (N=69)           (N=73)           (N=58)     #> ——————————————————————————————————————————————————————————————————————————————— #> 7 Months                                                                        #>   Patients remaining at risk         54               57               42       #>   Event Free Rate (%)              84.89            79.43            75.50      #>   95% CI                       (76.24, 93.53)   (70.15, 88.71)   (64.33, 86.67)  # Difference in survival at given time points. basic_table() %>%   split_cols_by(var = \"ARMCD\", ref_group = \"ARM A\") %>%   add_colcounts() %>%   surv_timepoint(     vars = \"AVAL\",     var_labels = \"Months\",     is_event = \"is_event\",     time_point = 9,     method = \"surv_diff\",     .indent_mods = c(\"rate_diff\" = 0L, \"rate_diff_ci\" = 2L, \"ztest_pval\" = 2L)   ) %>%   build_table(df = adtte_f) #>                                   ARM A        ARM B            ARM C      #>                                   (N=69)       (N=73)           (N=58)     #> —————————————————————————————————————————————————————————————————————————— #> 9 Months                                                                   #>   Difference in Event Free Rate                -9.64            -13.03     #>       95% CI                               (-22.80, 3.52)   (-27.59, 1.53) #>       p-value (Z-test)                         0.1511           0.0794      # Survival and difference in survival at given time points. basic_table() %>%   split_cols_by(var = \"ARMCD\", ref_group = \"ARM A\") %>%   add_colcounts() %>%   surv_timepoint(     vars = \"AVAL\",     var_labels = \"Months\",     is_event = \"is_event\",     time_point = 9,     method = \"both\"   ) %>%   build_table(df = adtte_f) #>                                       ARM A            ARM B            ARM C      #>                                       (N=69)           (N=73)           (N=58)     #> —————————————————————————————————————————————————————————————————————————————————— #> 9 Months                                                                           #>   Patients remaining at risk            53               53               39       #>   Event Free Rate (%)                 84.89            75.25            71.86      #>   95% CI                          (76.24, 93.53)   (65.32, 85.17)   (60.14, 83.57) #>   Difference in Event Free Rate                        -9.64            -13.03     #>     95% CI                                         (-22.80, 3.52)   (-27.59, 1.53) #>     p-value (Z-test)                                   0.1511           0.0794"},{"path":"https://insightsengineering.github.io/tern/reference/tern-package.html","id":null,"dir":"Reference","previous_headings":"","what":"tern Package — tern-package","title":"tern Package — tern-package","text":"Package create tables, listings graphs analyze clinical trials data.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/reference/tern-package.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"tern Package — tern-package","text":"Maintainer: Joe Zhu joe.zhu@roche.com Authors: Daniel Sabanés Bové daniel.sabanes_bove@roche.com Jana Stoilova jana.stoilova@roche.com Davide Garolini davide.garolini@roche.com Emily de la Rua emily.de_la_rua@contractors.roche.com Abinaya Yogasekaram abinaya.yogasekaram@contractors.roche.com Heng Wang wang.heng@gene.com Francois Collin Adrian Waddell adrian.waddell@gene.com Pawel Rucki pawel.rucki@roche.com Chendi Liao chendi.liao@roche.com Jennifer Li li.jing@gene.com contributors: F. Hoffmann-La Roche AG [copyright holder, funder]","code":""},{"path":"https://insightsengineering.github.io/tern/reference/tidy.glm.html","id":null,"dir":"Reference","previous_headings":"","what":"Custom tidy method for binomial GLM results — tidy.glm","title":"Custom tidy method for binomial GLM results — tidy.glm","text":"Helper method (broom::tidy()) prepare data frame glm object binomial family.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/tidy.glm.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Custom tidy method for binomial GLM results — tidy.glm","text":"","code":"# S3 method for class 'glm' tidy(x, conf_level = 0.95, at = NULL, ...)"},{"path":"https://insightsengineering.github.io/tern/reference/tidy.glm.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Custom tidy method for binomial GLM results — tidy.glm","text":"x (glm) logistic regression model fitted stats::glm() \"binomial\" family. conf_level (proportion) confidence level interval. (numeric NULL) optional values interaction variable. Otherwise median used. ... additional arguments lower level functions.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/tidy.glm.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Custom tidy method for binomial GLM results — tidy.glm","text":"data.frame containing tidied model.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/reference/tidy.glm.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Custom tidy method for binomial GLM results — tidy.glm","text":"","code":"library(dplyr) library(broom)  adrs_f <- tern_ex_adrs %>%   filter(PARAMCD == \"BESRSPI\") %>%   filter(RACE %in% c(\"ASIAN\", \"WHITE\", \"BLACK OR AFRICAN AMERICAN\")) %>%   mutate(     Response = case_when(AVALC %in% c(\"PR\", \"CR\") ~ 1, TRUE ~ 0),     RACE = factor(RACE),     SEX = factor(SEX)   ) formatters::var_labels(adrs_f) <- c(formatters::var_labels(tern_ex_adrs), Response = \"Response\") mod1 <- fit_logistic(   data = adrs_f,   variables = list(     response = \"Response\",     arm = \"ARMCD\",     covariates = c(\"AGE\", \"RACE\")   ) ) #> Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred mod2 <- fit_logistic(   data = adrs_f,   variables = list(     response = \"Response\",     arm = \"ARMCD\",     covariates = c(\"AGE\", \"RACE\"),     interaction = \"AGE\"   ) ) #> Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred  df <- tidy(mod1, conf_level = 0.99) df2 <- tidy(mod2, conf_level = 0.99)"},{"path":"https://insightsengineering.github.io/tern/reference/tidy.step.html","id":null,"dir":"Reference","previous_headings":"","what":"Custom tidy method for STEP results — tidy.step","title":"Custom tidy method for STEP results — tidy.step","text":"Tidy STEP results tibble format ready plotting.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/tidy.step.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Custom tidy method for STEP results — tidy.step","text":"","code":"# S3 method for class 'step' tidy(x, ...)"},{"path":"https://insightsengineering.github.io/tern/reference/tidy.step.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Custom tidy method for STEP results — tidy.step","text":"x (matrix) results fit_survival_step(). ... used.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/tidy.step.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Custom tidy method for STEP results — tidy.step","text":"tibble one row per STEP subgroup. estimates CIs HR scale, respectively. Additional attributes carry metadata also used plotting.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/reference/tidy.step.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Custom tidy method for STEP results — tidy.step","text":"","code":"library(survival) lung$sex <- factor(lung$sex) vars <- list(   time = \"time\",   event = \"status\",   arm = \"sex\",   biomarker = \"age\" ) step_matrix <- fit_survival_step(   variables = vars,   data = lung,   control = c(control_coxph(), control_step(num_points = 10, degree = 2)) ) broom::tidy(step_matrix) #> # A tibble: 10 × 12 #>    `Percentile Center` `Percentile Lower` `Percentile Upper` `Interval Center` #>  *               <dbl>              <dbl>              <dbl>             <dbl> #>  1              0.0909             0                   0.341              50   #>  2              0.182              0                   0.432              54   #>  3              0.273              0.0227              0.523              57   #>  4              0.364              0.114               0.614              59.5 #>  5              0.455              0.205               0.705              62   #>  6              0.545              0.295               0.795              64   #>  7              0.636              0.386               0.886              67   #>  8              0.727              0.477               0.977              69   #>  9              0.818              0.568               1                  71   #> 10              0.909              0.659               1                  74   #> # ℹ 8 more variables: `Interval Lower` <dbl>, `Interval Upper` <dbl>, n <dbl>, #> #   events <dbl>, `Hazard Ratio` <dbl>, se <dbl>, ci_lower <dbl>, #> #   ci_upper <dbl>"},{"path":[]},{"path":"https://insightsengineering.github.io/tern/reference/tidy_coxreg.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Custom tidy methods for Cox regression — tidy_coxreg","text":"","code":"# S3 method for class 'summary.coxph' tidy(x, ...)  # S3 method for class 'coxreg.univar' tidy(x, ...)  # S3 method for class 'coxreg.multivar' tidy(x, ...)"},{"path":"https://insightsengineering.github.io/tern/reference/tidy_coxreg.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Custom tidy methods for Cox regression — tidy_coxreg","text":"x (list) result Cox regression model fitted fit_coxreg_univar() (univariate models) fit_coxreg_multivar() (multivariate models). ... additional arguments lower level functions.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/tidy_coxreg.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Custom tidy methods for Cox regression — tidy_coxreg","text":"broom::tidy() returns: summary.coxph objects,  data.frame columns: Pr(>|z|), exp(coef), exp(-coef), lower .95, upper .95, level, n. coxreg.univar objects, data.frame columns: effect, term, term_label, level, n, hr, lcl, ucl, pval, ci. coxreg.multivar objects, data.frame columns: term, pval, term_label, hr, lcl, ucl, level, ci.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/tidy_coxreg.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Custom tidy methods for Cox regression — tidy_coxreg","text":"tidy(summary.coxph): Custom tidy method survival::coxph() summary results. Tidy survival::coxph() results data.frame extract model results. tidy(coxreg.univar): Custom tidy method univariate Cox regression. Tidy result Cox regression model fitted fit_coxreg_univar(). tidy(coxreg.multivar): Custom tidy method multivariate Cox regression. Tidy result Cox regression model fitted fit_coxreg_multivar().","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/reference/tidy_coxreg.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Custom tidy methods for Cox regression — tidy_coxreg","text":"","code":"library(survival) library(broom)  set.seed(1, kind = \"Mersenne-Twister\")  dta_bladder <- with(   data = bladder[bladder$enum < 5, ],   data.frame(     time = stop,     status = event,     armcd = as.factor(rx),     covar1 = as.factor(enum),     covar2 = factor(       sample(as.factor(enum)),       levels = 1:4, labels = c(\"F\", \"F\", \"M\", \"M\")     )   ) ) labels <- c(\"armcd\" = \"ARM\", \"covar1\" = \"A Covariate Label\", \"covar2\" = \"Sex (F/M)\") formatters::var_labels(dta_bladder)[names(labels)] <- labels dta_bladder$age <- sample(20:60, size = nrow(dta_bladder), replace = TRUE)  formula <- \"survival::Surv(time, status) ~ armcd + covar1\" msum <- summary(coxph(stats::as.formula(formula), data = dta_bladder)) tidy(msum) #>       Pr(>|z|) exp(coef) exp(-coef)  lower .95 upper .95   level   n #> 1 1.287954e-02 0.6110123   1.636628 0.41442417 0.9008549  armcd2 340 #> 2 6.407916e-04 0.4460731   2.241785 0.28061816 0.7090818 covar12 340 #> 3 5.272933e-06 0.3075864   3.251119 0.18517346 0.5109230 covar13 340 #> 4 2.125359e-08 0.1808795   5.528541 0.09943722 0.3290258 covar14 340  ## Cox regression: arm + 1 covariate. mod1 <- fit_coxreg_univar(   variables = list(     time = \"time\", event = \"status\", arm = \"armcd\",     covariates = \"covar1\"   ),   data = dta_bladder,   control = control_coxreg(conf_level = 0.91) )  ## Cox regression: arm + 1 covariate + interaction, 2 candidate covariates. mod2 <- fit_coxreg_univar(   variables = list(     time = \"time\", event = \"status\", arm = \"armcd\",     covariates = c(\"covar1\", \"covar2\")   ),   data = dta_bladder,   control = control_coxreg(conf_level = 0.91, interaction = TRUE) )  tidy(mod1) #>            effect   term        term_label level   n        hr       lcl #> ref    Treatment:  armcd  2 vs control (1)     2 340 0.6386426 0.4557586 #> covar1 Covariate: covar1 A Covariate Label     2 340  0.607037 0.4324571 #>              ucl       pval                   ci #> ref    0.8949131 0.02423805 0.4557586, 0.8949131 #> covar1 0.8520935 0.01257339 0.4324571, 0.8520935 tidy(mod2) #>                           effect   term        term_label level   n        hr #> ref                   Treatment:  armcd  2 vs control (1)     2 340 0.6386426 #> covar1.1              Covariate: covar1 A Covariate Label       340           #> covar1.armcd2/covar11 Covariate: covar1                 1     1     0.6284569 #> covar1.armcd2/covar12 Covariate: covar1                 2     2     0.5806499 #> covar1.armcd2/covar13 Covariate: covar1                 3     3     0.5486103 #> covar1.armcd2/covar14 Covariate: covar1                 4     4     0.6910725 #> covar2.1              Covariate: covar2         Sex (F/M)       340           #> covar2.armcd2/covar2F Covariate: covar2                 F     F     0.6678243 #> covar2.armcd2/covar2M Covariate: covar2                 M     M     0.5954021 #>                             lcl       ucl       pval pval_inter #> ref                   0.4557586 0.8949131 0.02423805            #> covar1.1                     NA        NA             0.9883021 #> covar1.armcd2/covar11 0.3450471 1.1446499                       #> covar1.armcd2/covar12 0.2684726 1.2558239                       #> covar1.armcd2/covar13 0.2226814 1.3515868                       #> covar1.armcd2/covar14 0.2308006 2.0692373                       #> covar2.1                     NA        NA             0.7759013 #> covar2.armcd2/covar2F 0.3649842 1.2219413                       #> covar2.armcd2/covar2M 0.3572772 0.9922368                       #>                                         ci #> ref                   0.4557586, 0.8949131 #> covar1.1                                   #> covar1.armcd2/covar11 0.3450471, 1.1446499 #> covar1.armcd2/covar12 0.2684726, 1.2558239 #> covar1.armcd2/covar13 0.2226814, 1.3515868 #> covar1.armcd2/covar14 0.2308006, 2.0692373 #> covar2.1                                   #> covar2.armcd2/covar2F 0.3649842, 1.2219413 #> covar2.armcd2/covar2M 0.3572772, 0.9922368  multivar_model <- fit_coxreg_multivar(   variables = list(     time = \"time\", event = \"status\", arm = \"armcd\",     covariates = c(\"covar1\", \"covar2\")   ),   data = dta_bladder ) broom::tidy(multivar_model) #>                       term         pval                        term_label #> armcd.1              armcd                            ARM (reference = 1) #> armcd.2                ARM   0.01232761                                 2 #> covar1.1            covar1 7.209956e-09 A Covariate Label (reference = 1) #> covar1.2 A Covariate Label  0.001120332                                 2 #> covar1.3 A Covariate Label 6.293725e-06                                 3 #> covar1.4 A Covariate Label 3.013875e-08                                 4 #> covar2.1            covar2                      Sex (F/M) (reference = F) #> covar2.2         Sex (F/M)    0.1910521                                 M #>                 hr        lcl       ucl level                     ci #> armcd.1                    NA        NA  <NA>                        #> armcd.2  0.6062777 0.40970194 0.8971710     2   0.4097019, 0.8971710 #> covar1.1                   NA        NA  <NA>                        #> covar1.2 0.4564763 0.28481052 0.7316115     2   0.2848105, 0.7316115 #> covar1.3 0.3069612 0.18386073 0.5124813     3   0.1838607, 0.5124813 #> covar1.4 0.1817017 0.09939435 0.3321668     4 0.09939435, 0.33216684 #> covar2.1                   NA        NA  <NA>                        #> covar2.2  1.289373 0.88087820 1.8873019     M   0.8808782, 1.8873019"},{"path":"https://insightsengineering.github.io/tern/reference/to_n.html","id":null,"dir":"Reference","previous_headings":"","what":"Replicate entries of a vector if required — to_n","title":"Replicate entries of a vector if required — to_n","text":"Replicate entries vector required.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/to_n.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Replicate entries of a vector if required — to_n","text":"","code":"to_n(x, n)"},{"path":"https://insightsengineering.github.io/tern/reference/to_n.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Replicate entries of a vector if required — to_n","text":"x (numeric) vector numbers want analyze. n (integer(1)) number entries needed.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/to_n.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Replicate entries of a vector if required — to_n","text":"x required length already NULL, otherwise scalar replicated version n entries.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/to_n.html","id":"note","dir":"Reference","previous_headings":"","what":"Note","title":"Replicate entries of a vector if required — to_n","text":"function fail x length n /scalar.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/to_string_matrix.html","id":null,"dir":"Reference","previous_headings":"","what":"Convert table into matrix of strings — to_string_matrix","title":"Convert table into matrix of strings — to_string_matrix","text":"Helper function use mostly within tests. with_spacesparameter allows test content also indentation table structure. print_txt_to_copy instead facilitate testing development returning well formatted text needs copied pasted expected output.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/to_string_matrix.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Convert table into matrix of strings — to_string_matrix","text":"","code":"to_string_matrix(   x,   widths = NULL,   max_width = NULL,   hsep = formatters::default_hsep(),   with_spaces = TRUE,   print_txt_to_copy = FALSE )"},{"path":"https://insightsengineering.github.io/tern/reference/to_string_matrix.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Convert table into matrix of strings — to_string_matrix","text":"x (VTableTree)rtables table object. widths (numeric  NULL) Proposed widths columns x. expected length numeric vector can retrieved ncol(x) + 1 column row names must also considered. max_width (integer(1), string NULL) width title footer (including footnotes) materials word-wrapped . NULL, set current print width session (getOption(\"width\")). set \"auto\", width table (plus table inset) used. Parameter ignored tf_wrap = FALSE. hsep (string) character repeat create header/body separator line. NULL, object value used. \" \", empty separator printed. See default_hsep() information. with_spaces (flag) whether tested table keep indentation relevant spaces. print_txt_to_copy (flag) utility way copy input table directly expected variable instead copying manually.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/to_string_matrix.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Convert table into matrix of strings — to_string_matrix","text":"matrix strings. print_txt_to_copy = TRUE well formatted printout table printed console, ready copied expected value.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/to_string_matrix.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Convert table into matrix of strings — to_string_matrix","text":"","code":"tbl <- basic_table() %>%   split_rows_by(\"SEX\") %>%   split_cols_by(\"ARM\") %>%   analyze(\"AGE\") %>%   build_table(tern_ex_adsl)  to_string_matrix(tbl, widths = ceiling(propose_column_widths(tbl) / 2)) #>  [1] \"       A:                    \" \"      Drug    B: Pl   C: Comb\" #>  [3] \"        X     acebo   ination\" \"—————————————————————————————\" #>  [5] \"F                            \" \"  M   33.68   35.98    36.02 \" #>  [7] \"  e                          \" \"  a                          \" #>  [9] \"  n                          \" \"M                            \" #> [11] \"  M   34.70   35.68    36.28 \" \"  e                          \" #> [13] \"  a                          \" \"  n                          \""},{"path":"https://insightsengineering.github.io/tern/reference/try_car_anova.html","id":null,"dir":"Reference","previous_headings":"","what":"tryCatch around car::Anova — try_car_anova","title":"tryCatch around car::Anova — try_car_anova","text":"Captures warnings executing car::Anova.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/try_car_anova.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"tryCatch around car::Anova — try_car_anova","text":"","code":"try_car_anova(mod, test.statistic)"},{"path":"https://insightsengineering.github.io/tern/reference/try_car_anova.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"tryCatch around car::Anova — try_car_anova","text":"mod lm, aov, glm, multinom, polr     mlm, coxph, coxme, lme, mer, merMod, svyglm, svycoxph,     rlm, clm, clmm, suitable model object. test.statistic generalized linear model, whether calculate     \"LR\" (likelihood-ratio), \"Wald\", \"F\" tests; Cox     Cox mixed-effects model, whether calculate \"LR\" (partial-likelihood ratio)     \"Wald\" tests (\"LR\" tests unavailable Cox models using tt argument); default case linear mixed models fit     lmer, whether calculate Wald \"Chisq\" Kenward-Roger     \"F\" tests Satterthwaite degrees freedom (warning: KR F-tests     can time-consuming).     multivariate linear model, multivariate test statistic compute — one     \"Pillai\", \"Wilks\", \"Hotelling-Lawley\", \"Roy\",     \"Pillai\" default. summary method Anova.mlm     objects permits specification one multivariate     test statistic, default report four.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/try_car_anova.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"tryCatch around car::Anova — try_car_anova","text":"list item aov result model error_text captured warnings.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/try_car_anova.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"tryCatch around car::Anova — try_car_anova","text":"","code":"# `car::Anova` on cox regression model including strata and expected # a likelihood ratio test triggers a warning as only Wald method is # accepted.  library(survival)  mod <- coxph(   formula = Surv(time = futime, event = fustat) ~ factor(rx) + strata(ecog.ps),   data = ovarian )"},{"path":"https://insightsengineering.github.io/tern/reference/ungroup_stats.html","id":null,"dir":"Reference","previous_headings":"","what":"Ungroup non-numeric statistics — ungroup_stats","title":"Ungroup non-numeric statistics — ungroup_stats","text":"Ungroups grouped non-numeric statistics within input vectors .formats, .labels, .indent_mods.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/ungroup_stats.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Ungroup non-numeric statistics — ungroup_stats","text":"","code":"ungroup_stats(x, .formats, .labels, .indent_mods)"},{"path":"https://insightsengineering.github.io/tern/reference/ungroup_stats.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Ungroup non-numeric statistics — ungroup_stats","text":"x (named list numeric) list numeric statistics containing statistics ungroup. .formats (named character list) formats statistics. See Details analyze_vars information \"auto\" setting. .labels (named character) labels statistics (without indent). .indent_mods (named integer) indent modifiers labels. Defaults 0, corresponds unmodified default behavior. Can negative.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/ungroup_stats.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Ungroup non-numeric statistics — ungroup_stats","text":"list modified elements x, .formats, .labels, .indent_mods.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/reference/univariate.html","id":null,"dir":"Reference","previous_headings":"","what":"Univariate formula special term — univariate","title":"Univariate formula special term — univariate","text":"special term univariate indicate model fitted individually every variable included univariate.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/univariate.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Univariate formula special term — univariate","text":"","code":"univariate(x)"},{"path":"https://insightsengineering.github.io/tern/reference/univariate.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Univariate formula special term — univariate","text":"x (character) vector variable names separated commas.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/univariate.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Univariate formula special term — univariate","text":"used within model formula, produces univariate models variable provided.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/univariate.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Univariate formula special term — univariate","text":"provided alongside pairwise specification, model y ~ ARM + univariate(SEX, AGE, RACE) lead study comparison models y ~ ARM y ~ ARM + SEX y ~ ARM + AGE y ~ ARM + RACE","code":""},{"path":"https://insightsengineering.github.io/tern/reference/unlist_and_blank_na.html","id":null,"dir":"Reference","previous_headings":"","what":"Blank for missing input — unlist_and_blank_na","title":"Blank for missing input — unlist_and_blank_na","text":"Helper function use tabulating model results.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/unlist_and_blank_na.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Blank for missing input — unlist_and_blank_na","text":"","code":"unlist_and_blank_na(x)"},{"path":"https://insightsengineering.github.io/tern/reference/unlist_and_blank_na.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Blank for missing input — unlist_and_blank_na","text":"x (vector) input cell.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/unlist_and_blank_na.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Blank for missing input — unlist_and_blank_na","text":"empty character vector entries x missing (NA), otherwise unlisted version x.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/update_weights_strat_wilson.html","id":null,"dir":"Reference","previous_headings":"","what":"Helper function for the estimation of weights for prop_strat_wilson() — update_weights_strat_wilson","title":"Helper function for the estimation of weights for prop_strat_wilson() — update_weights_strat_wilson","text":"function wraps iteration procedure allows estimate weights proportional strata. assumes minimize weighted squared length confidence interval.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/update_weights_strat_wilson.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Helper function for the estimation of weights for prop_strat_wilson() — update_weights_strat_wilson","text":"","code":"update_weights_strat_wilson(   vars,   strata_qnorm,   initial_weights,   n_per_strata,   max_iterations = 50,   conf_level = 0.95,   tol = 0.001 )"},{"path":"https://insightsengineering.github.io/tern/reference/update_weights_strat_wilson.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Helper function for the estimation of weights for prop_strat_wilson() — update_weights_strat_wilson","text":"vars (numeric) normalized proportions strata. strata_qnorm (numeric(1)) initial estimation identical weights quantiles. initial_weights (numeric) initial weights used calculate strata_qnorm. can optimized future need estimate better initial weights. n_per_strata (numeric) number elements strata. max_iterations (integer(1)) maximum number iterations tried. Convergence always checked. conf_level (proportion) confidence level interval. tol (numeric(1)) tolerance threshold convergence.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/update_weights_strat_wilson.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Helper function for the estimation of weights for prop_strat_wilson() — update_weights_strat_wilson","text":"list 3 elements: n_it, weights, diff_v.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/reference/update_weights_strat_wilson.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Helper function for the estimation of weights for prop_strat_wilson() — update_weights_strat_wilson","text":"","code":"vs <- c(0.011, 0.013, 0.012, 0.014, 0.017, 0.018) sq <- 0.674 ws <- rep(1 / length(vs), length(vs)) ns <- c(22, 18, 17, 17, 14, 12)  update_weights_strat_wilson(vs, sq, ws, ns, 100, 0.95, 0.001) #> $n_it #> [1] 3 #>  #> $weights #> [1] 0.2067191 0.1757727 0.1896962 0.1636346 0.1357615 0.1284160 #>  #> $diff_v #> [1] 1.458717e-01 1.497223e-03 1.442189e-06 #>"},{"path":"https://insightsengineering.github.io/tern/reference/util_handling_additional_fun_params.html","id":null,"dir":"Reference","previous_headings":"","what":"Utilities to handle extra arguments in analysis functions — util_handling_additional_fun_params","title":"Utilities to handle extra arguments in analysis functions — util_handling_additional_fun_params","text":"Important additional parameters, useful modify behavior analysis summary functions listed rtables::additional_fun_params. utility functions can retrieve curated list parameters environment, pass analysis functions dedicated ...; notice final s_* function get argument matching.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/util_handling_additional_fun_params.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Utilities to handle extra arguments in analysis functions — util_handling_additional_fun_params","text":"","code":"retrieve_extra_afun_params(extra_afun_params)  get_additional_afun_params(add_alt_df = FALSE)"},{"path":"https://insightsengineering.github.io/tern/reference/util_handling_additional_fun_params.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Utilities to handle extra arguments in analysis functions — util_handling_additional_fun_params","text":"extra_afun_params (list) list additional parameters (character) retrieved environment. Curated list present rtables::additional_fun_params. add_alt_df (logical) TRUE, function also add .alt_df .alt_df_row parameters.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/util_handling_additional_fun_params.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Utilities to handle extra arguments in analysis functions — util_handling_additional_fun_params","text":"retrieve_extra_afun_params returns list values parameters environment. get_additional_afun_params returns list additional parameters.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/util_handling_additional_fun_params.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Utilities to handle extra arguments in analysis functions — util_handling_additional_fun_params","text":"retrieve_extra_afun_params(): Retrieve additional parameters environment. get_additional_afun_params(): Curated list additional parameters analysis functions. Please check rtables::additional_fun_params precise descriptions.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/utils_split_funs.html","id":null,"dir":"Reference","previous_headings":"","what":"Custom split functions — utils_split_funs","title":"Custom split functions — utils_split_funs","text":"Collection useful functions expanding core list functions provided rtables. See rtables::custom_split_funs rtables::make_split_fun() information make custom split function. functions work rtables::split_rows_by() argument split_fun modify way split happens. split functions, consider consulting rtables::split_funcs.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/utils_split_funs.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Custom split functions — utils_split_funs","text":"","code":"ref_group_position(position = \"first\")  level_order(order)"},{"path":"https://insightsengineering.github.io/tern/reference/utils_split_funs.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Custom split functions — utils_split_funs","text":"position (string integer) position use reference group facet. Can \"first\", \"last\", specific position. order (character numeric) vector ordering indices split facets.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/utils_split_funs.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Custom split functions — utils_split_funs","text":"ref_group_position() returns utility function puts reference group first, last certain position needs assigned split_fun. level_order() returns utility function changes original levels' order, depending input order split levels.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/utils_split_funs.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Custom split functions — utils_split_funs","text":"ref_group_position(): Split function place reference group facet specific position post-processing stage. level_order(): Split function change level order based integer vector character vector represent split variable's factor levels.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/reference/utils_split_funs.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Custom split functions — utils_split_funs","text":"","code":"library(dplyr)  dat <- data.frame(   x = factor(letters[1:5], levels = letters[5:1]),   y = 1:5 )  # With rtables layout functions basic_table() %>%   split_cols_by(\"x\", ref_group = \"c\", split_fun = ref_group_position(\"last\")) %>%   analyze(\"y\") %>%   build_table(dat) #>         e      d      b      a      c   #> ——————————————————————————————————————— #> Mean   5.00   4.00   2.00   1.00   3.00  # With tern layout funcitons adtte_f <- tern_ex_adtte %>%   filter(PARAMCD == \"OS\") %>%   mutate(     AVAL = day2month(AVAL),     is_event = CNSR == 0   )  basic_table() %>%   split_cols_by(var = \"ARMCD\", ref_group = \"ARM B\", split_fun = ref_group_position(\"first\")) %>%   add_colcounts() %>%   surv_time(     vars = \"AVAL\",     var_labels = \"Survival Time (Months)\",     is_event = \"is_event\",   ) %>%   build_table(df = adtte_f) #>                             ARM B          ARM A          ARM C     #>                             (N=73)         (N=69)         (N=58)    #> ——————————————————————————————————————————————————————————————————— #> Survival Time (Months)                                              #>   Median                     23.9           32.0           20.8     #>     95% CI               (18.3, 32.9)   (22.5, 49.3)   (12.9, 26.0) #>   25% and 75%-ile         9.8, 42.0      17.4, 65.3     7.3, 37.1   #>   Range                  0.1 to 154.1   0.3 to 155.5   0.6 to 80.7   basic_table() %>%   split_cols_by(var = \"ARMCD\", ref_group = \"ARM B\", split_fun = ref_group_position(2)) %>%   add_colcounts() %>%   surv_time(     vars = \"AVAL\",     var_labels = \"Survival Time (Months)\",     is_event = \"is_event\",   ) %>%   build_table(df = adtte_f) #>                             ARM A          ARM B          ARM C     #>                             (N=69)         (N=73)         (N=58)    #> ——————————————————————————————————————————————————————————————————— #> Survival Time (Months)                                              #>   Median                     32.0           23.9           20.8     #>     95% CI               (22.5, 49.3)   (18.3, 32.9)   (12.9, 26.0) #>   25% and 75%-ile         17.4, 65.3     9.8, 42.0      7.3, 37.1   #>   Range                  0.3 to 155.5   0.1 to 154.1   0.6 to 80.7   # level_order -------- # Even if default would bring ref_group first, the original order puts it last basic_table() %>%   split_cols_by(\"Species\", split_fun = level_order(c(1, 3, 2))) %>%   analyze(\"Sepal.Length\") %>%   build_table(iris) #>        setosa   virginica   versicolor #> —————————————————————————————————————— #> Mean    5.01      6.59         5.94     # character vector new_order <- level_order(levels(iris$Species)[c(1, 3, 2)]) basic_table() %>%   split_cols_by(\"Species\", ref_group = \"virginica\", split_fun = new_order) %>%   analyze(\"Sepal.Length\") %>%   build_table(iris) #>        setosa   virginica   versicolor #> —————————————————————————————————————— #> Mean    5.01      6.59         5.94"},{"path":[]},{"path":"https://insightsengineering.github.io/tern/news/index.html","id":"enhancements-0-9-6-9016","dir":"Changelog","previous_headings":"","what":"Enhancements","title":"tern 0.9.6.9016","text":"Added denom parameter s_count_cumulative(), s_count_missed_doses(), s_count_occurrences_by_grade(). Added \"N_row\" optional input denom s_count_occurrences(). Refactored a_count_occurrences_by_grade(), a_count_patients_with_event(), a_count_patients_with_flags() longer use make_afun(). Added rel_height_plot parameter g_lineplot() control line plot height relative annotation table height. Updated table_font_size parameter g_lineplot() control size text annotation table, including labels. Added as_list parameter g_lineplot() allow users return line plot annotation table elements list instead stacked complex customization. Refactored summarize_change() work without make_afun() access additional function parameter. Added vignette “Understanding tern functions” future reference.","code":""},{"path":"https://insightsengineering.github.io/tern/news/index.html","id":"bug-fixes-0-9-6-9016","dir":"Changelog","previous_headings":"","what":"Bug Fixes","title":"tern 0.9.6.9016","text":"Fixed bug a_summary() causing non-unique row_name values occur multiple statistics selected count variables.","code":""},{"path":"https://insightsengineering.github.io/tern/news/index.html","id":"miscellaneous-0-9-6-9016","dir":"Changelog","previous_headings":"","what":"Miscellaneous","title":"tern 0.9.6.9016","text":"Reverted deprecation quick get functions summary_formats() summary_labels(). Added disclaimer underlying use get_stats. Corrected handling extra arguments NA summarize_change().","code":""},{"path":"https://insightsengineering.github.io/tern/news/index.html","id":"tern-096","dir":"Changelog","previous_headings":"","what":"tern 0.9.6","title":"tern 0.9.6","text":"CRAN release: 2024-09-24","code":""},{"path":"https://insightsengineering.github.io/tern/news/index.html","id":"enhancements-0-9-6","dir":"Changelog","previous_headings":"","what":"Enhancements","title":"tern 0.9.6","text":"Added median_ci_3d s_summary includes estimate confidence interval one statistic. Added median_ci_3d, quantiles_lower quantiles_upper s_surv_time includes estimate confidence interval one statistic. Added hr_ci_3d s_coxph_pairwise includes estimate confidence interval one statistic. Added event_free_rate_3d s_surv_timepoint includes estimate confidence interval one statistic. Added rate_diff_ci_3d s_surv_timepoint_diff includes estimate confidence interval one statistic. Added errorbar_width linetype parameters g_lineplot. Added .formats argument tabulate_rsp_subgroups tabulate_survival_subgroups allow users specify formats. Added riskdiff argument tabulate_rsp_subgroups tabulate_survival_subgroups allow users add risk difference table column, function control_riskdiff specify settings risk difference column. Added warning tabulate_rsp_subgroups pval statistic selected df correctly generated add p-values output table. Added n_rate statistic non-default option estimate_incidence_rate returns number events observed estimated incidence rate. Added n_unique statistic non-default option estimate_incidence_rate returns total number patients least one event observed. Refactored estimate_incidence_rate work analyze function summarize function, controlled added summarize parameter. summarize = TRUE, labels can fine-tuned via new label_fmt argument function. Added fraction statistic analyze_var_count method group. Improved summarize_glm_count() documentation associated functions better describe results functions’ purpose. Added method argument s_odds_ratio() estimate_odds_ratio() control whether exact approximate conditional likelihood calculations used.","code":""},{"path":"https://insightsengineering.github.io/tern/news/index.html","id":"bug-fixes-0-9-6","dir":"Changelog","previous_headings":"","what":"Bug Fixes","title":"tern 0.9.6","text":"Added defaults d_count_cumulative parameters described documentation. Fixed bug empty levels g_lineplot x-axis shown either plots. Fixed bug a_surv_time threw error split \"is_event\". Fixed disappearing line g_lineplot using one group strata level. Fixed defaults formats labels get_formats_from_stats get_labels_from_stats. Fixed bug linear scaling factor (scale parameter) applied response rate h_glm_count distributions logarithmic link function. Fixed bug decorate_grob handle well empty strings NULL values title footers. Fixed bug g_km caused error multiple records data estimates max time. Fixed issue wrong wrapping due different \\n vector behavior cope well split_string().","code":""},{"path":"https://insightsengineering.github.io/tern/news/index.html","id":"miscellaneous-0-9-6","dir":"Changelog","previous_headings":"","what":"Miscellaneous","title":"tern 0.9.6","text":"Began deprecation confusing functions summary_formats summary_labels. Enhanced general descriptions analyze summarize functions throughout package documentation. Finalized deprecation strata cohort_id arguments g_lineplot. Moved incidence rate helper functions separate h_incidence_rate.R file.","code":""},{"path":"https://insightsengineering.github.io/tern/news/index.html","id":"tern-095","dir":"Changelog","previous_headings":"","what":"tern 0.9.5","title":"tern 0.9.5","text":"CRAN release: 2024-06-21","code":""},{"path":"https://insightsengineering.github.io/tern/news/index.html","id":"enhancements-0-9-5","dir":"Changelog","previous_headings":"","what":"Enhancements","title":"tern 0.9.5","text":"Added facet_var g_lineplot allow plot faceting factor variable. Added examples tests label_all parameter extract_survival_biomarkers extract_survival_subgroups. Added xticks, xlim, ylim arguments g_lineplot allow customization x y axes. Updated g_lineplot legend follow factor levels set users.","code":""},{"path":"https://insightsengineering.github.io/tern/news/index.html","id":"bug-fixes-0-9-5","dir":"Changelog","previous_headings":"","what":"Bug Fixes","title":"tern 0.9.5","text":"Fixed bug s_ancova prevented statistics printed arm levels include special characters. Fixed bug decorate_grob prevented right margins respected adding title footers decorations.","code":""},{"path":"https://insightsengineering.github.io/tern/news/index.html","id":"miscellaneous-0-9-5","dir":"Changelog","previous_headings":"","what":"Miscellaneous","title":"tern 0.9.5","text":"Began deprecation unused label_all parameter tabulate_survival_biomarkers tabulate_survival_subgroups, redirection parameter associated extract_* functions.","code":""},{"path":"https://insightsengineering.github.io/tern/news/index.html","id":"tern-094","dir":"Changelog","previous_headings":"","what":"tern 0.9.4","title":"tern 0.9.4","text":"CRAN release: 2024-04-17","code":""},{"path":"https://insightsengineering.github.io/tern/news/index.html","id":"new-features-0-9-4","dir":"Changelog","previous_headings":"","what":"New Features","title":"tern 0.9.4","text":"Added h_glm_negbin h_glm_count enable count data analysis using negative binomial model. Added argument grade_groups_only count_occurrences_by_grade allow users display rows specified grade groups. Added internal function df2gg converts data.frame objects ggplot objects. Added functions control_surv_med_annot control_coxph_annot configure g_km annotation table sizes/positions. Refactored g_km output ggplot object instead grob object. Refactored g_forest output ggplot object instead grob object.","code":""},{"path":"https://insightsengineering.github.io/tern/news/index.html","id":"enhancements-0-9-4","dir":"Changelog","previous_headings":"","what":"Enhancements","title":"tern 0.9.4","text":"Default format mean p-values (mean_pval) updated \"xx.xx\" \"x.xxxx | (<0.0001)\".","code":""},{"path":"https://insightsengineering.github.io/tern/news/index.html","id":"bug-fixes-0-9-4","dir":"Changelog","previous_headings":"","what":"Bug Fixes","title":"tern 0.9.4","text":"Fixed nested column split label overlay issue rtable2gg clean appearance text labels. Fixed bug s_ancova causing incorrect difference calculations arm variables irregular levels. Fixed bug format_count_fraction_fixed_dp print fraction 1 (100%). Fixed bug g_lineplot causing default labels update according specified control settings. Fixed bug causing error automatic value formatting applied NA values.","code":""},{"path":"https://insightsengineering.github.io/tern/news/index.html","id":"miscellaneous-0-9-4","dir":"Changelog","previous_headings":"","what":"Miscellaneous","title":"tern 0.9.4","text":"Added function expect_snapshot_ggplot test setup file process plot snapshot tests allow plot dimensions set. Adapted argument renames introduced ggplot2 3.5.0. Renamed individual_patient_plot.R g_ipp.R. Removed instances deprecated parameters time_unit_input, time_unit_output, na_level indent_mod. Removed deprecated functions summarize_vars, control_summarize_vars, a_compare, create_afun_summary, create_afun_compare, summary_custom. Removed vdiffr package Suggests DESCRIPTION file. Began deprecation named element strat, renamed strata, within variables argument h_rsp_to_logistic_variables, h_logistic_mult_cont_df, h_odds_ratio_subgroups_df, h_coxreg_mult_cont_df, h_coxph_subgroups_df, h_tbl_coxph_pairwise, extract_rsp_biomarkers, extract_rsp_subgroups, extract_survival_biomarkers, extract_survival_subgroups. Began deprecation strat argument s_coxph_pairwise replaced strata argument. Began deprecation forest_grob, forest_dot_line, forest_viewport, vp_forest_table_part, grid.forest functions. Began deprecation longer used Kaplan-Meier helper functions h_ggkm, h_decompose_gg, h_km_layout, h_grob_tbl_at_risk, h_grob_median_surv, h_grob_y_annot, h_grob_coxph. Began deprecation grob/grid related functions stack_grobs, arrange_grobs, draw_grob longer used tern.","code":""},{"path":"https://insightsengineering.github.io/tern/news/index.html","id":"tern-093","dir":"Changelog","previous_headings":"","what":"tern 0.9.3","title":"tern 0.9.3","text":"CRAN release: 2023-12-08","code":""},{"path":"https://insightsengineering.github.io/tern/news/index.html","id":"new-features-0-9-3","dir":"Changelog","previous_headings":"","what":"New Features","title":"tern 0.9.3","text":"Added ref_group_position function place reference group facet last, first certain position. Added keep_level_order split function retain original order levels split. Added level_order split function reorder manually levels. Added function get_indents_from_stats format return indent modifiers given set statistics. Added internal utility function apply_auto_formatting check \"auto\" formats replace implementation format_auto analyze functions. Added utility function labels_use_control modify labels control specifications. Added list containing default statistics method group, tern_default_stats. Added summarize function version count_occurrences analyze function, summarize_occurrences. Added referential footnotes surv_time censored range observations, controlled via ref_fn_censor parameter. Added helper function h_adlb_abnormal_by_worst_grade prepare ADLB data use input count_abnormal_by_worst_grade. Added s_bland_altman function assess agreement two numerical vectors. Added function rtable2gg converts rtable objects ggplot objects. Added helper function set default na_str globally set_default_na_str() added default_na_str() interested functions.","code":""},{"path":"https://insightsengineering.github.io/tern/news/index.html","id":"enhancements-0-9-3","dir":"Changelog","previous_headings":"","what":"Enhancements","title":"tern 0.9.3","text":"Added ref_group_coxph parameter g_km specify reference group used pairwise Cox-PH calculations annot_coxph = TRUE. Added annot_coxph_ref_lbls parameter g_km enable printing reference group table labels annot_coxph = TRUE. Added x_lab parameter g_lineplot customize x-axis label. Remove 25% padding y-axis g_lineplot. Added support creating multiple risk difference columns, comparing single comparison group. Multiple comparison groups can specified vector via arm_y argument. Allowed numeric vector count_by input analyze_num_patients summarize_num_patients. Aligned plot table vertically g_lineplot.","code":""},{"path":"https://insightsengineering.github.io/tern/news/index.html","id":"bug-fixes-0-9-3","dir":"Changelog","previous_headings":"","what":"Bug Fixes","title":"tern 0.9.3","text":"Fixed bug decorate_grob preventing text wrapping accounting font size. Fixed implementation na_str argument column-wise analysis tabulation functions.","code":""},{"path":"https://insightsengineering.github.io/tern/news/index.html","id":"miscellaneous-0-9-3","dir":"Changelog","previous_headings":"","what":"Miscellaneous","title":"tern 0.9.3","text":"Specified minimal version package dependencies. Upgraded to_string_matrix take account widths printing parameters.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/news/index.html","id":"new-features-0-9-2","dir":"Changelog","previous_headings":"","what":"New Features","title":"tern 0.9.2","text":"Added na_str argument analyze & summarize_row_groups wrapper functions count_abnormal, count_abnormal_by_baseline, count_abnormal_by_marked, count_abnormal_by_worst_grade, count_abnormal_lab_worsen_by_baseline, count_cumulative, count_missed_doses, count_occurrences, count_occurrences_by_grade, summarize_occurrences_by_grade, summarize_patients_events_in_cols, count_patients_with_event, count_patients_with_flags, count_values, estimate_multinomial_response, estimate_proportion, h_tab_one_biomarker, estimate_incidence_rate, logistic_summary_by_flag, estimate_odds_ratio, estimate_proportion_diff, test_proportion_diff, summarize_ancova, summarize_change, summarize_glm_count, summarize_num_patients, analyze_num_patients, summarize_patients_exposure_in_cols, coxph_pairwise, tabulate_survival_subgroups, surv_time, surv_timepoint.","code":""},{"path":"https://insightsengineering.github.io/tern/news/index.html","id":"enhancements-0-9-2","dir":"Changelog","previous_headings":"","what":"Enhancements","title":"tern 0.9.2","text":"Added formatting function format_count_fraction_lt10 formatting count_fraction special consideration count less 10. Updated s_summary.logical output count_fraction denominator zero display NA instead 0 tables. Updated analyze_vars_in_cols allow character input indicate whether nominal time point post-dose pre-dose applying 1/3 imputation rule.","code":""},{"path":"https://insightsengineering.github.io/tern/news/index.html","id":"bug-fixes-0-9-2","dir":"Changelog","previous_headings":"","what":"Bug Fixes","title":"tern 0.9.2","text":"Fixed bug g_km causing error converting certain annotation width units.","code":""},{"path":"https://insightsengineering.github.io/tern/news/index.html","id":"miscellaneous-0-9-2","dir":"Changelog","previous_headings":"","what":"Miscellaneous","title":"tern 0.9.2","text":"Began deprecation na_level argument s_count_abnormal_by_baseline, a_summary, analyze_vars, analyze_vars_in_cols, compare_vars, h_map_for_count_abnormal, h_stack_by_baskets, summarize_colvars, a_coxreg, summarize_coxreg replaced na_str argument. strata cohort_id parameters renamed group_var subject_var respectively g_lineplot control_lineplot_vars .","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/news/index.html","id":"new-features-0-9-1","dir":"Changelog","previous_headings":"","what":"New Features","title":"tern 0.9.1","text":"Added imputation_rule function apply imputation rule data. Added new format function format_sigfig allow numeric value formatting specified number significant figures. Added vectors containing default statistic formats labels tern_default_formats tern_default_labels, respectively. Added function get_stats return methods given statistical method groups. Added function get_formats_from_stats return formats get_labels_from_stats return labels given set statistics. Added \"auto\" option .formats. uses format_auto determine automatically number digits. Added title argument h_grob_tbl_at_risk annot_at_risk_title argument g_km h_km_layout allows user add “Patients Risk” title Kaplan-Meier risk annotation table.","code":""},{"path":"https://insightsengineering.github.io/tern/news/index.html","id":"enhancements-0-9-1","dir":"Changelog","previous_headings":"","what":"Enhancements","title":"tern 0.9.1","text":"Refactored tabulate_rsp_subgroups pass sanitation checks preventing creation degenerate subtables. Updated analyze_vars_in_cols use caching, allow implementation imputation rule via imp_rule argument, allow user specify cell alignment via .aligns argument. Updated add_rowcounts allow addition row counts alt_counts_df using alt_counts argument. Added gp argument g_forest control graphical parameters font size.","code":""},{"path":"https://insightsengineering.github.io/tern/news/index.html","id":"miscellaneous-0-9-1","dir":"Changelog","previous_headings":"","what":"Miscellaneous","title":"tern 0.9.1","text":"Grouped functions relating valid method names default formats labels new source file utils_defaults_handling.R. Started deprecation summary_custom() a_summary() S3 method. Renamed statistical method p-value discrete case pval_counts. Removed a_summary_internal() favor one main a_summary().","code":""},{"path":"https://insightsengineering.github.io/tern/news/index.html","id":"tern-090","dir":"Changelog","previous_headings":"","what":"tern 0.9.0","title":"tern 0.9.0","text":"CRAN release: 2023-09-01","code":""},{"path":"https://insightsengineering.github.io/tern/news/index.html","id":"new-features-0-9-0","dir":"Changelog","previous_headings":"","what":"New Features","title":"tern 0.9.0","text":"Added stat_propdiff_ci function calculate proportion/risk difference CI. Added risk difference column functionality via riskdiff argument functions count_occurrences, count_occurrences_by_grade, count_patients_with_event, count_patients_with_flags, analyze_num_patients, summarize_num_patients.","code":""},{"path":"https://insightsengineering.github.io/tern/news/index.html","id":"enhancements-0-9-0","dir":"Changelog","previous_headings":"","what":"Enhancements","title":"tern 0.9.0","text":"Refactored function a_summary longer use helper function create_afun_summary. Refactored functions summarize_vars compare_vars use refactored a_summary function. Created new internal helper functions ungroup_stats ungroup statistics calculated factor variables, a_summary_internal perform calculations a_summary.","code":""},{"path":"https://insightsengineering.github.io/tern/news/index.html","id":"bug-fixes-0-9-0","dir":"Changelog","previous_headings":"","what":"Bug Fixes","title":"tern 0.9.0","text":"Fixed bug s_count_occurrences_by_grade “missing” grade always appears final level. Fixed bug analyze_vars_in_cols categorical data used. Fixed bug s_count_occurrences_by_grade levels relabeled reordering account “missing” grades.","code":""},{"path":"https://insightsengineering.github.io/tern/news/index.html","id":"miscellaneous-0-9-0","dir":"Changelog","previous_headings":"","what":"Miscellaneous","title":"tern 0.9.0","text":"Fixed swapped descriptions .N_row .N_col parameters. Removed internal calls df_explicit_na. Changes NA values happen externally tern functions, depending users’ needs. Reinstated correct soft deprecation create_afun_summary create_afun_compare.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/news/index.html","id":"enhancements-0-8-5","dir":"Changelog","previous_headings":"","what":"Enhancements","title":"tern 0.8.5","text":"Added ylim argument g_km allow user set custom limits y-axis. Added assertion g_km checks whether one arm present data annot_coxph true. Added flag_labels argument s_count_patients_with_flags enable label handling options count_patients_by_flags. Added nested argument analyze wrapper functions count_abnormal, count_abnormal_by_baseline, count_abnormal_by_marked, count_abnormal_by_worst_grade, count_abnormal_lab_worsen_by_baseline, count_cumulative, count_missed_doses, count_occurrences, count_occurrences_by_grade, count_patients_with_event, count_patients_with_flags, count_values, estimate_multinomial_response, estimate_proportion, estimate_incidence_rate, estimate_odds_ratio, estimate_proportion_diff, test_proportion_diff, summarize_ancova, summarize_change, summarize_glm_count, analyze_num_patients, coxph_pairwise, surv_time, surv_timepoint.","code":""},{"path":"https://insightsengineering.github.io/tern/news/index.html","id":"miscellaneous-0-8-5","dir":"Changelog","previous_headings":"","what":"Miscellaneous","title":"tern 0.8.5","text":"Started deprecation cycle summarize_vars control_summarize_vars. Renamed analyze_vars control_analyze_vars reflect underlying rtables machinery keeping backward compatibility aliases.","code":""},{"path":"https://insightsengineering.github.io/tern/news/index.html","id":"tern-084","dir":"Changelog","previous_headings":"","what":"tern 0.8.4","title":"tern 0.8.4","text":"CRAN release: 2023-06-27","code":""},{"path":"https://insightsengineering.github.io/tern/news/index.html","id":"enhancements-0-8-4","dir":"Changelog","previous_headings":"","what":"Enhancements","title":"tern 0.8.4","text":"Added method character class h_coxreg_inter_effect enabling character covariates summarize_coxreg.","code":""},{"path":"https://insightsengineering.github.io/tern/news/index.html","id":"miscellaneous-0-8-4","dir":"Changelog","previous_headings":"","what":"Miscellaneous","title":"tern 0.8.4","text":"Began deprecation time_unit_input time_unit_output arguments replaced input_time_unit num_pt_year, respectively, control_incidence_rate. Removed deprecated pairwise function. Deprecated a_compare replaced a_summary argument compare = TRUE. Deprecated helper functions create_afun_summary create_afun_compare longer used a_summary a_compare respectively.","code":""},{"path":"https://insightsengineering.github.io/tern/news/index.html","id":"bug-fixes-0-8-4","dir":"Changelog","previous_headings":"","what":"Bug Fixes","title":"tern 0.8.4","text":"Fixed long double assertion check sum(weights) M1mac installation.","code":""},{"path":"https://insightsengineering.github.io/tern/news/index.html","id":"tern-083","dir":"Changelog","previous_headings":"","what":"tern 0.8.3","title":"tern 0.8.3","text":"CRAN release: 2023-06-19","code":""},{"path":"https://insightsengineering.github.io/tern/news/index.html","id":"enhancements-0-8-3","dir":"Changelog","previous_headings":"","what":"Enhancements","title":"tern 0.8.3","text":"Added explicit zero counts g_km plot “risk” annotation tables. Added flag total level split analyze_patients_exposure_in_cols. Implemented .indent_mods argument functions h_tab_one_biomarker, h_tab_rsp_one_biomarker, h_tab_surv_one_biomarker, summarize_logistic, logistic_summary_by_flag, tabulate_rsp_biomarkers, a_coxreg, summarize_coxreg, tabulate_survival_biomarkers, surv_time, surv_timepoint, cfun_by_flag. Updated summarize_coxreg print covariates data rows univariate Cox regression interactions content rows otherwise. Removed “baseline status” text d_count_abnormal_by_baseline labels. Improved default sizing annotation tables g_km added dynamic scaling surv_med coxph annotation tables, customization via width_annots argument.","code":""},{"path":"https://insightsengineering.github.io/tern/news/index.html","id":"bug-fixes-0-8-3","dir":"Changelog","previous_headings":"","what":"Bug Fixes","title":"tern 0.8.3","text":"Fixed bug split_text_grob preventing titles footnotes properly formatted printed decorate_grob. Fixed bug g_lineplot preventing addition lines plot midpoint statistic calculations result NA value(s). Fixed tern:::tidy.glm formals respect broom:::tidy.default formals.","code":""},{"path":"https://insightsengineering.github.io/tern/news/index.html","id":"miscellaneous-0-8-3","dir":"Changelog","previous_headings":"","what":"Miscellaneous","title":"tern 0.8.3","text":"Updated README include installation instructions CRAN. Remove examples unexported functions. Export functions has_count_in_cols, has_counts_difference, combine_counts, h_tab_rsp_one_biomarker, arrange_grobs, a_count_patients_sum_exposure, a_coxreg, groups_list_to_df, forest_viewport. Updated README include installation instructions CRAN. Began deprecation indent_mod argument replaced .indent_mods argument summarize_num_patients analyze_num_patients.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/news/index.html","id":"breaking-changes-0-8-2","dir":"Changelog","previous_headings":"","what":"Breaking Changes","title":"tern 0.8.2","text":"Refactored s_coxreg summarize_coxregto work new analysis function a_coxreg.","code":""},{"path":"https://insightsengineering.github.io/tern/news/index.html","id":"enhancements-0-8-2","dir":"Changelog","previous_headings":"","what":"Enhancements","title":"tern 0.8.2","text":"Added section_div na_level arguments summarize_vars. Added median_range numeric variable statistic option summarize_vars. Corrected ordering factor levels d_onco_rsp_label. Added new “Analyze Functions”, “Summarize Functions”, “Analyze Functions Columns” overview pages. Consolidated KM plot documentation within g_km function. Added a_count_patients_sum_exposure summarize_patients_exposure_in_cols new analyze function analyze_patients_exposure_in_cols. Added informative error user selects invalid method unstratified analyses s_proportion_diff. Updated s_summary s_compare allow NA values input variables. factor variables NAs, na.rm = FALSE explicit NA level automatically added. na.rm = TRUE also consider \"<Missing>\" values exclude . Updated purpose na_level parameter s_summary s_compare align tern functions. Instead string consider NA setting na.rm = TRUE, now defines string print place NA values output table.","code":""},{"path":"https://insightsengineering.github.io/tern/news/index.html","id":"bug-fixes-0-8-2","dir":"Changelog","previous_headings":"","what":"Bug Fixes","title":"tern 0.8.2","text":"Fixed missing label TRTEDTM tern datasets. Fixed improper implementation na_level argument summarize_vars preventing effect.","code":""},{"path":"https://insightsengineering.github.io/tern/news/index.html","id":"miscellaneous-0-8-2","dir":"Changelog","previous_headings":"","what":"Miscellaneous","title":"tern 0.8.2","text":"Implemented lubridate package date variables tern datasets. Organized .gitignore .Rbuildignore files. Removed deprecated footnotes functions related files. Started deprecation cycle pairwise function. Moved count_patients_with_flags functions count_patients_with_event.R count_patients_with_flags.R.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/news/index.html","id":"enhancements-0-8-0","dir":"Changelog","previous_headings":"","what":"Enhancements","title":"tern 0.8.0","text":"Added summarize_glm_count function analyze count data using linear model. Added legend g_step. Added formatting functions format_fraction_fixed_dp format_count_fraction_fixed_dp fixed single decimal place percentages. Added na_level labelstr arguments summarize_vars_in_cols. Added analyze_num_patients include summary beginning repeat paginating. Added h_row_first_values function general helper function retrieve first values specific rows. Added option remove \"(n)\" suffix unique_count labels s_num_patients. Added options g_km annotate statistics (annot_stats) add corresponding vertical lines (annot_stats_lines).","code":""},{"path":"https://insightsengineering.github.io/tern/news/index.html","id":"bug-fixes-0-8-0","dir":"Changelog","previous_headings":"","what":"Bug Fixes","title":"tern 0.8.0","text":"Fixed bug causing incorrect ordering numeric grade levels missing grades present s_count_occurrences_by_grade. Refactored summarize_vars_in_cols work pagination machinery. Fixed bug allow passing conf_level argument emmeans::contrast() s_ancova. Fixed bugs rtables_access.R caused checking specific combinations (also standard values never used) column indices names. Fixed single applicable record bug count_abnormal_by_grade. Fixed bug add_rowcounts caused row count row values count zero. Fixed bug h_col_indices causing error pruning combination columns. Fixed bug test_proportion_diff missing argument var_labels.","code":""},{"path":"https://insightsengineering.github.io/tern/news/index.html","id":"documentation-and-tests-0-8-0","dir":"Changelog","previous_headings":"","what":"Documentation and Tests","title":"tern 0.8.0","text":"Added tests increase code coverage. Created separate documentation files functions different sections pkgdown reference. Created separate .R files logistic regression cox regression helper functions. Fixed table tests using analyze_num_patients generate initial summary repetition paginating. Updated tests use testthat 3rd edition replaced applicable tests snapshot testing. Updated summarize_ancova examples use iris dataset instead scda data. Created vignette saves cached synthetic CDISC dataset files data/ folder generated cached synthetic datasets. Updated examples/tests use datasets data/ folder instead scda datasets. Removed template tests tern. tests internal repo scda.test.","code":""},{"path":"https://insightsengineering.github.io/tern/news/index.html","id":"miscellaneous-0-8-0","dir":"Changelog","previous_headings":"","what":"Miscellaneous","title":"tern 0.8.0","text":"Renamed summarize_vars_in_cols analyze_vars_in_cols reflect appropriate analyze logic. Removed redundant summary_in_cols helper functions. Exported function format_xx. Replaced deprecated ggplot2 functions/arguments fix warnings. Replaced deprecated function forcats::fct_explicit_na forcats::fct_na_value_to_level. Removed deprecated wrap_text function related files. Started deprecation cycle footnotes functions.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/news/index.html","id":"new-features-0-7-10","dir":"Changelog","previous_headings":"","what":"New Features","title":"tern 0.7.10","text":"Added stratified Newcombe stratified Wilson statistics estimate_proportion estimate_proportion_diff relative tests. Added stat_mean_pval, new summary statistic calculate p-value mean. Added statistic mean_se (mean standard error) summarize_variables related functions. Introduced Rdpack references.","code":""},{"path":"https://insightsengineering.github.io/tern/news/index.html","id":"enhancements-0-7-10","dir":"Changelog","previous_headings":"","what":"Enhancements","title":"tern 0.7.10","text":"Redesign data handling tests removing repetitive data loads library calls. Added DescTools::BinomDiffCI function within tern. Added new parameter summarize_logistic specify pivoted value use analysis. Updated s_coxph_pairwise generate log-rank p-value using original log-rank test instead Cox Proportional-Hazards Model. Implemented nestcolor examples adapting g_km, g_ipp, g_waterfall, g_step, g_lineplot, g_forest. Added parameters interaction_y interaction_item ANCOVA make interaction calculations available. Added new parameter footnotes add footnotes g_km.","code":""},{"path":"https://insightsengineering.github.io/tern/news/index.html","id":"migration-from-assertthat-to-checkmate-0-7-10","dir":"Changelog","previous_headings":"","what":"Migration from assertthat to checkmate","title":"tern 0.7.10","text":"Implemented checkmate::assert_vector, checkmate::assert_set_equal, checkmate::assert_int check vector type, length, values. Replaced standard assertions checkmate following functions: all_elements_in_ref, is_df_with_nlevels_factor, is_df_with_no_na_level, is_proportion_vector, is_quantiles_vector, is_character_or_factor, is_nonnegative_count, is_valid_character, assert_character_or_factor, assert_equal_length has_tabletree_colnames. Modified is_proportion, is_equal_length, is_df_with_no_na_level, is_df_with_nlevels_factor, is_variables, is_df_with_variables, is_df_with_factors, is_valid_factor use assertion logic. Added verbose warnings as_factor_keep_attributes. Made assert_df_with_factors assert_proportion_value internal functions. Renamed assertthat.R test-assertthat.R utils_checkmate.R test-utils_checkmate.R.","code":""},{"path":"https://insightsengineering.github.io/tern/news/index.html","id":"documentation-and-namespace-polishing-0-7-10","dir":"Changelog","previous_headings":"","what":"Documentation and NAMESPACE Polishing","title":"tern 0.7.10","text":"count_abnormal_by_marked (reference abnormal_by_marked), count_abnormal_lab_worsen_by_baseline h_adlb_worsen (reference abnormal_by_worst_grade_worsen_from_baseline), count_abnormal_by_worst_grade (reference abnormal_by_worst_grade), to_string_matrix, tidy.summary.coxph, tidy.step, surv_timepoint, (reference survival_timepoint), surv_time (reference survival_time), coxph_pairwise (reference survival_coxph_pairwise), extract_survival_subgroups tabulate_survival_subgroups (reference survival_duration_subgroups), extract_survival_biomarkers tabulate_survival_biomarkers (reference survival_biomarkers_subgroups), control_summarize_vars, s_summary a_summary (reference summarize_variables) kept S3 method tree. summarize_patients_exposure_in_cols, summarize_num_patients s_num_patients, s_num_patients_content, summarize_num_patients. count_cumulative, count_missed_doses, count_patients_events_in_cols, summarize_colvars, summarize_change, summarize_ancova,.rtable, color_palette, add_footnotes. (statistical function controls) control_coxreg, control_coxph, control_incidence_rate, control_lineplot_vars, control_surv_time, control_surv_timepoint, control_logisitic, control_step. stat_mean_ci, stat_median_ci, split_cols_by_groups, explicit_na, sas_na, extract_rsp_subgroups, tabulate_rsp_subgroups, extract_rsp_biomarkers, tabulate_rsp_biomarkers, keep_rows, keep_content_rows, has_count_in_any_col, has_fraction_in_cols, has_fraction_in_any_col, has_fractions_difference, test_proportion_diff, pairwise, logistic_regression, estimate_incidence_rate, control_incidence_rate (reference incidence_rate), cut_quantile_bins, estimate_multinomial_rsp, decorate_grob_set, extreme_format, fit_rsp_step, fit_survival_step, footnotes, footnotes-set, format_count_fraction, format_fraction_threshold, formatting_functions, format_fraction, combination_function (S4 method), compare_variables (S3 method), kaplan_meier. (chain functions, reference abnormal_by_marked) s_count_abnormal_by_marked, a_count_abnormal_by_marked. (chain functions, reference abnormal_by_worst_grade_worsen_from_baseline) a_count_abnormal_lab_worsen_by_baseline, s_count_abnormal_lab_worsen_by_baseline. (chain functions, reference abnormal_by_worst_grade) s_count_abnormal_by_worst_grade, a_count_abnormal_by_worst_grade. (chain functions, reference survival_timepoint) s_surv_timepoint, s_surv_timepoint_diff, a_surv_timepoint, a_surv_timepoint_diff. (chain functions, reference survival_time) s_surv_time, a_surv_time. (chain functions, reference survival_coxph_pairwise) s_coxph_pairwise, a_coxph_pairwise. (chain functions, reference survival_duration_subgroups) a_survival_subgroups. (chain functions, reference count_cumulative) s_count_cumulative, a_count_cumulative. (chain functions, reference count_missed_doses) s_count_nonmissing, s_count_missed_doses, a_count_missed_doses. (chain functions, reference count_patients_events_in_cols) s_count_patients_and_multiple_events, summarize_patients_events_in_cols. (chain functions, reference incidence_rate) s_incidence_rate, a_incidence_rate. (cox regression helper) cox_regression_inter, decorate_grob_factory, draw_grob, estimate_coef. summary_labels, summary_formats, s_count_patients_sum_exposure, a_change_from_baseline s_change_from_baseline, a_ancova, s_ancova, arrange_grobs, as_factor_keep_attributes, combine_levels, split_text_grob, groups_list_to_df, s_cox_multivariate, is_leaf_table, a_response_subgroups, range_noinf, has_count_in_cols, has_counts_difference, prop_chisq, prop_cmh, prop_schouten, prop_fisher, s_test_proportion_diff, a_test_proportion_diff, fct_discard, fct_explicit_na_if.","code":""},{"path":"https://insightsengineering.github.io/tern/news/index.html","id":"bug-fixes-0-7-10","dir":"Changelog","previous_headings":"","what":"Bug Fixes","title":"tern 0.7.10","text":"Fixed retrieval method stats::ancova output due version inconsistency. Fixed tests respect new standard print NA coming rtables. Fixed error tests coming changes formatters::var_labels. Fixed prop_diff functions respect success responses (TRUE values). Fixed error coming comparing factors vector characters vector. Fixed empty vector exception cut_quantile_bins. Fixed exception error empty strings present pivoted columns (rtables split functions) Fixed bug s_ancova causing error first level arm factor control arm. Fixed bug s_abnormal_by_worst_grade one PARAM level. Fixed bug prop_diff_wald selecting responders, updated tests accordingly. Fixed bug h_ancova caused error deselecting covariates.","code":""},{"path":"https://insightsengineering.github.io/tern/news/index.html","id":"miscellaneous-0-7-10","dir":"Changelog","previous_headings":"","what":"Miscellaneous","title":"tern 0.7.10","text":"Added deprecated badge g_mmrm. Removed internal function calls examples (tern:::) added dontrun internal function examples. Removed warnings messages console occurring examples tests. Deprecated functions color_palette h_set_nest_theme favor nestcolor::color_palette nestcolor::theme_nest, respectively. Removed deprecated functions: color_palette, color_palette_core, h_set_nest_theme, s_cox_univariate. Removed deprecated MMRM functions: fit_mmrm, g_mmrm_diagnostic, g_mmrm_lsmeans, .rtable.mmrm, h_mmrm_fixed, h_mmrm_cov, h_mmrm_diagnostic, tidy.mmrm, s_mmrm_lsmeans, s_mmrm_lsmeans_single, summarize_lsmeans. Renamed functions arm study_arm extract extract_by_name. Renamed rtables.R utils_rtables.R. Extracted cox_regression_inter separate file cox_regression. Renamed estimate_incidence_rate.R incidence_rate.R match documentation grouping name. Extracted control_incidence_rate separate file produces separate documentation file. Added @md removed @order incidence_rate.R. Modified examples accordingly. Removed hyperlink prop_schouten function documentation. Exported draw_grob function.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/news/index.html","id":"fix-0-7-8","dir":"Changelog","previous_headings":"","what":"Fix","title":"tern 0.7.8","text":"h_split_by_subgroups documentation warning fix wrong placing example block","code":""},{"path":"https://insightsengineering.github.io/tern/news/index.html","id":"documentation-and-namespace-polishing-0-7-8","dir":"Changelog","previous_headings":"","what":"Documentation and NAMESPACE polishing","title":"tern 0.7.8","text":"Adopting standard badges @description instead every @descriptionIn function. Corrected accordingly summarize_variables_in_cols Added stable badge g_lineplot, g_step, g_waterfall, cox_regression, score_occurrences, add_rowcounts, odds_ratio, count_occurrences, count_occurrences_by_grade, explicit_na, df_explicit_na, count_patients_with_event, decorate_grob, combine_groups, append_varlabels, univariate, stack_grobs, count_abnormal (reference abnormal), count_abnormal_by_baseline (reference abnormal_by_baseline). (helper functions) h_format_row, h_map_for_count_abnormal (utils functions) make_names, month2day, day2month empty_vector_if_na, aesi_label, n_available, format_xx, arm. count_values_funs, prop_difference, combine_counts. (chain functions) s_count_abnormal, a_count_abnormal. (chain functions) s_count_abnormal_by_baseline, a_count_abnormal_by_baseline, d_count_abnormal_by_baseline. Deprecated s_cox_univariate function now deprecated badge.","code":""},{"path":"https://insightsengineering.github.io/tern/news/index.html","id":"enhancements-0-7-8","dir":"Changelog","previous_headings":"","what":"Enhancements","title":"tern 0.7.8","text":"Enhanced g_lineplot table automatically scale table height return ggplot object. Enhanced g_ipp caption argument adjust position. Enhanced prop_diff, tern function related functions able apply continuity correction Newcombe method. Enhanced summarize_numeric_in_columns summarize_variables allow factor/character summary able summarize number BLQs AVALC ADPC dataset. Updated order summarize variables stats manual order consistency. Added sum option summarize_variables. Use consistent color palette plotting (stream default). Enhanced h_pkparam_sort function argument key_var allow data different column names.","code":""},{"path":"https://insightsengineering.github.io/tern/news/index.html","id":"miscellaneous-0-7-8","dir":"Changelog","previous_headings":"","what":"Miscellaneous","title":"tern 0.7.8","text":"Updated test-table_aet02.R variant 12. Changed scda data version ‘2022-02-28’. Added template pkgdown site. Removed package dependencies grDevices, stringr, viridisLite. Renaming summarize_numeric_in_columns summarize_variables_in_columns. Renaming summarize_vars_numeric_in_cols summarize_vars_in_cols. Fixed bug points g_lineplot plot connected missing values. Updated package authors.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/news/index.html","id":"breaking-changes-0-7-7","dir":"Changelog","previous_headings":"","what":"Breaking changes","title":"tern 0.7.7","text":"Move MMRM separate package tern.mmrm.","code":""},{"path":"https://insightsengineering.github.io/tern/news/index.html","id":"new-features-0-7-7","dir":"Changelog","previous_headings":"","what":"New features","title":"tern 0.7.7","text":"Added h_pkparam_sort order PK PARAM value based order dataset generated d_pkparam(). Added d_pkparam generate PK parameter map sorting.","code":""},{"path":"https://insightsengineering.github.io/tern/news/index.html","id":"enhancements-0-7-7","dir":"Changelog","previous_headings":"","what":"Enhancements","title":"tern 0.7.7","text":"Changed nudge_y argument h_g_ipp dependent data, fixing issue whereby baseline labels offset incorrectly. Enhanced stat_mean_ci s_summary.numeric calculate geometric mean confidence intervals.","code":""},{"path":"https://insightsengineering.github.io/tern/news/index.html","id":"miscellaneous-0-7-7","dir":"Changelog","previous_headings":"","what":"Miscellaneous","title":"tern 0.7.7","text":"Updated dependencies internal adjustments rtables package refactor. Removed with_label, var_labels, var_labels<- resolve conflict formatters package, new dependency. Added new “Introduction tern” “tern tabulation” vignettes.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/news/index.html","id":"new-features-0-7-6","dir":"Changelog","previous_headings":"","what":"New features","title":"tern 0.7.6","text":"Added h_map_for_count_abnormal create map used trim_levels_to_map split function calling helper function. supports two methods: one observed mapping, one least low limit zero least one non missing high limit. Added s_summary_numeric_in_cols summarize_vars_numeric_in_cols functions generate summary statistics columns, mainly used PK datasets. Added five statistics s_summary.numeric use s_summary_numeric_in_cols.","code":""},{"path":"https://insightsengineering.github.io/tern/news/index.html","id":"enhancements-0-7-6","dir":"Changelog","previous_headings":"","what":"Enhancements","title":"tern 0.7.6","text":"Enhanced functions tabulate_survival_subgroups tabulate_rsp_subgroups (Survival Duration Best Response analyses) calculate N-s based records considered create model. Enhanced function estimate_proportion related functions able apply continuity correction Wilson method. Refactored count_abnormal_by_marked related statistics formatting functions use efficient layout .spl_context argument used determining denominators trim_levels_to_map split function split_rows_by show desired levels table. breaking change. Refactored count_abnormal_by_worst_grade related statistics formatting functions use efficient layout .spl_context argument used determining denominators trim_levels_to_map split function split_rows_by show desired levels table. breaking change. Refactored count_abnormal function related statistics formatting functions use efficient layout trim_levels_to_map split function split_rows_by show desired levels table. Also updated abnormal argument able consider one level direction. breaking change. Enhanced function estimate_incidence_rate related functions consider week time unit data input.","code":""},{"path":"https://insightsengineering.github.io/tern/news/index.html","id":"bug-fixes-0-7-6","dir":"Changelog","previous_headings":"","what":"Bug fixes","title":"tern 0.7.6","text":"Fixed bug assertthat functions output wrong data frame names limited length failure message outputs.","code":""},{"path":"https://insightsengineering.github.io/tern/news/index.html","id":"miscellaneous-0-7-6","dir":"Changelog","previous_headings":"","what":"Miscellaneous","title":"tern 0.7.6","text":"Removed dependency utils.nest using checkmate purrr packages validation moved get_free_cores skip_if_too_deep functions utils.nest tern.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/news/index.html","id":"new-features-0-7-5","dir":"Changelog","previous_headings":"","what":"New features","title":"tern 0.7.5","text":"Added functions estimate continuous biomarker effects across subgroups survival binary response endpoints, used produce corresponding forest plots, see survival_biomarkers_subgroups response_biomarkers_subgroups. Added g_lineplot plot function, including new h_format_row helper function control_lineplot_vars function. Removed g_summary_by. Added new safety helper function h_stack_by_baskets stack events SMQ /CQ basket flag ADAE data set.","code":""},{"path":"https://insightsengineering.github.io/tern/news/index.html","id":"enhancements-0-7-5","dir":"Changelog","previous_headings":"","what":"Enhancements","title":"tern 0.7.5","text":"Added couple new statistics s_summary.numeric. Added names attribute element final list returned s_summary.numeric function. Added summary_formats summary_labels helper functions. Added option also convert logical variables factor variables df_explicit_na. Refactored h_append_grade_groups improve flexibility, robustness clearness, make sure result ordering according order grade_groups. Also, added remove_single argument controls whether elements one-element grade groups output removed. Added var_labels show_labels arguments count_occurrences count_patients_with_flags allow creation title row. Added na_level argument count_abnormal_by_baseline. Updated h_append_grade_groups longer fill-empty grade groups zeros.","code":""},{"path":"https://insightsengineering.github.io/tern/news/index.html","id":"bug-fixes-0-7-5","dir":"Changelog","previous_headings":"","what":"Bug Fixes","title":"tern 0.7.5","text":"Fixed prop_diff_cmh handle edge case FALSE (TRUE) responses. Enhanced g_mmrm_diagnostic improve error handling data amenable Locally Weighted Scatterplot Smoothing. Plot can now display combination annotation tables number patients risk, median survival time, Cox-PH summary. Function return warning instead error arm variable includes single level annot_coxph = TRUE. Lines plot now start time 0 probability 1. Category labels can include equals sign.","code":""},{"path":"https://insightsengineering.github.io/tern/news/index.html","id":"miscellaneous-0-7-5","dir":"Changelog","previous_headings":"","what":"Miscellaneous","title":"tern 0.7.5","text":"Fixed day2month month2day work NA data. Added parameters stat_mean_ci stat_median_ci may return different outputs. Added functionality h_row_counts handle analysis rows NULL cells. Updated LICENCE README new package references. Added error_on_lint: TRUE .lintr.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/news/index.html","id":"new-features-0-7-4","dir":"Changelog","previous_headings":"","what":"New features","title":"tern 0.7.4","text":"count_abnormal_by_marked tabulates marked laboratory abnormalities. summarize_patients_exposure_in_cols tabulates patient counts sum exposure across patients.","code":""},{"path":"https://insightsengineering.github.io/tern/news/index.html","id":"enhancements-0-7-4","dir":"Changelog","previous_headings":"","what":"Enhancements","title":"tern 0.7.4","text":"Enhanced MMRM-related functions fitting models without arm variable. Updated cox_regression work without covariates. Also case interaction model summary, p-values main effect coefficients longer displayed. Descriptive statistics returned summarize_vars now include quantiles. summarize_vars now accepts control function control_summarize_vars specify details confidence level mean median quantile details. control argument replaces conf_level. Added var_labels show_labels arguments count_occurrences_by_grade. Changed indent argument append_varlabels accept non-negative integer represent indent space defined user. Previous calls Boolean indent integer conversion produce warning.","code":""},{"path":"https://insightsengineering.github.io/tern/news/index.html","id":"bug-fixes-0-7-4","dir":"Changelog","previous_headings":"","what":"Bug Fixes","title":"tern 0.7.4","text":"Corrected tabulate_survival_subgroups related survival forest plot functions use total number events, instead observations, default scaling symbol sizes plot. (user might still use total number observations manually wish .) Helper function h_adsl_adlb_merge_using_worst_flag now impute BTOXGR missing visits.","code":""},{"path":"https://insightsengineering.github.io/tern/news/index.html","id":"miscellaneous-0-7-4","dir":"Changelog","previous_headings":"","what":"Miscellaneous","title":"tern 0.7.4","text":"Deleted count_abnormal_by_worst_grade_by_baseline related statistic analysis functions simpler design create lab abnormality tables. Switched data examples use scda instead random.cdisc.data package.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/news/index.html","id":"new-features-0-7-3","dir":"Changelog","previous_headings":"","what":"New Features","title":"tern 0.7.3","text":"Added Subgroup Treatment Effect Pattern (STEP) model fitting functions fit_rsp_step fit_survival_step, corresponding tidy method tidy.step well graph function g_step. Added new layout function compare_vars compares variables different types columns produces p-value comparison reference column. Function built top summarize_vars functionality. cut_quantile_bins cuts numeric vector quantile bins. fct_collapse_only collapses levels factor keeps order provided. fct_explicit_na_if inserts explicit missings factor based condition. range_noinf kind wrapper function base::range. returns c(NA, NA) instead c(-Inf, Inf) zero-length data.","code":""},{"path":"https://insightsengineering.github.io/tern/news/index.html","id":"enhancements-0-7-3","dir":"Changelog","previous_headings":"","what":"Enhancements","title":"tern 0.7.3","text":"Cox regression via fit_coxreg_univar fit_coxreg_multivar now also possible without treatment arm. univariate case means fits separate univariate models provided covariates tabulation corresponding effect estimates can later occur. Added fraction result returned s_count_occurrences. contains list numerators denominators one element per occurrence. Updated sum_num_patients count_occurrences result unique count_fraction return (0, 0) input empty. Added new argument groups_lists extract_survival_subgroups, extract_rsp_subgroups associated helper functions allows group factor levels subgroup variables manually defined groups, enhancing flexibility resulting forest graphs. Forest graph function g_forest now extracts default arguments attributes input table produced tabulate_rsp_subgroups tabulate_survival_subgroups user manually anymore. Remove arm variable name arm labels plot legend annotation tables. Show symbol used mark censored cases match order arm variable factor levels legend. Display hazard ratio confidence interval two decimal places. Updated default position hazard ratio table stay left bottom corner x-axis. Use arm value strata name treatment arm variable single level. Updated s_surv_time function use newly created function range_noinf instead base::range. New argument no_fillin_visits added h_adsl_adlb_merge_using_worst_flag specify excluded visits post-baseline worst toxicity grade output. Improved h_adsl_adlb_merge_using_worst_flag include variables shared adsl adlb, along PARAM, PARAMCD, ATOXGR, BTOXGR optionally AVISIT, AVISITN by_visit = TRUE. Prior output contained USUBJID, ARMCD, PARAMCD, ATOXGR, BTOXGR.","code":""},{"path":"https://insightsengineering.github.io/tern/news/index.html","id":"bug-fixes-0-7-3","dir":"Changelog","previous_headings":"","what":"Bug Fixes","title":"tern 0.7.3","text":"Fix bug s_surv_timepoint cases zero patients risk. Modified stat_median_ci function passing empty var empty name, row names contain missing values error show.","code":""},{"path":"https://insightsengineering.github.io/tern/news/index.html","id":"miscellaneous-0-7-3","dir":"Changelog","previous_headings":"","what":"Miscellaneous","title":"tern 0.7.3","text":"Deprecated s_cox_univariate function, use fit_coxreg_univar function instead. Updated default formats hr hr_ci a_coxph_pairwise median s_surv_time align STREAM. Updated pre-processing code files test-table_ttet01.R test-table_dort01.R make sure analysis variable EVNT1 levels factor defined. Improved error message number levels factor variable data frame expected.","code":""},{"path":"https://insightsengineering.github.io/tern/news/index.html","id":"tern-072","dir":"Changelog","previous_headings":"","what":"tern 0.7.2","title":"tern 0.7.2","text":"Fixed column label internal test errors.","code":""},{"path":"https://insightsengineering.github.io/tern/news/index.html","id":"tern-071","dir":"Changelog","previous_headings":"","what":"tern 0.7.1","title":"tern 0.7.1","text":"New argument position_surv_med added g_km move position annotation table median survival times. Fixed bug g_km related ignored arguments pch size passed helper function h_ggkm. Updated xticks max_time arguments g_km greater functionality. max_time added argument h_xticks allow . Fixed bug prop_diff_cmh led NaN weighted proportion difference estimates missing confidence intervals. change, including patients one treatment arm least one stratum estimation lead numeric results. Fixed bug prop_cmh giving error case least one stratum containing less two observations. New argument n_events added estimate_incidence_rate. New argument denom added count_occurrences. New arguments yval ci_ribbon added g_km. Add new individual patient plot function g_ipp along helpers h_g_ipp h_set_nest_theme. Fixed bug count_patients_with_events, now shows zero counts without percentage. Fixed bug get_mmrm_lsmeans allow MMRM analysis 3000 observations. Updated stat_mean_ci stat_median_ci handle edge cases number elements input series equal 1. cases, NA_real_ now returned, instead NA +/-Inf confidence interval (CI) estimates. Rename n_lim argument stat_mean_ci n_min better reflect desired meaning.","code":""},{"path":"https://insightsengineering.github.io/tern/news/index.html","id":"tern-070","dir":"Changelog","previous_headings":"","what":"tern 0.7.0","title":"tern 0.7.0","text":"version tern introduces major rewriting tern due change layout based tabulation rtables. tern now build tables directly anymore, instead provides analysis functions build tables, see examples. * Counting patients abnormal values post-baseline count_abnormal. * Counting patients graded abnormal values count_abnormal_by_worst_grade. * Counting patients abnormal values baseline status count_abnormal_by_baseline. * Counting patients missed doses s_count_missed_doses count_missed_doses. * Counting patients event flags count_patients_with_event count_patients_with_flags. * Summarizing variables summarize_vars (supports numeric, factor, character logical variables). Note factors need NAs converted na_level use. * Summarizing change baseline summarize_change. * Summarizing variables columns summarize_colvars. * Estimating difference responder proportions estimate_proportion_diff. * Estimating difference Odds Ratio estimate_odds_ratio. * Testing difference responder proportions test_proportion_diff. * Estimating responder proportion level factor estimate_multinomial_response. * Fitting tabulating results Cox regressions fit_coxreg_univar, fit_coxreg_multivar summarize_coxreg, respectively. * Pruning occurrence tables (tables counts fractions) flexible rules, see ?prune_occurrences details. * Sorting occurrence tables using different options, see ?score_occurrences details. * Fitting tabulating MMRM models fit_mmrm .rtable summarize_lsmeans, see ?tabulate_mmrm details. * Counting number unique non-unique patients summarize_num_patients. * Counting occurrences count_occurrences. * Counting occurrences grade summarize_occurrences_by_grade count_occurrences_by_grade. * Counting patients events columns summarize_patients_events_in_cols. * Tabulating binary outcome response subgroup extract_rsp_subgroups tabulate_rsp_subgroups. * Tabulating survival duration subgroup extract_survival_subgroups tabulate_survival_subgroups.","code":""},{"path":"https://insightsengineering.github.io/tern/news/index.html","id":"tern-069","dir":"Changelog","previous_headings":"","what":"tern 0.6.9","title":"tern 0.6.9","text":"Removing used imports.","code":""},{"path":"https://insightsengineering.github.io/tern/news/index.html","id":"tern-068","dir":"Changelog","previous_headings":"","what":"tern 0.6.8","title":"tern 0.6.8","text":"Improved handling missing data aggregation functions: a_mean_sd, a_median, a_n_true_and_freq, a_count, a_q1q3, a_iqr, a_range. New default p-value method s_test_proportion_diff: Chi-Squared Test Schouten Correction. Add new function t_contingency contingency tables. Renamed class splitText dynamicSplitText resolve name conflict package ggpubr. Add rreplace_format tabulation post-processing. Add new tern function t_ancova create ANCOVA tables, well corresponding elementary table function t_el_ancova summary function s_ancova. Add new tern function s_odds_ratio estimate Odds Ratio response categories, well corresponding elementary table function t_el_odds_ratio. Added new CI methods (agresti-coull, jeffreys) s_proportion. Added new CI methods anderson-hauck newcombe s_proportion_diff. Added new p-value methods (Fisher’s Exact, Chi-Squared Test Schouten Correction) s_test_proportion_diff. binary summary table function t_binary_outcome takes now lists (instead character vectors) specified helper function control_binary_comparison arguments strat_analysis unstrat_analysis. Odds Ratio estimates CIs now removable included default, similarly subsections arm comparison analyses. Also added argument rsp_multinomial. Add new table function t_el_multinomial_proportion. Add new table function t_abn_shift. Add new MMRM analysis function s_mmrm, well corresponding table functions t_mmrm_lsmeans, t_mmrm_cov, t_mmrm_diagnostic, t_mmrm_fixed, plot functions g_mmrm_lsmeans, g_mmrm_diagnostic. results match SAS results (numeric precision). Deprecated old MMRM functions a_mmrm t_mmrm (give deprecation warning still work) remove next release. reason results functions don’t match SAS results. Fix bug g_km related numbers patients risk table correct numbers integer time--event variable inputs.","code":""},{"path":"https://insightsengineering.github.io/tern/news/index.html","id":"tern-067","dir":"Changelog","previous_headings":"","what":"tern 0.6.7","title":"tern 0.6.7","text":"functions row_by argument, inputs longer require use nested_by. Add stat_mean_ci stat_median_ci error bars ggplot2. Add new tern function t_coxreg single interface diverse cox regression types. Add compound table binary endpoint: t_binary_endpoint elementary functions: t_el_proportion, t_el_proportion_diff t_el_test_proportion_diff. supporting summary functions added : s_proportion, s_adj_proportion_diff, s_proportion_diff s_test_proportion_diff. Added new tern function t_events_patyear create event table adjusted person-years. Added new tern function t_abnormality elementary table function t_el_abnormality. Removed grade_levels argument t_events_term_grade_id functions. Post-processing reordering leaves table tree creates different ordering rows required. Creating helper function occur later time. Added prune_zero_rows argument t_events_per_term_grade_id t_max_grade_per_id show rows zeros can clutter visualization Shiny app make slower. Fixed position (N=xx) t_summary_by output summarizing numeric columns parallel compare_in_header. Rename t_coxph t_coxph_pairwise reflect model process, add details documentation. Remove test.nest dependency. Keep column labels splitting data tree.","code":""},{"path":"https://insightsengineering.github.io/tern/news/index.html","id":"tern-066","dir":"Changelog","previous_headings":"","what":"tern 0.6.6","title":"tern 0.6.6","text":"Remove test.nest dependency.","code":""},{"path":"https://insightsengineering.github.io/tern/news/index.html","id":"tern-065","dir":"Changelog","previous_headings":"","what":"tern 0.6.5","title":"tern 0.6.5","text":"Change default option denominator N t_summary. Fix IQR bug: IQR Q3 minus Q1. Add new function t_logistic multi-variable logistic regression table. Add new function df_explicit_na replace NA explicit values. Added possibility t_tte specify confidence level independent survfit, coxph, ztest, see manual. Fixed bug t_rsp showing p-value, odds ratio CIs strata_data NULL. Added stratified analysis t_forest_rsp t_forest_tte, footnotes g_forest. Added footnotes, footnotes<- add_footnotes<- functions deal footnotes. Added argument conf_int confidence interval level t_el_forest_rps, t_forest_rsp, t_el_forest_tte, t_forest_tte. Added argument col_symbol_size g_forest control relative size symbols used plot. Added s_coxph_pairwise function perform pairwise testing, used t_tte t_coxph. Added methods t_count_true replacing t_summary_true. Updated t_count_unique create analysis subsets, added t_el_count_unique vectors. Fixed bug t_events_term_id table sort order decreasing frequency instead alphabetical. Added function color_palette new nest color palette.","code":""},{"path":"https://insightsengineering.github.io/tern/news/index.html","id":"tern-064","dir":"Changelog","previous_headings":"","what":"tern 0.6.4","title":"tern 0.6.4","text":"Refactored renaming functions utils.nest. Added event_type argument t_events_per_term_grade_id. Added one/two-arm t-test functions. Improvements t_summary_by. Internal code refactoring.","code":""},{"path":"https://insightsengineering.github.io/tern/news/index.html","id":"tern-063","dir":"Changelog","previous_headings":"","what":"tern 0.6.3","title":"tern 0.6.3","text":"related tree functions see reference trees. Moved label functions rtables. Deleted keys keys<- functions. Exported tabulate_pairwise. get_N, col_N_add_total, check_id. na_as_level. as_factor_keep_attributes. r_by. Disposition elementary table t_el_disposition. t_el_forest_tte, t_el_forest_rsp. Added table_tree argument returns node object. Added f_numeric choose statistics calculate. denominator now also allows omit wanting omit percentages. Renamed row_by. Changed functionality group_data using row_by_list. Removed na_omit_group. Removed indent argument, use indent function rtables. instead","code":""},{"path":"https://insightsengineering.github.io/tern/news/index.html","id":"tern-062","dir":"Changelog","previous_headings":"","what":"tern 0.6.2","title":"tern 0.6.2","text":"Use cached data random.cdisc.data speed testing. Added t_summary.Date method. Added save_join.","code":""},{"path":"https://insightsengineering.github.io/tern/news/index.html","id":"tern-061","dir":"Changelog","previous_headings":"","what":"tern 0.6.1","title":"tern 0.6.1","text":"Fixed colors Kaplan-Meier Plot Changed width_row.names argument g_forest function width_row_names. Changed censor.show argument g_km function censor_show. Changed col.legend.title argument g_waterfall function col_legend_title. Changed na.rm argument t_count_unique function na_rm. Changed row.name argument t_count_unique function row_name. Changed na.omit.group argument t_forest_rsp function na_omit_group. Changed na.omit.group argument t_forest_tte function na_omit_group. Changed row.name.TRUE row.name.FALSE arguments t_summary.logical row_name_true row_name_false respectively. Rename splotTextGrob split_text_grob. Fix examples. Refactor internal functions code.","code":""},{"path":"https://insightsengineering.github.io/tern/news/index.html","id":"tern-060","dir":"Changelog","previous_headings":"","what":"tern 0.6.0","title":"tern 0.6.0","text":"Removed functions addTable, t_summarize_by_visit, t_summarize_variables. Added t_summary_by function. Refactor g_km function, renamed kmGrob kmCurveGrob. Refactor t_events_* family functions. Updated examples.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/news/index.html","id":"new-tlgs-0-5-0-3","dir":"Changelog","previous_headings":"","what":"New TLGs","title":"tern 0.5.0.3","text":"t_summary methods data.frame, numeric, logical, character, factor, Date objects. t_events_per_term_id, t_events_per_term_grade_id: Adverse Events & Concomitant Treatment Tables. t_max_grade_per_id, t_count_unique, t_events_summary elementary tables used Adverse Events & Concomitant Treatment Tables. g_waterfall: Horizontal Waterfall Plot.","code":""},{"path":"https://insightsengineering.github.io/tern/news/index.html","id":"new-helper-functions-0-5-0-3","dir":"Changelog","previous_headings":"","what":"New Helper Functions","title":"tern 0.5.0.3","text":"decorate_grob, decorate_grob_set, decorate_grob_factory, splitTextGrob. stack_grobs, arrange_grobs, draw_grob.","code":""},{"path":"https://insightsengineering.github.io/tern/news/index.html","id":"tlg-changes-0-5-0-3","dir":"Changelog","previous_headings":"","what":"TLG changes","title":"tern 0.5.0.3","text":"t_tte now shows two rows ranges event censored times, respectively. g_km works one arm survfit objects. forest plot functions, added formatting display extreme values “>999.9”. t_summarise_variables uses now n instead N denominator calculating percentages factors default. t_rsp now works response values TRUE FALSE.","code":""},{"path":"https://insightsengineering.github.io/tern/news/index.html","id":"deprecated-functions-0-5-0-3","dir":"Changelog","previous_headings":"","what":"Deprecated Functions","title":"tern 0.5.0.3","text":"Deprecated t_summarize_variables t_summary powerful. Replacing t_summarize_by_visit t_summary_by occur upcoming release.","code":""},{"path":"https://insightsengineering.github.io/tern/news/index.html","id":"tern-050","dir":"Changelog","previous_headings":"","what":"tern 0.5.0","title":"tern 0.5.0","text":"First version harmonized analysis functions names arguments.","code":""}]
+[{"path":[]},{"path":"https://insightsengineering.github.io/tern/main/CODE_OF_CONDUCT.html","id":"our-pledge","dir":"","previous_headings":"","what":"Our Pledge","title":"Contributor Covenant Code of Conduct","text":"members, contributors, leaders pledge make participation community harassment-free experience everyone, regardless age, body size, visible invisible disability, ethnicity, sex characteristics, gender identity expression, level experience, education, socio-economic status, nationality, personal appearance, race, caste, color, religion, sexual identity orientation. pledge act interact ways contribute open, welcoming, diverse, inclusive, healthy community.","code":""},{"path":"https://insightsengineering.github.io/tern/main/CODE_OF_CONDUCT.html","id":"our-standards","dir":"","previous_headings":"","what":"Our Standards","title":"Contributor Covenant Code of Conduct","text":"Examples behavior contributes positive environment community include: Demonstrating empathy kindness toward people respectful differing opinions, viewpoints, experiences Giving gracefully accepting constructive feedback Accepting responsibility apologizing affected mistakes, learning experience Focusing best just us individuals, overall community Examples unacceptable behavior include: use sexualized language imagery, sexual attention advances kind Trolling, insulting derogatory comments, personal political attacks Public private harassment Publishing others’ private information, physical email address, without explicit permission conduct reasonably considered inappropriate professional setting","code":""},{"path":"https://insightsengineering.github.io/tern/main/CODE_OF_CONDUCT.html","id":"enforcement-responsibilities","dir":"","previous_headings":"","what":"Enforcement Responsibilities","title":"Contributor Covenant Code of Conduct","text":"Community leaders responsible clarifying enforcing standards acceptable behavior take appropriate fair corrective action response behavior deem inappropriate, threatening, offensive, harmful. Community leaders right responsibility remove, edit, reject comments, commits, code, wiki edits, issues, contributions aligned Code Conduct, communicate reasons moderation decisions appropriate.","code":""},{"path":"https://insightsengineering.github.io/tern/main/CODE_OF_CONDUCT.html","id":"scope","dir":"","previous_headings":"","what":"Scope","title":"Contributor Covenant Code of Conduct","text":"Code Conduct applies within community spaces, also applies individual officially representing community public spaces. Examples representing community include using official e-mail address, posting via official social media account, acting appointed representative online offline event.","code":""},{"path":"https://insightsengineering.github.io/tern/main/CODE_OF_CONDUCT.html","id":"enforcement","dir":"","previous_headings":"","what":"Enforcement","title":"Contributor Covenant Code of Conduct","text":"Instances abusive, harassing, otherwise unacceptable behavior may reported community leaders responsible enforcement [INSERT CONTACT METHOD]. complaints reviewed investigated promptly fairly. community leaders obligated respect privacy security reporter incident.","code":""},{"path":"https://insightsengineering.github.io/tern/main/CODE_OF_CONDUCT.html","id":"enforcement-guidelines","dir":"","previous_headings":"","what":"Enforcement Guidelines","title":"Contributor Covenant Code of Conduct","text":"Community leaders follow Community Impact Guidelines determining consequences action deem violation Code Conduct:","code":""},{"path":"https://insightsengineering.github.io/tern/main/CODE_OF_CONDUCT.html","id":"id_1-correction","dir":"","previous_headings":"Enforcement Guidelines","what":"1. Correction","title":"Contributor Covenant Code of Conduct","text":"Community Impact: Use inappropriate language behavior deemed unprofessional unwelcome community. Consequence: private, written warning community leaders, providing clarity around nature violation explanation behavior inappropriate. public apology may requested.","code":""},{"path":"https://insightsengineering.github.io/tern/main/CODE_OF_CONDUCT.html","id":"id_2-warning","dir":"","previous_headings":"Enforcement Guidelines","what":"2. Warning","title":"Contributor Covenant Code of Conduct","text":"Community Impact: violation single incident series actions. Consequence: warning consequences continued behavior. interaction people involved, including unsolicited interaction enforcing Code Conduct, specified period time. includes avoiding interactions community spaces well external channels like social media. Violating terms may lead temporary permanent ban.","code":""},{"path":"https://insightsengineering.github.io/tern/main/CODE_OF_CONDUCT.html","id":"id_3-temporary-ban","dir":"","previous_headings":"Enforcement Guidelines","what":"3. Temporary Ban","title":"Contributor Covenant Code of Conduct","text":"Community Impact: serious violation community standards, including sustained inappropriate behavior. Consequence: temporary ban sort interaction public communication community specified period time. public private interaction people involved, including unsolicited interaction enforcing Code Conduct, allowed period. Violating terms may lead permanent ban.","code":""},{"path":"https://insightsengineering.github.io/tern/main/CODE_OF_CONDUCT.html","id":"id_4-permanent-ban","dir":"","previous_headings":"Enforcement Guidelines","what":"4. Permanent Ban","title":"Contributor Covenant Code of Conduct","text":"Community Impact: Demonstrating pattern violation community standards, including sustained inappropriate behavior, harassment individual, aggression toward disparagement classes individuals. Consequence: permanent ban sort public interaction within community.","code":""},{"path":"https://insightsengineering.github.io/tern/main/CODE_OF_CONDUCT.html","id":"attribution","dir":"","previous_headings":"","what":"Attribution","title":"Contributor Covenant Code of Conduct","text":"Code Conduct adapted Contributor Covenant, version 2.1, available https://www.contributor-covenant.org/version/2/1/code_of_conduct.html. Community Impact Guidelines inspired Mozilla’s code conduct enforcement ladder. answers common questions code conduct, see FAQ https://www.contributor-covenant.org/faq. Translations available https://www.contributor-covenant.org/translations.","code":""},{"path":"https://insightsengineering.github.io/tern/main/CONTRIBUTING.html","id":null,"dir":"","previous_headings":"","what":"Contribution Guidelines","title":"Contribution Guidelines","text":"🙏 Thank taking time contribute! input deeply valued, whether issue, pull request, even feedback, regardless size, content scope.","code":""},{"path":"https://insightsengineering.github.io/tern/main/CONTRIBUTING.html","id":"table-of-contents","dir":"","previous_headings":"","what":"Table of contents","title":"Contribution Guidelines","text":"👶 Getting started 📔 Code Conduct 🗃 License 📜 Issues 🚩 Pull requests 💻 Coding guidelines 🏆 Recognition model ❓ Questions","code":""},{"path":"https://insightsengineering.github.io/tern/main/CONTRIBUTING.html","id":"getting-started","dir":"","previous_headings":"","what":"Getting started","title":"Contribution Guidelines","text":"Please refer project documentation brief introduction. Please also see articles within project documentation additional information.","code":""},{"path":"https://insightsengineering.github.io/tern/main/CONTRIBUTING.html","id":"code-of-conduct","dir":"","previous_headings":"","what":"Code of Conduct","title":"Contribution Guidelines","text":"Code Conduct governs project. Participants contributors expected follow rules outlined therein.","code":""},{"path":"https://insightsengineering.github.io/tern/main/CONTRIBUTING.html","id":"license","dir":"","previous_headings":"","what":"License","title":"Contribution Guidelines","text":"contributions covered project’s license.","code":""},{"path":"https://insightsengineering.github.io/tern/main/CONTRIBUTING.html","id":"issues","dir":"","previous_headings":"","what":"Issues","title":"Contribution Guidelines","text":"use GitHub track issues, feature requests, bugs. submitting new issue, please check issue already reported. issue already exists, please upvote existing issue 👍. new feature requests, please elaborate context benefit feature users, developers, relevant personas.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/main/CONTRIBUTING.html","id":"github-flow","dir":"","previous_headings":"Pull requests","what":"GitHub Flow","title":"Contribution Guidelines","text":"repository uses GitHub Flow model collaboration. submit pull request: Create branch Please see branch naming convention . don’t write access repository, please fork . Make changes Make sure code passes checks imposed GitHub Actions well documented well tested unit tests sufficiently covering changes introduced Create pull request (PR) pull request description, please link relevant issue (), provide detailed description change, include assumptions. Address review comments, Post approval Merge PR write access. Otherwise, reviewer merge PR behalf. Pat back Congratulations! 🎉 now official contributor project! grateful contribution.","code":""},{"path":"https://insightsengineering.github.io/tern/main/CONTRIBUTING.html","id":"branch-naming-convention","dir":"","previous_headings":"Pull requests","what":"Branch naming convention","title":"Contribution Guidelines","text":"Suppose changes related current issue current project; please name branch follows: <issue_id>_<short_description>. Please use underscore (_) delimiter word separation. example, 420_fix_ui_bug suitable branch name change resolving UI-related bug reported issue number 420 current project. change affects multiple repositories, please name branches follows: <issue_id>_<issue_repo>_<short description>. example, 69_awesomeproject_fix_spelling_error reference issue 69 reported project awesomeproject aims resolve one spelling errors multiple (likely related) repositories.","code":""},{"path":"https://insightsengineering.github.io/tern/main/CONTRIBUTING.html","id":"monorepo-and-stageddependencies","dir":"","previous_headings":"Pull requests","what":"monorepo and staged.dependencies","title":"Contribution Guidelines","text":"Sometimes might need change upstream dependent package(s) able submit meaningful change. using staged.dependencies functionality simulate monorepo behavior. dependency configuration already specified project’s staged_dependencies.yaml file. need name feature branches appropriately. exception branch naming convention described . Please refer staged.dependencies package documentation details.","code":""},{"path":"https://insightsengineering.github.io/tern/main/CONTRIBUTING.html","id":"coding-guidelines","dir":"","previous_headings":"","what":"Coding guidelines","title":"Contribution Guidelines","text":"repository follows unified processes standards adopted maintainers ensure software development carried consistently within teams cohesively across repositories.","code":""},{"path":"https://insightsengineering.github.io/tern/main/CONTRIBUTING.html","id":"style-guide","dir":"","previous_headings":"Coding guidelines","what":"Style guide","title":"Contribution Guidelines","text":"repository follows standard tidyverse style guide uses lintr lint checks. Customized lint configurations available repository’s .lintr file.","code":""},{"path":"https://insightsengineering.github.io/tern/main/CONTRIBUTING.html","id":"dependency-management","dir":"","previous_headings":"Coding guidelines","what":"Dependency management","title":"Contribution Guidelines","text":"Lightweight right weight. repository follows tinyverse recommedations limiting dependencies minimum.","code":""},{"path":"https://insightsengineering.github.io/tern/main/CONTRIBUTING.html","id":"dependency-version-management","dir":"","previous_headings":"Coding guidelines","what":"Dependency version management","title":"Contribution Guidelines","text":"code compatible (!) historical versions given dependenct package, required specify minimal version DESCRIPTION file. particular: development version requires (imports) development version another package - required put abc (>= 1.2.3.9000).","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/main/CONTRIBUTING.html","id":"r--package-versions","dir":"","previous_headings":"Coding guidelines > Recommended development environment & tools","what":"R & package versions","title":"Contribution Guidelines","text":"continuously test packages newest R version along recent dependencies CRAN BioConductor. recommend working environment also set way. can find details R version packages used R CMD check GitHub Action execution log - step prints R sessionInfo(). discover bugs older R versions older set dependencies, please create relevant bug reports.","code":""},{"path":"https://insightsengineering.github.io/tern/main/CONTRIBUTING.html","id":"pre-commit","dir":"","previous_headings":"Coding guidelines > Recommended development environment & tools","what":"pre-commit","title":"Contribution Guidelines","text":"highly recommend use pre-commit tool combined R hooks pre-commit execute checks committing pushing changes. Pre-commit hooks already available repository’s .pre-commit-config.yaml file.","code":""},{"path":"https://insightsengineering.github.io/tern/main/CONTRIBUTING.html","id":"recognition-model","dir":"","previous_headings":"","what":"Recognition model","title":"Contribution Guidelines","text":"mentioned previously, contributions deeply valued appreciated. contribution data available part repository insights, recognize significant contribution hence add contributor package authors list, following rules enforced: Minimum 5% lines code authored* (determined git blame query) top 5 contributors terms number commits lines added lines removed* *Excluding auto-generated code, including limited roxygen comments renv.lock files. package maintainer also reserves right adjust criteria recognize contributions.","code":""},{"path":"https://insightsengineering.github.io/tern/main/CONTRIBUTING.html","id":"questions","dir":"","previous_headings":"","what":"Questions","title":"Contribution Guidelines","text":"questions regarding contribution guidelines, please contact package/repository maintainer.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/main/SECURITY.html","id":"reporting-security-issues","dir":"","previous_headings":"","what":"Reporting Security Issues","title":"Security Policy","text":"believe found security vulnerability repositories organization, please report us coordinated disclosure. Please report security vulnerabilities public GitHub issues, discussions, pull requests. Instead, please send email vulnerability.management[@]roche.com. Please include much information listed can help us better understand resolve issue: type issue (e.g., buffer overflow, SQL injection, cross-site scripting) Full paths source file(s) related manifestation issue location affected source code (tag/branch/commit direct URL) special configuration required reproduce issue Step--step instructions reproduce issue Proof--concept exploit code (possible) Impact issue, including attacker might exploit issue information help us triage report quickly.","code":""},{"path":"https://insightsengineering.github.io/tern/main/SECURITY.html","id":"data-security-standards-dss","dir":"","previous_headings":"","what":"Data Security Standards (DSS)","title":"Security Policy","text":"Please make sure reporting issues form bug, feature, pull request, sensitive information PII, PHI, PCI completely removed text attachments, including pictures videos.","code":""},{"path":"https://insightsengineering.github.io/tern/main/articles/missing_values.html","id":"variable-class-conversion","dir":"Articles","previous_headings":"","what":"Variable Class Conversion","title":"Missing Values in Tern","text":"rtables requires split variables factors. try split variable isn’t, warning message appear. purposefully convert SEX variable character demonstrate happens try splitting rows variable. fix , df_explict_na convert factor resulting table generated.","code":"adsl <- tern_ex_adsl adsl$SEX <- as.character(adsl$SEX)  vars <- c(\"AGE\", \"SEX\", \"RACE\", \"BMRKR1\") var_labels <- c(   \"Age (yr)\",   \"Sex\",   \"Race\",   \"Continous Level Biomarker 1\" )  result <- basic_table(show_colcounts = TRUE) %>%   split_cols_by(var = \"ARM\") %>%   add_overall_col(\"All Patients\") %>%   analyze_vars(     vars = vars,     var_labels = var_labels   ) %>%   build_table(adsl) #> Warning in as_factor_keep_attributes(x, verbose = verbose): automatically #> converting character variable x to factor, better manually convert to factor to #> avoid failures #> Warning in as_factor_keep_attributes(x, verbose = verbose): automatically #> converting character variable x to factor, better manually convert to factor to #> avoid failures #> Warning in as_factor_keep_attributes(x, verbose = verbose): automatically #> converting character variable x to factor, better manually convert to factor to #> avoid failures #> Warning in as_factor_keep_attributes(x, verbose = verbose): automatically #> converting character variable x to factor, better manually convert to factor to #> avoid failures result #>                                                A: Drug X    B: Placebo    C: Combination   All Patients #>                                                 (N=69)        (N=73)          (N=58)         (N=200)    #> ——————————————————————————————————————————————————————————————————————————————————————————————————————— #> Age (yr)                                                                                                #>   n                                               69            73              58             200      #>   Mean (SD)                                   34.1 (6.8)    35.8 (7.1)      36.1 (7.4)      35.3 (7.1)  #>   Median                                         32.8          35.4            36.2            34.8     #>   Min - Max                                   22.4 - 48.0   23.3 - 57.5    23.0 - 58.3     22.4 - 58.3  #> Sex                                                                                                     #>   n                                               69            73              58             200      #>   F                                           38 (55.1%)    40 (54.8%)      32 (55.2%)      110 (55%)   #>   M                                           31 (44.9%)    33 (45.2%)      26 (44.8%)       90 (45%)   #> Race                                                                                                    #>   n                                               69            73              58             200      #>   ASIAN                                       38 (55.1%)    43 (58.9%)       29 (50%)       110 (55%)   #>   BLACK OR AFRICAN AMERICAN                   15 (21.7%)    13 (17.8%)      12 (20.7%)       40 (20%)   #>   WHITE                                       11 (15.9%)    12 (16.4%)       11 (19%)        34 (17%)   #>   AMERICAN INDIAN OR ALASKA NATIVE             4 (5.8%)      3 (4.1%)       6 (10.3%)       13 (6.5%)   #>   MULTIPLE                                     1 (1.4%)      1 (1.4%)           0             2 (1%)    #>   NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER        0         1 (1.4%)           0            1 (0.5%)   #>   OTHER                                            0             0              0               0       #>   UNKNOWN                                          0             0              0               0       #> Continous Level Biomarker 1                                                                             #>   n                                               69            73              58             200      #>   Mean (SD)                                    6.3 (3.6)     6.7 (3.5)      6.2 (3.3)       6.4 (3.5)   #>   Median                                          5.4           6.3            5.4             5.6      #>   Min - Max                                   0.4 - 17.8    1.0 - 18.5      2.4 - 19.1      0.4 - 19.1"},{"path":"https://insightsengineering.github.io/tern/main/articles/missing_values.html","id":"including-missing-values-in-rtables","dir":"Articles","previous_headings":"","what":"Including Missing Values in rtables","title":"Missing Values in Tern","text":"purposefully convert M values NA SEX variable. running df_explicit_na NA values encoded <Missing> included table. well, missing values included n count included denominator value calculating percent values. want Na values displayed table included n count denominator calculating percent values, use na_level argument.","code":"adsl <- tern_ex_adsl adsl$SEX[adsl$SEX == \"M\"] <- NA adsl <- df_explicit_na(adsl)  vars <- c(\"AGE\", \"SEX\") var_labels <- c(   \"Age (yr)\",   \"Sex\" )  result <- basic_table(show_colcounts = TRUE) %>%   split_cols_by(var = \"ARM\") %>%   add_overall_col(\"All Patients\") %>%   analyze_vars(     vars = vars,     var_labels = var_labels   ) %>%   build_table(adsl) result #>                A: Drug X    B: Placebo    C: Combination   All Patients #>                 (N=69)        (N=73)          (N=58)         (N=200)    #> ——————————————————————————————————————————————————————————————————————— #> Age (yr)                                                                #>   n               69            73              58             200      #>   Mean (SD)   34.1 (6.8)    35.8 (7.1)      36.1 (7.4)      35.3 (7.1)  #>   Median         32.8          35.4            36.2            34.8     #>   Min - Max   22.4 - 48.0   23.3 - 57.5    23.0 - 58.3     22.4 - 58.3  #> Sex                                                                     #>   n               38            40              32             110      #>   F            38 (100%)     40 (100%)      32 (100%)       110 (100%)  #>   M                0             0              0               0 adsl <- tern_ex_adsl adsl$SEX[adsl$SEX == \"M\"] <- NA adsl <- df_explicit_na(adsl, na_level = \"Missing Values\")  result <- basic_table(show_colcounts = TRUE) %>%   split_cols_by(var = \"ARM\") %>%   add_overall_col(\"All Patients\") %>%   analyze_vars(     vars = vars,     var_labels = var_labels   ) %>%   build_table(adsl) result #>                     A: Drug X    B: Placebo    C: Combination   All Patients #>                      (N=69)        (N=73)          (N=58)         (N=200)    #> ———————————————————————————————————————————————————————————————————————————— #> Age (yr)                                                                     #>   n                    69            73              58             200      #>   Mean (SD)        34.1 (6.8)    35.8 (7.1)      36.1 (7.4)      35.3 (7.1)  #>   Median              32.8          35.4            36.2            34.8     #>   Min - Max        22.4 - 48.0   23.3 - 57.5    23.0 - 58.3     22.4 - 58.3  #> Sex                                                                          #>   n                    69            73              58             200      #>   F                38 (55.1%)    40 (54.8%)      32 (55.2%)      110 (55%)   #>   M                     0             0              0               0       #>   Missing Values   31 (44.9%)    33 (45.2%)      26 (44.8%)       90 (45%)"},{"path":"https://insightsengineering.github.io/tern/main/articles/missing_values.html","id":"missing-values-in-numeric-variables","dir":"Articles","previous_headings":"","what":"Missing Values in Numeric Variables","title":"Missing Values in Tern","text":"Numeric variables missing values altered. means NA value numeric variable included summary statistics, included denominator value calculating percent values. make value less 30 missing AGE variable valued greater 30 included table .","code":"adsl <- tern_ex_adsl adsl$AGE[adsl$AGE < 30] <- NA adsl <- df_explicit_na(adsl)  vars <- c(\"AGE\", \"SEX\") var_labels <- c(   \"Age (yr)\",   \"Sex\" )  result <- basic_table(show_colcounts = TRUE) %>%   split_cols_by(var = \"ARM\") %>%   add_overall_col(\"All Patients\") %>%   analyze_vars(     vars = vars,     var_labels = var_labels   ) %>%   build_table(adsl) result #>                A: Drug X    B: Placebo    C: Combination   All Patients #>                 (N=69)        (N=73)          (N=58)         (N=200)    #> ——————————————————————————————————————————————————————————————————————— #> Age (yr)                                                                #>   n               46            56              44             146      #>   Mean (SD)   37.8 (5.2)    38.3 (6.3)      39.1 (5.9)      38.3 (5.8)  #>   Median         37.2          37.3            37.5            37.5     #>   Min - Max   30.3 - 48.0   30.0 - 57.5    30.5 - 58.3     30.0 - 58.3  #> Sex                                                                     #>   n               69            73              58             200      #>   F           38 (55.1%)    40 (54.8%)      32 (55.2%)      110 (55%)   #>   M           31 (44.9%)    33 (45.2%)      26 (44.8%)       90 (45%)"},{"path":"https://insightsengineering.github.io/tern/main/articles/tables.html","id":"tern-tabulation","dir":"Articles","previous_headings":"","what":"tern Tabulation","title":"Tabulation","text":"tern R package provides functions create common analyses clinical trials R. core functionality tabulation built general purpose rtables package. New users first begin reading “Introduction tern” “Introduction rtables” vignettes. packages used vignette : datasets used vignette :","code":"library(rtables) library(tern) library(dplyr) adsl <- ex_adsl adae <- ex_adae adrs <- ex_adrs"},{"path":"https://insightsengineering.github.io/tern/main/articles/tables.html","id":"tern-analyze-functions","dir":"Articles","previous_headings":"","what":"tern Analyze Functions","title":"Tabulation","text":"Analyze functions used combination rtables layout functions, pipeline creates rtables table. apply statistical logic layout rtables table. table layout materialized rtables::build_table function data. tern analyze functions wrappers around rtables::analyze function, offer various methods useful perspective clinical trials statistical projects. Examples tern analyze functions count_occurrences, summarize_ancova analyze_vars. one prefix identify tern analyze functions recommended use tern website functions reference.","code":""},{"path":"https://insightsengineering.github.io/tern/main/articles/tables.html","id":"internals-of-tern-analyze-functions","dir":"Articles","previous_headings":"tern Analyze Functions","what":"Internals of tern Analyze Functions","title":"Tabulation","text":"Please skip subsection interested internals tern analyze functions. Internally tern analyze functions like summarize_ancova mainly built 4 elements chain: descriptions function type: analysis helper functions h_*. functions useful help define analysis. statistics function s_*. Statistics functions computation numbers tabulated later. order separate computation formatting, take care rcell type formatting . formatted analysis functions a_*. arguments corresponding statistics functions, can customized calling rtables::make_afun() . used afun rtables::analyze(). analyze functions rtables::analyze(..., afun = make_afun(tern::a_*)). Analyze functions used combination rtables layout functions, pipeline creates table. last element chain. use native rtables::analyze function tern formatted analysis functions afun parameter. rtables::make_afun function helpful somebody wants attach format formatted analysis function.","code":"h_ancova() -> tern:::s_ancova() -> tern:::a_ancova() -> summarize_ancova() l <- basic_table() %>%     split_cols_by(var = \"ARM\") %>%     split_rows_by(var = \"AVISIT\") %>%     analyze(vars = \"AVAL\", afun = a_summary)  build_table(l, df = adrs) afun <- make_afun(     a_summary,     .stats = NULL,     .formats = c(median = \"xx.\"),     .labels = c(median = \"My median\"),     .indent_mods = c(median = 1L) )  l2 <- basic_table() %>%     split_cols_by(var = \"ARM\") %>%     split_rows_by(var = \"AVISIT\") %>%     analyze(vars = \"AVAL\", afun = afun)  build_table(l2, df = adrs)"},{"path":"https://insightsengineering.github.io/tern/main/articles/tables.html","id":"tabulation-examples","dir":"Articles","previous_headings":"","what":"Tabulation Examples","title":"Tabulation","text":"going create 3 different tables using tern analyze functions rtables interface.","code":""},{"path":"https://insightsengineering.github.io/tern/main/articles/tables.html","id":"demographic-table","dir":"Articles","previous_headings":"Tabulation Examples","what":"Demographic Table","title":"Tabulation","text":"Demographic tables provide summary characteristics patients enrolled clinical trial. Typically table columns represent treatment arms variables summarized table demographic properties age, sex, race, etc. example function tern analyze_vars() remaining layout functions rtables. change display order categorical variables table use factor variables explicitly set order levels. case display order columns rows. Note forcats package many useful functions help types data processing steps (used ). tern package includes many functions similar analyze_vars(). functions called layout creating functions used combination rtables layout functions just like examples . Layout creating functions wrapping calls rtables analyze(), analyze_colvars() summarize_row_groups() provide options easy formatting analysis modifications. customize display demographics table, can via arguments analyze_vars(). layout creating functions tern include standard arguments .stats, .formats, .labels .indent_mods control statistics displayed numbers formatted. Refer package help help(\"analyze_vars\") ?analyze_vars see full set options. example change default summary numeric variables include number records, mean standard deviation (single statistic, .e. within single cell). categorical variables modify summary include number records counts categories. also modify display format mean standard deviation print two decimal places instead just one. One feature layout can used different datasets create different summaries. example, can easily create summary demographics Brazil China subgroups, respectively:","code":"# Select variables to include in table. vars <- c(\"AGE\", \"SEX\") var_labels <- c(\"Age (yr)\", \"Sex\")  basic_table() %>%   split_cols_by(var = \"ARM\") %>%   add_overall_col(\"All Patients\") %>%   add_colcounts() %>%   analyze_vars(     vars = vars,     var_labels = var_labels   ) %>%   build_table(adsl) #>                       A: Drug X    B: Placebo    C: Combination   All Patients #>                        (N=134)       (N=134)        (N=132)         (N=400)    #> —————————————————————————————————————————————————————————————————————————————— #> Age (yr)                                                                       #>   n                      134           134            132             400      #>   Mean (SD)          33.8 (6.6)    35.4 (7.9)      35.4 (7.7)      34.9 (7.4)  #>   Median                33.0          35.0            35.0            34.0     #>   Min - Max          21.0 - 50.0   21.0 - 62.0    20.0 - 69.0     20.0 - 69.0  #> Sex                                                                            #>   n                      134           134            132             400      #>   F                   79 (59%)     77 (57.5%)       66 (50%)      222 (55.5%)  #>   M                  51 (38.1%)     55 (41%)       60 (45.5%)     166 (41.5%)  #>   U                   3 (2.2%)      2 (1.5%)         4 (3%)         9 (2.2%)   #>   UNDIFFERENTIATED    1 (0.7%)          0           2 (1.5%)        3 (0.8%) # Reorder the levels in the ARM variable. adsl$ARM <- factor(adsl$ARM, levels = c(\"B: Placebo\", \"A: Drug X\", \"C: Combination\"))  # Reorder the levels in the SEX variable. adsl$SEX <- factor(adsl$SEX, levels = c(\"M\", \"F\", \"U\", \"UNDIFFERENTIATED\"))  basic_table() %>%   split_cols_by(var = \"ARM\") %>%   add_overall_col(\"All Patients\") %>%   add_colcounts() %>%   analyze_vars(     vars = vars,     var_labels = var_labels   ) %>%   build_table(adsl) #>                      B: Placebo     A: Drug X    C: Combination   All Patients #>                        (N=134)       (N=134)        (N=132)         (N=400)    #> —————————————————————————————————————————————————————————————————————————————— #> Age (yr)                                                                       #>   n                      134           134            132             400      #>   Mean (SD)          35.4 (7.9)    33.8 (6.6)      35.4 (7.7)      34.9 (7.4)  #>   Median                35.0          33.0            35.0            34.0     #>   Min - Max          21.0 - 62.0   21.0 - 50.0    20.0 - 69.0     20.0 - 69.0  #> Sex                                                                            #>   n                      134           134            132             400      #>   M                   55 (41%)     51 (38.1%)      60 (45.5%)     166 (41.5%)  #>   F                  77 (57.5%)     79 (59%)        66 (50%)      222 (55.5%)  #>   U                   2 (1.5%)      3 (2.2%)         4 (3%)         9 (2.2%)   #>   UNDIFFERENTIATED        0         1 (0.7%)        2 (1.5%)        3 (0.8%) # Select statistics and modify default formats. basic_table() %>%   split_cols_by(var = \"ARM\") %>%   add_overall_col(\"All Patients\") %>%   add_colcounts() %>%   analyze_vars(     vars = vars,     var_labels = var_labels,     .stats = c(\"n\", \"mean_sd\", \"count\"),     .formats = c(mean_sd = \"xx.xx (xx.xx)\")   ) %>%   build_table(adsl) #>                       B: Placebo     A: Drug X     C: Combination   All Patients #>                        (N=134)        (N=134)         (N=132)         (N=400)    #> ———————————————————————————————————————————————————————————————————————————————— #> Age (yr)                                                                         #>   n                      134            134             132             400      #>   Mean (SD)          35.43 (7.90)   33.77 (6.55)    35.43 (7.72)    34.88 (7.44) #> Sex                                                                              #>   n                      134            134             132             400      #>   M                       55             51              60             166      #>   F                       77             79              66             222      #>   U                       2              3               4               9       #>   UNDIFFERENTIATED        0              1               2               3 lyt <- basic_table() %>%   split_cols_by(var = \"ARM\") %>%   add_overall_col(\"All Patients\") %>%   add_colcounts() %>%   analyze_vars(     vars = vars,     var_labels = var_labels   )  build_table(lyt, df = adsl %>% dplyr::filter(COUNTRY == \"BRA\")) #>                      B: Placebo     A: Drug X    C: Combination   All Patients #>                         (N=7)        (N=13)          (N=10)          (N=30)    #> —————————————————————————————————————————————————————————————————————————————— #> Age (yr)                                                                       #>   n                       7            13              10              30      #>   Mean (SD)          32.0 (6.1)    36.7 (6.4)     38.3 (10.6)      36.1 (8.1)  #>   Median                32.0          37.0            35.0            35.5     #>   Min - Max          25.0 - 42.0   24.0 - 47.0    25.0 - 64.0     24.0 - 64.0  #> Sex                                                                            #>   n                       7            13              10              30      #>   M                   4 (57.1%)     8 (61.5%)       5 (50%)        17 (56.7%)  #>   F                   3 (42.9%)     5 (38.5%)       5 (50%)        13 (43.3%)  #>   U                       0             0              0               0       #>   UNDIFFERENTIATED        0             0              0               0  build_table(lyt, df = adsl %>% dplyr::filter(COUNTRY == \"CHN\")) #>                      B: Placebo     A: Drug X    C: Combination   All Patients #>                        (N=81)        (N=74)          (N=64)         (N=219)    #> —————————————————————————————————————————————————————————————————————————————— #> Age (yr)                                                                       #>   n                      81            74              64             219      #>   Mean (SD)          35.7 (7.3)    33.0 (6.4)      35.2 (6.4)      34.6 (6.8)  #>   Median                36.0          32.0            35.0            34.0     #>   Min - Max          21.0 - 58.0   23.0 - 48.0    21.0 - 49.0     21.0 - 58.0  #> Sex                                                                            #>   n                      81            74              64             219      #>   M                  35 (43.2%)    27 (36.5%)      30 (46.9%)       92 (42%)   #>   F                  45 (55.6%)    44 (59.5%)      29 (45.3%)     118 (53.9%)  #>   U                   1 (1.2%)      2 (2.7%)        3 (4.7%)        6 (2.7%)   #>   UNDIFFERENTIATED        0         1 (1.4%)        2 (3.1%)        3 (1.4%)"},{"path":"https://insightsengineering.github.io/tern/main/articles/tables.html","id":"adverse-event-table","dir":"Articles","previous_headings":"Tabulation Examples","what":"Adverse Event Table","title":"Tabulation","text":"standard table adverse events summary system organ class preferred term. frequency counts preferred term, multiple occurrences AE individual count . create table need use combination several layout creating functions tabulation pipeline. start creating high-level summary. layout creating function tern can summarize_num_patients(): Note table, denominator used percentages shown header table (N = xx) defined based subject-level dataset adsl. done using alt_df_counts argument build_table(), provides alternative data set deriving counts header. often required work data sets include multiple records per patient df, adae .","code":"basic_table() %>%   split_cols_by(var = \"ACTARM\") %>%   add_colcounts() %>%   add_overall_col(label = \"All Patients\") %>%   summarize_num_patients(     var = \"USUBJID\",     .stats = c(\"unique\", \"nonunique\"),     .labels = c(       unique = \"Total number of patients with at least one AE\",       nonunique = \"Overall total number of events\"     )   ) %>%   build_table(     df = adae,     alt_counts_df = adsl   ) #>                                                  A: Drug X    B: Placebo    C: Combination   All Patients #>                                                   (N=134)       (N=134)        (N=132)         (N=400)    #> ————————————————————————————————————————————————————————————————————————————————————————————————————————— #> Total number of patients with at least one AE   122 (91.0%)   123 (91.8%)    120 (90.9%)     365 (91.2%)  #> Overall total number of events                      609           622            703             1934"},{"path":"https://insightsengineering.github.io/tern/main/articles/tables.html","id":"statistics-functions","dir":"Articles","previous_headings":"Tabulation Examples > Adverse Event Table","what":"Statistics Functions","title":"Tabulation","text":"building rest AE table helpful introduce tern package design conventions. layout creating function tern wrapper Statistics function. Statistics functions ones actual computation numbers table. functions always return named lists whose elements statistics available include layout via .stats argument layout creating function level. Statistics functions follow naming convention always begin s_* ease use documented page layout creating function counterpart. helpful review Statistic function understand logic used calculate numbers table see options may available modify analysis. example, Statistics function calculating numbers summarize_num_patients() s_num_patients(). results Statistics function list elements unique, nonunique unique_count: results can see unique nonunique statistics displayed “Patients” column initial AE table output . Also can see raw numbers formatted way. formatting functionality handled layout creating function level .formats argument. Now know types statistics can derived s_num_patients(), can try modifying default layout returned summarize_num_patients(). Instead reporting unique nonqunie statistics, specify analysis include unique_count statistic. result show counts unique patients. Note make update .stats .labels argument summarize_num_patients(). Let’s now continue building layout adverse event table. top-level summary, can repeat summary system organ class level. split analysis data split_rows_by() calling summarize_num_patients(). table looks almost ready. final step, need layout creating function can produce count table event frequencies. layout creating function count_occurrences(). Let’s first try using function simpler layout without row splits: Putting everything together, final AE table looks like :","code":"s_num_patients(x = adae$USUBJID, labelstr = \"\", .N_col = nrow(adae)) #> $unique #> [1] 365.000000   0.188728 #> attr(,\"label\") #> [1] \"\" #>  #> $nonunique #> [1] 1934 #> attr(,\"label\") #> [1] \"\" #>  #> $unique_count #> [1] 365 #> attr(,\"label\") #> [1] \"(n)\" basic_table() %>%   split_cols_by(var = \"ACTARM\") %>%   add_colcounts() %>%   add_overall_col(label = \"All Patients\") %>%   summarize_num_patients(     var = \"USUBJID\",     .stats = \"unique_count\",     .labels = c(unique_count = \"Total number of patients with at least one AE\")   ) %>%   build_table(     df = adae,     alt_counts_df = adsl   ) #>                                                 A: Drug X   B: Placebo   C: Combination   All Patients #>                                                  (N=134)     (N=134)        (N=132)         (N=400)    #> —————————————————————————————————————————————————————————————————————————————————————————————————————— #> Total number of patients with at least one AE      122         123            120             365 basic_table() %>%   split_cols_by(var = \"ACTARM\") %>%   add_colcounts() %>%   add_overall_col(label = \"All Patients\") %>%   summarize_num_patients(     var = \"USUBJID\",     .stats = c(\"unique\", \"nonunique\"),     .labels = c(       unique = \"Total number of patients with at least one AE\",       nonunique = \"Overall total number of events\"     )   ) %>%   split_rows_by(     \"AEBODSYS\",     child_labels = \"visible\",     nested = FALSE,     indent_mod = -1L,     split_fun = drop_split_levels   ) %>%   summarize_num_patients(     var = \"USUBJID\",     .stats = c(\"unique\", \"nonunique\"),     .labels = c(       unique = \"Total number of patients with at least one AE\",       nonunique = \"Overall total number of events\"     )   ) %>%   build_table(     df = adae,     alt_counts_df = adsl   ) #>                                                    A: Drug X    B: Placebo    C: Combination   All Patients #>                                                     (N=134)       (N=134)        (N=132)         (N=400)    #> ——————————————————————————————————————————————————————————————————————————————————————————————————————————— #> Total number of patients with at least one AE     122 (91.0%)   123 (91.8%)    120 (90.9%)     365 (91.2%)  #> Overall total number of events                        609           622            703             1934     #> cl A.1                                                                                                      #>   Total number of patients with at least one AE   78 (58.2%)    75 (56.0%)      89 (67.4%)     242 (60.5%)  #>   Overall total number of events                      132           130            160             422      #> cl B.1                                                                                                      #>   Total number of patients with at least one AE   47 (35.1%)    49 (36.6%)      43 (32.6%)     139 (34.8%)  #>   Overall total number of events                      56            60              62             178      #> cl B.2                                                                                                      #>   Total number of patients with at least one AE   79 (59.0%)    74 (55.2%)      85 (64.4%)     238 (59.5%)  #>   Overall total number of events                      129           138            143             410      #> cl C.1                                                                                                      #>   Total number of patients with at least one AE   43 (32.1%)    46 (34.3%)      43 (32.6%)     132 (33.0%)  #>   Overall total number of events                      55            63              64             182      #> cl C.2                                                                                                      #>   Total number of patients with at least one AE   35 (26.1%)    48 (35.8%)      55 (41.7%)     138 (34.5%)  #>   Overall total number of events                      48            53              65             166      #> cl D.1                                                                                                      #>   Total number of patients with at least one AE   79 (59.0%)    67 (50.0%)      80 (60.6%)     226 (56.5%)  #>   Overall total number of events                      127           106            135             368      #> cl D.2                                                                                                      #>   Total number of patients with at least one AE   47 (35.1%)    58 (43.3%)      57 (43.2%)     162 (40.5%)  #>   Overall total number of events                      62            72              74             208 basic_table() %>%   split_cols_by(var = \"ACTARM\") %>%   add_colcounts() %>%   add_overall_col(label = \"All Patients\") %>%   count_occurrences(vars = \"AEDECOD\") %>%   build_table(     df = adae,     alt_counts_df = adsl   ) #>                 A: Drug X    B: Placebo   C: Combination   All Patients #>                  (N=134)      (N=134)        (N=132)         (N=400)    #> ——————————————————————————————————————————————————————————————————————— #> dcd A.1.1.1.1   50 (37.3%)   45 (33.6%)     63 (47.7%)     158 (39.5%)  #> dcd A.1.1.1.2   48 (35.8%)   48 (35.8%)     50 (37.9%)     146 (36.5%)  #> dcd B.1.1.1.1   47 (35.1%)   49 (36.6%)     43 (32.6%)     139 (34.8%)  #> dcd B.2.1.2.1   49 (36.6%)   44 (32.8%)     52 (39.4%)     145 (36.2%)  #> dcd B.2.2.3.1   48 (35.8%)   54 (40.3%)     51 (38.6%)     153 (38.2%)  #> dcd C.1.1.1.3   43 (32.1%)   46 (34.3%)     43 (32.6%)     132 (33.0%)  #> dcd C.2.1.2.1   35 (26.1%)   48 (35.8%)     55 (41.7%)     138 (34.5%)  #> dcd D.1.1.1.1   50 (37.3%)   42 (31.3%)     51 (38.6%)     143 (35.8%)  #> dcd D.1.1.4.2   48 (35.8%)   42 (31.3%)     50 (37.9%)     140 (35.0%)  #> dcd D.2.1.5.3   47 (35.1%)   58 (43.3%)     57 (43.2%)     162 (40.5%) basic_table() %>%   split_cols_by(var = \"ACTARM\") %>%   add_colcounts() %>%   add_overall_col(label = \"All Patients\") %>%   summarize_num_patients(     var = \"USUBJID\",     .stats = c(\"unique\", \"nonunique\"),     .labels = c(       unique = \"Total number of patients with at least one AE\",       nonunique = \"Overall total number of events\"     )   ) %>%   split_rows_by(     \"AEBODSYS\",     child_labels = \"visible\",     nested = FALSE,     indent_mod = -1L,     split_fun = drop_split_levels   ) %>%   summarize_num_patients(     var = \"USUBJID\",     .stats = c(\"unique\", \"nonunique\"),     .labels = c(       unique = \"Total number of patients with at least one AE\",       nonunique = \"Overall total number of events\"     )   ) %>%   count_occurrences(vars = \"AEDECOD\") %>%   build_table(     df = adae,     alt_counts_df = adsl   ) #>                                                    A: Drug X    B: Placebo    C: Combination   All Patients #>                                                     (N=134)       (N=134)        (N=132)         (N=400)    #> ——————————————————————————————————————————————————————————————————————————————————————————————————————————— #> Total number of patients with at least one AE     122 (91.0%)   123 (91.8%)    120 (90.9%)     365 (91.2%)  #> Overall total number of events                        609           622            703             1934     #> cl A.1                                                                                                      #>   Total number of patients with at least one AE   78 (58.2%)    75 (56.0%)      89 (67.4%)     242 (60.5%)  #>   Overall total number of events                      132           130            160             422      #>     dcd A.1.1.1.1                                 50 (37.3%)    45 (33.6%)      63 (47.7%)     158 (39.5%)  #>     dcd A.1.1.1.2                                 48 (35.8%)    48 (35.8%)      50 (37.9%)     146 (36.5%)  #> cl B.1                                                                                                      #>   Total number of patients with at least one AE   47 (35.1%)    49 (36.6%)      43 (32.6%)     139 (34.8%)  #>   Overall total number of events                      56            60              62             178      #>     dcd B.1.1.1.1                                 47 (35.1%)    49 (36.6%)      43 (32.6%)     139 (34.8%)  #> cl B.2                                                                                                      #>   Total number of patients with at least one AE   79 (59.0%)    74 (55.2%)      85 (64.4%)     238 (59.5%)  #>   Overall total number of events                      129           138            143             410      #>     dcd B.2.1.2.1                                 49 (36.6%)    44 (32.8%)      52 (39.4%)     145 (36.2%)  #>     dcd B.2.2.3.1                                 48 (35.8%)    54 (40.3%)      51 (38.6%)     153 (38.2%)  #> cl C.1                                                                                                      #>   Total number of patients with at least one AE   43 (32.1%)    46 (34.3%)      43 (32.6%)     132 (33.0%)  #>   Overall total number of events                      55            63              64             182      #>     dcd C.1.1.1.3                                 43 (32.1%)    46 (34.3%)      43 (32.6%)     132 (33.0%)  #> cl C.2                                                                                                      #>   Total number of patients with at least one AE   35 (26.1%)    48 (35.8%)      55 (41.7%)     138 (34.5%)  #>   Overall total number of events                      48            53              65             166      #>     dcd C.2.1.2.1                                 35 (26.1%)    48 (35.8%)      55 (41.7%)     138 (34.5%)  #> cl D.1                                                                                                      #>   Total number of patients with at least one AE   79 (59.0%)    67 (50.0%)      80 (60.6%)     226 (56.5%)  #>   Overall total number of events                      127           106            135             368      #>     dcd D.1.1.1.1                                 50 (37.3%)    42 (31.3%)      51 (38.6%)     143 (35.8%)  #>     dcd D.1.1.4.2                                 48 (35.8%)    42 (31.3%)      50 (37.9%)     140 (35.0%)  #> cl D.2                                                                                                      #>   Total number of patients with at least one AE   47 (35.1%)    58 (43.3%)      57 (43.2%)     162 (40.5%)  #>   Overall total number of events                      62            72              74             208      #>     dcd D.2.1.5.3                                 47 (35.1%)    58 (43.3%)      57 (43.2%)     162 (40.5%)"},{"path":"https://insightsengineering.github.io/tern/main/articles/tables.html","id":"response-table","dir":"Articles","previous_headings":"Tabulation Examples","what":"Response Table","title":"Tabulation","text":"typical response table binary clinical trial endpoint may composed several different analyses: Proportion responders treatment group Difference proportion responders comparison groups vs. control group Chi-Square test difference response rates comparison groups vs. control group can build table layout like following approach used AE table: table section produced using different layout creating function tern. First start data preparation steps set analysis dataset. select endpoint analyze PARAMCD define logical variable is_rsp indicates whether patient classified responder . create summary proportion responders treatment group, use estimate_proportion() layout creating function: specify arm table used reference, use argument ref_group split_cols_by(). change reference arm “B: Placebo” arm displayed first column: customize analysis, can use method conf_level arguments modify type confidence interval calculated: next table section needed summarize difference response rates reference arm comparison arm. Use estimate_proportion_diff() layout creating function : final section needed complete table includes statistical test difference response rates. Use test_proportion_diff() layout creating function : customize output, use method argument select Chi-Squared test Schouten correction. Now can put table sections together one layout pipeline. Note one small change needed. Since primary analysis variable table sections (is_rsp), need give sub-table unique name. done adding table_names argument providing unique names :","code":"# Preprocessing to select an analysis endpoint. anl <- adrs %>%   dplyr::filter(PARAMCD == \"BESRSPI\") %>%   dplyr::mutate(is_rsp = AVALC %in% c(\"CR\", \"PR\")) basic_table() %>%   split_cols_by(var = \"ARM\") %>%   add_colcounts() %>%   estimate_proportion(     vars = \"is_rsp\",     table_names = \"est_prop\"   ) %>%   build_table(anl) #>                                   A: Drug X      B: Placebo    C: Combination #>                                    (N=134)        (N=134)         (N=132)     #> ————————————————————————————————————————————————————————————————————————————— #> Responders                       114 (85.1%)     90 (67.2%)     120 (90.9%)   #> 95% CI (Wald, with correction)   (78.7, 91.5)   (58.8, 75.5)    (85.6, 96.2) basic_table() %>%   split_cols_by(var = \"ARM\", ref_group = \"B: Placebo\") %>%   add_colcounts() %>%   estimate_proportion(     vars = \"is_rsp\"   ) %>%   build_table(anl) #>                                   A: Drug X      B: Placebo    C: Combination #>                                    (N=134)        (N=134)         (N=132)     #> ————————————————————————————————————————————————————————————————————————————— #> Responders                       114 (85.1%)     90 (67.2%)     120 (90.9%)   #> 95% CI (Wald, with correction)   (78.7, 91.5)   (58.8, 75.5)    (85.6, 96.2) basic_table() %>%   split_cols_by(var = \"ARM\", ref_group = \"B: Placebo\") %>%   add_colcounts() %>%   estimate_proportion(     vars = \"is_rsp\",     method = \"clopper-pearson\",     conf_level = 0.9   ) %>%   build_table(anl) #>                             A: Drug X      B: Placebo    C: Combination #>                              (N=134)        (N=134)         (N=132)     #> ——————————————————————————————————————————————————————————————————————— #> Responders                 114 (85.1%)     90 (67.2%)     120 (90.9%)   #> 90% CI (Clopper-Pearson)   (79.1, 89.9)   (59.9, 73.9)    (85.7, 94.7) basic_table() %>%   split_cols_by(var = \"ARM\", ref_group = \"B: Placebo\") %>%   add_colcounts() %>%   estimate_proportion_diff(     vars = \"is_rsp\",     show_labels = \"visible\",     var_labels = \"Unstratified Analysis\"   ) %>%   build_table(anl) #>                                       A: Drug X    B: Placebo   C: Combination #>                                        (N=134)      (N=134)        (N=132)     #> —————————————————————————————————————————————————————————————————————————————— #> Unstratified Analysis                                                          #>   Difference in Response rate (%)       17.9                         23.7      #>     95% CI (Wald, with correction)   (7.2, 28.6)                 (13.7, 33.8) basic_table() %>%   split_cols_by(var = \"ARM\", ref_group = \"B: Placebo\") %>%   add_colcounts() %>%   test_proportion_diff(vars = \"is_rsp\") %>%   build_table(anl) #>                                A: Drug X   B: Placebo   C: Combination #>                                 (N=134)     (N=134)        (N=132)     #> —————————————————————————————————————————————————————————————————————— #>   p-value (Chi-Squared Test)    0.0006                     <0.0001 basic_table() %>%   split_cols_by(var = \"ARM\", ref_group = \"B: Placebo\") %>%   add_colcounts() %>%   test_proportion_diff(     vars = \"is_rsp\",     method = \"schouten\"   ) %>%   build_table(anl) #>                                                         A: Drug X   B: Placebo   C: Combination #>                                                          (N=134)     (N=134)        (N=132)     #> ——————————————————————————————————————————————————————————————————————————————————————————————— #>   p-value (Chi-Squared Test with Schouten Correction)    0.0008                     <0.0001 basic_table() %>%   split_cols_by(var = \"ARM\", ref_group = \"B: Placebo\") %>%   add_colcounts() %>%   estimate_proportion(     vars = \"is_rsp\",     method = \"clopper-pearson\",     conf_level = 0.9,     table_names = \"est_prop\"   ) %>%   estimate_proportion_diff(     vars = \"is_rsp\",     show_labels = \"visible\",     var_labels = \"Unstratified Analysis\",     table_names = \"est_prop_diff\"   ) %>%   test_proportion_diff(     vars = \"is_rsp\",     method = \"schouten\",     table_names = \"test_prop_diff\"   ) %>%   build_table(anl) #>                                                          A: Drug X      B: Placebo    C: Combination #>                                                           (N=134)        (N=134)         (N=132)     #> ———————————————————————————————————————————————————————————————————————————————————————————————————— #> Responders                                              114 (85.1%)     90 (67.2%)     120 (90.9%)   #> 90% CI (Clopper-Pearson)                                (79.1, 89.9)   (59.9, 73.9)    (85.7, 94.7)  #> Unstratified Analysis                                                                                #>   Difference in Response rate (%)                           17.9                           23.7      #>     95% CI (Wald, with correction)                      (7.2, 28.6)                    (13.7, 33.8)  #>   p-value (Chi-Squared Test with Schouten Correction)      0.0008                        <0.0001"},{"path":"https://insightsengineering.github.io/tern/main/articles/tables.html","id":"summary","dir":"Articles","previous_headings":"","what":"Summary","title":"Tabulation","text":"Tabulation tern builds top layout tabulation framework rtables. Complex tables built step step pipeline combining layout creating functions perform specific type analysis. tern analyze functions introduced vignette : analyze_vars() summarize_num_patients() count_occurrences() estimate_proportion() estimate_proportion_diff() test_proportion_diff() Layout creating functions build formatted layout controlling features labels, numerical display formats indentation. functions wrappers Statistics functions calculate raw summaries analysis. can easily spot Statistics functions documentation always begin prefix s_. can helpful inspect run Statistics functions understand ways analysis can customized.","code":""},{"path":"https://insightsengineering.github.io/tern/main/articles/tern.html","id":"common-clinical-trials-analyses","dir":"Articles","previous_headings":"","what":"Common Clinical Trials Analyses","title":"Introduction to tern","text":"package provides large range functionality create tables graphs used clinical trial statistical analysis. rtables tabulation extended clinical trials specific functions: demographics unique patients exposure across patients change baseline parameters statistical model fits: MMRM, logistic regression, Cox regression, … … rtables tabulation helper functions: pre-processing conversions transformations … data visualizations connected clinical trials: Kaplan-Meier plots forest plots line plots … data visualizations helper functions: arrange/stack multiple graphs embellishing graphs/tables metadata details, adding titles, footnotes, page number, etc. … reference tern functions available tern website functions reference.","code":""},{"path":"https://insightsengineering.github.io/tern/main/articles/tern.html","id":"analytical-functions-for-rtables","dir":"Articles","previous_headings":"","what":"Analytical Functions for rtables","title":"Introduction to tern","text":"Analytical functions used combination rtables layout functions, pipeline creates rtables table. apply statistical logic layout rtables table. table layout materialized rtables::build_table function data. tern analytical functions wrappers around rtables::analyze function; offer various methods useful perspective clinical trials statistical projects. Examples tern analytical functions count_occurrences, summarize_ancova analyze_vars. one prefix identify tern analytical functions recommended use reference subsection tern website. rtables code first describe two tables assign descriptions variables lyt lyt2. built tables using actual data rtables::build_table. description table called table layout. analyze instruction adds layout ARM variable analyzed mean analysis function result rounded 1 decimal place. Hence, layout “pre-data”; , ’s description build table get data. Defining table layout pure rtables code: , tern function used analyze_vars replaces rtables::analyze function used . see tern offers advanced analysis extending rtables function calls one additional function call. examples tabulation analyze functions presented Tabulation vignette.","code":"library(tern) library(dplyr) # Create table layout pure rtables lyt <- rtables::basic_table() %>%   rtables::split_cols_by(var = \"ARM\") %>%   rtables::split_rows_by(var = \"AVISIT\") %>%   rtables::analyze(vars = \"AVAL\", mean, format = \"xx.x\") # Create table layout with tern analyze_vars analyze function lyt2 <- rtables::basic_table() %>%   rtables::split_cols_by(var = \"ARM\") %>%   rtables::split_rows_by(var = \"AVISIT\") %>%   analyze_vars(vars = \"AVAL\", .formats = c(\"mean_sd\" = \"(xx.xx, xx.xx)\")) # Apply table layout to data and produce `rtables` object  adrs <- formatters::ex_adrs  rtables::build_table(lyt, df = adrs) #>                    A: Drug X   B: Placebo   C: Combination #> —————————————————————————————————————————————————————————— #> SCREENING                                                  #>   mean                3.0         3.0            3.0       #> BASELINE                                                   #>   mean                2.5         2.8            2.5       #> END OF INDUCTION                                           #>   mean                1.7         2.1            1.6       #> FOLLOW UP                                                  #>   mean                2.2         2.9            2.0 rtables::build_table(lyt2, df = adrs) #>                     A: Drug X      B: Placebo    C: Combination #> ——————————————————————————————————————————————————————————————— #> SCREENING                                                       #>   n                    154            178             144       #>   Mean (SD)        (3.00, 0.00)   (3.00, 0.00)    (3.00, 0.00)  #>   Median               3.0            3.0             3.0       #>   Min - Max         3.0 - 3.0      3.0 - 3.0       3.0 - 3.0    #> BASELINE                                                        #>   n                    136            146             124       #>   Mean (SD)        (2.46, 0.88)   (2.77, 1.00)    (2.46, 1.08)  #>   Median               3.0            3.0             3.0       #>   Min - Max         1.0 - 4.0      1.0 - 5.0       1.0 - 5.0    #> END OF INDUCTION                                                #>   n                    218            205             217       #>   Mean (SD)        (1.75, 0.90)   (2.14, 1.28)    (1.65, 1.06)  #>   Median               2.0            2.0             1.0       #>   Min - Max         1.0 - 4.0      1.0 - 5.0       1.0 - 5.0    #> FOLLOW UP                                                       #>   n                    164            153             167       #>   Mean (SD)        (2.23, 1.26)   (2.89, 1.29)    (1.97, 1.01)  #>   Median               2.0            4.0             2.0       #>   Min - Max         1.0 - 4.0      1.0 - 4.0       1.0 - 4.0"},{"path":"https://insightsengineering.github.io/tern/main/articles/tern.html","id":"clinical-trial-visualizations","dir":"Articles","previous_headings":"","what":"Clinical Trial Visualizations","title":"Introduction to tern","text":"Clinical trial related plots complement rich palette tern tabulation analysis functions. Thus tern package delivers full-featured tool clinical trial reporting. tern plot functions return graphs ggplot2 objects. nestcolor package can loaded apply standardized NEST color palette tern plots. Line plot without table generated g_lineplot function.  Line plot table generated g_lineplot function.  tern functions used plot generation g_ prefixed listed tern website functions reference.","code":"adsl <- formatters::ex_adsl adlb <- formatters::ex_adlb adlb <- dplyr::filter(adlb, PARAMCD == \"ALT\", AVISIT != \"SCREENING\") library(nestcolor) # Mean with CI g_lineplot(adlb, adsl, subtitle = \"Laboratory Test:\") # Mean with CI, table, and customized confidence level g_lineplot(   adlb,   adsl,   table = c(\"n\", \"mean\", \"mean_ci\"),   title = \"Plot of Mean and 80% Confidence Limits by Visit\" )"},{"path":"https://insightsengineering.github.io/tern/main/articles/tern.html","id":"interactive-apps","dir":"Articles","previous_headings":"","what":"Interactive Apps","title":"Introduction to tern","text":"tern outputs can easily converted shiny apps. recommend building apps using teal package, shiny-based interactive exploration framework analyzing data. variety pre-made teal shiny apps tern outputs available teal.modules.clinical package.","code":""},{"path":"https://insightsengineering.github.io/tern/main/articles/tern.html","id":"summary","dir":"Articles","previous_headings":"","what":"Summary","title":"Introduction to tern","text":"summary, tern contains many additional functions creating tables, listings, graphs used clinical trials statistical analyses. design package gives users flexibility meet analysis needs regulatory exploratory reporting contexts. information please explore tern website.","code":""},{"path":"https://insightsengineering.github.io/tern/main/articles/tern_formats.html","id":"tern-formatting-functions-overview","dir":"Articles","previous_headings":"","what":"tern Formatting Functions Overview","title":"Formatting Functions","text":"tern R package provides functions create common analyses clinical trials R functions default formatting arguments displaying values output specific way. tern formatting differs compared formatting available formatters package tern formats capable handling logical statements, allowing fine-tuning output displayed. Depending type value displayed, value , format output change. Whereas using formatters package, specified format applied regardless value. see available formatting functions available tern see ?formatting_functions. see available format strings available formatters see formatters::list_valid_format_labels().","code":""},{"path":"https://insightsengineering.github.io/tern/main/articles/tern_formats.html","id":"comparing-tern-formatters-formats","dir":"Articles","previous_headings":"","what":"Comparing tern & formatters Formats","title":"Formatting Functions","text":"packages used vignette : example demonstrates use tern formatting count_abnormal() function. example “low” category non-zero numerator value fraction percentage value displayed, “high” value numerator value zero fraction value displayed without also displaying redundant zero percentage value. following example count_abnormal() function utilized . time “low” values “high” values non-zero numerator show percentage. following example demonstrates difference formatters used instead format output. choose use \"xx / xx\" value format. “high” value zero numerator value “low” value non-zero numerator, yet displayed format. concept occurs using available formats formatters package. following example displays result using \"xx.x / xx.x\" format instead. Use formatters::list_valid_format_labels() see full list available formats formatters.","code":"library(rtables) library(formatters) library(tern) library(dplyr) df2 <- data.frame(   ID = as.character(c(1, 1, 2, 2)),   RANGE = factor(c(\"NORMAL\", \"LOW\", \"HIGH\", \"LOW\")),   BL_RANGE = factor(c(\"NORMAL\", \"NORMAL\", \"HIGH\", \"HIGH\")),   ONTRTFL = c(\"\", \"Y\", \"\", \"Y\"),   stringsAsFactors = FALSE )  df2 <- df2 %>%   filter(ONTRTFL == \"Y\")  basic_table() %>%   count_abnormal(     var = \"RANGE\",     abnormal = list(low = \"LOW\", high = \"HIGH\"),     variables = list(id = \"ID\", baseline = \"BL_RANGE\"),     exclude_base_abn = FALSE,     .formats = list(fraction = format_fraction)   ) %>%   build_table(df2) #>         all obs   #> ————————————————— #> low    2/2 (100%) #> high      0/2 df2 <- data.frame(   ID = as.character(c(1, 1, 2, 2)),   RANGE = factor(c(\"NORMAL\", \"LOW\", \"HIGH\", \"HIGH\")),   BL_RANGE = factor(c(\"NORMAL\", \"NORMAL\", \"HIGH\", \"HIGH\")),   ONTRTFL = c(\"\", \"Y\", \"\", \"Y\"),   stringsAsFactors = FALSE )  df2 <- df2 %>%   filter(ONTRTFL == \"Y\")  basic_table() %>%   count_abnormal(     var = \"RANGE\",     abnormal = list(low = \"LOW\", high = \"HIGH\"),     variables = list(id = \"ID\", baseline = \"BL_RANGE\"),     exclude_base_abn = FALSE,     .formats = list(fraction = format_fraction)   ) %>%   build_table(df2) #>         all obs  #> ———————————————— #> low    1/2 (50%) #> high   1/2 (50%) df2 <- data.frame(   ID = as.character(c(1, 1, 2, 2)),   RANGE = factor(c(\"NORMAL\", \"LOW\", \"HIGH\", \"LOW\")),   BL_RANGE = factor(c(\"NORMAL\", \"NORMAL\", \"HIGH\", \"HIGH\")),   ONTRTFL = c(\"\", \"Y\", \"\", \"Y\"),   stringsAsFactors = FALSE ) df2 <- df2 %>%   filter(ONTRTFL == \"Y\")  basic_table() %>%   count_abnormal(     var = \"RANGE\",     abnormal = list(low = \"LOW\", high = \"HIGH\"),     variables = list(id = \"ID\", baseline = \"BL_RANGE\"),     exclude_base_abn = FALSE,     .formats = list(fraction = \"xx / xx\")   ) %>%   build_table(df2) #>        all obs #> —————————————— #> low     2 / 2  #> high    0 / 2 df2 <- data.frame(   ID = as.character(c(1, 1, 2, 2)),   RANGE = factor(c(\"NORMAL\", \"LOW\", \"HIGH\", \"LOW\")),   BL_RANGE = factor(c(\"NORMAL\", \"NORMAL\", \"HIGH\", \"HIGH\")),   ONTRTFL = c(\"\", \"Y\", \"\", \"Y\"),   stringsAsFactors = FALSE ) df2 <- df2 %>%   filter(ONTRTFL == \"Y\")  basic_table() %>%   count_abnormal(     var = \"RANGE\",     abnormal = list(low = \"LOW\", high = \"HIGH\"),     variables = list(id = \"ID\", baseline = \"BL_RANGE\"),     exclude_base_abn = FALSE,     .formats = list(fraction = \"xx.x / xx.x\")   ) %>%   build_table(df2) #>         all obs  #> ———————————————— #> low    2.0 / 2.0 #> high   0.0 / 2.0"},{"path":"https://insightsengineering.github.io/tern/main/articles/tern_formats.html","id":"formatting-function-basics","dir":"Articles","previous_headings":"","what":"Formatting Function Basics","title":"Formatting Functions","text":"Current tern formatting functions consider following aspects setting custom behaviors: Missing values - custom value string can set display missing values instead NA. 0’s - cell value zero, tern fraction formatting functions exclude accompanying percentage value. Number decimal places display - number decimal places can fixed needed. Value thresholds - different format value can displayed depending whether value within certain threshold.","code":""},{"path":"https://insightsengineering.github.io/tern/main/articles/tern_formats.html","id":"number-of-decimal-places-to-display","dir":"Articles","previous_headings":"Formatting Function Basics","what":"Number of Decimal Places to Display","title":"Formatting Functions","text":"Two functions set fixed number decimal places (specifically 1) format_fraction_fixed_dp() format_count_fraction_fixed_dp(). default, formatting functions remove trailing zeros, two functions always one decimal place percentage, even digit zero. See following example:","code":"format_fraction_fixed_dp(x = c(num = 1L, denom = 3L)) #> [1] \"1/3 (33.3%)\" format_fraction_fixed_dp(x = c(num = 1L, denom = 2L)) #> [1] \"1/2 (50.0%)\"  format_count_fraction_fixed_dp(x = c(2, 0.6667)) #> [1] \"2 (66.7%)\" format_count_fraction_fixed_dp(x = c(2, 0.25)) #> [1] \"2 (25.0%)\""},{"path":"https://insightsengineering.github.io/tern/main/articles/tern_formats.html","id":"value-thresholds","dir":"Articles","previous_headings":"Formatting Function Basics","what":"Value Thresholds","title":"Formatting Functions","text":"Functions set custom values according certain threshold include format_extreme_values(), format_extreme_values_ci(), format_fraction_threshold(). extreme value formats work similarly allow user specify maximum number digits include, large small values given special string value. example: format_fraction_threshold() function allows user specify lower percentage threshold, values instead assigned special string value. example: See documentation function specific details behavior customize .","code":"extreme_format <- format_extreme_values(digits = 2) extreme_format(0.235) #> [1] \"0.23\" extreme_format(0.001) #> [1] \"<0.01\" extreme_format(Inf) #> [1] \">999.99\" fraction_format <- format_fraction_threshold(0.05) fraction_format(x = c(20, 0.1)) #> [1] 10 fraction_format(x = c(2, 0.01)) #> [1] \"<5\""},{"path":"https://insightsengineering.github.io/tern/main/articles/tern_formats.html","id":"creating-custom-formatting-functions","dir":"Articles","previous_headings":"","what":"Creating Custom Formatting Functions","title":"Formatting Functions","text":"table requires customized output displayed using one pre-existing tern formatting functions, may want consider creating new formatting function. creating formatting function important consider aspects listed Formatting Function Customization section . section create custom formatting function derived format_fraction_fixed_dp() function. First take look function detail customize . see numerator value greater 0, fraction percentage displayed. numerator 0, fraction shown. Percent values always display 1 decimal place. create dummy dataset observe output value behavior formatting function applied. Now modify function make custom formatting function, custom_format. want display 3 decimal places percent value, numerator value 0 want display 0 value (without denominator).","code":"# First we will see how the format_fraction_fixed_dp code works and displays the outputs format_fraction_fixed_dp <- function(x, ...) {   attr(x, \"label\") <- NULL   checkmate::assert_vector(x)   checkmate::assert_count(x[\"num\"])   checkmate::assert_count(x[\"denom\"])    result <- if (x[\"num\"] == 0) {     paste0(x[\"num\"], \"/\", x[\"denom\"])   } else {     paste0(       x[\"num\"], \"/\", x[\"denom\"],       \" (\", sprintf(\"%.1f\", round(x[\"num\"] / x[\"denom\"] * 100, 1)), \"%)\"     )   }   return(result) } df2 <- data.frame(   ID = as.character(c(1, 1, 2, 2)),   RANGE = factor(c(\"NORMAL\", \"LOW\", \"HIGH\", \"LOW\")),   BL_RANGE = factor(c(\"NORMAL\", \"NORMAL\", \"HIGH\", \"HIGH\")),   ONTRTFL = c(\"\", \"Y\", \"\", \"Y\"),   stringsAsFactors = FALSE ) %>%   filter(ONTRTFL == \"Y\")  basic_table() %>%   count_abnormal(     var = \"RANGE\",     abnormal = list(low = \"LOW\", high = \"HIGH\"),     variables = list(id = \"ID\", baseline = \"BL_RANGE\"),     exclude_base_abn = FALSE,     .formats = list(fraction = format_fraction_fixed_dp)   ) %>%   build_table(df2) #>          all obs    #> ——————————————————— #> low    2/2 (100.0%) #> high       0/2 custom_format <- function(x, ...) {   attr(x, \"label\") <- NULL   checkmate::assert_vector(x)   checkmate::assert_count(x[\"num\"])   checkmate::assert_count(x[\"denom\"])    result <- if (x[\"num\"] == 0) {     paste0(x[\"num\"]) # We remove the denominator on this line so that only a 0 is displayed   } else {     paste0(       x[\"num\"], \"/\", x[\"denom\"],       \" (\", sprintf(\"%.3f\", round(x[\"num\"] / x[\"denom\"] * 100, 1)), \"%)\" # We include 3 decimal places with %.3f     )   }   return(result) }  basic_table() %>%   count_abnormal(     var = \"RANGE\",     abnormal = list(low = \"LOW\", high = \"HIGH\"),     variables = list(id = \"ID\", baseline = \"BL_RANGE\"),     exclude_base_abn = FALSE,     .formats = list(fraction = custom_format) # Here we implement our new custom_format function   ) %>%   build_table(df2) #>           all obs     #> ————————————————————— #> low    2/2 (100.000%) #> high         0"},{"path":"https://insightsengineering.github.io/tern/main/articles/tern_formats.html","id":"summary","dir":"Articles","previous_headings":"","what":"Summary","title":"Formatting Functions","text":"tern analysis function pre-specified default format functions implement generating output, taken formatters package custom formatting functions stored tern. tern functions differ compared formatters logical statements can used set value-dependent customized formats. like create custom formatting function use tern, sure carefully consider rules want implement handle different input values.","code":""},{"path":"https://insightsengineering.github.io/tern/main/articles/tern_functions_guide.html","id":"understanding-tern-functions","dir":"Articles","previous_headings":"","what":"Understanding tern functions","title":"Understanding `tern` functions","text":"Every function tern package designed certain structure can cooperate well every user’s need, maintaining consistent predictable behavior. document guide example function package, explaining purpose many building blocks can used. recently worked consider summarize_change() example. function used calculate change baseline value given variable. realistic example can found LBT03 TLG-catalog. summarize_change() main function available user. can find lists functions ?tern::analyze_functions. build around rtables::analyze() function, core analysis function rtables. wrapper functions call specific analysis functions (always written a_*) meant handle statistic functions (always written s_*) format results rtables::in_row() function. can summarize structure follows: summarize_change() (1)-> a_change_from_baseline() (2)-> [s_change_from_baseline() + rtables::in_row()] main questions may arise : Handling NA. Handling formats. Additional statistics. Data set library loading. Classic use summarize_change(). .formats, .labels, .indent_mods depend names .stats. can change default formatting. want something special format? Adding custom statistic (custom format):","code":"library(dplyr) #>  #> Attaching package: 'dplyr' #> The following objects are masked from 'package:stats': #>  #>     filter, lag #> The following objects are masked from 'package:base': #>  #>     intersect, setdiff, setequal, union library(tern) #> Loading required package: rtables #> Loading required package: formatters #>  #> Attaching package: 'formatters' #> The following object is masked from 'package:base': #>  #>     %||% #> Loading required package: magrittr #>  #> Attaching package: 'rtables' #> The following object is masked from 'package:utils': #>  #>     str #> Registered S3 method overwritten by 'tern': #>   method   from  #>   tidy.glm broom  ## Fabricate dataset dta_test <- data.frame(   USUBJID = rep(1:6, each = 3),   AVISIT = rep(paste0(\"V\", 1:3), 6),   ARM = rep(LETTERS[1:3], rep(6, 3)),   AVAL = c(9:1, rep(NA, 9)) ) %>%   mutate(ABLFLL = AVISIT == \"V1\") %>%   group_by(USUBJID) %>%   mutate(     BLVAL = AVAL[ABLFLL],     CHG = AVAL - BLVAL   ) %>%   ungroup() fix_layout <- basic_table() %>%   split_cols_by(\"ARM\") %>%   split_rows_by(\"AVISIT\")   # Dealing with NAs: na_rm = TRUE fix_layout %>%   summarize_change(\"CHG\", variables = list(value = \"AVAL\", baseline_flag = \"ABLFLL\")) %>%   build_table(dta_test) %>%   print() #>                     A               B         C  #> ———————————————————————————————————————————————— #> V1                                               #>   n                 2               1         0  #>   Mean (SD)    7.50 (2.12)      3.00 (NA)     NA #>   Median          7.50            3.00        NA #>   Min - Max    6.00 - 9.00     3.00 - 3.00    NA #> V2                                               #>   n                 2               1         0  #>   Mean (SD)   -1.00 (0.00)     -1.00 (NA)     NA #>   Median          -1.00           -1.00       NA #>   Min - Max   -1.00 - -1.00   -1.00 - -1.00   NA #> V3                                               #>   n                 2               1         0  #>   Mean (SD)   -2.00 (0.00)     -2.00 (NA)     NA #>   Median          -2.00           -2.00       NA #>   Min - Max   -2.00 - -2.00   -2.00 - -2.00   NA  # Dealing with NAs: na_rm = FALSE fix_layout %>%   summarize_change(\"CHG\", variables = list(value = \"AVAL\", baseline_flag = \"ABLFLL\"), na_rm = FALSE) %>%   build_table(dta_test) %>%   print() #>                     A               B         C  #> ———————————————————————————————————————————————— #> V1                                               #>   n                 2               1         0  #>   Mean (SD)    7.50 (2.12)      3.00 (NA)     NA #>   Median          7.50            3.00        NA #>   Min - Max    6.00 - 9.00     3.00 - 3.00    NA #> V2                                               #>   n                 2               1         0  #>   Mean (SD)   -1.00 (0.00)     -1.00 (NA)     NA #>   Median          -1.00           -1.00       NA #>   Min - Max   -1.00 - -1.00   -1.00 - -1.00   NA #> V3                                               #>   n                 2               1         0  #>   Mean (SD)   -2.00 (0.00)     -2.00 (NA)     NA #>   Median          -2.00           -2.00       NA #>   Min - Max   -2.00 - -2.00   -2.00 - -2.00   NA  # changing the NA string (it is done on all levels) fix_layout %>%   summarize_change(\"CHG\", variables = list(value = \"AVAL\", baseline_flag = \"ABLFLL\"), na_str = \"my_na\") %>%   build_table(dta_test) %>%   print() #>                     A               B           C   #> ——————————————————————————————————————————————————— #> V1                                                  #>   n                 2               1           0   #>   Mean (SD)    7.50 (2.12)    3.00 (my_na)    my_na #>   Median          7.50            3.00        my_na #>   Min - Max    6.00 - 9.00     3.00 - 3.00    my_na #> V2                                                  #>   n                 2               1           0   #>   Mean (SD)   -1.00 (0.00)    -1.00 (my_na)   my_na #>   Median          -1.00           -1.00       my_na #>   Min - Max   -1.00 - -1.00   -1.00 - -1.00   my_na #> V3                                                  #>   n                 2               1           0   #>   Mean (SD)   -2.00 (0.00)    -2.00 (my_na)   my_na #>   Median          -2.00           -2.00       my_na #>   Min - Max   -2.00 - -2.00   -2.00 - -2.00   my_na # changing n count format and label and indentation fix_layout %>%   summarize_change(\"CHG\",     variables = list(value = \"AVAL\", baseline_flag = \"ABLFLL\"),     .stats = c(\"n\", \"mean\"), # reducing the number of stats for visual appreciation     .formats = c(n = \"xx.xx\"),     .labels = c(n = \"NnNn\"),     .indent_mods = c(n = 5), na_str = \"nA\"   ) %>%   build_table(dta_test) %>%   print() #>                     A      B      C   #> ————————————————————————————————————— #> V1                                    #>             NnNn   2.00   1.00   0.00 #>   Mean             7.5    3.0     nA  #> V2                                    #>             NnNn   2.00   1.00   0.00 #>   Mean             -1.0   -1.0    nA  #> V3                                    #>             NnNn   2.00   1.00   0.00 #>   Mean             -2.0   -2.0    nA # changing n count format and label and indentation fix_layout %>%   summarize_change(\"CHG\",     variables = list(value = \"AVAL\", baseline_flag = \"ABLFLL\"),     .stats = c(\"n\", \"mean\"), # reducing the number of stats for visual appreciation     .formats = c(n = function(x, ...) as.character(x * 100))   ) %>% # Note you need ...!!!   build_table(dta_test) %>%   print() #>           A      B     C  #> ————————————————————————— #> V1                        #>   n      200    100    0  #>   Mean   7.5    3.0    NA #> V2                        #>   n      200    100    0  #>   Mean   -1.0   -1.0   NA #> V3                        #>   n      200    100    0  #>   Mean   -2.0   -2.0   NA # changing n count format and label and indentation fix_layout %>%   summarize_change(     \"CHG\",     variables = list(value = \"AVAL\", baseline_flag = \"ABLFLL\"),     .stats = c(\"n\", \"my_stat\" = function(df, ...) {       a <- mean(df$AVAL, na.rm = TRUE)       b <- list(...)$.N_row # It has access at all `?rtables::additional_fun_params`       a / b     }),     .formats = c(\"my_stat\" = function(x, ...) sprintf(\"%.2f\", x))   ) %>%   build_table(dta_test) #>              A      B     C  #> ———————————————————————————— #> V1                           #>   n          2      1     0  #>   my_stat   1.25   0.50   NA #> V2                           #>   n          2      1     0  #>   my_stat   1.08   0.33   NA #> V3                           #>   n          2      1     0  #>   my_stat   0.92   0.17   NA"},{"path":"https://insightsengineering.github.io/tern/main/articles/tern_functions_guide.html","id":"for-developers","dir":"Articles","previous_headings":"","what":"For Developers","title":"Understanding `tern` functions","text":"layers specific parameters need available, , rtables multiple way handle formatting NA values, decide correctly handle additional extra arguments. follow following scheme: Level 1: summarize_change(): parameters without starting dot .* used added extra_args. Specifically, solve NA values using inclNAs option rtables::analyze(). add ... na.rm = inclNAs. Also na_str set. may want statistic dependent future, still need think accomplish . add rtables::additional_fun_params analysis function make available ... next level. Level 2: a_change_from_baseline(): parameters starting dot . used. Mainly .stats, .formats, .labels, .indent_mods used. also add extra_afun_params ... list statistical function. Notice handling additional parameters .call() function.","code":""},{"path":"https://insightsengineering.github.io/tern/main/authors.html","id":null,"dir":"","previous_headings":"","what":"Authors","title":"Authors and Citation","text":"Joe Zhu. Author, maintainer. Daniel Sabanés Bové. Author. Jana Stoilova. Author. Davide Garolini. Author. Emily de la Rua. Author. Abinaya Yogasekaram. Author. Heng Wang. Author. Francois Collin. Author. Adrian Waddell. Author. Pawel Rucki. Author. Chendi Liao. Author. Jennifer Li. Author. F. Hoffmann-La Roche AG. Copyright holder, funder.","code":""},{"path":"https://insightsengineering.github.io/tern/main/authors.html","id":"citation","dir":"","previous_headings":"","what":"Citation","title":"Authors and Citation","text":"Zhu J, Sabanés Bové D, Stoilova J, Garolini D, de la Rua E, Yogasekaram , Wang H, Collin F, Waddell , Rucki P, Liao C, Li J (2024). tern: Create Common TLGs Used Clinical Trials. R package version 0.9.6.9016, https://github.com/insightsengineering/tern/, https://insightsengineering.github.io/tern/main/.","code":"@Manual{,   title = {tern: Create Common TLGs Used in Clinical Trials},   author = {Joe Zhu and Daniel {Sabanés Bové} and Jana Stoilova and Davide Garolini and Emily {de la Rua} and Abinaya Yogasekaram and Heng Wang and Francois Collin and Adrian Waddell and Pawel Rucki and Chendi Liao and Jennifer Li},   year = {2024},   note = {R package version 0.9.6.9016,     https://github.com/insightsengineering/tern/},   url = {https://insightsengineering.github.io/tern/main/}, }"},{"path":"https://insightsengineering.github.io/tern/main/index.html","id":"tern-","dir":"","previous_headings":"","what":"Create Common TLGs Used in Clinical Trials","title":"Create Common TLGs Used in Clinical Trials","text":"tern R package contains analysis functions create tables graphs used clinical trial reporting. package provides large range functionality, : Data visualizations: Line plots (g_lineplot) Kaplan-Meier plots (g_km) Forest plots (g_forest) STEP graphs (g_step) Individual patient plots (g_ipp) Waterfall plots (g_waterfall) Bland-Altman plots (g_bland_altman) Statistical model fit summaries: Logistic regression (summarize_logistic) Cox regression (summarize_coxreg) Analysis tables: See list available analyze functions See list available summarize functions See list available column-wise analysis functions Many outputs available added teal shiny applications interactive exploration data. teal modules available teal.modules.clinical package. See TLG Catalog extensive catalog example clinical trial tables, listings, graphs created using tern functionality.","code":""},{"path":"https://insightsengineering.github.io/tern/main/index.html","id":"installation","dir":"","previous_headings":"","what":"Installation","title":"Create Common TLGs Used in Clinical Trials","text":"tern available CRAN can install latest released version : can install latest development version directly GitHub running following:","code":"install.packages(\"tern\") # install.packages(\"pak\") pak::pak(\"insightsengineering/tern\")"},{"path":"https://insightsengineering.github.io/tern/main/index.html","id":"usage","dir":"","previous_headings":"","what":"Usage","title":"Create Common TLGs Used in Clinical Trials","text":"understand use package, please refer Introduction tern article, provides multiple examples code implementation. See package vignettes browseVignettes(package = \"tern\") usage package.","code":""},{"path":"https://insightsengineering.github.io/tern/main/index.html","id":"related","dir":"","previous_headings":"","what":"Related","title":"Create Common TLGs Used in Clinical Trials","text":"rtables - table engine used tlg-catalog - website showcasing many examples clinical trial tables, listings, graphs teal.modules.clinical - teal modules interactive data analysis","code":""},{"path":"https://insightsengineering.github.io/tern/main/index.html","id":"acknowledgment","dir":"","previous_headings":"","what":"Acknowledgment","title":"Create Common TLGs Used in Clinical Trials","text":"package result joint efforts many developers stakeholders. like thank everyone contributed far!","code":""},{"path":[]},{"path":[]},{"path":[]},{"path":"https://insightsengineering.github.io/tern/main/reference/abnormal.html","id":null,"dir":"Reference","previous_headings":"","what":"Count patients with abnormal range values — abnormal","title":"Count patients with abnormal range values — abnormal","text":"analyze function count_abnormal() creates layout element count patients abnormal analysis range values direction. function analyzes primary analysis variable var indicates abnormal range results. Additional analysis variables can supplied list via variables parameter id (defaults USUBJID), variable indicate unique subject identifiers, baseline (defaults BNRIND), variable indicate baseline reference ranges. direction specified via abnormal parameter (e.g. High Low), fraction patient counts returned, numerator denominator calculated follows: num: number patients abnormality recorded treatment. denom: total number patients least one post-baseline assessment. function assumes df filtered include post-baseline records.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/abnormal.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Count patients with abnormal range values — abnormal","text":"","code":"count_abnormal(   lyt,   var,   abnormal = list(Low = \"LOW\", High = \"HIGH\"),   variables = list(id = \"USUBJID\", baseline = \"BNRIND\"),   exclude_base_abn = FALSE,   na_str = default_na_str(),   nested = TRUE,   ...,   table_names = var,   .stats = NULL,   .formats = NULL,   .labels = NULL,   .indent_mods = NULL )  s_count_abnormal(   df,   .var,   abnormal = list(Low = \"LOW\", High = \"HIGH\"),   variables = list(id = \"USUBJID\", baseline = \"BNRIND\"),   exclude_base_abn = FALSE )  a_count_abnormal(   df,   .var,   abnormal = list(Low = \"LOW\", High = \"HIGH\"),   variables = list(id = \"USUBJID\", baseline = \"BNRIND\"),   exclude_base_abn = FALSE )"},{"path":"https://insightsengineering.github.io/tern/main/reference/abnormal.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Count patients with abnormal range values — abnormal","text":"lyt (PreDataTableLayouts) layout analyses added . abnormal (named list) list identifying abnormal range level(s) var. Defaults list(Low = \"LOW\", High = \"HIGH\") can also group different levels named list, example, abnormal = list(Low = c(\"LOW\", \"LOW LOW\"), High = c(\"HIGH\", \"HIGH HIGH\")). variables (named list string) list additional analysis variables. exclude_base_abn (flag) whether exclude subjects baseline abnormality numerator denominator. na_str (string) string used replace NA empty values output. nested (flag) whether layout instruction applied within existing layout structure _if possible (TRUE, default) new top-level element (FALSE). Ignored nest split. underneath analyses, allowed. ... additional arguments lower level functions. table_names (character) can customized case vars analyzed multiple times, avoid warnings rtables. .stats (character) statistics select table. Options : 'fraction' .formats (named character list) formats statistics. See Details analyze_vars information \"auto\" setting. .labels (named character) labels statistics (without indent). .indent_mods (named integer) indent modifiers labels. Defaults 0, corresponds unmodified default behavior. Can negative. df (data.frame) data set containing analysis variables. .var, var (string) single variable name passed rtables requested statistics function.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/abnormal.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Count patients with abnormal range values — abnormal","text":"count_abnormal() returns layout object suitable passing layouting functions, rtables::build_table(). Adding function rtable layout add formatted rows containing statistics s_count_abnormal() table layout. s_count_abnormal() returns statistic fraction vector num denom counts patients. a_count_abnormal() returns corresponding list formatted rtables::CellValue().","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/abnormal.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Count patients with abnormal range values — abnormal","text":"count_abnormal(): Layout-creating function can take statistics function arguments additional format arguments. function wrapper rtables::analyze(). s_count_abnormal(): Statistics function counts patients abnormal range values single abnormal level. a_count_abnormal(): Formatted analysis function used afun count_abnormal().","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/abnormal.html","id":"note","dir":"Reference","previous_headings":"","what":"Note","title":"Count patients with abnormal range values — abnormal","text":"count_abnormal() considers single variable contains multiple abnormal levels. df filtered include post-baseline records. denominator includes patients may abnormal levels baseline, patients missing baseline records. Patients abnormalities baseline can optionally excluded numerator denominator via exclude_base_abn parameter.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/abnormal.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Count patients with abnormal range values — abnormal","text":"","code":"library(dplyr) #>  #> Attaching package: ‘dplyr’ #> The following object is masked from ‘package:testthat’: #>  #>     matches #> The following objects are masked from ‘package:stats’: #>  #>     filter, lag #> The following objects are masked from ‘package:base’: #>  #>     intersect, setdiff, setequal, union  df <- data.frame(   USUBJID = as.character(c(1, 1, 2, 2)),   ANRIND = factor(c(\"NORMAL\", \"LOW\", \"HIGH\", \"HIGH\")),   BNRIND = factor(c(\"NORMAL\", \"NORMAL\", \"HIGH\", \"HIGH\")),   ONTRTFL = c(\"\", \"Y\", \"\", \"Y\"),   stringsAsFactors = FALSE )  # Select only post-baseline records. df <- df %>%   filter(ONTRTFL == \"Y\")  # Layout creating function. basic_table() %>%   count_abnormal(var = \"ANRIND\", abnormal = list(high = \"HIGH\", low = \"LOW\")) %>%   build_table(df) #>         all obs  #> ———————————————— #> high   1/2 (50%) #> low    1/2 (50%)  # Passing of statistics function and formatting arguments. df2 <- data.frame(   ID = as.character(c(1, 1, 2, 2)),   RANGE = factor(c(\"NORMAL\", \"LOW\", \"HIGH\", \"HIGH\")),   BL_RANGE = factor(c(\"NORMAL\", \"NORMAL\", \"HIGH\", \"HIGH\")),   ONTRTFL = c(\"\", \"Y\", \"\", \"Y\"),   stringsAsFactors = FALSE )  # Select only post-baseline records. df2 <- df2 %>%   filter(ONTRTFL == \"Y\")  basic_table() %>%   count_abnormal(     var = \"RANGE\",     abnormal = list(low = \"LOW\", high = \"HIGH\"),     variables = list(id = \"ID\", baseline = \"BL_RANGE\")   ) %>%   build_table(df2) #>         all obs  #> ———————————————— #> low    1/2 (50%) #> high   1/2 (50%)"},{"path":"https://insightsengineering.github.io/tern/main/reference/abnormal_by_baseline.html","id":null,"dir":"Reference","previous_headings":"","what":"Count patients with abnormal analysis range values by baseline status — abnormal_by_baseline","title":"Count patients with abnormal analysis range values by baseline status — abnormal_by_baseline","text":"analyze function count_abnormal_by_baseline() creates layout element count patients abnormal analysis range values, categorized baseline status. function analyzes primary analysis variable var indicates abnormal range results. Additional analysis variables can supplied list via variables parameter id (defaults USUBJID), variable indicate unique subject identifiers, baseline (defaults BNRIND), variable indicate baseline reference ranges. direction specified via abnormal parameter (e.g. High Low), condition baseline range result count patients numerator denominator follows following categories: <abnormality> num:  number patients without abnormality baseline (excluding missing baseline) least one abnormality post-baseline. denom: number patients without abnormality baseline (excluding missing baseline). <Abnormality> num: number patients abnormality baseline least one abnormality post-baseline. denom: number patients abnormality baseline. Total num: number patients least one post-baseline record least one abnormality post-baseline. denom: number patients least one post-baseline record. function assumes df filtered include post-baseline records.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/abnormal_by_baseline.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Count patients with abnormal analysis range values by baseline status — abnormal_by_baseline","text":"","code":"count_abnormal_by_baseline(   lyt,   var,   abnormal,   variables = list(id = \"USUBJID\", baseline = \"BNRIND\"),   na_str = \"<Missing>\",   nested = TRUE,   ...,   table_names = abnormal,   .stats = NULL,   .formats = NULL,   .labels = NULL,   .indent_mods = NULL )  s_count_abnormal_by_baseline(   df,   .var,   abnormal,   na_str = \"<Missing>\",   variables = list(id = \"USUBJID\", baseline = \"BNRIND\") )  a_count_abnormal_by_baseline(   df,   .var,   abnormal,   na_str = \"<Missing>\",   variables = list(id = \"USUBJID\", baseline = \"BNRIND\") )"},{"path":"https://insightsengineering.github.io/tern/main/reference/abnormal_by_baseline.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Count patients with abnormal analysis range values by baseline status — abnormal_by_baseline","text":"lyt (PreDataTableLayouts) layout analyses added . abnormal (character) values identifying abnormal range level(s) .var. variables (named list string) list additional analysis variables. na_str (string) explicit na_level argument used pre-processing steps (maybe df_explicit_na()). default \"<Missing>\". nested (flag) whether layout instruction applied within existing layout structure _if possible (TRUE, default) new top-level element (FALSE). Ignored nest split. underneath analyses, allowed. ... additional arguments lower level functions. table_names (character) can customized case vars analyzed multiple times, avoid warnings rtables. .stats (character) statistics select table. Options : 'fraction' .formats (named character list) formats statistics. See Details analyze_vars information \"auto\" setting. .labels (named character) labels statistics (without indent). .indent_mods (named integer) indent modifiers labels. Defaults 0, corresponds unmodified default behavior. Can negative. df (data.frame) data set containing analysis variables. .var, var (string) single variable name passed rtables requested statistics function.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/abnormal_by_baseline.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Count patients with abnormal analysis range values by baseline status — abnormal_by_baseline","text":"count_abnormal_by_baseline() returns layout object suitable passing layouting functions, rtables::build_table(). Adding function rtable layout add formatted rows containing statistics s_count_abnormal_by_baseline() table layout. s_count_abnormal_by_baseline() returns statistic fraction named list 3 labeled elements: not_abnormal, abnormal, total. element contains vector num denom patient counts. a_count_abnormal_by_baseline() returns corresponding list formatted rtables::CellValue().","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/abnormal_by_baseline.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Count patients with abnormal analysis range values by baseline status — abnormal_by_baseline","text":"count_abnormal_by_baseline(): Layout-creating function can take statistics function arguments additional format arguments. function wrapper rtables::analyze(). s_count_abnormal_by_baseline(): Statistics function single abnormal level. a_count_abnormal_by_baseline(): Formatted analysis function used afun count_abnormal_by_baseline().","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/abnormal_by_baseline.html","id":"note","dir":"Reference","previous_headings":"","what":"Note","title":"Count patients with abnormal analysis range values by baseline status — abnormal_by_baseline","text":"df filtered include post-baseline records. baseline variable analysis variable contains NA records, expected df pre-processed using df_explicit_na() explicit_na().","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/main/reference/abnormal_by_baseline.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Count patients with abnormal analysis range values by baseline status — abnormal_by_baseline","text":"","code":"df <- data.frame(   USUBJID = as.character(c(1:6)),   ANRIND = factor(c(rep(\"LOW\", 4), \"NORMAL\", \"HIGH\")),   BNRIND = factor(c(\"LOW\", \"NORMAL\", \"HIGH\", NA, \"LOW\", \"NORMAL\")) ) df <- df_explicit_na(df)  # Layout creating function. basic_table() %>%   count_abnormal_by_baseline(var = \"ANRIND\", abnormal = c(High = \"HIGH\")) %>%   build_table(df) #>                all obs   #> ———————————————————————— #> High                     #>   Not high    1/4 (25%)  #>   High           0/1     #>   Total      1/6 (16.7%)  # Passing of statistics function and formatting arguments. df2 <- data.frame(   ID = as.character(c(1, 2, 3, 4)),   RANGE = factor(c(\"NORMAL\", \"LOW\", \"HIGH\", \"HIGH\")),   BLRANGE = factor(c(\"LOW\", \"HIGH\", \"HIGH\", \"NORMAL\")) )  basic_table() %>%   count_abnormal_by_baseline(     var = \"RANGE\",     abnormal = c(Low = \"LOW\"),     variables = list(id = \"ID\", baseline = \"BLRANGE\"),     .formats = c(fraction = \"xx / xx\"),     .indent_mods = c(fraction = 2L)   ) %>%   build_table(df2) #>                 all obs #> ——————————————————————— #> Low                     #>       Not low    1 / 3  #>       Low        0 / 1  #>       Total      1 / 4"},{"path":"https://insightsengineering.github.io/tern/main/reference/abnormal_by_marked.html","id":null,"dir":"Reference","previous_headings":"","what":"Count patients with marked laboratory abnormalities — abnormal_by_marked","title":"Count patients with marked laboratory abnormalities — abnormal_by_marked","text":"analyze function count_abnormal_by_marked() creates layout element count patients marked laboratory abnormalities direction abnormality, categorized parameter value. function analyzes primary analysis variable var indicates whether single, replicated, last marked laboratory abnormality observed. Levels var include marked lab abnormality (single last_replicated) can supplied via category parameter. Additional analysis variables can supplied list via variables parameter id (defaults USUBJID), variable indicate unique subject identifiers, param (defaults PARAM), variable indicate parameter values, direction (defaults abn_dir), variable indicate abnormality directions. combination param direction levels, marked lab abnormality counts calculated follows: Single, last & Last replicated: number patients Single, last Last replicated values, respectively. : number patients either single replicated marked abnormalities. Fractions calculated dividing counts number patients least one valid measurement recorded analysis. Prior using function table layout must use rtables::split_rows_by() create two row splits, one variable param one variable direction.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/abnormal_by_marked.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Count patients with marked laboratory abnormalities — abnormal_by_marked","text":"","code":"count_abnormal_by_marked(   lyt,   var,   category = list(single = \"SINGLE\", last_replicated = c(\"LAST\", \"REPLICATED\")),   variables = list(id = \"USUBJID\", param = \"PARAM\", direction = \"abn_dir\"),   na_str = default_na_str(),   nested = TRUE,   ...,   .stats = NULL,   .formats = NULL,   .labels = NULL,   .indent_mods = NULL )  s_count_abnormal_by_marked(   df,   .var = \"AVALCAT1\",   .spl_context,   category = list(single = \"SINGLE\", last_replicated = c(\"LAST\", \"REPLICATED\")),   variables = list(id = \"USUBJID\", param = \"PARAM\", direction = \"abn_dir\") )  a_count_abnormal_by_marked(   df,   .var = \"AVALCAT1\",   .spl_context,   category = list(single = \"SINGLE\", last_replicated = c(\"LAST\", \"REPLICATED\")),   variables = list(id = \"USUBJID\", param = \"PARAM\", direction = \"abn_dir\") )"},{"path":"https://insightsengineering.github.io/tern/main/reference/abnormal_by_marked.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Count patients with marked laboratory abnormalities — abnormal_by_marked","text":"lyt (PreDataTableLayouts) layout analyses added . category (list) list different marked category names single last replicated. variables (named list string) list additional analysis variables. na_str (string) string used replace NA empty values output. nested (flag) whether layout instruction applied within existing layout structure _if possible (TRUE, default) new top-level element (FALSE). Ignored nest split. underneath analyses, allowed. ... additional arguments lower level functions. .stats (character) statistics select table. Options : 'count_fraction', 'count_fraction_fixed_dp' .formats (named character list) formats statistics. See Details analyze_vars information \"auto\" setting. .labels (named character) labels statistics (without indent). .indent_mods (named integer) indent modifiers labels. Defaults 0, corresponds unmodified default behavior. Can negative. df (data.frame) data set containing analysis variables. .var, var (string) single variable name passed rtables requested statistics function. .spl_context (data.frame) gives information ancestor split states passed rtables.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/abnormal_by_marked.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Count patients with marked laboratory abnormalities — abnormal_by_marked","text":"count_abnormal_by_marked() returns layout object suitable passing layouting functions, rtables::build_table(). Adding function rtable layout add formatted rows containing statistics s_count_abnormal_by_marked() table layout. s_count_abnormal_by_marked() returns statistic count_fraction Single, last, Last replicated, results. a_count_abnormal_by_marked() returns corresponding list formatted rtables::CellValue().","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/abnormal_by_marked.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Count patients with marked laboratory abnormalities — abnormal_by_marked","text":"count_abnormal_by_marked(): Layout-creating function can take statistics function arguments additional format arguments. function wrapper rtables::analyze(). s_count_abnormal_by_marked(): Statistics function patients marked lab abnormalities. a_count_abnormal_by_marked(): Formatted analysis function used afun count_abnormal_by_marked().","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/abnormal_by_marked.html","id":"note","dir":"Reference","previous_headings":"","what":"Note","title":"Count patients with marked laboratory abnormalities — abnormal_by_marked","text":"Single, last Last replicated levels mutually exclusive. patient abnormalities meet Single, last Last replicated criteria, patient counted Last replicated category.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/abnormal_by_marked.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Count patients with marked laboratory abnormalities — abnormal_by_marked","text":"","code":"library(dplyr)  df <- data.frame(   USUBJID = as.character(c(rep(1, 5), rep(2, 5), rep(1, 5), rep(2, 5))),   ARMCD = factor(c(rep(\"ARM A\", 5), rep(\"ARM B\", 5), rep(\"ARM A\", 5), rep(\"ARM B\", 5))),   ANRIND = factor(c(     \"NORMAL\", \"HIGH\", \"HIGH\", \"HIGH HIGH\", \"HIGH\",     \"HIGH\", \"HIGH\", \"HIGH HIGH\", \"NORMAL\", \"HIGH HIGH\", \"NORMAL\", \"LOW\", \"LOW\", \"LOW LOW\", \"LOW\",     \"LOW\", \"LOW\", \"LOW LOW\", \"NORMAL\", \"LOW LOW\"   )),   ONTRTFL = rep(c(\"\", \"Y\", \"Y\", \"Y\", \"Y\", \"Y\", \"Y\", \"Y\", \"Y\", \"Y\"), 2),   PARAMCD = factor(c(rep(\"CRP\", 10), rep(\"ALT\", 10))),   AVALCAT1 = factor(rep(c(\"\", \"\", \"\", \"SINGLE\", \"REPLICATED\", \"\", \"\", \"LAST\", \"\", \"SINGLE\"), 2)),   stringsAsFactors = FALSE )  df <- df %>%   mutate(abn_dir = factor(     case_when(       ANRIND == \"LOW LOW\" ~ \"Low\",       ANRIND == \"HIGH HIGH\" ~ \"High\",       TRUE ~ \"\"     ),     levels = c(\"Low\", \"High\")   ))  # Select only post-baseline records. df <- df %>% filter(ONTRTFL == \"Y\") df_crp <- df %>%   filter(PARAMCD == \"CRP\") %>%   droplevels() full_parent_df <- list(df_crp, \"not_needed\") cur_col_subset <- list(rep(TRUE, nrow(df_crp)), \"not_needed\") spl_context <- data.frame(   split = c(\"PARAMCD\", \"GRADE_DIR\"),   full_parent_df = I(full_parent_df),   cur_col_subset = I(cur_col_subset) )  map <- unique(   df[df$abn_dir %in% c(\"Low\", \"High\") & df$AVALCAT1 != \"\", c(\"PARAMCD\", \"abn_dir\")] ) %>%   lapply(as.character) %>%   as.data.frame() %>%   arrange(PARAMCD, abn_dir)  basic_table() %>%   split_cols_by(\"ARMCD\") %>%   split_rows_by(\"PARAMCD\") %>%   summarize_num_patients(     var = \"USUBJID\",     .stats = \"unique_count\"   ) %>%   split_rows_by(     \"abn_dir\",     split_fun = trim_levels_to_map(map)   ) %>%   count_abnormal_by_marked(     var = \"AVALCAT1\",     variables = list(       id = \"USUBJID\",       param = \"PARAMCD\",       direction = \"abn_dir\"     )   ) %>%   build_table(df = df) #>                           ARM A      ARM B   #> ———————————————————————————————————————————— #> ALT (n)                     1          1     #>   Low                                        #>     Single, not last     1 (100%)      0     #>     Last or replicated      0       1 (100%) #>     Any Abnormality      1 (100%)   1 (100%) #> CRP (n)                     1          1     #>   High                                       #>     Single, not last     1 (100%)      0     #>     Last or replicated      0       1 (100%) #>     Any Abnormality      1 (100%)   1 (100%)  basic_table() %>%   split_cols_by(\"ARMCD\") %>%   split_rows_by(\"PARAMCD\") %>%   summarize_num_patients(     var = \"USUBJID\",     .stats = \"unique_count\"   ) %>%   split_rows_by(     \"abn_dir\",     split_fun = trim_levels_in_group(\"abn_dir\")   ) %>%   count_abnormal_by_marked(     var = \"AVALCAT1\",     variables = list(       id = \"USUBJID\",       param = \"PARAMCD\",       direction = \"abn_dir\"     )   ) %>%   build_table(df = df) #>                           ARM A      ARM B   #> ———————————————————————————————————————————— #> ALT (n)                     1          1     #>   Low                                        #>     Single, not last     1 (100%)      0     #>     Last or replicated      0       1 (100%) #>     Any Abnormality      1 (100%)   1 (100%) #> CRP (n)                     1          1     #>   High                                       #>     Single, not last     1 (100%)      0     #>     Last or replicated      0       1 (100%) #>     Any Abnormality      1 (100%)   1 (100%)"},{"path":"https://insightsengineering.github.io/tern/main/reference/abnormal_by_worst_grade.html","id":null,"dir":"Reference","previous_headings":"","what":"Count patients by most extreme post-baseline toxicity grade per direction of abnormality — abnormal_by_worst_grade","title":"Count patients by most extreme post-baseline toxicity grade per direction of abnormality — abnormal_by_worst_grade","text":"analyze function count_abnormal_by_worst_grade() creates layout element count patients highest (worst) analysis toxicity grade post-baseline direction, categorized parameter value. function analyzes primary analysis variable var indicates toxicity grades. Additional analysis variables can supplied list via variables parameter id (defaults USUBJID), variable indicate unique subject identifiers, param (defaults PARAM), variable indicate parameter values, grade_dir (defaults GRADE_DIR), variable indicate directions (e.g. High Low) toxicity grade supplied var. combination param grade_dir levels, patient counts worst grade calculated follows: 1 4: number patients worst grades 1-4, respectively. : number patients least one abnormality (.e. grade 0). Fractions calculated dividing counts number patients least one valid measurement recorded treatment. Pre-processing crucial using function can done automatically using h_adlb_abnormal_by_worst_grade() helper function. See description function details necessary pre-processing steps. Prior using function table layout must use rtables::split_rows_by() create two row splits, one variable param one variable grade_dir.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/abnormal_by_worst_grade.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Count patients by most extreme post-baseline toxicity grade per direction of abnormality — abnormal_by_worst_grade","text":"","code":"count_abnormal_by_worst_grade(   lyt,   var,   variables = list(id = \"USUBJID\", param = \"PARAM\", grade_dir = \"GRADE_DIR\"),   na_str = default_na_str(),   nested = TRUE,   ...,   .stats = NULL,   .formats = NULL,   .labels = NULL,   .indent_mods = NULL )  s_count_abnormal_by_worst_grade(   df,   .var = \"GRADE_ANL\",   .spl_context,   variables = list(id = \"USUBJID\", param = \"PARAM\", grade_dir = \"GRADE_DIR\") )  a_count_abnormal_by_worst_grade(   df,   .var = \"GRADE_ANL\",   .spl_context,   variables = list(id = \"USUBJID\", param = \"PARAM\", grade_dir = \"GRADE_DIR\") )"},{"path":"https://insightsengineering.github.io/tern/main/reference/abnormal_by_worst_grade.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Count patients by most extreme post-baseline toxicity grade per direction of abnormality — abnormal_by_worst_grade","text":"lyt (PreDataTableLayouts) layout analyses added . variables (named list string) list additional analysis variables. na_str (string) string used replace NA empty values output. nested (flag) whether layout instruction applied within existing layout structure _if possible (TRUE, default) new top-level element (FALSE). Ignored nest split. underneath analyses, allowed. ... additional arguments lower level functions. .stats (character) statistics select table. Options : 'count_fraction', 'count_fraction_fixed_dp' .formats (named character list) formats statistics. See Details analyze_vars information \"auto\" setting. .labels (named character) labels statistics (without indent). .indent_mods (named integer) indent modifiers labels. Defaults 0, corresponds unmodified default behavior. Can negative. df (data.frame) data set containing analysis variables. .var, var (string) single variable name passed rtables requested statistics function. .spl_context (data.frame) gives information ancestor split states passed rtables.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/abnormal_by_worst_grade.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Count patients by most extreme post-baseline toxicity grade per direction of abnormality — abnormal_by_worst_grade","text":"count_abnormal_by_worst_grade() returns layout object suitable passing layouting functions, rtables::build_table(). Adding function rtable layout add formatted rows containing statistics s_count_abnormal_by_worst_grade() table layout. s_count_abnormal_by_worst_grade() returns single statistic count_fraction grades 1 4 \"\" results. a_count_abnormal_by_worst_grade() returns corresponding list formatted rtables::CellValue().","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/abnormal_by_worst_grade.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Count patients by most extreme post-baseline toxicity grade per direction of abnormality — abnormal_by_worst_grade","text":"count_abnormal_by_worst_grade(): Layout-creating function can take statistics function arguments additional format arguments. function wrapper rtables::analyze(). s_count_abnormal_by_worst_grade(): Statistics function counts patients worst grade. a_count_abnormal_by_worst_grade(): Formatted analysis function used afun count_abnormal_by_worst_grade().","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/main/reference/abnormal_by_worst_grade.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Count patients by most extreme post-baseline toxicity grade per direction of abnormality — abnormal_by_worst_grade","text":"","code":"library(dplyr) library(forcats) adlb <- tern_ex_adlb  # Data is modified in order to have some parameters with grades only in one direction # and simulate the real data. adlb$ATOXGR[adlb$PARAMCD == \"ALT\" & adlb$ATOXGR %in% c(\"1\", \"2\", \"3\", \"4\")] <- \"-1\" adlb$ANRIND[adlb$PARAMCD == \"ALT\" & adlb$ANRIND == \"HIGH\"] <- \"LOW\" adlb$WGRHIFL[adlb$PARAMCD == \"ALT\"] <- \"\"  adlb$ATOXGR[adlb$PARAMCD == \"IGA\" & adlb$ATOXGR %in% c(\"-1\", \"-2\", \"-3\", \"-4\")] <- \"1\" adlb$ANRIND[adlb$PARAMCD == \"IGA\" & adlb$ANRIND == \"LOW\"] <- \"HIGH\" adlb$WGRLOFL[adlb$PARAMCD == \"IGA\"] <- \"\"  # Pre-processing adlb_f <- adlb %>% h_adlb_abnormal_by_worst_grade()  # Map excludes records without abnormal grade since they should not be displayed # in the table. map <- unique(adlb_f[adlb_f$GRADE_DIR != \"ZERO\", c(\"PARAM\", \"GRADE_DIR\", \"GRADE_ANL\")]) %>%   lapply(as.character) %>%   as.data.frame() %>%   arrange(PARAM, desc(GRADE_DIR), GRADE_ANL)  basic_table() %>%   split_cols_by(\"ARMCD\") %>%   split_rows_by(\"PARAM\") %>%   split_rows_by(\"GRADE_DIR\", split_fun = trim_levels_to_map(map)) %>%   count_abnormal_by_worst_grade(     var = \"GRADE_ANL\",     variables = list(id = \"USUBJID\", param = \"PARAM\", grade_dir = \"GRADE_DIR\")   ) %>%   build_table(df = adlb_f) #>                                          ARM A        ARM B        ARM C    #> ——————————————————————————————————————————————————————————————————————————— #> Alanine Aminotransferase Measurement                                        #>   LOW                                                                       #>     1                                  12 (17.4%)    5 (6.8%)    8 (13.8%)  #>     2                                   9 (13%)     13 (17.8%)   6 (10.3%)  #>     3                                   6 (8.7%)     4 (5.5%)    6 (10.3%)  #>     4                                  7 (10.1%)     7 (9.6%)    6 (10.3%)  #>     Any                                34 (49.3%)   29 (39.7%)   26 (44.8%) #> C-Reactive Protein Measurement                                              #>   LOW                                                                       #>     1                                  11 (15.9%)   12 (16.4%)   7 (12.1%)  #>     2                                  8 (11.6%)     2 (2.7%)    6 (10.3%)  #>     3                                   4 (5.8%)    9 (12.3%)    6 (10.3%)  #>     4                                  7 (10.1%)     6 (8.2%)     4 (6.9%)  #>     Any                                30 (43.5%)   29 (39.7%)   23 (39.7%) #>   HIGH                                                                      #>     1                                  8 (11.6%)    11 (15.1%)    2 (3.4%)  #>     2                                   9 (13%)     11 (15.1%)    11 (19%)  #>     3                                  14 (20.3%)   10 (13.7%)    5 (8.6%)  #>     4                                   2 (2.9%)     4 (5.5%)    6 (10.3%)  #>     Any                                33 (47.8%)   36 (49.3%)   24 (41.4%) #> Immunoglobulin A Measurement                                                #>   HIGH                                                                      #>     1                                  7 (10.1%)     7 (9.6%)    6 (10.3%)  #>     2                                  8 (11.6%)     6 (8.2%)    8 (13.8%)  #>     3                                  7 (10.1%)     5 (6.8%)    9 (15.5%)  #>     4                                   6 (8.7%)     2 (2.7%)     3 (5.2%)  #>     Any                                28 (40.6%)   20 (27.4%)   26 (44.8%)"},{"path":"https://insightsengineering.github.io/tern/main/reference/abnormal_by_worst_grade_worsen.html","id":null,"dir":"Reference","previous_headings":"","what":"Count patients with toxicity grades that have worsened from baseline by highest grade post-baseline — abnormal_by_worst_grade_worsen","title":"Count patients with toxicity grades that have worsened from baseline by highest grade post-baseline — abnormal_by_worst_grade_worsen","text":"analyze function count_abnormal_lab_worsen_by_baseline() creates layout element count patients analysis toxicity grades worsened baseline, categorized highest (worst) grade post-baseline. function analyzes primary analysis variable var indicates analysis toxicity grades. Additional analysis variables can supplied list via variables parameter id (defaults USUBJID), variable indicate unique subject identifiers, baseline_var (defaults BTOXGR), variable indicate baseline toxicity grades, direction_var (defaults GRADDIR), variable indicate toxicity grade directions interest include (e.g. \"H\" (high), \"L\" (low), \"B\" ()). direction(s) specified direction_var, patient counts worst grade patients worsened baseline calculated follows: 1 4: number patients worsened baseline grades worst grades 1-4, respectively. : total number patients worsened baseline grades. Fractions calculated dividing counts number patients analysis toxicity grades worsened baseline toxicity grades treatment. Prior using function table layout must use rtables::split_rows_by() create row split variable direction_var.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/abnormal_by_worst_grade_worsen.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Count patients with toxicity grades that have worsened from baseline by highest grade post-baseline — abnormal_by_worst_grade_worsen","text":"","code":"count_abnormal_lab_worsen_by_baseline(   lyt,   var,   variables = list(id = \"USUBJID\", baseline_var = \"BTOXGR\", direction_var = \"GRADDR\"),   na_str = default_na_str(),   nested = TRUE,   ...,   table_names = NULL,   .stats = NULL,   .formats = NULL,   .labels = NULL,   .indent_mods = NULL )  s_count_abnormal_lab_worsen_by_baseline(   df,   .var = \"ATOXGR\",   variables = list(id = \"USUBJID\", baseline_var = \"BTOXGR\", direction_var = \"GRADDR\") )  a_count_abnormal_lab_worsen_by_baseline(   df,   .var = \"ATOXGR\",   variables = list(id = \"USUBJID\", baseline_var = \"BTOXGR\", direction_var = \"GRADDR\") )"},{"path":"https://insightsengineering.github.io/tern/main/reference/abnormal_by_worst_grade_worsen.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Count patients with toxicity grades that have worsened from baseline by highest grade post-baseline — abnormal_by_worst_grade_worsen","text":"lyt (PreDataTableLayouts) layout analyses added . variables (named list string) list additional analysis variables including: id (string) subject variable name. baseline_var (string) name data column containing baseline toxicity variable. direction_var (string) see direction_var details. na_str (string) string used replace NA empty values output. nested (flag) whether layout instruction applied within existing layout structure _if possible (TRUE, default) new top-level element (FALSE). Ignored nest split. underneath analyses, allowed. ... additional arguments lower level functions. table_names (character) can customized case vars analyzed multiple times, avoid warnings rtables. .stats (character) statistics select table. Options : 'fraction' .formats (named character list) formats statistics. See Details analyze_vars information \"auto\" setting. .labels (named character) labels statistics (without indent). .indent_mods (named integer) indent modifiers labels. Defaults 0, corresponds unmodified default behavior. Can negative. df (data.frame) data set containing analysis variables. .var, var (string) single variable name passed rtables requested statistics function.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/abnormal_by_worst_grade_worsen.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Count patients with toxicity grades that have worsened from baseline by highest grade post-baseline — abnormal_by_worst_grade_worsen","text":"count_abnormal_lab_worsen_by_baseline() returns layout object suitable passing layouting functions, rtables::build_table(). Adding function rtable layout add formatted rows containing statistics s_count_abnormal_lab_worsen_by_baseline() table layout. s_count_abnormal_lab_worsen_by_baseline() returns counts fraction patients whose worst post-baseline lab grades worse baseline grades, post-baseline worst grades \"1\", \"2\", \"3\", \"4\" \"\". a_count_abnormal_lab_worsen_by_baseline() returns corresponding list formatted rtables::CellValue().","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/abnormal_by_worst_grade_worsen.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Count patients with toxicity grades that have worsened from baseline by highest grade post-baseline — abnormal_by_worst_grade_worsen","text":"count_abnormal_lab_worsen_by_baseline(): Layout-creating function can take statistics function arguments additional format arguments. function wrapper rtables::analyze(). s_count_abnormal_lab_worsen_by_baseline(): Statistics function patients whose worst post-baseline lab grades worse baseline grades. a_count_abnormal_lab_worsen_by_baseline(): Formatted analysis function used afun count_abnormal_lab_worsen_by_baseline().","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/main/reference/abnormal_by_worst_grade_worsen.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Count patients with toxicity grades that have worsened from baseline by highest grade post-baseline — abnormal_by_worst_grade_worsen","text":"","code":"library(dplyr)  # The direction variable, GRADDR, is based on metadata adlb <- tern_ex_adlb %>%   mutate(     GRADDR = case_when(       PARAMCD == \"ALT\" ~ \"B\",       PARAMCD == \"CRP\" ~ \"L\",       PARAMCD == \"IGA\" ~ \"H\"     )   ) %>%   filter(SAFFL == \"Y\" & ONTRTFL == \"Y\" & GRADDR != \"\")  df <- h_adlb_worsen(   adlb,   worst_flag_low = c(\"WGRLOFL\" = \"Y\"),   worst_flag_high = c(\"WGRHIFL\" = \"Y\"),   direction_var = \"GRADDR\" )  basic_table() %>%   split_cols_by(\"ARMCD\") %>%   add_colcounts() %>%   split_rows_by(\"PARAMCD\") %>%   split_rows_by(\"GRADDR\") %>%   count_abnormal_lab_worsen_by_baseline(     var = \"ATOXGR\",     variables = list(       id = \"USUBJID\",       baseline_var = \"BTOXGR\",       direction_var = \"GRADDR\"     )   ) %>%   append_topleft(\"Direction of Abnormality\") %>%   build_table(df = df, alt_counts_df = tern_ex_adsl) #>                                ARM A           ARM B           ARM C     #> Direction of Abnormality      (N=69)          (N=73)          (N=58)     #> ———————————————————————————————————————————————————————————————————————— #> IGA                                                                      #>   High                                                                   #>     1                       6/63 (9.5%)     6/64 (9.4%)      4/50 (8%)   #>     2                      8/64 (12.5%)     5/67 (7.5%)    8/53 (15.1%)  #>     3                      7/66 (10.6%)     5/68 (7.4%)    9/57 (15.8%)  #>     4                       6/68 (8.8%)     2/72 (2.8%)     3/58 (5.2%)  #>     Any                    27/68 (39.7%)    18/72 (25%)    24/58 (41.4%) #> ALT                                                                      #>   High                                                                   #>     1                      7/63 (11.1%)     6/62 (9.7%)     2/48 (4.2%)  #>     2                       12/63 (19%)      4/67 (6%)      11/50 (22%)  #>     3                       4/65 (6.2%)    11/71 (15.5%)   7/56 (12.5%)  #>     4                       1/67 (1.5%)    8/71 (11.3%)      4/57 (7%)   #>     Any                    24/67 (35.8%)   29/71 (40.8%)   24/57 (42.1%) #>   Low                                                                    #>     1                      12/67 (17.9%)    4/66 (6.1%)    7/52 (13.5%)  #>     2                      9/68 (13.2%)    12/69 (17.4%)   6/55 (10.9%)  #>     3                       6/69 (8.7%)     4/71 (5.6%)     5/56 (8.9%)  #>     4                      7/69 (10.1%)     7/73 (9.6%)    6/58 (10.3%)  #>     Any                    34/69 (49.3%)    27/73 (37%)    24/58 (41.4%) #> CRP                                                                      #>   Low                                                                    #>     1                      11/66 (16.7%)   10/67 (14.9%)    4/47 (8.5%)  #>     2                      8/66 (12.1%)     1/70 (1.4%)     6/50 (12%)   #>     3                       4/68 (5.9%)    9/70 (12.9%)     5/53 (9.4%)  #>     4                      7/69 (10.1%)     6/72 (8.3%)     4/55 (7.3%)  #>     Any                    30/69 (43.5%)   26/72 (36.1%)   19/55 (34.5%)"},{"path":"https://insightsengineering.github.io/tern/main/reference/add_riskdiff.html","id":null,"dir":"Reference","previous_headings":"","what":"Split function to configure risk difference column — add_riskdiff","title":"Split function to configure risk difference column — add_riskdiff","text":"Wrapper function rtables::add_combo_levels() configures settings risk difference column added rtables object. add risk difference column table, function used split_fun calls rtables::split_cols_by(), followed setting argument riskdiff TRUE following analyze function calls.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/add_riskdiff.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Split function to configure risk difference column — add_riskdiff","text":"","code":"add_riskdiff(   arm_x,   arm_y,   col_label = paste0(\"Risk Difference (%) (95% CI)\", if (length(arm_y) > 1)     paste0(\"\\n\", arm_x, \" vs. \", arm_y)),   pct = TRUE )"},{"path":"https://insightsengineering.github.io/tern/main/reference/add_riskdiff.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Split function to configure risk difference column — add_riskdiff","text":"arm_x (string) name reference arm use risk difference calculations. arm_y (character) names one arms compare reference arm risk difference calculations. new column added value arm_y. col_label (character) labels use rendering risk difference column within table. one comparison arm specified arm_y, default labels specify two arms compared (reference arm vs. comparison arm). pct (flag) whether output returned percentages. Defaults TRUE.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/add_riskdiff.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Split function to configure risk difference column — add_riskdiff","text":"closure suitable use split function (split_fun) within rtables::split_cols_by() creating table layout.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/main/reference/add_riskdiff.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Split function to configure risk difference column — add_riskdiff","text":"","code":"adae <- tern_ex_adae adae$AESEV <- factor(adae$AESEV)  lyt <- basic_table() %>%   split_cols_by(\"ARMCD\", split_fun = add_riskdiff(arm_x = \"ARM A\", arm_y = c(\"ARM B\", \"ARM C\"))) %>%   count_occurrences_by_grade(     var = \"AESEV\",     riskdiff = TRUE   )  tbl <- build_table(lyt, df = adae) tbl #>                                                   Risk Difference (%) (95% CI)   Risk Difference (%) (95% CI) #>              ARM A        ARM B        ARM C            ARM A vs. ARM B                ARM A vs. ARM C        #> ————————————————————————————————————————————————————————————————————————————————————————————————————————————— #> MILD        6 (3.0%)     4 (2.3%)     2 (1.2%)          0.7 (-2.5 - 3.9)               1.7 (-1.2 - 4.6)       #> MODERATE   19 (9.4%)    15 (8.5%)    14 (8.6%)          0.9 (-4.8 - 6.7)               0.8 (-5.1 - 6.7)       #> SEVERE     34 (16.8%)   38 (21.5%)   32 (19.8%)        -4.6 (-12.6 - 3.3)             -2.9 (-10.9 - 5.1)"},{"path":"https://insightsengineering.github.io/tern/main/reference/add_rowcounts.html","id":null,"dir":"Reference","previous_headings":"","what":"Layout-creating function to add row total counts — add_rowcounts","title":"Layout-creating function to add row total counts — add_rowcounts","text":"works analogously rtables::add_colcounts() rows. function wrapper rtables::summarize_row_groups().","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/add_rowcounts.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Layout-creating function to add row total counts — add_rowcounts","text":"","code":"add_rowcounts(lyt, alt_counts = FALSE)"},{"path":"https://insightsengineering.github.io/tern/main/reference/add_rowcounts.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Layout-creating function to add row total counts — add_rowcounts","text":"lyt (PreDataTableLayouts) layout analyses added . alt_counts (flag) whether row counts taken alt_counts_df (TRUE) df (FALSE). Defaults FALSE.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/add_rowcounts.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Layout-creating function to add row total counts — add_rowcounts","text":"modified layout latest row split labels now row-wise total counts (.e. without column-based subsetting) attached parentheses.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/add_rowcounts.html","id":"note","dir":"Reference","previous_headings":"","what":"Note","title":"Layout-creating function to add row total counts — add_rowcounts","text":"Row count values contained row count rows displayed considered zero rows default pruning.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/add_rowcounts.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Layout-creating function to add row total counts — add_rowcounts","text":"","code":"basic_table() %>%   split_cols_by(\"ARM\") %>%   add_colcounts() %>%   split_rows_by(\"RACE\", split_fun = drop_split_levels) %>%   add_rowcounts() %>%   analyze(\"AGE\", afun = list_wrap_x(summary), format = \"xx.xx\") %>%   build_table(DM) #>                                    A: Drug X   B: Placebo   C: Combination #>                                     (N=121)     (N=106)        (N=129)     #> —————————————————————————————————————————————————————————————————————————— #> ASIAN (N=231)                                                              #>   Min.                               20.00       21.00          22.00      #>   1st Qu.                            29.00       28.00          30.00      #>   Median                             33.00       32.50          33.50      #>   Mean                               34.20       32.68          34.63      #>   3rd Qu.                            38.50       36.00          38.00      #>   Max.                               58.00       55.00          53.00      #> BLACK OR AFRICAN AMERICAN (N=79)                                           #>   Min.                               23.00       21.00          24.00      #>   1st Qu.                            29.00       28.75          29.00      #>   Median                             33.00       30.00          32.00      #>   Mean                               34.68       31.71          34.00      #>   3rd Qu.                            37.25       36.25          39.00      #>   Max.                               60.00       42.00          51.00      #> WHITE (N=46)                                                               #>   Min.                               30.00       25.00          28.00      #>   1st Qu.                            38.00       31.00          30.25      #>   Median                             40.50       37.50          35.00      #>   Mean                               39.36       36.93          35.11      #>   3rd Qu.                            43.50       40.00          37.50      #>   Max.                               47.00       55.00          47.00"},{"path":[]},{"path":"https://insightsengineering.github.io/tern/main/reference/aesi_label.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Labels for adverse event baskets — aesi_label","text":"","code":"aesi_label(aesi, scope = NULL)"},{"path":"https://insightsengineering.github.io/tern/main/reference/aesi_label.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Labels for adverse event baskets — aesi_label","text":"aesi (character) vector standardized MedDRA query name (e.g. SMQxxNAM) customized query name (e.g. CQxxNAM). scope (character) vector scope query (e.g. SMQxxSC).","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/aesi_label.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Labels for adverse event baskets — aesi_label","text":"string standard label AE basket.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/aesi_label.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Labels for adverse event baskets — aesi_label","text":"","code":"adae <- tern_ex_adae  # Standardized query label includes scope. aesi_label(adae$SMQ01NAM, scope = adae$SMQ01SC) #> [1] \"C.1.1.1.3/B.2.2.3.1 aesi (BROAD)\"  # Customized query label. aesi_label(adae$CQ01NAM) #> [1] \"D.2.1.5.3/A.1.1.1.1 aesi\""},{"path":"https://insightsengineering.github.io/tern/main/reference/afun_riskdiff.html","id":null,"dir":"Reference","previous_headings":"","what":"Analysis function to calculate risk difference column values — afun_riskdiff","title":"Analysis function to calculate risk difference column values — afun_riskdiff","text":"risk difference column, function uses statistics function associated afun calculates risk difference values arm X (reference group) arm Y. arms specified configuring risk difference column done using add_riskdiff() split function previous call rtables::split_cols_by(). columns, applies afun usual. function utilizes stat_propdiff_ci() function perform risk difference calculations.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/afun_riskdiff.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Analysis function to calculate risk difference column values — afun_riskdiff","text":"","code":"afun_riskdiff(   df,   labelstr = \"\",   .var,   .N_col,   .N_row,   .df_row,   .spl_context,   .all_col_counts,   .stats,   .formats = NULL,   .labels = NULL,   .indent_mods = NULL,   na_str = default_na_str(),   afun,   s_args = list() )"},{"path":"https://insightsengineering.github.io/tern/main/reference/afun_riskdiff.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Analysis function to calculate risk difference column values — afun_riskdiff","text":"df (data.frame) data set containing analysis variables. labelstr (string) label level parent split currently summarized (must present second argument Content Row Functions). See rtables::summarize_row_groups() information. .var (string) single variable name passed rtables requested statistics function. .N_col (integer(1)) column-wise N (column count) full column analyzed typically passed rtables. .N_row (integer(1)) row-wise N (row group count) group observations analyzed (.e. column-based subsetting) typically passed rtables. .df_row (data.frame) data frame across columns given row split. .spl_context (data.frame) gives information ancestor split states passed rtables. .all_col_counts (integer) vector value represents global count column. Values taken alt_counts_df specified (see rtables::build_table()). .stats (character) statistics select table. .formats (named character list) formats statistics. See Details analyze_vars information \"auto\" setting. .labels (named character) labels statistics (without indent). .indent_mods (named integer) indent modifiers labels. Defaults 0, corresponds unmodified default behavior. Can negative. na_str (string) string used replace NA empty values output. afun (named list) named list containing one name-value pair name corresponds name statistics function used calculations value corresponding analysis function. s_args (named list) additional arguments passed statistics function analysis function supplied afun.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/afun_riskdiff.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Analysis function to calculate risk difference column values — afun_riskdiff","text":"list formatted rtables::CellValue().","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/main/reference/afun_selected_stats.html","id":null,"dir":"Reference","previous_headings":"","what":"Get selected statistics names — afun_selected_stats","title":"Get selected statistics names — afun_selected_stats","text":"Helper function used creating afun.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/afun_selected_stats.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get selected statistics names — afun_selected_stats","text":"","code":"afun_selected_stats(.stats, all_stats)"},{"path":"https://insightsengineering.github.io/tern/main/reference/afun_selected_stats.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get selected statistics names — afun_selected_stats","text":".stats (vector NULL) input layout creating function. Note NULL means context default statistics used. all_stats (character) statistics can selected potentially.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/afun_selected_stats.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get selected statistics names — afun_selected_stats","text":"character vector selected statistics.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/analyze_colvars_functions.html","id":null,"dir":"Reference","previous_headings":"","what":"Analyze functions in columns — analyze_colvars_functions","title":"Analyze functions in columns — analyze_colvars_functions","text":"functions wrappers rtables::analyze_colvars() apply corresponding tern statistics functions add analysis given table layout. particular, functions designed analysis methods split different columns. analyze_vars_in_cols(): fundamental tabulation analysis methods onto columns. words, analysis methods defined column space, .e. become column labels. changing variable vector, list functions can applied different variables, caveat number statistical functions. tabulate_rsp_subgroups(): similarly analyze_vars_in_cols, function combines analyze_colvars summarize_row_groups compact way produce standard tables show analysis methods columns. tabulate_survival_subgroups(): function similar , used tables. analyze_patients_exposure_in_cols(): based analyze_colvars. needs summarize_patients_exposure_in_cols() leverage nesting label rows analysis rtables::summarize_row_groups(). summarize_coxreg(): generally based rtables::summarize_row_groups(), behaves similarly tabulate_* functions described designed provide specific standard tables may contain nested structure combination summarize_row_groups() rtables::analyze_colvars().","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/main/reference/analyze_functions.html","id":null,"dir":"Reference","previous_headings":"","what":"Analyze functions — analyze_functions","title":"Analyze functions — analyze_functions","text":"functions wrappers rtables::analyze() apply corresponding tern statistics functions add analysis given table layout: analyze_num_patients() analyze_vars() compare_vars() count_abnormal() count_abnormal_by_baseline() count_abnormal_by_marked() count_abnormal_by_worst_grade() count_cumulative() count_missed_doses() count_occurrences() count_occurrences_by_grade() count_patients_events_in_cols() count_patients_with_event() count_patients_with_flags() count_values() coxph_pairwise() estimate_incidence_rate() estimate_multinomial_rsp() estimate_odds_ratio() estimate_proportion() estimate_proportion_diff() summarize_ancova() summarize_colvars(): even function uses rtables::analyze_colvars(), applies analysis methods different rows one variables split different columns. comparison, analyze_colvars_functions leverage analyze_colvars context split rows analysis methods columns. summarize_change() surv_time() surv_timepoint() test_proportion_diff()","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/main/reference/analyze_variables.html","id":null,"dir":"Reference","previous_headings":"","what":"Analyze variables — analyze_variables","title":"Analyze variables — analyze_variables","text":"analyze function analyze_vars() creates layout element summarize one variables, using S3 generic function s_summary() calculate list summary statistics. list available statistics numeric variables can viewed running get_stats(\"analyze_vars_numeric\") non-numeric variables running get_stats(\"analyze_vars_counts\"). Use .stats parameter specify statistics include output summary table.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/analyze_variables.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Analyze variables — analyze_variables","text":"","code":"analyze_vars(   lyt,   vars,   var_labels = vars,   na_str = default_na_str(),   nested = TRUE,   ...,   na.rm = TRUE,   show_labels = \"default\",   table_names = vars,   section_div = NA_character_,   .stats = c(\"n\", \"mean_sd\", \"median\", \"range\", \"count_fraction\"),   .formats = NULL,   .labels = NULL,   .indent_mods = NULL )  s_summary(x, na.rm = TRUE, denom, .N_row, .N_col, .var, ...)  # S3 method for class 'numeric' s_summary(   x,   na.rm = TRUE,   denom,   .N_row,   .N_col,   .var,   control = control_analyze_vars(),   ... )  # S3 method for class 'factor' s_summary(   x,   na.rm = TRUE,   denom = c(\"n\", \"N_col\", \"N_row\"),   .N_row,   .N_col,   ... )  # S3 method for class 'character' s_summary(   x,   na.rm = TRUE,   denom = c(\"n\", \"N_col\", \"N_row\"),   .N_row,   .N_col,   .var,   verbose = TRUE,   ... )  # S3 method for class 'logical' s_summary(   x,   na.rm = TRUE,   denom = c(\"n\", \"N_col\", \"N_row\"),   .N_row,   .N_col,   ... )  a_summary(   x,   .N_col,   .N_row,   .var = NULL,   .df_row = NULL,   .ref_group = NULL,   .in_ref_col = FALSE,   compare = FALSE,   .stats = NULL,   .formats = NULL,   .labels = NULL,   .indent_mods = NULL,   na.rm = TRUE,   na_str = default_na_str(),   ... )"},{"path":"https://insightsengineering.github.io/tern/main/reference/analyze_variables.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Analyze variables — analyze_variables","text":"lyt (PreDataTableLayouts) layout analyses added . vars (character) variable names primary analysis variable iterated . var_labels (character) variable labels. na_str (string) string used replace NA empty values output. nested (flag) whether layout instruction applied within existing layout structure _if possible (TRUE, default) new top-level element (FALSE). Ignored nest split. underneath analyses, allowed. ... arguments passed s_summary(). na.rm (flag) whether NA values removed x prior analysis. show_labels (string) label visibility: one \"default\", \"visible\" \"hidden\". table_names (character) can customized case vars analyzed multiple times, avoid warnings rtables. section_div (string) string repeated section divider group defined split instruction, NA_character_ (default) section divider. .stats (character) statistics select table. Options numeric variables : 'n', 'sum', 'mean', 'sd', 'se', 'mean_sd', 'mean_se', 'mean_ci', 'mean_sei', 'mean_sdi', 'mean_pval', 'median', 'mad', 'median_ci', 'quantiles', 'iqr', 'range', 'min', 'max', 'median_range', 'cv', 'geom_mean', 'geom_mean_ci', 'geom_cv', 'median_ci_3d', 'mean_ci_3d', 'geom_mean_ci_3d' Options non-numeric variables : 'n', 'count', 'count_fraction', 'count_fraction_fixed_dp', 'fraction', 'n_blq' .formats (named character list) formats statistics. See Details analyze_vars information \"auto\" setting. .labels (named character) labels statistics (without indent). .indent_mods (named integer) indent modifiers labels. element vector name-value pair name corresponding statistic specified .stats value indentation statistic's row label. x (numeric) vector numbers want analyze. denom (string) choice denominator proportion. Options : n: number values row column intersection. N_row: total number values row across columns. N_col: total number values column across rows. .N_row (integer(1)) row-wise N (row group count) group observations analyzed (.e. column-based subsetting) typically passed rtables. .N_col (integer(1)) column-wise N (column count) full column analyzed typically passed rtables. .var (string) single variable name passed rtables requested statistics function. control (list) parameters descriptive statistics details, specified using helper function control_analyze_vars(). possible parameter options : conf_level (proportion) confidence level interval mean median. quantiles (numeric(2)) vector length two specify quantiles. quantile_type (numeric(1)) 1 9 selecting quantile algorithms used. See type stats::quantile(). test_mean (numeric(1)) value test mean null hypothesis calculating p-value. verbose (flag) defaults TRUE, prints warnings messages. mainly used print information factor casting. .df_row (data.frame) data frame across columns given row split. .ref_group (data.frame vector) data corresponding reference group. .in_ref_col (flag)TRUE working reference level, FALSE otherwise. compare (flag) whether comparison statistics analyzed instead summary statistics (compare = TRUE adds pval statistic comparing reference group).","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/analyze_variables.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Analyze variables — analyze_variables","text":"analyze_vars() returns layout object suitable passing layouting functions, rtables::build_table(). Adding function rtable layout add formatted rows containing statistics s_summary() table layout. s_summary() returns different statistics depending class x. x class numeric, returns list following named numeric items: n: length() x. sum: sum() x. mean: mean() x. sd: stats::sd() x. se: standard error x mean, .e.: (sd(x) / sqrt(length(x))). mean_sd: mean() stats::sd() x. mean_se: mean() x standard error (see ). mean_ci: CI mean x (stat_mean_ci()). mean_sei: SE interval mean x, .e.: (mean() -/+ stats::sd() / sqrt()). mean_sdi: SD interval mean x, .e.: (mean() -/+ stats::sd()). mean_pval: two-sided p-value mean x (stat_mean_pval()). median: stats::median() x. mad: median absolute deviation x, .e.: (stats::median() xc, xc = x - stats::median()). median_ci: CI median x (stat_median_ci()). quantiles: Two sample quantiles x (stats::quantile()). iqr: stats::IQR() x. range: range_noinf() x. min: max() x. max: min() x. median_range: median() range_noinf() x. cv: coefficient variation x, .e.: (stats::sd() / mean() * 100). geom_mean: geometric mean x, .e.: (exp(mean(log(x)))). geom_cv: geometric coefficient variation x, .e.: (sqrt(exp(sd(log(x)) ^ 2) - 1) * 100). x class factor converted character, returns list named numeric items: n: length() x. count: list number cases level factor x. count_fraction: Similar count also includes proportion cases level factor x relative denominator, NA denominator zero. x class logical, returns list named numeric items: n: length() x (possibly removing NAs). count: Count TRUE x. count_fraction: Count proportion TRUE x relative denominator, NA denominator zero. Note NAs x never counted leading NA . a_summary() returns corresponding list formatted rtables::CellValue().","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/analyze_variables.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Analyze variables — analyze_variables","text":"Automatic digit formatting: number digits display can automatically determined analyzed variable(s) (vars) certain statistics setting statistic format \"auto\" .formats. utilizes format_auto() formatting function. Note data current row & variable (columns) considered (.df_row[[.var]], see rtables::additional_fun_params) whole dataset.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/analyze_variables.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Analyze variables — analyze_variables","text":"analyze_vars(): Layout-creating function can take statistics function arguments additional format arguments. function wrapper rtables::analyze(). s_summary(): S3 generic function produces variable summary. s_summary(numeric): Method numeric class. s_summary(factor): Method factor class. s_summary(character): Method character class. makes automatic conversion factor (warning) forwards method factors. s_summary(logical): Method logical class. a_summary(): Formatted analysis function used afun analyze_vars() compare_vars() cfun summarize_colvars().","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/analyze_variables.html","id":"note","dir":"Reference","previous_headings":"","what":"Note","title":"Analyze variables — analyze_variables","text":"x empty vector, NA returned. expected feature return rcell content rtables intersection column row delimits empty data selection. mean function applied empty vector, NA returned instead NaN, latter standard behavior R. x empty factor, list still returned counts one element per factor level. levels x, function fails. factor variables contain NA, NA values excluded default. include NA values set na.rm = FALSE missing values displayed NA level. Alternatively, explicit factor level can defined NA values pre-processing via df_explicit_na() - default na_level (\"<Missing>\") also excluded na.rm set TRUE. Automatic conversion character factor guarantee table can generated correctly. particular sparse tables likely can fail. therefore better always pre-process dataset factors manually created character variables passing dataset rtables::build_table(). use comparison (additional p-value statistic), parameter compare must set TRUE. Ensure either NA values converted explicit NA level NA values left .","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/analyze_variables.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Analyze variables — analyze_variables","text":"","code":"## Fabricated dataset. dta_test <- data.frame(   USUBJID = rep(1:6, each = 3),   PARAMCD = rep(\"lab\", 6 * 3),   AVISIT  = rep(paste0(\"V\", 1:3), 6),   ARM     = rep(LETTERS[1:3], rep(6, 3)),   AVAL    = c(9:1, rep(NA, 9)) )  # `analyze_vars()` in `rtables` pipelines ## Default output within a `rtables` pipeline. l <- basic_table() %>%   split_cols_by(var = \"ARM\") %>%   split_rows_by(var = \"AVISIT\") %>%   analyze_vars(vars = \"AVAL\")  build_table(l, df = dta_test) #>                   A           B       C  #> ———————————————————————————————————————— #> V1                                       #>   n               2           1       0  #>   Mean (SD)   7.5 (2.1)   3.0 (NA)    NA #>   Median         7.5         3.0      NA #>   Min - Max   6.0 - 9.0   3.0 - 3.0   NA #> V2                                       #>   n               2           1       0  #>   Mean (SD)   6.5 (2.1)   2.0 (NA)    NA #>   Median         6.5         2.0      NA #>   Min - Max   5.0 - 8.0   2.0 - 2.0   NA #> V3                                       #>   n               2           1       0  #>   Mean (SD)   5.5 (2.1)   1.0 (NA)    NA #>   Median         5.5         1.0      NA #>   Min - Max   4.0 - 7.0   1.0 - 1.0   NA  ## Select and format statistics output. l <- basic_table() %>%   split_cols_by(var = \"ARM\") %>%   split_rows_by(var = \"AVISIT\") %>%   analyze_vars(     vars = \"AVAL\",     .stats = c(\"n\", \"mean_sd\", \"quantiles\"),     .formats = c(\"mean_sd\" = \"xx.x, xx.x\"),     .labels = c(n = \"n\", mean_sd = \"Mean, SD\", quantiles = c(\"Q1 - Q3\"))   )  build_table(l, df = dta_test) #>                  A           B       C  #> ——————————————————————————————————————— #> V1                                      #>   n              2           1       0  #>   Mean, SD   7.5, 2.1     3.0, NA    NA #>   Q1 - Q3    6.0 - 9.0   3.0 - 3.0   NA #> V2                                      #>   n              2           1       0  #>   Mean, SD   6.5, 2.1     2.0, NA    NA #>   Q1 - Q3    5.0 - 8.0   2.0 - 2.0   NA #> V3                                      #>   n              2           1       0  #>   Mean, SD   5.5, 2.1     1.0, NA    NA #>   Q1 - Q3    4.0 - 7.0   1.0 - 1.0   NA  ## Use arguments interpreted by `s_summary`. l <- basic_table() %>%   split_cols_by(var = \"ARM\") %>%   split_rows_by(var = \"AVISIT\") %>%   analyze_vars(vars = \"AVAL\", na.rm = FALSE)  build_table(l, df = dta_test) #>                   A       B    C  #> ————————————————————————————————— #> V1                                #>   n               2       2    2  #>   Mean (SD)   7.5 (2.1)   NA   NA #>   Median         7.5      NA   NA #>   Min - Max   6.0 - 9.0   NA   NA #> V2                                #>   n               2       2    2  #>   Mean (SD)   6.5 (2.1)   NA   NA #>   Median         6.5      NA   NA #>   Min - Max   5.0 - 8.0   NA   NA #> V3                                #>   n               2       2    2  #>   Mean (SD)   5.5 (2.1)   NA   NA #>   Median         5.5      NA   NA #>   Min - Max   4.0 - 7.0   NA   NA  ## Handle `NA` levels first when summarizing factors. dta_test$AVISIT <- NA_character_ dta_test <- df_explicit_na(dta_test) l <- basic_table() %>%   split_cols_by(var = \"ARM\") %>%   analyze_vars(vars = \"AVISIT\", na.rm = FALSE)  build_table(l, df = dta_test) #>                A          B          C     #> —————————————————————————————————————————— #> n              6          6          6     #> <Missing>   6 (100%)   6 (100%)   6 (100%)  # auto format dt <- data.frame(\"VAR\" = c(0.001, 0.2, 0.0011000, 3, 4)) basic_table() %>%   analyze_vars(     vars = \"VAR\",     .stats = c(\"n\", \"mean\", \"mean_sd\", \"range\"),     .formats = c(\"mean_sd\" = \"auto\", \"range\" = \"auto\")   ) %>%   build_table(dt) #>                  all obs      #> ————————————————————————————— #> n                   5         #> Mean               1.4        #> Mean (SD)   1.44042 (1.91481) #> Min - Max    0.0010 - 4.0000   # `s_summary.numeric`  ## Basic usage: empty numeric returns NA-filled items. s_summary(numeric()) #> $n #> n  #> 0  #>  #> $sum #> sum  #>  NA  #>  #> $mean #> mean  #>   NA  #>  #> $sd #> sd  #> NA  #>  #> $se #> se  #> NA  #>  #> $mean_sd #> mean   sd  #>   NA   NA  #>  #> $mean_se #> mean   se  #>   NA   NA  #>  #> $mean_ci #> mean_ci_lwr mean_ci_upr  #>          NA          NA  #> attr(,\"label\") #> [1] \"Mean 95% CI\" #>  #> $mean_sei #> mean_sei_lwr mean_sei_upr  #>           NA           NA  #> attr(,\"label\") #> [1] \"Mean -/+ 1xSE\" #>  #> $mean_sdi #> mean_sdi_lwr mean_sdi_upr  #>           NA           NA  #> attr(,\"label\") #> [1] \"Mean -/+ 1xSD\" #>  #> $mean_ci_3d #>        mean mean_ci_lwr mean_ci_upr  #>          NA          NA          NA  #> attr(,\"label\") #> [1] \"Mean (95% CI)\" #>  #> $mean_pval #> p_value  #>      NA  #> attr(,\"label\") #> [1] \"Mean p-value (H0: mean = 0)\" #>  #> $median #> median  #>     NA  #>  #> $mad #> mad  #>  NA  #>  #> $median_ci #> median_ci_lwr median_ci_upr  #>            NA            NA  #> attr(,\"conf_level\") #> [1] NA #> attr(,\"label\") #> [1] \"Median 95% CI\" #>  #> $median_ci_3d #>        median median_ci_lwr median_ci_upr  #>            NA            NA            NA  #> attr(,\"label\") #> [1] \"Median (95% CI)\" #>  #> $quantiles #> quantile_0.25 quantile_0.75  #>            NA            NA  #> attr(,\"label\") #> [1] \"25% and 75%-ile\" #>  #> $iqr #> iqr  #>  NA  #>  #> $range #> min max  #>  NA  NA  #>  #> $min #> min  #>  NA  #>  #> $max #> max  #>  NA  #>  #> $median_range #> median    min    max  #>     NA     NA     NA  #> attr(,\"label\") #> [1] \"Median (Min - Max)\" #>  #> $cv #> cv  #> NA  #>  #> $geom_mean #> geom_mean  #>       NaN  #>  #> $geom_mean_ci #> mean_ci_lwr mean_ci_upr  #>          NA          NA  #> attr(,\"label\") #> [1] \"Geometric Mean 95% CI\" #>  #> $geom_cv #> geom_cv  #>      NA  #>  #> $geom_mean_ci_3d #>   geom_mean mean_ci_lwr mean_ci_upr  #>         NaN          NA          NA  #> attr(,\"label\") #> [1] \"Geometric Mean (95% CI)\" #>   ## Management of NA values. x <- c(NA_real_, 1) s_summary(x, na.rm = TRUE) #> $n #> n  #> 1  #>  #> $sum #> sum  #>   1  #>  #> $mean #> mean  #>    1  #>  #> $sd #> sd  #> NA  #>  #> $se #> se  #> NA  #>  #> $mean_sd #> mean   sd  #>    1   NA  #>  #> $mean_se #> mean   se  #>    1   NA  #>  #> $mean_ci #> mean_ci_lwr mean_ci_upr  #>          NA          NA  #> attr(,\"label\") #> [1] \"Mean 95% CI\" #>  #> $mean_sei #> mean_sei_lwr mean_sei_upr  #>           NA           NA  #> attr(,\"label\") #> [1] \"Mean -/+ 1xSE\" #>  #> $mean_sdi #> mean_sdi_lwr mean_sdi_upr  #>           NA           NA  #> attr(,\"label\") #> [1] \"Mean -/+ 1xSD\" #>  #> $mean_ci_3d #>        mean mean_ci_lwr mean_ci_upr  #>           1          NA          NA  #> attr(,\"label\") #> [1] \"Mean (95% CI)\" #>  #> $mean_pval #> p_value  #>      NA  #> attr(,\"label\") #> [1] \"Mean p-value (H0: mean = 0)\" #>  #> $median #> median  #>      1  #>  #> $mad #> mad  #>   0  #>  #> $median_ci #> median_ci_lwr median_ci_upr  #>            NA            NA  #> attr(,\"conf_level\") #> [1] NA #> attr(,\"label\") #> [1] \"Median 95% CI\" #>  #> $median_ci_3d #>        median median_ci_lwr median_ci_upr  #>             1            NA            NA  #> attr(,\"label\") #> [1] \"Median (95% CI)\" #>  #> $quantiles #> quantile_0.25 quantile_0.75  #>             1             1  #> attr(,\"label\") #> [1] \"25% and 75%-ile\" #>  #> $iqr #> iqr  #>   0  #>  #> $range #> min max  #>   1   1  #>  #> $min #> min  #>   1  #>  #> $max #> max  #>   1  #>  #> $median_range #> median    min    max  #>      1      1      1  #> attr(,\"label\") #> [1] \"Median (Min - Max)\" #>  #> $cv #> cv  #> NA  #>  #> $geom_mean #> geom_mean  #>         1  #>  #> $geom_mean_ci #> mean_ci_lwr mean_ci_upr  #>          NA          NA  #> attr(,\"label\") #> [1] \"Geometric Mean 95% CI\" #>  #> $geom_cv #> geom_cv  #>      NA  #>  #> $geom_mean_ci_3d #>   geom_mean mean_ci_lwr mean_ci_upr  #>           1          NA          NA  #> attr(,\"label\") #> [1] \"Geometric Mean (95% CI)\" #>  s_summary(x, na.rm = FALSE) #> $n #> n  #> 2  #>  #> $sum #> sum  #>  NA  #>  #> $mean #> mean  #>   NA  #>  #> $sd #> sd  #> NA  #>  #> $se #> se  #> NA  #>  #> $mean_sd #> mean   sd  #>   NA   NA  #>  #> $mean_se #> mean   se  #>   NA   NA  #>  #> $mean_ci #> mean_ci_lwr mean_ci_upr  #>          NA          NA  #> attr(,\"label\") #> [1] \"Mean 95% CI\" #>  #> $mean_sei #> mean_sei_lwr mean_sei_upr  #>           NA           NA  #> attr(,\"label\") #> [1] \"Mean -/+ 1xSE\" #>  #> $mean_sdi #> mean_sdi_lwr mean_sdi_upr  #>           NA           NA  #> attr(,\"label\") #> [1] \"Mean -/+ 1xSD\" #>  #> $mean_ci_3d #>        mean mean_ci_lwr mean_ci_upr  #>          NA          NA          NA  #> attr(,\"label\") #> [1] \"Mean (95% CI)\" #>  #> $mean_pval #> p_value  #>      NA  #> attr(,\"label\") #> [1] \"Mean p-value (H0: mean = 0)\" #>  #> $median #> median  #>     NA  #>  #> $mad #> mad  #>  NA  #>  #> $median_ci #> median_ci_lwr median_ci_upr  #>            NA            NA  #> attr(,\"conf_level\") #> [1] NA #> attr(,\"label\") #> [1] \"Median 95% CI\" #>  #> $median_ci_3d #>        median median_ci_lwr median_ci_upr  #>            NA            NA            NA  #> attr(,\"label\") #> [1] \"Median (95% CI)\" #>  #> $quantiles #> quantile_0.25 quantile_0.75  #>            NA            NA  #> attr(,\"label\") #> [1] \"25% and 75%-ile\" #>  #> $iqr #> iqr  #>  NA  #>  #> $range #> min max  #>  NA  NA  #>  #> $min #> min  #>  NA  #>  #> $max #> max  #>  NA  #>  #> $median_range #> median    min    max  #>     NA     NA     NA  #> attr(,\"label\") #> [1] \"Median (Min - Max)\" #>  #> $cv #> cv  #> NA  #>  #> $geom_mean #> geom_mean  #>        NA  #>  #> $geom_mean_ci #> mean_ci_lwr mean_ci_upr  #>          NA          NA  #> attr(,\"label\") #> [1] \"Geometric Mean 95% CI\" #>  #> $geom_cv #> geom_cv  #>      NA  #>  #> $geom_mean_ci_3d #>   geom_mean mean_ci_lwr mean_ci_upr  #>          NA          NA          NA  #> attr(,\"label\") #> [1] \"Geometric Mean (95% CI)\" #>   x <- c(NA_real_, 1, 2) s_summary(x, stats = NULL) #> $n #> n  #> 2  #>  #> $sum #> sum  #>   3  #>  #> $mean #> mean  #>  1.5  #>  #> $sd #>        sd  #> 0.7071068  #>  #> $se #>  se  #> 0.5  #>  #> $mean_sd #>      mean        sd  #> 1.5000000 0.7071068  #>  #> $mean_se #> mean   se  #>  1.5  0.5  #>  #> $mean_ci #> mean_ci_lwr mean_ci_upr  #>   -4.853102    7.853102  #> attr(,\"label\") #> [1] \"Mean 95% CI\" #>  #> $mean_sei #> mean_sei_lwr mean_sei_upr  #>            1            2  #> attr(,\"label\") #> [1] \"Mean -/+ 1xSE\" #>  #> $mean_sdi #> mean_sdi_lwr mean_sdi_upr  #>    0.7928932    2.2071068  #> attr(,\"label\") #> [1] \"Mean -/+ 1xSD\" #>  #> $mean_ci_3d #>        mean mean_ci_lwr mean_ci_upr  #>    1.500000   -4.853102    7.853102  #> attr(,\"label\") #> [1] \"Mean (95% CI)\" #>  #> $mean_pval #>   p_value  #> 0.2048328  #> attr(,\"label\") #> [1] \"Mean p-value (H0: mean = 0)\" #>  #> $median #> median  #>    1.5  #>  #> $mad #> mad  #>   0  #>  #> $median_ci #> median_ci_lwr median_ci_upr  #>            NA            NA  #> attr(,\"conf_level\") #> [1] NA #> attr(,\"label\") #> [1] \"Median 95% CI\" #>  #> $median_ci_3d #>        median median_ci_lwr median_ci_upr  #>           1.5            NA            NA  #> attr(,\"label\") #> [1] \"Median (95% CI)\" #>  #> $quantiles #> quantile_0.25 quantile_0.75  #>             1             2  #> attr(,\"label\") #> [1] \"25% and 75%-ile\" #>  #> $iqr #> iqr  #>   1  #>  #> $range #> min max  #>   1   2  #>  #> $min #> min  #>   1  #>  #> $max #> max  #>   2  #>  #> $median_range #> median    min    max  #>    1.5    1.0    2.0  #> attr(,\"label\") #> [1] \"Median (Min - Max)\" #>  #> $cv #>       cv  #> 47.14045  #>  #> $geom_mean #> geom_mean  #>  1.414214  #>  #> $geom_mean_ci #>  mean_ci_lwr  mean_ci_upr  #>   0.01729978 115.60839614  #> attr(,\"label\") #> [1] \"Geometric Mean 95% CI\" #>  #> $geom_cv #>  geom_cv  #> 52.10922  #>  #> $geom_mean_ci_3d #>    geom_mean  mean_ci_lwr  mean_ci_upr  #>   1.41421356   0.01729978 115.60839614  #> attr(,\"label\") #> [1] \"Geometric Mean (95% CI)\" #>   ## Benefits in `rtables` contructions: dta_test <- data.frame(   Group = rep(LETTERS[1:3], each = 2),   sub_group = rep(letters[1:2], each = 3),   x = 1:6 )  ## The summary obtained in with `rtables`: basic_table() %>%   split_cols_by(var = \"Group\") %>%   split_rows_by(var = \"sub_group\") %>%   analyze(vars = \"x\", afun = s_summary) %>%   build_table(df = dta_test) #>                                                           A                                  B                                C                           #> ————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————— #> a                                                                                                                                                         #>   n                                                       2                                  1                                0                           #>   sum                                                     3                                  3                                NA                          #>   mean                                                   1.5                                 3                                NA                          #>   sd                                              0.707106781186548                         NA                                NA                          #>   se                                                     0.5                                NA                                NA                          #>   mean_sd                                       1.5, 0.707106781186548                     3, NA                              NA                          #>   mean_se                                              1.5, 0.5                            3, NA                              NA                          #>   Mean 95% CI                            -4.85310236808735, 7.85310236808735                NA                                NA                          #>   Mean -/+ 1xSE                                          1, 2                               NA                                NA                          #>   Mean -/+ 1xSD                          0.792893218813452, 2.20710678118655                NA                                NA                          #>   Mean (95% CI)                        1.5, -4.85310236808735, 7.85310236808735          3, NA, NA                            NA                          #>   Mean p-value (H0: mean = 0)                     0.204832764699133                         NA                                NA                          #>   median                                                 1.5                                 3                                NA                          #>   mad                                                     0                                  0                                NA                          #>   Median 95% CI                                           NA                                NA                                NA                          #>   Median (95% CI)                                    1.5, NA, NA                         3, NA, NA                            NA                          #>   25% and 75%-ile                                        1, 2                              3, 3                               NA                          #>   iqr                                                     1                                  0                                NA                          #>   range                                                  1, 2                              3, 3                               NA                          #>   min                                                     1                                  3                                NA                          #>   max                                                     2                                  3                                NA                          #>   Median (Min - Max)                                  1.5, 1, 2                           3, 3, 3                             NA                          #>   cv                                               47.1404520791032                         NA                                NA                          #>   geom_mean                                        1.41421356237309                          3                                NA                          #>   Geometric Mean 95% CI                  0.0172997815631007, 115.608396135236               NA                                NA                          #>   geom_cv                                          52.1092246837487                         NA                                NA                          #>   Geometric Mean (95% CI)       1.41421356237309, 0.0172997815631007, 115.608396135236   3, NA, NA                            NA                          #> b                                                                                                                                                         #>   n                                                       0                                  1                                2                           #>   sum                                                     NA                                 4                                11                          #>   mean                                                    NA                                 4                               5.5                          #>   sd                                                      NA                                NA                        0.707106781186548                   #>   se                                                      NA                                NA                               0.5                          #>   mean_sd                                                 NA                               4, NA                    5.5, 0.707106781186548                #>   mean_se                                                 NA                               4, NA                           5.5, 0.5                       #>   Mean 95% CI                                             NA                                NA               -0.853102368087347, 11.8531023680873         #>   Mean -/+ 1xSE                                           NA                                NA                               5, 6                         #>   Mean -/+ 1xSD                                           NA                                NA                4.79289321881345, 6.20710678118655          #>   Mean (95% CI)                                           NA                             4, NA, NA        5.5, -0.853102368087347, 11.8531023680873       #>   Mean p-value (H0: mean = 0)                             NA                                NA                        0.0577158767526089                  #>   median                                                  NA                                 4                               5.5                          #>   mad                                                     NA                                 0                                0                           #>   Median 95% CI                                           NA                                NA                                NA                          #>   Median (95% CI)                                         NA                             4, NA, NA                       5.5, NA, NA                      #>   25% and 75%-ile                                         NA                               4, 4                              5, 6                         #>   iqr                                                     NA                                 0                                1                           #>   range                                                   NA                               4, 4                              5, 6                         #>   min                                                     NA                                 4                                5                           #>   max                                                     NA                                 4                                6                           #>   Median (Min - Max)                                      NA                              4, 4, 4                         5.5, 5, 6                       #>   cv                                                      NA                                NA                         12.8564869306645                   #>   geom_mean                                               NA                                 4                         5.47722557505166                   #>   Geometric Mean 95% CI                                   NA                                NA                1.71994304449266, 17.4424380482025          #>   geom_cv                                                 NA                                NA                         12.945835316564                    #>   Geometric Mean (95% CI)                                 NA                             4, NA, NA   5.47722557505166, 1.71994304449266, 17.4424380482025  ## By comparison with `lapply`: X <- split(dta_test, f = with(dta_test, interaction(Group, sub_group))) lapply(X, function(x) s_summary(x$x)) #> $A.a #> $A.a$n #> n  #> 2  #>  #> $A.a$sum #> sum  #>   3  #>  #> $A.a$mean #> mean  #>  1.5  #>  #> $A.a$sd #>        sd  #> 0.7071068  #>  #> $A.a$se #>  se  #> 0.5  #>  #> $A.a$mean_sd #>      mean        sd  #> 1.5000000 0.7071068  #>  #> $A.a$mean_se #> mean   se  #>  1.5  0.5  #>  #> $A.a$mean_ci #> mean_ci_lwr mean_ci_upr  #>   -4.853102    7.853102  #> attr(,\"label\") #> [1] \"Mean 95% CI\" #>  #> $A.a$mean_sei #> mean_sei_lwr mean_sei_upr  #>            1            2  #> attr(,\"label\") #> [1] \"Mean -/+ 1xSE\" #>  #> $A.a$mean_sdi #> mean_sdi_lwr mean_sdi_upr  #>    0.7928932    2.2071068  #> attr(,\"label\") #> [1] \"Mean -/+ 1xSD\" #>  #> $A.a$mean_ci_3d #>        mean mean_ci_lwr mean_ci_upr  #>    1.500000   -4.853102    7.853102  #> attr(,\"label\") #> [1] \"Mean (95% CI)\" #>  #> $A.a$mean_pval #>   p_value  #> 0.2048328  #> attr(,\"label\") #> [1] \"Mean p-value (H0: mean = 0)\" #>  #> $A.a$median #> median  #>    1.5  #>  #> $A.a$mad #> mad  #>   0  #>  #> $A.a$median_ci #> median_ci_lwr median_ci_upr  #>            NA            NA  #> attr(,\"conf_level\") #> [1] NA #> attr(,\"label\") #> [1] \"Median 95% CI\" #>  #> $A.a$median_ci_3d #>        median median_ci_lwr median_ci_upr  #>           1.5            NA            NA  #> attr(,\"label\") #> [1] \"Median (95% CI)\" #>  #> $A.a$quantiles #> quantile_0.25 quantile_0.75  #>             1             2  #> attr(,\"label\") #> [1] \"25% and 75%-ile\" #>  #> $A.a$iqr #> iqr  #>   1  #>  #> $A.a$range #> min max  #>   1   2  #>  #> $A.a$min #> min  #>   1  #>  #> $A.a$max #> max  #>   2  #>  #> $A.a$median_range #> median    min    max  #>    1.5    1.0    2.0  #> attr(,\"label\") #> [1] \"Median (Min - Max)\" #>  #> $A.a$cv #>       cv  #> 47.14045  #>  #> $A.a$geom_mean #> geom_mean  #>  1.414214  #>  #> $A.a$geom_mean_ci #>  mean_ci_lwr  mean_ci_upr  #>   0.01729978 115.60839614  #> attr(,\"label\") #> [1] \"Geometric Mean 95% CI\" #>  #> $A.a$geom_cv #>  geom_cv  #> 52.10922  #>  #> $A.a$geom_mean_ci_3d #>    geom_mean  mean_ci_lwr  mean_ci_upr  #>   1.41421356   0.01729978 115.60839614  #> attr(,\"label\") #> [1] \"Geometric Mean (95% CI)\" #>  #>  #> $B.a #> $B.a$n #> n  #> 1  #>  #> $B.a$sum #> sum  #>   3  #>  #> $B.a$mean #> mean  #>    3  #>  #> $B.a$sd #> sd  #> NA  #>  #> $B.a$se #> se  #> NA  #>  #> $B.a$mean_sd #> mean   sd  #>    3   NA  #>  #> $B.a$mean_se #> mean   se  #>    3   NA  #>  #> $B.a$mean_ci #> mean_ci_lwr mean_ci_upr  #>          NA          NA  #> attr(,\"label\") #> [1] \"Mean 95% CI\" #>  #> $B.a$mean_sei #> mean_sei_lwr mean_sei_upr  #>           NA           NA  #> attr(,\"label\") #> [1] \"Mean -/+ 1xSE\" #>  #> $B.a$mean_sdi #> mean_sdi_lwr mean_sdi_upr  #>           NA           NA  #> attr(,\"label\") #> [1] \"Mean -/+ 1xSD\" #>  #> $B.a$mean_ci_3d #>        mean mean_ci_lwr mean_ci_upr  #>           3          NA          NA  #> attr(,\"label\") #> [1] \"Mean (95% CI)\" #>  #> $B.a$mean_pval #> p_value  #>      NA  #> attr(,\"label\") #> [1] \"Mean p-value (H0: mean = 0)\" #>  #> $B.a$median #> median  #>      3  #>  #> $B.a$mad #> mad  #>   0  #>  #> $B.a$median_ci #> median_ci_lwr median_ci_upr  #>            NA            NA  #> attr(,\"conf_level\") #> [1] NA #> attr(,\"label\") #> [1] \"Median 95% CI\" #>  #> $B.a$median_ci_3d #>        median median_ci_lwr median_ci_upr  #>             3            NA            NA  #> attr(,\"label\") #> [1] \"Median (95% CI)\" #>  #> $B.a$quantiles #> quantile_0.25 quantile_0.75  #>             3             3  #> attr(,\"label\") #> [1] \"25% and 75%-ile\" #>  #> $B.a$iqr #> iqr  #>   0  #>  #> $B.a$range #> min max  #>   3   3  #>  #> $B.a$min #> min  #>   3  #>  #> $B.a$max #> max  #>   3  #>  #> $B.a$median_range #> median    min    max  #>      3      3      3  #> attr(,\"label\") #> [1] \"Median (Min - Max)\" #>  #> $B.a$cv #> cv  #> NA  #>  #> $B.a$geom_mean #> geom_mean  #>         3  #>  #> $B.a$geom_mean_ci #> mean_ci_lwr mean_ci_upr  #>          NA          NA  #> attr(,\"label\") #> [1] \"Geometric Mean 95% CI\" #>  #> $B.a$geom_cv #> geom_cv  #>      NA  #>  #> $B.a$geom_mean_ci_3d #>   geom_mean mean_ci_lwr mean_ci_upr  #>           3          NA          NA  #> attr(,\"label\") #> [1] \"Geometric Mean (95% CI)\" #>  #>  #> $C.a #> $C.a$n #> n  #> 0  #>  #> $C.a$sum #> sum  #>  NA  #>  #> $C.a$mean #> mean  #>   NA  #>  #> $C.a$sd #> sd  #> NA  #>  #> $C.a$se #> se  #> NA  #>  #> $C.a$mean_sd #> mean   sd  #>   NA   NA  #>  #> $C.a$mean_se #> mean   se  #>   NA   NA  #>  #> $C.a$mean_ci #> mean_ci_lwr mean_ci_upr  #>          NA          NA  #> attr(,\"label\") #> [1] \"Mean 95% CI\" #>  #> $C.a$mean_sei #> mean_sei_lwr mean_sei_upr  #>           NA           NA  #> attr(,\"label\") #> [1] \"Mean -/+ 1xSE\" #>  #> $C.a$mean_sdi #> mean_sdi_lwr mean_sdi_upr  #>           NA           NA  #> attr(,\"label\") #> [1] \"Mean -/+ 1xSD\" #>  #> $C.a$mean_ci_3d #>        mean mean_ci_lwr mean_ci_upr  #>          NA          NA          NA  #> attr(,\"label\") #> [1] \"Mean (95% CI)\" #>  #> $C.a$mean_pval #> p_value  #>      NA  #> attr(,\"label\") #> [1] \"Mean p-value (H0: mean = 0)\" #>  #> $C.a$median #> median  #>     NA  #>  #> $C.a$mad #> mad  #>  NA  #>  #> $C.a$median_ci #> median_ci_lwr median_ci_upr  #>            NA            NA  #> attr(,\"conf_level\") #> [1] NA #> attr(,\"label\") #> [1] \"Median 95% CI\" #>  #> $C.a$median_ci_3d #>        median median_ci_lwr median_ci_upr  #>            NA            NA            NA  #> attr(,\"label\") #> [1] \"Median (95% CI)\" #>  #> $C.a$quantiles #> quantile_0.25 quantile_0.75  #>            NA            NA  #> attr(,\"label\") #> [1] \"25% and 75%-ile\" #>  #> $C.a$iqr #> iqr  #>  NA  #>  #> $C.a$range #> min max  #>  NA  NA  #>  #> $C.a$min #> min  #>  NA  #>  #> $C.a$max #> max  #>  NA  #>  #> $C.a$median_range #> median    min    max  #>     NA     NA     NA  #> attr(,\"label\") #> [1] \"Median (Min - Max)\" #>  #> $C.a$cv #> cv  #> NA  #>  #> $C.a$geom_mean #> geom_mean  #>       NaN  #>  #> $C.a$geom_mean_ci #> mean_ci_lwr mean_ci_upr  #>          NA          NA  #> attr(,\"label\") #> [1] \"Geometric Mean 95% CI\" #>  #> $C.a$geom_cv #> geom_cv  #>      NA  #>  #> $C.a$geom_mean_ci_3d #>   geom_mean mean_ci_lwr mean_ci_upr  #>         NaN          NA          NA  #> attr(,\"label\") #> [1] \"Geometric Mean (95% CI)\" #>  #>  #> $A.b #> $A.b$n #> n  #> 0  #>  #> $A.b$sum #> sum  #>  NA  #>  #> $A.b$mean #> mean  #>   NA  #>  #> $A.b$sd #> sd  #> NA  #>  #> $A.b$se #> se  #> NA  #>  #> $A.b$mean_sd #> mean   sd  #>   NA   NA  #>  #> $A.b$mean_se #> mean   se  #>   NA   NA  #>  #> $A.b$mean_ci #> mean_ci_lwr mean_ci_upr  #>          NA          NA  #> attr(,\"label\") #> [1] \"Mean 95% CI\" #>  #> $A.b$mean_sei #> mean_sei_lwr mean_sei_upr  #>           NA           NA  #> attr(,\"label\") #> [1] \"Mean -/+ 1xSE\" #>  #> $A.b$mean_sdi #> mean_sdi_lwr mean_sdi_upr  #>           NA           NA  #> attr(,\"label\") #> [1] \"Mean -/+ 1xSD\" #>  #> $A.b$mean_ci_3d #>        mean mean_ci_lwr mean_ci_upr  #>          NA          NA          NA  #> attr(,\"label\") #> [1] \"Mean (95% CI)\" #>  #> $A.b$mean_pval #> p_value  #>      NA  #> attr(,\"label\") #> [1] \"Mean p-value (H0: mean = 0)\" #>  #> $A.b$median #> median  #>     NA  #>  #> $A.b$mad #> mad  #>  NA  #>  #> $A.b$median_ci #> median_ci_lwr median_ci_upr  #>            NA            NA  #> attr(,\"conf_level\") #> [1] NA #> attr(,\"label\") #> [1] \"Median 95% CI\" #>  #> $A.b$median_ci_3d #>        median median_ci_lwr median_ci_upr  #>            NA            NA            NA  #> attr(,\"label\") #> [1] \"Median (95% CI)\" #>  #> $A.b$quantiles #> quantile_0.25 quantile_0.75  #>            NA            NA  #> attr(,\"label\") #> [1] \"25% and 75%-ile\" #>  #> $A.b$iqr #> iqr  #>  NA  #>  #> $A.b$range #> min max  #>  NA  NA  #>  #> $A.b$min #> min  #>  NA  #>  #> $A.b$max #> max  #>  NA  #>  #> $A.b$median_range #> median    min    max  #>     NA     NA     NA  #> attr(,\"label\") #> [1] \"Median (Min - Max)\" #>  #> $A.b$cv #> cv  #> NA  #>  #> $A.b$geom_mean #> geom_mean  #>       NaN  #>  #> $A.b$geom_mean_ci #> mean_ci_lwr mean_ci_upr  #>          NA          NA  #> attr(,\"label\") #> [1] \"Geometric Mean 95% CI\" #>  #> $A.b$geom_cv #> geom_cv  #>      NA  #>  #> $A.b$geom_mean_ci_3d #>   geom_mean mean_ci_lwr mean_ci_upr  #>         NaN          NA          NA  #> attr(,\"label\") #> [1] \"Geometric Mean (95% CI)\" #>  #>  #> $B.b #> $B.b$n #> n  #> 1  #>  #> $B.b$sum #> sum  #>   4  #>  #> $B.b$mean #> mean  #>    4  #>  #> $B.b$sd #> sd  #> NA  #>  #> $B.b$se #> se  #> NA  #>  #> $B.b$mean_sd #> mean   sd  #>    4   NA  #>  #> $B.b$mean_se #> mean   se  #>    4   NA  #>  #> $B.b$mean_ci #> mean_ci_lwr mean_ci_upr  #>          NA          NA  #> attr(,\"label\") #> [1] \"Mean 95% CI\" #>  #> $B.b$mean_sei #> mean_sei_lwr mean_sei_upr  #>           NA           NA  #> attr(,\"label\") #> [1] \"Mean -/+ 1xSE\" #>  #> $B.b$mean_sdi #> mean_sdi_lwr mean_sdi_upr  #>           NA           NA  #> attr(,\"label\") #> [1] \"Mean -/+ 1xSD\" #>  #> $B.b$mean_ci_3d #>        mean mean_ci_lwr mean_ci_upr  #>           4          NA          NA  #> attr(,\"label\") #> [1] \"Mean (95% CI)\" #>  #> $B.b$mean_pval #> p_value  #>      NA  #> attr(,\"label\") #> [1] \"Mean p-value (H0: mean = 0)\" #>  #> $B.b$median #> median  #>      4  #>  #> $B.b$mad #> mad  #>   0  #>  #> $B.b$median_ci #> median_ci_lwr median_ci_upr  #>            NA            NA  #> attr(,\"conf_level\") #> [1] NA #> attr(,\"label\") #> [1] \"Median 95% CI\" #>  #> $B.b$median_ci_3d #>        median median_ci_lwr median_ci_upr  #>             4            NA            NA  #> attr(,\"label\") #> [1] \"Median (95% CI)\" #>  #> $B.b$quantiles #> quantile_0.25 quantile_0.75  #>             4             4  #> attr(,\"label\") #> [1] \"25% and 75%-ile\" #>  #> $B.b$iqr #> iqr  #>   0  #>  #> $B.b$range #> min max  #>   4   4  #>  #> $B.b$min #> min  #>   4  #>  #> $B.b$max #> max  #>   4  #>  #> $B.b$median_range #> median    min    max  #>      4      4      4  #> attr(,\"label\") #> [1] \"Median (Min - Max)\" #>  #> $B.b$cv #> cv  #> NA  #>  #> $B.b$geom_mean #> geom_mean  #>         4  #>  #> $B.b$geom_mean_ci #> mean_ci_lwr mean_ci_upr  #>          NA          NA  #> attr(,\"label\") #> [1] \"Geometric Mean 95% CI\" #>  #> $B.b$geom_cv #> geom_cv  #>      NA  #>  #> $B.b$geom_mean_ci_3d #>   geom_mean mean_ci_lwr mean_ci_upr  #>           4          NA          NA  #> attr(,\"label\") #> [1] \"Geometric Mean (95% CI)\" #>  #>  #> $C.b #> $C.b$n #> n  #> 2  #>  #> $C.b$sum #> sum  #>  11  #>  #> $C.b$mean #> mean  #>  5.5  #>  #> $C.b$sd #>        sd  #> 0.7071068  #>  #> $C.b$se #>  se  #> 0.5  #>  #> $C.b$mean_sd #>      mean        sd  #> 5.5000000 0.7071068  #>  #> $C.b$mean_se #> mean   se  #>  5.5  0.5  #>  #> $C.b$mean_ci #> mean_ci_lwr mean_ci_upr  #>  -0.8531024  11.8531024  #> attr(,\"label\") #> [1] \"Mean 95% CI\" #>  #> $C.b$mean_sei #> mean_sei_lwr mean_sei_upr  #>            5            6  #> attr(,\"label\") #> [1] \"Mean -/+ 1xSE\" #>  #> $C.b$mean_sdi #> mean_sdi_lwr mean_sdi_upr  #>     4.792893     6.207107  #> attr(,\"label\") #> [1] \"Mean -/+ 1xSD\" #>  #> $C.b$mean_ci_3d #>        mean mean_ci_lwr mean_ci_upr  #>   5.5000000  -0.8531024  11.8531024  #> attr(,\"label\") #> [1] \"Mean (95% CI)\" #>  #> $C.b$mean_pval #>    p_value  #> 0.05771588  #> attr(,\"label\") #> [1] \"Mean p-value (H0: mean = 0)\" #>  #> $C.b$median #> median  #>    5.5  #>  #> $C.b$mad #> mad  #>   0  #>  #> $C.b$median_ci #> median_ci_lwr median_ci_upr  #>            NA            NA  #> attr(,\"conf_level\") #> [1] NA #> attr(,\"label\") #> [1] \"Median 95% CI\" #>  #> $C.b$median_ci_3d #>        median median_ci_lwr median_ci_upr  #>           5.5            NA            NA  #> attr(,\"label\") #> [1] \"Median (95% CI)\" #>  #> $C.b$quantiles #> quantile_0.25 quantile_0.75  #>             5             6  #> attr(,\"label\") #> [1] \"25% and 75%-ile\" #>  #> $C.b$iqr #> iqr  #>   1  #>  #> $C.b$range #> min max  #>   5   6  #>  #> $C.b$min #> min  #>   5  #>  #> $C.b$max #> max  #>   6  #>  #> $C.b$median_range #> median    min    max  #>    5.5    5.0    6.0  #> attr(,\"label\") #> [1] \"Median (Min - Max)\" #>  #> $C.b$cv #>       cv  #> 12.85649  #>  #> $C.b$geom_mean #> geom_mean  #>  5.477226  #>  #> $C.b$geom_mean_ci #> mean_ci_lwr mean_ci_upr  #>    1.719943   17.442438  #> attr(,\"label\") #> [1] \"Geometric Mean 95% CI\" #>  #> $C.b$geom_cv #>  geom_cv  #> 12.94584  #>  #> $C.b$geom_mean_ci_3d #>   geom_mean mean_ci_lwr mean_ci_upr  #>    5.477226    1.719943   17.442438  #> attr(,\"label\") #> [1] \"Geometric Mean (95% CI)\" #>  #>   # `s_summary.factor`  ## Basic usage: s_summary(factor(c(\"a\", \"a\", \"b\", \"c\", \"a\"))) #> $n #> [1] 5 #>  #> $count #> $count$a #> [1] 3 #>  #> $count$b #> [1] 1 #>  #> $count$c #> [1] 1 #>  #>  #> $count_fraction #> $count_fraction$a #> [1] 3.0 0.6 #>  #> $count_fraction$b #> [1] 1.0 0.2 #>  #> $count_fraction$c #> [1] 1.0 0.2 #>  #>  #> $fraction #> $fraction$a #>   num denom  #>     3     5  #>  #> $fraction$b #>   num denom  #>     1     5  #>  #> $fraction$c #>   num denom  #>     1     5  #>  #>  #> $n_blq #> [1] 0 #>   # Empty factor returns zero-filled items. s_summary(factor(levels = c(\"a\", \"b\", \"c\"))) #> $n #> [1] 0 #>  #> $count #> $count$a #> [1] 0 #>  #> $count$b #> [1] 0 #>  #> $count$c #> [1] 0 #>  #>  #> $count_fraction #> $count_fraction$a #> [1] 0 0 #>  #> $count_fraction$b #> [1] 0 0 #>  #> $count_fraction$c #> [1] 0 0 #>  #>  #> $fraction #> $fraction$a #>   num denom  #>     0     0  #>  #> $fraction$b #>   num denom  #>     0     0  #>  #> $fraction$c #>   num denom  #>     0     0  #>  #>  #> $n_blq #> [1] 0 #>   ## Management of NA values. x <- factor(c(NA, \"Female\")) x <- explicit_na(x) s_summary(x, na.rm = TRUE) #> $n #> [1] 1 #>  #> $count #> $count$Female #> [1] 1 #>  #>  #> $count_fraction #> $count_fraction$Female #> [1] 1 1 #>  #>  #> $fraction #> $fraction$Female #>   num denom  #>     1     1  #>  #>  #> $n_blq #> [1] 0 #>  s_summary(x, na.rm = FALSE) #> $n #> [1] 2 #>  #> $count #> $count$Female #> [1] 1 #>  #> $count$`<Missing>` #> [1] 1 #>  #>  #> $count_fraction #> $count_fraction$Female #> [1] 1.0 0.5 #>  #> $count_fraction$`<Missing>` #> [1] 1.0 0.5 #>  #>  #> $fraction #> $fraction$Female #>   num denom  #>     1     2  #>  #> $fraction$`<Missing>` #>   num denom  #>     1     2  #>  #>  #> $n_blq #> [1] 0 #>   ## Different denominators. x <- factor(c(\"a\", \"a\", \"b\", \"c\", \"a\")) s_summary(x, denom = \"N_row\", .N_row = 10L) #> $n #> [1] 5 #>  #> $count #> $count$a #> [1] 3 #>  #> $count$b #> [1] 1 #>  #> $count$c #> [1] 1 #>  #>  #> $count_fraction #> $count_fraction$a #> [1] 3.0 0.3 #>  #> $count_fraction$b #> [1] 1.0 0.1 #>  #> $count_fraction$c #> [1] 1.0 0.1 #>  #>  #> $fraction #> $fraction$a #>   num denom  #>     3    10  #>  #> $fraction$b #>   num denom  #>     1    10  #>  #> $fraction$c #>   num denom  #>     1    10  #>  #>  #> $n_blq #> [1] 0 #>  s_summary(x, denom = \"N_col\", .N_col = 20L) #> $n #> [1] 5 #>  #> $count #> $count$a #> [1] 3 #>  #> $count$b #> [1] 1 #>  #> $count$c #> [1] 1 #>  #>  #> $count_fraction #> $count_fraction$a #> [1] 3.00 0.15 #>  #> $count_fraction$b #> [1] 1.00 0.05 #>  #> $count_fraction$c #> [1] 1.00 0.05 #>  #>  #> $fraction #> $fraction$a #>   num denom  #>     3    20  #>  #> $fraction$b #>   num denom  #>     1    20  #>  #> $fraction$c #>   num denom  #>     1    20  #>  #>  #> $n_blq #> [1] 0 #>   # `s_summary.character`  ## Basic usage: s_summary(c(\"a\", \"a\", \"b\", \"c\", \"a\"), .var = \"x\", verbose = FALSE) #> $n #> [1] 5 #>  #> $count #> $count$a #> [1] 3 #>  #> $count$b #> [1] 1 #>  #> $count$c #> [1] 1 #>  #>  #> $count_fraction #> $count_fraction$a #> [1] 3.0 0.6 #>  #> $count_fraction$b #> [1] 1.0 0.2 #>  #> $count_fraction$c #> [1] 1.0 0.2 #>  #>  #> $fraction #> $fraction$a #>   num denom  #>     3     5  #>  #> $fraction$b #>   num denom  #>     1     5  #>  #> $fraction$c #>   num denom  #>     1     5  #>  #>  #> $n_blq #> [1] 0 #>  s_summary(c(\"a\", \"a\", \"b\", \"c\", \"a\", \"\"), .var = \"x\", na.rm = FALSE, verbose = FALSE) #> $n #> [1] 6 #>  #> $count #> $count$a #> [1] 3 #>  #> $count$b #> [1] 1 #>  #> $count$c #> [1] 1 #>  #> $count$`NA` #> [1] 1 #>  #>  #> $count_fraction #> $count_fraction$a #> [1] 3.0 0.5 #>  #> $count_fraction$b #> [1] 1.0000000 0.1666667 #>  #> $count_fraction$c #> [1] 1.0000000 0.1666667 #>  #> $count_fraction$`NA` #> [1] 1.0000000 0.1666667 #>  #>  #> $fraction #> $fraction$a #>   num denom  #>     3     6  #>  #> $fraction$b #>   num denom  #>     1     6  #>  #> $fraction$c #>   num denom  #>     1     6  #>  #> $fraction$`NA` #>   num denom  #>     1     6  #>  #>  #> $n_blq #> [1] 0 #>   # `s_summary.logical`  ## Basic usage: s_summary(c(TRUE, FALSE, TRUE, TRUE)) #> $n #> [1] 4 #>  #> $count #> [1] 3 #>  #> $count_fraction #> [1] 3.00 0.75 #>  #> $n_blq #> [1] 0 #>   # Empty factor returns zero-filled items. s_summary(as.logical(c())) #> $n #> [1] 0 #>  #> $count #> [1] 0 #>  #> $count_fraction #> [1] 0 0 #>  #> $n_blq #> [1] 0 #>   ## Management of NA values. x <- c(NA, TRUE, FALSE) s_summary(x, na.rm = TRUE) #> $n #> [1] 2 #>  #> $count #> [1] 1 #>  #> $count_fraction #> [1] 1.0 0.5 #>  #> $n_blq #> [1] 0 #>  s_summary(x, na.rm = FALSE) #> $n #> [1] 3 #>  #> $count #> [1] 1 #>  #> $count_fraction #> [1] 1.0000000 0.3333333 #>  #> $n_blq #> [1] 0 #>   ## Different denominators. x <- c(TRUE, FALSE, TRUE, TRUE) s_summary(x, denom = \"N_row\", .N_row = 10L) #> $n #> [1] 4 #>  #> $count #> [1] 3 #>  #> $count_fraction #> [1] 3.0 0.3 #>  #> $n_blq #> [1] 0 #>  s_summary(x, denom = \"N_col\", .N_col = 20L) #> $n #> [1] 4 #>  #> $count #> [1] 3 #>  #> $count_fraction #> [1] 3.00 0.15 #>  #> $n_blq #> [1] 0 #>   a_summary(factor(c(\"a\", \"a\", \"b\", \"c\", \"a\")), .N_row = 10, .N_col = 10) #> RowsVerticalSection (in_rows) object print method: #> ---------------------------- #>                     row_name formatted_cell indent_mod row_label #> 1                          n              5          0         n #> 2                    count.a              3          0         a #> 3                    count.b              1          0         b #> 4                    count.c              1          0         c #> 5           count_fraction.a        3 (60%)          0         a #> 6           count_fraction.b        1 (20%)          0         b #> 7           count_fraction.c        1 (20%)          0         c #> 8  count_fraction_fixed_dp.a      3 (60.0%)          0         a #> 9  count_fraction_fixed_dp.b      1 (20.0%)          0         b #> 10 count_fraction_fixed_dp.c      1 (20.0%)          0         c #> 11                fraction.a    3/5 (60.0%)          0         a #> 12                fraction.b    1/5 (20.0%)          0         b #> 13                fraction.c    1/5 (20.0%)          0         c #> 14                     n_blq              0          0     n_blq a_summary(   factor(c(\"a\", \"a\", \"b\", \"c\", \"a\")),   .ref_group = factor(c(\"a\", \"a\", \"b\", \"c\")), compare = TRUE ) #> RowsVerticalSection (in_rows) object print method: #> ---------------------------- #>                     row_name formatted_cell indent_mod #> 1                          n              5          0 #> 2                    count.a              3          0 #> 3                    count.b              1          0 #> 4                    count.c              1          0 #> 5           count_fraction.a        3 (60%)          0 #> 6           count_fraction.b        1 (20%)          0 #> 7           count_fraction.c        1 (20%)          0 #> 8  count_fraction_fixed_dp.a      3 (60.0%)          0 #> 9  count_fraction_fixed_dp.b      1 (20.0%)          0 #> 10 count_fraction_fixed_dp.c      1 (20.0%)          0 #> 11                fraction.a    3/5 (60.0%)          0 #> 12                fraction.b    1/5 (20.0%)          0 #> 13                fraction.c    1/5 (20.0%)          0 #> 14                     n_blq              0          0 #> 15               pval_counts         0.9560          0 #>                     row_label #> 1                           n #> 2                           a #> 3                           b #> 4                           c #> 5                           a #> 6                           b #> 7                           c #> 8                           a #> 9                           b #> 10                          c #> 11                          a #> 12                          b #> 13                          c #> 14                      n_blq #> 15 p-value (chi-squared test)  a_summary(c(\"A\", \"B\", \"A\", \"C\"), .var = \"x\", .N_col = 10, .N_row = 10, verbose = FALSE) #> RowsVerticalSection (in_rows) object print method: #> ---------------------------- #>                     row_name formatted_cell indent_mod row_label #> 1                          n              4          0         n #> 2                    count.A              2          0         A #> 3                    count.B              1          0         B #> 4                    count.C              1          0         C #> 5           count_fraction.A        2 (50%)          0         A #> 6           count_fraction.B        1 (25%)          0         B #> 7           count_fraction.C        1 (25%)          0         C #> 8  count_fraction_fixed_dp.A      2 (50.0%)          0         A #> 9  count_fraction_fixed_dp.B      1 (25.0%)          0         B #> 10 count_fraction_fixed_dp.C      1 (25.0%)          0         C #> 11                fraction.A    2/4 (50.0%)          0         A #> 12                fraction.B    1/4 (25.0%)          0         B #> 13                fraction.C    1/4 (25.0%)          0         C #> 14                     n_blq              0          0     n_blq a_summary(   c(\"A\", \"B\", \"A\", \"C\"),   .ref_group = c(\"B\", \"A\", \"C\"), .var = \"x\", compare = TRUE, verbose = FALSE ) #> RowsVerticalSection (in_rows) object print method: #> ---------------------------- #>                     row_name formatted_cell indent_mod #> 1                          n              4          0 #> 2                    count.A              2          0 #> 3                    count.B              1          0 #> 4                    count.C              1          0 #> 5           count_fraction.A        2 (50%)          0 #> 6           count_fraction.B        1 (25%)          0 #> 7           count_fraction.C        1 (25%)          0 #> 8  count_fraction_fixed_dp.A      2 (50.0%)          0 #> 9  count_fraction_fixed_dp.B      1 (25.0%)          0 #> 10 count_fraction_fixed_dp.C      1 (25.0%)          0 #> 11                fraction.A    2/4 (50.0%)          0 #> 12                fraction.B    1/4 (25.0%)          0 #> 13                fraction.C    1/4 (25.0%)          0 #> 14                     n_blq              0          0 #> 15               pval_counts         0.9074          0 #>                     row_label #> 1                           n #> 2                           A #> 3                           B #> 4                           C #> 5                           A #> 6                           B #> 7                           C #> 8                           A #> 9                           B #> 10                          C #> 11                          A #> 12                          B #> 13                          C #> 14                      n_blq #> 15 p-value (chi-squared test)  a_summary(c(TRUE, FALSE, FALSE, TRUE, TRUE), .N_row = 10, .N_col = 10) #> RowsVerticalSection (in_rows) object print method: #> ---------------------------- #>                  row_name formatted_cell indent_mod      row_label #> 1                       n              5          0              n #> 2                   count              3          0          count #> 3          count_fraction        3 (60%)          0 count_fraction #> 4 count_fraction_fixed_dp      3 (60.0%)          0 count_fraction #> 5                fraction                         0       fraction #> 6                   n_blq              0          0          n_blq a_summary(   c(TRUE, FALSE, FALSE, TRUE, TRUE),   .ref_group = c(TRUE, FALSE), .in_ref_col = TRUE, compare = TRUE ) #> RowsVerticalSection (in_rows) object print method: #> ---------------------------- #>                  row_name formatted_cell indent_mod                  row_label #> 1                       n              5          0                          n #> 2                   count              3          0                      count #> 3          count_fraction        3 (60%)          0             count_fraction #> 4 count_fraction_fixed_dp      3 (60.0%)          0             count_fraction #> 5                fraction                         0                   fraction #> 6                   n_blq              0          0                      n_blq #> 7             pval_counts                         0 p-value (chi-squared test)  a_summary(rnorm(10), .N_col = 10, .N_row = 20, .var = \"bla\") #> RowsVerticalSection (in_rows) object print method: #> ---------------------------- #>           row_name       formatted_cell indent_mod                   row_label #> 1                n                   10          0                           n #> 2              sum                 -4.4          0                         Sum #> 3             mean                 -0.4          0                        Mean #> 4               sd                  1.1          0                          SD #> 5               se                  0.4          0                          SE #> 6          mean_sd           -0.4 (1.1)          0                   Mean (SD) #> 7          mean_se           -0.4 (0.4)          0                   Mean (SE) #> 8          mean_ci        (-1.24, 0.36)          0                 Mean 95% CI #> 9         mean_sei       (-0.79, -0.09)          0               Mean -/+ 1xSE #> 10        mean_sdi        (-1.56, 0.68)          0               Mean -/+ 1xSD #> 11       mean_pval               0.2432          0 Mean p-value (H0: mean = 0) #> 12          median                 -0.2          0                      Median #> 13             mad                  0.0          0   Median Absolute Deviation #> 14       median_ci        (-1.82, 0.62)          0               Median 95% CI #> 15       quantiles           -1.4 - 0.3          0             25% and 75%-ile #> 16             iqr                  1.7          0                         IQR #> 17           range           -2.4 - 1.1          0                   Min - Max #> 18             min                 -2.4          0                     Minimum #> 19             max                  1.1          0                     Maximum #> 20    median_range    -0.2 (-2.4 - 1.1)          0          Median (Min - Max) #> 21              cv               -253.2          0                      CV (%) #> 22       geom_mean                   NA          0              Geometric Mean #> 23    geom_mean_ci                   NA          0       Geometric Mean 95% CI #> 24         geom_cv                   NA          0         CV % Geometric Mean #> 25    median_ci_3d -0.25 (-1.82 - 0.62)          0             Median (95% CI) #> 26      mean_ci_3d -0.44 (-1.24 - 0.36)          0               Mean (95% CI) #> 27 geom_mean_ci_3d                   NA          0     Geometric Mean (95% CI) a_summary(rnorm(10, 5, 1), .ref_group = rnorm(20, -5, 1), .var = \"bla\", compare = TRUE) #> RowsVerticalSection (in_rows) object print method: #> ---------------------------- #>           row_name     formatted_cell indent_mod                   row_label #> 1                n                 10          0                           n #> 2              sum               48.2          0                         Sum #> 3             mean                4.8          0                        Mean #> 4               sd                1.2          0                          SD #> 5               se                0.4          0                          SE #> 6          mean_sd          4.8 (1.2)          0                   Mean (SD) #> 7          mean_se          4.8 (0.4)          0                   Mean (SE) #> 8          mean_ci       (3.98, 5.66)          0                 Mean 95% CI #> 9         mean_sei       (4.45, 5.19)          0               Mean -/+ 1xSE #> 10        mean_sdi       (3.65, 6.00)          0               Mean -/+ 1xSD #> 11       mean_pval            <0.0001          0 Mean p-value (H0: mean = 0) #> 12          median                4.7          0                      Median #> 13             mad                0.0          0   Median Absolute Deviation #> 14       median_ci       (3.37, 5.63)          0               Median 95% CI #> 15       quantiles          4.1 - 5.5          0             25% and 75%-ile #> 16             iqr                1.5          0                         IQR #> 17           range          3.1 - 7.1          0                   Min - Max #> 18             min                3.1          0                     Minimum #> 19             max                7.1          0                     Maximum #> 20    median_range    4.7 (3.1 - 7.1)          0          Median (Min - Max) #> 21              cv               24.4          0                      CV (%) #> 22       geom_mean                4.7          0              Geometric Mean #> 23    geom_mean_ci       (3.93, 5.60)          0       Geometric Mean 95% CI #> 24         geom_cv               25.2          0         CV % Geometric Mean #> 25    median_ci_3d 4.71 (3.37 - 5.63)          0             Median (95% CI) #> 26      mean_ci_3d 4.82 (3.98 - 5.66)          0               Mean (95% CI) #> 27 geom_mean_ci_3d 4.69 (3.93 - 5.60)          0     Geometric Mean (95% CI) #> 28            pval            <0.0001          0            p-value (t-test)"},{"path":"https://insightsengineering.github.io/tern/main/reference/analyze_vars_in_cols.html","id":null,"dir":"Reference","previous_headings":"","what":"Analyze numeric variables in columns — analyze_vars_in_cols","title":"Analyze numeric variables in columns — analyze_vars_in_cols","text":"layout-creating function analyze_vars_in_cols() creates layout element generate column-wise analysis table. function sets analysis methods column labels wrapper rtables::analyze_colvars(). designed principally PK tables.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/analyze_vars_in_cols.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Analyze numeric variables in columns — analyze_vars_in_cols","text":"","code":"analyze_vars_in_cols(   lyt,   vars,   ...,   .stats = c(\"n\", \"mean\", \"sd\", \"se\", \"cv\", \"geom_cv\"),   .labels = c(n = \"n\", mean = \"Mean\", sd = \"SD\", se = \"SE\", cv = \"CV (%)\", geom_cv =     \"CV % Geometric Mean\"),   row_labels = NULL,   do_summarize_row_groups = FALSE,   split_col_vars = TRUE,   imp_rule = NULL,   avalcat_var = \"AVALCAT1\",   cache = FALSE,   .indent_mods = NULL,   na_str = default_na_str(),   nested = TRUE,   .formats = NULL,   .aligns = NULL )"},{"path":"https://insightsengineering.github.io/tern/main/reference/analyze_vars_in_cols.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Analyze numeric variables in columns — analyze_vars_in_cols","text":"lyt (PreDataTableLayouts) layout analyses added . vars (character) variable names primary analysis variable iterated . ... additional arguments lower level functions. .stats (character) statistics select table. .labels (named character) labels statistics (without indent). row_labels (character) function works columns space, usually .labels character vector applies column space. can change row labels defining parameter named character vector names corresponding split values. defaults NULL contains one string, duplicate row label. do_summarize_row_groups (flag) defaults FALSE applies analysis current label rows. wrapper rtables::summarize_row_groups() can accept labelstr define row labels. behavior supported never need overload row labels. split_col_vars (flag) defaults TRUE puts analysis results onto columns. option allows add multiple instances functions, also nested fashion, without adding splits. split must happen one time single layout. imp_rule (string NULL) imputation rule setting. Defaults NULL imputation rule. Can also \"1/3\" implement 1/3 imputation rule \"1/2\" implement 1/2 imputation rule. order use imputation rule, avalcat_var argument must specified. See imputation_rule() details imputation. avalcat_var (string) imp_rule NULL, name variable indicates whether row data corresponds analysis value category \"BLQ\", \"LTR\", \"<PCLLOQ\", none (defaults \"AVALCAT1\"). Variable must present data match variable used calculate n_blq statistic (included .stats). cache (flag) whether store computed values temporary caching environment. speed calculations large tables, set FALSE rtable layout used multiple tables different data. Defaults FALSE. .indent_mods (named integer) indent modifiers labels. Defaults 0, corresponds unmodified default behavior. Can negative. na_str (string) string used replace NA empty values output. nested (flag) whether layout instruction applied within existing layout structure _if possible (TRUE, default) new top-level element (FALSE). Ignored nest split. underneath analyses, allowed. .formats (named character list) formats statistics. See Details analyze_vars information \"auto\" setting. .aligns (character NULL) alignment table contents (including labels). NULL, \"center\" applied. See formatters::list_valid_aligns() list currently supported alignments.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/analyze_vars_in_cols.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Analyze numeric variables in columns — analyze_vars_in_cols","text":"layout object suitable passing layouting functions, rtables::build_table(). Adding function rtable layout summarize given variables, arrange output columns, add table layout.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/analyze_vars_in_cols.html","id":"note","dir":"Reference","previous_headings":"","what":"Note","title":"Analyze numeric variables in columns — analyze_vars_in_cols","text":"experimental implementation rtables::summarize_row_groups() rtables::analyze_colvars() may subjected changes rtables extends support complex analysis pipelines column space. encourage users read examples carefully file issues different use cases. function, labelstr behaves atypically. labelstr = NULL (default), row labels assigned automatically split values do_summarize_row_groups = FALSE (default), group label do_summarize_row_groups = TRUE.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/main/reference/analyze_vars_in_cols.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Analyze numeric variables in columns — analyze_vars_in_cols","text":"","code":"library(dplyr)  # Data preparation adpp <- tern_ex_adpp %>% h_pkparam_sort()  lyt <- basic_table() %>%   split_rows_by(var = \"STRATA1\", label_pos = \"topleft\") %>%   split_rows_by(     var = \"SEX\",     label_pos = \"topleft\",     child_labels = \"hidden\"   ) %>% # Removes duplicated labels   analyze_vars_in_cols(vars = \"AGE\") result <- build_table(lyt = lyt, df = adpp) result #> STRATA1                                                          #>   SEX      n    Mean    SD    SE    CV (%)   CV % Geometric Mean #> ———————————————————————————————————————————————————————————————— #> A                                                                #>   F       81    38.8   5.4    0.6    13.8           14.3         #>   M       81    38.9   5.9    0.7    15.1           14.9         #> B                                                                #>   F       90    36.0   6.4    0.7    17.7           17.9         #>   M       81    36.4   6.5    0.7    17.9           17.8         #> C                                                                #>   F       117   34.1   6.2    0.6    18.2           18.3         #>   M       72    33.2   11.5   1.4    34.6           31.6          # By selecting just some statistics and ad-hoc labels lyt <- basic_table() %>%   split_rows_by(var = \"ARM\", label_pos = \"topleft\") %>%   split_rows_by(     var = \"SEX\",     label_pos = \"topleft\",     child_labels = \"hidden\",     split_fun = drop_split_levels   ) %>%   analyze_vars_in_cols(     vars = \"AGE\",     .stats = c(\"n\", \"cv\", \"geom_mean\"),     .labels = c(       n = \"aN\",       cv = \"aCV\",       geom_mean = \"aGeomMean\"     )   ) result <- build_table(lyt = lyt, df = adpp) result #> ARM                                     #>   SEX            aN    aCV    aGeomMean #> ——————————————————————————————————————— #> A: Drug X                               #> B: Placebo                              #> C: Combination                          #>   F              288   17.6     35.5    #>   M              234   23.4     35.3     # Changing row labels lyt <- basic_table() %>%   analyze_vars_in_cols(     vars = \"AGE\",     row_labels = \"some custom label\"   ) result <- build_table(lyt, df = adpp) result #>                      n    Mean   SD    SE    CV (%)   CV % Geometric Mean #> ————————————————————————————————————————————————————————————————————————— #> some custom label   522   36.1   7.4   0.3    20.4           20.6          # Pharmacokinetic parameters lyt <- basic_table() %>%   split_rows_by(     var = \"TLG_DISPLAY\",     split_label = \"PK Parameter\",     label_pos = \"topleft\",     child_labels = \"hidden\"   ) %>%   analyze_vars_in_cols(     vars = \"AVAL\"   ) result <- build_table(lyt, df = adpp) result #> PK Parameter   n    Mean     SD    SE    CV (%)   CV % Geometric Mean #> ————————————————————————————————————————————————————————————————————— #> Cmax           58   29.7    5.6    0.7    19.0           19.3         #> AUCinf obs     58   207.5   34.9   4.6    16.8           17.3         #> CL obs         58    5.1    1.0    0.1    20.6           22.7         #> Ae             58    1.5    0.3    0.0    21.3           24.1         #> Fe             58   15.7    3.6    0.5    22.7           24.0         #> CLR            58    0.0    0.0    0.0    19.9           22.2         #> Rmax           58    9.6    2.0    0.3    21.1           21.6         #> Tonset         58    3.0    0.7    0.1    22.4           23.3         #> RENALCLD       58    0.0    0.0    0.0    19.0           19.4          # Multiple calls (summarize label and analyze underneath) lyt <- basic_table() %>%   split_rows_by(     var = \"TLG_DISPLAY\",     split_label = \"PK Parameter\",     label_pos = \"topleft\"   ) %>%   analyze_vars_in_cols(     vars = \"AVAL\",     do_summarize_row_groups = TRUE # does a summarize level   ) %>%   split_rows_by(\"SEX\",     child_labels = \"hidden\",     label_pos = \"topleft\"   ) %>%   analyze_vars_in_cols(     vars = \"AVAL\",     split_col_vars = FALSE # avoids re-splitting the columns   ) result <- build_table(lyt, df = adpp) result #> PK Parameter                                                          #>   SEX          n    Mean     SD    SE    CV (%)   CV % Geometric Mean #> ————————————————————————————————————————————————————————————————————— #> Cmax           58   29.7    5.6    0.7    19.0           19.3         #>   F            32   30.1    6.1    1.1    20.4           21.0         #>   M            26   29.2    5.0    1.0    17.2           17.2         #> AUCinf obs     58   207.5   34.9   4.6    16.8           17.3         #>   F            32   209.5   43.3   7.7    20.7           21.6         #>   M            26   205.0   20.9   4.1    10.2           10.4         #> CL obs         58    5.1    1.0    0.1    20.6           22.7         #>   F            32    5.1    1.1    0.2    20.8           23.2         #>   M            26    5.1    1.1    0.2    20.7           22.5         #> Ae             58    1.5    0.3    0.0    21.3           24.1         #>   F            32    1.5    0.3    0.1    19.3           20.8         #>   M            26    1.5    0.4    0.1    23.9           27.9         #> Fe             58   15.7    3.6    0.5    22.7           24.0         #>   F            32   16.3    3.4    0.6    20.9           22.3         #>   M            26   15.0    3.7    0.7    24.7           25.6         #> CLR            58    0.0    0.0    0.0    19.9           22.2         #>   F            32    0.0    0.0    0.0    20.5           24.8         #>   M            26    0.0    0.0    0.0    19.5           18.9         #> Rmax           58    9.6    2.0    0.3    21.1           21.6         #>   F            32    9.6    2.2    0.4    22.4           23.5         #>   M            26    9.6    1.9    0.4    19.7           19.5         #> Tonset         58    3.0    0.7    0.1    22.4           23.3         #>   F            32    3.0    0.7    0.1    24.7           25.9         #>   M            26    3.0    0.6    0.1    19.8           20.0         #> RENALCLD       58    0.0    0.0    0.0    19.0           19.4         #>   F            32    0.0    0.0    0.0    19.6           20.4         #>   M            26    0.0    0.0    0.0    18.0           17.6"},{"path":"https://insightsengineering.github.io/tern/main/reference/append_varlabels.html","id":null,"dir":"Reference","previous_headings":"","what":"Add variable labels to top left corner in table — append_varlabels","title":"Add variable labels to top left corner in table — append_varlabels","text":"Helper layout-creating function append variable labels given variables vector given dataset top left corner. variable label found variable name used instead. Multiple variable labels concatenated slashes.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/append_varlabels.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Add variable labels to top left corner in table — append_varlabels","text":"","code":"append_varlabels(lyt, df, vars, indent = 0L)"},{"path":"https://insightsengineering.github.io/tern/main/reference/append_varlabels.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Add variable labels to top left corner in table — append_varlabels","text":"lyt (PreDataTableLayouts) layout analyses added . df (data.frame) data set containing analysis variables. vars (character) variable names labels looked df. indent (integer(1)) non-negative number nested indent space, default 0L means indent. 1L means two spaces indent, 2L means four spaces indent .","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/append_varlabels.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Add variable labels to top left corner in table — append_varlabels","text":"modified layout new variable label(s) added top-left material.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/append_varlabels.html","id":"note","dir":"Reference","previous_headings":"","what":"Note","title":"Add variable labels to top left corner in table — append_varlabels","text":"optimal implementation course, since using data set layout creation. mature rtables implementation also improved necessary anymore.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/append_varlabels.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Add variable labels to top left corner in table — append_varlabels","text":"","code":"lyt <- basic_table() %>%   split_cols_by(\"ARM\") %>%   add_colcounts() %>%   split_rows_by(\"SEX\") %>%   append_varlabels(DM, \"SEX\") %>%   analyze(\"AGE\", afun = mean) %>%   append_varlabels(DM, \"AGE\", indent = 1) build_table(lyt, DM) #> SEX                   A: Drug X          B: Placebo       C: Combination  #>   Age                  (N=121)            (N=106)            (N=129)      #> ————————————————————————————————————————————————————————————————————————— #> F                                                                         #>   mean             33.7142857142857   33.8392857142857   34.8852459016393 #> M                                                                         #>   mean             36.5490196078431         32.1         34.2794117647059 #> U                                                                         #>   mean                    NA                 NA                 NA        #> UNDIFFERENTIATED                                                          #>   mean                    NA                 NA                 NA         lyt <- basic_table() %>%   split_cols_by(\"ARM\") %>%   split_rows_by(\"SEX\") %>%   analyze(\"AGE\", afun = mean) %>%   append_varlabels(DM, c(\"SEX\", \"AGE\")) build_table(lyt, DM) #> SEX / Age             A: Drug X          B: Placebo       C: Combination  #> ————————————————————————————————————————————————————————————————————————— #> F                                                                         #>   mean             33.7142857142857   33.8392857142857   34.8852459016393 #> M                                                                         #>   mean             36.5490196078431         32.1         34.2794117647059 #> U                                                                         #>   mean                    NA                 NA                 NA        #> UNDIFFERENTIATED                                                          #>   mean                    NA                 NA                 NA"},{"path":"https://insightsengineering.github.io/tern/main/reference/apply_auto_formatting.html","id":null,"dir":"Reference","previous_headings":"","what":"Apply automatic formatting — apply_auto_formatting","title":"Apply automatic formatting — apply_auto_formatting","text":"Checks listed formats .formats \"auto\", replaces \"auto\" correct implementation format_auto given statistics, data, variable.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/apply_auto_formatting.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Apply automatic formatting — apply_auto_formatting","text":"","code":"apply_auto_formatting(.formats, x_stats, .df_row, .var)"},{"path":"https://insightsengineering.github.io/tern/main/reference/apply_auto_formatting.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Apply automatic formatting — apply_auto_formatting","text":".formats (named character list) formats statistics. See Details analyze_vars information \"auto\" setting. x_stats (named list) named list statistics element corresponds element .formats, matching names. .df_row (data.frame) data frame across columns given row split. .var (string) single variable name passed rtables requested statistics function.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/argument_convention.html","id":null,"dir":"Reference","previous_headings":"","what":"Standard arguments — argument_convention","title":"Standard arguments — argument_convention","text":"documentation function lists arguments tern used repeatedly express analysis.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/argument_convention.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Standard arguments — argument_convention","text":"... additional arguments lower level functions. .aligns (character NULL) alignment table contents (including labels). NULL, \"center\" applied. See formatters::list_valid_aligns() list currently supported alignments. .all_col_counts (integer) vector value represents global count column. Values taken alt_counts_df specified (see rtables::build_table()). .df_row (data.frame) data frame across columns given row split. .formats (named character list) formats statistics. See Details analyze_vars information \"auto\" setting. .in_ref_col (flag)TRUE working reference level, FALSE otherwise. .indent_mods (named integer) indent modifiers labels. Defaults 0, corresponds unmodified default behavior. Can negative. .labels (named character) labels statistics (without indent). .N_col (integer(1)) column-wise N (column count) full column analyzed typically passed rtables. .N_row (integer(1)) row-wise N (row group count) group observations analyzed (.e. column-based subsetting) typically passed rtables. .ref_group (data.frame vector) data corresponding reference group. .spl_context (data.frame) gives information ancestor split states passed rtables. .stats (character) statistics select table. .var (string) single variable name passed rtables requested statistics function. add_total_level (flag) adds \"total\" level others includes levels constitute split. custom label can set level via custom_label argument. col_by (factor) defining column groups. conf_level (proportion) confidence level interval. data (data.frame) dataset containing variables summarize. denom (string) choice denominator proportion. Options : n: number values row column intersection. N_row: total number values row across columns. N_col: total number values column across rows. df (data.frame) data set containing analysis variables. groups_lists (named list list) optionally contains subgroups variable list, specifies new group levels via names levels belong character vectors elements list. id (string) subject variable name. is_event (flag)TRUE event, FALSE time event censored. label_all (string) label total population analysis. labelstr (string) label level parent split currently summarized (must present second argument Content Row Functions). See rtables::summarize_row_groups() information. lyt (PreDataTableLayouts) layout analyses added . method (string NULL) specifies test used calculate p-value difference two proportions. options, see test_proportion_diff(). Default NULL test performed. na.rm (flag) whether NA values removed x prior analysis. na_str (string) string used replace NA empty values output. nested (flag) whether layout instruction applied within existing layout structure _if possible (TRUE, default) new top-level element (FALSE). Ignored nest split. underneath analyses, allowed. prune_zero_rows (flag) whether prune zero rows. riskdiff (flag) whether risk difference column present. set TRUE, add_riskdiff() must used split_fun prior column split table layout, specifying columns compared. See stat_propdiff_ci() details risk difference calculation. rsp (logical) vector indicating whether subject responder . show_labels (string) label visibility: one \"default\", \"visible\" \"hidden\". section_div (string) string repeated section divider group defined split instruction, NA_character_ (default) section divider. table_names (character) can customized case vars analyzed multiple times, avoid warnings rtables. tte (numeric) vector time--event duration values. var_labels (character) variable labels. variables (named list string) list additional analysis variables. vars (character) variable names primary analysis variable iterated . var (string) single variable name primary analysis variable. x (numeric) vector numbers want analyze. xlim (numeric(2)) vector containing lower upper limits x-axis, respectively. NULL (default), default scale range used. ylim (numeric(2)) vector containing lower upper limits y-axis, respectively. NULL (default), default scale range used.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/argument_convention.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Standard arguments — argument_convention","text":"Although function just returns NULL two uses, tern users provides documentation arguments commonly consistently used framework. developer adds single reference point import roxygen argument description : @inheritParams argument_convention","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/arrange_grobs.html","id":null,"dir":"Reference","previous_headings":"","what":"Arrange multiple grobs — arrange_grobs","title":"Arrange multiple grobs — arrange_grobs","text":"Arrange grobs new grob n * m (rows * cols) layout.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/arrange_grobs.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Arrange multiple grobs — arrange_grobs","text":"","code":"arrange_grobs(   ...,   grobs = list(...),   ncol = NULL,   nrow = NULL,   padding_ht = grid::unit(2, \"line\"),   padding_wt = grid::unit(2, \"line\"),   vp = NULL,   gp = NULL,   name = NULL )"},{"path":"https://insightsengineering.github.io/tern/main/reference/arrange_grobs.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Arrange multiple grobs — arrange_grobs","text":"... grobs. grobs (list grob) list grobs. ncol (integer(1)) number columns layout. nrow (integer(1)) number rows layout. padding_ht (grid::unit) unit length 1, vertical space grob. padding_wt (grid::unit) unit length 1, horizontal space grob. vp (viewport NULL) viewport() object (NULL). gp (gpar) gpar() object. name (string) character identifier grob.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/arrange_grobs.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Arrange multiple grobs — arrange_grobs","text":"grob.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/arrange_grobs.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Arrange multiple grobs — arrange_grobs","text":"","code":"library(grid)  # \\donttest{ num <- lapply(1:9, textGrob) grid::grid.newpage() grid.draw(arrange_grobs(grobs = num, ncol = 2)) #> Warning: `arrange_grobs()` was deprecated in tern 0.9.4. #> ℹ `tern` plotting functions no longer generate `grob` objects.  showViewport()   g1 <- circleGrob(gp = gpar(col = \"blue\")) g2 <- circleGrob(gp = gpar(col = \"red\")) g3 <- textGrob(\"TEST TEXT\") grid::grid.newpage() grid.draw(arrange_grobs(g1, g2, g3, nrow = 2))  showViewport()   grid::grid.newpage() grid.draw(arrange_grobs(g1, g2, g3, ncol = 3))   grid::grid.newpage() grid::pushViewport(grid::viewport(layout = grid::grid.layout(1, 2))) vp1 <- grid::viewport(layout.pos.row = 1, layout.pos.col = 2) grid.draw(arrange_grobs(g1, g2, g3, ncol = 2, vp = vp1))  showViewport()  # }"},{"path":"https://insightsengineering.github.io/tern/main/reference/as.rtable.html","id":null,"dir":"Reference","previous_headings":"","what":"Convert to rtable — as.rtable","title":"Convert to rtable — as.rtable","text":"new generic function convert objects rtable tables.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/as.rtable.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Convert to rtable — as.rtable","text":"","code":"as.rtable(x, ...)  # S3 method for class 'data.frame' as.rtable(x, format = \"xx.xx\", ...)"},{"path":"https://insightsengineering.github.io/tern/main/reference/as.rtable.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Convert to rtable — as.rtable","text":"x (data.frame) object converted rtable. ... additional arguments methods. format (string function) format used columns.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/as.rtable.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Convert to rtable — as.rtable","text":"rtables table object. Note concrete class depend method used.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/as.rtable.html","id":"methods-by-class-","dir":"Reference","previous_headings":"","what":"Methods (by class)","title":"Convert to rtable — as.rtable","text":".rtable(data.frame): Method converting data.frame contains numeric columns rtable.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/as.rtable.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Convert to rtable — as.rtable","text":"","code":"x <- data.frame(   a = 1:10,   b = rnorm(10) ) as.rtable(x) #>        a       b   #> —————————————————— #> 1    1.00    0.07  #> 2    2.00    -0.64 #> 3    3.00    -0.05 #> 4    4.00    -0.25 #> 5    5.00    0.44  #> 6    6.00    2.76  #> 7    7.00    0.05  #> 8    8.00    0.58  #> 9    9.00    0.12  #> 10   10.00   -1.91"},{"path":"https://insightsengineering.github.io/tern/main/reference/as_factor_keep_attributes.html","id":null,"dir":"Reference","previous_headings":"","what":"Conversion of a vector to a factor — as_factor_keep_attributes","title":"Conversion of a vector to a factor — as_factor_keep_attributes","text":"Converts x factor keeps attributes. Warns appropriately user can decide whether prefer converting factor manually (e.g. full control factor levels).","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/as_factor_keep_attributes.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Conversion of a vector to a factor — as_factor_keep_attributes","text":"","code":"as_factor_keep_attributes(   x,   x_name = deparse(substitute(x)),   na_level = \"<Missing>\",   verbose = TRUE )"},{"path":"https://insightsengineering.github.io/tern/main/reference/as_factor_keep_attributes.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Conversion of a vector to a factor — as_factor_keep_attributes","text":"x (vector) object convert. x_name (string) name x. na_level (string) explicit missing level used converting character vector. verbose (flag) defaults TRUE. prints warnings messages.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/as_factor_keep_attributes.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Conversion of a vector to a factor — as_factor_keep_attributes","text":"factor attributes (except class) x. modify x already factor.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/assertions.html","id":null,"dir":"Reference","previous_headings":"","what":"Additional assertions to use with checkmate — assertions","title":"Additional assertions to use with checkmate — assertions","text":"Additional assertion functions can used together checkmate package.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/assertions.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Additional assertions to use with checkmate — assertions","text":"","code":"assert_list_of_variables(x, .var.name = checkmate::vname(x), add = NULL)  assert_df_with_variables(   df,   variables,   na_level = NULL,   .var.name = checkmate::vname(df),   add = NULL )  assert_valid_factor(   x,   min.levels = 1,   max.levels = NULL,   null.ok = TRUE,   any.missing = TRUE,   n.levels = NULL,   len = NULL,   .var.name = checkmate::vname(x),   add = NULL )  assert_df_with_factors(   df,   variables,   min.levels = 1,   max.levels = NULL,   any.missing = TRUE,   na_level = NULL,   .var.name = checkmate::vname(df),   add = NULL )  assert_proportion_value(x, include_boundaries = FALSE)"},{"path":"https://insightsengineering.github.io/tern/main/reference/assertions.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Additional assertions to use with checkmate — assertions","text":"x () object test. .var.name [character(1)] Name checked object print assertions. Defaults heuristic implemented vname. add [AssertCollection] Collection store assertion messages. See AssertCollection. df (data.frame) data set test. variables (named list character) list variables test. na_level (string) string using represent NA missing data. NA values please consider using directly .na() similar approaches. min.levels [integer(1)] Minimum number factor levels. Default NULL (check). max.levels [integer(1)] Maximum number factor levels. Default NULL (check). null.ok [logical(1)] set TRUE, x may also NULL. case type check x performed, additional checks disabled. .missing [logical(1)] vectors missing values allowed? Default TRUE. n.levels [integer(1)] Exact number factor levels. Default NULL (check). len [integer(1)] Exact expected length x. include_boundaries (flag) whether include boundaries testing proportions.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/assertions.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Additional assertions to use with checkmate — assertions","text":"Nothing assertion passes, otherwise prints error message.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/assertions.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Additional assertions to use with checkmate — assertions","text":"assert_list_of_variables(): Checks whether x valid list variable names. NULL elements list x dropped Filter(Negate(.null), x). assert_df_with_variables(): Check whether df data frame analysis variables. Please notice produces error variables present data.frame opposite required. assert_valid_factor(): Check whether x valid factor (.e. levels empty string levels). Note NULL NA elements allowed. assert_df_with_factors(): Check whether df data frame analysis variables factors. Note creation NA direct call factor() trim NA levels vector list . assert_proportion_value(): Check whether x proportion: number 0 1.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/bins_percent_labels.html","id":null,"dir":"Reference","previous_headings":"","what":"Labels for bins in percent — bins_percent_labels","title":"Labels for bins in percent — bins_percent_labels","text":"creates labels quantile based bins percent. assumes right-closed intervals produced cut_quantile_bins().","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/bins_percent_labels.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Labels for bins in percent — bins_percent_labels","text":"","code":"bins_percent_labels(probs, digits = 0)"},{"path":"https://insightsengineering.github.io/tern/main/reference/bins_percent_labels.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Labels for bins in percent — bins_percent_labels","text":"probs (numeric) probabilities identifying quantiles. sorted vector unique proportion values, .e. 0 1, boundaries 0 1 must included. digits (integer(1)) number decimal places round percent numbers.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/bins_percent_labels.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Labels for bins in percent — bins_percent_labels","text":"character vector labels format [0%,20%], (20%,50%], etc.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/c_label_n.html","id":null,"dir":"Reference","previous_headings":"","what":"Content row function to add row total to labels — c_label_n","title":"Content row function to add row total to labels — c_label_n","text":"takes label latest row split level adds row total df parentheses. function differs c_label_n_alt() taking row counts df rather alt_counts_df, used add_rowcounts() alt_counts set FALSE.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/c_label_n.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Content row function to add row total to labels — c_label_n","text":"","code":"c_label_n(df, labelstr, .N_row)"},{"path":"https://insightsengineering.github.io/tern/main/reference/c_label_n.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Content row function to add row total to labels — c_label_n","text":"df (data.frame) data set containing analysis variables. labelstr (string) label level parent split currently summarized (must present second argument Content Row Functions). See rtables::summarize_row_groups() information. .N_row (integer(1)) row-wise N (row group count) group observations analyzed (.e. column-based subsetting) typically passed rtables.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/c_label_n.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Content row function to add row total to labels — c_label_n","text":"list formatted rtables::CellValue() row count value correct label.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/c_label_n.html","id":"note","dir":"Reference","previous_headings":"","what":"Note","title":"Content row function to add row total to labels — c_label_n","text":"important use df rather .N_row implementation, former already split columns refer first column data .","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/main/reference/c_label_n_alt.html","id":null,"dir":"Reference","previous_headings":"","what":"Content row function to add alt_counts_df row total to labels — c_label_n_alt","title":"Content row function to add alt_counts_df row total to labels — c_label_n_alt","text":"takes label latest row split level adds row total alt_counts_df parentheses. function differs c_label_n() taking row counts alt_counts_df rather df, used add_rowcounts() alt_counts set TRUE.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/c_label_n_alt.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Content row function to add alt_counts_df row total to labels — c_label_n_alt","text":"","code":"c_label_n_alt(df, labelstr, .alt_df_row)"},{"path":"https://insightsengineering.github.io/tern/main/reference/c_label_n_alt.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Content row function to add alt_counts_df row total to labels — c_label_n_alt","text":"df (data.frame) data set containing analysis variables. labelstr (string) label level parent split currently summarized (must present second argument Content Row Functions). See rtables::summarize_row_groups() information.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/c_label_n_alt.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Content row function to add alt_counts_df row total to labels — c_label_n_alt","text":"list formatted rtables::CellValue() row count value correct label.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/main/reference/cfun_by_flag.html","id":null,"dir":"Reference","previous_headings":"","what":"Constructor for content functions given a data frame with flag input — cfun_by_flag","title":"Constructor for content functions given a data frame with flag input — cfun_by_flag","text":"can useful tabulating model results.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/cfun_by_flag.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Constructor for content functions given a data frame with flag input — cfun_by_flag","text":"","code":"cfun_by_flag(analysis_var, flag_var, format = \"xx\", .indent_mods = NULL)"},{"path":"https://insightsengineering.github.io/tern/main/reference/cfun_by_flag.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Constructor for content functions given a data frame with flag input — cfun_by_flag","text":"analysis_var (string) variable name column containing values returned content function. flag_var (string) variable name logical column identifying row returned. format (string)rtables format use.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/cfun_by_flag.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Constructor for content functions given a data frame with flag input — cfun_by_flag","text":"content function gives df$analysis_var row identified .df_row$flag given format.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/check_diff_prop_ci.html","id":null,"dir":"Reference","previous_headings":"","what":"Check proportion difference arguments — check_diff_prop_ci","title":"Check proportion difference arguments — check_diff_prop_ci","text":"Verifies /convert arguments valid values used estimation difference responder proportions.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/check_diff_prop_ci.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Check proportion difference arguments — check_diff_prop_ci","text":"","code":"check_diff_prop_ci(rsp, grp, strata = NULL, conf_level, correct = NULL)"},{"path":"https://insightsengineering.github.io/tern/main/reference/check_diff_prop_ci.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Check proportion difference arguments — check_diff_prop_ci","text":"rsp (logical) vector indicating whether subject responder . grp (factor) vector assigning observations one two groups (e.g. reference treatment group). strata (factor) variable one level per stratum length rsp. conf_level (proportion) confidence level interval. correct (flag) whether include continuity correction. information, see stats::prop.test().","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/check_same_n.html","id":null,"dir":"Reference","previous_headings":"","what":"Check element dimension — check_same_n","title":"Check element dimension — check_same_n","text":"Checks elements ... dimension.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/check_same_n.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Check element dimension — check_same_n","text":"","code":"check_same_n(..., omit_null = TRUE)"},{"path":"https://insightsengineering.github.io/tern/main/reference/check_same_n.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Check element dimension — check_same_n","text":"... (data.frame vector) data frames vectors. omit_null (flag) whether NULL elements ... omitted check.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/check_same_n.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Check element dimension — check_same_n","text":"logical value.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/combination_function.html","id":null,"dir":"Reference","previous_headings":"","what":"Class for CombinationFunction — combination_function","title":"Class for CombinationFunction — combination_function","text":"CombinationFunction S4 class extends standard functions. special functions can combined negated logical operators.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/combination_function.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Class for CombinationFunction — combination_function","text":"","code":"# S4 method for class 'CombinationFunction,CombinationFunction' e1 & e2  # S4 method for class 'CombinationFunction,CombinationFunction' e1 | e2  # S4 method for class 'CombinationFunction' !x"},{"path":"https://insightsengineering.github.io/tern/main/reference/combination_function.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Class for CombinationFunction — combination_function","text":"e1 (CombinationFunction) left hand side logical operator. e2 (CombinationFunction) right hand side logical operator. x (CombinationFunction) function negated.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/combination_function.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Class for CombinationFunction — combination_function","text":"logical value indicating whether left hand side equation equals right hand side.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/combination_function.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Class for CombinationFunction — combination_function","text":"e1 & e2: Logical \"\" combination CombinationFunction functions. resulting object class, evaluates two argument functions. result \"\" two individual results. e1 | e2: Logical \"\" combination CombinationFunction functions. resulting object class, evaluates two argument functions. result \"\" two individual results. `!`(CombinationFunction): Logical negation CombinationFunction functions. resulting object class, evaluates original function. result opposite results.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/combination_function.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Class for CombinationFunction — combination_function","text":"","code":"higher <- function(a) {   force(a)   CombinationFunction(     function(x) {       x > a     }   ) }  lower <- function(b) {   force(b)   CombinationFunction(     function(x) {       x < b     }   ) }  c1 <- higher(5) c2 <- lower(10) c3 <- higher(5) & lower(10) c3(7) #> [1] TRUE"},{"path":"https://insightsengineering.github.io/tern/main/reference/combine_counts.html","id":null,"dir":"Reference","previous_headings":"","what":"Combine counts — combine_counts","title":"Combine counts — combine_counts","text":"Simplifies estimation column counts, especially group combination required.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/combine_counts.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Combine counts — combine_counts","text":"","code":"combine_counts(fct, groups_list = NULL)"},{"path":"https://insightsengineering.github.io/tern/main/reference/combine_counts.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Combine counts — combine_counts","text":"fct (factor) variable levels needs grouped. groups_list (named list character) specifies new group levels via names levels belong character vectors elements list.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/combine_counts.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Combine counts — combine_counts","text":"vector column counts.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/main/reference/combine_counts.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Combine counts — combine_counts","text":"","code":"ref <- c(\"A: Drug X\", \"B: Placebo\") groups <- combine_groups(fct = DM$ARM, ref = ref)  col_counts <- combine_counts(   fct = DM$ARM,   groups_list = groups )  basic_table() %>%   split_cols_by_groups(\"ARM\", groups) %>%   add_colcounts() %>%   analyze_vars(\"AGE\") %>%   build_table(DM, col_counts = col_counts) #>             A: Drug X/B: Placebo   C: Combination #>                   (N=227)             (N=129)     #> ————————————————————————————————————————————————— #> n                   227                 129       #> Mean (SD)        34.0 (7.2)          34.6 (6.5)   #> Median              33.0                33.0      #> Min - Max       20.0 - 60.0         22.0 - 53.0    ref <- \"A: Drug X\" groups <- combine_groups(fct = DM$ARM, ref = ref) col_counts <- combine_counts(   fct = DM$ARM,   groups_list = groups )  basic_table() %>%   split_cols_by_groups(\"ARM\", groups) %>%   add_colcounts() %>%   analyze_vars(\"AGE\") %>%   build_table(DM, col_counts = col_counts) #>              A: Drug X    B: Placebo/C: Combination #>               (N=121)              (N=235)          #> ——————————————————————————————————————————————————— #> n               121                  235            #> Mean (SD)   34.9 (7.8)           33.9 (6.5)         #> Median         33.0                 33.0            #> Min - Max   20.0 - 60.0          21.0 - 55.0"},{"path":"https://insightsengineering.github.io/tern/main/reference/combine_groups.html","id":null,"dir":"Reference","previous_headings":"","what":"Reference and treatment group combination — combine_groups","title":"Reference and treatment group combination — combine_groups","text":"Facilitate re-combination groups divided reference treatment groups; helps arranging groups columns rtables framework teal modules.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/combine_groups.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Reference and treatment group combination — combine_groups","text":"","code":"combine_groups(fct, ref = NULL, collapse = \"/\")"},{"path":"https://insightsengineering.github.io/tern/main/reference/combine_groups.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Reference and treatment group combination — combine_groups","text":"fct (factor) variable levels needs grouped. ref (character) reference level(s). collapse (string) character string separate fct ref.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/combine_groups.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Reference and treatment group combination — combine_groups","text":"list first item ref (reference) second item trt (treatment).","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/combine_groups.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Reference and treatment group combination — combine_groups","text":"","code":"groups <- combine_groups(   fct = DM$ARM,   ref = c(\"B: Placebo\") )  basic_table() %>%   split_cols_by_groups(\"ARM\", groups) %>%   add_colcounts() %>%   analyze_vars(\"AGE\") %>%   build_table(DM) #>             B: Placebo    A: Drug X/C: Combination #>               (N=106)             (N=250)          #> —————————————————————————————————————————————————— #> n               106                 250            #> Mean (SD)   33.0 (6.3)           34.7 (7.1)        #> Median         32.0                 33.0           #> Min - Max   21.0 - 55.0         20.0 - 60.0"},{"path":"https://insightsengineering.github.io/tern/main/reference/combine_levels.html","id":null,"dir":"Reference","previous_headings":"","what":"Combine factor levels — combine_levels","title":"Combine factor levels — combine_levels","text":"Combine specified old factor Levels single new level.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/combine_levels.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Combine factor levels — combine_levels","text":"","code":"combine_levels(x, levels, new_level = paste(levels, collapse = \"/\"))"},{"path":"https://insightsengineering.github.io/tern/main/reference/combine_levels.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Combine factor levels — combine_levels","text":"x (factor) factor variable. levels (character) level names combined. new_level (string) name new level.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/combine_levels.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Combine factor levels — combine_levels","text":"factor new levels.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/combine_levels.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Combine factor levels — combine_levels","text":"","code":"x <- factor(letters[1:5], levels = letters[5:1]) combine_levels(x, levels = c(\"a\", \"b\")) #> [1] a/b a/b c   d   e   #> Levels: e d c a/b  combine_levels(x, c(\"e\", \"b\")) #> [1] a   e/b c   d   e/b #> Levels: e/b d c a"},{"path":"https://insightsengineering.github.io/tern/main/reference/combine_vectors.html","id":null,"dir":"Reference","previous_headings":"","what":"Element-wise combination of two vectors — combine_vectors","title":"Element-wise combination of two vectors — combine_vectors","text":"Element-wise combination two vectors","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/combine_vectors.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Element-wise combination of two vectors — combine_vectors","text":"","code":"combine_vectors(x, y)"},{"path":"https://insightsengineering.github.io/tern/main/reference/combine_vectors.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Element-wise combination of two vectors — combine_vectors","text":"x (vector) first vector combine. y (vector) second vector combine.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/combine_vectors.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Element-wise combination of two vectors — combine_vectors","text":"list element combines corresponding elements x y.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/combine_vectors.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Element-wise combination of two vectors — combine_vectors","text":"","code":"combine_vectors(1:3, 4:6) #> [[1]] #> [1] 1 4 #>  #> [[2]] #> [1] 2 5 #>  #> [[3]] #> [1] 3 6 #>"},{"path":"https://insightsengineering.github.io/tern/main/reference/compare_variables.html","id":null,"dir":"Reference","previous_headings":"","what":"Compare variables between groups — compare_variables","title":"Compare variables between groups — compare_variables","text":"analyze function compare_vars() creates layout element summarize compare one variables, using S3 generic function s_summary() calculate list summary statistics. list available statistics numeric variables can viewed running get_stats(\"analyze_vars_numeric\", add_pval = TRUE) non-numeric variables running get_stats(\"analyze_vars_counts\", add_pval = TRUE). Use .stats parameter specify statistics include output summary table. Prior using function table layout must use rtables::split_cols_by() create column split variable used comparisons, specify reference group via ref_group parameter. Comparisons can performed group (column) specified reference group including p-value statistic.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/compare_variables.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Compare variables between groups — compare_variables","text":"","code":"compare_vars(   lyt,   vars,   var_labels = vars,   na_str = default_na_str(),   nested = TRUE,   ...,   na.rm = TRUE,   show_labels = \"default\",   table_names = vars,   section_div = NA_character_,   .stats = c(\"n\", \"mean_sd\", \"count_fraction\", \"pval\"),   .formats = NULL,   .labels = NULL,   .indent_mods = NULL )  s_compare(x, .ref_group, .in_ref_col, ...)  # S3 method for class 'numeric' s_compare(x, .ref_group, .in_ref_col, ...)  # S3 method for class 'factor' s_compare(x, .ref_group, .in_ref_col, denom = \"n\", na.rm = TRUE, ...)  # S3 method for class 'character' s_compare(   x,   .ref_group,   .in_ref_col,   denom = \"n\",   na.rm = TRUE,   .var,   verbose = TRUE,   ... )  # S3 method for class 'logical' s_compare(x, .ref_group, .in_ref_col, na.rm = TRUE, denom = \"n\", ...)"},{"path":"https://insightsengineering.github.io/tern/main/reference/compare_variables.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Compare variables between groups — compare_variables","text":"lyt (PreDataTableLayouts) layout analyses added . vars (character) variable names primary analysis variable iterated . var_labels (character) variable labels. na_str (string) string used replace NA empty values output. nested (flag) whether layout instruction applied within existing layout structure _if possible (TRUE, default) new top-level element (FALSE). Ignored nest split. underneath analyses, allowed. ... arguments passed s_compare(). na.rm (flag) whether NA values removed x prior analysis. show_labels (string) label visibility: one \"default\", \"visible\" \"hidden\". table_names (character) can customized case vars analyzed multiple times, avoid warnings rtables. section_div (string) string repeated section divider group defined split instruction, NA_character_ (default) section divider. .stats (character) statistics select table. Options numeric variables : 'n', 'sum', 'mean', 'sd', 'se', 'mean_sd', 'mean_se', 'mean_ci', 'mean_sei', 'mean_sdi', 'mean_pval', 'median', 'mad', 'median_ci', 'quantiles', 'iqr', 'range', 'min', 'max', 'median_range', 'cv', 'geom_mean', 'geom_mean_ci', 'geom_cv', 'median_ci_3d', 'mean_ci_3d', 'geom_mean_ci_3d', 'pval' Options non-numeric variables : 'n', 'count', 'count_fraction', 'count_fraction_fixed_dp', 'fraction', 'n_blq', 'pval_counts' .formats (named character list) formats statistics. See Details analyze_vars information \"auto\" setting. .labels (named character) labels statistics (without indent). .indent_mods (named integer) indent modifiers labels. element vector name-value pair name corresponding statistic specified .stats value indentation statistic's row label. x (numeric) vector numbers want analyze. .ref_group (data.frame vector) data corresponding reference group. .in_ref_col (flag)TRUE working reference level, FALSE otherwise. denom (string) choice denominator factor proportions, can n (number values row column intersection). .var (string) single variable name passed rtables requested statistics function. verbose (flag) whether warnings messages printed. Mainly used print information factor casting. Defaults TRUE.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/compare_variables.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Compare variables between groups — compare_variables","text":"compare_vars() returns layout object suitable passing layouting functions, rtables::build_table(). Adding function rtable layout add formatted rows containing statistics s_compare() table layout. s_compare() returns output s_summary() comparisons versus reference group form p-values.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/compare_variables.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Compare variables between groups — compare_variables","text":"compare_vars(): Layout-creating function can take statistics function arguments additional format arguments. function wrapper rtables::analyze(). s_compare(): S3 generic function produce comparison summary. s_compare(numeric): Method numeric class. uses standard t-test calculate p-value. s_compare(factor): Method factor class. uses chi-squared test calculate p-value. s_compare(character): Method character class. makes automatic conversion factor (warning) forwards method factors. s_compare(logical): Method logical class. chi-squared test used. missing values removed, counted FALSE.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/compare_variables.html","id":"note","dir":"Reference","previous_headings":"","what":"Note","title":"Compare variables between groups — compare_variables","text":"factor variables, denom factor proportions can n since purpose compare proportions columns, therefore row-based proportion make sense. Proportion based N_col difficult since use counts chi-squared test statistic, therefore missing values accounted explicit factor levels. factor variables contain NA, NA values excluded default. include NA values set na.rm = FALSE missing values displayed NA level. Alternatively, explicit factor level can defined NA values pre-processing via df_explicit_na() - default na_level (\"<Missing>\") also excluded na.rm set TRUE. character variables, automatic conversion factor guarantee table generated correctly. particular sparse tables likely can fail. Therefore always better manually convert character variables factors pre-processing. compare_vars(), column split must define reference group via ref_group comparison well defined.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/main/reference/compare_variables.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Compare variables between groups — compare_variables","text":"","code":"# `compare_vars()` in `rtables` pipelines  ## Default output within a `rtables` pipeline. lyt <- basic_table() %>%   split_cols_by(\"ARMCD\", ref_group = \"ARM B\") %>%   compare_vars(c(\"AGE\", \"SEX\")) build_table(lyt, tern_ex_adsl) #>                                  ARM A        ARM B        ARM C    #> ——————————————————————————————————————————————————————————————————— #> AGE                                                                 #>   n                                69           73           58     #>   Mean (SD)                    34.1 (6.8)   35.8 (7.1)   36.1 (7.4) #>   p-value (t-test)               0.1446                    0.8212   #> SEX                                                                 #>   n                                69           73           58     #>   F                            38 (55.1%)   40 (54.8%)   32 (55.2%) #>   M                            31 (44.9%)   33 (45.2%)   26 (44.8%) #>   p-value (chi-squared test)     1.0000                    1.0000    ## Select and format statistics output. lyt <- basic_table() %>%   split_cols_by(\"ARMCD\", ref_group = \"ARM C\") %>%   compare_vars(     vars = \"AGE\",     .stats = c(\"mean_sd\", \"pval\"),     .formats = c(mean_sd = \"xx.x, xx.x\"),     .labels = c(mean_sd = \"Mean, SD\")   ) build_table(lyt, df = tern_ex_adsl) #>                      ARM A       ARM B       ARM C   #> ———————————————————————————————————————————————————— #> Mean, SD           34.1, 6.8   35.8, 7.1   36.1, 7.4 #> p-value (t-test)    0.1176      0.8212                # `s_compare.numeric`  ## Usual case where both this and the reference group vector have more than 1 value. s_compare(rnorm(10, 5, 1), .ref_group = rnorm(5, -5, 1), .in_ref_col = FALSE) #> $n #>  n  #> 10  #>  #> $sum #>      sum  #> 51.27191  #>  #> $mean #>     mean  #> 5.127191  #>  #> $sd #>       sd  #> 1.226119  #>  #> $se #>       se  #> 0.387733  #>  #> $mean_sd #>     mean       sd  #> 5.127191 1.226119  #>  #> $mean_se #>     mean       se  #> 5.127191 0.387733  #>  #> $mean_ci #> mean_ci_lwr mean_ci_upr  #>    4.250078    6.004304  #> attr(,\"label\") #> [1] \"Mean 95% CI\" #>  #> $mean_sei #> mean_sei_lwr mean_sei_upr  #>     4.739458     5.514924  #> attr(,\"label\") #> [1] \"Mean -/+ 1xSE\" #>  #> $mean_sdi #> mean_sdi_lwr mean_sdi_upr  #>     3.901071     6.353310  #> attr(,\"label\") #> [1] \"Mean -/+ 1xSD\" #>  #> $mean_ci_3d #>        mean mean_ci_lwr mean_ci_upr  #>    5.127191    4.250078    6.004304  #> attr(,\"label\") #> [1] \"Mean (95% CI)\" #>  #> $mean_pval #>      p_value  #> 3.353908e-07  #> attr(,\"label\") #> [1] \"Mean p-value (H0: mean = 0)\" #>  #> $median #>   median  #> 5.024369  #>  #> $mad #>           mad  #> -4.440892e-16  #>  #> $median_ci #> median_ci_lwr median_ci_upr  #>      4.638779      5.862086  #> attr(,\"conf_level\") #> [1] 0.9785156 #> attr(,\"label\") #> [1] \"Median 95% CI\" #>  #> $median_ci_3d #>        median median_ci_lwr median_ci_upr  #>      5.024369      4.638779      5.862086  #> attr(,\"label\") #> [1] \"Median (95% CI)\" #>  #> $quantiles #> quantile_0.25 quantile_0.75  #>      4.756763      5.549828  #> attr(,\"label\") #> [1] \"25% and 75%-ile\" #>  #> $iqr #>       iqr  #> 0.7930643  #>  #> $range #>      min      max  #> 2.725885 7.682557  #>  #> $min #>      min  #> 2.725885  #>  #> $max #>      max  #> 7.682557  #>  #> $median_range #>   median      min      max  #> 5.024369 2.725885 7.682557  #> attr(,\"label\") #> [1] \"Median (Min - Max)\" #>  #> $cv #>       cv  #> 23.91406  #>  #> $geom_mean #> geom_mean  #>  4.985435  #>  #> $geom_mean_ci #> mean_ci_lwr mean_ci_upr  #>    4.144463    5.997052  #> attr(,\"label\") #> [1] \"Geometric Mean 95% CI\" #>  #> $geom_cv #>  geom_cv  #> 26.26258  #>  #> $geom_mean_ci_3d #>   geom_mean mean_ci_lwr mean_ci_upr  #>    4.985435    4.144463    5.997052  #> attr(,\"label\") #> [1] \"Geometric Mean (95% CI)\" #>  #> $pval #> [1] 2.25779e-08 #>   ## If one group has not more than 1 value, then p-value is not calculated. s_compare(rnorm(10, 5, 1), .ref_group = 1, .in_ref_col = FALSE) #> $n #>  n  #> 10  #>  #> $sum #>      sum  #> 50.71578  #>  #> $mean #>     mean  #> 5.071578  #>  #> $sd #>       sd  #> 1.105832  #>  #> $se #>        se  #> 0.3496948  #>  #> $mean_sd #>     mean       sd  #> 5.071578 1.105832  #>  #> $mean_se #>      mean        se  #> 5.0715780 0.3496948  #>  #> $mean_ci #> mean_ci_lwr mean_ci_upr  #>    4.280513    5.862643  #> attr(,\"label\") #> [1] \"Mean 95% CI\" #>  #> $mean_sei #> mean_sei_lwr mean_sei_upr  #>     4.721883     5.421273  #> attr(,\"label\") #> [1] \"Mean -/+ 1xSE\" #>  #> $mean_sdi #> mean_sdi_lwr mean_sdi_upr  #>     3.965746     6.177410  #> attr(,\"label\") #> [1] \"Mean -/+ 1xSD\" #>  #> $mean_ci_3d #>        mean mean_ci_lwr mean_ci_upr  #>    5.071578    4.280513    5.862643  #> attr(,\"label\") #> [1] \"Mean (95% CI)\" #>  #> $mean_pval #>      p_value  #> 1.511204e-07  #> attr(,\"label\") #> [1] \"Mean p-value (H0: mean = 0)\" #>  #> $median #>   median  #> 5.260423  #>  #> $mad #> mad  #>   0  #>  #> $median_ci #> median_ci_lwr median_ci_upr  #>      3.529264      6.318293  #> attr(,\"conf_level\") #> [1] 0.9785156 #> attr(,\"label\") #> [1] \"Median 95% CI\" #>  #> $median_ci_3d #>        median median_ci_lwr median_ci_upr  #>      5.260423      3.529264      6.318293  #> attr(,\"label\") #> [1] \"Median (95% CI)\" #>  #> $quantiles #> quantile_0.25 quantile_0.75  #>      4.024149      6.065057  #> attr(,\"label\") #> [1] \"25% and 75%-ile\" #>  #> $iqr #>      iqr  #> 2.040908  #>  #> $range #>      min      max  #> 3.300549 6.337320  #>  #> $min #>      min  #> 3.300549  #>  #> $max #>     max  #> 6.33732  #>  #> $median_range #>   median      min      max  #> 5.260423 3.300549 6.337320  #> attr(,\"label\") #> [1] \"Median (Min - Max)\" #>  #> $cv #>      cv  #> 21.8045  #>  #> $geom_mean #> geom_mean  #>  4.952266  #>  #> $geom_mean_ci #> mean_ci_lwr mean_ci_upr  #>    4.181833    5.864639  #> attr(,\"label\") #> [1] \"Geometric Mean 95% CI\" #>  #> $geom_cv #>  geom_cv  #> 23.97201  #>  #> $geom_mean_ci_3d #>   geom_mean mean_ci_lwr mean_ci_upr  #>    4.952266    4.181833    5.864639  #> attr(,\"label\") #> [1] \"Geometric Mean (95% CI)\" #>  #> $pval #> character(0) #>   ## Empty numeric does not fail, it returns NA-filled items and no p-value. s_compare(numeric(), .ref_group = numeric(), .in_ref_col = FALSE) #> $n #> n  #> 0  #>  #> $sum #> sum  #>  NA  #>  #> $mean #> mean  #>   NA  #>  #> $sd #> sd  #> NA  #>  #> $se #> se  #> NA  #>  #> $mean_sd #> mean   sd  #>   NA   NA  #>  #> $mean_se #> mean   se  #>   NA   NA  #>  #> $mean_ci #> mean_ci_lwr mean_ci_upr  #>          NA          NA  #> attr(,\"label\") #> [1] \"Mean 95% CI\" #>  #> $mean_sei #> mean_sei_lwr mean_sei_upr  #>           NA           NA  #> attr(,\"label\") #> [1] \"Mean -/+ 1xSE\" #>  #> $mean_sdi #> mean_sdi_lwr mean_sdi_upr  #>           NA           NA  #> attr(,\"label\") #> [1] \"Mean -/+ 1xSD\" #>  #> $mean_ci_3d #>        mean mean_ci_lwr mean_ci_upr  #>          NA          NA          NA  #> attr(,\"label\") #> [1] \"Mean (95% CI)\" #>  #> $mean_pval #> p_value  #>      NA  #> attr(,\"label\") #> [1] \"Mean p-value (H0: mean = 0)\" #>  #> $median #> median  #>     NA  #>  #> $mad #> mad  #>  NA  #>  #> $median_ci #> median_ci_lwr median_ci_upr  #>            NA            NA  #> attr(,\"conf_level\") #> [1] NA #> attr(,\"label\") #> [1] \"Median 95% CI\" #>  #> $median_ci_3d #>        median median_ci_lwr median_ci_upr  #>            NA            NA            NA  #> attr(,\"label\") #> [1] \"Median (95% CI)\" #>  #> $quantiles #> quantile_0.25 quantile_0.75  #>            NA            NA  #> attr(,\"label\") #> [1] \"25% and 75%-ile\" #>  #> $iqr #> iqr  #>  NA  #>  #> $range #> min max  #>  NA  NA  #>  #> $min #> min  #>  NA  #>  #> $max #> max  #>  NA  #>  #> $median_range #> median    min    max  #>     NA     NA     NA  #> attr(,\"label\") #> [1] \"Median (Min - Max)\" #>  #> $cv #> cv  #> NA  #>  #> $geom_mean #> geom_mean  #>       NaN  #>  #> $geom_mean_ci #> mean_ci_lwr mean_ci_upr  #>          NA          NA  #> attr(,\"label\") #> [1] \"Geometric Mean 95% CI\" #>  #> $geom_cv #> geom_cv  #>      NA  #>  #> $geom_mean_ci_3d #>   geom_mean mean_ci_lwr mean_ci_upr  #>         NaN          NA          NA  #> attr(,\"label\") #> [1] \"Geometric Mean (95% CI)\" #>  #> $pval #> character(0) #>   # `s_compare.factor`  ## Basic usage: x <- factor(c(\"a\", \"a\", \"b\", \"c\", \"a\")) y <- factor(c(\"a\", \"b\", \"c\")) s_compare(x = x, .ref_group = y, .in_ref_col = FALSE) #> $n #> [1] 5 #>  #> $count #> $count$a #> [1] 3 #>  #> $count$b #> [1] 1 #>  #> $count$c #> [1] 1 #>  #>  #> $count_fraction #> $count_fraction$a #> [1] 3.0 0.6 #>  #> $count_fraction$b #> [1] 1.0 0.2 #>  #> $count_fraction$c #> [1] 1.0 0.2 #>  #>  #> $fraction #> $fraction$a #>   num denom  #>     3     5  #>  #> $fraction$b #>   num denom  #>     1     5  #>  #> $fraction$c #>   num denom  #>     1     5  #>  #>  #> $n_blq #> [1] 0 #>  #> $pval_counts #> [1] 0.7659283 #>   ## Management of NA values. x <- explicit_na(factor(c(\"a\", \"a\", \"b\", \"c\", \"a\", NA, NA))) y <- explicit_na(factor(c(\"a\", \"b\", \"c\", NA))) s_compare(x = x, .ref_group = y, .in_ref_col = FALSE, na.rm = TRUE) #> $n #> [1] 5 #>  #> $count #> $count$a #> [1] 3 #>  #> $count$b #> [1] 1 #>  #> $count$c #> [1] 1 #>  #>  #> $count_fraction #> $count_fraction$a #> [1] 3.0 0.6 #>  #> $count_fraction$b #> [1] 1.0 0.2 #>  #> $count_fraction$c #> [1] 1.0 0.2 #>  #>  #> $fraction #> $fraction$a #>   num denom  #>     3     5  #>  #> $fraction$b #>   num denom  #>     1     5  #>  #> $fraction$c #>   num denom  #>     1     5  #>  #>  #> $n_blq #> [1] 0 #>  #> $pval_counts #> [1] 0.7659283 #>  s_compare(x = x, .ref_group = y, .in_ref_col = FALSE, na.rm = FALSE) #> $n #> [1] 7 #>  #> $count #> $count$a #> [1] 3 #>  #> $count$b #> [1] 1 #>  #> $count$c #> [1] 1 #>  #> $count$`<Missing>` #> [1] 2 #>  #>  #> $count_fraction #> $count_fraction$a #> [1] 3.0000000 0.4285714 #>  #> $count_fraction$b #> [1] 1.0000000 0.1428571 #>  #> $count_fraction$c #> [1] 1.0000000 0.1428571 #>  #> $count_fraction$`<Missing>` #> [1] 2.0000000 0.2857143 #>  #>  #> $fraction #> $fraction$a #>   num denom  #>     3     7  #>  #> $fraction$b #>   num denom  #>     1     7  #>  #> $fraction$c #>   num denom  #>     1     7  #>  #> $fraction$`<Missing>` #>   num denom  #>     2     7  #>  #>  #> $n_blq #> [1] 0 #>  #> $pval_counts #> [1] 0.9063036 #>   # `s_compare.character`  ## Basic usage: x <- c(\"a\", \"a\", \"b\", \"c\", \"a\") y <- c(\"a\", \"b\", \"c\") s_compare(x, .ref_group = y, .in_ref_col = FALSE, .var = \"x\", verbose = FALSE) #> $n #> [1] 5 #>  #> $count #> $count$a #> [1] 3 #>  #> $count$b #> [1] 1 #>  #> $count$c #> [1] 1 #>  #>  #> $count_fraction #> $count_fraction$a #> [1] 3.0 0.6 #>  #> $count_fraction$b #> [1] 1.0 0.2 #>  #> $count_fraction$c #> [1] 1.0 0.2 #>  #>  #> $fraction #> $fraction$a #>   num denom  #>     3     5  #>  #> $fraction$b #>   num denom  #>     1     5  #>  #> $fraction$c #>   num denom  #>     1     5  #>  #>  #> $n_blq #> [1] 0 #>  #> $pval_counts #> [1] 0.7659283 #>   ## Note that missing values handling can make a large difference: x <- c(\"a\", \"a\", \"b\", \"c\", \"a\", NA) y <- c(\"a\", \"b\", \"c\", rep(NA, 20)) s_compare(x,   .ref_group = y, .in_ref_col = FALSE,   .var = \"x\", verbose = FALSE ) #> $n #> [1] 5 #>  #> $count #> $count$a #> [1] 3 #>  #> $count$b #> [1] 1 #>  #> $count$c #> [1] 1 #>  #>  #> $count_fraction #> $count_fraction$a #> [1] 3.0 0.6 #>  #> $count_fraction$b #> [1] 1.0 0.2 #>  #> $count_fraction$c #> [1] 1.0 0.2 #>  #>  #> $fraction #> $fraction$a #>   num denom  #>     3     5  #>  #> $fraction$b #>   num denom  #>     1     5  #>  #> $fraction$c #>   num denom  #>     1     5  #>  #>  #> $n_blq #> [1] 0 #>  #> $pval_counts #> [1] 0.7659283 #>  s_compare(x,   .ref_group = y, .in_ref_col = FALSE, .var = \"x\",   na.rm = FALSE, verbose = FALSE ) #> $n #> [1] 6 #>  #> $count #> $count$a #> [1] 3 #>  #> $count$b #> [1] 1 #>  #> $count$c #> [1] 1 #>  #> $count$`<Missing>` #> [1] 1 #>  #>  #> $count_fraction #> $count_fraction$a #> [1] 3.0 0.5 #>  #> $count_fraction$b #> [1] 1.0000000 0.1666667 #>  #> $count_fraction$c #> [1] 1.0000000 0.1666667 #>  #> $count_fraction$`<Missing>` #> [1] 1.0000000 0.1666667 #>  #>  #> $fraction #> $fraction$a #>   num denom  #>     3     6  #>  #> $fraction$b #>   num denom  #>     1     6  #>  #> $fraction$c #>   num denom  #>     1     6  #>  #> $fraction$`<Missing>` #>   num denom  #>     1     6  #>  #>  #> $n_blq #> [1] 0 #>  #> $pval_counts #> [1] 0.005768471 #>   # `s_compare.logical`  ## Basic usage: x <- c(TRUE, FALSE, TRUE, TRUE) y <- c(FALSE, FALSE, TRUE) s_compare(x, .ref_group = y, .in_ref_col = FALSE) #> $n #> [1] 4 #>  #> $count #> [1] 3 #>  #> $count_fraction #> [1] 3.00 0.75 #>  #> $n_blq #> [1] 0 #>  #> $pval_counts #> [1] 0.2702894 #>   ## Management of NA values. x <- c(NA, TRUE, FALSE) y <- c(NA, NA, NA, NA, FALSE) s_compare(x, .ref_group = y, .in_ref_col = FALSE, na.rm = TRUE) #> $n #> [1] 2 #>  #> $count #> [1] 1 #>  #> $count_fraction #> [1] 1.0 0.5 #>  #> $n_blq #> [1] 0 #>  #> $pval_counts #> [1] 0.3864762 #>  s_compare(x, .ref_group = y, .in_ref_col = FALSE, na.rm = FALSE) #> $n #> [1] 3 #>  #> $count #> [1] 1 #>  #> $count_fraction #> [1] 1.0000000 0.3333333 #>  #> $n_blq #> [1] 0 #>  #> $pval_counts #> [1] 0.1675463 #>"},{"path":"https://insightsengineering.github.io/tern/main/reference/control_analyze_vars.html","id":null,"dir":"Reference","previous_headings":"","what":"Control function for descriptive statistics — control_analyze_vars","title":"Control function for descriptive statistics — control_analyze_vars","text":"Sets list parameters summaries descriptive statistics. Typically used internally specify details s_summary(). function family mainly used analyze_vars().","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/control_analyze_vars.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Control function for descriptive statistics — control_analyze_vars","text":"","code":"control_analyze_vars(   conf_level = 0.95,   quantiles = c(0.25, 0.75),   quantile_type = 2,   test_mean = 0 )"},{"path":"https://insightsengineering.github.io/tern/main/reference/control_analyze_vars.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Control function for descriptive statistics — control_analyze_vars","text":"conf_level (proportion) confidence level interval. quantiles (numeric(2)) vector length two specify quantiles calculate. quantile_type (numeric(1)) number 1 9 selecting quantile algorithms used. Default set 2 matches default quantile algorithm SAS proc univariate set QNTLDEF=5. differs R's default. See type stats::quantile(). test_mean (numeric(1)) number test mean null hypothesis calculating p-value.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/control_analyze_vars.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Control function for descriptive statistics — control_analyze_vars","text":"list components names arguments.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/control_annot.html","id":null,"dir":"Reference","previous_headings":"","what":"Control functions for Kaplan-Meier plot annotation tables — control_annot","title":"Control functions for Kaplan-Meier plot annotation tables — control_annot","text":"Auxiliary functions controlling arguments formatting annotation tables can added plots generated via g_km().","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/control_annot.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Control functions for Kaplan-Meier plot annotation tables — control_annot","text":"","code":"control_surv_med_annot(x = 0.8, y = 0.85, w = 0.32, h = 0.16, fill = TRUE)  control_coxph_annot(   x = 0.29,   y = 0.51,   w = 0.4,   h = 0.125,   fill = TRUE,   ref_lbls = FALSE )"},{"path":"https://insightsengineering.github.io/tern/main/reference/control_annot.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Control functions for Kaplan-Meier plot annotation tables — control_annot","text":"x (proportion) x-coordinate center annotation table. y (proportion) y-coordinate center annotation table. w (proportion) relative width annotation table. h (proportion) relative height annotation table. fill (flag character) whether annotation table background fill color. Can also color code use background fill color. TRUE, color code defaults \"#00000020\". ref_lbls (flag) whether reference group explicitly printed labels annotation table. FALSE (default), comparison groups printed table labels.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/control_annot.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Control functions for Kaplan-Meier plot annotation tables — control_annot","text":"list components names arguments.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/control_annot.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Control functions for Kaplan-Meier plot annotation tables — control_annot","text":"control_surv_med_annot(): Control function formatting median survival time annotation table. annotation table can added g_km() setting annot_surv_med=TRUE, can configured using control_surv_med_annot() function setting control_annot_surv_med argument. control_coxph_annot(): Control function formatting Cox-PH annotation table. annotation table can added g_km() setting annot_coxph=TRUE, can configured using control_coxph_annot() function setting control_annot_coxph argument.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/main/reference/control_annot.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Control functions for Kaplan-Meier plot annotation tables — control_annot","text":"","code":"control_surv_med_annot() #> $x #> [1] 0.8 #>  #> $y #> [1] 0.85 #>  #> $w #> [1] 0.32 #>  #> $h #> [1] 0.16 #>  #> $fill #> [1] TRUE #>   control_coxph_annot() #> $x #> [1] 0.29 #>  #> $y #> [1] 0.51 #>  #> $w #> [1] 0.4 #>  #> $h #> [1] 0.125 #>  #> $fill #> [1] TRUE #>  #> $ref_lbls #> [1] FALSE #>"},{"path":"https://insightsengineering.github.io/tern/main/reference/control_coxph.html","id":null,"dir":"Reference","previous_headings":"","what":"Control function for Cox-PH model — control_coxph","title":"Control function for Cox-PH model — control_coxph","text":"auxiliary function controlling arguments Cox-PH model, typically used internally specify details Cox-PH model s_coxph_pairwise(). conf_level refers Hazard Ratio estimation.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/control_coxph.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Control function for Cox-PH model — control_coxph","text":"","code":"control_coxph(   pval_method = c(\"log-rank\", \"wald\", \"likelihood\"),   ties = c(\"efron\", \"breslow\", \"exact\"),   conf_level = 0.95 )"},{"path":"https://insightsengineering.github.io/tern/main/reference/control_coxph.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Control function for Cox-PH model — control_coxph","text":"pval_method (string) p-value method testing hazard ratio = 1. Default method \"log-rank\", can also set \"wald\" \"likelihood\". ties (string) string specifying method tie handling. Default \"efron\", can also set \"breslow\" \"exact\". See survival::coxph(). conf_level (proportion) confidence level interval.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/control_coxph.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Control function for Cox-PH model — control_coxph","text":"list components names arguments.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/control_coxreg.html","id":null,"dir":"Reference","previous_headings":"","what":"Control function for Cox regression — control_coxreg","title":"Control function for Cox regression — control_coxreg","text":"Sets list parameters Cox regression fit. Used internally.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/control_coxreg.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Control function for Cox regression — control_coxreg","text":"","code":"control_coxreg(   pval_method = c(\"wald\", \"likelihood\"),   ties = c(\"exact\", \"efron\", \"breslow\"),   conf_level = 0.95,   interaction = FALSE )"},{"path":"https://insightsengineering.github.io/tern/main/reference/control_coxreg.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Control function for Cox regression — control_coxreg","text":"pval_method (string) method used estimation p.values; wald (default) likelihood. ties (string) among exact (equivalent DISCRETE SAS), efron breslow, see survival::coxph(). Note: equivalent SAS EXACT method R. conf_level (proportion) confidence level interval. interaction (flag) TRUE, model includes interaction studied treatment candidate covariate. Note univariate models without treatment arm, multivariate models, interaction can used needs FALSE.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/control_coxreg.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Control function for Cox regression — control_coxreg","text":"list items names corresponding arguments.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/main/reference/control_coxreg.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Control function for Cox regression — control_coxreg","text":"","code":"control_coxreg() #> $pval_method #> [1] \"wald\" #>  #> $ties #> [1] \"exact\" #>  #> $conf_level #> [1] 0.95 #>  #> $interaction #> [1] FALSE #>"},{"path":"https://insightsengineering.github.io/tern/main/reference/control_incidence_rate.html","id":null,"dir":"Reference","previous_headings":"","what":"Control function for incidence rate — control_incidence_rate","title":"Control function for incidence rate — control_incidence_rate","text":"auxiliary function controlling arguments incidence rate, used internally specify details s_incidence_rate().","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/control_incidence_rate.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Control function for incidence rate — control_incidence_rate","text":"","code":"control_incidence_rate(   conf_level = 0.95,   conf_type = c(\"normal\", \"normal_log\", \"exact\", \"byar\"),   input_time_unit = c(\"year\", \"day\", \"week\", \"month\"),   num_pt_year = 100 )"},{"path":"https://insightsengineering.github.io/tern/main/reference/control_incidence_rate.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Control function for incidence rate — control_incidence_rate","text":"conf_level (proportion) confidence level interval. conf_type (string)normal (default), normal_log, exact, byar confidence interval type. input_time_unit (string)day, week, month, year (default) indicating time unit data input. num_pt_year (numeric(1)) number patient-years use calculating adverse event rates.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/control_incidence_rate.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Control function for incidence rate — control_incidence_rate","text":"list components names arguments.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/main/reference/control_incidence_rate.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Control function for incidence rate — control_incidence_rate","text":"","code":"control_incidence_rate(0.9, \"exact\", \"month\", 100) #> $conf_level #> [1] 0.9 #>  #> $conf_type #> [1] \"exact\" #>  #> $input_time_unit #> [1] \"month\" #>  #> $num_pt_year #> [1] 100 #>"},{"path":"https://insightsengineering.github.io/tern/main/reference/control_lineplot_vars.html","id":null,"dir":"Reference","previous_headings":"","what":"Control function for g_lineplot() — control_lineplot_vars","title":"Control function for g_lineplot() — control_lineplot_vars","text":"Default values variables parameter g_lineplot function. variable's default value can overwritten variable.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/control_lineplot_vars.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Control function for g_lineplot() — control_lineplot_vars","text":"","code":"control_lineplot_vars(   x = \"AVISIT\",   y = \"AVAL\",   group_var = \"ARM\",   facet_var = NA,   paramcd = \"PARAMCD\",   y_unit = \"AVALU\",   subject_var = \"USUBJID\" )"},{"path":"https://insightsengineering.github.io/tern/main/reference/control_lineplot_vars.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Control function for g_lineplot() — control_lineplot_vars","text":"x (string) x-variable name. y (string) y-variable name. group_var (string NA) group variable name. facet_var (string NA) faceting variable name. paramcd (string NA) parameter code variable name. y_unit (string NA) y-axis unit variable name. subject_var (string NA) subject variable name.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/control_lineplot_vars.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Control function for g_lineplot() — control_lineplot_vars","text":"named character vector variable names.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/control_lineplot_vars.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Control function for g_lineplot() — control_lineplot_vars","text":"","code":"control_lineplot_vars() #>           x           y   group_var     paramcd      y_unit subject_var  #>    \"AVISIT\"      \"AVAL\"       \"ARM\"   \"PARAMCD\"     \"AVALU\"   \"USUBJID\"  #>   facet_var  #>          NA  control_lineplot_vars(group_var = NA) #>           x           y   group_var     paramcd      y_unit subject_var  #>    \"AVISIT\"      \"AVAL\"          NA   \"PARAMCD\"     \"AVALU\"   \"USUBJID\"  #>   facet_var  #>          NA"},{"path":"https://insightsengineering.github.io/tern/main/reference/control_logistic.html","id":null,"dir":"Reference","previous_headings":"","what":"Control function for logistic regression model fitting — control_logistic","title":"Control function for logistic regression model fitting — control_logistic","text":"auxiliary function controlling arguments logistic regression models. conf_level refers confidence level used Odds Ratio CIs.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/control_logistic.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Control function for logistic regression model fitting — control_logistic","text":"","code":"control_logistic(response_definition = \"response\", conf_level = 0.95)"},{"path":"https://insightsengineering.github.io/tern/main/reference/control_logistic.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Control function for logistic regression model fitting — control_logistic","text":"response_definition (string) definition event terms response. used fitting logistic regression model left hand side formula. Note evaluated expression result either logical vector factor 2 levels. default just \"response\" original response variable used modified . conf_level (proportion) confidence level interval.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/control_logistic.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Control function for logistic regression model fitting — control_logistic","text":"list components names arguments.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/control_logistic.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Control function for logistic regression model fitting — control_logistic","text":"","code":"# Standard options. control_logistic() #> $response_definition #> [1] \"response\" #>  #> $conf_level #> [1] 0.95 #>   # Modify confidence level. control_logistic(conf_level = 0.9) #> $response_definition #> [1] \"response\" #>  #> $conf_level #> [1] 0.9 #>   # Use a different response definition. control_logistic(response_definition = \"I(response %in% c('CR', 'PR'))\") #> $response_definition #> [1] \"I(response %in% c('CR', 'PR'))\" #>  #> $conf_level #> [1] 0.95 #>"},{"path":"https://insightsengineering.github.io/tern/main/reference/control_riskdiff.html","id":null,"dir":"Reference","previous_headings":"","what":"Control function for risk difference column — control_riskdiff","title":"Control function for risk difference column — control_riskdiff","text":"Sets list parameters use generating risk (proportion) difference column. Used input riskdiff parameter tabulate_rsp_subgroups() tabulate_survival_subgroups().","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/control_riskdiff.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Control function for risk difference column — control_riskdiff","text":"","code":"control_riskdiff(   arm_x = NULL,   arm_y = NULL,   format = \"xx.x (xx.x - xx.x)\",   col_label = \"Risk Difference (%) (95% CI)\",   pct = TRUE )"},{"path":"https://insightsengineering.github.io/tern/main/reference/control_riskdiff.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Control function for risk difference column — control_riskdiff","text":"arm_x (string) name reference arm use risk difference calculations. arm_y (character) names one arms compare reference arm risk difference calculations. new column added value arm_y. format (string function) format label (string) formatting function apply risk difference statistic. See 3d string options formatters::list_valid_format_labels() possible format strings. Defaults \"xx.x (xx.x - xx.x)\". col_label (character) labels use rendering risk difference column within table. one comparison arm specified arm_y, default labels specify two arms compared (reference arm vs. comparison arm). pct (flag) whether output returned percentages. Defaults TRUE.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/control_riskdiff.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Control function for risk difference column — control_riskdiff","text":"list items names corresponding arguments.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/main/reference/control_riskdiff.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Control function for risk difference column — control_riskdiff","text":"","code":"control_riskdiff() #> $arm_x #> NULL #>  #> $arm_y #> NULL #>  #> $format #> [1] \"xx.x (xx.x - xx.x)\" #>  #> $col_label #> [1] \"Risk Difference (%) (95% CI)\" #>  #> $pct #> [1] TRUE #>  control_riskdiff(arm_x = \"ARM A\", arm_y = \"ARM B\") #> $arm_x #> [1] \"ARM A\" #>  #> $arm_y #> [1] \"ARM B\" #>  #> $format #> [1] \"xx.x (xx.x - xx.x)\" #>  #> $col_label #> [1] \"Risk Difference (%) (95% CI)\" #>  #> $pct #> [1] TRUE #>"},{"path":"https://insightsengineering.github.io/tern/main/reference/control_step.html","id":null,"dir":"Reference","previous_headings":"","what":"Control function for subgroup treatment effect pattern (STEP) calculations — control_step","title":"Control function for subgroup treatment effect pattern (STEP) calculations — control_step","text":"auxiliary function controlling arguments STEP calculations.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/control_step.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Control function for subgroup treatment effect pattern (STEP) calculations — control_step","text":"","code":"control_step(   biomarker = NULL,   use_percentile = TRUE,   bandwidth,   degree = 0L,   num_points = 39L )"},{"path":"https://insightsengineering.github.io/tern/main/reference/control_step.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Control function for subgroup treatment effect pattern (STEP) calculations — control_step","text":"biomarker (numeric NULL) optional provision numeric biomarker variable, used infer bandwidth, see . use_percentile (flag) TRUE, running windows created according quantiles rather actual values, .e. bandwidth refers percentage data covered window. Suggest TRUE biomarker variable uniformly distributed. bandwidth (numeric(1) NULL) indicating bandwidth window. Depending argument use_percentile, can either length actual-value windows real biomarker scale, percentage windows. use_percentile = TRUE, number 0 1. NULL, treat bandwidth infinity, means one global model fitted. default, 0.25 used percentage windows one quarter range biomarker variable actual-value windows. degree (integer(1)) degree polynomial function biomarker interaction term treatment arm fitted window. 0 (default), biomarker variable included model fitted biomarker window. num_points (integer(1)) number points hazard ratios estimated. smallest number 2.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/control_step.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Control function for subgroup treatment effect pattern (STEP) calculations — control_step","text":"list components names arguments, except biomarker just used calculate bandwidth case actual biomarker windows requested.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/control_step.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Control function for subgroup treatment effect pattern (STEP) calculations — control_step","text":"","code":"# Provide biomarker values and request actual values to be used, # so that bandwidth is chosen from range. control_step(biomarker = 1:10, use_percentile = FALSE) #> $use_percentile #> [1] FALSE #>  #> $bandwidth #> [1] 2.25 #>  #> $degree #> [1] 0 #>  #> $num_points #> [1] 39 #>   # Use a global model with quadratic biomarker interaction term. control_step(bandwidth = NULL, degree = 2) #> $use_percentile #> [1] TRUE #>  #> $bandwidth #> NULL #>  #> $degree #> [1] 2 #>  #> $num_points #> [1] 39 #>   # Reduce number of points to be used. control_step(num_points = 10) #> $use_percentile #> [1] TRUE #>  #> $bandwidth #> [1] 0.25 #>  #> $degree #> [1] 0 #>  #> $num_points #> [1] 10 #>"},{"path":"https://insightsengineering.github.io/tern/main/reference/control_surv_time.html","id":null,"dir":"Reference","previous_headings":"","what":"Control function for survfit models for survival time — control_surv_time","title":"Control function for survfit models for survival time — control_surv_time","text":"auxiliary function controlling arguments survfit model, typically used internally specify details survfit model s_surv_time(). conf_level refers survival time estimation.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/control_surv_time.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Control function for survfit models for survival time — control_surv_time","text":"","code":"control_surv_time(   conf_level = 0.95,   conf_type = c(\"plain\", \"log\", \"log-log\"),   quantiles = c(0.25, 0.75) )"},{"path":"https://insightsengineering.github.io/tern/main/reference/control_surv_time.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Control function for survfit models for survival time — control_surv_time","text":"conf_level (proportion) confidence level interval. conf_type (string) confidence interval type. Options \"plain\" (default), \"log\", \"log-log\", see survival::survfit(). Note option \"none\" longer supported. quantiles (numeric(2)) vector length two specifying quantiles survival time.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/control_surv_time.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Control function for survfit models for survival time — control_surv_time","text":"list components names arguments.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/control_surv_timepoint.html","id":null,"dir":"Reference","previous_headings":"","what":"Control function for survfit models for patients' survival rate at time points — control_surv_timepoint","title":"Control function for survfit models for patients' survival rate at time points — control_surv_timepoint","text":"auxiliary function controlling arguments survfit model, typically used internally specify details survfit model s_surv_timepoint(). conf_level refers patient risk estimation time point.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/control_surv_timepoint.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Control function for survfit models for patients' survival rate at time points — control_surv_timepoint","text":"","code":"control_surv_timepoint(   conf_level = 0.95,   conf_type = c(\"plain\", \"log\", \"log-log\") )"},{"path":"https://insightsengineering.github.io/tern/main/reference/control_surv_timepoint.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Control function for survfit models for patients' survival rate at time points — control_surv_timepoint","text":"conf_level (proportion) confidence level interval. conf_type (string) confidence interval type. Options \"plain\" (default), \"log\", \"log-log\", see survival::survfit(). Note option \"none\" longer supported.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/control_surv_timepoint.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Control function for survfit models for patients' survival rate at time points — control_surv_timepoint","text":"list components names arguments.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/count_cumulative.html","id":null,"dir":"Reference","previous_headings":"","what":"Cumulative counts of numeric variable by thresholds — count_cumulative","title":"Cumulative counts of numeric variable by thresholds — count_cumulative","text":"analyze function count_cumulative() creates layout element calculate cumulative counts values numeric variable less , less equal , greater , greater equal user-specified threshold values. function analyzes numeric variable vars threshold values supplied thresholds argument numeric vector. Whether counts include threshold values, whether count values lower higher threshold values can set via include_eq lower_tail parameters, respectively.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/count_cumulative.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Cumulative counts of numeric variable by thresholds — count_cumulative","text":"","code":"count_cumulative(   lyt,   vars,   thresholds,   lower_tail = TRUE,   include_eq = TRUE,   var_labels = vars,   show_labels = \"visible\",   na_str = default_na_str(),   nested = TRUE,   ...,   table_names = vars,   .stats = NULL,   .formats = NULL,   .labels = NULL,   .indent_mods = NULL )  s_count_cumulative(   x,   thresholds,   lower_tail = TRUE,   include_eq = TRUE,   .N_col,   .N_row,   denom = c(\"N_col\", \"n\", \"N_row\"),   ... )  a_count_cumulative(   x,   thresholds,   lower_tail = TRUE,   include_eq = TRUE,   .N_col,   .N_row,   denom = c(\"N_col\", \"n\", \"N_row\"),   ... )"},{"path":"https://insightsengineering.github.io/tern/main/reference/count_cumulative.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Cumulative counts of numeric variable by thresholds — count_cumulative","text":"lyt (PreDataTableLayouts) layout analyses added . vars (character) variable names primary analysis variable iterated . thresholds (numeric) vector cutoff values counts. lower_tail (flag) whether count lower tail, default TRUE. include_eq (flag) whether include value equal threshold count, default TRUE. var_labels (character) variable labels. show_labels (string) label visibility: one \"default\", \"visible\" \"hidden\". na_str (string) string used replace NA empty values output. nested (flag) whether layout instruction applied within existing layout structure _if possible (TRUE, default) new top-level element (FALSE). Ignored nest split. underneath analyses, allowed. ... additional arguments lower level functions. table_names (character) can customized case vars analyzed multiple times, avoid warnings rtables. .stats (character) statistics select table. Options : 'count_fraction', 'count_fraction_fixed_dp' .formats (named character list) formats statistics. See Details analyze_vars information \"auto\" setting. .labels (named character) labels statistics (without indent). .indent_mods (named integer) indent modifiers labels. Defaults 0, corresponds unmodified default behavior. Can negative. x (numeric) vector numbers want analyze. .N_col (integer(1)) column-wise N (column count) full column analyzed typically passed rtables. .N_row (integer(1)) row-wise N (row group count) group observations analyzed (.e. column-based subsetting) typically passed rtables. denom (string) choice denominator proportion. Options : n: number values row column intersection. N_row: total number values row across columns. N_col: total number values column across rows.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/count_cumulative.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Cumulative counts of numeric variable by thresholds — count_cumulative","text":"count_cumulative() returns layout object suitable passing layouting functions, rtables::build_table(). Adding function rtable layout add formatted rows containing statistics s_count_cumulative() table layout. s_count_cumulative() returns named list count_fractions: list thresholds value component, component containing vector count fraction. a_count_cumulative() returns corresponding list formatted rtables::CellValue().","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/count_cumulative.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Cumulative counts of numeric variable by thresholds — count_cumulative","text":"count_cumulative(): Layout-creating function can take statistics function arguments additional format arguments. function wrapper rtables::analyze(). s_count_cumulative(): Statistics function produces named list given numeric vector thresholds. a_count_cumulative(): Formatted analysis function used afun count_cumulative().","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/main/reference/count_cumulative.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Cumulative counts of numeric variable by thresholds — count_cumulative","text":"","code":"basic_table() %>%   split_cols_by(\"ARM\") %>%   add_colcounts() %>%   count_cumulative(     vars = \"AGE\",     thresholds = c(40, 60)   ) %>%   build_table(tern_ex_adsl) #>           A: Drug X    B: Placebo   C: Combination #>             (N=69)       (N=73)         (N=58)     #> —————————————————————————————————————————————————— #> AGE                                                #>   <= 40   52 (75.4%)   58 (79.5%)     41 (70.7%)   #>   <= 60   69 (100%)    73 (100%)      58 (100%)"},{"path":"https://insightsengineering.github.io/tern/main/reference/count_missed_doses.html","id":null,"dir":"Reference","previous_headings":"","what":"Count number of patients with missed doses by thresholds — count_missed_doses","title":"Count number of patients with missed doses by thresholds — count_missed_doses","text":"analyze function creates layout element calculate cumulative counts patients number missed doses least equal user-specified threshold values. function analyzes numeric variable vars, variable numbers missed doses, threshold values supplied thresholds argument numeric vector. function assumes every row given data frame corresponds unique patient.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/count_missed_doses.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Count number of patients with missed doses by thresholds — count_missed_doses","text":"","code":"count_missed_doses(   lyt,   vars,   thresholds,   var_labels = vars,   show_labels = \"visible\",   na_str = default_na_str(),   nested = TRUE,   ...,   table_names = vars,   .stats = NULL,   .formats = NULL,   .labels = NULL,   .indent_mods = NULL )  s_count_nonmissing(x)  s_count_missed_doses(   x,   thresholds,   .N_col,   .N_row,   denom = c(\"N_col\", \"n\", \"N_row\") )  a_count_missed_doses(   x,   thresholds,   .N_col,   .N_row,   denom = c(\"N_col\", \"n\", \"N_row\") )"},{"path":"https://insightsengineering.github.io/tern/main/reference/count_missed_doses.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Count number of patients with missed doses by thresholds — count_missed_doses","text":"lyt (PreDataTableLayouts) layout analyses added . vars (character) variable names primary analysis variable iterated . thresholds (numeric) minimum number missed doses patients . var_labels (character) variable labels. show_labels (string) label visibility: one \"default\", \"visible\" \"hidden\". na_str (string) string used replace NA empty values output. nested (flag) whether layout instruction applied within existing layout structure _if possible (TRUE, default) new top-level element (FALSE). Ignored nest split. underneath analyses, allowed. ... additional arguments lower level functions. table_names (character) can customized case vars analyzed multiple times, avoid warnings rtables. .stats (character) statistics select table. Options : 'n', 'count_fraction', 'count_fraction_fixed_dp' .formats (named character list) formats statistics. See Details analyze_vars information \"auto\" setting. .labels (named character) labels statistics (without indent). .indent_mods (named integer) indent modifiers labels. Defaults 0, corresponds unmodified default behavior. Can negative. x (numeric) vector numbers want analyze. .N_col (integer(1)) column-wise N (column count) full column analyzed typically passed rtables. .N_row (integer(1)) row-wise N (row group count) group observations analyzed (.e. column-based subsetting) typically passed rtables. denom (string) choice denominator proportion. Options : n: number values row column intersection. N_row: total number values row across columns. N_col: total number values column across rows.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/count_missed_doses.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Count number of patients with missed doses by thresholds — count_missed_doses","text":"count_missed_doses() returns layout object suitable passing layouting functions, rtables::build_table(). Adding function rtable layout add formatted rows containing statistics s_count_missed_doses() table layout. s_count_nonmissing() returns statistic n count non-missing values x. s_count_missed_doses() returns statistics n count_fraction one element threshold. a_count_missed_doses() returns corresponding list formatted rtables::CellValue().","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/count_missed_doses.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Count number of patients with missed doses by thresholds — count_missed_doses","text":"count_missed_doses(): Layout-creating function can take statistics function arguments additional format arguments. function wrapper rtables::analyze(). s_count_nonmissing(): Statistics function count non-missing values. s_count_missed_doses(): Statistics function count patients missed doses. a_count_missed_doses(): Formatted analysis function used afun count_missed_doses().","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/main/reference/count_missed_doses.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Count number of patients with missed doses by thresholds — count_missed_doses","text":"","code":"library(dplyr)  anl <- tern_ex_adsl %>%   distinct(STUDYID, USUBJID, ARM) %>%   mutate(     PARAMCD = \"TNDOSMIS\",     PARAM = \"Total number of missed doses during study\",     AVAL = sample(0:20, size = nrow(tern_ex_adsl), replace = TRUE),     AVALC = \"\"   )  basic_table() %>%   split_cols_by(\"ARM\") %>%   add_colcounts() %>%   count_missed_doses(\"AVAL\", thresholds = c(1, 5, 10, 15), var_labels = \"Missed Doses\") %>%   build_table(anl, alt_counts_df = tern_ex_adsl) #>                              A: Drug X    B: Placebo   C: Combination #>                                (N=69)       (N=73)         (N=58)     #> ————————————————————————————————————————————————————————————————————— #> Missed Doses                                                          #>   n                              69           73             58       #>   At least 1 missed dose     69 (100%)    69 (94.5%)     55 (94.8%)   #>   At least 5 missed doses    57 (82.6%)   55 (75.3%)     50 (86.2%)   #>   At least 10 missed doses    40 (58%)    40 (54.8%)     32 (55.2%)   #>   At least 15 missed doses   26 (37.7%)   25 (34.2%)     13 (22.4%)"},{"path":"https://insightsengineering.github.io/tern/main/reference/count_occurrences.html","id":null,"dir":"Reference","previous_headings":"","what":"Count occurrences — count_occurrences","title":"Count occurrences — count_occurrences","text":"analyze function count_occurrences() creates layout element calculate occurrence counts patients. function analyzes variable(s) supplied vars returns table occurrence counts unique value (level) variable(s). variable (variables) must non-numeric. id variable used indicate unique subject identifiers (defaults USUBJID). multiple occurrences value recorded patient, value counted . summarize function summarize_occurrences() performs function count_occurrences() except creates content rows, data rows, summarize current table row/column context operates level latest row split root table row splits occurred.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/count_occurrences.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Count occurrences — count_occurrences","text":"","code":"count_occurrences(   lyt,   vars,   id = \"USUBJID\",   drop = TRUE,   var_labels = vars,   show_labels = \"hidden\",   riskdiff = FALSE,   na_str = default_na_str(),   nested = TRUE,   ...,   table_names = vars,   .stats = \"count_fraction_fixed_dp\",   .formats = NULL,   .labels = NULL,   .indent_mods = NULL )  summarize_occurrences(   lyt,   var,   id = \"USUBJID\",   drop = TRUE,   riskdiff = FALSE,   na_str = default_na_str(),   ...,   .stats = \"count_fraction_fixed_dp\",   .formats = NULL,   .indent_mods = NULL,   .labels = NULL )  s_count_occurrences(   df,   denom = c(\"N_col\", \"n\", \"N_row\"),   .N_col,   .N_row,   .df_row,   drop = TRUE,   .var = \"MHDECOD\",   id = \"USUBJID\" )  a_count_occurrences(   df,   labelstr = \"\",   id = \"USUBJID\",   denom = c(\"N_col\", \"n\", \"N_row\"),   drop = TRUE,   .N_col,   .N_row,   .var = NULL,   .df_row = NULL,   .stats = NULL,   .formats = NULL,   .labels = NULL,   .indent_mods = NULL,   na_str = default_na_str() )"},{"path":"https://insightsengineering.github.io/tern/main/reference/count_occurrences.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Count occurrences — count_occurrences","text":"lyt (PreDataTableLayouts) layout analyses added . vars (character) variable names primary analysis variable iterated . id (string) subject variable name. drop (flag) whether non-appearing occurrence levels dropped resulting table. Note case remaining occurrence levels table sorted alphabetically. var_labels (character) variable labels. show_labels (string) label visibility: one \"default\", \"visible\" \"hidden\". riskdiff (flag) whether risk difference column present. set TRUE, add_riskdiff() must used split_fun prior column split table layout, specifying columns compared. See stat_propdiff_ci() details risk difference calculation. na_str (string) string used replace NA empty values output. nested (flag) whether layout instruction applied within existing layout structure _if possible (TRUE, default) new top-level element (FALSE). Ignored nest split. underneath analyses, allowed. ... additional arguments lower level functions. table_names (character) can customized case vars analyzed multiple times, avoid warnings rtables. .stats (character) statistics select table. Options : 'count', 'count_fraction', 'count_fraction_fixed_dp', 'fraction' .formats (named character list) formats statistics. See Details analyze_vars information \"auto\" setting. .labels (named character) labels statistics (without indent). .indent_mods (named integer) indent modifiers labels. Defaults 0, corresponds unmodified default behavior. Can negative. df (data.frame) data set containing analysis variables. denom (string) choice denominator proportion. Options : N_col: total number patients column across rows. n: number patients occurrences. N_row: total number patients row across columns. .N_col (integer(1)) column-wise N (column count) full column analyzed typically passed rtables. .N_row (integer(1)) row-wise N (row group count) group observations analyzed (.e. column-based subsetting) typically passed rtables. .df_row (data.frame) data frame across columns given row split. .var, var (string) single variable name passed rtables requested statistics function. labelstr (string) label level parent split currently summarized (must present second argument Content Row Functions). See rtables::summarize_row_groups() information.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/count_occurrences.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Count occurrences — count_occurrences","text":"count_occurrences() returns layout object suitable passing layouting functions, rtables::build_table(). Adding function rtable layout add formatted rows containing statistics s_count_occurrences() table layout. summarize_occurrences() returns layout object suitable passing layouting functions, rtables::build_table(). Adding function rtable layout add formatted content rows containing statistics s_count_occurrences() table layout. s_count_occurrences() returns list : count: list counts one element per occurrence. count_fraction: list counts fractions one element per occurrence. fraction: list numerators denominators one element per occurrence. a_count_occurrences() returns corresponding list formatted rtables::CellValue().","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/count_occurrences.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Count occurrences — count_occurrences","text":"count_occurrences(): Layout-creating function can take statistics function arguments additional format arguments. function wrapper rtables::analyze(). summarize_occurrences(): Layout-creating function can take content function arguments additional format arguments. function wrapper rtables::summarize_row_groups(). s_count_occurrences(): Statistics function counts number patients report occurrence. a_count_occurrences(): Formatted analysis function used afun count_occurrences().","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/count_occurrences.html","id":"note","dir":"Reference","previous_headings":"","what":"Note","title":"Count occurrences — count_occurrences","text":"default, occurrences appear given row split dropped table occurrences table sorted alphabetically per row split. Therefore, corresponding layout needs use split_fun = drop_split_levels split_rows_by calls. Use drop = FALSE like show occurrences.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/count_occurrences.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Count occurrences — count_occurrences","text":"","code":"library(dplyr) df <- data.frame(   USUBJID = as.character(c(     1, 1, 2, 4, 4, 4,     6, 6, 6, 7, 7, 8   )),   MHDECOD = c(     \"MH1\", \"MH2\", \"MH1\", \"MH1\", \"MH1\", \"MH3\",     \"MH2\", \"MH2\", \"MH3\", \"MH1\", \"MH2\", \"MH4\"   ),   ARM = rep(c(\"A\", \"B\"), each = 6),   SEX = c(\"F\", \"F\", \"M\", \"M\", \"M\", \"M\", \"F\", \"F\", \"F\", \"M\", \"M\", \"F\") ) df_adsl <- df %>%   select(USUBJID, ARM) %>%   unique()  # Create table layout lyt <- basic_table() %>%   split_cols_by(\"ARM\") %>%   add_colcounts() %>%   count_occurrences(vars = \"MHDECOD\", .stats = c(\"count_fraction\"))  # Apply table layout to data and produce `rtable` object tbl <- lyt %>%   build_table(df, alt_counts_df = df_adsl) %>%   prune_table()  tbl #>           A           B     #>         (N=3)       (N=3)   #> ——————————————————————————— #> MH1   3 (100%)    1 (33.3%) #> MH2   1 (33.3%)   2 (66.7%) #> MH3   1 (33.3%)   1 (33.3%) #> MH4       0       1 (33.3%)  # Layout creating function with custom format. basic_table() %>%   add_colcounts() %>%   split_rows_by(\"SEX\", child_labels = \"visible\") %>%   summarize_occurrences(     var = \"MHDECOD\",     .formats = c(\"count_fraction\" = \"xx.xx (xx.xx%)\")   ) %>%   build_table(df, alt_counts_df = df_adsl) #>          all obs  #>           (N=6)   #> ————————————————— #> F                 #>   MH1   1 (16.7%) #>   MH2   2 (33.3%) #>   MH3   1 (16.7%) #>   MH4   1 (16.7%) #> M                 #>   MH1   3 (50.0%) #>   MH2   1 (16.7%) #>   MH3   1 (16.7%)  # Count unique occurrences per subject. s_count_occurrences(   df,   .N_col = 4L,   .N_row = 4L,   .df_row = df,   .var = \"MHDECOD\",   id = \"USUBJID\" ) #> $count #> $count$MH1 #> [1] 4 #>  #> $count$MH2 #> [1] 3 #>  #> $count$MH3 #> [1] 2 #>  #> $count$MH4 #> [1] 1 #>  #>  #> $count_fraction #> $count_fraction$MH1 #> [1] 4 1 #>  #> $count_fraction$MH2 #> [1] 3.00 0.75 #>  #> $count_fraction$MH3 #> [1] 2.0 0.5 #>  #> $count_fraction$MH4 #> [1] 1.00 0.25 #>  #>  #> $fraction #> $fraction$MH1 #>   num denom  #>     4     4  #>  #> $fraction$MH2 #>   num denom  #>     3     4  #>  #> $fraction$MH3 #>   num denom  #>     2     4  #>  #> $fraction$MH4 #>   num denom  #>     1     4  #>  #>   a_count_occurrences(   df,   .N_col = 4L,   .df_row = df,   .var = \"MHDECOD\",   id = \"USUBJID\" ) #> RowsVerticalSection (in_rows) object print method: #> ---------------------------- #>    row_name formatted_cell indent_mod row_label #> 1       MH1              4          0       MH1 #> 2       MH2              3          0       MH2 #> 3       MH3              2          0       MH3 #> 4       MH4              1          0       MH4 #> 5       MH1       4 (100%)          0       MH1 #> 6       MH2        3 (75%)          0       MH2 #> 7       MH3        2 (50%)          0       MH3 #> 8       MH4        1 (25%)          0       MH4 #> 9       MH1       4 (100%)          0       MH1 #> 10      MH2      3 (75.0%)          0       MH2 #> 11      MH3      2 (50.0%)          0       MH3 #> 12      MH4      1 (25.0%)          0       MH4 #> 13      MH1   4/4 (100.0%)          0       MH1 #> 14      MH2    3/4 (75.0%)          0       MH2 #> 15      MH3    2/4 (50.0%)          0       MH3 #> 16      MH4    1/4 (25.0%)          0       MH4"},{"path":"https://insightsengineering.github.io/tern/main/reference/count_occurrences_by_grade.html","id":null,"dir":"Reference","previous_headings":"","what":"Count occurrences by grade — count_occurrences_by_grade","title":"Count occurrences by grade — count_occurrences_by_grade","text":"analyze function count_occurrences_by_grade() creates layout element calculate occurrence counts grade. function analyzes primary analysis variable var indicates toxicity grades. id variable used indicate unique subject identifiers (defaults USUBJID). user can also supply list custom groups grades analyze via grade_groups parameter. remove_single  argument remove single grades analysis grade groups analyzed. multiple grades recorded one patient highest grade level counted. summarize function summarize_occurrences_by_grade() performs function count_occurrences_by_grade() except creates content rows, data rows, summarize current table row/column context operates level latest row split root table row splits occurred.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/count_occurrences_by_grade.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Count occurrences by grade — count_occurrences_by_grade","text":"","code":"count_occurrences_by_grade(   lyt,   var,   id = \"USUBJID\",   grade_groups = list(),   remove_single = TRUE,   only_grade_groups = FALSE,   var_labels = var,   show_labels = \"default\",   riskdiff = FALSE,   na_str = default_na_str(),   nested = TRUE,   ...,   table_names = var,   .stats = \"count_fraction\",   .formats = list(count_fraction = format_count_fraction_fixed_dp),   .indent_mods = NULL,   .labels = NULL )  summarize_occurrences_by_grade(   lyt,   var,   id = \"USUBJID\",   grade_groups = list(),   remove_single = TRUE,   only_grade_groups = FALSE,   riskdiff = FALSE,   na_str = default_na_str(),   ...,   .stats = \"count_fraction\",   .formats = list(count_fraction = format_count_fraction_fixed_dp),   .indent_mods = NULL,   .labels = NULL )  s_count_occurrences_by_grade(   df,   .var,   .N_row,   .N_col,   id = \"USUBJID\",   grade_groups = list(),   remove_single = TRUE,   only_grade_groups = FALSE,   denom = c(\"N_col\", \"n\", \"N_row\"),   labelstr = \"\" )  a_count_occurrences_by_grade(   df,   labelstr = \"\",   id = \"USUBJID\",   grade_groups = list(),   remove_single = TRUE,   only_grade_groups = FALSE,   denom = c(\"N_col\", \"n\", \"N_row\"),   .N_col,   .N_row,   .df_row,   .var = NULL,   .stats = NULL,   .formats = NULL,   .labels = NULL,   .indent_mods = NULL,   na_str = default_na_str() )"},{"path":"https://insightsengineering.github.io/tern/main/reference/count_occurrences_by_grade.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Count occurrences by grade — count_occurrences_by_grade","text":"lyt (PreDataTableLayouts) layout analyses added . id (string) subject variable name. grade_groups (named list character) list containing groupings grades. remove_single (flag)TRUE include elements one-element grade groups output list; case grade groups names included output. only_grade_groups set TRUE argument ignored. only_grade_groups (flag) whether specified grade groups included, individual grade rows removed (TRUE), grades grade groups displayed (FALSE). var_labels (character) variable labels. show_labels (string) label visibility: one \"default\", \"visible\" \"hidden\". riskdiff (flag) whether risk difference column present. set TRUE, add_riskdiff() must used split_fun prior column split table layout, specifying columns compared. See stat_propdiff_ci() details risk difference calculation. na_str (string) string used replace NA empty values output. nested (flag) whether layout instruction applied within existing layout structure _if possible (TRUE, default) new top-level element (FALSE). Ignored nest split. underneath analyses, allowed. ... additional arguments lower level functions. table_names (character) can customized case vars analyzed multiple times, avoid warnings rtables. .stats (character) statistics select table. Options : 'count_fraction', 'count_fraction_fixed_dp' .formats (named character list) formats statistics. See Details analyze_vars information \"auto\" setting. .indent_mods (named integer) indent modifiers labels. Defaults 0, corresponds unmodified default behavior. Can negative. .labels (named character) labels statistics (without indent). df (data.frame) data set containing analysis variables. .var, var (string) single variable name passed rtables requested statistics function. .N_row (integer(1)) row-wise N (row group count) group observations analyzed (.e. column-based subsetting) typically passed rtables. .N_col (integer(1)) column-wise N (column count) full column analyzed typically passed rtables. denom (string) choice denominator proportion. Options : N_col: total number patients column across rows. n: number patients occurrences. N_row: total number patients row across columns. labelstr (string) label level parent split currently summarized (must present second argument Content Row Functions). See rtables::summarize_row_groups() information. .df_row (data.frame) data frame across columns given row split.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/count_occurrences_by_grade.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Count occurrences by grade — count_occurrences_by_grade","text":"count_occurrences_by_grade() returns layout object suitable passing layouting functions, rtables::build_table(). Adding function rtable layout add formatted rows containing statistics s_count_occurrences_by_grade() table layout. summarize_occurrences_by_grade() returns layout object suitable passing layouting functions, rtables::build_table(). Adding function rtable layout add formatted content rows containing statistics s_count_occurrences_by_grade() table layout. s_count_occurrences_by_grade() returns list counts fractions one element per grade level grade level grouping. a_count_occurrences_by_grade() returns corresponding list formatted rtables::CellValue().","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/count_occurrences_by_grade.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Count occurrences by grade — count_occurrences_by_grade","text":"count_occurrences_by_grade(): Layout-creating function can take statistics function arguments additional format arguments. function wrapper rtables::analyze(). summarize_occurrences_by_grade(): Layout-creating function can take content function arguments additional format arguments. function wrapper rtables::summarize_row_groups(). s_count_occurrences_by_grade(): Statistics function counts number patients highest grade. a_count_occurrences_by_grade(): Formatted analysis function used afun count_occurrences_by_grade().","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/main/reference/count_occurrences_by_grade.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Count occurrences by grade — count_occurrences_by_grade","text":"","code":"library(dplyr)  df <- data.frame(   USUBJID = as.character(c(1:6, 1)),   ARM = factor(c(\"A\", \"A\", \"A\", \"B\", \"B\", \"B\", \"A\"), levels = c(\"A\", \"B\")),   AETOXGR = factor(c(1, 2, 3, 4, 1, 2, 3), levels = c(1:5)),   AESEV = factor(     x = c(\"MILD\", \"MODERATE\", \"SEVERE\", \"MILD\", \"MILD\", \"MODERATE\", \"SEVERE\"),     levels = c(\"MILD\", \"MODERATE\", \"SEVERE\")   ),   stringsAsFactors = FALSE )  df_adsl <- df %>%   select(USUBJID, ARM) %>%   unique()  # Layout creating function with custom format. basic_table() %>%   split_cols_by(\"ARM\") %>%   add_colcounts() %>%   count_occurrences_by_grade(     var = \"AESEV\",     .formats = c(\"count_fraction\" = \"xx.xx (xx.xx%)\")   ) %>%   build_table(df, alt_counts_df = df_adsl) #>                  A               B       #>                (N=3)           (N=3)     #> ———————————————————————————————————————— #> MILD       0.00 (0.00%)    2.00 (66.67%) #> MODERATE   1.00 (33.33%)   1.00 (33.33%) #> SEVERE     2.00 (66.67%)   0.00 (0.00%)   # Define additional grade groupings. grade_groups <- list(   \"-Any-\" = c(\"1\", \"2\", \"3\", \"4\", \"5\"),   \"Grade 1-2\" = c(\"1\", \"2\"),   \"Grade 3-5\" = c(\"3\", \"4\", \"5\") )  basic_table() %>%   split_cols_by(\"ARM\") %>%   add_colcounts() %>%   count_occurrences_by_grade(     var = \"AETOXGR\",     grade_groups = grade_groups,     only_grade_groups = TRUE   ) %>%   build_table(df, alt_counts_df = df_adsl) #>                 A           B     #>               (N=3)       (N=3)   #> ————————————————————————————————— #> -Any-       3 (100%)    3 (100%)  #> Grade 1-2   1 (33.3%)   2 (66.7%) #> Grade 3-5   2 (66.7%)   1 (33.3%)  # Layout creating function with custom format. basic_table() %>%   add_colcounts() %>%   split_rows_by(\"ARM\", child_labels = \"visible\", nested = TRUE) %>%   summarize_occurrences_by_grade(     var = \"AESEV\",     .formats = c(\"count_fraction\" = \"xx.xx (xx.xx%)\")   ) %>%   build_table(df, alt_counts_df = df_adsl) #>                 all obs    #>                  (N=6)     #> —————————————————————————— #> A                          #>   MILD       0.00 (0.00%)  #>   MODERATE   1.00 (16.67%) #>   SEVERE     2.00 (33.33%) #> B                          #>   MILD       2.00 (33.33%) #>   MODERATE   1.00 (16.67%) #>   SEVERE     0.00 (0.00%)   basic_table() %>%   add_colcounts() %>%   split_rows_by(\"ARM\", child_labels = \"visible\", nested = TRUE) %>%   summarize_occurrences_by_grade(     var = \"AETOXGR\",     grade_groups = grade_groups   ) %>%   build_table(df, alt_counts_df = df_adsl) #>                all obs  #>                 (N=6)   #> ——————————————————————— #> A                       #>   -Any-       3 (50.0%) #>   Grade 1-2   1 (16.7%) #>   1               0     #>   2           1 (16.7%) #>   Grade 3-5   2 (33.3%) #>   3           2 (33.3%) #>   4               0     #>   5               0     #> B                       #>   -Any-       3 (50.0%) #>   Grade 1-2   2 (33.3%) #>   1           1 (16.7%) #>   2           1 (16.7%) #>   Grade 3-5   1 (16.7%) #>   3               0     #>   4           1 (16.7%) #>   5               0      s_count_occurrences_by_grade(   df,   .N_col = 10L,   .var = \"AETOXGR\",   id = \"USUBJID\",   grade_groups = list(\"ANY\" = levels(df$AETOXGR)) ) #> $count_fraction #> $count_fraction$ANY #> [1] 6.0 0.6 #>  #> $count_fraction$`1` #> [1] 1.0 0.1 #>  #> $count_fraction$`2` #> [1] 2.0 0.2 #>  #> $count_fraction$`3` #> [1] 2.0 0.2 #>  #> $count_fraction$`4` #> [1] 1.0 0.1 #>  #> $count_fraction$`5` #> [1] 0 0 #>  #>   a_count_occurrences_by_grade(   df,   .N_col = 10L,   .N_row = 10L,   .var = \"AETOXGR\",   id = \"USUBJID\",   grade_groups = list(\"ANY\" = levels(df$AETOXGR)) ) #> RowsVerticalSection (in_rows) object print method: #> ---------------------------- #>    row_name formatted_cell indent_mod row_label #> 1       ANY        6 (60%)          0       ANY #> 2         1        1 (10%)          0         1 #> 3         2        2 (20%)          0         2 #> 4         3        2 (20%)          0         3 #> 5         4        1 (10%)          0         4 #> 6         5              0          0         5 #> 7       ANY      6 (60.0%)          0       ANY #> 8         1      1 (10.0%)          0         1 #> 9         2      2 (20.0%)          0         2 #> 10        3      2 (20.0%)          0         3 #> 11        4      1 (10.0%)          0         4 #> 12        5              0          0         5"},{"path":"https://insightsengineering.github.io/tern/main/reference/count_patients_events_in_cols.html","id":null,"dir":"Reference","previous_headings":"","what":"Count patient events in columns — count_patients_events_in_cols","title":"Count patient events in columns — count_patients_events_in_cols","text":"summarize function summarize_patients_events_in_cols() creates layout element summarize patient event counts columns. function analyzes elements (events) supplied via filters_list parameter returns row counts number patients event well total numbers patients events. id variable used indicate unique subject identifiers (defaults USUBJID). multiple occurrences event recorded patient, event counted .","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/count_patients_events_in_cols.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Count patient events in columns — count_patients_events_in_cols","text":"","code":"summarize_patients_events_in_cols(   lyt,   id = \"USUBJID\",   filters_list = list(),   empty_stats = character(),   na_str = default_na_str(),   ...,   .stats = c(\"unique\", \"all\", names(filters_list)),   .labels = c(unique = \"Patients (All)\", all = \"Events (All)\",     labels_or_names(filters_list)),   col_split = TRUE )  s_count_patients_and_multiple_events(   df,   id,   filters_list,   empty_stats = character(),   labelstr = \"\",   custom_label = NULL )"},{"path":"https://insightsengineering.github.io/tern/main/reference/count_patients_events_in_cols.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Count patient events in columns — count_patients_events_in_cols","text":"lyt (PreDataTableLayouts) layout analyses added . id (string) subject variable name. filters_list (named list character) list element list describes one type event describe filters, format s_count_patients_with_event(). label, used column title. empty_stats (character) optional names statistics returned empty corresponding table cells stay blank. na_str (string) string used replace NA empty values output. ... additional arguments lower level functions. .stats (character) statistics select table. addition statistics added using filters_list, statistic options : 'unique', '' .labels (named character) labels statistics (without indent). col_split (flag) whether columns split. Set FALSE required column split done already earlier layout pipe. df (data.frame) data set containing analysis variables. labelstr (string) label level parent split currently summarized (must present second argument Content Row Functions). See rtables::summarize_row_groups() information. custom_label (string NULL) provided labelstr empty used label.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/count_patients_events_in_cols.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Count patient events in columns — count_patients_events_in_cols","text":"summarize_patients_events_in_cols() returns layout object suitable passing layouting functions, rtables::build_table(). Adding function rtable layout add formatted content rows containing statistics s_count_patients_and_multiple_events() table layout. s_count_patients_and_multiple_events() returns list statistics: unique: number unique patients df. : number rows df. one element name filters_list: number rows df, .e. events, fulfilling filter condition.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/count_patients_events_in_cols.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Count patient events in columns — count_patients_events_in_cols","text":"summarize_patients_events_in_cols(): Layout-creating function can take statistics function arguments additional format arguments. function wrapper rtables::summarize_row_groups(). s_count_patients_and_multiple_events(): Statistics function counts numbers patients multiple events defined filters. Used analysis function afun summarize_patients_events_in_cols().","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/count_patients_events_in_cols.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Count patient events in columns — count_patients_events_in_cols","text":"","code":"df <- data.frame(   USUBJID = rep(c(\"id1\", \"id2\", \"id3\", \"id4\"), c(2, 3, 1, 1)),   ARM = c(\"A\", \"A\", \"B\", \"B\", \"B\", \"B\", \"A\"),   AESER = rep(\"Y\", 7),   AESDTH = c(\"Y\", \"Y\", \"N\", \"Y\", \"Y\", \"N\", \"N\"),   AEREL = c(\"Y\", \"Y\", \"N\", \"Y\", \"Y\", \"N\", \"Y\"),   AEDECOD = c(\"A\", \"A\", \"A\", \"B\", \"B\", \"C\", \"D\"),   AEBODSYS = rep(c(\"SOC1\", \"SOC2\", \"SOC3\"), c(3, 3, 1)) )  # `summarize_patients_events_in_cols()` basic_table() %>%   summarize_patients_events_in_cols(     filters_list = list(       related = formatters::with_label(c(AEREL = \"Y\"), \"Events (Related)\"),       fatal = c(AESDTH = \"Y\"),       fatal_related = c(AEREL = \"Y\", AESDTH = \"Y\")     ),     custom_label = \"%s Total number of patients and events\"   ) %>%   build_table(df) #>                                          Patients (All)   Events (All)   Events (Related)   fatal   fatal_related #> ————————————————————————————————————————————————————————————————————————————————————————————————————————————————— #> %s Total number of patients and events         4               7                5             4           4"},{"path":"https://insightsengineering.github.io/tern/main/reference/count_patients_with_event.html","id":null,"dir":"Reference","previous_headings":"","what":"Count the number of patients with a particular event — count_patients_with_event","title":"Count the number of patients with a particular event — count_patients_with_event","text":"analyze function count_patients_with_event() creates layout element calculate patient counts user-specified set events. function analyzes primary analysis variable vars indicates unique subject identifiers. Events defined user named vector via filters argument, name corresponds variable value value(s) variable takes event. multiple records event recorded patient, one occurrence counted.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/count_patients_with_event.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Count the number of patients with a particular event — count_patients_with_event","text":"","code":"count_patients_with_event(   lyt,   vars,   filters,   riskdiff = FALSE,   na_str = default_na_str(),   nested = TRUE,   ...,   table_names = vars,   .stats = \"count_fraction\",   .formats = list(count_fraction = format_count_fraction_fixed_dp),   .labels = NULL,   .indent_mods = NULL )  s_count_patients_with_event(   df,   .var,   filters,   .N_col,   .N_row,   denom = c(\"n\", \"N_col\", \"N_row\") )  a_count_patients_with_event(   df,   labelstr = \"\",   filters,   denom = c(\"n\", \"N_col\", \"N_row\"),   .N_col,   .N_row,   .df_row,   .var = NULL,   .stats = NULL,   .formats = NULL,   .labels = NULL,   .indent_mods = NULL,   na_str = default_na_str() )"},{"path":"https://insightsengineering.github.io/tern/main/reference/count_patients_with_event.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Count the number of patients with a particular event — count_patients_with_event","text":"lyt (PreDataTableLayouts) layout analyses added . vars (character) variable names primary analysis variable iterated . filters (character) character vector specifying column names flag variables used counting number unique identifiers satisfying conditions. Multiple column names flags accepted format c(\"column_name1\" = \"flag1\", \"column_name2\" = \"flag2\"). Note equality accepted condition. riskdiff (flag) whether risk difference column present. set TRUE, add_riskdiff() must used split_fun prior column split table layout, specifying columns compared. See stat_propdiff_ci() details risk difference calculation. na_str (string) string used replace NA empty values output. nested (flag) whether layout instruction applied within existing layout structure _if possible (TRUE, default) new top-level element (FALSE). Ignored nest split. underneath analyses, allowed. ... additional arguments lower level functions. table_names (character) can customized case vars analyzed multiple times, avoid warnings rtables. .stats (character) statistics select table. Options : 'n', 'count', 'count_fraction', 'count_fraction_fixed_dp', 'n_blq' .formats (named character list) formats statistics. See Details analyze_vars information \"auto\" setting. .labels (named character) labels statistics (without indent). .indent_mods (named integer) indent modifiers labels. Defaults 0, corresponds unmodified default behavior. Can negative. df (data.frame) data set containing analysis variables. .var (string) name column contains unique identifier. .N_col (integer(1)) column-wise N (column count) full column analyzed typically passed rtables. .N_row (integer(1)) row-wise N (row group count) group observations analyzed (.e. column-based subsetting) typically passed rtables. denom (string) choice denominator proportion. Options : n: number values row column intersection. N_row: total number values row across columns. N_col: total number values column across rows. labelstr (string) label level parent split currently summarized (must present second argument Content Row Functions). See rtables::summarize_row_groups() information. .df_row (data.frame) data frame across columns given row split.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/count_patients_with_event.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Count the number of patients with a particular event — count_patients_with_event","text":"count_patients_with_event() returns layout object suitable passing layouting functions, rtables::build_table(). Adding function rtable layout add formatted rows containing statistics s_count_patients_with_event() table layout. s_count_patients_with_event() returns count fraction unique identifiers defined event. a_count_patients_with_event() returns corresponding list formatted rtables::CellValue().","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/count_patients_with_event.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Count the number of patients with a particular event — count_patients_with_event","text":"count_patients_with_event(): Layout-creating function can take statistics function arguments additional format arguments. function wrapper rtables::analyze(). s_count_patients_with_event(): Statistics function counts number patients defined event occurred. a_count_patients_with_event(): Formatted analysis function used afun count_patients_with_event().","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/main/reference/count_patients_with_event.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Count the number of patients with a particular event — count_patients_with_event","text":"","code":"lyt <- basic_table() %>%   split_cols_by(\"ARM\") %>%   add_colcounts() %>%   count_values(     \"STUDYID\",     values = \"AB12345\",     .stats = \"count\",     .labels = c(count = \"Total AEs\")   ) %>%   count_patients_with_event(     \"SUBJID\",     filters = c(\"TRTEMFL\" = \"Y\"),     .labels = c(count_fraction = \"Total number of patients with at least one adverse event\"),     table_names = \"tbl_all\"   ) %>%   count_patients_with_event(     \"SUBJID\",     filters = c(\"TRTEMFL\" = \"Y\", \"AEOUT\" = \"FATAL\"),     .labels = c(count_fraction = \"Total number of patients with fatal AEs\"),     table_names = \"tbl_fatal\"   ) %>%   count_patients_with_event(     \"SUBJID\",     filters = c(\"TRTEMFL\" = \"Y\", \"AEOUT\" = \"FATAL\", \"AEREL\" = \"Y\"),     .labels = c(count_fraction = \"Total number of patients with related fatal AEs\"),     .indent_mods = c(count_fraction = 2L),     table_names = \"tbl_rel_fatal\"   )  build_table(lyt, tern_ex_adae, alt_counts_df = tern_ex_adsl) #>                                                            A: Drug X    B: Placebo   C: Combination #>                                                              (N=69)       (N=73)         (N=58)     #> ——————————————————————————————————————————————————————————————————————————————————————————————————— #> Total AEs                                                     202          177            162       #> Total number of patients with at least one adverse event   59 (100%)    57 (100%)      48 (100%)    #> Total number of patients with fatal AEs                    28 (47.5%)   31 (54.4%)     20 (41.7%)   #>     Total number of patients with related fatal AEs        28 (47.5%)   31 (54.4%)     20 (41.7%)    s_count_patients_with_event(   tern_ex_adae,   .var = \"SUBJID\",   filters = c(\"TRTEMFL\" = \"Y\") ) #> $n #> [1] 164 #>  #> $count #> [1] 164 #>  #> $count_fraction #> [1] 164   1 #>  #> $n_blq #> [1] 0 #>   s_count_patients_with_event(   tern_ex_adae,   .var = \"SUBJID\",   filters = c(\"TRTEMFL\" = \"Y\", \"AEOUT\" = \"FATAL\") ) #> $n #> [1] 164 #>  #> $count #> [1] 79 #>  #> $count_fraction #> [1] 79.0000000  0.4817073 #>  #> $n_blq #> [1] 0 #>   s_count_patients_with_event(   tern_ex_adae,   .var = \"SUBJID\",   filters = c(\"TRTEMFL\" = \"Y\", \"AEOUT\" = \"FATAL\"),   denom = \"N_col\",   .N_col = 456 ) #> $n #> [1] 164 #>  #> $count #> [1] 79 #>  #> $count_fraction #> [1] 79.0000000  0.1732456 #>  #> $n_blq #> [1] 0 #>   a_count_patients_with_event(   tern_ex_adae,   .var = \"SUBJID\",   filters = c(\"TRTEMFL\" = \"Y\"),   .N_col = 100,   .N_row = 100 ) #> RowsVerticalSection (in_rows) object print method: #> ---------------------------- #>                  row_name formatted_cell indent_mod      row_label #> 1                       n            164          0              n #> 2                   count            164          0          count #> 3          count_fraction     164 (100%)          0 count_fraction #> 4 count_fraction_fixed_dp     164 (100%)          0 count_fraction #> 5                   n_blq              0          0          n_blq"},{"path":"https://insightsengineering.github.io/tern/main/reference/count_patients_with_flags.html","id":null,"dir":"Reference","previous_headings":"","what":"Count the number of patients with particular flags — count_patients_with_flags","title":"Count the number of patients with particular flags — count_patients_with_flags","text":"analyze function count_patients_with_flags() creates layout element calculate counts patients user-specified flags present. function analyzes primary analysis variable var indicates unique subject identifiers. Flags variables analyze specified user via flag_variables argument, must either take value TRUE (flag present) FALSE (flag absent) record. multiple records flag present patient, one occurrence counted.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/count_patients_with_flags.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Count the number of patients with particular flags — count_patients_with_flags","text":"","code":"count_patients_with_flags(   lyt,   var,   flag_variables,   flag_labels = NULL,   var_labels = var,   show_labels = \"hidden\",   riskdiff = FALSE,   na_str = default_na_str(),   nested = TRUE,   ...,   table_names = paste0(\"tbl_flags_\", var),   .stats = \"count_fraction\",   .formats = list(count_fraction = format_count_fraction_fixed_dp),   .indent_mods = NULL,   .labels = NULL )  s_count_patients_with_flags(   df,   .var,   flag_variables,   flag_labels = NULL,   .N_col,   .N_row,   denom = c(\"n\", \"N_col\", \"N_row\") )  a_count_patients_with_flags(   df,   labelstr = \"\",   flag_variables,   flag_labels = NULL,   denom = c(\"n\", \"N_col\", \"N_row\"),   .N_col,   .N_row,   .df_row,   .var = NULL,   .stats = NULL,   .formats = NULL,   .labels = NULL,   .indent_mods = NULL,   na_str = default_na_str() )"},{"path":"https://insightsengineering.github.io/tern/main/reference/count_patients_with_flags.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Count the number of patients with particular flags — count_patients_with_flags","text":"lyt (PreDataTableLayouts) layout analyses added . var (string) single variable name passed rtables requested statistics function. flag_variables (character) vector specifying names logical variables analysis dataset used counting number unique identifiers. flag_labels (character) vector labels use flag variables. labels also specified via .labels parameter, .labels values take precedence replace labels. var_labels (character) variable labels. show_labels (string) label visibility: one \"default\", \"visible\" \"hidden\". riskdiff (flag) whether risk difference column present. set TRUE, add_riskdiff() must used split_fun prior column split table layout, specifying columns compared. See stat_propdiff_ci() details risk difference calculation. na_str (string) string used replace NA empty values output. nested (flag) whether layout instruction applied within existing layout structure _if possible (TRUE, default) new top-level element (FALSE). Ignored nest split. underneath analyses, allowed. ... additional arguments lower level functions. table_names (character) can customized case vars analyzed multiple times, avoid warnings rtables. .stats (character) statistics select table. Options : 'n', 'count', 'count_fraction', 'count_fraction_fixed_dp', 'n_blq' .formats (named character list) formats statistics. See Details analyze_vars information \"auto\" setting. .indent_mods (named integer) indent modifiers labels. Defaults 0, corresponds unmodified default behavior. Can negative. .labels (named character) labels statistics (without indent). df (data.frame) data set containing analysis variables. .var (string) name column contains unique identifier. .N_col (integer(1)) column-wise N (column count) full column analyzed typically passed rtables. .N_row (integer(1)) row-wise N (row group count) group observations analyzed (.e. column-based subsetting) typically passed rtables. denom (string) choice denominator proportion. Options : n: number values row column intersection. N_row: total number values row across columns. N_col: total number values column across rows. labelstr (string) label level parent split currently summarized (must present second argument Content Row Functions). See rtables::summarize_row_groups() information. .df_row (data.frame) data frame across columns given row split.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/count_patients_with_flags.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Count the number of patients with particular flags — count_patients_with_flags","text":"count_patients_with_flags() returns layout object suitable passing layouting functions, rtables::build_table(). Adding function rtable layout add formatted rows containing statistics s_count_patients_with_flags() table layout. s_count_patients_with_flags() returns count fraction unique identifiers particular flag list statistics n, count, count_fraction, n_blq, one element per flag. a_count_patients_with_flags() returns corresponding list formatted rtables::CellValue().","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/count_patients_with_flags.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Count the number of patients with particular flags — count_patients_with_flags","text":"count_patients_with_flags(): Layout-creating function can take statistics function arguments additional format arguments. function wrapper rtables::analyze(). s_count_patients_with_flags(): Statistics function counts number patients particular flag variable TRUE. a_count_patients_with_flags(): Formatted analysis function used afun count_patients_with_flags().","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/count_patients_with_flags.html","id":"note","dir":"Reference","previous_headings":"","what":"Note","title":"Count the number of patients with particular flags — count_patients_with_flags","text":"flag_labels specified, variables labels extracted df. variables labeled, variable names used instead. Alternatively, named vector can supplied flag_variables within name-value pair name corresponds variable name value label use variable.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/main/reference/count_patients_with_flags.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Count the number of patients with particular flags — count_patients_with_flags","text":"","code":"# Add labelled flag variables to analysis dataset. adae <- tern_ex_adae %>%   dplyr::mutate(     fl1 = TRUE %>% with_label(\"Total AEs\"),     fl2 = (TRTEMFL == \"Y\") %>%       with_label(\"Total number of patients with at least one adverse event\"),     fl3 = (TRTEMFL == \"Y\" & AEOUT == \"FATAL\") %>%       with_label(\"Total number of patients with fatal AEs\"),     fl4 = (TRTEMFL == \"Y\" & AEOUT == \"FATAL\" & AEREL == \"Y\") %>%       with_label(\"Total number of patients with related fatal AEs\")   )  lyt <- basic_table() %>%   split_cols_by(\"ARM\") %>%   add_colcounts() %>%   count_patients_with_flags(     \"SUBJID\",     flag_variables = c(\"fl1\", \"fl2\", \"fl3\", \"fl4\"),     denom = \"N_col\"   )  build_table(lyt, adae, alt_counts_df = tern_ex_adsl) #>                                                            A: Drug X    B: Placebo   C: Combination #>                                                              (N=69)       (N=73)         (N=58)     #> ——————————————————————————————————————————————————————————————————————————————————————————————————— #> Total AEs                                                  59 (85.5%)   57 (78.1%)     48 (82.8%)   #> Total number of patients with at least one adverse event   59 (85.5%)   57 (78.1%)     48 (82.8%)   #> Total number of patients with fatal AEs                    28 (40.6%)   31 (42.5%)     20 (34.5%)   #> Total number of patients with related fatal AEs            28 (40.6%)   31 (42.5%)     20 (34.5%)    # `s_count_patients_with_flags()`  s_count_patients_with_flags(   adae,   \"SUBJID\",   flag_variables = c(\"fl1\", \"fl2\", \"fl3\", \"fl4\"),   denom = \"N_col\",   .N_col = 1000 ) #> $n #> $n$`Total AEs` #> [1] 164 #>  #> $n$`Total number of patients with at least one adverse event` #> [1] 164 #>  #> $n$`Total number of patients with fatal AEs` #> [1] 164 #>  #> $n$`Total number of patients with related fatal AEs` #> [1] 164 #>  #>  #> $count #> $count$`Total AEs` #> [1] 164 #>  #> $count$`Total number of patients with at least one adverse event` #> [1] 164 #>  #> $count$`Total number of patients with fatal AEs` #> [1] 79 #>  #> $count$`Total number of patients with related fatal AEs` #> [1] 79 #>  #>  #> $count_fraction #> $count_fraction$`Total AEs` #> [1] 164.000   0.164 #>  #> $count_fraction$`Total number of patients with at least one adverse event` #> [1] 164.000   0.164 #>  #> $count_fraction$`Total number of patients with fatal AEs` #> [1] 79.000  0.079 #>  #> $count_fraction$`Total number of patients with related fatal AEs` #> [1] 79.000  0.079 #>  #>  #> $n_blq #> $n_blq$`Total AEs` #> [1] 0 #>  #> $n_blq$`Total number of patients with at least one adverse event` #> [1] 0 #>  #> $n_blq$`Total number of patients with fatal AEs` #> [1] 0 #>  #> $n_blq$`Total number of patients with related fatal AEs` #> [1] 0 #>  #>   a_count_patients_with_flags(   adae,   .N_col = 10L,   .N_row = 10L,   .var = \"USUBJID\",   flag_variables = c(\"fl1\", \"fl2\", \"fl3\", \"fl4\") ) #> RowsVerticalSection (in_rows) object print method: #> ---------------------------- #>                       row_name formatted_cell indent_mod #> 1                        n.fl1            164          0 #> 2                        n.fl2            164          0 #> 3                        n.fl3            164          0 #> 4                        n.fl4            164          0 #> 5                    count.fl1            164          0 #> 6                    count.fl2            164          0 #> 7                    count.fl3             79          0 #> 8                    count.fl4             79          0 #> 9           count_fraction.fl1     164 (100%)          0 #> 10          count_fraction.fl2     164 (100%)          0 #> 11          count_fraction.fl3     79 (48.2%)          0 #> 12          count_fraction.fl4     79 (48.2%)          0 #> 13 count_fraction_fixed_dp.fl1     164 (100%)          0 #> 14 count_fraction_fixed_dp.fl2     164 (100%)          0 #> 15 count_fraction_fixed_dp.fl3     79 (48.2%)          0 #> 16 count_fraction_fixed_dp.fl4     79 (48.2%)          0 #> 17                   n_blq.fl1              0          0 #> 18                   n_blq.fl2              0          0 #> 19                   n_blq.fl3              0          0 #> 20                   n_blq.fl4              0          0 #>                                                   row_label #> 1                                                 Total AEs #> 2  Total number of patients with at least one adverse event #> 3                   Total number of patients with fatal AEs #> 4           Total number of patients with related fatal AEs #> 5                                                 Total AEs #> 6  Total number of patients with at least one adverse event #> 7                   Total number of patients with fatal AEs #> 8           Total number of patients with related fatal AEs #> 9                                                 Total AEs #> 10 Total number of patients with at least one adverse event #> 11                  Total number of patients with fatal AEs #> 12          Total number of patients with related fatal AEs #> 13                                                Total AEs #> 14 Total number of patients with at least one adverse event #> 15                  Total number of patients with fatal AEs #> 16          Total number of patients with related fatal AEs #> 17                                                Total AEs #> 18 Total number of patients with at least one adverse event #> 19                  Total number of patients with fatal AEs #> 20          Total number of patients with related fatal AEs"},{"path":"https://insightsengineering.github.io/tern/main/reference/count_values.html","id":null,"dir":"Reference","previous_headings":"","what":"Count specific values — count_values","title":"Count specific values — count_values","text":"analyze function count_values() creates layout element calculate counts specific values within variable interest. function analyzes one variables interest supplied vector vars. Values count variable(s) vars can given vector via values argument. One row counts generated variable.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/count_values.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Count specific values — count_values","text":"","code":"count_values(   lyt,   vars,   values,   na_str = default_na_str(),   nested = TRUE,   ...,   table_names = vars,   .stats = \"count_fraction\",   .formats = NULL,   .labels = c(count_fraction = paste(values, collapse = \", \")),   .indent_mods = NULL )  s_count_values(   x,   values,   na.rm = TRUE,   .N_col,   .N_row,   denom = c(\"n\", \"N_col\", \"N_row\") )  # S3 method for class 'character' s_count_values(x, values = \"Y\", na.rm = TRUE, ...)  # S3 method for class 'factor' s_count_values(x, values = \"Y\", ...)  # S3 method for class 'logical' s_count_values(x, values = TRUE, ...)  a_count_values(   x,   values,   na.rm = TRUE,   .N_col,   .N_row,   denom = c(\"n\", \"N_col\", \"N_row\") )"},{"path":"https://insightsengineering.github.io/tern/main/reference/count_values.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Count specific values — count_values","text":"lyt (PreDataTableLayouts) layout analyses added . vars (character) variable names primary analysis variable iterated . values (character) specific values counted. na_str (string) string used replace NA empty values output. nested (flag) whether layout instruction applied within existing layout structure _if possible (TRUE, default) new top-level element (FALSE). Ignored nest split. underneath analyses, allowed. ... additional arguments lower level functions. table_names (character) can customized case vars analyzed multiple times, avoid warnings rtables. .stats (character) statistics select table. Options : 'n', 'count', 'count_fraction', 'count_fraction_fixed_dp', 'n_blq' .formats (named character list) formats statistics. See Details analyze_vars information \"auto\" setting. .labels (named character) labels statistics (without indent). .indent_mods (named integer) indent modifiers labels. Defaults 0, corresponds unmodified default behavior. Can negative. x (numeric) vector numbers want analyze. na.rm (flag) whether NA values removed x prior analysis. .N_col (integer(1)) column-wise N (column count) full column analyzed typically passed rtables. .N_row (integer(1)) row-wise N (row group count) group observations analyzed (.e. column-based subsetting) typically passed rtables. denom (string) choice denominator proportion. Options : n: number values row column intersection. N_row: total number values row across columns. N_col: total number values column across rows.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/count_values.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Count specific values — count_values","text":"count_values() returns layout object suitable passing layouting functions, rtables::build_table(). Adding function rtable layout add formatted rows containing statistics s_count_values() table layout. s_count_values() returns output s_summary() specified values non-numeric variable. a_count_values() returns corresponding list formatted rtables::CellValue().","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/count_values.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Count specific values — count_values","text":"count_values(): Layout-creating function can take statistics function arguments additional format arguments. function wrapper rtables::analyze(). s_count_values(): S3 generic function count values. s_count_values(character): Method character class. s_count_values(factor): Method factor class. makes automatic conversion character forwards method characters. s_count_values(logical): Method logical class. a_count_values(): Formatted analysis function used afun count_values().","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/count_values.html","id":"note","dir":"Reference","previous_headings":"","what":"Note","title":"Count specific values — count_values","text":"factor variables, s_count_values checks whether values included levels x fails otherwise. count_values(), variable labels shown one element vars, otherwise hidden.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/count_values.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Count specific values — count_values","text":"","code":"# `count_values` basic_table() %>%   count_values(\"Species\", values = \"setosa\") %>%   build_table(iris) #>            all obs   #> ———————————————————— #> setosa   50 (33.33%)  # `s_count_values.character` s_count_values(x = c(\"a\", \"b\", \"a\"), values = \"a\") #> $n #> [1] 3 #>  #> $count #> [1] 2 #>  #> $count_fraction #> [1] 2.0000000 0.6666667 #>  #> $n_blq #> [1] 0 #>  s_count_values(x = c(\"a\", \"b\", \"a\", NA, NA), values = \"b\", na.rm = FALSE) #> $n #> [1] 5 #>  #> $count #> [1] 1 #>  #> $count_fraction #> [1] 1.0 0.2 #>  #> $n_blq #> [1] 0 #>   # `s_count_values.factor` s_count_values(x = factor(c(\"a\", \"b\", \"a\")), values = \"a\") #> $n #> [1] 3 #>  #> $count #> [1] 2 #>  #> $count_fraction #> [1] 2.0000000 0.6666667 #>  #> $n_blq #> [1] 0 #>   # `s_count_values.logical` s_count_values(x = c(TRUE, FALSE, TRUE)) #> $n #> [1] 3 #>  #> $count #> [1] 2 #>  #> $count_fraction #> [1] 2.0000000 0.6666667 #>  #> $n_blq #> [1] 0 #>   # `a_count_values` a_count_values(x = factor(c(\"a\", \"b\", \"a\")), values = \"a\", .N_col = 10, .N_row = 10) #> RowsVerticalSection (in_rows) object print method: #> ---------------------------- #>         row_name formatted_cell indent_mod      row_label #> 1              n              3          0              n #> 2          count              2          0          count #> 3 count_fraction     2 (66.67%)          0 count_fraction #> 4          n_blq              0          0          n_blq"},{"path":"https://insightsengineering.github.io/tern/main/reference/cox_regression.html","id":null,"dir":"Reference","previous_headings":"","what":"Cox proportional hazards regression — cox_regression","title":"Cox proportional hazards regression — cox_regression","text":"Fits Cox regression model estimates hazard ratio describe effect size survival analysis.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/cox_regression.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Cox proportional hazards regression — cox_regression","text":"","code":"summarize_coxreg(   lyt,   variables,   control = control_coxreg(),   at = list(),   multivar = FALSE,   common_var = \"STUDYID\",   .stats = c(\"n\", \"hr\", \"ci\", \"pval\", \"pval_inter\"),   .formats = c(n = \"xx\", hr = \"xx.xx\", ci = \"(xx.xx, xx.xx)\", pval =     \"x.xxxx | (<0.0001)\", pval_inter = \"x.xxxx | (<0.0001)\"),   varlabels = NULL,   .indent_mods = NULL,   na_str = \"\",   .section_div = NA_character_ )  s_coxreg(model_df, .stats, .which_vars = \"all\", .var_nms = NULL)  a_coxreg(   df,   labelstr,   eff = FALSE,   var_main = FALSE,   multivar = FALSE,   variables,   at = list(),   control = control_coxreg(),   .spl_context,   .stats,   .formats,   .indent_mods = NULL,   na_str = \"\",   cache_env = NULL )"},{"path":"https://insightsengineering.github.io/tern/main/reference/cox_regression.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Cox proportional hazards regression — cox_regression","text":"lyt (PreDataTableLayouts) layout analyses added . variables (named list string) list additional analysis variables. control (list) list parameters returned helper function control_coxreg(). (list numeric) candidate covariate numeric, use specify value covariate effect estimated. multivar (flag) whether multivariate Cox regression run (defaults FALSE), otherwise univariate Cox regression run. common_var (string) name factor variable dataset takes value rows. created pre-processing variable currently exists. .stats (character) names statistics reported among: n: number observations (univariate ) hr: hazard ratio ci: confidence interval pval: p-value treatment effect pval_inter: p-value interaction effect treatment covariate (univariate ) .formats (named character list) formats statistics. See Details analyze_vars information \"auto\" setting. varlabels (list) named list corresponds names variables found data, passed named list corresponding time, event, arm, strata, covariates terms. arm missing variables, Cox model(s) including covariates fitted corresponding effect estimates tabulated later. .indent_mods (named integer) indent modifiers labels. Defaults 0, corresponds unmodified default behavior. Can negative. na_str (string) custom string replace NA values . Defaults \"\". .section_div (string NA) string repeated section divider sections. Defaults NA section divider. vector two strings given, first used treatment covariate sections second different covariates. model_df (data.frame) contains resulting model fit fit_coxreg function tidying applied via broom::tidy(). .which_vars (character) rows statistics returned given model. Defaults \"\". options include \"var_main\" main effects, \"inter\" interaction effects, \"multi_lvl\" multivariate model covariate level rows. .which_vars \"\", specific variables can selected specifying .var_nms. .var_nms (character) term value rows df .stats returned. Typically name variable. using variable labels, var vector desired variable name variable label order see .stats related variable. .which_vars \"var_main\", .var_nms variable name. df (data.frame) data set containing analysis variables. labelstr (string) label level parent split currently summarized (must present second argument Content Row Functions). See rtables::summarize_row_groups() information. eff (flag) whether treatment effect calculated. Defaults FALSE. var_main (flag) whether main effects calculated. Defaults FALSE. .spl_context (data.frame) gives information ancestor split states passed rtables. cache_env (environment) environment object used cache regression model order avoid repeatedly fitting model every row table. Defaults NULL (caching).","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/cox_regression.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Cox proportional hazards regression — cox_regression","text":"summarize_coxreg() returns layout object suitable passing layouting functions, rtables::build_table(). Adding function rtable layout add Cox regression table containing chosen statistics table layout. s_coxreg() returns selected statistic Cox regression model selected variable(s). a_coxreg() returns formatted rtables::CellValue().","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/cox_regression.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Cox proportional hazards regression — cox_regression","text":"Cox models commonly used methods estimate magnitude effect survival analysis. assumes proportional hazards: ratio hazards groups (e.g., two arms) constant time. ratio referred \"hazard ratio\" (HR) one commonly reported metrics describe effect size survival analysis (NEST Team, 2020).","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/cox_regression.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Cox proportional hazards regression — cox_regression","text":"summarize_coxreg(): Layout-creating function creates Cox regression summary table layout. function wrapper several rtables layouting functions. function wrapper rtables::analyze_colvars() rtables::summarize_row_groups(). s_coxreg(): Statistics function transforms results tabulated fit_coxreg_univar() fit_coxreg_multivar() list. a_coxreg(): Analysis function used afun rtables::analyze() cfun rtables::summarize_row_groups() within summarize_coxreg().","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/main/reference/cox_regression.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Cox proportional hazards regression — cox_regression","text":"","code":"library(survival)  # Testing dataset [survival::bladder]. set.seed(1, kind = \"Mersenne-Twister\") dta_bladder <- with(   data = bladder[bladder$enum < 5, ],   tibble::tibble(     TIME = stop,     STATUS = event,     ARM = as.factor(rx),     COVAR1 = as.factor(enum) %>% formatters::with_label(\"A Covariate Label\"),     COVAR2 = factor(       sample(as.factor(enum)),       levels = 1:4, labels = c(\"F\", \"F\", \"M\", \"M\")     ) %>% formatters::with_label(\"Sex (F/M)\")   ) ) dta_bladder$AGE <- sample(20:60, size = nrow(dta_bladder), replace = TRUE) dta_bladder$STUDYID <- factor(\"X\")  u1_variables <- list(   time = \"TIME\", event = \"STATUS\", arm = \"ARM\", covariates = c(\"COVAR1\", \"COVAR2\") )  u2_variables <- list(time = \"TIME\", event = \"STATUS\", covariates = c(\"COVAR1\", \"COVAR2\"))  m1_variables <- list(   time = \"TIME\", event = \"STATUS\", arm = \"ARM\", covariates = c(\"COVAR1\", \"COVAR2\") )  m2_variables <- list(time = \"TIME\", event = \"STATUS\", covariates = c(\"COVAR1\", \"COVAR2\"))  # summarize_coxreg  result_univar <- basic_table() %>%   summarize_coxreg(variables = u1_variables) %>%   build_table(dta_bladder) result_univar #>                        n    Hazard Ratio      95% CI      p-value #> ————————————————————————————————————————————————————————————————— #> Treatment:                                                        #>   2 vs control (1)    340       0.64       (0.43, 0.94)   0.0242  #> Covariate:                                                        #>   A Covariate Label   340       0.61       (0.41, 0.90)   0.0126  #>   Sex (F/M)           340       0.62       (0.42, 0.92)   0.0182   result_univar_covs <- basic_table() %>%   summarize_coxreg(     variables = u2_variables,   ) %>%   build_table(dta_bladder) result_univar_covs #>                                       Hazard Ratio      95% CI      p-value #> ——————————————————————————————————————————————————————————————————————————— #> Covariate:                                                                  #>   A Covariate Label (reference = 1)                                 <0.0001 #>     2                                     0.45       (0.28, 0.71)   0.0007  #>     3                                     0.31       (0.19, 0.52)   <0.0001 #>     4                                     0.18       (0.10, 0.33)   <0.0001 #>   Sex (F/M) (reference = F)                                                 #>     M                                     1.33       (0.91, 1.94)   0.1414   result_multivar <- basic_table() %>%   summarize_coxreg(     variables = m1_variables,     multivar = TRUE,   ) %>%   build_table(dta_bladder) result_multivar #>                                       Hazard Ratio      95% CI      p-value #> ——————————————————————————————————————————————————————————————————————————— #> Treatment:                                                                  #>   ARM (reference = 1)                                                       #>     2                                     0.61       (0.41, 0.90)   0.0123  #> Covariate:                                                                  #>   A Covariate Label (reference = 1)                                 <0.0001 #>     2                                     0.46       (0.28, 0.73)   0.0011  #>     3                                     0.31       (0.18, 0.51)   <0.0001 #>     4                                     0.18       (0.10, 0.33)   <0.0001 #>   Sex (F/M) (reference = F)                                                 #>     M                                     1.29       (0.88, 1.89)   0.1911   result_multivar_covs <- basic_table() %>%   summarize_coxreg(     variables = m2_variables,     multivar = TRUE,     varlabels = c(\"Covariate 1\", \"Covariate 2\") # custom labels   ) %>%   build_table(dta_bladder) result_multivar_covs #>                                 Hazard Ratio      95% CI      p-value #> ————————————————————————————————————————————————————————————————————— #> Covariate:                                                            #>   Covariate 1 (reference = 1)                                 <0.0001 #>     2                               0.46       (0.29, 0.74)   0.0012  #>     3                               0.31       (0.19, 0.52)   <0.0001 #>     4                               0.19       (0.10, 0.34)   <0.0001 #>   Covariate 2 (reference = F)                                         #>     M                               1.29       (0.88, 1.88)   0.1958   # s_coxreg  # Univariate univar_model <- fit_coxreg_univar(variables = u1_variables, data = dta_bladder) df1 <- broom::tidy(univar_model)  s_coxreg(model_df = df1, .stats = \"hr\") #> $hr #> $hr$`2 vs control (1)` #> [1] 0.6386426 #>  #>  #> $hr #> $hr$`A Covariate Label` #> [1] 0.607037 #>  #>  #> $hr #> $hr$`Sex (F/M)` #> [1] 0.6242738 #>  #>   # Univariate with interactions univar_model_inter <- fit_coxreg_univar(   variables = u1_variables, control = control_coxreg(interaction = TRUE), data = dta_bladder ) df1_inter <- broom::tidy(univar_model_inter)  s_coxreg(model_df = df1_inter, .stats = \"hr\", .which_vars = \"inter\", .var_nms = \"COVAR1\") #> $hr #> $hr$`  1` #> [1] 0.6284569 #>  #> $hr$`  2` #> [1] 0.5806499 #>  #> $hr$`  3` #> [1] 0.5486103 #>  #> $hr$`  4` #> [1] 0.6910725 #>  #>   # Univariate without treatment arm - only \"COVAR2\" covariate effects univar_covs_model <- fit_coxreg_univar(variables = u2_variables, data = dta_bladder) df1_covs <- broom::tidy(univar_covs_model)  s_coxreg(model_df = df1_covs, .stats = \"hr\", .var_nms = c(\"COVAR2\", \"Sex (F/M)\")) #> $hr #> $hr$`Sex (F/M) (reference = F)` #> numeric(0) #>  #>  #> $hr #> $hr$M #> [1] 1.3271 #>  #>   # Multivariate. multivar_model <- fit_coxreg_multivar(variables = m1_variables, data = dta_bladder) df2 <- broom::tidy(multivar_model)  s_coxreg(model_df = df2, .stats = \"pval\", .which_vars = \"var_main\", .var_nms = \"COVAR1\") #> $pval #> $pval$`A Covariate Label (reference = 1)` #> [1] 7.209956e-09 #>  #>  s_coxreg(   model_df = df2, .stats = \"pval\", .which_vars = \"multi_lvl\",   .var_nms = c(\"COVAR1\", \"A Covariate Label\") ) #> $pval #> $pval$`2` #> [1] 0.001120332 #>  #> $pval$`3` #> [1] 6.293725e-06 #>  #> $pval$`4` #> [1] 3.013875e-08 #>  #>   # Multivariate without treatment arm - only \"COVAR1\" main effect multivar_covs_model <- fit_coxreg_multivar(variables = m2_variables, data = dta_bladder) df2_covs <- broom::tidy(multivar_covs_model)  s_coxreg(model_df = df2_covs, .stats = \"hr\") #> $hr #> $hr$`2` #> [1] 0.4600728 #>  #> $hr$`3` #> [1] 0.3100455 #>  #> $hr$`4` #> [1] 0.1854177 #>  #>  #> $hr #> $hr$`A Covariate Label (reference = 1)` #> numeric(0) #>  #>  #> $hr #> $hr$`Sex (F/M) (reference = F)` #> numeric(0) #>  #>  #> $hr #> $hr$M #> [1] 1.285406 #>  #>   a_coxreg(   df = dta_bladder,   labelstr = \"Label 1\",   variables = u1_variables,   .spl_context = list(value = \"COVAR1\"),   .stats = \"n\",   .formats = \"xx\" ) #> RowsVerticalSection (in_rows) object print method: #> ---------------------------- #>   row_name formatted_cell indent_mod row_label #> 1  Label 1            340          0   Label 1  a_coxreg(   df = dta_bladder,   labelstr = \"\",   variables = u1_variables,   .spl_context = list(value = \"COVAR2\"),   .stats = \"pval\",   .formats = \"xx.xxxx\" ) #> RowsVerticalSection (in_rows) object print method: #> ---------------------------- #>    row_name formatted_cell indent_mod row_label #> 1 Sex (F/M)         0.0182          0 Sex (F/M)"},{"path":"https://insightsengineering.github.io/tern/main/reference/cox_regression_inter.html","id":null,"dir":"Reference","previous_headings":"","what":"Cox regression helper function for interactions — cox_regression_inter","title":"Cox regression helper function for interactions — cox_regression_inter","text":"Test estimate effect treatment interaction covariate. effect estimated HR tested treatment given level covariate, comparison treatment control.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/cox_regression_inter.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Cox regression helper function for interactions — cox_regression_inter","text":"","code":"h_coxreg_inter_effect(x, effect, covar, mod, label, control, ...)  # S3 method for class 'numeric' h_coxreg_inter_effect(x, effect, covar, mod, label, control, at, ...)  # S3 method for class 'factor' h_coxreg_inter_effect(x, effect, covar, mod, label, control, data, ...)  # S3 method for class 'character' h_coxreg_inter_effect(x, effect, covar, mod, label, control, data, ...)  h_coxreg_extract_interaction(effect, covar, mod, data, at, control)  h_coxreg_inter_estimations(   variable,   given,   lvl_var,   lvl_given,   mod,   conf_level = 0.95 )"},{"path":"https://insightsengineering.github.io/tern/main/reference/cox_regression_inter.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Cox regression helper function for interactions — cox_regression_inter","text":"x (numeric factor) values covariate tested. effect (string) name effect tested estimated. covar (string) name covariate model. mod (coxph) fitted Cox regression model (see survival::coxph()). label (string) label returned term_label. control (list) list controls returned control_coxreg(). ... see methods. (list) list items named covariate, every item vector levels interaction estimated. data (data.frame) data frame model fit. variable, given (string) name variables interaction. seek estimation levels variable given levels given. lvl_var, lvl_given (character) corresponding levels given levels(). conf_level (proportion) confidence level interval.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/cox_regression_inter.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Cox regression helper function for interactions — cox_regression_inter","text":"h_coxreg_inter_effect() returns data.frame covariate interaction effects consisting following variables: effect, term, term_label, level, n, hr, lcl, ucl, pval, pval_inter. h_coxreg_extract_interaction() returns result interaction test estimated values. interaction, h_coxreg_univar_extract() applied instead. h_coxreg_inter_estimations() returns list matrices (one per level variable) rows corresponding combinations variable given, columns: coef_hat: Estimation coefficient. coef_se: Standard error estimation. hr: Hazard ratio. lcl, ucl: Lower/upper confidence limit hazard ratio.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/cox_regression_inter.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Cox regression helper function for interactions — cox_regression_inter","text":"Given cox regression investigating effect Arm (, B, C; reference ) Sex (F, M; reference Female) model abbreviated: y ~ Arm + Sex + Arm:Sex. cox regression estimates coefficients along variance-covariance matrix : b1 (arm b), b2 (arm c) b3 (sex m) b4 (arm b: sex m), b5 (arm c: sex m) estimation Hazard Ratio arm C/sex M given reference arm /Sex M exp(b2 + b3 + b5)/ exp(b3) = exp(b2 + b5). interaction coefficient deduced b2 + b5 standard error obtained $sqrt(Var b2 + Var b5 + 2 * covariance (b2,b5))$.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/cox_regression_inter.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Cox regression helper function for interactions — cox_regression_inter","text":"h_coxreg_inter_effect(): S3 generic helper function determine interaction effect. h_coxreg_inter_effect(numeric): Method numeric class. Estimates interaction numeric covariate. h_coxreg_inter_effect(factor): Method factor class. Estimate interaction factor covariate. h_coxreg_inter_effect(character): Method character class. Estimate interaction character covariate. makes automatic conversion factor forwards method factors. h_coxreg_extract_interaction(): higher level function get results interaction test estimated values. h_coxreg_inter_estimations(): Hazard ratio estimation interactions.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/cox_regression_inter.html","id":"note","dir":"Reference","previous_headings":"","what":"Note","title":"Cox regression helper function for interactions — cox_regression_inter","text":"Automatic conversion character factor guarantee results can generated correctly. therefore better always pre-process dataset factors manually created character variables passing dataset rtables::build_table().","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/cox_regression_inter.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Cox regression helper function for interactions — cox_regression_inter","text":"","code":"library(survival)  set.seed(1, kind = \"Mersenne-Twister\")  # Testing dataset [survival::bladder]. dta_bladder <- with(   data = bladder[bladder$enum < 5, ],   data.frame(     time = stop,     status = event,     armcd = as.factor(rx),     covar1 = as.factor(enum),     covar2 = factor(       sample(as.factor(enum)),       levels = 1:4,       labels = c(\"F\", \"F\", \"M\", \"M\")     )   ) ) labels <- c(\"armcd\" = \"ARM\", \"covar1\" = \"A Covariate Label\", \"covar2\" = \"Sex (F/M)\") formatters::var_labels(dta_bladder)[names(labels)] <- labels dta_bladder$age <- sample(20:60, size = nrow(dta_bladder), replace = TRUE)  plot(   survfit(Surv(time, status) ~ armcd + covar1, data = dta_bladder),   lty = 2:4,   xlab = \"Months\",   col = c(\"blue1\", \"blue2\", \"blue3\", \"blue4\", \"red1\", \"red2\", \"red3\", \"red4\") )   mod <- coxph(Surv(time, status) ~ armcd * covar1, data = dta_bladder) h_coxreg_extract_interaction(   mod = mod, effect = \"armcd\", covar = \"covar1\", data = dta_bladder,   control = control_coxreg() ) #>                    effect   term        term_label level   n        hr #> 1              Covariate: covar1 A Covariate Label       340        NA #> armcd2/covar11 Covariate: covar1                 1     1  NA 0.6341111 #> armcd2/covar12 Covariate: covar1                 2     2  NA 0.5845305 #> armcd2/covar13 Covariate: covar1                 3     3  NA 0.5507703 #> armcd2/covar14 Covariate: covar1                 4     4  NA 0.6910643 #>                      lcl      ucl      pval pval_inter #> 1                     NA       NA 0.1302825   0.988245 #> armcd2/covar11 0.3514676 1.144051        NA         NA #> armcd2/covar12 0.2716689 1.257692        NA         NA #> armcd2/covar13 0.2244668 1.351415        NA         NA #> armcd2/covar14 0.2315248 2.062715        NA         NA  mod <- coxph(Surv(time, status) ~ armcd * covar1, data = dta_bladder) result <- h_coxreg_inter_estimations(   variable = \"armcd\", given = \"covar1\",   lvl_var = levels(dta_bladder$armcd),   lvl_given = levels(dta_bladder$covar1),   mod = mod, conf_level = .95 ) result #> $armcd2 #>                      coef  se(coef)        hr       lcl      ucl #> armcd2/covar11 -0.4555312 0.3010803 0.6341111 0.3514676 1.144051 #> armcd2/covar12 -0.5369464 0.3909383 0.5845305 0.2716689 1.257692 #> armcd2/covar13 -0.5964375 0.4579624 0.5507703 0.2244668 1.351415 #> armcd2/covar14 -0.3695225 0.5579418 0.6910643 0.2315248 2.062715 #>  #> attr(,\"details\") #> [1] \"Estimations of armcd hazard ratio given the level of covar1 compared to armcd level 1.\""},{"path":"https://insightsengineering.github.io/tern/main/reference/cut_quantile_bins.html","id":null,"dir":"Reference","previous_headings":"","what":"Cut numeric vector into empirical quantile bins — cut_quantile_bins","title":"Cut numeric vector into empirical quantile bins — cut_quantile_bins","text":"cuts numeric vector sample quantile bins.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/cut_quantile_bins.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Cut numeric vector into empirical quantile bins — cut_quantile_bins","text":"","code":"cut_quantile_bins(   x,   probs = c(0.25, 0.5, 0.75),   labels = NULL,   type = 7,   ordered = TRUE )"},{"path":"https://insightsengineering.github.io/tern/main/reference/cut_quantile_bins.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Cut numeric vector into empirical quantile bins — cut_quantile_bins","text":"x (numeric) continuous variable values cut quantile bins. may contain NA values, used quantile calculations, included return vector. probs (numeric) probabilities identifying quantiles. sorted vector unique proportion values, .e. 0 1, boundaries 0 1 must included. labels (character) unique labels quantile bins. n probabilities probs, must n + 1 long. type (integer(1)) type quantiles use, see stats::quantile() details. ordered (flag) result ordered factor.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/cut_quantile_bins.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Cut numeric vector into empirical quantile bins — cut_quantile_bins","text":"factor variable appropriately-labeled bins levels.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/cut_quantile_bins.html","id":"note","dir":"Reference","previous_headings":"","what":"Note","title":"Cut numeric vector into empirical quantile bins — cut_quantile_bins","text":"Intervals closed right side. , first bin interval [-Inf, q1] q1 first quantile, second bin (q1, q2], etc., last bin (qn, +Inf] qn last quantile.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/cut_quantile_bins.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Cut numeric vector into empirical quantile bins — cut_quantile_bins","text":"","code":"# Default is to cut into quartile bins. cut_quantile_bins(cars$speed) #>  [1] [0%,25%]   [0%,25%]   [0%,25%]   [0%,25%]   [0%,25%]   [0%,25%]   #>  [7] [0%,25%]   [0%,25%]   [0%,25%]   [0%,25%]   [0%,25%]   [0%,25%]   #> [13] [0%,25%]   [0%,25%]   [0%,25%]   (25%,50%]  (25%,50%]  (25%,50%]  #> [19] (25%,50%]  (25%,50%]  (25%,50%]  (25%,50%]  (25%,50%]  (25%,50%]  #> [25] (25%,50%]  (25%,50%]  (50%,75%]  (50%,75%]  (50%,75%]  (50%,75%]  #> [31] (50%,75%]  (50%,75%]  (50%,75%]  (50%,75%]  (50%,75%]  (50%,75%]  #> [37] (50%,75%]  (50%,75%]  (75%,100%] (75%,100%] (75%,100%] (75%,100%] #> [43] (75%,100%] (75%,100%] (75%,100%] (75%,100%] (75%,100%] (75%,100%] #> [49] (75%,100%] (75%,100%] #> Levels: [0%,25%] < (25%,50%] < (50%,75%] < (75%,100%]  # Use custom quantiles. cut_quantile_bins(cars$speed, probs = c(0.1, 0.2, 0.6, 0.88)) #>  [1] [0%,10%]   [0%,10%]   [0%,10%]   [0%,10%]   [0%,10%]   (10%,20%]  #>  [7] (10%,20%]  (10%,20%]  (10%,20%]  (10%,20%]  (10%,20%]  (20%,60%]  #> [13] (20%,60%]  (20%,60%]  (20%,60%]  (20%,60%]  (20%,60%]  (20%,60%]  #> [19] (20%,60%]  (20%,60%]  (20%,60%]  (20%,60%]  (20%,60%]  (20%,60%]  #> [25] (20%,60%]  (20%,60%]  (20%,60%]  (20%,60%]  (20%,60%]  (20%,60%]  #> [31] (20%,60%]  (60%,88%]  (60%,88%]  (60%,88%]  (60%,88%]  (60%,88%]  #> [37] (60%,88%]  (60%,88%]  (60%,88%]  (60%,88%]  (60%,88%]  (60%,88%]  #> [43] (60%,88%]  (60%,88%]  (88%,100%] (88%,100%] (88%,100%] (88%,100%] #> [49] (88%,100%] (88%,100%] #> Levels: [0%,10%] < (10%,20%] < (20%,60%] < (60%,88%] < (88%,100%]  # Use custom labels. cut_quantile_bins(cars$speed, labels = paste0(\"Q\", 1:4)) #>  [1] Q1 Q1 Q1 Q1 Q1 Q1 Q1 Q1 Q1 Q1 Q1 Q1 Q1 Q1 Q1 Q2 Q2 Q2 Q2 Q2 Q2 Q2 Q2 Q2 Q2 #> [26] Q2 Q3 Q3 Q3 Q3 Q3 Q3 Q3 Q3 Q3 Q3 Q3 Q3 Q4 Q4 Q4 Q4 Q4 Q4 Q4 Q4 Q4 Q4 Q4 Q4 #> Levels: Q1 < Q2 < Q3 < Q4  # NAs are preserved in result factor. ozone_binned <- cut_quantile_bins(airquality$Ozone) which(is.na(ozone_binned)) #>  [1]   5  10  25  26  27  32  33  34  35  36  37  39  42  43  45  46  52  53  54 #> [20]  55  56  57  58  59  60  61  65  72  75  83  84 102 103 107 115 119 150 # So you might want to make these explicit. explicit_na(ozone_binned) #>   [1] (50%,75%]  (50%,75%]  [0%,25%]   [0%,25%]   <Missing>  (25%,50%]  #>   [7] (25%,50%]  (25%,50%]  [0%,25%]   <Missing>  [0%,25%]   [0%,25%]   #>  [13] [0%,25%]   [0%,25%]   [0%,25%]   [0%,25%]   (50%,75%]  [0%,25%]   #>  [19] (25%,50%]  [0%,25%]   [0%,25%]   [0%,25%]   [0%,25%]   (50%,75%]  #>  [25] <Missing>  <Missing>  <Missing>  (25%,50%]  (50%,75%]  (75%,100%] #>  [31] (50%,75%]  <Missing>  <Missing>  <Missing>  <Missing>  <Missing>  #>  [37] <Missing>  (25%,50%]  <Missing>  (75%,100%] (50%,75%]  <Missing>  #>  [43] <Missing>  (25%,50%]  <Missing>  <Missing>  (25%,50%]  (50%,75%]  #>  [49] (25%,50%]  [0%,25%]   [0%,25%]   <Missing>  <Missing>  <Missing>  #>  [55] <Missing>  <Missing>  <Missing>  <Missing>  <Missing>  <Missing>  #>  [61] <Missing>  (75%,100%] (50%,75%]  (50%,75%]  <Missing>  (75%,100%] #>  [67] (50%,75%]  (75%,100%] (75%,100%] (75%,100%] (75%,100%] <Missing>  #>  [73] [0%,25%]   (25%,50%]  <Missing>  [0%,25%]   (50%,75%]  (50%,75%]  #>  [79] (50%,75%]  (75%,100%] (50%,75%]  [0%,25%]   <Missing>  <Missing>  #>  [85] (75%,100%] (75%,100%] (25%,50%]  (50%,75%]  (75%,100%] (50%,75%]  #>  [91] (75%,100%] (50%,75%]  (50%,75%]  [0%,25%]   [0%,25%]   (75%,100%] #>  [97] (50%,75%]  (75%,100%] (75%,100%] (75%,100%] (75%,100%] <Missing>  #> [103] <Missing>  (50%,75%]  (25%,50%]  (75%,100%] <Missing>  (25%,50%]  #> [109] (50%,75%]  (25%,50%]  (25%,50%]  (50%,75%]  (25%,50%]  [0%,25%]   #> [115] <Missing>  (50%,75%]  (75%,100%] (75%,100%] <Missing>  (75%,100%] #> [121] (75%,100%] (75%,100%] (75%,100%] (75%,100%] (75%,100%] (75%,100%] #> [127] (75%,100%] (50%,75%]  (50%,75%]  (25%,50%]  (25%,50%]  (25%,50%]  #> [133] (25%,50%]  (50%,75%]  (25%,50%]  (25%,50%]  [0%,25%]   [0%,25%]   #> [139] (50%,75%]  [0%,25%]   [0%,25%]   (25%,50%]  [0%,25%]   [0%,25%]   #> [145] (25%,50%]  (50%,75%]  [0%,25%]   [0%,25%]   (25%,50%]  <Missing>  #> [151] [0%,25%]   [0%,25%]   (25%,50%]  #> Levels: [0%,25%] < (25%,50%] < (50%,75%] < (75%,100%] < <Missing>"},{"path":"https://insightsengineering.github.io/tern/main/reference/d_count_abnormal_by_baseline.html","id":null,"dir":"Reference","previous_headings":"","what":"Description function for s_count_abnormal_by_baseline() — d_count_abnormal_by_baseline","title":"Description function for s_count_abnormal_by_baseline() — d_count_abnormal_by_baseline","text":"Description function produces labels s_count_abnormal_by_baseline().","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/d_count_abnormal_by_baseline.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Description function for s_count_abnormal_by_baseline() — d_count_abnormal_by_baseline","text":"","code":"d_count_abnormal_by_baseline(abnormal)"},{"path":"https://insightsengineering.github.io/tern/main/reference/d_count_abnormal_by_baseline.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Description function for s_count_abnormal_by_baseline() — d_count_abnormal_by_baseline","text":"abnormal (character) values identifying abnormal range level(s) .var.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/d_count_abnormal_by_baseline.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Description function for s_count_abnormal_by_baseline() — d_count_abnormal_by_baseline","text":"Abnormal category labels s_count_abnormal_by_baseline().","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/d_count_abnormal_by_baseline.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Description function for s_count_abnormal_by_baseline() — d_count_abnormal_by_baseline","text":"","code":"d_count_abnormal_by_baseline(\"LOW\") #> $not_abnormal #> [1] \"Not low\" #>  #> $abnormal #> [1] \"Low\" #>  #> $total #> [1] \"Total\" #>"},{"path":"https://insightsengineering.github.io/tern/main/reference/d_count_cumulative.html","id":null,"dir":"Reference","previous_headings":"","what":"Description of cumulative count — d_count_cumulative","title":"Description of cumulative count — d_count_cumulative","text":"helper function describes analysis s_count_cumulative().","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/d_count_cumulative.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Description of cumulative count — d_count_cumulative","text":"","code":"d_count_cumulative(threshold, lower_tail = TRUE, include_eq = TRUE)"},{"path":"https://insightsengineering.github.io/tern/main/reference/d_count_cumulative.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Description of cumulative count — d_count_cumulative","text":"threshold (numeric(1)) cutoff value threshold count values x. lower_tail (flag) whether count lower tail, default TRUE. include_eq (flag) whether include value equal threshold count, default TRUE.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/d_count_cumulative.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Description of cumulative count — d_count_cumulative","text":"Labels s_count_cumulative().","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/main/reference/d_count_missed_doses.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Description function that calculates labels for s_count_missed_doses() — d_count_missed_doses","text":"","code":"d_count_missed_doses(thresholds)"},{"path":"https://insightsengineering.github.io/tern/main/reference/d_count_missed_doses.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Description function that calculates labels for s_count_missed_doses() — d_count_missed_doses","text":"thresholds (numeric) minimum number missed doses patients .","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/d_count_missed_doses.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Description function that calculates labels for s_count_missed_doses() — d_count_missed_doses","text":"d_count_missed_doses() returns named character vector labels.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/main/reference/d_onco_rsp_label.html","id":null,"dir":"Reference","previous_headings":"","what":"Description of standard oncology response — d_onco_rsp_label","title":"Description of standard oncology response — d_onco_rsp_label","text":"Describe oncology response standard way.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/d_onco_rsp_label.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Description of standard oncology response — d_onco_rsp_label","text":"","code":"d_onco_rsp_label(x)"},{"path":"https://insightsengineering.github.io/tern/main/reference/d_onco_rsp_label.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Description of standard oncology response — d_onco_rsp_label","text":"x (character) standard oncology codes described.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/d_onco_rsp_label.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Description of standard oncology response — d_onco_rsp_label","text":"Response labels.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/main/reference/d_onco_rsp_label.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Description of standard oncology response — d_onco_rsp_label","text":"","code":"d_onco_rsp_label(   c(\"CR\", \"PR\", \"SD\", \"NON CR/PD\", \"PD\", \"NE\", \"Missing\", \"<Missing>\", \"NE/Missing\") ) #>                           CR                           PR  #>       Complete Response (CR)        Partial Response (PR)  #>                           SD                    NON CR/PD  #>          Stable Disease (SD) Non-CR or Non-PD (NON CR/PD)  #>                           PD                           NE  #>     Progressive Disease (PD)           Not Evaluable (NE)  #>                      Missing                    <Missing>  #>                      Missing                    <Missing>  #>                   NE/Missing  #>       Missing or unevaluable  #> 9 Levels: Complete Response (CR) Partial Response (PR) ... <Missing>  # Adding some values not considered in d_onco_rsp_label  d_onco_rsp_label(   c(\"CR\", \"PR\", \"hello\", \"hi\") ) #>                     CR                     PR                  hello  #> Complete Response (CR)  Partial Response (PR)                  hello  #>                     hi  #>                     hi  #> Levels: Complete Response (CR) Partial Response (PR) hello hi"},{"path":[]},{"path":"https://insightsengineering.github.io/tern/main/reference/d_pkparam.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Generate PK reference dataset — d_pkparam","text":"","code":"d_pkparam()"},{"path":"https://insightsengineering.github.io/tern/main/reference/d_pkparam.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Generate PK reference dataset — d_pkparam","text":"data.frame PK parameters.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/d_pkparam.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Generate PK reference dataset — d_pkparam","text":"","code":"pk_reference_dataset <- d_pkparam()"},{"path":"https://insightsengineering.github.io/tern/main/reference/d_proportion.html","id":null,"dir":"Reference","previous_headings":"","what":"Description of the proportion summary — d_proportion","title":"Description of the proportion summary — d_proportion","text":"helper function describes analysis s_proportion().","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/d_proportion.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Description of the proportion summary — d_proportion","text":"","code":"d_proportion(conf_level, method, long = FALSE)"},{"path":"https://insightsengineering.github.io/tern/main/reference/d_proportion.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Description of the proportion summary — d_proportion","text":"conf_level (proportion) confidence level interval. method (string) method used construct confidence interval proportion successful outcomes; one waldcc, wald, clopper-pearson, wilson, wilsonc, strat_wilson, strat_wilsonc, agresti-coull jeffreys. long (flag) whether long short (default) description required.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/d_proportion.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Description of the proportion summary — d_proportion","text":"String describing analysis.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/d_proportion_diff.html","id":null,"dir":"Reference","previous_headings":"","what":"Description of method used for proportion comparison — d_proportion_diff","title":"Description of method used for proportion comparison — d_proportion_diff","text":"auxiliary function describes analysis s_proportion_diff().","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/d_proportion_diff.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Description of method used for proportion comparison — d_proportion_diff","text":"","code":"d_proportion_diff(conf_level, method, long = FALSE)"},{"path":"https://insightsengineering.github.io/tern/main/reference/d_proportion_diff.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Description of method used for proportion comparison — d_proportion_diff","text":"conf_level (proportion) confidence level interval. method (string) method used confidence interval estimation. long (flag) whether long (TRUE) short (FALSE, default) description required.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/d_proportion_diff.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Description of method used for proportion comparison — d_proportion_diff","text":"string describing analysis.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/main/reference/d_rsp_subgroups_colvars.html","id":null,"dir":"Reference","previous_headings":"","what":"Labels for column variables in binary response by subgroup table — d_rsp_subgroups_colvars","title":"Labels for column variables in binary response by subgroup table — d_rsp_subgroups_colvars","text":"Internal function check variables included tabulate_rsp_subgroups() create column labels.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/d_rsp_subgroups_colvars.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Labels for column variables in binary response by subgroup table — d_rsp_subgroups_colvars","text":"","code":"d_rsp_subgroups_colvars(vars, conf_level = NULL, method = NULL)"},{"path":"https://insightsengineering.github.io/tern/main/reference/d_rsp_subgroups_colvars.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Labels for column variables in binary response by subgroup table — d_rsp_subgroups_colvars","text":"vars (character) variable names primary analysis variable iterated . conf_level (proportion) confidence level interval. method (string NULL) specifies test used calculate p-value difference two proportions. options, see test_proportion_diff(). Default NULL test performed.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/d_rsp_subgroups_colvars.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Labels for column variables in binary response by subgroup table — d_rsp_subgroups_colvars","text":"list variables tabulate labels.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/d_survival_subgroups_colvars.html","id":null,"dir":"Reference","previous_headings":"","what":"Labels for column variables in survival duration by subgroup table — d_survival_subgroups_colvars","title":"Labels for column variables in survival duration by subgroup table — d_survival_subgroups_colvars","text":"Internal function check variables included tabulate_survival_subgroups() create column labels.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/d_survival_subgroups_colvars.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Labels for column variables in survival duration by subgroup table — d_survival_subgroups_colvars","text":"","code":"d_survival_subgroups_colvars(vars, conf_level, method, time_unit = NULL)"},{"path":"https://insightsengineering.github.io/tern/main/reference/d_survival_subgroups_colvars.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Labels for column variables in survival duration by subgroup table — d_survival_subgroups_colvars","text":"vars (character) names statistics reported among: n_tot_events: Total number events per group. n_events: Number events per group. n_tot: Total number observations per group. n: Number observations per group. median: Median survival time. hr: Hazard ratio. ci: Confidence interval hazard ratio. pval: p-value effect. Note, one statistics n_tot n_tot_events, well hr ci required. conf_level (proportion) confidence level interval. method (string) p-value method testing hazard ratio = 1. time_unit (string) label unit median survival time. Default NULL skips displaying unit.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/d_survival_subgroups_colvars.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Labels for column variables in survival duration by subgroup table — d_survival_subgroups_colvars","text":"list variables labels tabulate.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/d_survival_subgroups_colvars.html","id":"note","dir":"Reference","previous_headings":"","what":"Note","title":"Labels for column variables in survival duration by subgroup table — d_survival_subgroups_colvars","text":"least one n_tot n_tot_events must provided vars.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/d_test_proportion_diff.html","id":null,"dir":"Reference","previous_headings":"","what":"Description of the difference test between two proportions — d_test_proportion_diff","title":"Description of the difference test between two proportions — d_test_proportion_diff","text":"auxiliary function describes analysis s_test_proportion_diff.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/d_test_proportion_diff.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Description of the difference test between two proportions — d_test_proportion_diff","text":"","code":"d_test_proportion_diff(method)"},{"path":"https://insightsengineering.github.io/tern/main/reference/d_test_proportion_diff.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Description of the difference test between two proportions — d_test_proportion_diff","text":"method (string) one chisq, cmh, fisher, schouten; specifies test used calculate p-value.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/d_test_proportion_diff.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Description of the difference test between two proportions — d_test_proportion_diff","text":"string describing test p-value derived.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/day2month.html","id":null,"dir":"Reference","previous_headings":"","what":"Conversion of days to months — day2month","title":"Conversion of days to months — day2month","text":"Conversion days months","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/day2month.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Conversion of days to months — day2month","text":"","code":"day2month(x)"},{"path":"https://insightsengineering.github.io/tern/main/reference/day2month.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Conversion of days to months — day2month","text":"x (numeric(1)) time days.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/day2month.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Conversion of days to months — day2month","text":"numeric vector time months.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/day2month.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Conversion of days to months — day2month","text":"","code":"x <- c(403, 248, 30, 86) day2month(x) #> [1] 13.2402464  8.1478439  0.9856263  2.8254620"},{"path":"https://insightsengineering.github.io/tern/main/reference/decorate_grob.html","id":null,"dir":"Reference","previous_headings":"","what":"Add titles, footnotes, page Number, and a bounding box to a grid grob — decorate_grob","title":"Add titles, footnotes, page Number, and a bounding box to a grid grob — decorate_grob","text":"function useful label grid grobs (also ggplot2, lattice plots) title, footnote, page numbers.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/decorate_grob.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Add titles, footnotes, page Number, and a bounding box to a grid grob — decorate_grob","text":"","code":"decorate_grob(   grob,   titles,   footnotes,   page = \"\",   width_titles = grid::unit(1, \"npc\"),   width_footnotes = grid::unit(1, \"npc\"),   border = TRUE,   padding = grid::unit(rep(1, 4), \"lines\"),   margins = grid::unit(c(1, 0, 1, 0), \"lines\"),   outer_margins = grid::unit(c(2, 1.5, 3, 1.5), \"cm\"),   gp_titles = grid::gpar(),   gp_footnotes = grid::gpar(fontsize = 8),   name = NULL,   gp = grid::gpar(),   vp = NULL )"},{"path":"https://insightsengineering.github.io/tern/main/reference/decorate_grob.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Add titles, footnotes, page Number, and a bounding box to a grid grob — decorate_grob","text":"grob (grob) grid grob object, optionally NULL grob decoration shown. titles (character) titles given vector strings separated newline wrapped according page width. footnotes (character) footnotes. Uses formatting rules titles. page (string NULL) page numeration. NULL page number displayed. width_titles (grid::unit) width titles. Usually defined available space grid::unit(1, \"npc\"), affected parameter outer_margins. Right margins (outer_margins[4]) need subtracted allowed width. width_footnotes (grid::unit) width footnotes. default margin correction width_titles. border (flag) whether border drawn around plot . padding (grid::unit) padding. unit object length 4. Innermost margin plot (grob) , possibly, border plot. Usually expressed 4 identical values (usually \"lines\"). defaults grid::unit(rep(1, 4), \"lines\"). margins (grid::unit) margins. unit object length 4. Margins plot elements list (e.g. titles, plot, footers). usually expressed 4 \"lines\", lateral ones 0s, top bottom 1s. defaults grid::unit(c(1, 0, 1, 0), \"lines\"). outer_margins (grid::unit) outer margins. unit object length 4. defines general margin plot, considering also decorations like titles, footnotes, page numbers. defaults grid::unit(c(2, 1.5, 3, 1.5), \"cm\"). gp_titles (gpar) gpar object. Mainly used set different \"fontsize\". gp_footnotes (gpar) gpar object. Mainly used set different \"fontsize\". name character identifier grob.  Used find     grob display list /child another grob. gp \"gpar\" object, typically output     call function gpar.  basically     list graphical parameter settings. vp viewport object (NULL).","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/decorate_grob.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Add titles, footnotes, page Number, and a bounding box to a grid grob — decorate_grob","text":"grid grob (gTree).","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/decorate_grob.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Add titles, footnotes, page Number, and a bounding box to a grid grob — decorate_grob","text":"titles footnotes ragged, .e. title wrapped individually.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/decorate_grob.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Add titles, footnotes, page Number, and a bounding box to a grid grob — decorate_grob","text":"","code":"library(grid)  titles <- c(   \"Edgar Anderson's Iris Data\",   paste(     \"This famous (Fisher's or Anderson's) iris data set gives the measurements\",     \"in centimeters of the variables sepal length and width and petal length\",     \"and width, respectively, for 50 flowers from each of 3 species of iris.\"   ) )  footnotes <- c(   \"The species are Iris setosa, versicolor, and virginica.\",   paste(     \"iris is a data frame with 150 cases (rows) and 5 variables (columns) named\",     \"Sepal.Length, Sepal.Width, Petal.Length, Petal.Width, and Species.\"   ) )  ## empty plot grid.newpage()  grid.draw(   decorate_grob(     NULL,     titles = titles,     footnotes = footnotes,     page = \"Page 4 of 10\"   ) )   # grid p <- gTree(   children = gList(     rectGrob(),     xaxisGrob(),     yaxisGrob(),     textGrob(\"Sepal.Length\", y = unit(-4, \"lines\")),     textGrob(\"Petal.Length\", x = unit(-3.5, \"lines\"), rot = 90),     pointsGrob(iris$Sepal.Length, iris$Petal.Length, gp = gpar(col = iris$Species), pch = 16)   ),   vp = vpStack(plotViewport(), dataViewport(xData = iris$Sepal.Length, yData = iris$Petal.Length)) ) grid.newpage() grid.draw(p)   grid.newpage() grid.draw(   decorate_grob(     grob = p,     titles = titles,     footnotes = footnotes,     page = \"Page 6 of 129\"   ) )   ## with ggplot2 library(ggplot2)  p_gg <- ggplot2::ggplot(iris, aes(Sepal.Length, Sepal.Width, col = Species)) +   ggplot2::geom_point() p_gg  p <- ggplotGrob(p_gg) grid.newpage() grid.draw(   decorate_grob(     grob = p,     titles = titles,     footnotes = footnotes,     page = \"Page 6 of 129\"   ) )   ## with lattice library(lattice)  xyplot(Sepal.Length ~ Petal.Length, data = iris, col = iris$Species)  p <- grid.grab()  grid.newpage() grid.draw(   decorate_grob(     grob = p,     titles = titles,     footnotes = footnotes,     page = \"Page 6 of 129\"   ) )   # with gridExtra - no borders library(gridExtra) #>  #> Attaching package: ‘gridExtra’ #> The following object is masked from ‘package:dplyr’: #>  #>     combine grid.newpage() grid.draw(   decorate_grob(     tableGrob(       head(mtcars)     ),     titles = \"title\",     footnotes = \"footnote\",     border = FALSE   ) )"},{"path":"https://insightsengineering.github.io/tern/main/reference/decorate_grob_factory.html","id":null,"dir":"Reference","previous_headings":"","what":"Update page number — decorate_grob_factory","title":"Update page number — decorate_grob_factory","text":"Automatically updates page number.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/decorate_grob_factory.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Update page number — decorate_grob_factory","text":"","code":"decorate_grob_factory(npages, ...)"},{"path":"https://insightsengineering.github.io/tern/main/reference/decorate_grob_factory.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Update page number — decorate_grob_factory","text":"npages (numeric(1)) total number pages. ... arguments passed decorate_grob().","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/decorate_grob_factory.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Update page number — decorate_grob_factory","text":"Closure increments page number.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/decorate_grob_set.html","id":null,"dir":"Reference","previous_headings":"","what":"Decorate set of grobs and add page numbering — decorate_grob_set","title":"Decorate set of grobs and add page numbering — decorate_grob_set","text":"Note uses decorate_grob_factory() function.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/decorate_grob_set.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Decorate set of grobs and add page numbering — decorate_grob_set","text":"","code":"decorate_grob_set(grobs, ...)"},{"path":"https://insightsengineering.github.io/tern/main/reference/decorate_grob_set.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Decorate set of grobs and add page numbering — decorate_grob_set","text":"grobs (list grob) list grid grobs. ... arguments passed decorate_grob().","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/decorate_grob_set.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Decorate set of grobs and add page numbering — decorate_grob_set","text":"decorated grob.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/decorate_grob_set.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Decorate set of grobs and add page numbering — decorate_grob_set","text":"","code":"library(ggplot2) library(grid) g <- with(data = iris, {   list(     ggplot2::ggplotGrob(       ggplot2::ggplot(mapping = aes(Sepal.Length, Sepal.Width, col = Species)) +         ggplot2::geom_point()     ),     ggplot2::ggplotGrob(       ggplot2::ggplot(mapping = aes(Sepal.Length, Petal.Length, col = Species)) +         ggplot2::geom_point()     ),     ggplot2::ggplotGrob(       ggplot2::ggplot(mapping = aes(Sepal.Length, Petal.Width, col = Species)) +         ggplot2::geom_point()     ),     ggplot2::ggplotGrob(       ggplot2::ggplot(mapping = aes(Sepal.Width, Petal.Length, col = Species)) +         ggplot2::geom_point()     ),     ggplot2::ggplotGrob(       ggplot2::ggplot(mapping = aes(Sepal.Width, Petal.Width, col = Species)) +         ggplot2::geom_point()     ),     ggplot2::ggplotGrob(       ggplot2::ggplot(mapping = aes(Petal.Length, Petal.Width, col = Species)) +         ggplot2::geom_point()     )   ) }) lg <- decorate_grob_set(grobs = g, titles = \"Hello\\nOne\\nTwo\\nThree\", footnotes = \"\")  draw_grob(lg[[1]]) #> Warning: `draw_grob()` was deprecated in tern 0.9.4. #> ℹ `tern` plotting functions no longer generate `grob` objects.  draw_grob(lg[[2]])  draw_grob(lg[[6]])"},{"path":"https://insightsengineering.github.io/tern/main/reference/default_na_str.html","id":null,"dir":"Reference","previous_headings":"","what":"Default string replacement for NA values — default_na_str","title":"Default string replacement for NA values — default_na_str","text":"default string used represent NA values. value used default value na_str argument throughout tern package, printed place NA values output tables. specified tern function user via na_str argument, R environment options via set_default_na_str(), NA used.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/default_na_str.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Default string replacement for NA values — default_na_str","text":"","code":"default_na_str()  set_default_na_str(na_str)"},{"path":"https://insightsengineering.github.io/tern/main/reference/default_na_str.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Default string replacement for NA values — default_na_str","text":"na_str (string) single string value set R environment options default value replace NAs. Use getOption(\"tern_default_na_str\") check current value set R environment (defaults NULL set).","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/default_na_str.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Default string replacement for NA values — default_na_str","text":"default_na_str returns current value R environment option set \"tern_default_na_str\", NA_character_ otherwise. set_default_na_str return value.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/default_na_str.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Default string replacement for NA values — default_na_str","text":"default_na_str(): Accessor default NA value replacement string. set_default_na_str(): Setter default NA value replacement string. Sets option \"tern_default_na_str\" within R environment.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/default_na_str.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Default string replacement for NA values — default_na_str","text":"","code":"# Default settings default_na_str() #> [1] NA getOption(\"tern_default_na_str\") #> NULL  # Set custom value set_default_na_str(\"<Missing>\")  # Settings after value has been set default_na_str() #> [1] \"<Missing>\" getOption(\"tern_default_na_str\") #> [1] \"<Missing>\""},{"path":"https://insightsengineering.github.io/tern/main/reference/default_stats_formats_labels.html","id":null,"dir":"Reference","previous_headings":"","what":"Get default statistical methods and their associated formats, labels, and indent modifiers — default_stats_formats_labels","title":"Get default statistical methods and their associated formats, labels, and indent modifiers — default_stats_formats_labels","text":"Utility functions get valid statistic methods different method groups (.stats) associated formats (.formats), labels (.labels), indent modifiers (.indent_mods). utility used across tern, working principles can seen analyze_vars(). See notes understand experimental.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/default_stats_formats_labels.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get default statistical methods and their associated formats, labels, and indent modifiers — default_stats_formats_labels","text":"","code":"get_stats(   method_groups = \"analyze_vars_numeric\",   stats_in = NULL,   add_pval = FALSE )  get_formats_from_stats(stats, formats_in = NULL)  get_labels_from_stats(stats, labels_in = NULL, row_nms = NULL)  get_indents_from_stats(stats, indents_in = NULL, row_nms = NULL)  tern_default_stats  tern_default_formats  tern_default_labels  summary_formats(type = \"numeric\", include_pval = FALSE)  summary_labels(type = \"numeric\", include_pval = FALSE)"},{"path":"https://insightsengineering.github.io/tern/main/reference/default_stats_formats_labels.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Get default statistical methods and their associated formats, labels, and indent modifiers — default_stats_formats_labels","text":"tern_default_stats named list available statistics, element named corresponding statistical method group. tern_default_formats named vector available default formats, element named corresponding statistic. tern_default_labels named character vector available default labels, element named corresponding statistic.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/default_stats_formats_labels.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get default statistical methods and their associated formats, labels, and indent modifiers — default_stats_formats_labels","text":"method_groups (character) indicates statistical method group (tern analyze function) retrieve default statistics . character vector can used specify one statistical method group. stats_in (character) statistics retrieve selected method group. add_pval (flag) \"pval\" (\"pval_counts\" method_groups contains \"analyze_vars_counts\") added statistical methods? stats (character) statistical methods get defaults . formats_in (named vector) inserted formats replace defaults. can character vector formatters::list_valid_format_labels() custom format function. labels_in (named character) inserted labels replace defaults. row_nms (character) row names. Levels factor character variable, statistics .stats calculated . parameter set, variable levels used defaults, names given custom values correspond levels (format statistic.level) instead statistics. Can also variable names rows correspond different variables instead levels. Defaults NULL. indents_in (named vector) inserted indent modifiers replace defaults (default 0L). type (string)\"numeric\" \"counts\". include_pval (flag) add_pval argument get_stats().","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/default_stats_formats_labels.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get default statistical methods and their associated formats, labels, and indent modifiers — default_stats_formats_labels","text":"get_stats() returns character vector statistical methods. get_formats_from_stats() returns named vector formats (present either tern_default_formats formats_in, otherwise NULL). Values can taken formatters::list_valid_format_labels() custom function (e.g. formatting_functions). get_labels_from_stats() returns named character vector labels (present either tern_default_labels labels_in, otherwise NULL). get_indents_from_stats() returns single indent modifier value apply rows named numeric vector indent modifiers (present, otherwise NULL). summary_formats() returns named vector default statistic formats given data type. summary_labels returns named vector default statistic labels given data type.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/default_stats_formats_labels.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Get default statistical methods and their associated formats, labels, and indent modifiers — default_stats_formats_labels","text":"Current choices type counts numeric analyze_vars() affect get_stats(). summary_* quick get functions labels formats uses get_stats get_labels_from_stats get_formats_from_stats respectively retrieve relevant information.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/default_stats_formats_labels.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Get default statistical methods and their associated formats, labels, and indent modifiers — default_stats_formats_labels","text":"get_stats(): Get statistics available given method group (analyze function). check available defaults see tern::tern_default_stats list. get_formats_from_stats(): Get formats corresponding list statistics. check available defaults see tern::tern_default_formats list. get_labels_from_stats(): Get labels corresponding list statistics. check available defaults see tern::tern_default_labels list. available , statistics name used label. get_indents_from_stats(): Format indent modifiers given vector/list statistics. defaults 0L values. tern_default_stats: Named list available statistics method group tern. tern_default_formats: Named vector default formats tern. tern_default_labels: Named character vector default labels tern. summary_formats():  Quick function retrieve default formats summary statistics: analyze_vars() analyze_vars_in_cols() principally. summary_labels():  Quick function retrieve default labels summary statistics. Returns labels descriptive statistics understood rtables. Similar summary_formats.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/default_stats_formats_labels.html","id":"note","dir":"Reference","previous_headings":"","what":"Note","title":"Get default statistical methods and their associated formats, labels, and indent modifiers — default_stats_formats_labels","text":"defaults experimental use names functions retrieve default statistics. generalized groups methods according reasonable groupings. Formats tern rtables can functions take table cell value return string. well documented vignette(\"custom_appearance\", package = \"rtables\").","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/main/reference/default_stats_formats_labels.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get default statistical methods and their associated formats, labels, and indent modifiers — default_stats_formats_labels","text":"","code":"# analyze_vars is numeric num_stats <- get_stats(\"analyze_vars_numeric\") # also the default  # Other type cnt_stats <- get_stats(\"analyze_vars_counts\")  # Weirdly taking the pval from count_occurrences only_pval <- get_stats(\"count_occurrences\", add_pval = TRUE, stats_in = \"pval\")  # All count_occurrences all_cnt_occ <- get_stats(\"count_occurrences\")  # Multiple get_stats(c(\"count_occurrences\", \"analyze_vars_counts\")) #> [1] \"count\"                   \"count_fraction\"          #> [3] \"count_fraction_fixed_dp\" \"fraction\"                #> [5] \"n\"                       \"n_blq\"                    # Defaults formats get_formats_from_stats(num_stats) #> $n #> [1] \"xx.\" #>  #> $sum #> [1] \"xx.x\" #>  #> $mean #> [1] \"xx.x\" #>  #> $sd #> [1] \"xx.x\" #>  #> $se #> [1] \"xx.x\" #>  #> $mean_sd #> [1] \"xx.x (xx.x)\" #>  #> $mean_se #> [1] \"xx.x (xx.x)\" #>  #> $mean_ci #> [1] \"(xx.xx, xx.xx)\" #>  #> $mean_sei #> [1] \"(xx.xx, xx.xx)\" #>  #> $mean_sdi #> [1] \"(xx.xx, xx.xx)\" #>  #> $mean_pval #> [1] \"x.xxxx | (<0.0001)\" #>  #> $median #> [1] \"xx.x\" #>  #> $mad #> [1] \"xx.x\" #>  #> $median_ci #> [1] \"(xx.xx, xx.xx)\" #>  #> $quantiles #> [1] \"xx.x - xx.x\" #>  #> $iqr #> [1] \"xx.x\" #>  #> $range #> [1] \"xx.x - xx.x\" #>  #> $min #> [1] \"xx.x\" #>  #> $max #> [1] \"xx.x\" #>  #> $median_range #> [1] \"xx.x (xx.x - xx.x)\" #>  #> $cv #> [1] \"xx.x\" #>  #> $geom_mean #> [1] \"xx.x\" #>  #> $geom_mean_ci #> [1] \"(xx.xx, xx.xx)\" #>  #> $geom_cv #> [1] \"xx.x\" #>  #> $median_ci_3d #> [1] \"xx.xx (xx.xx - xx.xx)\" #>  #> $mean_ci_3d #> [1] \"xx.xx (xx.xx - xx.xx)\" #>  #> $geom_mean_ci_3d #> [1] \"xx.xx (xx.xx - xx.xx)\" #>  get_formats_from_stats(cnt_stats) #> $n #> [1] \"xx.\" #>  #> $count #> [1] \"xx.\" #>  #> $count_fraction #> function(x, ...) { #>   attr(x, \"label\") <- NULL #>  #>   if (any(is.na(x))) { #>     return(\"NA\") #>   } #>  #>   checkmate::assert_vector(x) #>   checkmate::assert_integerish(x[1]) #>   assert_proportion_value(x[2], include_boundaries = TRUE) #>  #>   result <- if (x[1] == 0) { #>     \"0\" #>   } else { #>     paste0(x[1], \" (\", round(x[2] * 100, 1), \"%)\") #>   } #>  #>   return(result) #> } #> <environment: namespace:tern> #>  #> $count_fraction_fixed_dp #> function(x, ...) { #>   attr(x, \"label\") <- NULL #>  #>   if (any(is.na(x))) { #>     return(\"NA\") #>   } #>  #>   checkmate::assert_vector(x) #>   checkmate::assert_integerish(x[1]) #>   assert_proportion_value(x[2], include_boundaries = TRUE) #>  #>   result <- if (x[1] == 0) { #>     \"0\" #>   } else if (.is_equal_float(x[2], 1)) { #>     sprintf(\"%d (100%%)\", x[1]) #>   } else { #>     sprintf(\"%d (%.1f%%)\", x[1], x[2] * 100) #>   } #>  #>   return(result) #> } #> <environment: namespace:tern> #>  #> $fraction #> function(x, ...) { #>   attr(x, \"label\") <- NULL #>   checkmate::assert_vector(x) #>   checkmate::assert_count(x[\"num\"]) #>   checkmate::assert_count(x[\"denom\"]) #>  #>   result <- if (x[\"num\"] == 0) { #>     paste0(x[\"num\"], \"/\", x[\"denom\"]) #>   } else { #>     paste0( #>       x[\"num\"], \"/\", x[\"denom\"], #>       \" (\", sprintf(\"%.1f\", round(x[\"num\"] / x[\"denom\"] * 100, 1)), \"%)\" #>     ) #>   } #>   return(result) #> } #> <environment: namespace:tern> #>  #> $n_blq #> [1] \"xx.\" #>  get_formats_from_stats(only_pval) #> $pval #> [1] \"x.xxxx | (<0.0001)\" #>  get_formats_from_stats(all_cnt_occ) #> $count #> [1] \"xx.\" #>  #> $count_fraction #> function(x, ...) { #>   attr(x, \"label\") <- NULL #>  #>   if (any(is.na(x))) { #>     return(\"NA\") #>   } #>  #>   checkmate::assert_vector(x) #>   checkmate::assert_integerish(x[1]) #>   assert_proportion_value(x[2], include_boundaries = TRUE) #>  #>   result <- if (x[1] == 0) { #>     \"0\" #>   } else { #>     paste0(x[1], \" (\", round(x[2] * 100, 1), \"%)\") #>   } #>  #>   return(result) #> } #> <environment: namespace:tern> #>  #> $count_fraction_fixed_dp #> function(x, ...) { #>   attr(x, \"label\") <- NULL #>  #>   if (any(is.na(x))) { #>     return(\"NA\") #>   } #>  #>   checkmate::assert_vector(x) #>   checkmate::assert_integerish(x[1]) #>   assert_proportion_value(x[2], include_boundaries = TRUE) #>  #>   result <- if (x[1] == 0) { #>     \"0\" #>   } else if (.is_equal_float(x[2], 1)) { #>     sprintf(\"%d (100%%)\", x[1]) #>   } else { #>     sprintf(\"%d (%.1f%%)\", x[1], x[2] * 100) #>   } #>  #>   return(result) #> } #> <environment: namespace:tern> #>  #> $fraction #> function(x, ...) { #>   attr(x, \"label\") <- NULL #>   checkmate::assert_vector(x) #>   checkmate::assert_count(x[\"num\"]) #>   checkmate::assert_count(x[\"denom\"]) #>  #>   result <- if (x[\"num\"] == 0) { #>     paste0(x[\"num\"], \"/\", x[\"denom\"]) #>   } else { #>     paste0( #>       x[\"num\"], \"/\", x[\"denom\"], #>       \" (\", sprintf(\"%.1f\", round(x[\"num\"] / x[\"denom\"] * 100, 1)), \"%)\" #>     ) #>   } #>   return(result) #> } #> <environment: namespace:tern> #>   # Addition of customs get_formats_from_stats(all_cnt_occ, formats_in = c(\"fraction\" = c(\"xx\"))) #> $count #> [1] \"xx.\" #>  #> $count_fraction #> function(x, ...) { #>   attr(x, \"label\") <- NULL #>  #>   if (any(is.na(x))) { #>     return(\"NA\") #>   } #>  #>   checkmate::assert_vector(x) #>   checkmate::assert_integerish(x[1]) #>   assert_proportion_value(x[2], include_boundaries = TRUE) #>  #>   result <- if (x[1] == 0) { #>     \"0\" #>   } else { #>     paste0(x[1], \" (\", round(x[2] * 100, 1), \"%)\") #>   } #>  #>   return(result) #> } #> <environment: namespace:tern> #>  #> $count_fraction_fixed_dp #> function(x, ...) { #>   attr(x, \"label\") <- NULL #>  #>   if (any(is.na(x))) { #>     return(\"NA\") #>   } #>  #>   checkmate::assert_vector(x) #>   checkmate::assert_integerish(x[1]) #>   assert_proportion_value(x[2], include_boundaries = TRUE) #>  #>   result <- if (x[1] == 0) { #>     \"0\" #>   } else if (.is_equal_float(x[2], 1)) { #>     sprintf(\"%d (100%%)\", x[1]) #>   } else { #>     sprintf(\"%d (%.1f%%)\", x[1], x[2] * 100) #>   } #>  #>   return(result) #> } #> <environment: namespace:tern> #>  #> $fraction #> [1] \"xx\" #>  get_formats_from_stats(all_cnt_occ, formats_in = list(\"fraction\" = c(\"xx.xx\", \"xx\"))) #> $count #> [1] \"xx.\" #>  #> $count_fraction #> function(x, ...) { #>   attr(x, \"label\") <- NULL #>  #>   if (any(is.na(x))) { #>     return(\"NA\") #>   } #>  #>   checkmate::assert_vector(x) #>   checkmate::assert_integerish(x[1]) #>   assert_proportion_value(x[2], include_boundaries = TRUE) #>  #>   result <- if (x[1] == 0) { #>     \"0\" #>   } else { #>     paste0(x[1], \" (\", round(x[2] * 100, 1), \"%)\") #>   } #>  #>   return(result) #> } #> <environment: namespace:tern> #>  #> $count_fraction_fixed_dp #> function(x, ...) { #>   attr(x, \"label\") <- NULL #>  #>   if (any(is.na(x))) { #>     return(\"NA\") #>   } #>  #>   checkmate::assert_vector(x) #>   checkmate::assert_integerish(x[1]) #>   assert_proportion_value(x[2], include_boundaries = TRUE) #>  #>   result <- if (x[1] == 0) { #>     \"0\" #>   } else if (.is_equal_float(x[2], 1)) { #>     sprintf(\"%d (100%%)\", x[1]) #>   } else { #>     sprintf(\"%d (%.1f%%)\", x[1], x[2] * 100) #>   } #>  #>   return(result) #> } #> <environment: namespace:tern> #>  #> $fraction #> [1] \"xx.xx\" \"xx\"    #>   # Defaults labels get_labels_from_stats(num_stats) #>                             n                           sum  #>                           \"n\"                         \"Sum\"  #>                          mean                            sd  #>                        \"Mean\"                          \"SD\"  #>                            se                       mean_sd  #>                          \"SE\"                   \"Mean (SD)\"  #>                       mean_se                       mean_ci  #>                   \"Mean (SE)\"                 \"Mean 95% CI\"  #>                      mean_sei                      mean_sdi  #>               \"Mean -/+ 1xSE\"               \"Mean -/+ 1xSD\"  #>                     mean_pval                        median  #> \"Mean p-value (H0: mean = 0)\"                      \"Median\"  #>                           mad                     median_ci  #>   \"Median Absolute Deviation\"               \"Median 95% CI\"  #>                     quantiles                           iqr  #>             \"25% and 75%-ile\"                         \"IQR\"  #>                         range                           min  #>                   \"Min - Max\"                     \"Minimum\"  #>                           max                  median_range  #>                     \"Maximum\"          \"Median (Min - Max)\"  #>                            cv                     geom_mean  #>                      \"CV (%)\"              \"Geometric Mean\"  #>                  geom_mean_ci                       geom_cv  #>       \"Geometric Mean 95% CI\"         \"CV % Geometric Mean\"  #>                  median_ci_3d                    mean_ci_3d  #>             \"Median (95% CI)\"               \"Mean (95% CI)\"  #>               geom_mean_ci_3d  #>     \"Geometric Mean (95% CI)\"  get_labels_from_stats(cnt_stats) #>                       n                   count          count_fraction  #>                     \"n\"                 \"count\"        \"count_fraction\"  #> count_fraction_fixed_dp                fraction                   n_blq  #>        \"count_fraction\"              \"fraction\"                 \"n_blq\"  get_labels_from_stats(only_pval) #>               pval  #> \"p-value (t-test)\"  get_labels_from_stats(all_cnt_occ) #>                   count          count_fraction count_fraction_fixed_dp  #>                 \"count\"        \"count_fraction\"        \"count_fraction\"  #>                fraction  #>              \"fraction\"   # Addition of customs get_labels_from_stats(all_cnt_occ, labels_in = c(\"fraction\" = \"Fraction\")) #>                   count          count_fraction count_fraction_fixed_dp  #>                 \"count\"        \"count_fraction\"        \"count_fraction\"  #>                fraction  #>              \"Fraction\"  get_labels_from_stats(all_cnt_occ, labels_in = list(\"fraction\" = c(\"Some more fractions\"))) #> $count #> [1] \"count\" #>  #> $count_fraction #> [1] \"count_fraction\" #>  #> $count_fraction_fixed_dp #> [1] \"count_fraction\" #>  #> $fraction #> [1] \"Some more fractions\" #>   get_indents_from_stats(all_cnt_occ, indents_in = 3L) #> [1] 3 3 3 3 get_indents_from_stats(all_cnt_occ, indents_in = list(count = 2L, count_fraction = 5L)) #> $count #> [1] 2 #>  #> $count_fraction #> [1] 5 #>  #> $count_fraction_fixed_dp #> [1] 0 #>  #> $fraction #> [1] 0 #>  get_indents_from_stats(   all_cnt_occ,   indents_in = list(a = 2L, count.a = 1L, count.b = 5L), row_nms = c(\"a\", \"b\") ) #> $count.a #> [1] 1 #>  #> $count.b #> [1] 5 #>  #> $count_fraction.a #> [1] 2 #>  #> $count_fraction.b #> [1] 0 #>  #> $count_fraction_fixed_dp.a #> [1] 2 #>  #> $count_fraction_fixed_dp.b #> [1] 0 #>  #> $fraction.a #> [1] 2 #>  #> $fraction.b #> [1] 0 #>   summary_formats() #> $n #> [1] \"xx.\" #>  #> $sum #> [1] \"xx.x\" #>  #> $mean #> [1] \"xx.x\" #>  #> $sd #> [1] \"xx.x\" #>  #> $se #> [1] \"xx.x\" #>  #> $mean_sd #> [1] \"xx.x (xx.x)\" #>  #> $mean_se #> [1] \"xx.x (xx.x)\" #>  #> $mean_ci #> [1] \"(xx.xx, xx.xx)\" #>  #> $mean_sei #> [1] \"(xx.xx, xx.xx)\" #>  #> $mean_sdi #> [1] \"(xx.xx, xx.xx)\" #>  #> $mean_pval #> [1] \"x.xxxx | (<0.0001)\" #>  #> $median #> [1] \"xx.x\" #>  #> $mad #> [1] \"xx.x\" #>  #> $median_ci #> [1] \"(xx.xx, xx.xx)\" #>  #> $quantiles #> [1] \"xx.x - xx.x\" #>  #> $iqr #> [1] \"xx.x\" #>  #> $range #> [1] \"xx.x - xx.x\" #>  #> $min #> [1] \"xx.x\" #>  #> $max #> [1] \"xx.x\" #>  #> $median_range #> [1] \"xx.x (xx.x - xx.x)\" #>  #> $cv #> [1] \"xx.x\" #>  #> $geom_mean #> [1] \"xx.x\" #>  #> $geom_mean_ci #> [1] \"(xx.xx, xx.xx)\" #>  #> $geom_cv #> [1] \"xx.x\" #>  #> $median_ci_3d #> [1] \"xx.xx (xx.xx - xx.xx)\" #>  #> $mean_ci_3d #> [1] \"xx.xx (xx.xx - xx.xx)\" #>  #> $geom_mean_ci_3d #> [1] \"xx.xx (xx.xx - xx.xx)\" #>  summary_formats(type = \"counts\", include_pval = TRUE) #> $n #> [1] \"xx.\" #>  #> $count #> [1] \"xx.\" #>  #> $count_fraction #> function(x, ...) { #>   attr(x, \"label\") <- NULL #>  #>   if (any(is.na(x))) { #>     return(\"NA\") #>   } #>  #>   checkmate::assert_vector(x) #>   checkmate::assert_integerish(x[1]) #>   assert_proportion_value(x[2], include_boundaries = TRUE) #>  #>   result <- if (x[1] == 0) { #>     \"0\" #>   } else { #>     paste0(x[1], \" (\", round(x[2] * 100, 1), \"%)\") #>   } #>  #>   return(result) #> } #> <environment: namespace:tern> #>  #> $count_fraction_fixed_dp #> function(x, ...) { #>   attr(x, \"label\") <- NULL #>  #>   if (any(is.na(x))) { #>     return(\"NA\") #>   } #>  #>   checkmate::assert_vector(x) #>   checkmate::assert_integerish(x[1]) #>   assert_proportion_value(x[2], include_boundaries = TRUE) #>  #>   result <- if (x[1] == 0) { #>     \"0\" #>   } else if (.is_equal_float(x[2], 1)) { #>     sprintf(\"%d (100%%)\", x[1]) #>   } else { #>     sprintf(\"%d (%.1f%%)\", x[1], x[2] * 100) #>   } #>  #>   return(result) #> } #> <environment: namespace:tern> #>  #> $fraction #> function(x, ...) { #>   attr(x, \"label\") <- NULL #>   checkmate::assert_vector(x) #>   checkmate::assert_count(x[\"num\"]) #>   checkmate::assert_count(x[\"denom\"]) #>  #>   result <- if (x[\"num\"] == 0) { #>     paste0(x[\"num\"], \"/\", x[\"denom\"]) #>   } else { #>     paste0( #>       x[\"num\"], \"/\", x[\"denom\"], #>       \" (\", sprintf(\"%.1f\", round(x[\"num\"] / x[\"denom\"] * 100, 1)), \"%)\" #>     ) #>   } #>   return(result) #> } #> <environment: namespace:tern> #>  #> $n_blq #> [1] \"xx.\" #>  #> $pval_counts #> [1] \"x.xxxx | (<0.0001)\" #>   summary_labels() #>                             n                           sum  #>                           \"n\"                         \"Sum\"  #>                          mean                            sd  #>                        \"Mean\"                          \"SD\"  #>                            se                       mean_sd  #>                          \"SE\"                   \"Mean (SD)\"  #>                       mean_se                       mean_ci  #>                   \"Mean (SE)\"                 \"Mean 95% CI\"  #>                      mean_sei                      mean_sdi  #>               \"Mean -/+ 1xSE\"               \"Mean -/+ 1xSD\"  #>                     mean_pval                        median  #> \"Mean p-value (H0: mean = 0)\"                      \"Median\"  #>                           mad                     median_ci  #>   \"Median Absolute Deviation\"               \"Median 95% CI\"  #>                     quantiles                           iqr  #>             \"25% and 75%-ile\"                         \"IQR\"  #>                         range                           min  #>                   \"Min - Max\"                     \"Minimum\"  #>                           max                  median_range  #>                     \"Maximum\"          \"Median (Min - Max)\"  #>                            cv                     geom_mean  #>                      \"CV (%)\"              \"Geometric Mean\"  #>                  geom_mean_ci                       geom_cv  #>       \"Geometric Mean 95% CI\"         \"CV % Geometric Mean\"  #>                  median_ci_3d                    mean_ci_3d  #>             \"Median (95% CI)\"               \"Mean (95% CI)\"  #>               geom_mean_ci_3d  #>     \"Geometric Mean (95% CI)\"  summary_labels(type = \"counts\", include_pval = TRUE) #>                            n                        count  #>                          \"n\"                      \"count\"  #>               count_fraction      count_fraction_fixed_dp  #>             \"count_fraction\"             \"count_fraction\"  #>                     fraction                        n_blq  #>                   \"fraction\"                      \"n_blq\"  #>                  pval_counts  #> \"p-value (chi-squared test)\""},{"path":"https://insightsengineering.github.io/tern/main/reference/desctools_binom.html","id":null,"dir":"Reference","previous_headings":"","what":"Confidence intervals for a difference of binomials — desctools_binom","title":"Confidence intervals for a difference of binomials — desctools_binom","text":"Several confidence intervals difference proportions.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/desctools_binom.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Confidence intervals for a difference of binomials — desctools_binom","text":"","code":"desctools_binom(   x1,   n1,   x2,   n2,   conf.level = 0.95,   sides = c(\"two.sided\", \"left\", \"right\"),   method = c(\"ac\", \"wald\", \"waldcc\", \"score\", \"scorecc\", \"mn\", \"mee\", \"blj\", \"ha\", \"hal\",     \"jp\") )  desctools_binomci(   x,   n,   conf.level = 0.95,   sides = c(\"two.sided\", \"left\", \"right\"),   method = c(\"wilson\", \"wald\", \"waldcc\", \"agresti-coull\", \"jeffreys\", \"modified wilson\",     \"wilsoncc\", \"modified jeffreys\", \"clopper-pearson\", \"arcsine\", \"logit\", \"witting\",     \"pratt\", \"midp\", \"lik\", \"blaker\"),   rand = 123,   tol = 1e-05 )"},{"path":"https://insightsengineering.github.io/tern/main/reference/desctools_binom.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Confidence intervals for a difference of binomials — desctools_binom","text":"conf.level (proportion) confidence level, defaults 0.95. sides (string) side confidence interval compute. Must one \"two-sided\" (default), \"left\", \"right\". method (string) method use. Can one : \"wald\", \"wilson\", \"wilsoncc\", \"agresti-coull\", \"jeffreys\", \"modified wilson\", \"modified jeffreys\", \"clopper-pearson\", \"arcsine\", \"logit\", \"witting\", \"pratt\", \"midp\", \"lik\", \"blaker\". x (integer(1)) number successes. n (integer(1)) number trials.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/desctools_binom.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Confidence intervals for a difference of binomials — desctools_binom","text":"matrix 3 values: est: estimate proportion difference. lwr.ci: estimate lower end confidence interval. upr.ci: estimate upper end confidence interval. matrix 3 columns containing: est: estimate proportion difference. lwr.ci: lower end confidence interval. upr.ci: upper end confidence interval.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/desctools_binom.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Confidence intervals for a difference of binomials — desctools_binom","text":"desctools_binom(): Several confidence intervals difference proportions. desctools_binomci(): Compute confidence intervals binomial proportions.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/df2gg.html","id":null,"dir":"Reference","previous_headings":"","what":"Convert data.frame object to ggplot object — df2gg","title":"Convert data.frame object to ggplot object — df2gg","text":"Given data.frame object, performs basic conversion ggplot2::ggplot() object built using functions ggplot2 package.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/df2gg.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Convert data.frame object to ggplot object — df2gg","text":"","code":"df2gg(   df,   colwidths = NULL,   font_size = 10,   col_labels = TRUE,   col_lab_fontface = \"bold\",   hline = TRUE,   bg_fill = NULL )"},{"path":"https://insightsengineering.github.io/tern/main/reference/df2gg.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Convert data.frame object to ggplot object — df2gg","text":"df (data.frame) data frame. colwidths (numeric NULL) vector column widths. element's position colwidths corresponds column df position. NULL, column widths calculated according maximum number characters per column. font_size (numeric(1)) font size. col_labels (flag) whether column names (labels) df used first row output table. col_lab_fontface (string) font face apply first row (column labels col_labels = TRUE). Defaults \"bold\". hline (flag) whether horizontal line printed first row table. bg_fill (string) table background fill color.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/df2gg.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Convert data.frame object to ggplot object — df2gg","text":"ggplot object.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/df2gg.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Convert data.frame object to ggplot object — df2gg","text":"","code":"if (FALSE) { # \\dontrun{ df2gg(head(iris, 5))  df2gg(head(iris, 5), font_size = 15, colwidths = c(1, 1, 1, 1, 1)) } # }"},{"path":"https://insightsengineering.github.io/tern/main/reference/df_explicit_na.html","id":null,"dir":"Reference","previous_headings":"","what":"Encode categorical missing values in a data frame — df_explicit_na","title":"Encode categorical missing values in a data frame — df_explicit_na","text":"helper function encode missing entries across groups categorical variables data frame.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/df_explicit_na.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Encode categorical missing values in a data frame — df_explicit_na","text":"","code":"df_explicit_na(   data,   omit_columns = NULL,   char_as_factor = TRUE,   logical_as_factor = FALSE,   na_level = \"<Missing>\" )"},{"path":"https://insightsengineering.github.io/tern/main/reference/df_explicit_na.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Encode categorical missing values in a data frame — df_explicit_na","text":"data (data.frame) data set. omit_columns (character) names variables data modified function. char_as_factor (flag) whether convert character variables data factors. logical_as_factor (flag) whether convert logical variables data factors. na_level (string) string used replace NA empty values inside non-omit_columns columns.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/df_explicit_na.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Encode categorical missing values in a data frame — df_explicit_na","text":"data.frame chosen modifications applied.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/df_explicit_na.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Encode categorical missing values in a data frame — df_explicit_na","text":"Missing entries NA empty strings replaced specified value. factor variables include missing values, missing value inserted last level. Similarly, case character logical variables converted factors char_as_factor logical_as_factor options, missing values set last level.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/main/reference/df_explicit_na.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Encode categorical missing values in a data frame — df_explicit_na","text":"","code":"my_data <- data.frame(   u = c(TRUE, FALSE, NA, TRUE),   v = factor(c(\"A\", NA, NA, NA), levels = c(\"Z\", \"A\")),   w = c(\"A\", \"B\", NA, \"C\"),   x = c(\"D\", \"E\", \"F\", NA),   y = c(\"G\", \"H\", \"I\", \"\"),   z = c(1, 2, 3, 4),   stringsAsFactors = FALSE )  # Example 1 # Encode missing values in all character or factor columns. df_explicit_na(my_data) #>       u         v         w         x         y z #> 1  TRUE         A         A         D         G 1 #> 2 FALSE <Missing>         B         E         H 2 #> 3    NA <Missing> <Missing>         F         I 3 #> 4  TRUE <Missing>         C <Missing> <Missing> 4 # Also convert logical columns to factor columns. df_explicit_na(my_data, logical_as_factor = TRUE) #>           u         v         w         x         y z #> 1      TRUE         A         A         D         G 1 #> 2     FALSE <Missing>         B         E         H 2 #> 3 <Missing> <Missing> <Missing>         F         I 3 #> 4      TRUE <Missing>         C <Missing> <Missing> 4 # Encode missing values in a subset of columns. df_explicit_na(my_data, omit_columns = c(\"x\", \"y\")) #>       u         v         w    x y z #> 1  TRUE         A         A    D G 1 #> 2 FALSE <Missing>         B    E H 2 #> 3    NA <Missing> <Missing>    F I 3 #> 4  TRUE <Missing>         C <NA>   4  # Example 2 # Here we purposefully convert all `M` values to `NA` in the `SEX` variable. # After running `df_explicit_na` the `NA` values are encoded as `<Missing>` but they are not # included when generating `rtables`. adsl <- tern_ex_adsl adsl$SEX[adsl$SEX == \"M\"] <- NA adsl <- df_explicit_na(adsl)  # If you want the `Na` values to be displayed in the table use the `na_level` argument. adsl <- tern_ex_adsl adsl$SEX[adsl$SEX == \"M\"] <- NA adsl <- df_explicit_na(adsl, na_level = \"Missing Values\")  # Example 3 # Numeric variables that have missing values are not altered. This means that any `NA` value in # a numeric variable will not be included in the summary statistics, nor will they be included # in the denominator value for calculating the percent values. adsl <- tern_ex_adsl adsl$AGE[adsl$AGE < 30] <- NA adsl <- df_explicit_na(adsl)"},{"path":"https://insightsengineering.github.io/tern/main/reference/dot-is_equal_float.html","id":null,"dir":"Reference","previous_headings":"","what":"Utility function to check if a float value is equal to another float value — .is_equal_float","title":"Utility function to check if a float value is equal to another float value — .is_equal_float","text":"Uses .Machine$double.eps tolerance comparison.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/dot-is_equal_float.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Utility function to check if a float value is equal to another float value — .is_equal_float","text":"","code":".is_equal_float(x, y)"},{"path":"https://insightsengineering.github.io/tern/main/reference/dot-is_equal_float.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Utility function to check if a float value is equal to another float value — .is_equal_float","text":"x (numeric(1)) float number. y (numeric(1)) float number.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/dot-is_equal_float.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Utility function to check if a float value is equal to another float value — .is_equal_float","text":"TRUE identical, otherwise FALSE.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/draw_grob.html","id":null,"dir":"Reference","previous_headings":"","what":"Draw grob — draw_grob","title":"Draw grob — draw_grob","text":"Draw grob device page.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/draw_grob.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Draw grob — draw_grob","text":"","code":"draw_grob(grob, newpage = TRUE, vp = NULL)"},{"path":"https://insightsengineering.github.io/tern/main/reference/draw_grob.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Draw grob — draw_grob","text":"grob (grob) grid object. newpage (flag) draw new page. vp (viewport NULL) viewport() object (NULL).","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/draw_grob.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Draw grob — draw_grob","text":"grob.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/draw_grob.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Draw grob — draw_grob","text":"","code":"library(dplyr) library(grid)  # \\donttest{ rect <- rectGrob(width = grid::unit(0.5, \"npc\"), height = grid::unit(0.5, \"npc\")) rect %>% draw_grob(vp = grid::viewport(angle = 45))   num <- lapply(1:10, textGrob) num %>%   arrange_grobs(grobs = .) %>%   draw_grob() #> Warning: `stack_grobs()` was deprecated in tern 0.9.4. #> ℹ `tern` plotting functions no longer generate `grob` objects. #> ℹ The deprecated feature was likely used in the tern package. #>   Please report the issue at #>   <https://github.com/insightsengineering/tern/issues>. showViewport()  # }"},{"path":"https://insightsengineering.github.io/tern/main/reference/empty_vector_if_na.html","id":null,"dir":"Reference","previous_headings":"","what":"Return an empty numeric if all elements are NA. — empty_vector_if_na","title":"Return an empty numeric if all elements are NA. — empty_vector_if_na","text":"Return empty numeric elements NA.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/empty_vector_if_na.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Return an empty numeric if all elements are NA. — empty_vector_if_na","text":"","code":"empty_vector_if_na(x)"},{"path":"https://insightsengineering.github.io/tern/main/reference/empty_vector_if_na.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Return an empty numeric if all elements are NA. — empty_vector_if_na","text":"x (numeric) vector.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/empty_vector_if_na.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Return an empty numeric if all elements are NA. — empty_vector_if_na","text":"empty numeric elements x NA, otherwise x.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/empty_vector_if_na.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Return an empty numeric if all elements are NA. — empty_vector_if_na","text":"","code":"x <- c(NA, NA, NA) # Internal function - empty_vector_if_na"},{"path":"https://insightsengineering.github.io/tern/main/reference/estimate_coef.html","id":null,"dir":"Reference","previous_headings":"","what":"Hazard ratio estimation in interactions — estimate_coef","title":"Hazard ratio estimation in interactions — estimate_coef","text":"function estimates hazard ratios arms interaction variable given specific values.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/estimate_coef.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Hazard ratio estimation in interactions — estimate_coef","text":"","code":"estimate_coef(   variable,   given,   lvl_var,   lvl_given,   coef,   mmat,   vcov,   conf_level = 0.95 )"},{"path":"https://insightsengineering.github.io/tern/main/reference/estimate_coef.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Hazard ratio estimation in interactions — estimate_coef","text":"variable, given (character(2)) names two variables interaction. seek estimation levels variable given levels given. lvl_var, lvl_given (character) corresponding levels given levels(). coef (numeric) vector estimated coefficients. mmat (named numeric) vector filled 0s used template obtain design matrix. vcov (matrix) variance-covariance matrix underlying model. conf_level (proportion) confidence level estimate intervals.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/estimate_coef.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Hazard ratio estimation in interactions — estimate_coef","text":"list matrices (one per level variable) rows corresponding combinations variable given, columns: coef_hat: Estimation coefficient. coef_se: Standard error estimation. hr: Hazard ratio. lcl, ucl: Lower/upper confidence limit hazard ratio.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/estimate_coef.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Hazard ratio estimation in interactions — estimate_coef","text":"Given cox regression investigating effect Arm (, B, C; reference ) Sex (F, M; reference Female). model abbreviated: y ~ Arm + Sex + Arm x Sex. cox regression estimates coefficients along variance-covariance matrix : b1 (arm b), b2 (arm c) b3 (sex m) b4 (arm b: sex m), b5 (arm c: sex m) Given want estimation Hazard Ratio arm C/sex M, estimation given reference arm /Sex M exp(b2 + b3 + b5)/ exp(b3) = exp(b2 + b5), therefore interaction coefficient given b2 + b5 standard error obtained $1.96 * sqrt(Var b2 + Var b5 + 2 * covariance (b2,b5))$ confidence level 0.95.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/main/reference/estimate_coef.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Hazard ratio estimation in interactions — estimate_coef","text":"","code":"library(dplyr) library(survival)  ADSL <- tern_ex_adsl %>%   filter(SEX %in% c(\"F\", \"M\"))  adtte <- tern_ex_adtte %>% filter(PARAMCD == \"PFS\") adtte$ARMCD <- droplevels(adtte$ARMCD) adtte$SEX <- droplevels(adtte$SEX)  mod <- coxph(   formula = Surv(time = AVAL, event = 1 - CNSR) ~ (SEX + ARMCD)^2,   data = adtte )  mmat <- stats::model.matrix(mod)[1, ] mmat[!mmat == 0] <- 0"},{"path":"https://insightsengineering.github.io/tern/main/reference/estimate_multinomial_rsp.html","id":null,"dir":"Reference","previous_headings":"","what":"Estimate proportions of each level of a variable — estimate_multinomial_rsp","title":"Estimate proportions of each level of a variable — estimate_multinomial_rsp","text":"analyze & summarize function estimate_multinomial_response() creates layout element estimate proportion proportion confidence interval level factor variable. primary analysis variable, var, factor variable, values used labels within output table.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/estimate_multinomial_rsp.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Estimate proportions of each level of a variable — estimate_multinomial_rsp","text":"","code":"estimate_multinomial_response(   lyt,   var,   na_str = default_na_str(),   nested = TRUE,   ...,   show_labels = \"hidden\",   table_names = var,   .stats = \"prop_ci\",   .formats = NULL,   .labels = NULL,   .indent_mods = NULL )  s_length_proportion(x, .N_col, ...)  a_length_proportion(x, .N_col, ...)"},{"path":"https://insightsengineering.github.io/tern/main/reference/estimate_multinomial_rsp.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Estimate proportions of each level of a variable — estimate_multinomial_rsp","text":"lyt (PreDataTableLayouts) layout analyses added . var (string) single variable name passed rtables requested statistics function. na_str (string) string used replace NA empty values output. nested (flag) whether layout instruction applied within existing layout structure _if possible (TRUE, default) new top-level element (FALSE). Ignored nest split. underneath analyses, allowed. ... additional arguments lower level functions. show_labels (string) label visibility: one \"default\", \"visible\" \"hidden\". table_names (character) can customized case vars analyzed multiple times, avoid warnings rtables. .stats (character) statistics select table. Options : 'n_prop', 'prop_ci' .formats (named character list) formats statistics. See Details analyze_vars information \"auto\" setting. .labels (named character) labels statistics (without indent). .indent_mods (named integer) indent modifiers labels. Defaults 0, corresponds unmodified default behavior. Can negative. x (numeric) vector numbers want analyze. .N_col (integer(1)) column-wise N (column count) full column analyzed typically passed rtables.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/estimate_multinomial_rsp.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Estimate proportions of each level of a variable — estimate_multinomial_rsp","text":"estimate_multinomial_response() returns layout object suitable passing layouting functions, rtables::build_table(). Adding function rtable layout add formatted rows containing statistics s_length_proportion() table layout. s_length_proportion() returns statistics s_proportion(). a_length_proportion() returns corresponding list formatted rtables::CellValue().","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/estimate_multinomial_rsp.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Estimate proportions of each level of a variable — estimate_multinomial_rsp","text":"estimate_multinomial_response(): Layout-creating function can take statistics function arguments additional format arguments. function wrapper rtables::analyze() rtables::summarize_row_groups(). s_length_proportion(): Statistics function feeds length x number successes, .N_col total number successes failures s_proportion(). a_length_proportion(): Formatted analysis function used afun estimate_multinomial_response().","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/main/reference/estimate_multinomial_rsp.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Estimate proportions of each level of a variable — estimate_multinomial_rsp","text":"","code":"library(dplyr)  # Use of the layout creating function. dta_test <- data.frame(   USUBJID = paste0(\"S\", 1:12),   ARM     = factor(rep(LETTERS[1:3], each = 4)),   AVAL    = c(A = c(1, 1, 1, 1), B = c(0, 0, 1, 1), C = c(0, 0, 0, 0)) ) %>% mutate(   AVALC = factor(AVAL,     levels = c(0, 1),     labels = c(\"Complete Response (CR)\", \"Partial Response (PR)\")   ) )  lyt <- basic_table() %>%   split_cols_by(\"ARM\") %>%   estimate_multinomial_response(var = \"AVALC\")  tbl <- build_table(lyt, dta_test)  tbl #>                                           A                B                 C        #> ————————————————————————————————————————————————————————————————————————————————————— #> Complete Response (CR)                0 (0.0%)         2 (50.0%)        4 (100.0%)    #>   95% CI (Wald, with correction)    (0.00, 12.50)    (0.00, 100.00)   (87.50, 100.00) #> Partial Response (PR)                4 (100.0%)        2 (50.0%)         0 (0.0%)     #>   95% CI (Wald, with correction)   (87.50, 100.00)   (0.00, 100.00)    (0.00, 12.50)   s_length_proportion(rep(\"CR\", 10), .N_col = 100) #> $n_prop #> [1] 10.0  0.1 #> attr(,\"label\") #> [1] \"Responders\" #>  #> $prop_ci #> [1]  3.620108 16.379892 #> attr(,\"label\") #> [1] \"95% CI (Wald, with correction)\" #>  s_length_proportion(factor(character(0)), .N_col = 100) #> $n_prop #> [1] 0 0 #> attr(,\"label\") #> [1] \"Responders\" #>  #> $prop_ci #> [1] 0.0 0.5 #> attr(,\"label\") #> [1] \"95% CI (Wald, with correction)\" #>   a_length_proportion(rep(\"CR\", 10), .N_col = 100) #> RowsVerticalSection (in_rows) object print method: #> ---------------------------- #>   row_name formatted_cell indent_mod                      row_label #> 1   n_prop     10 (10.0%)          0                     Responders #> 2  prop_ci  (3.62, 16.38)          0 95% CI (Wald, with correction) a_length_proportion(factor(character(0)), .N_col = 100) #> RowsVerticalSection (in_rows) object print method: #> ---------------------------- #>   row_name formatted_cell indent_mod                      row_label #> 1   n_prop       0 (0.0%)          0                     Responders #> 2  prop_ci   (0.00, 0.50)          0 95% CI (Wald, with correction)"},{"path":"https://insightsengineering.github.io/tern/main/reference/estimate_proportion.html","id":null,"dir":"Reference","previous_headings":"","what":"Proportion estimation — estimate_proportion","title":"Proportion estimation — estimate_proportion","text":"analyze function estimate_proportion() creates layout element estimate proportion responders within studied population. primary analysis variable, vars, indicates whether response occurred record. See method parameter options methods use constructing confidence interval proportion. Additionally, stratification variable can supplied via strata element variables argument.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/estimate_proportion.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Proportion estimation — estimate_proportion","text":"","code":"estimate_proportion(   lyt,   vars,   conf_level = 0.95,   method = c(\"waldcc\", \"wald\", \"clopper-pearson\", \"wilson\", \"wilsonc\", \"strat_wilson\",     \"strat_wilsonc\", \"agresti-coull\", \"jeffreys\"),   weights = NULL,   max_iterations = 50,   variables = list(strata = NULL),   long = FALSE,   na_str = default_na_str(),   nested = TRUE,   ...,   show_labels = \"hidden\",   table_names = vars,   .stats = NULL,   .formats = NULL,   .labels = NULL,   .indent_mods = NULL )  s_proportion(   df,   .var,   conf_level = 0.95,   method = c(\"waldcc\", \"wald\", \"clopper-pearson\", \"wilson\", \"wilsonc\", \"strat_wilson\",     \"strat_wilsonc\", \"agresti-coull\", \"jeffreys\"),   weights = NULL,   max_iterations = 50,   variables = list(strata = NULL),   long = FALSE )  a_proportion(   df,   .var,   conf_level = 0.95,   method = c(\"waldcc\", \"wald\", \"clopper-pearson\", \"wilson\", \"wilsonc\", \"strat_wilson\",     \"strat_wilsonc\", \"agresti-coull\", \"jeffreys\"),   weights = NULL,   max_iterations = 50,   variables = list(strata = NULL),   long = FALSE )"},{"path":"https://insightsengineering.github.io/tern/main/reference/estimate_proportion.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Proportion estimation — estimate_proportion","text":"lyt (PreDataTableLayouts) layout analyses added . vars (character) variable names primary analysis variable iterated . conf_level (proportion) confidence level interval. method (string) method used construct confidence interval proportion successful outcomes; one waldcc, wald, clopper-pearson, wilson, wilsonc, strat_wilson, strat_wilsonc, agresti-coull jeffreys. weights (numeric NULL) weights level strata. NULL, estimated using iterative algorithm proposed Yan2010-jt;textualtern minimizes weighted squared length confidence interval. max_iterations (count) maximum number iterations iterative procedure used find estimates optimal weights. variables (named list string) list additional analysis variables. long (flag) whether long description required. na_str (string) string used replace NA empty values output. nested (flag) whether layout instruction applied within existing layout structure _if possible (TRUE, default) new top-level element (FALSE). Ignored nest split. underneath analyses, allowed. ... additional arguments lower level functions. show_labels (string) label visibility: one \"default\", \"visible\" \"hidden\". table_names (character) can customized case vars analyzed multiple times, avoid warnings rtables. .stats (character) statistics select table. Options : 'n_prop', 'prop_ci' .formats (named character list) formats statistics. See Details analyze_vars information \"auto\" setting. .labels (named character) labels statistics (without indent). .indent_mods (named integer) indent modifiers labels. Defaults 0, corresponds unmodified default behavior. Can negative. df (logical data.frame) logical vector used, indicates whether subject responder . TRUE represents successful outcome. data.frame provided, also strata variable names must provided variables list element strata strings. case data.frame, logical vector responses must indicated variable name .var. .var (string) single variable name passed rtables requested statistics function.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/estimate_proportion.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Proportion estimation — estimate_proportion","text":"estimate_proportion() returns layout object suitable passing layouting functions, rtables::build_table(). Adding function rtable layout add formatted rows containing statistics s_proportion() table layout. s_proportion() returns statistics n_prop (n proportion) prop_ci (proportion CI) given variable. a_proportion() returns corresponding list formatted rtables::CellValue().","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/estimate_proportion.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Proportion estimation — estimate_proportion","text":"estimate_proportion(): Layout-creating function can take statistics function arguments additional format arguments. function wrapper rtables::analyze(). s_proportion(): Statistics function estimating proportion along confidence interval. a_proportion(): Formatted analysis function used afun estimate_proportion().","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/main/reference/estimate_proportion.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Proportion estimation — estimate_proportion","text":"","code":"dta_test <- data.frame(   USUBJID = paste0(\"S\", 1:12),   ARM     = rep(LETTERS[1:3], each = 4),   AVAL    = rep(LETTERS[1:3], each = 4) )  basic_table() %>%   split_cols_by(\"ARM\") %>%   estimate_proportion(vars = \"AVAL\") %>%   build_table(df = dta_test) #>                                      A           B           C     #> —————————————————————————————————————————————————————————————————— #> Responders                       <Missing>   <Missing>   <Missing> #> 95% CI (Wald, with correction)   <Missing>   <Missing>   <Missing>  # Case with only logical vector. rsp_v <- c(1, 0, 1, 0, 1, 1, 0, 0) s_proportion(rsp_v) #> $n_prop #> [1] 4.0 0.5 #> attr(,\"label\") #> [1] \"Responders\" #>  #> $prop_ci #> [1]  9.102404 90.897596 #> attr(,\"label\") #> [1] \"95% CI (Wald, with correction)\" #>   # Example for Stratified Wilson CI nex <- 100 # Number of example rows dta <- data.frame(   \"rsp\" = sample(c(TRUE, FALSE), nex, TRUE),   \"grp\" = sample(c(\"A\", \"B\"), nex, TRUE),   \"f1\" = sample(c(\"a1\", \"a2\"), nex, TRUE),   \"f2\" = sample(c(\"x\", \"y\", \"z\"), nex, TRUE),   stringsAsFactors = TRUE )  s_proportion(   df = dta,   .var = \"rsp\",   variables = list(strata = c(\"f1\", \"f2\")),   conf_level = 0.90,   method = \"strat_wilson\" ) #> $n_prop #> [1] 49.00  0.49 #> attr(,\"label\") #> [1] \"Responders\" #>  #> $prop_ci #>    lower    upper  #> 40.80675 56.65017  #> attr(,\"label\") #> [1] \"90% CI (Stratified Wilson, without correction)\" #>"},{"path":"https://insightsengineering.github.io/tern/main/reference/ex_data.html","id":null,"dir":"Reference","previous_headings":"","what":"Simulated CDISC data for examples — ex_data","title":"Simulated CDISC data for examples — ex_data","text":"Simulated CDISC data examples","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/ex_data.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Simulated CDISC data for examples — ex_data","text":"","code":"tern_ex_adsl  tern_ex_adae  tern_ex_adlb  tern_ex_adpp  tern_ex_adrs  tern_ex_adtte"},{"path":"https://insightsengineering.github.io/tern/main/reference/ex_data.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Simulated CDISC data for examples — ex_data","text":"rds (data.frame) object class tbl_df (inherits tbl, data.frame) 200 rows 21 columns. object class tbl_df (inherits tbl, data.frame) 541 rows 42 columns. object class tbl_df (inherits tbl, data.frame) 4200 rows 50 columns. object class tbl_df (inherits tbl, data.frame) 522 rows 25 columns. object class tbl_df (inherits tbl, data.frame) 1600 rows 29 columns. object class tbl_df (inherits tbl, data.frame) 1000 rows 28 columns.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/ex_data.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Simulated CDISC data for examples — ex_data","text":"tern_ex_adsl: ADSL data tern_ex_adae: ADAE data tern_ex_adlb: ADLB data tern_ex_adpp: ADPP data tern_ex_adrs: ADRS data tern_ex_adtte: ADTTE data","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/explicit_na.html","id":null,"dir":"Reference","previous_headings":"","what":"Missing data — explicit_na","title":"Missing data — explicit_na","text":"Substitute missing data string factor level.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/explicit_na.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Missing data — explicit_na","text":"","code":"explicit_na(x, label = \"<Missing>\")"},{"path":"https://insightsengineering.github.io/tern/main/reference/explicit_na.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Missing data — explicit_na","text":"x (factor character) values missing values substituted. label (string) string missing data replaced .","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/explicit_na.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Missing data — explicit_na","text":"x NA values substituted label.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/explicit_na.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Missing data — explicit_na","text":"","code":"explicit_na(c(NA, \"a\", \"b\")) #> [1] \"<Missing>\" \"a\"         \"b\"         is.na(explicit_na(c(NA, \"a\", \"b\"))) #> [1] FALSE FALSE FALSE  explicit_na(factor(c(NA, \"a\", \"b\"))) #> [1] <Missing> a         b         #> Levels: a b <Missing> is.na(explicit_na(factor(c(NA, \"a\", \"b\")))) #> [1] FALSE FALSE FALSE  explicit_na(sas_na(c(\"a\", \"\"))) #> [1] \"a\"         \"<Missing>\""},{"path":"https://insightsengineering.github.io/tern/main/reference/extract_by_name.html","id":null,"dir":"Reference","previous_headings":"","what":"Extract elements by name — extract_by_name","title":"Extract elements by name — extract_by_name","text":"utility function extracts elements vector x names. Differences standard [ function :","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/extract_by_name.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Extract elements by name — extract_by_name","text":"","code":"extract_by_name(x, names)"},{"path":"https://insightsengineering.github.io/tern/main/reference/extract_by_name.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Extract elements by name — extract_by_name","text":"x (named vector) extract named elements . names (character) vector names extract.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/extract_by_name.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Extract elements by name — extract_by_name","text":"NULL x NULL, otherwise extracted elements x.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/extract_by_name.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Extract elements by name — extract_by_name","text":"x NULL, still always NULL returned (base function). x NULL, intersection names made names elements returned. , names appear x returned NAs.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/extract_rsp_biomarkers.html","id":null,"dir":"Reference","previous_headings":"","what":"Prepare response data estimates for multiple biomarkers in a single data frame — extract_rsp_biomarkers","title":"Prepare response data estimates for multiple biomarkers in a single data frame — extract_rsp_biomarkers","text":"Prepares estimates number responses, patients overall response rate, well odds ratio estimates, confidence intervals p-values, multiple biomarkers across population subgroups single data frame. variables corresponds names variables found data, passed named list requires elements rsp biomarkers (vector continuous biomarker variables) optionally covariates, subgroups strata. groups_lists optionally specifies groupings subgroups variables.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/extract_rsp_biomarkers.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Prepare response data estimates for multiple biomarkers in a single data frame — extract_rsp_biomarkers","text":"","code":"extract_rsp_biomarkers(   variables,   data,   groups_lists = list(),   control = control_logistic(),   label_all = \"All Patients\" )"},{"path":"https://insightsengineering.github.io/tern/main/reference/extract_rsp_biomarkers.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Prepare response data estimates for multiple biomarkers in a single data frame — extract_rsp_biomarkers","text":"variables (named list string) list additional analysis variables. data (data.frame) dataset containing variables summarize. groups_lists (named list list) optionally contains subgroups variable list, specifies new group levels via names levels belong character vectors elements list. control (named list) controls response definition confidence level produced control_logistic(). label_all (string) label total population analysis.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/extract_rsp_biomarkers.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Prepare response data estimates for multiple biomarkers in a single data frame — extract_rsp_biomarkers","text":"data.frame columns biomarker, biomarker_label, n_tot, n_rsp, prop, , lcl, ucl, conf_level, pval, pval_label, subgroup, var, var_label, row_type.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/extract_rsp_biomarkers.html","id":"note","dir":"Reference","previous_headings":"","what":"Note","title":"Prepare response data estimates for multiple biomarkers in a single data frame — extract_rsp_biomarkers","text":"can also specify continuous variable rsp use response_definition control convert internally logical variable reflecting binary response.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/main/reference/extract_rsp_biomarkers.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Prepare response data estimates for multiple biomarkers in a single data frame — extract_rsp_biomarkers","text":"","code":"library(dplyr) library(forcats)  adrs <- tern_ex_adrs adrs_labels <- formatters::var_labels(adrs)  adrs_f <- adrs %>%   filter(PARAMCD == \"BESRSPI\") %>%   mutate(rsp = AVALC == \"CR\")  # Typical analysis of two continuous biomarkers `BMRKR1` and `AGE`, # in logistic regression models with one covariate `RACE`. The subgroups # are defined by the levels of `BMRKR2`. df <- extract_rsp_biomarkers(   variables = list(     rsp = \"rsp\",     biomarkers = c(\"BMRKR1\", \"AGE\"),     covariates = \"SEX\",     subgroups = \"BMRKR2\"   ),   data = adrs_f ) df #>   biomarker              biomarker_label n_tot n_rsp      prop        or #> 1    BMRKR1 Continuous Level Biomarker 1   200   164 0.8200000 0.9755036 #> 2       AGE                          Age   200   164 0.8200000 0.9952416 #> 3    BMRKR1 Continuous Level Biomarker 1    70    53 0.7571429 1.1524547 #> 4       AGE                          Age    70    53 0.7571429 0.9261012 #> 5    BMRKR1 Continuous Level Biomarker 1    68    58 0.8529412 0.8773122 #> 6       AGE                          Age    68    58 0.8529412 0.9867104 #> 7    BMRKR1 Continuous Level Biomarker 1    62    53 0.8548387 0.8792921 #> 8       AGE                          Age    62    53 0.8548387 1.0630262 #>         lcl      ucl conf_level      pval     pval_label     subgroup    var #> 1 0.8804862 1.080775       0.95 0.6352602 p-value (Wald) All Patients    ALL #> 2 0.9462617 1.046757       0.95 0.8530389 p-value (Wald) All Patients    ALL #> 3 0.9462127 1.403650       0.95 0.1584187 p-value (Wald)          LOW BMRKR2 #> 4 0.8487519 1.010500       0.95 0.0844837 p-value (Wald)          LOW BMRKR2 #> 5 0.7277189 1.057657       0.95 0.1699778 p-value (Wald)       MEDIUM BMRKR2 #> 6 0.8798911 1.106498       0.95 0.8189816 p-value (Wald)       MEDIUM BMRKR2 #> 7 0.7189748 1.075357       0.95 0.2103709 p-value (Wald)         HIGH BMRKR2 #> 8 0.9595973 1.177603       0.95 0.2418840 p-value (Wald)         HIGH BMRKR2 #>                      var_label row_type #> 1                 All Patients  content #> 2                 All Patients  content #> 3 Continuous Level Biomarker 2 analysis #> 4 Continuous Level Biomarker 2 analysis #> 5 Continuous Level Biomarker 2 analysis #> 6 Continuous Level Biomarker 2 analysis #> 7 Continuous Level Biomarker 2 analysis #> 8 Continuous Level Biomarker 2 analysis  # Here we group the levels of `BMRKR2` manually, and we add a stratification # variable `STRATA1`. We also here use a continuous variable `EOSDY` # which is then binarized internally (response is defined as this variable # being larger than 750). df_grouped <- extract_rsp_biomarkers(   variables = list(     rsp = \"EOSDY\",     biomarkers = c(\"BMRKR1\", \"AGE\"),     covariates = \"SEX\",     subgroups = \"BMRKR2\",     strata = \"STRATA1\"   ),   data = adrs_f,   groups_lists = list(     BMRKR2 = list(       \"low\" = \"LOW\",       \"low/medium\" = c(\"LOW\", \"MEDIUM\"),       \"low/medium/high\" = c(\"LOW\", \"MEDIUM\", \"HIGH\")     )   ),   control = control_logistic(     response_definition = \"I(response > 750)\"   ) ) df_grouped #>   biomarker              biomarker_label n_tot n_rsp prop or lcl ucl conf_level #> 1    BMRKR1 Continuous Level Biomarker 1   200     0    0 NA  NA  NA       0.95 #> 2       AGE                          Age   200     0    0 NA  NA  NA       0.95 #> 3    BMRKR1 Continuous Level Biomarker 1    70     0    0 NA  NA  NA       0.95 #> 4       AGE                          Age    70     0    0 NA  NA  NA       0.95 #> 5    BMRKR1 Continuous Level Biomarker 1   138     0    0 NA  NA  NA       0.95 #> 6       AGE                          Age   138     0    0 NA  NA  NA       0.95 #> 7    BMRKR1 Continuous Level Biomarker 1   200     0    0 NA  NA  NA       0.95 #> 8       AGE                          Age   200     0    0 NA  NA  NA       0.95 #>   pval     pval_label        subgroup    var                    var_label #> 1   NA p-value (Wald)    All Patients    ALL                 All Patients #> 2   NA p-value (Wald)    All Patients    ALL                 All Patients #> 3   NA p-value (Wald)             low BMRKR2 Continuous Level Biomarker 2 #> 4   NA p-value (Wald)             low BMRKR2 Continuous Level Biomarker 2 #> 5   NA p-value (Wald)      low/medium BMRKR2 Continuous Level Biomarker 2 #> 6   NA p-value (Wald)      low/medium BMRKR2 Continuous Level Biomarker 2 #> 7   NA p-value (Wald) low/medium/high BMRKR2 Continuous Level Biomarker 2 #> 8   NA p-value (Wald) low/medium/high BMRKR2 Continuous Level Biomarker 2 #>   row_type #> 1  content #> 2  content #> 3 analysis #> 4 analysis #> 5 analysis #> 6 analysis #> 7 analysis #> 8 analysis"},{"path":"https://insightsengineering.github.io/tern/main/reference/extract_rsp_subgroups.html","id":null,"dir":"Reference","previous_headings":"","what":"Prepare response data for population subgroups in data frames — extract_rsp_subgroups","title":"Prepare response data for population subgroups in data frames — extract_rsp_subgroups","text":"Prepares response rates odds ratios population subgroups data frames. Simple wrapper h_odds_ratio_subgroups_df() h_proportion_subgroups_df(). Result list two data.frames: prop . variables corresponds names variables found data, passed named list requires elements rsp, arm optionally subgroups strata. groups_lists optionally specifies groupings subgroups variables.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/extract_rsp_subgroups.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Prepare response data for population subgroups in data frames — extract_rsp_subgroups","text":"","code":"extract_rsp_subgroups(   variables,   data,   groups_lists = list(),   conf_level = 0.95,   method = NULL,   label_all = \"All Patients\" )"},{"path":"https://insightsengineering.github.io/tern/main/reference/extract_rsp_subgroups.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Prepare response data for population subgroups in data frames — extract_rsp_subgroups","text":"variables (named list string) list additional analysis variables. data (data.frame) dataset containing variables summarize. groups_lists (named list list) optionally contains subgroups variable list, specifies new group levels via names levels belong character vectors elements list. conf_level (proportion) confidence level interval. method (string NULL) specifies test used calculate p-value difference two proportions. options, see test_proportion_diff(). Default NULL test performed. label_all (string) label total population analysis.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/extract_rsp_subgroups.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Prepare response data for population subgroups in data frames — extract_rsp_subgroups","text":"named list two elements: prop: data.frame containing columns arm, n, n_rsp, prop, subgroup, var, var_label, row_type. : data.frame containing columns arm, n_tot, , lcl, ucl, conf_level, subgroup, var, var_label, row_type.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/main/reference/extract_survival_biomarkers.html","id":null,"dir":"Reference","previous_headings":"","what":"Prepare survival data estimates for multiple biomarkers in a single data frame — extract_survival_biomarkers","title":"Prepare survival data estimates for multiple biomarkers in a single data frame — extract_survival_biomarkers","text":"Prepares estimates number events, patients median survival times, well hazard ratio estimates, confidence intervals p-values, multiple biomarkers across population subgroups single data frame. variables corresponds names variables found data, passed named list requires elements tte, is_event, biomarkers (vector continuous biomarker variables), optionally subgroups strata. groups_lists optionally specifies groupings subgroups variables.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/extract_survival_biomarkers.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Prepare survival data estimates for multiple biomarkers in a single data frame — extract_survival_biomarkers","text":"","code":"extract_survival_biomarkers(   variables,   data,   groups_lists = list(),   control = control_coxreg(),   label_all = \"All Patients\" )"},{"path":"https://insightsengineering.github.io/tern/main/reference/extract_survival_biomarkers.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Prepare survival data estimates for multiple biomarkers in a single data frame — extract_survival_biomarkers","text":"variables (named list string) list additional analysis variables. data (data.frame) dataset containing variables summarize. groups_lists (named list list) optionally contains subgroups variable list, specifies new group levels via names levels belong character vectors elements list. control (list) list parameters returned helper function control_coxreg(). label_all (string) label total population analysis.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/extract_survival_biomarkers.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Prepare survival data estimates for multiple biomarkers in a single data frame — extract_survival_biomarkers","text":"data.frame columns biomarker, biomarker_label, n_tot, n_tot_events, median, hr, lcl, ucl, conf_level, pval, pval_label, subgroup, var, var_label, row_type.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/main/reference/extract_survival_subgroups.html","id":null,"dir":"Reference","previous_headings":"","what":"Prepare survival data for population subgroups in data frames — extract_survival_subgroups","title":"Prepare survival data for population subgroups in data frames — extract_survival_subgroups","text":"Prepares estimates median survival times treatment hazard ratios population subgroups data frames. Simple wrapper h_survtime_subgroups_df() h_coxph_subgroups_df(). Result list two data.frames: survtime hr. variables corresponds names variables found data, passed named list requires elements tte, is_event, arm optionally subgroups strata. groups_lists optionally specifies groupings subgroups variables.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/extract_survival_subgroups.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Prepare survival data for population subgroups in data frames — extract_survival_subgroups","text":"","code":"extract_survival_subgroups(   variables,   data,   groups_lists = list(),   control = control_coxph(),   label_all = \"All Patients\" )"},{"path":"https://insightsengineering.github.io/tern/main/reference/extract_survival_subgroups.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Prepare survival data for population subgroups in data frames — extract_survival_subgroups","text":"variables (named list string) list additional analysis variables. data (data.frame) dataset containing variables summarize. groups_lists (named list list) optionally contains subgroups variable list, specifies new group levels via names levels belong character vectors elements list. control (list) parameters comparison details, specified using helper function control_coxph(). possible parameter options : pval_method (string) p-value method testing null hypothesis hazard ratio = 1. Default method \"log-rank\" comes survival::survdiff(), can also set \"wald\" \"likelihood\" (survival::coxph()). ties (string) specifying method tie handling. Default \"efron\", can also set \"breslow\" \"exact\". See survival::coxph(). conf_level (proportion) confidence level interval HR. label_all (string) label total population analysis.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/extract_survival_subgroups.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Prepare survival data for population subgroups in data frames — extract_survival_subgroups","text":"named list two elements: survtime: data.frame containing columns arm, n, n_events, median, subgroup, var, var_label, row_type. hr: data.frame containing columns arm, n_tot, n_tot_events, hr, lcl, ucl, conf_level, pval, pval_label, subgroup, var, var_label, row_type.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/main/reference/extreme_format.html","id":null,"dir":"Reference","previous_headings":"","what":"Format extreme values — extreme_format","title":"Format extreme values — extreme_format","text":"rtables formatting functions handle extreme values.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/extreme_format.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Format extreme values — extreme_format","text":"","code":"h_get_format_threshold(digits = 2L)  h_format_threshold(x, digits = 2L)"},{"path":"https://insightsengineering.github.io/tern/main/reference/extreme_format.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Format extreme values — extreme_format","text":"digits (integer(1)) number decimal places display. x (numeric(1)) value format.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/extreme_format.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Format extreme values — extreme_format","text":"h_get_format_threshold() returns list 2 elements: threshold, low high thresholds, format_string, thresholds formatted strings. h_format_threshold() returns given value, value within digit threshold relation given value digit threshold, formatted string.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/extreme_format.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Format extreme values — extreme_format","text":"input, apply format specified number digits. value threshold, returns \"<0.01\" e.g. number digits 2. value threshold, returns \">999.99\" e.g. number digits 2. zero, returns \"0.00\".","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/extreme_format.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Format extreme values — extreme_format","text":"h_get_format_threshold(): Internal helper function calculate threshold create formatted strings used Formatting Functions. Returns list elements threshold format_string. h_format_threshold(): Internal helper function apply threshold format value. Creates formatted string used Formatting Functions.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/main/reference/extreme_format.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Format extreme values — extreme_format","text":"","code":"h_get_format_threshold(2L) #> $threshold #>    low   high  #>   0.01 999.99  #>  #> $format_string #>       low      high  #>   \"<0.01\" \">999.99\"  #>   h_format_threshold(0.001) #> [1] \"<0.01\" h_format_threshold(1000) #> [1] \">999.99\""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/main/reference/f_conf_level.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Utility function to create label for confidence interval — f_conf_level","text":"","code":"f_conf_level(conf_level)"},{"path":"https://insightsengineering.github.io/tern/main/reference/f_conf_level.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Utility function to create label for confidence interval — f_conf_level","text":"conf_level (proportion) confidence level interval.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/f_conf_level.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Utility function to create label for confidence interval — f_conf_level","text":"string.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/main/reference/f_pval.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Utility function to create label for p-value — f_pval","text":"","code":"f_pval(test_mean)"},{"path":"https://insightsengineering.github.io/tern/main/reference/f_pval.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Utility function to create label for p-value — f_pval","text":"test_mean (numeric(1)) mean value test null hypothesis.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/f_pval.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Utility function to create label for p-value — f_pval","text":"string.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/fct_collapse_only.html","id":null,"dir":"Reference","previous_headings":"","what":"Collapse factor levels and keep only those new group levels — fct_collapse_only","title":"Collapse factor levels and keep only those new group levels — fct_collapse_only","text":"collapses levels keeps new group levels, order provided. returned factor levels order given, possible missing level last (included missing values).","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/fct_collapse_only.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Collapse factor levels and keep only those new group levels — fct_collapse_only","text":"","code":"fct_collapse_only(.f, ..., .na_level = \"<Missing>\")"},{"path":"https://insightsengineering.github.io/tern/main/reference/fct_collapse_only.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Collapse factor levels and keep only those new group levels — fct_collapse_only","text":".f (factor character) original vector. ... (named character) levels vector provided collapsed new level given respective name. .na_level (string) level use levels, missing new factor. Note level must contained new levels specified ....","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/fct_collapse_only.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Collapse factor levels and keep only those new group levels — fct_collapse_only","text":"modified factor collapsed levels. Values levels included given character vector input set missing level .na_level.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/fct_collapse_only.html","id":"note","dir":"Reference","previous_headings":"","what":"Note","title":"Collapse factor levels and keep only those new group levels — fct_collapse_only","text":"existing NAs input vector replaced missing level. needed, explicit_na() can called separately result.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/main/reference/fct_collapse_only.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Collapse factor levels and keep only those new group levels — fct_collapse_only","text":"","code":"fct_collapse_only(factor(c(\"a\", \"b\", \"c\", \"d\")), TRT = \"b\", CTRL = c(\"c\", \"d\")) #> [1] <Missing> TRT       CTRL      CTRL      #> Levels: TRT CTRL <Missing>"},{"path":"https://insightsengineering.github.io/tern/main/reference/fct_discard.html","id":null,"dir":"Reference","previous_headings":"","what":"Discard specified levels of a factor — fct_discard","title":"Discard specified levels of a factor — fct_discard","text":"discards observations well levels specified factor.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/fct_discard.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Discard specified levels of a factor — fct_discard","text":"","code":"fct_discard(x, discard)"},{"path":"https://insightsengineering.github.io/tern/main/reference/fct_discard.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Discard specified levels of a factor — fct_discard","text":"x (factor) original factor. discard (character) levels discard.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/fct_discard.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Discard specified levels of a factor — fct_discard","text":"modified factor observations well levels discard dropped.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/fct_discard.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Discard specified levels of a factor — fct_discard","text":"","code":"fct_discard(factor(c(\"a\", \"b\", \"c\")), \"c\") #> [1] a b #> Levels: a b"},{"path":"https://insightsengineering.github.io/tern/main/reference/fct_explicit_na_if.html","id":null,"dir":"Reference","previous_headings":"","what":"Insertion of explicit missing values in a factor — fct_explicit_na_if","title":"Insertion of explicit missing values in a factor — fct_explicit_na_if","text":"inserts explicit missing values factor based condition. Additionally, existing NA values explicitly converted given na_level.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/fct_explicit_na_if.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Insertion of explicit missing values in a factor — fct_explicit_na_if","text":"","code":"fct_explicit_na_if(x, condition, na_level = \"<Missing>\")"},{"path":"https://insightsengineering.github.io/tern/main/reference/fct_explicit_na_if.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Insertion of explicit missing values in a factor — fct_explicit_na_if","text":"x (factor) original factor. condition (logical) positions insert missing values. na_level (string) level use missing values.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/fct_explicit_na_if.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Insertion of explicit missing values in a factor — fct_explicit_na_if","text":"modified factor inserted existing NA converted na_level.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/main/reference/fct_explicit_na_if.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Insertion of explicit missing values in a factor — fct_explicit_na_if","text":"","code":"fct_explicit_na_if(factor(c(\"a\", \"b\", NA)), c(TRUE, FALSE, FALSE)) #> [1] <Missing> b         <Missing> #> Levels: a b <Missing>"},{"path":"https://insightsengineering.github.io/tern/main/reference/fit_coxreg.html","id":null,"dir":"Reference","previous_headings":"","what":"Fitting functions for Cox proportional hazards regression — fit_coxreg","title":"Fitting functions for Cox proportional hazards regression — fit_coxreg","text":"Fitting functions univariate multivariate Cox regression models.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/fit_coxreg.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Fitting functions for Cox proportional hazards regression — fit_coxreg","text":"","code":"fit_coxreg_univar(variables, data, at = list(), control = control_coxreg())  fit_coxreg_multivar(variables, data, control = control_coxreg())"},{"path":"https://insightsengineering.github.io/tern/main/reference/fit_coxreg.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Fitting functions for Cox proportional hazards regression — fit_coxreg","text":"variables (named list) names variables found data, passed named list corresponding time, event, arm, strata, covariates terms. arm missing variables, Cox model(s) including covariates fitted corresponding effect estimates tabulated later. data (data.frame) dataset containing variables fit models. (list numeric) candidate covariate numeric, use specify value covariate effect estimated. control (list) list parameters returned helper function control_coxreg().","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/fit_coxreg.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Fitting functions for Cox proportional hazards regression — fit_coxreg","text":"fit_coxreg_univar() returns coxreg.univar class object named list 5 elements: mod: Cox regression models fitted survival::coxph(). data: original data frame input. control: original control input. vars: variables used model. : Value covariate effect estimated. fit_coxreg_multivar() returns coxreg.multivar class object named list 4 elements: mod: Cox regression model fitted survival::coxph(). data: original data frame input. control: original control input. vars: variables used model.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/fit_coxreg.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Fitting functions for Cox proportional hazards regression — fit_coxreg","text":"fit_coxreg_univar(): Fit series univariate Cox regression models given inputs. fit_coxreg_multivar(): Fit multivariate Cox regression model.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/fit_coxreg.html","id":"note","dir":"Reference","previous_headings":"","what":"Note","title":"Fitting functions for Cox proportional hazards regression — fit_coxreg","text":"using fit_coxreg_univar two study arms.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/main/reference/fit_coxreg.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Fitting functions for Cox proportional hazards regression — fit_coxreg","text":"","code":"library(survival)  set.seed(1, kind = \"Mersenne-Twister\")  # Testing dataset [survival::bladder]. dta_bladder <- with(   data = bladder[bladder$enum < 5, ],   data.frame(     time = stop,     status = event,     armcd = as.factor(rx),     covar1 = as.factor(enum),     covar2 = factor(       sample(as.factor(enum)),       levels = 1:4, labels = c(\"F\", \"F\", \"M\", \"M\")     )   ) ) labels <- c(\"armcd\" = \"ARM\", \"covar1\" = \"A Covariate Label\", \"covar2\" = \"Sex (F/M)\") formatters::var_labels(dta_bladder)[names(labels)] <- labels dta_bladder$age <- sample(20:60, size = nrow(dta_bladder), replace = TRUE)  plot(   survfit(Surv(time, status) ~ armcd + covar1, data = dta_bladder),   lty = 2:4,   xlab = \"Months\",   col = c(\"blue1\", \"blue2\", \"blue3\", \"blue4\", \"red1\", \"red2\", \"red3\", \"red4\") )   # fit_coxreg_univar  ## Cox regression: arm + 1 covariate. mod1 <- fit_coxreg_univar(   variables = list(     time = \"time\", event = \"status\", arm = \"armcd\",     covariates = \"covar1\"   ),   data = dta_bladder,   control = control_coxreg(conf_level = 0.91) )  ## Cox regression: arm + 1 covariate + interaction, 2 candidate covariates. mod2 <- fit_coxreg_univar(   variables = list(     time = \"time\", event = \"status\", arm = \"armcd\",     covariates = c(\"covar1\", \"covar2\")   ),   data = dta_bladder,   control = control_coxreg(conf_level = 0.91, interaction = TRUE) )  ## Cox regression: arm + 1 covariate, stratified analysis. mod3 <- fit_coxreg_univar(   variables = list(     time = \"time\", event = \"status\", arm = \"armcd\", strata = \"covar2\",     covariates = c(\"covar1\")   ),   data = dta_bladder,   control = control_coxreg(conf_level = 0.91) )  ## Cox regression: no arm, only covariates. mod4 <- fit_coxreg_univar(   variables = list(     time = \"time\", event = \"status\",     covariates = c(\"covar1\", \"covar2\")   ),   data = dta_bladder )  # fit_coxreg_multivar  ## Cox regression: multivariate Cox regression. multivar_model <- fit_coxreg_multivar(   variables = list(     time = \"time\", event = \"status\", arm = \"armcd\",     covariates = c(\"covar1\", \"covar2\")   ),   data = dta_bladder )  # Example without treatment arm. multivar_covs_model <- fit_coxreg_multivar(   variables = list(     time = \"time\", event = \"status\",     covariates = c(\"covar1\", \"covar2\")   ),   data = dta_bladder )"},{"path":"https://insightsengineering.github.io/tern/main/reference/fit_logistic.html","id":null,"dir":"Reference","previous_headings":"","what":"Fit for logistic regression — fit_logistic","title":"Fit for logistic regression — fit_logistic","text":"Fit (conditional) logistic regression model.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/fit_logistic.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Fit for logistic regression — fit_logistic","text":"","code":"fit_logistic(   data,   variables = list(response = \"Response\", arm = \"ARMCD\", covariates = NULL, interaction =     NULL, strata = NULL),   response_definition = \"response\" )"},{"path":"https://insightsengineering.github.io/tern/main/reference/fit_logistic.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Fit for logistic regression — fit_logistic","text":"data (data.frame) data frame model fit. variables (named list string) list additional analysis variables. response_definition (string) definition event terms response. used fitting (conditional) logistic regression model left hand side formula.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/fit_logistic.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Fit for logistic regression — fit_logistic","text":"fitted logistic regression model.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/fit_logistic.html","id":"model-specification","dir":"Reference","previous_headings":"","what":"Model Specification","title":"Fit for logistic regression — fit_logistic","text":"variables list needs include following elements: arm: Treatment arm variable name. response: response arm variable name. Usually 0/1 variable. covariates: either NULL (covariates) character vector covariate variable names. interaction: either NULL (interaction) string single covariate variable name already included covariates. interaction treatment arm included model.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/fit_logistic.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Fit for logistic regression — fit_logistic","text":"","code":"library(dplyr)  adrs_f <- tern_ex_adrs %>%   filter(PARAMCD == \"BESRSPI\") %>%   filter(RACE %in% c(\"ASIAN\", \"WHITE\", \"BLACK OR AFRICAN AMERICAN\")) %>%   mutate(     Response = case_when(AVALC %in% c(\"PR\", \"CR\") ~ 1, TRUE ~ 0),     RACE = factor(RACE),     SEX = factor(SEX)   ) formatters::var_labels(adrs_f) <- c(formatters::var_labels(tern_ex_adrs), Response = \"Response\") mod1 <- fit_logistic(   data = adrs_f,   variables = list(     response = \"Response\",     arm = \"ARMCD\",     covariates = c(\"AGE\", \"RACE\")   ) ) #> Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred mod2 <- fit_logistic(   data = adrs_f,   variables = list(     response = \"Response\",     arm = \"ARMCD\",     covariates = c(\"AGE\", \"RACE\"),     interaction = \"AGE\"   ) ) #> Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred"},{"path":"https://insightsengineering.github.io/tern/main/reference/fit_rsp_step.html","id":null,"dir":"Reference","previous_headings":"","what":"Subgroup treatment effect pattern (STEP) fit for binary (response) outcome — fit_rsp_step","title":"Subgroup treatment effect pattern (STEP) fit for binary (response) outcome — fit_rsp_step","text":"fits Subgroup Treatment Effect Pattern logistic regression models binary (response) outcome. treatment arm variable must exactly 2 levels, first one taken reference estimated odds ratios comparison second level vs. first one. (conditional) logistic regression model fit : response ~ arm * poly(biomarker, degree) + covariates + strata(strata) degree specified control_step().","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/fit_rsp_step.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Subgroup treatment effect pattern (STEP) fit for binary (response) outcome — fit_rsp_step","text":"","code":"fit_rsp_step(variables, data, control = c(control_step(), control_logistic()))"},{"path":"https://insightsengineering.github.io/tern/main/reference/fit_rsp_step.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Subgroup treatment effect pattern (STEP) fit for binary (response) outcome — fit_rsp_step","text":"variables (named list character) list analysis variables: needs response, arm, biomarker, optional covariates strata. data (data.frame) dataset containing variables summarize. control (named list) combined control list control_step() control_logistic().","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/fit_rsp_step.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Subgroup treatment effect pattern (STEP) fit for binary (response) outcome — fit_rsp_step","text":"matrix class step. first part columns describe subgroup intervals used biomarker variable, including center intervals bounds. second part columns contain estimates treatment arm comparison.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/fit_rsp_step.html","id":"note","dir":"Reference","previous_headings":"","what":"Note","title":"Subgroup treatment effect pattern (STEP) fit for binary (response) outcome — fit_rsp_step","text":"default degree 0 biomarker variable included model.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/main/reference/fit_rsp_step.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Subgroup treatment effect pattern (STEP) fit for binary (response) outcome — fit_rsp_step","text":"","code":"# Testing dataset with just two treatment arms. library(survival) library(dplyr)  adrs_f <- tern_ex_adrs %>%   filter(     PARAMCD == \"BESRSPI\",     ARM %in% c(\"B: Placebo\", \"A: Drug X\")   ) %>%   mutate(     # Reorder levels of ARM to have Placebo as reference arm for Odds Ratio calculations.     ARM = droplevels(forcats::fct_relevel(ARM, \"B: Placebo\")),     RSP = case_when(AVALC %in% c(\"PR\", \"CR\") ~ 1, TRUE ~ 0),     SEX = factor(SEX)   )  variables <- list(   arm = \"ARM\",   biomarker = \"BMRKR1\",   covariates = \"AGE\",   response = \"RSP\" )  # Fit default STEP models: Here a constant treatment effect is estimated in each subgroup. # We use a large enough bandwidth to avoid too small subgroups and linear separation in those. step_matrix <- fit_rsp_step(   variables = variables,   data = adrs_f,   control = c(control_logistic(), control_step(bandwidth = 0.9)) ) dim(step_matrix) #> [1] 39 11 head(step_matrix) #>      Percentile Center Percentile Lower Percentile Upper Interval Center #> [1,]             0.025                0            0.925        1.472755 #> [2,]             0.050                0            0.950        2.028546 #> [3,]             0.075                0            0.975        2.204086 #> [4,]             0.100                0            1.000        2.799776 #> [5,]             0.125                0            1.000        2.969998 #> [6,]             0.150                0            1.000        3.149068 #>      Interval Lower Interval Upper   n    logor       se   ci_lower ci_upper #> [1,]      0.4459546       11.74529 131 1.835008 1.134560 -0.3886885 4.058703 #> [2,]      0.4459546       12.73387 134 1.895158 1.136248 -0.3318481 4.122163 #> [3,]      0.4459546       14.75099 138 1.947699 1.136969 -0.2807193 4.176116 #> [4,]      0.4459546       18.49236 142 1.931001 1.135866 -0.2952561 4.157258 #> [5,]      0.4459546       18.49236 142 1.931001 1.135866 -0.2952561 4.157258 #> [6,]      0.4459546       18.49236 142 1.931001 1.135866 -0.2952561 4.157258  # Specify different polynomial degree for the biomarker interaction to use more flexible local # models. Or specify different logistic regression options, including confidence level. step_matrix2 <- fit_rsp_step(   variables = variables,   data = adrs_f,   control = c(control_logistic(conf_level = 0.9), control_step(bandwidth = NULL, degree = 1)) )  # Use a global constant model. This is helpful as a reference for the subgroup models. step_matrix3 <- fit_rsp_step(   variables = variables,   data = adrs_f,   control = c(control_logistic(), control_step(bandwidth = NULL, num_points = 2L)) )  # It is also possible to use strata, i.e. use conditional logistic regression models. variables2 <- list(   arm = \"ARM\",   biomarker = \"BMRKR1\",   covariates = \"AGE\",   response = \"RSP\",   strata = c(\"STRATA1\", \"STRATA2\") )  step_matrix4 <- fit_rsp_step(   variables = variables2,   data = adrs_f,   control = c(control_logistic(), control_step(bandwidth = NULL)) )"},{"path":"https://insightsengineering.github.io/tern/main/reference/fit_survival_step.html","id":null,"dir":"Reference","previous_headings":"","what":"Subgroup treatment effect pattern (STEP) fit for survival outcome — fit_survival_step","title":"Subgroup treatment effect pattern (STEP) fit for survival outcome — fit_survival_step","text":"fits subgroup treatment effect pattern (STEP) models survival outcome. treatment arm variable must exactly 2 levels, first one taken reference estimated hazard ratios comparison second level vs. first one. model fit : Surv(time, event) ~ arm * poly(biomarker, degree) + covariates + strata(strata) degree specified control_step().","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/fit_survival_step.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Subgroup treatment effect pattern (STEP) fit for survival outcome — fit_survival_step","text":"","code":"fit_survival_step(   variables,   data,   control = c(control_step(), control_coxph()) )"},{"path":"https://insightsengineering.github.io/tern/main/reference/fit_survival_step.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Subgroup treatment effect pattern (STEP) fit for survival outcome — fit_survival_step","text":"variables (named list character) list analysis variables: needs time, event, arm, biomarker, optional covariates strata. data (data.frame) dataset containing variables summarize. control (named list) combined control list control_step() control_coxph().","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/fit_survival_step.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Subgroup treatment effect pattern (STEP) fit for survival outcome — fit_survival_step","text":"matrix class step. first part columns describe subgroup intervals used biomarker variable, including center intervals bounds. second part columns contain estimates treatment arm comparison.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/fit_survival_step.html","id":"note","dir":"Reference","previous_headings":"","what":"Note","title":"Subgroup treatment effect pattern (STEP) fit for survival outcome — fit_survival_step","text":"default degree 0 biomarker variable included model.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/main/reference/fit_survival_step.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Subgroup treatment effect pattern (STEP) fit for survival outcome — fit_survival_step","text":"","code":"# Testing dataset with just two treatment arms. library(dplyr)  adtte_f <- tern_ex_adtte %>%   filter(     PARAMCD == \"OS\",     ARM %in% c(\"B: Placebo\", \"A: Drug X\")   ) %>%   mutate(     # Reorder levels of ARM to display reference arm before treatment arm.     ARM = droplevels(forcats::fct_relevel(ARM, \"B: Placebo\")),     is_event = CNSR == 0   ) labels <- c(\"ARM\" = \"Treatment Arm\", \"is_event\" = \"Event Flag\") formatters::var_labels(adtte_f)[names(labels)] <- labels  variables <- list(   arm = \"ARM\",   biomarker = \"BMRKR1\",   covariates = c(\"AGE\", \"BMRKR2\"),   event = \"is_event\",   time = \"AVAL\" )  # Fit default STEP models: Here a constant treatment effect is estimated in each subgroup. step_matrix <- fit_survival_step(   variables = variables,   data = adtte_f ) dim(step_matrix) #> [1] 39 12 head(step_matrix) #>      Percentile Center Percentile Lower Percentile Upper Interval Center #> [1,]             0.025                0            0.275        1.472755 #> [2,]             0.050                0            0.300        2.028546 #> [3,]             0.075                0            0.325        2.204086 #> [4,]             0.100                0            0.350        2.799776 #> [5,]             0.125                0            0.375        2.969998 #> [6,]             0.150                0            0.400        3.149068 #>      Interval Lower Interval Upper  n events      loghr        se   ci_lower #> [1,]      0.4459546       4.182444 39     29 0.03729601 0.4243013 -0.7943192 #> [2,]      0.4459546       4.349471 43     31 0.23246622 0.3881347 -0.5282639 #> [3,]      0.4459546       4.626913 46     32 0.07952492 0.3813113 -0.6678314 #> [4,]      0.4459546       4.805767 50     35 0.09020455 0.3638368 -0.6229026 #> [5,]      0.4459546       4.929816 53     37 0.15522702 0.3477999 -0.5264483 #> [6,]      0.4459546       5.020539 57     41 0.11135760 0.3332843 -0.5418676 #>       ci_upper #> [1,] 0.8689112 #> [2,] 0.9931963 #> [3,] 0.8268813 #> [4,] 0.8033117 #> [5,] 0.8369023 #> [6,] 0.7645828  # Specify different polynomial degree for the biomarker interaction to use more flexible local # models. Or specify different Cox regression options. step_matrix2 <- fit_survival_step(   variables = variables,   data = adtte_f,   control = c(control_coxph(conf_level = 0.9), control_step(degree = 2)) )  # Use a global model with cubic interaction and only 5 points. step_matrix3 <- fit_survival_step(   variables = variables,   data = adtte_f,   control = c(control_coxph(), control_step(bandwidth = NULL, degree = 3, num_points = 5L)) )"},{"path":[]},{"path":"https://insightsengineering.github.io/tern/main/reference/forest_viewport.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create a viewport tree for the forest plot — forest_viewport","text":"","code":"forest_viewport(   tbl,   width_row_names = NULL,   width_columns = NULL,   width_forest = grid::unit(1, \"null\"),   gap_column = grid::unit(1, \"lines\"),   gap_header = grid::unit(1, \"lines\"),   mat_form = NULL )"},{"path":"https://insightsengineering.github.io/tern/main/reference/forest_viewport.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create a viewport tree for the forest plot — forest_viewport","text":"tbl (VTableTree)rtables table object. width_row_names (grid::unit) width row names. width_columns (grid::unit) width column spans. width_forest (grid::unit) width forest plot. gap_column (grid::unit) gap width columns. gap_header (grid::unit) gap width header. mat_form (MatrixPrintForm) matrix print form table.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/forest_viewport.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Create a viewport tree for the forest plot — forest_viewport","text":"viewport tree.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/forest_viewport.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Create a viewport tree for the forest plot — forest_viewport","text":"","code":"library(grid)  tbl <- rtable(   header = rheader(     rrow(\"\", \"E\", rcell(\"CI\", colspan = 2)),     rrow(\"\", \"A\", \"B\", \"C\")   ),   rrow(\"row 1\", 1, 0.8, 1.1),   rrow(\"row 2\", 1.4, 0.8, 1.6),   rrow(\"row 3\", 1.2, 0.8, 1.2) )  # \\donttest{ v <- forest_viewport(tbl) #> Warning: `forest_viewport()` was deprecated in tern 0.9.4. #> ℹ `g_forest` now generates `ggplot` objects. This function is no longer used #>   within `tern`. #> Warning: `vp_forest_table_part()` was deprecated in tern 0.9.4. #> ℹ `g_forest` now generates `ggplot` objects. This function is no longer used #>   within `tern`. #> ℹ The deprecated feature was likely used in the tern package. #>   Please report the issue at #>   <https://github.com/insightsengineering/tern/issues>.  grid::grid.newpage() showViewport(v)  # }"},{"path":"https://insightsengineering.github.io/tern/main/reference/format_auto.html","id":null,"dir":"Reference","previous_headings":"","what":"Format automatically using data significant digits — format_auto","title":"Format automatically using data significant digits — format_auto","text":"Formatting function majority default methods used analyze_vars(). non-derived values, significant digits data used (e.g. range), derived values one digits (measure location dispersion like mean, standard deviation). function can called internally \"auto\" like, example, .formats = c(\"mean\" = \"auto\"). See details see works inner function.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/format_auto.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Format automatically using data significant digits — format_auto","text":"","code":"format_auto(dt_var, x_stat)"},{"path":"https://insightsengineering.github.io/tern/main/reference/format_auto.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Format automatically using data significant digits — format_auto","text":"dt_var (numeric) variable data statistics calculated . Used find significant digits. analyze_vars comes .df_row (see rtables::additional_fun_params), row data row splits. column split considered. x_stat (string) string indicating current statistical method used.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/format_auto.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Format automatically using data significant digits — format_auto","text":"string rtables prints table cell.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/format_auto.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Format automatically using data significant digits — format_auto","text":"internal function needed work rtables default structure format functions, .e. function(x, ...), x results statistical evaluation. can one element (e.g. .stats = \"mean_sd\").","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/main/reference/format_auto.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Format automatically using data significant digits — format_auto","text":"","code":"x_todo <- c(0.001, 0.2, 0.0011000, 3, 4) res <- c(mean(x_todo[1:3]), sd(x_todo[1:3]))  # x is the result coming into the formatting function -> res!! format_auto(dt_var = x_todo, x_stat = \"mean_sd\")(x = res) #> [1] \"0.06737 (0.11486)\" format_auto(x_todo, \"range\")(x = range(x_todo)) #> [1] \"0.0010 - 4.0000\" no_sc_x <- c(0.0000001, 1) format_auto(no_sc_x, \"range\")(x = no_sc_x) #> [1] \"0.0000001 - 1.0000000\""},{"path":"https://insightsengineering.github.io/tern/main/reference/format_count_fraction.html","id":null,"dir":"Reference","previous_headings":"","what":"Format count and fraction — format_count_fraction","title":"Format count and fraction — format_count_fraction","text":"Formats count together fraction special consideration count 0.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/format_count_fraction.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Format count and fraction — format_count_fraction","text":"","code":"format_count_fraction(x, ...)"},{"path":"https://insightsengineering.github.io/tern/main/reference/format_count_fraction.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Format count and fraction — format_count_fraction","text":"x (numeric(2)) vector length 2 count fraction, respectively. ... used. Required rtables interface.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/format_count_fraction.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Format count and fraction — format_count_fraction","text":"string format count (fraction %). count 0, format 0.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/main/reference/format_count_fraction.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Format count and fraction — format_count_fraction","text":"","code":"format_count_fraction(x = c(2, 0.6667)) #> [1] \"2 (66.7%)\" format_count_fraction(x = c(0, 0)) #> [1] \"0\""},{"path":"https://insightsengineering.github.io/tern/main/reference/format_count_fraction_fixed_dp.html","id":null,"dir":"Reference","previous_headings":"","what":"Format count and percentage with fixed single decimal place — format_count_fraction_fixed_dp","title":"Format count and percentage with fixed single decimal place — format_count_fraction_fixed_dp","text":"Formats count together fraction special consideration count 0.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/format_count_fraction_fixed_dp.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Format count and percentage with fixed single decimal place — format_count_fraction_fixed_dp","text":"","code":"format_count_fraction_fixed_dp(x, ...)"},{"path":"https://insightsengineering.github.io/tern/main/reference/format_count_fraction_fixed_dp.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Format count and percentage with fixed single decimal place — format_count_fraction_fixed_dp","text":"x (numeric(2)) vector length 2 count fraction, respectively. ... used. Required rtables interface.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/format_count_fraction_fixed_dp.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Format count and percentage with fixed single decimal place — format_count_fraction_fixed_dp","text":"string format count (fraction %). count 0, format 0.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/main/reference/format_count_fraction_fixed_dp.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Format count and percentage with fixed single decimal place — format_count_fraction_fixed_dp","text":"","code":"format_count_fraction_fixed_dp(x = c(2, 0.6667)) #> [1] \"2 (66.7%)\" format_count_fraction_fixed_dp(x = c(2, 0.5)) #> [1] \"2 (50.0%)\" format_count_fraction_fixed_dp(x = c(0, 0)) #> [1] \"0\""},{"path":"https://insightsengineering.github.io/tern/main/reference/format_count_fraction_lt10.html","id":null,"dir":"Reference","previous_headings":"","what":"Format count and fraction with special case for count < 10 — format_count_fraction_lt10","title":"Format count and fraction with special case for count < 10 — format_count_fraction_lt10","text":"Formats count together fraction special consideration count less 10.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/format_count_fraction_lt10.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Format count and fraction with special case for count < 10 — format_count_fraction_lt10","text":"","code":"format_count_fraction_lt10(x, ...)"},{"path":"https://insightsengineering.github.io/tern/main/reference/format_count_fraction_lt10.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Format count and fraction with special case for count < 10 — format_count_fraction_lt10","text":"x (numeric(2)) vector length 2 count fraction, respectively. ... used. Required rtables interface.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/format_count_fraction_lt10.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Format count and fraction with special case for count < 10 — format_count_fraction_lt10","text":"string format count (fraction %). count less 10, count printed.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/main/reference/format_count_fraction_lt10.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Format count and fraction with special case for count < 10 — format_count_fraction_lt10","text":"","code":"format_count_fraction_lt10(x = c(275, 0.9673)) #> [1] \"275 (96.7%)\" format_count_fraction_lt10(x = c(2, 0.6667)) #> [1] \"2\" format_count_fraction_lt10(x = c(9, 1)) #> [1] \"9\""},{"path":"https://insightsengineering.github.io/tern/main/reference/format_extreme_values.html","id":null,"dir":"Reference","previous_headings":"","what":"Format a single extreme value — format_extreme_values","title":"Format a single extreme value — format_extreme_values","text":"Create formatting function single extreme value.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/format_extreme_values.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Format a single extreme value — format_extreme_values","text":"","code":"format_extreme_values(digits = 2L)"},{"path":"https://insightsengineering.github.io/tern/main/reference/format_extreme_values.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Format a single extreme value — format_extreme_values","text":"digits (integer(1)) number decimal places display.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/format_extreme_values.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Format a single extreme value — format_extreme_values","text":"rtables formatting function uses threshold digits return formatted extreme value.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/main/reference/format_extreme_values.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Format a single extreme value — format_extreme_values","text":"","code":"format_fun <- format_extreme_values(2L) format_fun(x = 0.127) #> [1] \"0.13\" format_fun(x = Inf) #> [1] \">999.99\" format_fun(x = 0) #> [1] \"0.00\" format_fun(x = 0.009) #> [1] \"<0.01\""},{"path":"https://insightsengineering.github.io/tern/main/reference/format_extreme_values_ci.html","id":null,"dir":"Reference","previous_headings":"","what":"Format extreme values part of a confidence interval — format_extreme_values_ci","title":"Format extreme values part of a confidence interval — format_extreme_values_ci","text":"Formatting Function extreme values part confidence interval. Values formatted e.g. \"(xx.xx, xx.xx)\" number digits 2.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/format_extreme_values_ci.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Format extreme values part of a confidence interval — format_extreme_values_ci","text":"","code":"format_extreme_values_ci(digits = 2L)"},{"path":"https://insightsengineering.github.io/tern/main/reference/format_extreme_values_ci.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Format extreme values part of a confidence interval — format_extreme_values_ci","text":"digits (integer(1)) number decimal places display.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/format_extreme_values_ci.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Format extreme values part of a confidence interval — format_extreme_values_ci","text":"rtables formatting function uses threshold digits return formatted extreme values confidence interval.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/main/reference/format_extreme_values_ci.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Format extreme values part of a confidence interval — format_extreme_values_ci","text":"","code":"format_fun <- format_extreme_values_ci(2L) format_fun(x = c(0.127, Inf)) #> [1] \"(0.13, >999.99)\" format_fun(x = c(0, 0.009)) #> [1] \"(0.00, <0.01)\""},{"path":"https://insightsengineering.github.io/tern/main/reference/format_fraction.html","id":null,"dir":"Reference","previous_headings":"","what":"Format fraction and percentage — format_fraction","title":"Format fraction and percentage — format_fraction","text":"Formats fraction together ratio percent.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/format_fraction.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Format fraction and percentage — format_fraction","text":"","code":"format_fraction(x, ...)"},{"path":"https://insightsengineering.github.io/tern/main/reference/format_fraction.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Format fraction and percentage — format_fraction","text":"x (named integer) vector elements num denom. ... used. Required rtables interface.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/format_fraction.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Format fraction and percentage — format_fraction","text":"string format num / denom (ratio %). num 0, format num / denom.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/main/reference/format_fraction.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Format fraction and percentage — format_fraction","text":"","code":"format_fraction(x = c(num = 2L, denom = 3L)) #> [1] \"2/3 (66.7%)\" format_fraction(x = c(num = 0L, denom = 3L)) #> [1] \"0/3\""},{"path":"https://insightsengineering.github.io/tern/main/reference/format_fraction_fixed_dp.html","id":null,"dir":"Reference","previous_headings":"","what":"Format fraction and percentage with fixed single decimal place — format_fraction_fixed_dp","title":"Format fraction and percentage with fixed single decimal place — format_fraction_fixed_dp","text":"Formats fraction together ratio percent fixed single decimal place. Includes trailing zero case whole number percentages always keep one decimal place.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/format_fraction_fixed_dp.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Format fraction and percentage with fixed single decimal place — format_fraction_fixed_dp","text":"","code":"format_fraction_fixed_dp(x, ...)"},{"path":"https://insightsengineering.github.io/tern/main/reference/format_fraction_fixed_dp.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Format fraction and percentage with fixed single decimal place — format_fraction_fixed_dp","text":"x (named integer) vector elements num denom. ... used. Required rtables interface.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/format_fraction_fixed_dp.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Format fraction and percentage with fixed single decimal place — format_fraction_fixed_dp","text":"string format num / denom (ratio %). num 0, format num / denom.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/main/reference/format_fraction_fixed_dp.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Format fraction and percentage with fixed single decimal place — format_fraction_fixed_dp","text":"","code":"format_fraction_fixed_dp(x = c(num = 1L, denom = 2L)) #> [1] \"1/2 (50.0%)\" format_fraction_fixed_dp(x = c(num = 1L, denom = 4L)) #> [1] \"1/4 (25.0%)\" format_fraction_fixed_dp(x = c(num = 0L, denom = 3L)) #> [1] \"0/3\""},{"path":"https://insightsengineering.github.io/tern/main/reference/format_fraction_threshold.html","id":null,"dir":"Reference","previous_headings":"","what":"Format fraction with lower threshold — format_fraction_threshold","title":"Format fraction with lower threshold — format_fraction_threshold","text":"Formats fraction second element input x fraction. applies lower threshold, just stated fraction smaller .","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/format_fraction_threshold.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Format fraction with lower threshold — format_fraction_threshold","text":"","code":"format_fraction_threshold(threshold)"},{"path":"https://insightsengineering.github.io/tern/main/reference/format_fraction_threshold.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Format fraction with lower threshold — format_fraction_threshold","text":"threshold (proportion) lower threshold.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/format_fraction_threshold.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Format fraction with lower threshold — format_fraction_threshold","text":"rtables formatting function takes numeric input x second element fraction formatted. fraction equal threshold, displayed percentage. positive threshold, returns, e.g. \"<1\" threshold 0.01. zero, just \"0\" returned.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/main/reference/format_fraction_threshold.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Format fraction with lower threshold — format_fraction_threshold","text":"","code":"format_fun <- format_fraction_threshold(0.05) format_fun(x = c(20, 0.1)) #> [1] 10 format_fun(x = c(2, 0.01)) #> [1] \"<5\" format_fun(x = c(0, 0)) #> [1] \"0\""},{"path":"https://insightsengineering.github.io/tern/main/reference/format_sigfig.html","id":null,"dir":"Reference","previous_headings":"","what":"Format numeric values by significant figures — format_sigfig","title":"Format numeric values by significant figures — format_sigfig","text":"Format numeric values print specified number significant figures.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/format_sigfig.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Format numeric values by significant figures — format_sigfig","text":"","code":"format_sigfig(sigfig, format = \"xx\", num_fmt = \"fg\")"},{"path":"https://insightsengineering.github.io/tern/main/reference/format_sigfig.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Format numeric values by significant figures — format_sigfig","text":"sigfig (integer(1)) number significant figures display. format (string) format label (string) apply printing value. Decimal places string ignored favor formatting significant figures. Formats options : \"xx\", \"xx / xx\", \"(xx, xx)\", \"xx - xx\", \"xx (xx)\". num_fmt (string) numeric format modifiers apply value. Defaults \"fg\" standard significant figures formatting - fixed (non-scientific notation) format (\"f\") sigfig equal number significant figures instead decimal places (\"g\"). See formatC() format argument options.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/format_sigfig.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Format numeric values by significant figures — format_sigfig","text":"rtables formatting function.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/main/reference/format_sigfig.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Format numeric values by significant figures — format_sigfig","text":"","code":"fmt_3sf <- format_sigfig(3) fmt_3sf(1.658) #> [1] \"1.66\" fmt_3sf(1e1) #> [1] \"10.0\"  fmt_5sf <- format_sigfig(5) fmt_5sf(0.57) #> [1] \"0.57000\" fmt_5sf(0.000025645) #> [1] \"0.000025645\""},{"path":"https://insightsengineering.github.io/tern/main/reference/format_xx.html","id":null,"dir":"Reference","previous_headings":"","what":"Format XX as a formatting function — format_xx","title":"Format XX as a formatting function — format_xx","text":"Translate string x dots interpreted number place holders, others formatting elements.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/format_xx.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Format XX as a formatting function — format_xx","text":"","code":"format_xx(str)"},{"path":"https://insightsengineering.github.io/tern/main/reference/format_xx.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Format XX as a formatting function — format_xx","text":"str (string) template.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/format_xx.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Format XX as a formatting function — format_xx","text":"rtables formatting function.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/main/reference/format_xx.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Format XX as a formatting function — format_xx","text":"","code":"test <- list(c(1.658, 0.5761), c(1e1, 785.6))  z <- format_xx(\"xx (xx.x)\") sapply(test, z) #> [1] \"2 (0.6)\"    \"10 (785.6)\"  z <- format_xx(\"xx.x - xx.x\") sapply(test, z) #> [1] \"1.7 - 0.6\"  \"10 - 785.6\"  z <- format_xx(\"xx.x, incl. xx.x% NE\") sapply(test, z) #> [1] \"1.7, incl. 0.6% NE\"  \"10, incl. 785.6% NE\""},{"path":"https://insightsengineering.github.io/tern/main/reference/formatting_functions.html","id":null,"dir":"Reference","previous_headings":"","what":"Formatting functions — formatting_functions","title":"Formatting functions — formatting_functions","text":"See list formatting functions created tern work rtables.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/formatting_functions.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Formatting functions — formatting_functions","text":"available formats can listed via formatters::list_valid_format_labels(). Additional custom formats can created via formatters::sprintf_format() function.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/main/reference/g_bland_altman.html","id":null,"dir":"Reference","previous_headings":"","what":"Bland-Altman plot — g_bland_altman","title":"Bland-Altman plot — g_bland_altman","text":"Graphing function produces Bland-Altman plot.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/g_bland_altman.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Bland-Altman plot — g_bland_altman","text":"","code":"g_bland_altman(x, y, conf_level = 0.95)"},{"path":"https://insightsengineering.github.io/tern/main/reference/g_bland_altman.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Bland-Altman plot — g_bland_altman","text":"x (numeric) vector numbers want analyze. y (numeric) vector numbers want analyze, compared x. conf_level (proportion) confidence level interval.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/g_bland_altman.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Bland-Altman plot — g_bland_altman","text":"ggplot Bland-Altman plot.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/g_bland_altman.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Bland-Altman plot — g_bland_altman","text":"","code":"x <- seq(1, 60, 5) y <- seq(5, 50, 4)  g_bland_altman(x = x, y = y, conf_level = 0.9)"},{"path":[]},{"path":"https://insightsengineering.github.io/tern/main/reference/g_forest.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create a forest plot from an rtable — g_forest","text":"","code":"g_forest(   tbl,   col_x = attr(tbl, \"col_x\"),   col_ci = attr(tbl, \"col_ci\"),   vline = 1,   forest_header = attr(tbl, \"forest_header\"),   xlim = c(0.1, 10),   logx = TRUE,   x_at = c(0.1, 1, 10),   width_row_names = lifecycle::deprecated(),   width_columns = NULL,   width_forest = lifecycle::deprecated(),   lbl_col_padding = 0,   rel_width_forest = 0.25,   font_size = 12,   col_symbol_size = attr(tbl, \"col_symbol_size\"),   col = getOption(\"ggplot2.discrete.colour\")[1],   ggtheme = NULL,   as_list = FALSE,   gp = lifecycle::deprecated(),   draw = lifecycle::deprecated(),   newpage = lifecycle::deprecated() )"},{"path":"https://insightsengineering.github.io/tern/main/reference/g_forest.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create a forest plot from an rtable — g_forest","text":"tbl (VTableTree)rtables table least one column single value one column 2 values. col_x (integer(1) NULL) column index estimator. default tries get tbl attribute col_x, otherwise needs manually specified. NULL, points excluded forest plot. col_ci (integer(1) NULL) column index confidence intervals. default tries get tbl attribute col_ci, otherwise needs manually specified. NULL, lines excluded forest plot. vline (numeric(1) NULL) x coordinate vertical line, NULL line omitted. forest_header (character(2)) text displayed left right vline, respectively. vline = NULL forest_header printed. default tries get tbl attribute forest_header. NULL, defaults extracted table possible, set \"Comparison\\nBetter\" \"Treatment\\nBetter\" . xlim (numeric(2)) limits x axis. logx (flag) show x-values logarithm scale. x_at (numeric) x-tick locations, NULL, x_at set vline xlim values. width_row_names Please use lbl_col_padding argument instead. width_columns (numeric) vector column widths. element's position colwidths corresponds column tbl position. NULL, column widths calculated according maximum number characters per column. width_forest Please use rel_width_forest argument instead. lbl_col_padding (numeric) additional padding use calculating spacing first (label) column second column tbl. colwidths specified, width first column becomes colwidths[1] + lbl_col_padding. Defaults 0. rel_width_forest (proportion) proportion total width allocate forest plot. Relative width table 1 - rel_width_forest. as_list = TRUE, parameter ignored. font_size (numeric(1)) font size. col_symbol_size (numeric NULL) column index tbl containing data used determine relative size estimator plot symbol. Typically, symbol size proportional sample size used calculate estimator. NULL, symbol size used subgroups. default tries get tbl attribute col_symbol_size, otherwise needs manually specified. col (character) color(s). ggtheme (theme) graphical theme provided ggplot2 control styling plot. as_list (flag) whether two ggplot objects returned list. TRUE, named list two elements, table plot, returned. FALSE (default) table forest plot printed side--side via cowplot::plot_grid(). gp g_forest now generated ggplot object. argument longer used. draw g_forest now generated ggplot object. argument longer used. newpage g_forest now generated ggplot object. argument longer used.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/g_forest.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Create a forest plot from an rtable — g_forest","text":"ggplot forest plot table.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/g_forest.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Create a forest plot from an rtable — g_forest","text":"Given rtables::rtable() object least one column single value one column 2 values, converts table ggplot2::ggplot() object generates accompanying forest plot. table forest plot printed side--side.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/g_forest.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Create a forest plot from an rtable — g_forest","text":"","code":"library(dplyr) library(forcats)  adrs <- tern_ex_adrs n_records <- 20 adrs_labels <- formatters::var_labels(adrs, fill = TRUE) adrs <- adrs %>%   filter(PARAMCD == \"BESRSPI\") %>%   filter(ARM %in% c(\"A: Drug X\", \"B: Placebo\")) %>%   slice(seq_len(n_records)) %>%   droplevels() %>%   mutate(     # Reorder levels of factor to make the placebo group the reference arm.     ARM = fct_relevel(ARM, \"B: Placebo\"),     rsp = AVALC == \"CR\"   ) formatters::var_labels(adrs) <- c(adrs_labels, \"Response\") df <- extract_rsp_subgroups(   variables = list(rsp = \"rsp\", arm = \"ARM\", subgroups = c(\"SEX\", \"STRATA2\")),   data = adrs ) # Full commonly used response table.  tbl <- basic_table() %>%   tabulate_rsp_subgroups(df) g_forest(tbl)   # Odds ratio only table.  tbl_or <- basic_table() %>%   tabulate_rsp_subgroups(df, vars = c(\"n_tot\", \"or\", \"ci\")) g_forest(   tbl_or,   forest_header = c(\"Comparison\\nBetter\", \"Treatment\\nBetter\") )   # Survival forest plot example. adtte <- tern_ex_adtte # Save variable labels before data processing steps. adtte_labels <- formatters::var_labels(adtte, fill = TRUE) adtte_f <- adtte %>%   filter(     PARAMCD == \"OS\",     ARM %in% c(\"B: Placebo\", \"A: Drug X\"),     SEX %in% c(\"M\", \"F\")   ) %>%   mutate(     # Reorder levels of ARM to display reference arm before treatment arm.     ARM = droplevels(fct_relevel(ARM, \"B: Placebo\")),     SEX = droplevels(SEX),     AVALU = as.character(AVALU),     is_event = CNSR == 0   ) labels <- list(   \"ARM\" = adtte_labels[\"ARM\"],   \"SEX\" = adtte_labels[\"SEX\"],   \"AVALU\" = adtte_labels[\"AVALU\"],   \"is_event\" = \"Event Flag\" ) formatters::var_labels(adtte_f)[names(labels)] <- as.character(labels) df <- extract_survival_subgroups(   variables = list(     tte = \"AVAL\",     is_event = \"is_event\",     arm = \"ARM\", subgroups = c(\"SEX\", \"BMRKR2\")   ),   data = adtte_f ) table_hr <- basic_table() %>%   tabulate_survival_subgroups(df, time_unit = adtte_f$AVALU[1]) g_forest(table_hr)   # Works with any `rtable`. tbl <- rtable(   header = c(\"E\", \"CI\", \"N\"),   rrow(\"\", 1, c(.8, 1.2), 200),   rrow(\"\", 1.2, c(1.1, 1.4), 50) ) g_forest(   tbl = tbl,   col_x = 1,   col_ci = 2,   xlim = c(0.5, 2),   x_at = c(0.5, 1, 2),   col_symbol_size = 3 )   tbl <- rtable(   header = rheader(     rrow(\"\", rcell(\"A\", colspan = 2)),     rrow(\"\", \"c1\", \"c2\")   ),   rrow(\"row 1\", 1, c(.8, 1.2)),   rrow(\"row 2\", 1.2, c(1.1, 1.4)) ) g_forest(   tbl = tbl,   col_x = 1,   col_ci = 2,   xlim = c(0.5, 2),   x_at = c(0.5, 1, 2),   vline = 1,   forest_header = c(\"Hello\", \"World\") )"},{"path":"https://insightsengineering.github.io/tern/main/reference/g_ipp.html","id":null,"dir":"Reference","previous_headings":"","what":"Individual patient plots — g_ipp","title":"Individual patient plots — g_ipp","text":"Line plot(s) displaying trend patients' parameter values time rendered. Patients' individual baseline values can added plot(s) reference.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/g_ipp.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Individual patient plots — g_ipp","text":"","code":"g_ipp(   df,   xvar,   yvar,   xlab,   ylab,   id_var = \"USUBJID\",   title = \"Individual Patient Plots\",   subtitle = \"\",   caption = NULL,   add_baseline_hline = FALSE,   yvar_baseline = \"BASE\",   ggtheme = nestcolor::theme_nest(),   plotting_choices = c(\"all_in_one\", \"split_by_max_obs\", \"separate_by_obs\"),   max_obs_per_plot = 4,   col = NULL )"},{"path":"https://insightsengineering.github.io/tern/main/reference/g_ipp.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Individual patient plots — g_ipp","text":"df (data.frame) data set containing analysis variables. xvar (string) time point variable plotted x-axis. yvar (string) continuous analysis variable plotted y-axis. xlab (string) plot label x-axis. ylab (string) plot label y-axis. id_var (string) variable used patient identifier. title (string) title plot. subtitle (string) subtitle plot. caption (string) optional caption plot. add_baseline_hline (flag) adds horizontal line baseline y-value plot TRUE. yvar_baseline (string) variable baseline values . Ignored add_baseline_hline FALSE. ggtheme (theme) optional graphical theme function provided ggplot2 control outlook plot. Use ggplot2::theme() tweak display. plotting_choices (string) specifies options displaying plots. Must one \"all_in_one\", \"split_by_max_obs\", \"separate_by_obs\". max_obs_per_plot (integer(1)) number observations plotted one plot. Ignored plotting_choices \"separate_by_obs\". col (character) line colors.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/g_ipp.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Individual patient plots — g_ipp","text":"ggplot object list ggplot objects.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/g_ipp.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Individual patient plots — g_ipp","text":"g_ipp(): Plotting function individual patient plots , depending user preference, renders single graphic compiles list graphics show trends individual's parameter values time.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/main/reference/g_ipp.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Individual patient plots — g_ipp","text":"","code":"library(dplyr)  # Select a small sample of data to plot. adlb <- tern_ex_adlb %>%   filter(PARAMCD == \"ALT\", !(AVISIT %in% c(\"SCREENING\", \"BASELINE\"))) %>%   slice(1:36)  plot_list <- g_ipp(   df = adlb,   xvar = \"AVISIT\",   yvar = \"AVAL\",   xlab = \"Visit\",   ylab = \"SGOT/ALT (U/L)\",   title = \"Individual Patient Plots\",   add_baseline_hline = TRUE,   plotting_choices = \"split_by_max_obs\",   max_obs_per_plot = 5 ) plot_list #> [[1]]  #>  #> [[2]]  #>"},{"path":"https://insightsengineering.github.io/tern/main/reference/g_km.html","id":null,"dir":"Reference","previous_headings":"","what":"Kaplan-Meier plot — g_km","title":"Kaplan-Meier plot — g_km","text":"survival model, graphic rendered along tabulated annotation including number patient risk given time median survival per group.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/g_km.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Kaplan-Meier plot — g_km","text":"","code":"g_km(   df,   variables,   control_surv = control_surv_timepoint(),   col = NULL,   lty = NULL,   lwd = 0.5,   censor_show = TRUE,   pch = 3,   size = 2,   max_time = NULL,   xticks = NULL,   xlab = \"Days\",   yval = c(\"Survival\", \"Failure\"),   ylab = paste(yval, \"Probability\"),   ylim = NULL,   title = NULL,   footnotes = NULL,   font_size = 10,   ci_ribbon = FALSE,   annot_at_risk = TRUE,   annot_at_risk_title = TRUE,   annot_surv_med = TRUE,   annot_coxph = FALSE,   annot_stats = NULL,   annot_stats_vlines = FALSE,   control_coxph_pw = control_coxph(),   ref_group_coxph = NULL,   control_annot_surv_med = control_surv_med_annot(),   control_annot_coxph = control_coxph_annot(),   legend_pos = NULL,   rel_height_plot = 0.75,   ggtheme = NULL,   as_list = FALSE,   draw = lifecycle::deprecated(),   newpage = lifecycle::deprecated(),   gp = lifecycle::deprecated(),   vp = lifecycle::deprecated(),   name = lifecycle::deprecated(),   annot_coxph_ref_lbls = lifecycle::deprecated(),   position_coxph = lifecycle::deprecated(),   position_surv_med = lifecycle::deprecated(),   width_annots = lifecycle::deprecated() )"},{"path":"https://insightsengineering.github.io/tern/main/reference/g_km.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Kaplan-Meier plot — g_km","text":"df (data.frame) data set containing analysis variables. variables (named list) variable names. Details : tte (numeric) variable indicating time--event duration values. is_event (logical) event variable. TRUE event, FALSE time event censored. arm (factor) treatment group variable. strata (character NULL) variable names indicating stratification factors. control_surv (list) parameters comparison details, specified using helper function control_surv_timepoint(). possible parameter options : conf_level (proportion) confidence level interval survival rate. conf_type (string)\"plain\" (default), \"log\", \"log-log\" confidence interval type, see survival::survfit(). Note option \"none\" longer supported. col (character) lines colors. Length vector equal number strata survival::survfit(). lty (numeric) line type. vector given, length equal number strata survival::survfit(). lwd (numeric) line width. vector given, length equal number strata survival::survfit(). censor_show (flag) whether show censored observations. pch (string) name symbol character use point symbol indicate censored cases. size (numeric(1)) size censored point symbols. max_time (numeric(1)) maximum value show x-axis. data values less threshold value plotted (defaults NULL). xticks (numeric NULL) numeric vector tick positions single number spacing ticks x-axis. NULL (default), labeling::extended() used determine optimal tick positions x-axis. xlab (string) x-axis label. yval (string) type plot, plotted y-axis. Options Survival (default) Failure probability. ylab (string) y-axis label. ylim (numeric(2)) vector containing lower upper limits y-axis, respectively. NULL (default), default scale range used. title (string) plot title. footnotes (string) plot footnotes. font_size (numeric(1)) font size use text. ci_ribbon (flag) whether confidence interval drawn around Kaplan-Meier curve. annot_at_risk (flag) compute add annotation table reporting number patient risk matching main grid Kaplan-Meier curve. annot_at_risk_title (flag) whether \"Patients Risk\" title added annot_at_risk table. effect annot_at_risk FALSE. Defaults TRUE. annot_surv_med (flag) compute add annotation table Kaplan-Meier curve estimating median survival time per group. annot_coxph (flag) whether add annotation table survival::coxph() model. annot_stats (string NULL) statistics annotations add plot. Options median (median survival follow-time) min (minimum survival follow-time). annot_stats_vlines (flag) add vertical lines corresponding statistics specified annot_stats. annot_stats NULL lines added. control_coxph_pw (list) parameters comparison details, specified using helper function control_coxph(). possible parameter options : pval_method (string) p-value method testing hazard ratio = 1. Default method \"log-rank\", can also set \"wald\" \"likelihood\". ties (string) method tie handling. Default \"efron\", can also set \"breslow\" \"exact\". See survival::coxph() conf_level (proportion) confidence level interval HR. ref_group_coxph (string NULL) level arm variable use reference group calculations annot_coxph table. NULL (default), uses first level arm variable. control_annot_surv_med (list) parameters control position size annotation table added plot annot_surv_med = TRUE, specified using control_surv_med_annot() function. Parameter options : x, y, w, h, fill. See control_surv_med_annot() details. control_annot_coxph (list) parameters control position size annotation table added plot annot_coxph = TRUE, specified using control_coxph_annot() function. Parameter options : x, y, w, h, fill, ref_lbls. See control_coxph_annot() details. legend_pos (numeric(2) NULL) vector containing x- y-coordinates, respectively, legend position relative KM plot area. NULL (default), legend positioned bottom right corner plot, middle right plot needed prevent overlapping. rel_height_plot (proportion) proportion total figure height allocate Kaplan-Meier plot. Relative height patients risk table 1 - rel_height_plot. annot_at_risk = FALSE as_list = TRUE, parameter ignored. ggtheme (theme) graphical theme provided ggplot2 format Kaplan-Meier plot. as_list (flag) whether two ggplot objects returned list annot_at_risk = TRUE. TRUE, named list two elements, plot table, returned. FALSE (default) patients risk table printed plot via cowplot::plot_grid(). draw function longer generates grob objects. newpage function longer generates grob objects. gp function longer generates grob objects. vp function longer generates grob objects. name function longer generates grob objects. annot_coxph_ref_lbls Please use ref_lbls element control_annot_coxph instead. position_coxph Please use x y elements control_annot_coxph instead. position_surv_med Please use x y elements control_annot_surv_med instead. width_annots Please use w element control_annot_surv_med (surv_med) control_annot_coxph (coxph).\"","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/g_km.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Kaplan-Meier plot — g_km","text":"ggplot Kaplan-Meier plot (optionally) summary table.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/g_km.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Kaplan-Meier plot — g_km","text":"","code":"library(dplyr)  df <- tern_ex_adtte %>%   filter(PARAMCD == \"OS\") %>%   mutate(is_event = CNSR == 0) variables <- list(tte = \"AVAL\", is_event = \"is_event\", arm = \"ARMCD\")  # Basic examples g_km(df = df, variables = variables)  g_km(df = df, variables = variables, yval = \"Failure\")   # Examples with customization parameters applied g_km(   df = df,   variables = variables,   control_surv = control_surv_timepoint(conf_level = 0.9),   col = c(\"grey25\", \"grey50\", \"grey75\"),   annot_at_risk_title = FALSE,   lty = 1:3,   font_size = 8 )  g_km(   df = df,   variables = variables,   annot_stats = c(\"min\", \"median\"),   annot_stats_vlines = TRUE,   max_time = 3000,   ggtheme = ggplot2::theme_minimal() )   # Example with pairwise Cox-PH analysis annotation table, adjusted annotation tables g_km(   df = df, variables = variables,   annot_coxph = TRUE,   control_coxph = control_coxph(pval_method = \"wald\", ties = \"exact\", conf_level = 0.99),   control_annot_coxph = control_coxph_annot(x = 0.26, w = 0.35),   control_annot_surv_med = control_surv_med_annot(x = 0.8, y = 0.9, w = 0.35) )"},{"path":"https://insightsengineering.github.io/tern/main/reference/g_lineplot.html","id":null,"dir":"Reference","previous_headings":"","what":"Line plot with optional table — g_lineplot","title":"Line plot with optional table — g_lineplot","text":"Line plot optional table.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/g_lineplot.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Line plot with optional table — g_lineplot","text":"","code":"g_lineplot(   df,   alt_counts_df = NULL,   variables = control_lineplot_vars(),   mid = \"mean\",   interval = \"mean_ci\",   whiskers = c(\"mean_ci_lwr\", \"mean_ci_upr\"),   table = NULL,   sfun = s_summary,   ...,   mid_type = \"pl\",   mid_point_size = 2,   position = ggplot2::position_dodge(width = 0.4),   legend_title = NULL,   legend_position = \"bottom\",   ggtheme = nestcolor::theme_nest(),   xticks = NULL,   xlim = NULL,   ylim = NULL,   x_lab = obj_label(df[[variables[[\"x\"]]]]),   y_lab = NULL,   y_lab_add_paramcd = TRUE,   y_lab_add_unit = TRUE,   title = \"Plot of Mean and 95% Confidence Limits by Visit\",   subtitle = \"\",   subtitle_add_paramcd = TRUE,   subtitle_add_unit = TRUE,   caption = NULL,   table_format = NULL,   table_labels = NULL,   table_font_size = 3,   errorbar_width = 0.45,   newpage = lifecycle::deprecated(),   col = NULL,   linetype = NULL,   rel_height_plot = 0.5,   as_list = FALSE )"},{"path":"https://insightsengineering.github.io/tern/main/reference/g_lineplot.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Line plot with optional table — g_lineplot","text":"df (data.frame) data set containing analysis variables. alt_counts_df (data.frame NULL) data set used () counts objects groups stratification. variables (named character) vector variable names df include: x (string) name x-axis variable. y (string) name y-axis variable. group_var (string NULL) name grouping variable (strata), .e. treatment arm. Can NA indicate lack groups. subject_var (string NULL) name subject variable. applies group_var NULL. paramcd (string NA) name variable parameter's code. Used y-axis label plot's subtitle. Can NA paramcd added y-axis label subtitle. y_unit (string NA) name variable units y. Used y-axis label plot's subtitle. Can NA y unit added y-axis label subtitle. facet_var (string NA) name secondary grouping variable used plot faceting, .e. treatment arm. Can NA indicate lack groups. mid (character NULL) names statistics plotted midpoints. statistics indicated mid variable must present object returned sfun, double numeric type vector length one. interval (character NULL) names statistics plotted intervals. statistics indicated interval variable must present object returned sfun, double numeric type vector length two. Set interval = NULL intervals added plot. whiskers (character) names interval whiskers plotted. Names must match names list element interval returned sfun (e.g. mean_ci_lwr element sfun(x)[[\"mean_ci\"]]). possible specify one whisker , suppress whiskers setting interval = NULL. table (character NULL) names statistics displayed table plot. statistics indicated table variable must present object returned sfun. sfun (function) function compute values required statistics. must return named list atomic vectors. names list elements refer names statistics used mid, interval, table. must able accept input vector data statistics computed. ... optional arguments sfun. mid_type (string) controls type mid plot, can point (\"p\"), line (\"l\"), point line (\"pl\"). mid_point_size (numeric(1)) font size mid plot points. position (character call) geom element position adjustment, either string, result call position adjustment function. legend_title (string) legend title. legend_position (string) position plot legend (\"none\", \"left\", \"right\", \"bottom\", \"top\", two-element numeric vector). ggtheme (theme) graphical theme provided ggplot2 control styling plot. xticks (numeric NULL) numeric vector tick positions single number spacing ticks x-axis, use variables$x numeric. NULL (default), labeling::extended() used determine optimal tick positions x-axis. variables$x numeric, argument ignored. xlim (numeric(2)) vector containing lower upper limits x-axis, respectively. NULL (default), default scale range used. ylim (numeric(2)) vector containing lower upper limits y-axis, respectively. NULL (default), default scale range used. x_lab (string NULL) x-axis label. NULL label added. y_lab (string NULL) y-axis label. NULL label added. y_lab_add_paramcd (flag) whether paramcd, .e. unique(df[[variables[\"paramcd\"]]]) added y-axis label (y_lab). y_lab_add_unit (flag) whether y-axis unit, .e. unique(df[[variables[\"y_unit\"]]]) added y-axis label (y_lab). title (string) plot title. subtitle (string) plot subtitle. subtitle_add_paramcd (flag) whether paramcd, .e. unique(df[[variables[\"paramcd\"]]]) added plot's subtitle (subtitle). subtitle_add_unit (flag) whether y-axis unit, .e. unique(df[[variables[\"y_unit\"]]]) added plot's subtitle (subtitle). caption (string) optional caption plot. table_format (named character NULL) format patterns descriptive statistics used (optional) table appended plot. passed directly h_format_row function format parameter. Names table_format must match names statistics returned sfun function. table_labels (named character NULL) labels descriptive statistics used (optional) table appended plot. Names table_labels must match names statistics returned sfun function. table_font_size (numeric(1)) font size text table. errorbar_width (numeric(1)) width error bars. newpage used. col (character) color(s). See ?ggplot2::aes_colour_fill_alpha example values. linetype (character) line type(s). See ?ggplot2::aes_linetype_size_shape example values. rel_height_plot (proportion) proportion total figure height allocate line plot. Relative height annotation table 1 - rel_height_plot. table = NULL, parameter ignored. as_list (flag) whether two ggplot objects returned list table NULL. TRUE, named list two elements, plot table, returned. FALSE (default) annotation table printed plot via cowplot::plot_grid().","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/g_lineplot.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Line plot with optional table — g_lineplot","text":"ggplot line plot (statistics table applicable).","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/g_lineplot.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Line plot with optional table — g_lineplot","text":"","code":"adsl <- tern_ex_adsl adlb <- tern_ex_adlb %>% dplyr::filter(ANL01FL == \"Y\", PARAMCD == \"ALT\", AVISIT != \"SCREENING\") adlb$AVISIT <- droplevels(adlb$AVISIT) adlb <- dplyr::mutate(adlb, AVISIT = forcats::fct_reorder(AVISIT, AVISITN, min))  # Mean with CI g_lineplot(adlb, adsl, subtitle = \"Laboratory Test:\")   # Mean with CI, no stratification with group_var g_lineplot(adlb, variables = control_lineplot_vars(group_var = NA))   # Mean, upper whisker of CI, no group_var(strata) counts N g_lineplot(   adlb,   whiskers = \"mean_ci_upr\",   title = \"Plot of Mean and Upper 95% Confidence Limit by Visit\" )   # Median with CI g_lineplot(   adlb,   adsl,   mid = \"median\",   interval = \"median_ci\",   whiskers = c(\"median_ci_lwr\", \"median_ci_upr\"),   title = \"Plot of Median and 95% Confidence Limits by Visit\" )   # Mean, +/- SD g_lineplot(adlb, adsl,   interval = \"mean_sdi\",   whiskers = c(\"mean_sdi_lwr\", \"mean_sdi_upr\"),   title = \"Plot of Median +/- SD by Visit\" )   # Mean with CI plot with stats table g_lineplot(adlb, adsl, table = c(\"n\", \"mean\", \"mean_ci\"))   # Mean with CI, table and customized confidence level g_lineplot(   adlb,   adsl,   table = c(\"n\", \"mean\", \"mean_ci\"),   control = control_analyze_vars(conf_level = 0.80),   title = \"Plot of Mean and 80% Confidence Limits by Visit\" )   # Mean with CI, table, filtered data adlb_f <- dplyr::filter(adlb, ARMCD != \"ARM A\" | AVISIT == \"BASELINE\") g_lineplot(adlb_f, table = c(\"n\", \"mean\"))"},{"path":"https://insightsengineering.github.io/tern/main/reference/g_step.html","id":null,"dir":"Reference","previous_headings":"","what":"Create a STEP graph — g_step","title":"Create a STEP graph — g_step","text":"Based STEP results, creates ggplot graph showing estimated HR along continuous biomarker value subgroups.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/g_step.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create a STEP graph — g_step","text":"","code":"g_step(   df,   use_percentile = \"Percentile Center\" %in% names(df),   est = list(col = \"blue\", lty = 1),   ci_ribbon = list(fill = getOption(\"ggplot2.discrete.colour\")[1], alpha = 0.5),   col = getOption(\"ggplot2.discrete.colour\") )"},{"path":"https://insightsengineering.github.io/tern/main/reference/g_step.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create a STEP graph — g_step","text":"df (tibble) result tidy.step(). use_percentile (flag) whether use percentiles x axis actual biomarker values. est (named list)col lty settings estimate line. ci_ribbon (named list NULL)fill alpha settings confidence interval ribbon area, NULL plot CI ribbon. col (character) color(s).","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/g_step.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Create a STEP graph — g_step","text":"ggplot STEP graph.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/main/reference/g_step.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Create a STEP graph — g_step","text":"","code":"library(survival) lung$sex <- factor(lung$sex)  # Survival example. vars <- list(   time = \"time\",   event = \"status\",   arm = \"sex\",   biomarker = \"age\" )  step_matrix <- fit_survival_step(   variables = vars,   data = lung,   control = c(control_coxph(), control_step(num_points = 10, degree = 2)) ) step_data <- broom::tidy(step_matrix)  # Default plot. g_step(step_data)   # Add the reference 1 horizontal line. library(ggplot2) g_step(step_data) +   ggplot2::geom_hline(ggplot2::aes(yintercept = 1), linetype = 2)   # Use actual values instead of percentiles, different color for estimate and no CI, # use log scale for y axis. g_step(   step_data,   use_percentile = FALSE,   est = list(col = \"blue\", lty = 1),   ci_ribbon = NULL ) + scale_y_log10()   # Adding another curve based on additional column. step_data$extra <- exp(step_data$`Percentile Center`) g_step(step_data) +   ggplot2::geom_line(ggplot2::aes(y = extra), linetype = 2, color = \"green\")   # Response example. vars <- list(   response = \"status\",   arm = \"sex\",   biomarker = \"age\" )  step_matrix <- fit_rsp_step(   variables = vars,   data = lung,   control = c(     control_logistic(response_definition = \"I(response == 2)\"),     control_step()   ) ) step_data <- broom::tidy(step_matrix) g_step(step_data)"},{"path":"https://insightsengineering.github.io/tern/main/reference/g_waterfall.html","id":null,"dir":"Reference","previous_headings":"","what":"Horizontal waterfall plot — g_waterfall","title":"Horizontal waterfall plot — g_waterfall","text":"basic waterfall plot visualizes quantity height ordered value markup.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/g_waterfall.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Horizontal waterfall plot — g_waterfall","text":"","code":"g_waterfall(   height,   id,   col_var = NULL,   col = getOption(\"ggplot2.discrete.colour\"),   xlab = NULL,   ylab = NULL,   col_legend_title = NULL,   title = NULL )"},{"path":"https://insightsengineering.github.io/tern/main/reference/g_waterfall.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Horizontal waterfall plot — g_waterfall","text":"height (numeric) vector containing values plotted waterfall bars. id (character) vector containing identifiers use x-axis label waterfall bars. col_var (factor, character, NULL) categorical variable bar coloring. NULL default. col (character) color(s). xlab (string) x label. Default \"ID\". ylab (string) y label. Default \"Value\". col_legend_title (string) text displayed legend title. title (string) text displayed plot title.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/g_waterfall.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Horizontal waterfall plot — g_waterfall","text":"ggplot waterfall plot.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/g_waterfall.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Horizontal waterfall plot — g_waterfall","text":"","code":"library(dplyr)  g_waterfall(height = c(3, 5, -1), id = letters[1:3])   g_waterfall(   height = c(3, 5, -1),   id = letters[1:3],   col_var = letters[1:3] )   adsl_f <- tern_ex_adsl %>%   select(USUBJID, STUDYID, ARM, ARMCD, SEX)  adrs_f <- tern_ex_adrs %>%   filter(PARAMCD == \"OVRINV\") %>%   mutate(pchg = rnorm(n(), 10, 50))  adrs_f <- head(adrs_f, 30) adrs_f <- adrs_f[!duplicated(adrs_f$USUBJID), ] head(adrs_f) #> # A tibble: 5 × 30 #>   STUDYID COUNTRY SITEID SUBJID   AGE SEX   ARMCD ARM      ACTARMCD ACTARM RACE  #>   <chr>   <fct>   <chr>  <chr>  <dbl> <fct> <fct> <fct>    <fct>    <fct>  <fct> #> 1 AB12345 BRA     BRA-1  id-105  37.8 F     ARM A A: Drug… ARM A    A: Dr… ASIAN #> 2 AB12345 BRA     BRA-1  id-171  29.8 F     ARM B B: Plac… ARM B    B: Pl… ASIAN #> 3 AB12345 BRA     BRA-1  id-177  38.9 F     ARM B B: Plac… ARM B    B: Pl… ASIAN #> 4 AB12345 BRA     BRA-1  id-23   41.3 F     ARM A A: Drug… ARM A    A: Dr… AMER… #> 5 AB12345 BRA     BRA-1  id-59   26.7 F     ARM A A: Drug… ARM A    A: Dr… ASIAN #> # ℹ 19 more variables: TRTSDTM <dttm>, TRTEDTM <dttm>, EOSDY <dbl>, #> #   STRATA1 <fct>, STRATA2 <fct>, BMRKR1 <dbl>, BMRKR2 <fct>, REGION1 <fct>, #> #   SAFFL <fct>, USUBJID <chr>, AVISIT <fct>, PARAMCD <fct>, PARAM <fct>, #> #   AVALC <fct>, AVAL <int>, ADTM <date>, AVISITN <dbl>, DTHFL <fct>, #> #   pchg <dbl>  g_waterfall(   height = adrs_f$pchg,   id = adrs_f$USUBJID,   col_var = adrs_f$AVALC )   g_waterfall(   height = adrs_f$pchg,   id = paste(\"asdfdsfdsfsd\", adrs_f$USUBJID),   col_var = adrs_f$SEX )   g_waterfall(   height = adrs_f$pchg,   id = paste(\"asdfdsfdsfsd\", adrs_f$USUBJID),   xlab = \"ID\",   ylab = \"Percentage Change\",   title = \"Waterfall plot\" )"},{"path":"https://insightsengineering.github.io/tern/main/reference/get_covariates.html","id":null,"dir":"Reference","previous_headings":"","what":"Utility function to return a named list of covariate names — get_covariates","title":"Utility function to return a named list of covariate names — get_covariates","text":"Utility function return named list covariate names","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/get_covariates.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Utility function to return a named list of covariate names — get_covariates","text":"","code":"get_covariates(covariates)"},{"path":"https://insightsengineering.github.io/tern/main/reference/get_covariates.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Utility function to return a named list of covariate names — get_covariates","text":"covariates (character) vector can contain single variable names (\"X1\"), /interaction terms indicated \"X1 * X2\".","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/get_covariates.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Utility function to return a named list of covariate names — get_covariates","text":"named list character vector.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/get_smooths.html","id":null,"dir":"Reference","previous_headings":"","what":"Smooth function with optional grouping — get_smooths","title":"Smooth function with optional grouping — get_smooths","text":"produces loess smoothed estimates y Student confidence intervals.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/get_smooths.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Smooth function with optional grouping — get_smooths","text":"","code":"get_smooths(df, x, y, groups = NULL, level = 0.95)"},{"path":"https://insightsengineering.github.io/tern/main/reference/get_smooths.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Smooth function with optional grouping — get_smooths","text":"df (data.frame) data set containing analysis variables. x (string) x column name. y (string) y column name. groups (character NULL) vector optional grouping variables names. level (proportion) level confidence interval use (0.95 default).","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/get_smooths.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Smooth function with optional grouping — get_smooths","text":"data.frame original x, smoothed y, ylow, yhigh, optional groups variables formatted factor type.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/groups_list_to_df.html","id":null,"dir":"Reference","previous_headings":"","what":"Convert list of groups to a data frame — groups_list_to_df","title":"Convert list of groups to a data frame — groups_list_to_df","text":"converts list group levels data frame format expected rtables::add_combo_levels().","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/groups_list_to_df.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Convert list of groups to a data frame — groups_list_to_df","text":"","code":"groups_list_to_df(groups_list)"},{"path":"https://insightsengineering.github.io/tern/main/reference/groups_list_to_df.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Convert list of groups to a data frame — groups_list_to_df","text":"groups_list (named list character) specifies new group levels via names levels belong character vectors elements list.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/groups_list_to_df.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Convert list of groups to a data frame — groups_list_to_df","text":"tibble required format.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/groups_list_to_df.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Convert list of groups to a data frame — groups_list_to_df","text":"","code":"grade_groups <- list(   \"Any Grade (%)\" = c(\"1\", \"2\", \"3\", \"4\", \"5\"),   \"Grade 3-4 (%)\" = c(\"3\", \"4\"),   \"Grade 5 (%)\" = \"5\" ) groups_list_to_df(grade_groups) #> # A tibble: 3 × 4 #>   valname  label         levelcombo exargs     #>   <chr>    <chr>         <list>     <list>     #> 1 AnyGrade Any Grade (%) <chr [5]>  <list [0]> #> 2 Grade34  Grade 3-4 (%) <chr [2]>  <list [0]> #> 3 Grade5   Grade 5 (%)   <chr [1]>  <list [0]>"},{"path":"https://insightsengineering.github.io/tern/main/reference/h_adlb_abnormal_by_worst_grade.html","id":null,"dir":"Reference","previous_headings":"","what":"Helper function to prepare ADLB for count_abnormal_by_worst_grade() — h_adlb_abnormal_by_worst_grade","title":"Helper function to prepare ADLB for count_abnormal_by_worst_grade() — h_adlb_abnormal_by_worst_grade","text":"Helper function prepare ADLB data frame used input count_abnormal_by_worst_grade(). following pre-processing steps applied: adlb filtered variable avisit include post-baseline visits. adlb filtered variables worst_flag_low worst_flag_high worst grades (either direction) included. standard lab grade variable atoxgr, following two variables derived added adlb: grade direction variable (e.g. GRADE_DIR). variable takes value \"HIGH\" atoxgr > 0, \"LOW\" atoxgr < 0, \"ZERO\" otherwise. toxicity grade variable (e.g. GRADE_ANL) negative values atoxgr replaced absolute values. Unused factor levels dropped adlb via droplevels().","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/h_adlb_abnormal_by_worst_grade.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Helper function to prepare ADLB for count_abnormal_by_worst_grade() — h_adlb_abnormal_by_worst_grade","text":"","code":"h_adlb_abnormal_by_worst_grade(   adlb,   atoxgr = \"ATOXGR\",   avisit = \"AVISIT\",   worst_flag_low = \"WGRLOFL\",   worst_flag_high = \"WGRHIFL\" )"},{"path":"https://insightsengineering.github.io/tern/main/reference/h_adlb_abnormal_by_worst_grade.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Helper function to prepare ADLB for count_abnormal_by_worst_grade() — h_adlb_abnormal_by_worst_grade","text":"adlb (data.frame) ADLB data frame. atoxgr (string) name analysis toxicity grade variable. must factor variable. avisit (string) name analysis visit variable. worst_flag_low (string) name worst low lab grade flag variable. variable set \"Y\" indicating records worst low lab grades. worst_flag_high (string) name worst high lab grade flag variable. variable set \"Y\" indicating records worst high lab grades.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/h_adlb_abnormal_by_worst_grade.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Helper function to prepare ADLB for count_abnormal_by_worst_grade() — h_adlb_abnormal_by_worst_grade","text":"h_adlb_abnormal_by_worst_grade() returns adlb data frame two new variables: GRADE_DIR GRADE_ANL.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/main/reference/h_adlb_abnormal_by_worst_grade.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Helper function to prepare ADLB for count_abnormal_by_worst_grade() — h_adlb_abnormal_by_worst_grade","text":"","code":"h_adlb_abnormal_by_worst_grade(tern_ex_adlb) %>%   dplyr::select(ATOXGR, GRADE_DIR, GRADE_ANL) %>%   head(10) #> # A tibble: 10 × 3 #>    ATOXGR GRADE_DIR GRADE_ANL #>    <fct>  <fct>     <fct>     #>  1 -3     LOW       3         #>  2 0      ZERO      0         #>  3 0      ZERO      0         #>  4 2      HIGH      2         #>  5 0      ZERO      0         #>  6 0      ZERO      0         #>  7 -4     LOW       4         #>  8 1      HIGH      1         #>  9 -1     LOW       1         #> 10 0      ZERO      0"},{"path":"https://insightsengineering.github.io/tern/main/reference/h_adlb_worsen.html","id":null,"dir":"Reference","previous_headings":"","what":"Helper function to prepare ADLB with worst labs — h_adlb_worsen","title":"Helper function to prepare ADLB with worst labs — h_adlb_worsen","text":"Helper function prepare df generate patient count shift table.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/h_adlb_worsen.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Helper function to prepare ADLB with worst labs — h_adlb_worsen","text":"","code":"h_adlb_worsen(   adlb,   worst_flag_low = NULL,   worst_flag_high = NULL,   direction_var )"},{"path":"https://insightsengineering.github.io/tern/main/reference/h_adlb_worsen.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Helper function to prepare ADLB with worst labs — h_adlb_worsen","text":"adlb (data.frame) ADLB data frame. worst_flag_low (named vector) worst low post-baseline lab grade flag variable. See implemented following examples. worst_flag_high (named vector) worst high post-baseline lab grade flag variable. See implemented following examples. direction_var (string) name direction variable specifying direction shift table interest. lab records flagged L, H B included shift table. L: low direction H: high direction B: low high directions","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/h_adlb_worsen.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Helper function to prepare ADLB with worst labs — h_adlb_worsen","text":"h_adlb_worsen() returns adlb data.frame containing worst labs specified according worst_flag_low worst_flag_high direction specified according direction_var. instance, lab needed low direction , records flagged worst_flag_low selected. lab needed low high directions, worst low records selected low direction, worst high record selected high direction.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/main/reference/h_adlb_worsen.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Helper function to prepare ADLB with worst labs — h_adlb_worsen","text":"","code":"library(dplyr)  # The direction variable, GRADDR, is based on metadata adlb <- tern_ex_adlb %>%   mutate(     GRADDR = case_when(       PARAMCD == \"ALT\" ~ \"B\",       PARAMCD == \"CRP\" ~ \"L\",       PARAMCD == \"IGA\" ~ \"H\"     )   ) %>%   filter(SAFFL == \"Y\" & ONTRTFL == \"Y\" & GRADDR != \"\")  df <- h_adlb_worsen(   adlb,   worst_flag_low = c(\"WGRLOFL\" = \"Y\"),   worst_flag_high = c(\"WGRHIFL\" = \"Y\"),   direction_var = \"GRADDR\" )"},{"path":"https://insightsengineering.github.io/tern/main/reference/h_adsl_adlb_merge_using_worst_flag.html","id":null,"dir":"Reference","previous_headings":"","what":"Helper function for deriving analysis datasets for select laboratory tables — h_adsl_adlb_merge_using_worst_flag","title":"Helper function for deriving analysis datasets for select laboratory tables — h_adsl_adlb_merge_using_worst_flag","text":"Helper function merges ADSL ADLB datasets missing lab test records inserted output dataset. Remember na_level must match needed pre-processing done df_explicit_na() desired output.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/h_adsl_adlb_merge_using_worst_flag.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Helper function for deriving analysis datasets for select laboratory tables — h_adsl_adlb_merge_using_worst_flag","text":"","code":"h_adsl_adlb_merge_using_worst_flag(   adsl,   adlb,   worst_flag = c(WGRHIFL = \"Y\"),   by_visit = FALSE,   no_fillin_visits = c(\"SCREENING\", \"BASELINE\") )"},{"path":"https://insightsengineering.github.io/tern/main/reference/h_adsl_adlb_merge_using_worst_flag.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Helper function for deriving analysis datasets for select laboratory tables — h_adsl_adlb_merge_using_worst_flag","text":"adsl (data.frame) ADSL data frame. adlb (data.frame) ADLB data frame. worst_flag (named character) worst post-baseline lab flag variable. See implemented following examples. by_visit (flag) defaults FALSE generate worst grade per patient. worst grade per patient per visit specified worst_flag, by_visit TRUE generate worst grade patient per visit. no_fillin_visits (named character) visits considered post-baseline worst toxicity grade. Defaults c(\"SCREENING\", \"BASELINE\").","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/h_adsl_adlb_merge_using_worst_flag.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Helper function for deriving analysis datasets for select laboratory tables — h_adsl_adlb_merge_using_worst_flag","text":"df containing variables shared adlb adsl along variables PARAM, PARAMCD, ATOXGR, BTOXGR relevant analysis. Optionally, AVISIT AVISITN included by_visit = TRUE no_fillin_visits = c(\"SCREENING\", \"BASELINE\").","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/h_adsl_adlb_merge_using_worst_flag.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Helper function for deriving analysis datasets for select laboratory tables — h_adsl_adlb_merge_using_worst_flag","text":"result data missing records created following situations: Patients present adsl lab data adlb (baseline post-baseline). Patients post-baseline lab values. Patients without post-baseline values flagged worst.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/h_adsl_adlb_merge_using_worst_flag.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Helper function for deriving analysis datasets for select laboratory tables — h_adsl_adlb_merge_using_worst_flag","text":"","code":"# `h_adsl_adlb_merge_using_worst_flag` adlb_out <- h_adsl_adlb_merge_using_worst_flag(   tern_ex_adsl,   tern_ex_adlb,   worst_flag = c(\"WGRHIFL\" = \"Y\") )  # `h_adsl_adlb_merge_using_worst_flag` by visit example adlb_out_by_visit <- h_adsl_adlb_merge_using_worst_flag(   tern_ex_adsl,   tern_ex_adlb,   worst_flag = c(\"WGRLOVFL\" = \"Y\"),   by_visit = TRUE )"},{"path":[]},{"path":"https://insightsengineering.github.io/tern/main/reference/h_ancova.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Helper function to return results of a linear model — h_ancova","text":"","code":"h_ancova(.var, .df_row, variables, interaction_item = NULL)"},{"path":"https://insightsengineering.github.io/tern/main/reference/h_ancova.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Helper function to return results of a linear model — h_ancova","text":".var (string) single variable name passed rtables requested statistics function. .df_row (data.frame) data set includes variables called .var variables. variables (named list string) list additional analysis variables, expected elements: arm (string) group variable, covariate adjusted means multiple groups summarized. Specifically, first level arm variable taken reference group. covariates (character) vector can contain single variable names (\"X1\"), /interaction terms indicated \"X1 * X2\". interaction_item (string NULL) name variable interactions arm. interaction needed, default option NULL.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/h_ancova.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Helper function to return results of a linear model — h_ancova","text":"summary linear model.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/h_ancova.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Helper function to return results of a linear model — h_ancova","text":"","code":"h_ancova(   .var = \"Sepal.Length\",   .df_row = iris,   variables = list(arm = \"Species\", covariates = c(\"Petal.Length * Petal.Width\", \"Sepal.Width\")) ) #>  Species    emmean     SE  df lower.CL upper.CL #>  setosa       6.15 0.3370 143     5.49     6.82 #>  versicolor   5.72 0.0668 143     5.59     5.85 #>  virginica    5.41 0.1490 143     5.11     5.70 #>  #> Confidence level used: 0.95"},{"path":"https://insightsengineering.github.io/tern/main/reference/h_append_grade_groups.html","id":null,"dir":"Reference","previous_headings":"","what":"Helper function for s_count_occurrences_by_grade() — h_append_grade_groups","title":"Helper function for s_count_occurrences_by_grade() — h_append_grade_groups","text":"Helper function s_count_occurrences_by_grade() insert grade groupings list individual grade frequencies. order final result follows order grade_groups. elements -grade group (), .e. grade group equal refs moved end. Grade groups names must unique.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/h_append_grade_groups.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Helper function for s_count_occurrences_by_grade() — h_append_grade_groups","text":"","code":"h_append_grade_groups(   grade_groups,   refs,   remove_single = TRUE,   only_grade_groups = FALSE )"},{"path":"https://insightsengineering.github.io/tern/main/reference/h_append_grade_groups.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Helper function for s_count_occurrences_by_grade() — h_append_grade_groups","text":"grade_groups (named list character) list containing groupings grades. refs (named list numeric) named list name corresponds reference grade level entry represents count. remove_single (flag)TRUE include elements one-element grade groups output list; case grade groups names included output. only_grade_groups set TRUE argument ignored. only_grade_groups (flag) whether specified grade groups included, individual grade rows removed (TRUE), grades grade groups displayed (FALSE).","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/h_append_grade_groups.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Helper function for s_count_occurrences_by_grade() — h_append_grade_groups","text":"Formatted list grade groupings.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/h_append_grade_groups.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Helper function for s_count_occurrences_by_grade() — h_append_grade_groups","text":"","code":"h_append_grade_groups(   list(     \"Any Grade\" = as.character(1:5),     \"Grade 1-2\" = c(\"1\", \"2\"),     \"Grade 3-4\" = c(\"3\", \"4\")   ),   list(\"1\" = 10, \"2\" = 20, \"3\" = 30, \"4\" = 40, \"5\" = 50) ) #> $`Any Grade` #> [1] 150 #>  #> $`Grade 1-2` #> [1] 30 #>  #> $`1` #> [1] 10 #>  #> $`2` #> [1] 20 #>  #> $`Grade 3-4` #> [1] 70 #>  #> $`3` #> [1] 30 #>  #> $`4` #> [1] 40 #>  #> $`5` #> [1] 50 #>   h_append_grade_groups(   list(     \"Any Grade\" = as.character(5:1),     \"Grade A\" = \"5\",     \"Grade B\" = c(\"4\", \"3\")   ),   list(\"1\" = 10, \"2\" = 20, \"3\" = 30, \"4\" = 40, \"5\" = 50) ) #> $`Any Grade` #> [1] 150 #>  #> $`Grade A` #> [1] 50 #>  #> $`Grade B` #> [1] 70 #>  #> $`4` #> [1] 40 #>  #> $`3` #> [1] 30 #>  #> $`2` #> [1] 20 #>  #> $`1` #> [1] 10 #>   h_append_grade_groups(   list(     \"Any Grade\" = as.character(1:5),     \"Grade 1-2\" = c(\"1\", \"2\"),     \"Grade 3-4\" = c(\"3\", \"4\")   ),   list(\"1\" = 10, \"2\" = 5, \"3\" = 0) ) #> $`Any Grade` #> [1] 15 #>  #> $`Grade 1-2` #> [1] 15 #>  #> $`1` #> [1] 10 #>  #> $`2` #> [1] 5 #>  #> $`Grade 3-4` #> [1] 0 #>  #> $`3` #> [1] 0 #>"},{"path":"https://insightsengineering.github.io/tern/main/reference/h_col_indices.html","id":null,"dir":"Reference","previous_headings":"","what":"Obtain column indices — h_col_indices","title":"Obtain column indices — h_col_indices","text":"Helper function extract column indices VTableTree given vector column names.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/h_col_indices.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Obtain column indices — h_col_indices","text":"","code":"h_col_indices(table_tree, col_names)"},{"path":"https://insightsengineering.github.io/tern/main/reference/h_col_indices.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Obtain column indices — h_col_indices","text":"table_tree (VTableTree)rtables table object extract indices . col_names (character) vector column names.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/h_col_indices.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Obtain column indices — h_col_indices","text":"vector column indices.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/h_count_cumulative.html","id":null,"dir":"Reference","previous_headings":"","what":"Helper function for s_count_cumulative() — h_count_cumulative","title":"Helper function for s_count_cumulative() — h_count_cumulative","text":"Helper function calculate count fraction x values lower upper tail given threshold.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/h_count_cumulative.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Helper function for s_count_cumulative() — h_count_cumulative","text":"","code":"h_count_cumulative(   x,   threshold,   lower_tail = TRUE,   include_eq = TRUE,   na.rm = TRUE,   .N_col )"},{"path":"https://insightsengineering.github.io/tern/main/reference/h_count_cumulative.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Helper function for s_count_cumulative() — h_count_cumulative","text":"x (numeric) vector numbers want analyze. threshold (numeric(1)) cutoff value threshold count values x. lower_tail (flag) whether count lower tail, default TRUE. include_eq (flag) whether include value equal threshold count, default TRUE. na.rm (flag) whether NA values removed x prior analysis. .N_col (integer(1)) column-wise N (column count) full column analyzed typically passed rtables.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/h_count_cumulative.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Helper function for s_count_cumulative() — h_count_cumulative","text":"named vector items: count: count values less , less equal , greater , greater equal threshold user specification. fraction: fraction count.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/main/reference/h_count_cumulative.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Helper function for s_count_cumulative() — h_count_cumulative","text":"","code":"set.seed(1, kind = \"Mersenne-Twister\") x <- c(sample(1:10, 10), NA) .N_col <- length(x)  h_count_cumulative(x, 5, .N_col = .N_col) #>     count  fraction  #> 5.0000000 0.4545455  h_count_cumulative(x, 5, lower_tail = FALSE, include_eq = FALSE, na.rm = FALSE, .N_col = .N_col) #>     count  fraction  #> 6.0000000 0.5454545  h_count_cumulative(x, 0, lower_tail = FALSE, .N_col = .N_col) #>      count   fraction  #> 10.0000000  0.9090909  h_count_cumulative(x, 100, lower_tail = FALSE, .N_col = .N_col) #>    count fraction  #>        0        0"},{"path":"https://insightsengineering.github.io/tern/main/reference/h_cox_regression.html","id":null,"dir":"Reference","previous_headings":"","what":"Helper functions for Cox proportional hazards regression — h_cox_regression","title":"Helper functions for Cox proportional hazards regression — h_cox_regression","text":"Helper functions used fit_coxreg_univar() fit_coxreg_multivar().","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/h_cox_regression.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Helper functions for Cox proportional hazards regression — h_cox_regression","text":"","code":"h_coxreg_univar_formulas(variables, interaction = FALSE)  h_coxreg_multivar_formula(variables)  h_coxreg_univar_extract(effect, covar, data, mod, control = control_coxreg())  h_coxreg_multivar_extract(var, data, mod, control = control_coxreg())"},{"path":"https://insightsengineering.github.io/tern/main/reference/h_cox_regression.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Helper functions for Cox proportional hazards regression — h_cox_regression","text":"variables (named list string) list additional analysis variables. interaction (flag) TRUE, model includes interaction studied treatment candidate covariate. Note univariate models without treatment arm, multivariate models, interaction can used needs FALSE. effect (string) treatment variable. covar (string) name covariate model. data (data.frame) dataset containing variables summarize. mod (coxph) Cox regression model fitted survival::coxph(). control (list) list controls returned control_coxreg(). var (string) single variable name passed rtables requested statistics function.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/h_cox_regression.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Helper functions for Cox proportional hazards regression — h_cox_regression","text":"h_coxreg_univar_formulas() returns character vector coercible formulas (e.g stats::.formula()). h_coxreg_multivar_formula() returns string coercible formula (e.g stats::.formula()). h_coxreg_univar_extract() returns data.frame variables effect, term, term_label, level, n, hr, lcl, ucl, pval. h_coxreg_multivar_extract() returns data.frame variables pval, hr, lcl, ucl, level, n, term, term_label.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/h_cox_regression.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Helper functions for Cox proportional hazards regression — h_cox_regression","text":"h_coxreg_univar_formulas(): Helper Cox regression formula. Creates list formulas. used internally fit_coxreg_univar() comparison univariate Cox regression models. h_coxreg_multivar_formula(): Helper multivariate Cox regression formula. Creates formulas string. used internally fit_coxreg_multivar() comparison multivariate Cox regression models. Interactions included multivariate Cox regression model. h_coxreg_univar_extract(): Utility function help tabulate result univariate Cox regression model. h_coxreg_multivar_extract(): Tabulation multivariate Cox regressions. Utility function help tabulate result multivariate Cox regression model treatment/covariate variable.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/main/reference/h_cox_regression.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Helper functions for Cox proportional hazards regression — h_cox_regression","text":"","code":"# `h_coxreg_univar_formulas`  ## Simple formulas. h_coxreg_univar_formulas(   variables = list(     time = \"time\", event = \"status\", arm = \"armcd\", covariates = c(\"X\", \"y\")   ) ) #>                                        ref  #>     \"survival::Surv(time, status) ~ armcd\"  #>                                          X  #> \"survival::Surv(time, status) ~ armcd + X\"  #>                                          y  #> \"survival::Surv(time, status) ~ armcd + y\"   ## Addition of an optional strata. h_coxreg_univar_formulas(   variables = list(     time = \"time\", event = \"status\", arm = \"armcd\", covariates = c(\"X\", \"y\"),     strata = \"SITE\"   ) ) #>                                                       ref  #>     \"survival::Surv(time, status) ~ armcd + strata(SITE)\"  #>                                                         X  #> \"survival::Surv(time, status) ~ armcd + X + strata(SITE)\"  #>                                                         y  #> \"survival::Surv(time, status) ~ armcd + y + strata(SITE)\"   ## Inclusion of the interaction term. h_coxreg_univar_formulas(   variables = list(     time = \"time\", event = \"status\", arm = \"armcd\", covariates = c(\"X\", \"y\"),     strata = \"SITE\"   ),   interaction = TRUE ) #>                                                       ref  #>     \"survival::Surv(time, status) ~ armcd + strata(SITE)\"  #>                                                         X  #> \"survival::Surv(time, status) ~ armcd * X + strata(SITE)\"  #>                                                         y  #> \"survival::Surv(time, status) ~ armcd * y + strata(SITE)\"   ## Only covariates fitted in separate models. h_coxreg_univar_formulas(   variables = list(     time = \"time\", event = \"status\", covariates = c(\"X\", \"y\")   ) ) #>                                      X                                      y  #> \"survival::Surv(time, status) ~ 1 + X\" \"survival::Surv(time, status) ~ 1 + y\"   # `h_coxreg_multivar_formula`  h_coxreg_multivar_formula(   variables = list(     time = \"AVAL\", event = \"event\", arm = \"ARMCD\", covariates = c(\"RACE\", \"AGE\")   ) ) #> [1] \"survival::Surv(AVAL, event) ~ ARMCD + RACE + AGE\"  # Addition of an optional strata. h_coxreg_multivar_formula(   variables = list(     time = \"AVAL\", event = \"event\", arm = \"ARMCD\", covariates = c(\"RACE\", \"AGE\"),     strata = \"SITE\"   ) ) #> [1] \"survival::Surv(AVAL, event) ~ ARMCD + RACE + AGE + strata(SITE)\"  # Example without treatment arm. h_coxreg_multivar_formula(   variables = list(     time = \"AVAL\", event = \"event\", covariates = c(\"RACE\", \"AGE\"),     strata = \"SITE\"   ) ) #> [1] \"survival::Surv(AVAL, event) ~ 1 + RACE + AGE + strata(SITE)\"  library(survival)  dta_simple <- data.frame(   time = c(5, 5, 10, 10, 5, 5, 10, 10),   status = c(0, 0, 1, 0, 0, 1, 1, 1),   armcd = factor(LETTERS[c(1, 1, 1, 1, 2, 2, 2, 2)], levels = c(\"A\", \"B\")),   var1 = c(45, 55, 65, 75, 55, 65, 85, 75),   var2 = c(\"F\", \"M\", \"F\", \"M\", \"F\", \"M\", \"F\", \"U\") ) mod <- coxph(Surv(time, status) ~ armcd + var1, data = dta_simple) result <- h_coxreg_univar_extract(   effect = \"armcd\", covar = \"armcd\", mod = mod, data = dta_simple ) result #>       effect  term       term_label level n       hr       lcl      ucl #> 1 Treatment: armcd B vs control (A)     B 8 6.551448 0.4606904 93.16769 #>       pval #> 1 0.165209  mod <- coxph(Surv(time, status) ~ armcd + var1, data = dta_simple) result <- h_coxreg_multivar_extract(   var = \"var1\", mod = mod, data = dta_simple ) result #>        pval        hr      lcl      ucl level n term term_label #> 2 0.4456195 0.9423284 0.808931 1.097724  var1 8 var1       var1"},{"path":"https://insightsengineering.github.io/tern/main/reference/h_data_plot.html","id":null,"dir":"Reference","previous_headings":"","what":"Helper function to tidy survival fit data — h_data_plot","title":"Helper function to tidy survival fit data — h_data_plot","text":"Convert survival fit data data frame designed plotting within g_km. starts broom::tidy() result, : Post-processes strata column factor. Extends stratum additional first row time 0 probability 1 downstream plot lines start coordinates. Adds censor column. Filters rows max_time.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/h_data_plot.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Helper function to tidy survival fit data — h_data_plot","text":"","code":"h_data_plot(fit_km, armval = \"All\", max_time = NULL)"},{"path":"https://insightsengineering.github.io/tern/main/reference/h_data_plot.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Helper function to tidy survival fit data — h_data_plot","text":"fit_km (survfit) result survival::survfit(). armval (string) used strata name treatment arm variable one level. Default \"\". max_time (numeric(1)) maximum value show x-axis. data values less threshold value plotted (defaults NULL).","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/h_data_plot.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Helper function to tidy survival fit data — h_data_plot","text":"tibble columns time, n.risk, n.event, n.censor, estimate, std.error, conf.high, conf.low, strata, censor.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/h_data_plot.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Helper function to tidy survival fit data — h_data_plot","text":"","code":"library(dplyr) library(survival)  # Test with multiple arms tern_ex_adtte %>%   filter(PARAMCD == \"OS\") %>%   survfit(formula = Surv(AVAL, 1 - CNSR) ~ ARMCD, data = .) %>%   h_data_plot() #> # A tibble: 203 × 10 #>     time n.risk n.event n.censor estimate std.error conf.high conf.low strata #>    <dbl>  <dbl>   <dbl>    <dbl>    <dbl>     <dbl>     <dbl>    <dbl> <fct>  #>  1   0       70       0        0    1        0          1        1     ARM A  #>  2  10.4     69       1        0    0.986    0.0146     1        0.958 ARM A  #>  3  20.5     68       1        0    0.971    0.0208     1        0.932 ARM A  #>  4  21.5     67       1        0    0.957    0.0257     1        0.910 ARM A  #>  5  25.3     66       0        1    0.957    0.0257     1        0.910 ARM A  #>  6  48.1     65       1        0    0.942    0.0300     0.999    0.888 ARM A  #>  7  66.6     64       0        1    0.942    0.0300     0.999    0.888 ARM A  #>  8  73.9     63       0        1    0.942    0.0300     0.999    0.888 ARM A  #>  9  78.9     62       0        1    0.942    0.0300     0.999    0.888 ARM A  #> 10  90.3     61       1        0    0.926    0.0342     0.991    0.866 ARM A  #> # ℹ 193 more rows #> # ℹ 1 more variable: censor <dbl>  # Test with single arm tern_ex_adtte %>%   filter(PARAMCD == \"OS\", ARMCD == \"ARM B\") %>%   survfit(formula = Surv(AVAL, 1 - CNSR) ~ ARMCD, data = .) %>%   h_data_plot(armval = \"ARM B\") #> # A tibble: 74 × 10 #>      time n.risk n.event n.censor estimate std.error conf.high conf.low strata #>     <dbl>  <dbl>   <dbl>    <dbl>    <dbl>     <dbl>     <dbl>    <dbl> <chr>  #>  1   0        74       0        0    1        0          1        1     ARM B  #>  2   2.17     73       1        0    0.986    0.0138     1        0.960 ARM B  #>  3  16.9      72       1        0    0.973    0.0196     1        0.936 ARM B  #>  4  22.6      71       1        0    0.959    0.0242     1        0.914 ARM B  #>  5  26.3      70       1        0    0.945    0.0282     0.999    0.894 ARM B  #>  6  57.5      69       1        0    0.932    0.0317     0.991    0.875 ARM B  #>  7  80.0      68       1        0    0.918    0.0350     0.983    0.857 ARM B  #>  8  81.6      67       1        0    0.904    0.0381     0.974    0.839 ARM B  #>  9  88.6      66       1        0    0.890    0.0411     0.965    0.822 ARM B  #> 10 102.       65       1        0    0.877    0.0439     0.955    0.804 ARM B  #> # ℹ 64 more rows #> # ℹ 1 more variable: censor <dbl>"},{"path":"https://insightsengineering.github.io/tern/main/reference/h_decompose_gg.html","id":null,"dir":"Reference","previous_headings":"","what":"ggplot decomposition — h_decompose_gg","title":"ggplot decomposition — h_decompose_gg","text":"elements composing ggplot extracted organized list.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/h_decompose_gg.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"ggplot decomposition — h_decompose_gg","text":"","code":"h_decompose_gg(gg)"},{"path":"https://insightsengineering.github.io/tern/main/reference/h_decompose_gg.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"ggplot decomposition — h_decompose_gg","text":"gg (ggplot) graphic decompose.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/h_decompose_gg.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"ggplot decomposition — h_decompose_gg","text":"named list elements: panel: panel. yaxis: y-axis. xaxis: x-axis. xlab: x-axis label. ylab: y-axis label. guide: legend.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/h_decompose_gg.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"ggplot decomposition — h_decompose_gg","text":"","code":"# \\donttest{ library(dplyr) library(survival) library(grid)  fit_km <- tern_ex_adtte %>%   filter(PARAMCD == \"OS\") %>%   survfit(formula = Surv(AVAL, 1 - CNSR) ~ ARMCD, data = .) data_plot <- h_data_plot(fit_km = fit_km) xticks <- h_xticks(data = data_plot) gg <- h_ggkm(   data = data_plot,   yval = \"Survival\",   censor_show = TRUE,   xticks = xticks, xlab = \"Days\", ylab = \"Survival Probability\",   title = \"tt\",   footnotes = \"ff\" ) #> Warning: `h_ggkm()` was deprecated in tern 0.9.4. #> ℹ `g_km` now generates `ggplot` objects. This function is no longer used within #>   `tern`.  g_el <- h_decompose_gg(gg) #> Warning: `h_decompose_gg()` was deprecated in tern 0.9.4. #> ℹ `g_km` now generates `ggplot` objects. This function is no longer used within #>   `tern`. grid::grid.newpage() grid.rect(gp = grid::gpar(lty = 1, col = \"red\", fill = \"gray85\", lwd = 5)) grid::grid.draw(g_el$panel)   grid::grid.newpage() grid.rect(gp = grid::gpar(lty = 1, col = \"royalblue\", fill = \"gray85\", lwd = 5)) grid::grid.draw(with(g_el, cbind(ylab, yaxis)))  # }"},{"path":[]},{"path":"https://insightsengineering.github.io/tern/main/reference/h_format_row.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Helper function to format the optional g_lineplot table — h_format_row","text":"","code":"h_format_row(x, format, labels = NULL)"},{"path":"https://insightsengineering.github.io/tern/main/reference/h_format_row.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Helper function to format the optional g_lineplot table — h_format_row","text":"x (named list) list numerical values formatted optionally labeled. Elements x must numeric vectors. format (named character NULL) format patterns x. Names format must match names x. parameter passed directly rtables::format_rcell function format parameter. labels (named character NULL) optional labels x. Names labels must match names x. label specified element x, function tries use label names (order) attribute element (depending one exists NULL NA NaN). none attributes attached given element x, label automatically generated.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/h_format_row.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Helper function to format the optional g_lineplot table — h_format_row","text":"single row data.frame object.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/h_format_row.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Helper function to format the optional g_lineplot table — h_format_row","text":"","code":"mean_ci <- c(48, 51) x <- list(mean = 50, mean_ci = mean_ci) format <- c(mean = \"xx.x\", mean_ci = \"(xx.xx, xx.xx)\") labels <- c(mean = \"My Mean\") h_format_row(x, format, labels) #>   My Mean             V1 #> 1    50.0 (48.00, 51.00)  attr(mean_ci, \"label\") <- \"Mean 95% CI\" x <- list(mean = 50, mean_ci = mean_ci) h_format_row(x, format, labels) #>   My Mean    Mean 95% CI #> 1    50.0 (48.00, 51.00)"},{"path":"https://insightsengineering.github.io/tern/main/reference/h_g_ipp.html","id":null,"dir":"Reference","previous_headings":"","what":"Helper function to create simple line plot over time — h_g_ipp","title":"Helper function to create simple line plot over time — h_g_ipp","text":"Function generates simple line plot displaying parameter trends time.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/h_g_ipp.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Helper function to create simple line plot over time — h_g_ipp","text":"","code":"h_g_ipp(   df,   xvar,   yvar,   xlab,   ylab,   id_var,   title = \"Individual Patient Plots\",   subtitle = \"\",   caption = NULL,   add_baseline_hline = FALSE,   yvar_baseline = \"BASE\",   ggtheme = nestcolor::theme_nest(),   col = NULL )"},{"path":"https://insightsengineering.github.io/tern/main/reference/h_g_ipp.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Helper function to create simple line plot over time — h_g_ipp","text":"df (data.frame) data set containing analysis variables. xvar (string) time point variable plotted x-axis. yvar (string) continuous analysis variable plotted y-axis. xlab (string) plot label x-axis. ylab (string) plot label y-axis. id_var (string) variable used patient identifier. title (string) title plot. subtitle (string) subtitle plot. caption (string) optional caption plot. add_baseline_hline (flag) adds horizontal line baseline y-value plot TRUE. yvar_baseline (string) variable baseline values . Ignored add_baseline_hline FALSE. ggtheme (theme) optional graphical theme function provided ggplot2 control outlook plot. Use ggplot2::theme() tweak display. col (character) line colors.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/h_g_ipp.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Helper function to create simple line plot over time — h_g_ipp","text":"ggplot line plot.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/main/reference/h_g_ipp.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Helper function to create simple line plot over time — h_g_ipp","text":"","code":"library(dplyr)  # Select a small sample of data to plot. adlb <- tern_ex_adlb %>%   filter(PARAMCD == \"ALT\", !(AVISIT %in% c(\"SCREENING\", \"BASELINE\"))) %>%   slice(1:36)  p <- h_g_ipp(   df = adlb,   xvar = \"AVISIT\",   yvar = \"AVAL\",   xlab = \"Visit\",   id_var = \"USUBJID\",   ylab = \"SGOT/ALT (U/L)\",   add_baseline_hline = TRUE ) p"},{"path":"https://insightsengineering.github.io/tern/main/reference/h_ggkm.html","id":null,"dir":"Reference","previous_headings":"","what":"Helper function to create a KM plot — h_ggkm","title":"Helper function to create a KM plot — h_ggkm","text":"Draw Kaplan-Meier plot using ggplot2.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/h_ggkm.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Helper function to create a KM plot — h_ggkm","text":"","code":"h_ggkm(   data,   xticks = NULL,   yval = \"Survival\",   censor_show,   xlab,   ylab,   ylim = NULL,   title,   footnotes = NULL,   max_time = NULL,   lwd = 1,   lty = NULL,   pch = 3,   size = 2,   col = NULL,   ci_ribbon = FALSE,   ggtheme = nestcolor::theme_nest() )"},{"path":"https://insightsengineering.github.io/tern/main/reference/h_ggkm.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Helper function to create a KM plot — h_ggkm","text":"data (data.frame) survival data pre-processed h_data_plot. xticks (numeric NULL) numeric vector tick positions single number spacing ticks x-axis. NULL (default), labeling::extended() used determine optimal tick positions x-axis. yval (string) type plot, plotted y-axis. Options Survival (default) Failure probability. censor_show (flag) whether show censored observations. xlab (string) x-axis label. ylab (string) y-axis label. ylim (numeric(2)) vector containing lower upper limits y-axis, respectively. NULL (default), default scale range used. title (string) plot title. footnotes (string) plot footnotes. max_time (numeric(1)) maximum value show x-axis. data values less threshold value plotted (defaults NULL). lwd (numeric) line width. vector given, length equal number strata survival::survfit(). lty (numeric) line type. vector given, length equal number strata survival::survfit(). pch (string) name symbol character use point symbol indicate censored cases. size (numeric(1)) size censored point symbols. col (character) lines colors. Length vector equal number strata survival::survfit(). ci_ribbon (flag) whether confidence interval drawn around Kaplan-Meier curve. ggtheme (theme) graphical theme provided ggplot2 format Kaplan-Meier plot.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/h_ggkm.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Helper function to create a KM plot — h_ggkm","text":"ggplot object.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/h_ggkm.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Helper function to create a KM plot — h_ggkm","text":"","code":"# \\donttest{ library(dplyr) library(survival)  fit_km <- tern_ex_adtte %>%   filter(PARAMCD == \"OS\") %>%   survfit(formula = Surv(AVAL, 1 - CNSR) ~ ARMCD, data = .) data_plot <- h_data_plot(fit_km = fit_km) xticks <- h_xticks(data = data_plot) gg <- h_ggkm(   data = data_plot,   censor_show = TRUE,   xticks = xticks,   xlab = \"Days\",   yval = \"Survival\",   ylab = \"Survival Probability\",   title = \"Survival\" ) gg  # }"},{"path":"https://insightsengineering.github.io/tern/main/reference/h_glm_count.html","id":null,"dir":"Reference","previous_headings":"","what":"Helper functions for Poisson models — h_glm_count","title":"Helper functions for Poisson models — h_glm_count","text":"Helper functions returns results stats::glm() Poisson Quasi-Poisson distributions needed (see family parameter), MASS::glm.nb() Negative Binomial distributions. Link function GLM log.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/h_glm_count.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Helper functions for Poisson models — h_glm_count","text":"","code":"h_glm_count(.var, .df_row, variables, distribution, weights)  h_glm_poisson(.var, .df_row, variables, weights)  h_glm_quasipoisson(.var, .df_row, variables, weights)  h_glm_negbin(.var, .df_row, variables, weights)"},{"path":"https://insightsengineering.github.io/tern/main/reference/h_glm_count.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Helper functions for Poisson models — h_glm_count","text":".var (string) single variable name passed rtables requested statistics function. .df_row (data.frame) dataset includes variables called .var variables. variables (named list string) list additional analysis variables, expected elements: arm (string) group variable, covariate adjusted means multiple groups summarized. Specifically, first level arm variable taken reference group. covariates (character) vector can contain single variable names (\"X1\"), /interaction terms indicated \"X1 * X2\". offset (numeric) numeric vector scalar adding offset. distribution (character) character value specifying distribution used regression (Poisson, Quasi-Poisson, negative binomial). weights (character) character vector specifying weights used averaging predictions. Number weights must equal number levels included covariates. Weights option passed emmeans::emmeans().","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/h_glm_count.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Helper functions for Poisson models — h_glm_count","text":"h_glm_count() returns results selected model. h_glm_poisson() returns results Poisson model. h_glm_quasipoisson() returns results Quasi-Poisson model. h_glm_negbin() returns results negative binomial model.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/h_glm_count.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Helper functions for Poisson models — h_glm_count","text":"h_glm_count(): Helper function return results selected model (Poisson, Quasi-Poisson, negative binomial). h_glm_poisson(): Helper function return results Poisson model. h_glm_quasipoisson(): Helper function return results Quasi-Poisson model. h_glm_negbin(): Helper function return results negative binomial model.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/main/reference/h_grob_coxph.html","id":null,"dir":"Reference","previous_headings":"","what":"Helper function to create Cox-PH grobs — h_grob_coxph","title":"Helper function to create Cox-PH grobs — h_grob_coxph","text":"Grob rtable output h_tbl_coxph_pairwise()","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/h_grob_coxph.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Helper function to create Cox-PH grobs — h_grob_coxph","text":"","code":"h_grob_coxph(   ...,   x = 0,   y = 0,   width = grid::unit(0.4, \"npc\"),   ttheme = gridExtra::ttheme_default(padding = grid::unit(c(1, 0.5), \"lines\"), core =     list(bg_params = list(fill = c(\"grey95\", \"grey90\"), alpha = 0.5))) )"},{"path":"https://insightsengineering.github.io/tern/main/reference/h_grob_coxph.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Helper function to create Cox-PH grobs — h_grob_coxph","text":"... arguments pass h_tbl_coxph_pairwise(). x (proportion) value 0 1 specifying x-location. y (proportion) value 0 1 specifying y-location. width (grid::unit) width (unit) use printing grob. ttheme (list) see gridExtra::ttheme_default().","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/h_grob_coxph.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Helper function to create Cox-PH grobs — h_grob_coxph","text":"grob table containing statistics HR, XX% CI (XX taken control_coxph_pw), p-value (log-rank).","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/h_grob_coxph.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Helper function to create Cox-PH grobs — h_grob_coxph","text":"","code":"# \\donttest{ library(dplyr) library(survival) library(grid)  grid::grid.newpage() grid.rect(gp = grid::gpar(lty = 1, col = \"pink\", fill = \"gray85\", lwd = 1)) data <- tern_ex_adtte %>%   filter(PARAMCD == \"OS\") %>%   mutate(is_event = CNSR == 0) tbl_grob <- h_grob_coxph(   df = data,   variables = list(tte = \"AVAL\", is_event = \"is_event\", arm = \"ARMCD\"),   control_coxph_pw = control_coxph(conf_level = 0.9), x = 0.5, y = 0.5 ) #> Warning: `h_grob_coxph()` was deprecated in tern 0.9.4. #> ℹ `g_km` now generates `ggplot` objects. This function is no longer used within #>   `tern`. grid::grid.draw(tbl_grob)  # }"},{"path":"https://insightsengineering.github.io/tern/main/reference/h_grob_median_surv.html","id":null,"dir":"Reference","previous_headings":"","what":"Helper function to create survival estimation grobs — h_grob_median_surv","title":"Helper function to create survival estimation grobs — h_grob_median_surv","text":"survival fit transformed grob containing table groups rows characterized N, median 95% confidence interval.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/h_grob_median_surv.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Helper function to create survival estimation grobs — h_grob_median_surv","text":"","code":"h_grob_median_surv(   fit_km,   armval = \"All\",   x = 0.9,   y = 0.9,   width = grid::unit(0.3, \"npc\"),   ttheme = gridExtra::ttheme_default() )"},{"path":"https://insightsengineering.github.io/tern/main/reference/h_grob_median_surv.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Helper function to create survival estimation grobs — h_grob_median_surv","text":"fit_km (survfit) result survival::survfit(). armval (string) used strata name treatment arm variable one level. Default \"\". x (proportion) value 0 1 specifying x-location. y (proportion) value 0 1 specifying y-location. width (grid::unit) width (unit) use printing grob. ttheme (list) see gridExtra::ttheme_default().","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/h_grob_median_surv.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Helper function to create survival estimation grobs — h_grob_median_surv","text":"grob table containing statistics N, Median, XX% CI (XX taken fit_km).","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/h_grob_median_surv.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Helper function to create survival estimation grobs — h_grob_median_surv","text":"","code":"# \\donttest{ library(dplyr) library(survival) library(grid)  grid::grid.newpage() grid.rect(gp = grid::gpar(lty = 1, col = \"pink\", fill = \"gray85\", lwd = 1)) tern_ex_adtte %>%   filter(PARAMCD == \"OS\") %>%   survfit(formula = Surv(AVAL, 1 - CNSR) ~ ARMCD, data = .) %>%   h_grob_median_surv() %>%   grid::grid.draw() #> Warning: `h_grob_median_surv()` was deprecated in tern 0.9.4. #> ℹ `g_km` now generates `ggplot` objects. This function is no longer used within #>   `tern`.  # }"},{"path":"https://insightsengineering.github.io/tern/main/reference/h_grob_tbl_at_risk.html","id":null,"dir":"Reference","previous_headings":"","what":"Helper function to create patient-at-risk grobs — h_grob_tbl_at_risk","title":"Helper function to create patient-at-risk grobs — h_grob_tbl_at_risk","text":"Two graphical objects obtained, one corresponding row labeling second table numbers patients risk. title = TRUE, third object corresponding table title also obtained.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/h_grob_tbl_at_risk.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Helper function to create patient-at-risk grobs — h_grob_tbl_at_risk","text":"","code":"h_grob_tbl_at_risk(data, annot_tbl, xlim, title = TRUE)"},{"path":"https://insightsengineering.github.io/tern/main/reference/h_grob_tbl_at_risk.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Helper function to create patient-at-risk grobs — h_grob_tbl_at_risk","text":"data (data.frame) survival data pre-processed h_data_plot. annot_tbl (data.frame) annotation prepared survival::summary.survfit() includes number patients risk given time points. xlim (numeric(1)) maximum value x-axis (used ensure risk table aligns KM graph). title (flag) whether \"Patients Risk\" title added annot_at_risk table. effect annot_at_risk FALSE. Defaults TRUE.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/h_grob_tbl_at_risk.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Helper function to create patient-at-risk grobs — h_grob_tbl_at_risk","text":"named list two gTree objects title = FALSE: at_risk label, three gTree objects title = TRUE: at_risk, label, title.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/h_grob_tbl_at_risk.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Helper function to create patient-at-risk grobs — h_grob_tbl_at_risk","text":"","code":"# \\donttest{ library(dplyr) library(survival) library(grid)  fit_km <- tern_ex_adtte %>%   filter(PARAMCD == \"OS\") %>%   survfit(formula = Surv(AVAL, 1 - CNSR) ~ ARMCD, data = .)  data_plot <- h_data_plot(fit_km = fit_km)  xticks <- h_xticks(data = data_plot)  gg <- h_ggkm(   data = data_plot,   censor_show = TRUE,   xticks = xticks, xlab = \"Days\", ylab = \"Survival Probability\",   title = \"tt\", footnotes = \"ff\", yval = \"Survival\" )  # The annotation table reports the patient at risk for a given strata and # times (`xticks`). annot_tbl <- summary(fit_km, times = xticks) if (is.null(fit_km$strata)) {   annot_tbl <- with(annot_tbl, data.frame(n.risk = n.risk, time = time, strata = \"All\")) } else {   strata_lst <- strsplit(sub(\"=\", \"equals\", levels(annot_tbl$strata)), \"equals\")   levels(annot_tbl$strata) <- matrix(unlist(strata_lst), ncol = 2, byrow = TRUE)[, 2]   annot_tbl <- data.frame(     n.risk = annot_tbl$n.risk,     time = annot_tbl$time,     strata = annot_tbl$strata   ) }  # The annotation table is transformed into a grob. tbl <- h_grob_tbl_at_risk(data = data_plot, annot_tbl = annot_tbl, xlim = max(xticks)) #> Warning: `h_grob_tbl_at_risk()` was deprecated in tern 0.9.4. #> ℹ `g_km` now generates `ggplot` objects. This function is no longer used within #>   `tern`.  # For the representation, the layout is estimated for which the decomposition # of the graphic element is necessary. g_el <- h_decompose_gg(gg) lyt <- h_km_layout(data = data_plot, g_el = g_el, title = \"t\", footnotes = \"f\") #> Warning: `h_km_layout()` was deprecated in tern 0.9.4. #> ℹ `g_km` now generates `ggplot` objects. This function is no longer used within #>   `tern`.  grid::grid.newpage() pushViewport(viewport(layout = lyt, height = .95, width = .95)) grid.rect(gp = grid::gpar(lty = 1, col = \"purple\", fill = \"gray85\", lwd = 1)) pushViewport(viewport(layout.pos.row = 3:4, layout.pos.col = 2)) grid.rect(gp = grid::gpar(lty = 1, col = \"orange\", fill = \"gray85\", lwd = 1)) grid::grid.draw(tbl$at_risk) popViewport() pushViewport(viewport(layout.pos.row = 3:4, layout.pos.col = 1)) grid.rect(gp = grid::gpar(lty = 1, col = \"green3\", fill = \"gray85\", lwd = 1)) grid::grid.draw(tbl$label)  # }"},{"path":"https://insightsengineering.github.io/tern/main/reference/h_grob_y_annot.html","id":null,"dir":"Reference","previous_headings":"","what":"Helper function to create grid object with y-axis annotation — h_grob_y_annot","title":"Helper function to create grid object with y-axis annotation — h_grob_y_annot","text":"Build y-axis annotation decomposed ggplot.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/h_grob_y_annot.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Helper function to create grid object with y-axis annotation — h_grob_y_annot","text":"","code":"h_grob_y_annot(ylab, yaxis)"},{"path":"https://insightsengineering.github.io/tern/main/reference/h_grob_y_annot.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Helper function to create grid object with y-axis annotation — h_grob_y_annot","text":"ylab (gtable) y-lab graphical object derived ggplot. yaxis (gtable) y-axis graphical object derived ggplot.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/h_grob_y_annot.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Helper function to create grid object with y-axis annotation — h_grob_y_annot","text":"gTree object containing y-axis annotation ggplot.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/h_grob_y_annot.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Helper function to create grid object with y-axis annotation — h_grob_y_annot","text":"","code":"# \\donttest{ library(dplyr) library(survival) library(grid)  fit_km <- tern_ex_adtte %>%   filter(PARAMCD == \"OS\") %>%   survfit(formula = Surv(AVAL, 1 - CNSR) ~ ARMCD, data = .) data_plot <- h_data_plot(fit_km = fit_km) xticks <- h_xticks(data = data_plot) gg <- h_ggkm(   data = data_plot,   censor_show = TRUE,   xticks = xticks, xlab = \"Days\", ylab = \"Survival Probability\",   title = \"title\", footnotes = \"footnotes\", yval = \"Survival\" )  g_el <- h_decompose_gg(gg)  grid::grid.newpage() pvp <- grid::plotViewport(margins = c(5, 4, 2, 20)) pushViewport(pvp) grid::grid.draw(h_grob_y_annot(ylab = g_el$ylab, yaxis = g_el$yaxis)) #> Warning: `h_grob_y_annot()` was deprecated in tern 0.9.4. #> ℹ `g_km` now generates `ggplot` objects. This function is no longer used within #>   `tern`. grid.rect(gp = grid::gpar(lty = 1, col = \"gray35\", fill = NA))  # }"},{"path":[]},{"path":"https://insightsengineering.github.io/tern/main/reference/h_incidence_rate.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Helper functions for incidence rate — h_incidence_rate","text":"","code":"h_incidence_rate(person_years, n_events, control = control_incidence_rate())  h_incidence_rate_normal(person_years, n_events, alpha = 0.05)  h_incidence_rate_normal_log(person_years, n_events, alpha = 0.05)  h_incidence_rate_exact(person_years, n_events, alpha = 0.05)  h_incidence_rate_byar(person_years, n_events, alpha = 0.05)"},{"path":"https://insightsengineering.github.io/tern/main/reference/h_incidence_rate.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Helper functions for incidence rate — h_incidence_rate","text":"person_years (numeric(1)) total person-years risk. n_events (integer(1)) number events observed. control (list) parameters estimation details, specified using helper function control_incidence_rate(). Possible parameter options : conf_level: (proportion) confidence level estimated incidence rate. conf_type: (string)normal (default), normal_log, exact, byar confidence interval type. input_time_unit: (string)day, week, month, year (default) indicating time unit data input. num_pt_year: (numeric) time unit desired output (person-years). alpha (numeric(1)) two-sided alpha-level confidence interval.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/h_incidence_rate.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Helper functions for incidence rate — h_incidence_rate","text":"Estimated incidence rate, rate, associated confidence interval, rate_ci.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/h_incidence_rate.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Helper functions for incidence rate — h_incidence_rate","text":"h_incidence_rate(): Helper function estimate incidence rate associated confidence interval. h_incidence_rate_normal(): Helper function estimate incidence rate associated confidence interval based normal approximation incidence rate. Unit one person-year. h_incidence_rate_normal_log(): Helper function estimate incidence rate associated confidence interval based normal approximation logarithm incidence rate. Unit one person-year. h_incidence_rate_exact(): Helper function estimate incidence rate associated exact confidence interval. Unit one person-year. h_incidence_rate_byar(): Helper function estimate incidence rate associated Byar's confidence interval. Unit one person-year.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/main/reference/h_incidence_rate.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Helper functions for incidence rate — h_incidence_rate","text":"","code":"h_incidence_rate_normal(200, 2) #> $rate #> [1] 0.01 #>  #> $rate_ci #> [1] -0.003859038  0.023859038 #>   h_incidence_rate_normal_log(200, 2) #> $rate #> [1] 0.01 #>  #> $rate_ci #> [1] 0.002500977 0.039984382 #>   h_incidence_rate_exact(200, 2) #> $rate #> [1] 0.01 #>  #> $rate_ci #> [1] 0.001211046 0.036123438 #>   h_incidence_rate_byar(200, 2) #> $rate #> [1] 0.01 #>  #> $rate_ci #> [1] 0.001994207 0.032054171 #>"},{"path":"https://insightsengineering.github.io/tern/main/reference/h_km_layout.html","id":null,"dir":"Reference","previous_headings":"","what":"Helper function to prepare a KM layout — h_km_layout","title":"Helper function to prepare a KM layout — h_km_layout","text":"Prepares (5 rows) x (2 cols) layout Kaplan-Meier curve.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/h_km_layout.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Helper function to prepare a KM layout — h_km_layout","text":"","code":"h_km_layout(   data,   g_el,   title,   footnotes,   annot_at_risk = TRUE,   annot_at_risk_title = TRUE )"},{"path":"https://insightsengineering.github.io/tern/main/reference/h_km_layout.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Helper function to prepare a KM layout — h_km_layout","text":"data (data.frame) survival data pre-processed h_data_plot. g_el (list gtable) list obtained h_decompose_gg(). title (string) plot title. footnotes (string) plot footnotes. annot_at_risk (flag) compute add annotation table reporting number patient risk matching main grid Kaplan-Meier curve. annot_at_risk_title (flag) whether \"Patients Risk\" title added annot_at_risk table. effect annot_at_risk FALSE. Defaults TRUE.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/h_km_layout.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Helper function to prepare a KM layout — h_km_layout","text":"grid layout.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/h_km_layout.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Helper function to prepare a KM layout — h_km_layout","text":"layout corresponds grid two columns five rows unequal dimensions. dimension fixed, curve flexible accommodate remaining free space. left column gets annotation ggplot (y-axis) names strata patient risk tabulation. main constraint width columns must allow writing strata name. right column receive ggplot, legend, x-axis patient risk table.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/h_km_layout.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Helper function to prepare a KM layout — h_km_layout","text":"","code":"# \\donttest{ library(dplyr) library(survival) library(grid)  fit_km <- tern_ex_adtte %>%   filter(PARAMCD == \"OS\") %>%   survfit(formula = Surv(AVAL, 1 - CNSR) ~ ARMCD, data = .) data_plot <- h_data_plot(fit_km = fit_km) xticks <- h_xticks(data = data_plot) gg <- h_ggkm(   data = data_plot,   censor_show = TRUE,   xticks = xticks, xlab = \"Days\", ylab = \"Survival Probability\",   title = \"tt\", footnotes = \"ff\", yval = \"Survival\" ) g_el <- h_decompose_gg(gg) lyt <- h_km_layout(data = data_plot, g_el = g_el, title = \"t\", footnotes = \"f\") grid.show.layout(lyt)  # }"},{"path":"https://insightsengineering.github.io/tern/main/reference/h_logistic_regression.html","id":null,"dir":"Reference","previous_headings":"","what":"Helper functions for multivariate logistic regression — h_logistic_regression","title":"Helper functions for multivariate logistic regression — h_logistic_regression","text":"Helper functions used calculations logistic regression.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/h_logistic_regression.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Helper functions for multivariate logistic regression — h_logistic_regression","text":"","code":"h_get_interaction_vars(fit_glm)  h_interaction_coef_name(   interaction_vars,   first_var_with_level,   second_var_with_level )  h_or_cat_interaction(   odds_ratio_var,   interaction_var,   fit_glm,   conf_level = 0.95 )  h_or_cont_interaction(   odds_ratio_var,   interaction_var,   fit_glm,   at = NULL,   conf_level = 0.95 )  h_or_interaction(   odds_ratio_var,   interaction_var,   fit_glm,   at = NULL,   conf_level = 0.95 )  h_simple_term_labels(terms, table)  h_interaction_term_labels(terms1, terms2, table, any = FALSE)  h_glm_simple_term_extract(x, fit_glm)  h_glm_interaction_extract(x, fit_glm)  h_glm_inter_term_extract(odds_ratio_var, interaction_var, fit_glm, ...)  h_logistic_simple_terms(x, fit_glm, conf_level = 0.95)  h_logistic_inter_terms(x, fit_glm, conf_level = 0.95, at = NULL)"},{"path":"https://insightsengineering.github.io/tern/main/reference/h_logistic_regression.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Helper functions for multivariate logistic regression — h_logistic_regression","text":"fit_glm (glm) logistic regression model fitted stats::glm() \"binomial\" family. Limited functionality also available conditional logistic regression models fitted survival::clogit(), currently used extract_rsp_biomarkers(). interaction_vars (character(2)) interaction variable names. first_var_with_level (character(2)) first variable name interaction level. second_var_with_level (character(2)) second variable name interaction level. odds_ratio_var (string) odds ratio variable. interaction_var (string) interaction variable. conf_level (proportion) confidence level interval. (numeric NULL) optional values interaction variable. Otherwise median used. terms (character) simple terms. table (table) table containing numbers terms. terms1 (character) terms first dimension (rows). terms2 (character) terms second dimension (rows). (flag) whether term1 term2 can fulfilled count number patients. case can scalar (strings). x (character) variable interaction term fit_glm (depending helper function used). ... additional arguments lower level functions.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/h_logistic_regression.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Helper functions for multivariate logistic regression — h_logistic_regression","text":"Vector names interaction variables. Name coefficient. Odds ratio. Odds ratio. Odds ratio. Term labels containing numbers patients. Term labels containing numbers patients. Tabulated main effect results logistic regression model. Tabulated interaction term results logistic regression model. data.frame tabulated interaction term results logistic regression model. Tabulated statistics given variable(s) logistic regression model. Tabulated statistics given variable(s) logistic regression model.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/h_logistic_regression.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Helper functions for multivariate logistic regression — h_logistic_regression","text":"h_get_interaction_vars(): Helper function extract interaction variable names fitted model assuming one interaction term. h_interaction_coef_name(): Helper function get right coefficient name interaction variable names given levels. main value order first second variable checked interaction_vars input. h_or_cat_interaction(): Helper function calculate odds ratio estimates case odds ratio interaction variable categorical. h_or_cont_interaction(): Helper function calculate odds ratio estimates case either odds ratio interaction variable continuous. h_or_interaction(): Helper function calculate odds ratio estimates case interaction. wrapper h_or_cont_interaction() h_or_cat_interaction(). h_simple_term_labels(): Helper function construct term labels simple terms table numbers patients. h_interaction_term_labels(): Helper function construct term labels interaction terms table numbers patients. h_glm_simple_term_extract(): Helper function tabulate main effect results (conditional) logistic regression model. h_glm_interaction_extract(): Helper function tabulate interaction term results logistic regression model. h_glm_inter_term_extract(): Helper function tabulate interaction results logistic regression model. basically wrapper h_or_interaction() h_glm_simple_term_extract() puts results right data frame format. h_logistic_simple_terms(): Helper function tabulate results including odds ratios confidence intervals simple terms. h_logistic_inter_terms(): Helper function tabulate results including odds ratios confidence intervals interaction terms.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/h_logistic_regression.html","id":"note","dir":"Reference","previous_headings":"","what":"Note","title":"Helper functions for multivariate logistic regression — h_logistic_regression","text":"provide function case variables continuous arise table, treatment arm variable always involved categorical.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/h_logistic_regression.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Helper functions for multivariate logistic regression — h_logistic_regression","text":"","code":"library(dplyr) library(broom)  adrs_f <- tern_ex_adrs %>%   filter(PARAMCD == \"BESRSPI\") %>%   filter(RACE %in% c(\"ASIAN\", \"WHITE\", \"BLACK OR AFRICAN AMERICAN\")) %>%   mutate(     Response = case_when(AVALC %in% c(\"PR\", \"CR\") ~ 1, TRUE ~ 0),     RACE = factor(RACE),     SEX = factor(SEX)   ) formatters::var_labels(adrs_f) <- c(formatters::var_labels(tern_ex_adrs), Response = \"Response\") mod1 <- fit_logistic(   data = adrs_f,   variables = list(     response = \"Response\",     arm = \"ARMCD\",     covariates = c(\"AGE\", \"RACE\")   ) ) #> Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred mod2 <- fit_logistic(   data = adrs_f,   variables = list(     response = \"Response\",     arm = \"ARMCD\",     covariates = c(\"AGE\", \"RACE\"),     interaction = \"AGE\"   ) ) #> Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred  h_glm_simple_term_extract(\"AGE\", mod1) #>   variable variable_label term term_label interaction interaction_label #> 1      AGE            Age  AGE        Age                               #>   reference reference_label  estimate  std_error df     pvalue #> 1                           0.1698216 0.09524116  1 0.07457501 #>   is_variable_summary is_term_summary #> 1               FALSE            TRUE h_glm_simple_term_extract(\"ARMCD\", mod1) #>   variable   variable_label  term              term_label interaction #> 1    ARMCD Planned Arm Code ARM A Reference ARM A, n = 64             #> 2    ARMCD Planned Arm Code ARM B           ARM B, n = 68             #> 3    ARMCD Planned Arm Code ARM C           ARM C, n = 52             #>   interaction_label reference reference_label  estimate std_error df    pvalue #> 1                                                                  2 0.3004308 #> 2                                             -1.774769  1.144405  1 0.1209443 #> 3                                               17.1922  3626.588  1 0.9962176 #>   is_variable_summary is_term_summary #> 1                TRUE           FALSE #> 2               FALSE            TRUE #> 3               FALSE            TRUE  h_glm_interaction_extract(\"ARMCD:AGE\", mod2) #>    variable                        variable_label  term              term_label #> 1 ARMCD:AGE Interaction of Planned Arm Code * Age ARM A Reference ARM A, n = 64 #> 2 ARMCD:AGE Interaction of Planned Arm Code * Age ARM B           ARM B, n = 68 #> 3 ARMCD:AGE Interaction of Planned Arm Code * Age ARM C           ARM C, n = 52 #>   interaction interaction_label reference reference_label   estimate std_error #> 1                                                                              #> 2                                                          0.3081205 0.2062392 #> 3                                                         0.02948826  548.5923 #>   df    pvalue is_variable_summary is_term_summary #> 1  2 0.3275837                TRUE           FALSE #> 2  1 0.1351767               FALSE            TRUE #> 3  1 0.9999571               FALSE            TRUE  h_glm_inter_term_extract(\"AGE\", \"ARMCD\", mod2) #>   variable variable_label term term_label interaction interaction_label #> 1      AGE            Age  AGE        Age                               #> 2      AGE            Age  AGE        Age       ARMCD  Planned Arm Code #> 3      AGE            Age  AGE        Age       ARMCD  Planned Arm Code #> 4      AGE            Age  AGE        Age       ARMCD  Planned Arm Code #>   reference reference_label    estimate std_error odds_ratio       lcl      ucl #> 1                           -0.03873898 0.1514322         NA        NA       NA #> 2     ARM A           ARM A          NA        NA  0.9620018 0.7149514 1.294420 #> 3     ARM B           ARM B          NA        NA  1.3091545 1.0021802 1.710157 #> 4     ARM C           ARM C          NA        NA  0.9907919 0.0000000      Inf #>   df   pvalue is_variable_summary is_term_summary is_reference_summary #> 1  1 0.798092               FALSE            TRUE                FALSE #> 2 NA       NA               FALSE           FALSE                 TRUE #> 3 NA       NA               FALSE           FALSE                 TRUE #> 4 NA       NA               FALSE           FALSE                 TRUE  h_logistic_simple_terms(\"AGE\", mod1) #>   variable variable_label term term_label interaction interaction_label #> 1      AGE            Age  AGE        Age                               #>   reference reference_label  estimate  std_error df     pvalue #> 1                           0.1698216 0.09524116  1 0.07457501 #>   is_variable_summary is_term_summary odds_ratio       lcl      ucl #> 1               FALSE            TRUE   1.185093 0.9832935 1.428308 #>                     ci #> 1 0.9832935, 1.4283084  h_logistic_inter_terms(c(\"RACE\", \"AGE\", \"ARMCD\", \"AGE:ARMCD\"), mod2) #>        variable                        variable_label                      term #> 1          RACE                                  Race                     ASIAN #> 2          RACE                                  Race BLACK OR AFRICAN AMERICAN #> 3          RACE                                  Race                     WHITE #> 13        ARMCD                      Planned Arm Code                     ARM A #> 23        ARMCD                      Planned Arm Code                     ARM B #> ARM B     ARMCD                      Planned Arm Code                     ARM B #> 33        ARMCD                      Planned Arm Code                     ARM C #> ARM C     ARMCD                      Planned Arm Code                     ARM C #> 11          AGE                                   Age                       AGE #> 21          AGE                                   Age                       AGE #> 31          AGE                                   Age                       AGE #> 4           AGE                                   Age                       AGE #> 12    AGE:ARMCD Interaction of Planned Arm Code * Age                     ARM A #> 22    AGE:ARMCD Interaction of Planned Arm Code * Age                     ARM B #> 32    AGE:ARMCD Interaction of Planned Arm Code * Age                     ARM C #>                              term_label interaction interaction_label reference #> 1              Reference ASIAN, n = 110                                         #> 2     BLACK OR AFRICAN AMERICAN, n = 40                                         #> 3                         WHITE, n = 34                                         #> 13              Reference ARM A, n = 64                                         #> 23                        ARM B, n = 68                                         #> ARM B                     ARM B, n = 68         AGE               Age        35 #> 33                        ARM C, n = 52                                         #> ARM C                     ARM C, n = 52         AGE               Age        35 #> 11                                  Age                                         #> 21                                  Age       ARMCD  Planned Arm Code     ARM A #> 31                                  Age       ARMCD  Planned Arm Code     ARM B #> 4                                   Age       ARMCD  Planned Arm Code     ARM C #> 12              Reference ARM A, n = 64                                         #> 22                        ARM B, n = 68                                         #> 32                        ARM C, n = 52                                         #>       reference_label    estimate std_error df     pvalue odds_ratio        lcl #> 1                                            2  0.9361139                       #> 2                        18.15018  3944.701  1  0.9963288   76299564          0 #> 3                      -0.3727152  1.025808  1  0.7163522  0.6888614 0.09224926 #> 13                                           2   0.253914         NA         NA #> 23                      -11.52715   6.96188  1 0.09777185         NA         NA #> ARM B              35          NA        NA NA         NA  0.4757148 0.03361147 #> 33                       16.33327  20278.39  1  0.9993573         NA         NA #> ARM C              35          NA        NA NA         NA   34808099          0 #> 11                    -0.03873898 0.1514322  1   0.798092         NA         NA #> 21              ARM A          NA        NA NA         NA  0.9620018  0.7149514 #> 31              ARM B          NA        NA NA         NA   1.309155    1.00218 #> 4               ARM C          NA        NA NA         NA  0.9907919          0 #> 12                                          NA         NA         NA         NA #> 22                      0.3081205 0.2062392  1  0.1351767         NA         NA #> 32                     0.02948826  548.5923  1  0.9999571         NA         NA #>            ucl is_variable_summary is_term_summary is_reference_summary #> 1                             TRUE           FALSE                FALSE #> 2          Inf               FALSE            TRUE                FALSE #> 3     5.143998               FALSE            TRUE                FALSE #> 13          NA                TRUE           FALSE                FALSE #> 23          NA               FALSE            TRUE                FALSE #> ARM B 6.732956               FALSE           FALSE                 TRUE #> 33          NA               FALSE            TRUE                FALSE #> ARM C      Inf               FALSE           FALSE                 TRUE #> 11          NA               FALSE            TRUE                FALSE #> 21     1.29442               FALSE           FALSE                 TRUE #> 31    1.710157               FALSE           FALSE                 TRUE #> 4          Inf               FALSE           FALSE                 TRUE #> 12          NA                TRUE           FALSE                FALSE #> 22          NA               FALSE            TRUE                FALSE #> 32          NA               FALSE            TRUE                FALSE #>                           ci #> 1                            #> 2                     0, Inf #> 3     0.09224926, 5.14399810 #> 13                    NA, NA #> 23                    NA, NA #> ARM B 0.03361147, 6.73295611 #> 33                    NA, NA #> ARM C                 0, Inf #> 11                    NA, NA #> 21      0.7149514, 1.2944200 #> 31        1.002180, 1.710157 #> 4                     0, Inf #> 12                    NA, NA #> 22                    NA, NA #> 32                    NA, NA"},{"path":"https://insightsengineering.github.io/tern/main/reference/h_map_for_count_abnormal.html","id":null,"dir":"Reference","previous_headings":"","what":"Helper function to create a map data frame for trim_levels_to_map() — h_map_for_count_abnormal","title":"Helper function to create a map data frame for trim_levels_to_map() — h_map_for_count_abnormal","text":"Helper function create map data frame input dataset, can used argument trim_levels_to_map split function. Based different method, map constructed differently.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/h_map_for_count_abnormal.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Helper function to create a map data frame for trim_levels_to_map() — h_map_for_count_abnormal","text":"","code":"h_map_for_count_abnormal(   df,   variables = list(anl = \"ANRIND\", split_rows = c(\"PARAM\"), range_low = \"ANRLO\",     range_high = \"ANRHI\"),   abnormal = list(low = c(\"LOW\", \"LOW LOW\"), high = c(\"HIGH\", \"HIGH HIGH\")),   method = c(\"default\", \"range\"),   na_str = \"<Missing>\" )"},{"path":"https://insightsengineering.github.io/tern/main/reference/h_map_for_count_abnormal.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Helper function to create a map data frame for trim_levels_to_map() — h_map_for_count_abnormal","text":"df (data.frame) data set containing analysis variables. variables (named list string) list additional analysis variables. abnormal (named list) identifying abnormal range level(s) df. Based levels abnormality input dataset, can something like list(Low = \"LOW LOW\", High = \"HIGH HIGH\") abnormal = list(Low = \"LOW\", High = \"HIGH\")) method (string) indicates returned map constructed. Can \"default\" \"range\". na_str (string) string used replace NA empty values output.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/h_map_for_count_abnormal.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Helper function to create a map data frame for trim_levels_to_map() — h_map_for_count_abnormal","text":"map data.frame.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/h_map_for_count_abnormal.html","id":"note","dir":"Reference","previous_headings":"","what":"Note","title":"Helper function to create a map data frame for trim_levels_to_map() — h_map_for_count_abnormal","text":"method \"default\", returned map abnormal directions observed df, records normal values excluded avoid error creating layout. method \"range\", returned map based rule least one observation low range > 0 low direction least one observation high range missing high direction.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/h_map_for_count_abnormal.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Helper function to create a map data frame for trim_levels_to_map() — h_map_for_count_abnormal","text":"","code":"adlb <- df_explicit_na(tern_ex_adlb)  h_map_for_count_abnormal(   df = adlb,   variables = list(anl = \"ANRIND\", split_rows = c(\"LBCAT\", \"PARAM\")),   abnormal = list(low = c(\"LOW\"), high = c(\"HIGH\")),   method = \"default\",   na_str = \"<Missing>\" ) #>        LBCAT                                PARAM ANRIND #> 1  CHEMISTRY Alanine Aminotransferase Measurement    LOW #> 4  CHEMISTRY Alanine Aminotransferase Measurement   HIGH #> 7  CHEMISTRY Alanine Aminotransferase Measurement NORMAL #> 2  CHEMISTRY       C-Reactive Protein Measurement    LOW #> 3  CHEMISTRY       C-Reactive Protein Measurement   HIGH #> 8  CHEMISTRY       C-Reactive Protein Measurement NORMAL #> 5 IMMUNOLOGY         Immunoglobulin A Measurement    LOW #> 6 IMMUNOLOGY         Immunoglobulin A Measurement   HIGH #> 9 IMMUNOLOGY         Immunoglobulin A Measurement NORMAL  df <- data.frame(   USUBJID = c(rep(\"1\", 4), rep(\"2\", 4), rep(\"3\", 4)),   AVISIT = c(     rep(\"WEEK 1\", 2),     rep(\"WEEK 2\", 2),     rep(\"WEEK 1\", 2),     rep(\"WEEK 2\", 2),     rep(\"WEEK 1\", 2),     rep(\"WEEK 2\", 2)   ),   PARAM = rep(c(\"ALT\", \"CPR\"), 6),   ANRIND = c(     \"NORMAL\", \"NORMAL\", \"LOW\",     \"HIGH\", \"LOW\", \"LOW\", \"HIGH\", \"HIGH\", rep(\"NORMAL\", 4)   ),   ANRLO = rep(5, 12),   ANRHI = rep(20, 12) ) df$ANRIND <- factor(df$ANRIND, levels = c(\"LOW\", \"HIGH\", \"NORMAL\")) h_map_for_count_abnormal(   df = df,   variables = list(     anl = \"ANRIND\",     split_rows = c(\"PARAM\"),     range_low = \"ANRLO\",     range_high = \"ANRHI\"   ),   abnormal = list(low = c(\"LOW\"), high = c(\"HIGH\")),   method = \"range\",   na_str = \"<Missing>\" ) #>   PARAM ANRIND #> 1   ALT    LOW #> 3   ALT   HIGH #> 5   ALT NORMAL #> 2   CPR    LOW #> 4   CPR   HIGH #> 6   CPR NORMAL"},{"path":"https://insightsengineering.github.io/tern/main/reference/h_odds_ratio.html","id":null,"dir":"Reference","previous_headings":"","what":"Helper functions for odds ratio estimation — h_odds_ratio","title":"Helper functions for odds ratio estimation — h_odds_ratio","text":"Functions calculate odds ratios estimate_odds_ratio().","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/h_odds_ratio.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Helper functions for odds ratio estimation — h_odds_ratio","text":"","code":"or_glm(data, conf_level)  or_clogit(data, conf_level, method = \"exact\")"},{"path":"https://insightsengineering.github.io/tern/main/reference/h_odds_ratio.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Helper functions for odds ratio estimation — h_odds_ratio","text":"data (data.frame) data frame containing least variables rsp grp, optionally strata or_clogit(). conf_level (proportion) confidence level interval. method (string) whether use correct (\"exact\") calculation conditional likelihood one approximations. See survival::clogit() details.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/h_odds_ratio.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Helper functions for odds ratio estimation — h_odds_ratio","text":"named list elements or_ci n_tot.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/h_odds_ratio.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Helper functions for odds ratio estimation — h_odds_ratio","text":"or_glm(): Estimates odds ratio based stats::glm(). Note must exactly 2 groups data specified grp variable. or_clogit(): Estimates odds ratio based survival::clogit(). done whole data set including groups, since results pairwise comparisons groups.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/main/reference/h_odds_ratio.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Helper functions for odds ratio estimation — h_odds_ratio","text":"","code":"# Data with 2 groups. data <- data.frame(   rsp = as.logical(c(1, 1, 0, 1, 0, 0, 1, 1)),   grp = letters[c(1, 1, 1, 2, 2, 2, 1, 2)],   strata = letters[c(1, 2, 1, 2, 2, 2, 1, 2)],   stringsAsFactors = TRUE )  # Odds ratio based on glm. or_glm(data, conf_level = 0.95) #> $or_ci #>        est        lcl        ucl  #> 0.33333333 0.01669735 6.65441589  #>  #> $n_tot #> n_tot  #>     8  #>   # Data with 3 groups. data <- data.frame(   rsp = as.logical(c(1, 1, 0, 1, 0, 0, 1, 1, 0, 0, 1, 1, 0, 1, 0, 0, 1, 1, 0, 0)),   grp = letters[c(1, 1, 1, 2, 2, 2, 3, 3, 3, 3, 1, 1, 1, 2, 2, 2, 3, 3, 3, 3)],   strata = LETTERS[c(1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2)],   stringsAsFactors = TRUE )  # Odds ratio based on stratified estimation by conditional logistic regression. or_clogit(data, conf_level = 0.95) #> $or_ci #> $or_ci$b #>        est        lcl        ucl  #> 0.28814553 0.02981009 2.78522598  #>  #> $or_ci$c #>       est       lcl       ucl  #> 0.5367919 0.0673365 4.2791881  #>  #>  #> $n_tot #> n_tot  #>    20  #>"},{"path":[]},{"path":"https://insightsengineering.github.io/tern/main/reference/h_pkparam_sort.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Sort pharmacokinetic data by PARAM variable — h_pkparam_sort","text":"","code":"h_pkparam_sort(pk_data, key_var = \"PARAMCD\")"},{"path":"https://insightsengineering.github.io/tern/main/reference/h_pkparam_sort.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Sort pharmacokinetic data by PARAM variable — h_pkparam_sort","text":"pk_data (data.frame) pharmacokinetic data frame. key_var (string) key variable used merge pk_data metadata created d_pkparam().","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/h_pkparam_sort.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Sort pharmacokinetic data by PARAM variable — h_pkparam_sort","text":"pharmacokinetic data.frame sorted PARAM variable.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/h_pkparam_sort.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Sort pharmacokinetic data by PARAM variable — h_pkparam_sort","text":"","code":"library(dplyr)  adpp <- tern_ex_adpp %>% mutate(PKPARAM = factor(paste0(PARAM, \" (\", AVALU, \")\"))) pk_ordered_data <- h_pkparam_sort(adpp)"},{"path":"https://insightsengineering.github.io/tern/main/reference/h_ppmeans.html","id":null,"dir":"Reference","previous_headings":"","what":"Function to return the estimated means using predicted probabilities — h_ppmeans","title":"Function to return the estimated means using predicted probabilities — h_ppmeans","text":"arm level, predicted mean rate calculated using fitted model object, newdata set result stats::model.frame, reconstructed data original data, depending object formula (coming fit). confidence interval derived using conf_level parameter.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/h_ppmeans.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Function to return the estimated means using predicted probabilities — h_ppmeans","text":"","code":"h_ppmeans(obj, .df_row, arm, conf_level)"},{"path":"https://insightsengineering.github.io/tern/main/reference/h_ppmeans.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Function to return the estimated means using predicted probabilities — h_ppmeans","text":"obj (glm.fit) fitted model object used derive mean rate estimates treatment arm. .df_row (data.frame) dataset includes variables called .var variables. arm (string) group variable, covariate adjusted means multiple groups summarized. Specifically, first level arm variable taken reference group. conf_level (proportion) value used derive confidence interval rate.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/h_ppmeans.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Function to return the estimated means using predicted probabilities — h_ppmeans","text":"h_ppmeans() returns estimated means.","code":""},{"path":[]},{"path":[]},{"path":"https://insightsengineering.github.io/tern/main/reference/h_prop_diff.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Helper functions to calculate proportion difference — h_prop_diff","text":"","code":"prop_diff_wald(rsp, grp, conf_level = 0.95, correct = FALSE)  prop_diff_ha(rsp, grp, conf_level)  prop_diff_nc(rsp, grp, conf_level, correct = FALSE)  prop_diff_cmh(rsp, grp, strata, conf_level = 0.95)  prop_diff_strat_nc(   rsp,   grp,   strata,   weights_method = c(\"cmh\", \"wilson_h\"),   conf_level = 0.95,   correct = FALSE )"},{"path":"https://insightsengineering.github.io/tern/main/reference/h_prop_diff.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Helper functions to calculate proportion difference — h_prop_diff","text":"rsp (logical) vector indicating whether subject responder . grp (factor) vector assigning observations one two groups (e.g. reference treatment group). conf_level (proportion) confidence level interval. correct (flag) whether include continuity correction. information, see stats::prop.test(). strata (factor) variable one level per stratum length rsp. weights_method (string) weights method. Can either \"cmh\" \"heuristic\" directs way weights estimated.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/h_prop_diff.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Helper functions to calculate proportion difference — h_prop_diff","text":"named list elements diff (proportion difference) diff_ci (proportion difference confidence interval).","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/h_prop_diff.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Helper functions to calculate proportion difference — h_prop_diff","text":"prop_diff_wald(): Wald interval follows usual textbook definition single proportion confidence interval using normal approximation. possible include continuity correction Wald's interval. prop_diff_ha(): Anderson-Hauck confidence interval. prop_diff_nc(): Newcombe confidence interval. based Wilson score confidence interval single binomial proportion. prop_diff_cmh(): Calculates weighted difference. defined difference response rates experimental treatment group control treatment group, adjusted stratification factors applying Cochran-Mantel-Haenszel (CMH) weights. CMH chi-squared test, use stats::mantelhaen.test(). prop_diff_strat_nc(): Calculates stratified Newcombe confidence interval difference response rates experimental treatment group control treatment group, adjusted stratification factors. implementation follows closely one proposed Yan2010-jt;textualtern. Weights can estimated heuristic proposed prop_strat_wilson() CMH-derived weights (see prop_diff_cmh()).","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/h_prop_diff.html","id":"references","dir":"Reference","previous_headings":"","what":"References","title":"Helper functions to calculate proportion difference — h_prop_diff","text":"Yan2010-jttern","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/main/reference/h_prop_diff.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Helper functions to calculate proportion difference — h_prop_diff","text":"","code":"# Wald confidence interval set.seed(2) rsp <- sample(c(TRUE, FALSE), replace = TRUE, size = 20) grp <- factor(c(rep(\"A\", 10), rep(\"B\", 10)))  prop_diff_wald(rsp = rsp, grp = grp, conf_level = 0.95, correct = FALSE) #> $diff #> [1] 0 #>  #> $diff_ci #> [1] -0.4382613  0.4382613 #>   # Anderson-Hauck confidence interval ## \"Mid\" case: 3/4 respond in group A, 1/2 respond in group B. rsp <- c(TRUE, FALSE, FALSE, TRUE, TRUE, TRUE) grp <- factor(c(\"A\", \"B\", \"A\", \"B\", \"A\", \"A\"), levels = c(\"B\", \"A\"))  prop_diff_ha(rsp = rsp, grp = grp, conf_level = 0.90) #> $diff #> [1] 0.25 #>  #> $diff_ci #> [1] -0.9195011  1.0000000 #>   ## Edge case: Same proportion of response in A and B. rsp <- c(TRUE, FALSE, TRUE, FALSE) grp <- factor(c(\"A\", \"A\", \"B\", \"B\"), levels = c(\"A\", \"B\"))  prop_diff_ha(rsp = rsp, grp = grp, conf_level = 0.6) #> $diff #> [1] 0 #>  #> $diff_ci #> [1] -0.8451161  0.8451161 #>   # Newcombe confidence interval  set.seed(1) rsp <- c(   sample(c(TRUE, FALSE), size = 40, prob = c(3 / 4, 1 / 4), replace = TRUE),   sample(c(TRUE, FALSE), size = 40, prob = c(1 / 2, 1 / 2), replace = TRUE) ) grp <- factor(rep(c(\"A\", \"B\"), each = 40), levels = c(\"B\", \"A\")) table(rsp, grp) #>        grp #> rsp      B  A #>   FALSE 20 10 #>   TRUE  20 30  prop_diff_nc(rsp = rsp, grp = grp, conf_level = 0.9) #> $diff #> [1] 0.25 #>  #> $diff_ci #> [1] 0.07193388 0.40725819 #>   # Cochran-Mantel-Haenszel confidence interval  set.seed(2) rsp <- sample(c(TRUE, FALSE), 100, TRUE) grp <- sample(c(\"Placebo\", \"Treatment\"), 100, TRUE) grp <- factor(grp, levels = c(\"Placebo\", \"Treatment\")) strata_data <- data.frame(   \"f1\" = sample(c(\"a\", \"b\"), 100, TRUE),   \"f2\" = sample(c(\"x\", \"y\", \"z\"), 100, TRUE),   stringsAsFactors = TRUE )  prop_diff_cmh(   rsp = rsp, grp = grp, strata = interaction(strata_data),   conf_level = 0.90 ) #> $prop #>   Placebo Treatment  #> 0.5331117 0.3954251  #>  #> $prop_ci #> $prop_ci$Placebo #> [1] 0.4306536 0.6355698 #>  #> $prop_ci$Treatment #> [1] 0.2890735 0.5017768 #>  #>  #> $diff #> [1] -0.1376866 #>  #> $diff_ci #> [1] -0.285363076  0.009989872 #>  #> $weights #>       a.x       b.x       a.y       b.y       a.z       b.z  #> 0.1148388 0.2131696 0.1148388 0.2131696 0.1767914 0.1671918  #>  #> $n1 #> a.x b.x a.y b.y a.z b.z  #>   4  11   8  11  13  11  #>  #> $n2 #> a.x b.x a.y b.y a.z b.z  #>   8   9   4   9   6   6  #>   # Stratified Newcombe confidence interval  set.seed(2) data_set <- data.frame(   \"rsp\" = sample(c(TRUE, FALSE), 100, TRUE),   \"f1\" = sample(c(\"a\", \"b\"), 100, TRUE),   \"f2\" = sample(c(\"x\", \"y\", \"z\"), 100, TRUE),   \"grp\" = sample(c(\"Placebo\", \"Treatment\"), 100, TRUE),   stringsAsFactors = TRUE )  prop_diff_strat_nc(   rsp = data_set$rsp, grp = data_set$grp, strata = interaction(data_set[2:3]),   weights_method = \"cmh\",   conf_level = 0.90 ) #> $diff #> [1] -0.05777672 #>  #> $diff_ci #>      lower      upper  #> -0.2236537  0.1119331  #>   prop_diff_strat_nc(   rsp = data_set$rsp, grp = data_set$grp, strata = interaction(data_set[2:3]),   weights_method = \"wilson_h\",   conf_level = 0.90 ) #> $diff #> [1] -0.07771884 #>  #> $diff_ci #>      lower      upper  #> -0.2540844  0.1027720  #>"},{"path":"https://insightsengineering.github.io/tern/main/reference/h_prop_diff_test.html","id":null,"dir":"Reference","previous_headings":"","what":"Helper functions to test proportion differences — h_prop_diff_test","title":"Helper functions to test proportion differences — h_prop_diff_test","text":"Helper functions implement various tests difference two proportions.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/h_prop_diff_test.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Helper functions to test proportion differences — h_prop_diff_test","text":"","code":"prop_chisq(tbl)  prop_cmh(ary)  prop_schouten(tbl)  prop_fisher(tbl)"},{"path":"https://insightsengineering.github.io/tern/main/reference/h_prop_diff_test.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Helper functions to test proportion differences — h_prop_diff_test","text":"tbl (matrix) matrix two groups rows binary response (TRUE/FALSE) columns. ary (array, 3 dimensions) array two groups rows, binary response (TRUE/FALSE) columns, strata third dimension.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/h_prop_diff_test.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Helper functions to test proportion differences — h_prop_diff_test","text":"p-value.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/h_prop_diff_test.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Helper functions to test proportion differences — h_prop_diff_test","text":"prop_chisq(): Performs Chi-Squared test. Internally calls stats::prop.test(). prop_cmh(): Performs stratified Cochran-Mantel-Haenszel test. Internally calls stats::mantelhaen.test(). Note strata less two observations automatically discarded. prop_schouten(): Performs Chi-Squared test Schouten correction. prop_fisher(): Performs Fisher's exact test. Internally calls stats::fisher.test().","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/main/reference/h_proportions.html","id":null,"dir":"Reference","previous_headings":"","what":"Helper functions for calculating proportion confidence intervals — h_proportions","title":"Helper functions for calculating proportion confidence intervals — h_proportions","text":"Functions calculate different proportion confidence intervals use estimate_proportion().","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/h_proportions.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Helper functions for calculating proportion confidence intervals — h_proportions","text":"","code":"prop_wilson(rsp, conf_level, correct = FALSE)  prop_strat_wilson(   rsp,   strata,   weights = NULL,   conf_level = 0.95,   max_iterations = NULL,   correct = FALSE )  prop_clopper_pearson(rsp, conf_level)  prop_wald(rsp, conf_level, correct = FALSE)  prop_agresti_coull(rsp, conf_level)  prop_jeffreys(rsp, conf_level)"},{"path":"https://insightsengineering.github.io/tern/main/reference/h_proportions.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Helper functions for calculating proportion confidence intervals — h_proportions","text":"rsp (logical) vector indicating whether subject responder . conf_level (proportion) confidence level interval. correct (flag) whether apply continuity correction. strata (factor) variable one level per stratum length rsp. weights (numeric NULL) weights level strata. NULL, estimated using iterative algorithm proposed Yan2010-jt;textualtern minimizes weighted squared length confidence interval. max_iterations (count) maximum number iterations iterative procedure used find estimates optimal weights.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/h_proportions.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Helper functions for calculating proportion confidence intervals — h_proportions","text":"Confidence interval proportion.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/h_proportions.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Helper functions for calculating proportion confidence intervals — h_proportions","text":"prop_wilson(): Calculates Wilson interval calling stats::prop.test(). Also referred Wilson score interval. prop_strat_wilson(): Calculates stratified Wilson confidence interval unequal proportions described Yan2010-jt;textualtern prop_clopper_pearson(): Calculates Clopper-Pearson interval calling stats::binom.test(). Also referred exact method. prop_wald(): Calculates Wald interval following usual textbook definition single proportion confidence interval using normal approximation. prop_agresti_coull(): Calculates Agresti-Coull interval. Constructed (95% CI) adding two successes two failures data using Wald formula construct CI. prop_jeffreys(): Calculates Jeffreys interval, equal-tailed interval based non-informative Jeffreys prior binomial proportion.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/h_proportions.html","id":"references","dir":"Reference","previous_headings":"","what":"References","title":"Helper functions for calculating proportion confidence intervals — h_proportions","text":"Yan2010-jttern","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/main/reference/h_proportions.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Helper functions for calculating proportion confidence intervals — h_proportions","text":"","code":"rsp <- c(   TRUE, TRUE, TRUE, TRUE, TRUE,   FALSE, FALSE, FALSE, FALSE, FALSE ) prop_wilson(rsp, conf_level = 0.9) #> [1] 0.2692718 0.7307282  # Stratified Wilson confidence interval with unequal probabilities  set.seed(1) rsp <- sample(c(TRUE, FALSE), 100, TRUE) strata_data <- data.frame(   \"f1\" = sample(c(\"a\", \"b\"), 100, TRUE),   \"f2\" = sample(c(\"x\", \"y\", \"z\"), 100, TRUE),   stringsAsFactors = TRUE ) strata <- interaction(strata_data) n_strata <- ncol(table(rsp, strata)) # Number of strata  prop_strat_wilson(   rsp = rsp, strata = strata,   conf_level = 0.90 ) #> $conf_int #>     lower     upper  #> 0.4072891 0.5647887  #>  #> $weights #>       a.x       b.x       a.y       b.y       a.z       b.z  #> 0.2074199 0.1776464 0.1915610 0.1604678 0.1351096 0.1277952  #>   # Not automatic setting of weights prop_strat_wilson(   rsp = rsp, strata = strata,   weights = rep(1 / n_strata, n_strata),   conf_level = 0.90 ) #> $conf_int #>     lower     upper  #> 0.4190436 0.5789733  #>   prop_clopper_pearson(rsp, conf_level = .95) #> [1] 0.3886442 0.5919637  prop_wald(rsp, conf_level = 0.95) #> [1] 0.3920214 0.5879786 prop_wald(rsp, conf_level = 0.95, correct = TRUE) #> [1] 0.3870214 0.5929786  prop_agresti_coull(rsp, conf_level = 0.95) #> [1] 0.3942193 0.5865206  prop_jeffreys(rsp, conf_level = 0.95) #> [1] 0.3934779 0.5870917"},{"path":"https://insightsengineering.github.io/tern/main/reference/h_response_biomarkers_subgroups.html","id":null,"dir":"Reference","previous_headings":"","what":"Helper functions for tabulating biomarker effects on binary response by subgroup — h_response_biomarkers_subgroups","title":"Helper functions for tabulating biomarker effects on binary response by subgroup — h_response_biomarkers_subgroups","text":"Helper functions documented separately confuse user reading user-facing functions.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/h_response_biomarkers_subgroups.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Helper functions for tabulating biomarker effects on binary response by subgroup — h_response_biomarkers_subgroups","text":"","code":"h_rsp_to_logistic_variables(variables, biomarker)  h_logistic_mult_cont_df(variables, data, control = control_logistic())  h_tab_rsp_one_biomarker(df, vars, na_str = default_na_str(), .indent_mods = 0L)"},{"path":"https://insightsengineering.github.io/tern/main/reference/h_response_biomarkers_subgroups.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Helper functions for tabulating biomarker effects on binary response by subgroup — h_response_biomarkers_subgroups","text":"variables (named list string) list additional analysis variables. biomarker (string) name biomarker variable. data (data.frame) dataset containing variables summarize. control (named list) controls response definition confidence level produced control_logistic(). df (data.frame) results single biomarker, part returned extract_rsp_biomarkers() (needs couple columns added high-level function relative returned h_logistic_mult_cont_df(), see example). vars (character) names statistics reported among: n_tot: Total number patients per group. n_rsp: Total number responses per group. prop: Total response proportion per group. : Odds ratio. ci: Confidence interval odds ratio. pval: p-value effect. Note, statistics n_tot, ci required. na_str (string) string used replace NA empty values output. .indent_mods (named integer) indent modifiers labels. Defaults 0, corresponds unmodified default behavior. Can negative.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/h_response_biomarkers_subgroups.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Helper functions for tabulating biomarker effects on binary response by subgroup — h_response_biomarkers_subgroups","text":"h_rsp_to_logistic_variables() returns named list elements response, arm, covariates, strata. h_logistic_mult_cont_df() returns data.frame containing estimates statistics selected biomarkers. h_tab_rsp_one_biomarker() returns rtables table object given statistics arranged columns.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/h_response_biomarkers_subgroups.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Helper functions for tabulating biomarker effects on binary response by subgroup — h_response_biomarkers_subgroups","text":"h_rsp_to_logistic_variables(): helps converting \"response\" function variable list \"logistic regression\" variable list. reason currently inconsistency variable names accepted extract_rsp_subgroups() fit_logistic(). h_logistic_mult_cont_df(): prepares estimates number responses, patients overall response rate, well odds ratio estimates, confidence intervals p-values, multiple biomarkers given single data set. variables corresponds names variables found data, passed named list requires elements rsp biomarkers (vector continuous biomarker variables) optionally covariates strata. h_tab_rsp_one_biomarker(): Prepares single sub-table given df_sub containing results single biomarker.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/h_response_biomarkers_subgroups.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Helper functions for tabulating biomarker effects on binary response by subgroup — h_response_biomarkers_subgroups","text":"","code":"library(dplyr) library(forcats)  adrs <- tern_ex_adrs adrs_labels <- formatters::var_labels(adrs)  adrs_f <- adrs %>%   filter(PARAMCD == \"BESRSPI\") %>%   mutate(rsp = AVALC == \"CR\") formatters::var_labels(adrs_f) <- c(adrs_labels, \"Response\")  # This is how the variable list is converted internally. h_rsp_to_logistic_variables(   variables = list(     rsp = \"RSP\",     covariates = c(\"A\", \"B\"),     strata = \"D\"   ),   biomarker = \"AGE\" ) #> $response #> [1] \"RSP\" #>  #> $arm #> [1] \"AGE\" #>  #> $covariates #> [1] \"A\" \"B\" #>  #> $strata #> [1] \"D\" #>   # For a single population, estimate separately the effects # of two biomarkers. df <- h_logistic_mult_cont_df(   variables = list(     rsp = \"rsp\",     biomarkers = c(\"BMRKR1\", \"AGE\"),     covariates = \"SEX\"   ),   data = adrs_f ) df #>   biomarker              biomarker_label n_tot n_rsp prop        or       lcl #> 1    BMRKR1 Continuous Level Biomarker 1   200   164 0.82 0.9755036 0.8804862 #> 2       AGE                          Age   200   164 0.82 0.9952416 0.9462617 #>        ucl conf_level      pval     pval_label #> 1 1.080775       0.95 0.6352602 p-value (Wald) #> 2 1.046757       0.95 0.8530389 p-value (Wald)  # If the data set is empty, still the corresponding rows with missings are returned. h_coxreg_mult_cont_df(   variables = list(     rsp = \"rsp\",     biomarkers = c(\"BMRKR1\", \"AGE\"),     covariates = \"SEX\",     strata = \"STRATA1\"   ),   data = adrs_f[NULL, ] ) #>   biomarker              biomarker_label n_tot n_tot_events median hr lcl ucl #> 1    BMRKR1 Continuous Level Biomarker 1     0            0     NA NA  NA  NA #> 2       AGE                          Age     0            0     NA NA  NA  NA #>   conf_level pval     pval_label #> 1       0.95   NA p-value (Wald) #> 2       0.95   NA p-value (Wald)  # Starting from above `df`, zoom in on one biomarker and add required columns. df1 <- df[1, ] df1$subgroup <- \"All patients\" df1$row_type <- \"content\" df1$var <- \"ALL\" df1$var_label <- \"All patients\"  h_tab_rsp_one_biomarker(   df1,   vars = c(\"n_tot\", \"n_rsp\", \"prop\", \"or\", \"ci\", \"pval\") ) #>                Total n   Responders   Response (%)   Odds Ratio      95% CI      p-value (Wald) #> ——————————————————————————————————————————————————————————————————————————————————————————————— #> All patients     200        164          82.0%          0.98      (0.88, 1.08)       0.6353"},{"path":"https://insightsengineering.github.io/tern/main/reference/h_response_subgroups.html","id":null,"dir":"Reference","previous_headings":"","what":"Helper functions for tabulating binary response by subgroup — h_response_subgroups","title":"Helper functions for tabulating binary response by subgroup — h_response_subgroups","text":"Helper functions tabulate data frame statistics response rate odds ratio population subgroups.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/h_response_subgroups.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Helper functions for tabulating binary response by subgroup — h_response_subgroups","text":"","code":"h_proportion_df(rsp, arm)  h_proportion_subgroups_df(   variables,   data,   groups_lists = list(),   label_all = \"All Patients\" )  h_odds_ratio_df(rsp, arm, strata_data = NULL, conf_level = 0.95, method = NULL)  h_odds_ratio_subgroups_df(   variables,   data,   groups_lists = list(),   conf_level = 0.95,   method = NULL,   label_all = \"All Patients\" )"},{"path":"https://insightsengineering.github.io/tern/main/reference/h_response_subgroups.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Helper functions for tabulating binary response by subgroup — h_response_subgroups","text":"rsp (logical) vector indicating whether subject responder . arm (factor) treatment group variable. variables (named list string) list additional analysis variables. data (data.frame) dataset containing variables summarize. groups_lists (named list list) optionally contains subgroups variable list, specifies new group levels via names levels belong character vectors elements list. label_all (string) label total population analysis. strata_data (factor, data.frame, NULL) required stratified analysis performed. conf_level (proportion) confidence level interval. method (string NULL) specifies test used calculate p-value difference two proportions. options, see test_proportion_diff(). Default NULL test performed.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/h_response_subgroups.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Helper functions for tabulating binary response by subgroup — h_response_subgroups","text":"h_proportion_df() returns data.frame columns arm, n, n_rsp, prop. h_proportion_subgroups_df() returns data.frame columns arm, n, n_rsp, prop, subgroup, var, var_label, row_type. h_odds_ratio_df() returns data.frame columns arm, n_tot, , lcl, ucl, conf_level, optionally pval pval_label. h_odds_ratio_subgroups_df() returns data.frame columns arm, n_tot, , lcl, ucl, conf_level, subgroup, var, var_label, row_type.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/h_response_subgroups.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Helper functions for tabulating binary response by subgroup — h_response_subgroups","text":"Main functionality prepare data use layout-creating function.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/h_response_subgroups.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Helper functions for tabulating binary response by subgroup — h_response_subgroups","text":"h_proportion_df(): Helper prepare data frame binary responses arm. h_proportion_subgroups_df(): Summarizes proportion binary responses arm across subgroups data frame. variables corresponds names variables found data, passed named list requires elements rsp, arm optionally subgroups. groups_lists optionally specifies groupings subgroups variables. h_odds_ratio_df(): Helper prepare data frame estimates odds ratio treatment control arm. h_odds_ratio_subgroups_df(): Summarizes estimates odds ratio treatment control arm across subgroups data frame. variables corresponds names variables found data, passed named list requires elements rsp, arm optionally subgroups strata. groups_lists optionally specifies groupings subgroups variables.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/h_response_subgroups.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Helper functions for tabulating binary response by subgroup — h_response_subgroups","text":"","code":"library(dplyr) library(forcats)  adrs <- tern_ex_adrs adrs_labels <- formatters::var_labels(adrs)  adrs_f <- adrs %>%   filter(PARAMCD == \"BESRSPI\") %>%   filter(ARM %in% c(\"A: Drug X\", \"B: Placebo\")) %>%   droplevels() %>%   mutate(     # Reorder levels of factor to make the placebo group the reference arm.     ARM = fct_relevel(ARM, \"B: Placebo\"),     rsp = AVALC == \"CR\"   ) formatters::var_labels(adrs_f) <- c(adrs_labels, \"Response\")  h_proportion_df(   c(TRUE, FALSE, FALSE),   arm = factor(c(\"A\", \"A\", \"B\"), levels = c(\"A\", \"B\")) ) #>   arm n n_rsp prop #> 1   A 2     1  0.5 #> 2   B 1     0  0.0  h_proportion_subgroups_df(   variables = list(rsp = \"rsp\", arm = \"ARM\", subgroups = c(\"SEX\", \"BMRKR2\")),   data = adrs_f ) #>           arm  n n_rsp      prop     subgroup    var #> 1  B: Placebo 73    50 0.6849315 All Patients    ALL #> 2   A: Drug X 69    59 0.8550725 All Patients    ALL #> 3  B: Placebo 40    25 0.6250000            F    SEX #> 4   A: Drug X 38    36 0.9473684            F    SEX #> 5  B: Placebo 33    25 0.7575758            M    SEX #> 6   A: Drug X 31    23 0.7419355            M    SEX #> 7  B: Placebo 24    13 0.5416667          LOW BMRKR2 #> 8   A: Drug X 26    21 0.8076923          LOW BMRKR2 #> 9  B: Placebo 23    17 0.7391304       MEDIUM BMRKR2 #> 10  A: Drug X 26    23 0.8846154       MEDIUM BMRKR2 #> 11 B: Placebo 26    20 0.7692308         HIGH BMRKR2 #> 12  A: Drug X 17    15 0.8823529         HIGH BMRKR2 #>                       var_label row_type #> 1                  All Patients  content #> 2                  All Patients  content #> 3                           Sex analysis #> 4                           Sex analysis #> 5                           Sex analysis #> 6                           Sex analysis #> 7  Continuous Level Biomarker 2 analysis #> 8  Continuous Level Biomarker 2 analysis #> 9  Continuous Level Biomarker 2 analysis #> 10 Continuous Level Biomarker 2 analysis #> 11 Continuous Level Biomarker 2 analysis #> 12 Continuous Level Biomarker 2 analysis  # Define groupings for BMRKR2 levels. h_proportion_subgroups_df(   variables = list(rsp = \"rsp\", arm = \"ARM\", subgroups = c(\"SEX\", \"BMRKR2\")),   data = adrs_f,   groups_lists = list(     BMRKR2 = list(       \"low\" = \"LOW\",       \"low/medium\" = c(\"LOW\", \"MEDIUM\"),       \"low/medium/high\" = c(\"LOW\", \"MEDIUM\", \"HIGH\")     )   ) ) #>           arm  n n_rsp      prop        subgroup    var #> 1  B: Placebo 73    50 0.6849315    All Patients    ALL #> 2   A: Drug X 69    59 0.8550725    All Patients    ALL #> 3  B: Placebo 40    25 0.6250000               F    SEX #> 4   A: Drug X 38    36 0.9473684               F    SEX #> 5  B: Placebo 33    25 0.7575758               M    SEX #> 6   A: Drug X 31    23 0.7419355               M    SEX #> 7  B: Placebo 24    13 0.5416667             low BMRKR2 #> 8   A: Drug X 26    21 0.8076923             low BMRKR2 #> 9  B: Placebo 47    30 0.6382979      low/medium BMRKR2 #> 10  A: Drug X 52    44 0.8461538      low/medium BMRKR2 #> 11 B: Placebo 73    50 0.6849315 low/medium/high BMRKR2 #> 12  A: Drug X 69    59 0.8550725 low/medium/high BMRKR2 #>                       var_label row_type #> 1                  All Patients  content #> 2                  All Patients  content #> 3                           Sex analysis #> 4                           Sex analysis #> 5                           Sex analysis #> 6                           Sex analysis #> 7  Continuous Level Biomarker 2 analysis #> 8  Continuous Level Biomarker 2 analysis #> 9  Continuous Level Biomarker 2 analysis #> 10 Continuous Level Biomarker 2 analysis #> 11 Continuous Level Biomarker 2 analysis #> 12 Continuous Level Biomarker 2 analysis  # Unstratatified analysis. h_odds_ratio_df(   c(TRUE, FALSE, FALSE, TRUE),   arm = factor(c(\"A\", \"A\", \"B\", \"B\"), levels = c(\"A\", \"B\")) ) #>   arm n_tot or        lcl      ucl conf_level #> 1         4  1 0.01984252 50.39681       0.95  # Include p-value. h_odds_ratio_df(adrs_f$rsp, adrs_f$ARM, method = \"chisq\") #>   arm n_tot    or      lcl      ucl conf_level       pval #> 1       142 2.714 1.180449 6.239827       0.95 0.01643036 #>                   pval_label #> 1 p-value (Chi-Squared Test)  # Stratatified analysis. h_odds_ratio_df(   rsp = adrs_f$rsp,   arm = adrs_f$ARM,   strata_data = adrs_f[, c(\"STRATA1\", \"STRATA2\")],   method = \"cmh\" ) #>   arm n_tot       or      lcl      ucl conf_level       pval #> 1       142 2.665586 1.146149 6.199324       0.95 0.02019665 #>                               pval_label #> 1 p-value (Cochran-Mantel-Haenszel Test)  # Unstratified analysis. h_odds_ratio_subgroups_df(   variables = list(rsp = \"rsp\", arm = \"ARM\", subgroups = c(\"SEX\", \"BMRKR2\")),   data = adrs_f ) #>   arm n_tot        or       lcl       ucl conf_level     subgroup    var #> 1       142  2.714000 1.1804488  6.239827       0.95 All Patients    ALL #> 2        78 10.800000 2.2669576 51.452218       0.95            F    SEX #> 3        64  0.920000 0.2966470  2.853223       0.95            M    SEX #> 4        50  3.553846 1.0047370 12.570277       0.95          LOW BMRKR2 #> 5        49  2.705882 0.5911718 12.385232       0.95       MEDIUM BMRKR2 #> 6        43  2.250000 0.3970298 12.750933       0.95         HIGH BMRKR2 #>                      var_label row_type #> 1                 All Patients  content #> 2                          Sex analysis #> 3                          Sex analysis #> 4 Continuous Level Biomarker 2 analysis #> 5 Continuous Level Biomarker 2 analysis #> 6 Continuous Level Biomarker 2 analysis  # Stratified analysis. h_odds_ratio_subgroups_df(   variables = list(     rsp = \"rsp\",     arm = \"ARM\",     subgroups = c(\"SEX\", \"BMRKR2\"),     strata = c(\"STRATA1\", \"STRATA2\")   ),   data = adrs_f ) #>   arm n_tot        or       lcl       ucl conf_level     subgroup    var #> 1       142 2.6655860 1.1461490  6.199324       0.95 All Patients    ALL #> 2        78 7.7065093 1.5817529 37.547132       0.95            F    SEX #> 3        64 0.9572284 0.2990954  3.063525       0.95            M    SEX #> 4        50 3.0323726 0.8833232 10.409875       0.95          LOW BMRKR2 #> 5        49 2.1264996 0.4312008 10.486995       0.95       MEDIUM BMRKR2 #> 6        43 2.5134820 0.4351747 14.517370       0.95         HIGH BMRKR2 #>                      var_label row_type #> 1                 All Patients  content #> 2                          Sex analysis #> 3                          Sex analysis #> 4 Continuous Level Biomarker 2 analysis #> 5 Continuous Level Biomarker 2 analysis #> 6 Continuous Level Biomarker 2 analysis  # Define groupings of BMRKR2 levels. h_odds_ratio_subgroups_df(   variables = list(     rsp = \"rsp\",     arm = \"ARM\",     subgroups = c(\"SEX\", \"BMRKR2\")   ),   data = adrs_f,   groups_lists = list(     BMRKR2 = list(       \"low\" = \"LOW\",       \"low/medium\" = c(\"LOW\", \"MEDIUM\"),       \"low/medium/high\" = c(\"LOW\", \"MEDIUM\", \"HIGH\")     )   ) ) #>   arm n_tot        or      lcl       ucl conf_level        subgroup    var #> 1       142  2.714000 1.180449  6.239827       0.95    All Patients    ALL #> 2        78 10.800000 2.266958 51.452218       0.95               F    SEX #> 3        64  0.920000 0.296647  2.853223       0.95               M    SEX #> 4        50  3.553846 1.004737 12.570277       0.95             low BMRKR2 #> 5        99  3.116667 1.193409  8.139385       0.95      low/medium BMRKR2 #> 6       142  2.714000 1.180449  6.239827       0.95 low/medium/high BMRKR2 #>                      var_label row_type #> 1                 All Patients  content #> 2                          Sex analysis #> 3                          Sex analysis #> 4 Continuous Level Biomarker 2 analysis #> 5 Continuous Level Biomarker 2 analysis #> 6 Continuous Level Biomarker 2 analysis"},{"path":"https://insightsengineering.github.io/tern/main/reference/h_split_by_subgroups.html","id":null,"dir":"Reference","previous_headings":"","what":"Split data frame by subgroups — h_split_by_subgroups","title":"Split data frame by subgroups — h_split_by_subgroups","text":"Split data frame non-nested list subsets.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/h_split_by_subgroups.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Split data frame by subgroups — h_split_by_subgroups","text":"","code":"h_split_by_subgroups(data, subgroups, groups_lists = list())"},{"path":"https://insightsengineering.github.io/tern/main/reference/h_split_by_subgroups.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Split data frame by subgroups — h_split_by_subgroups","text":"data (data.frame) dataset split. subgroups (character) names factor variables data used create subsets. Unused levels present data dropped. Note order vector determines order downstream table. groups_lists (named list list) optionally contains subgroups variable list, specifies new group levels via names levels belong character vectors elements list.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/h_split_by_subgroups.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Split data frame by subgroups — h_split_by_subgroups","text":"list subset data (df) metadata subset (df_labels).","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/h_split_by_subgroups.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Split data frame by subgroups — h_split_by_subgroups","text":"Main functionality prepare data use forest plot layouts.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/h_split_by_subgroups.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Split data frame by subgroups — h_split_by_subgroups","text":"","code":"df <- data.frame(   x = c(1:5),   y = factor(c(\"A\", \"B\", \"A\", \"B\", \"A\"), levels = c(\"A\", \"B\", \"C\")),   z = factor(c(\"C\", \"C\", \"D\", \"D\", \"D\"), levels = c(\"D\", \"C\")) ) formatters::var_labels(df) <- paste(\"label for\", names(df))  h_split_by_subgroups(   data = df,   subgroups = c(\"y\", \"z\") ) #> $y.A #> $y.A$df #>   x y z #> 1 1 A C #> 2 3 A D #> 3 5 A D #>  #> $y.A$df_labels #>   subgroup var   var_label #> 1        A   y label for y #>  #>  #> $y.B #> $y.B$df #>   x y z #> 1 2 B C #> 2 4 B D #>  #> $y.B$df_labels #>   subgroup var   var_label #> 1        B   y label for y #>  #>  #> $z.D #> $z.D$df #>   x y z #> 1 3 A D #> 2 4 B D #> 3 5 A D #>  #> $z.D$df_labels #>   subgroup var   var_label #> 1        D   z label for z #>  #>  #> $z.C #> $z.C$df #>   x y z #> 1 1 A C #> 2 2 B C #>  #> $z.C$df_labels #>   subgroup var   var_label #> 1        C   z label for z #>  #>   h_split_by_subgroups(   data = df,   subgroups = c(\"y\", \"z\"),   groups_lists = list(     y = list(\"AB\" = c(\"A\", \"B\"), \"C\" = \"C\")   ) ) #> $y.AB #> $y.AB$df #>   x y z #> 1 1 A C #> 2 2 B C #> 3 3 A D #> 4 4 B D #> 5 5 A D #>  #> $y.AB$df_labels #>   subgroup var   var_label #> 1       AB   y label for y #>  #>  #> $z.D #> $z.D$df #>   x y z #> 1 3 A D #> 2 4 B D #> 3 5 A D #>  #> $z.D$df_labels #>   subgroup var   var_label #> 1        D   z label for z #>  #>  #> $z.C #> $z.C$df #>   x y z #> 1 1 A C #> 2 2 B C #>  #> $z.C$df_labels #>   subgroup var   var_label #> 1        C   z label for z #>  #>"},{"path":"https://insightsengineering.github.io/tern/main/reference/h_split_param.html","id":null,"dir":"Reference","previous_headings":"","what":"Split parameters — h_split_param","title":"Split parameters — h_split_param","text":"divides data vector param groups defined f based specified values. relevant rtables layers distribute parameters .stats ' .formats lists items corresponding specific analysis function.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/h_split_param.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Split parameters — h_split_param","text":"","code":"h_split_param(param, value, f)"},{"path":"https://insightsengineering.github.io/tern/main/reference/h_split_param.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Split parameters — h_split_param","text":"param (vector) parameter split. value (vector) value used split. f (list) reference make split.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/h_split_param.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Split parameters — h_split_param","text":"named list element names f, containing elements specified .stats.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/h_split_param.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Split parameters — h_split_param","text":"","code":"f <- list(   surv = c(\"pt_at_risk\", \"event_free_rate\", \"rate_se\", \"rate_ci\"),   surv_diff = c(\"rate_diff\", \"rate_diff_ci\", \"ztest_pval\") )  .stats <- c(\"pt_at_risk\", \"rate_diff\") h_split_param(.stats, .stats, f = f) #> $surv #> [1] \"pt_at_risk\" #>  #> $surv_diff #> [1] \"rate_diff\" #>   # $surv # [1] \"pt_at_risk\" # # $surv_diff # [1] \"rate_diff\"  .formats <- c(\"pt_at_risk\" = \"xx\", \"event_free_rate\" = \"xxx\") h_split_param(.formats, names(.formats), f = f) #> $surv #>      pt_at_risk event_free_rate  #>            \"xx\"           \"xxx\"  #>  #> $surv_diff #> NULL #>   # $surv # pt_at_risk event_free_rate # \"xx\"           \"xxx\" # # $surv_diff # NULL"},{"path":"https://insightsengineering.github.io/tern/main/reference/h_stack_by_baskets.html","id":null,"dir":"Reference","previous_headings":"","what":"Helper function to create a new SMQ variable in ADAE by stacking SMQ and/or CQ records. — h_stack_by_baskets","title":"Helper function to create a new SMQ variable in ADAE by stacking SMQ and/or CQ records. — h_stack_by_baskets","text":"Helper function create new SMQ variable ADAE consists adverse events belonging selected Standardized/Customized queries. new dataset contain records adverse events belonging selected baskets. Remember na_str must match needed pre-processing done df_explicit_na() desired output.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/h_stack_by_baskets.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Helper function to create a new SMQ variable in ADAE by stacking SMQ and/or CQ records. — h_stack_by_baskets","text":"","code":"h_stack_by_baskets(   df,   baskets = grep(\"^(SMQ|CQ).+NAM$\", names(df), value = TRUE),   smq_varlabel = \"Standardized MedDRA Query\",   keys = c(\"STUDYID\", \"USUBJID\", \"ASTDTM\", \"AEDECOD\", \"AESEQ\"),   aag_summary = NULL,   na_str = \"<Missing>\" )"},{"path":"https://insightsengineering.github.io/tern/main/reference/h_stack_by_baskets.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Helper function to create a new SMQ variable in ADAE by stacking SMQ and/or CQ records. — h_stack_by_baskets","text":"df (data.frame) data set containing analysis variables. baskets (character) variable names selected Standardized/Customized queries. smq_varlabel (string) label new variable created. keys (character) names key variables returned along new variable created. aag_summary (data.frame) containing SMQ baskets levels interest final SMQ variable. useful levels interest observed df dataset. two columns dataset named basket basket_name. na_str (string) string used replace NA empty values output.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/h_stack_by_baskets.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Helper function to create a new SMQ variable in ADAE by stacking SMQ and/or CQ records. — h_stack_by_baskets","text":"data.frame variables keys taken df new variable SMQ containing records belonging baskets selected via baskets argument.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/h_stack_by_baskets.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Helper function to create a new SMQ variable in ADAE by stacking SMQ and/or CQ records. — h_stack_by_baskets","text":"","code":"adae <- tern_ex_adae[1:20, ] %>% df_explicit_na() h_stack_by_baskets(df = adae) #> # A tibble: 8 × 6 #>   STUDYID USUBJID               ASTDTM              AEDECOD       AESEQ SMQ      #>   <fct>   <fct>                 <dttm>              <fct>         <int> <fct>    #> 1 AB12345 AB12345-BRA-11-id-8   2021-12-05 02:02:07 dcd D.2.1.5.3     2 D.2.1.5… #> 2 AB12345 AB12345-BRA-12-id-120 2020-02-05 01:42:29 dcd D.2.1.5.3     2 D.2.1.5… #> 3 AB12345 AB12345-BRA-1-id-171  2022-11-29 12:18:31 dcd C.1.1.1.3     2 C.1.1.1… #> 4 AB12345 AB12345-BRA-1-id-23   2020-07-10 07:32:49 dcd B.2.2.3.1     3 C.1.1.1… #> 5 AB12345 AB12345-BRA-1-id-59   2021-10-10 23:54:46 dcd C.1.1.1.3     4 C.1.1.1… #> 6 AB12345 AB12345-BRA-1-id-9    2021-06-01 14:39:09 dcd C.1.1.1.3     1 C.1.1.1… #> 7 AB12345 AB12345-BRA-11-id-8   2021-12-21 02:02:07 dcd C.1.1.1.3     3 C.1.1.1… #> 8 AB12345 AB12345-BRA-12-id-120 2020-10-01 01:42:29 dcd C.1.1.1.3     3 C.1.1.1…  aag <- data.frame(   NAMVAR = c(\"CQ01NAM\", \"CQ02NAM\", \"SMQ01NAM\", \"SMQ02NAM\"),   REFNAME = c(     \"D.2.1.5.3/A.1.1.1.1 aesi\", \"X.9.9.9.9/Y.8.8.8.8 aesi\",     \"C.1.1.1.3/B.2.2.3.1 aesi\", \"C.1.1.1.3/B.3.3.3.3 aesi\"   ),   SCOPE = c(\"\", \"\", \"BROAD\", \"BROAD\"),   stringsAsFactors = FALSE )  basket_name <- character(nrow(aag)) cq_pos <- grep(\"^(CQ).+NAM$\", aag$NAMVAR) smq_pos <- grep(\"^(SMQ).+NAM$\", aag$NAMVAR) basket_name[cq_pos] <- aag$REFNAME[cq_pos] basket_name[smq_pos] <- paste0(   aag$REFNAME[smq_pos], \"(\", aag$SCOPE[smq_pos], \")\" )  aag_summary <- data.frame(   basket = aag$NAMVAR,   basket_name = basket_name,   stringsAsFactors = TRUE )  result <- h_stack_by_baskets(df = adae, aag_summary = aag_summary) all(levels(aag_summary$basket_name) %in% levels(result$SMQ)) #> [1] TRUE  h_stack_by_baskets(   df = adae,   aag_summary = NULL,   keys = c(\"STUDYID\", \"USUBJID\", \"AEDECOD\", \"ARM\"),   baskets = \"SMQ01NAM\" ) #> # A tibble: 6 × 5 #>   STUDYID USUBJID               AEDECOD       ARM            SMQ                 #>   <fct>   <fct>                 <fct>         <fct>          <fct>               #> 1 AB12345 AB12345-BRA-1-id-171  dcd C.1.1.1.3 B: Placebo     C.1.1.1.3/B.2.2.3.… #> 2 AB12345 AB12345-BRA-1-id-23   dcd B.2.2.3.1 A: Drug X      C.1.1.1.3/B.2.2.3.… #> 3 AB12345 AB12345-BRA-1-id-59   dcd C.1.1.1.3 A: Drug X      C.1.1.1.3/B.2.2.3.… #> 4 AB12345 AB12345-BRA-1-id-9    dcd C.1.1.1.3 C: Combination C.1.1.1.3/B.2.2.3.… #> 5 AB12345 AB12345-BRA-11-id-8   dcd C.1.1.1.3 A: Drug X      C.1.1.1.3/B.2.2.3.… #> 6 AB12345 AB12345-BRA-12-id-120 dcd C.1.1.1.3 A: Drug X      C.1.1.1.3/B.2.2.3.…"},{"path":"https://insightsengineering.github.io/tern/main/reference/h_step.html","id":null,"dir":"Reference","previous_headings":"","what":"Helper functions for subgroup treatment effect pattern (STEP) calculations — h_step","title":"Helper functions for subgroup treatment effect pattern (STEP) calculations — h_step","text":"Helper functions used internally STEP calculations.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/h_step.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Helper functions for subgroup treatment effect pattern (STEP) calculations — h_step","text":"","code":"h_step_window(x, control = control_step())  h_step_trt_effect(data, model, variables, x)  h_step_survival_formula(variables, control = control_step())  h_step_survival_est(   formula,   data,   variables,   x,   subset = rep(TRUE, nrow(data)),   control = control_coxph() )  h_step_rsp_formula(variables, control = c(control_step(), control_logistic()))  h_step_rsp_est(   formula,   data,   variables,   x,   subset = rep(TRUE, nrow(data)),   control = control_logistic() )"},{"path":"https://insightsengineering.github.io/tern/main/reference/h_step.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Helper functions for subgroup treatment effect pattern (STEP) calculations — h_step","text":"x (numeric) biomarker value(s) use (without NA). control (named list) output control_step(). data (data.frame) dataset containing variables summarize. model (coxph glm) regression model object. variables (named list string) list additional analysis variables. formula (formula) regression model formula. subset (logical) subset vector.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/h_step.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Helper functions for subgroup treatment effect pattern (STEP) calculations — h_step","text":"h_step_window() returns list containing window-selection matrix sel interval information matrix interval. h_step_trt_effect() returns vector elements est se. h_step_survival_formula() returns model formula. h_step_survival_est() returns matrix number observations n, events, log hazard ratio estimates loghr, standard error se, Wald confidence interval bounds ci_lower ci_upper. One row included biomarker value x. h_step_rsp_formula() returns model formula. h_step_rsp_est() returns matrix number observations n, log odds ratio estimates logor, standard error se, Wald confidence interval bounds ci_lower ci_upper. One row included biomarker value x.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/h_step.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Helper functions for subgroup treatment effect pattern (STEP) calculations — h_step","text":"h_step_window(): Creates windows STEP, based control settings provided. h_step_trt_effect(): Calculates estimated treatment effect estimate linear predictor scale corresponding standard error STEP model fitted data given variables specification, single biomarker value x. works coxph glm models, .e. calculating log hazard ratio log odds ratio estimates. h_step_survival_formula(): Builds model formula used survival STEP calculations. h_step_survival_est(): Estimates model formula built based variables data given subset control parameters Cox regression. h_step_rsp_formula(): Builds model formula used response STEP calculations. h_step_rsp_est(): Estimates model formula built based variables data given subset control parameters logistic regression.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/h_survival_biomarkers_subgroups.html","id":null,"dir":"Reference","previous_headings":"","what":"Helper functions for tabulating biomarker effects on survival by subgroup — h_survival_biomarkers_subgroups","title":"Helper functions for tabulating biomarker effects on survival by subgroup — h_survival_biomarkers_subgroups","text":"Helper functions documented separately confuse user reading user-facing functions.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/h_survival_biomarkers_subgroups.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Helper functions for tabulating biomarker effects on survival by subgroup — h_survival_biomarkers_subgroups","text":"","code":"h_surv_to_coxreg_variables(variables, biomarker)  h_coxreg_mult_cont_df(variables, data, control = control_coxreg())  h_tab_surv_one_biomarker(   df,   vars,   time_unit,   na_str = default_na_str(),   .indent_mods = 0L,   ... )"},{"path":"https://insightsengineering.github.io/tern/main/reference/h_survival_biomarkers_subgroups.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Helper functions for tabulating biomarker effects on survival by subgroup — h_survival_biomarkers_subgroups","text":"variables (named list string) list additional analysis variables. biomarker (string) name biomarker variable. data (data.frame) dataset containing variables summarize. control (list) list parameters returned helper function control_coxreg(). df (data.frame) results single biomarker, part returned extract_survival_biomarkers() (needs couple columns added high-level function relative returned h_coxreg_mult_cont_df(), see example). vars (character) names statistics reported among: n_tot_events: Total number events per group. n_tot: Total number observations per group. median: Median survival time. hr: Hazard ratio. ci: Confidence interval hazard ratio. pval: p-value effect. Note, one statistics n_tot n_tot_events, well hr ci required. time_unit (string) label unit median survival time. Default NULL skips displaying unit. na_str (string) string used replace NA empty values output. .indent_mods (named integer) indent modifiers labels. Defaults 0, corresponds unmodified default behavior. Can negative. ... additional arguments lower level functions.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/h_survival_biomarkers_subgroups.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Helper functions for tabulating biomarker effects on survival by subgroup — h_survival_biomarkers_subgroups","text":"h_surv_to_coxreg_variables() returns named list elements time, event, arm, covariates, strata. h_coxreg_mult_cont_df() returns data.frame containing estimates statistics selected biomarkers. h_tab_surv_one_biomarker() returns rtables table object given statistics arranged columns.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/h_survival_biomarkers_subgroups.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Helper functions for tabulating biomarker effects on survival by subgroup — h_survival_biomarkers_subgroups","text":"h_surv_to_coxreg_variables(): Helps converting \"survival\" function variable list \"Cox regression\" variable list. reason currently inconsistency variable names accepted extract_survival_subgroups() fit_coxreg_multivar(). h_coxreg_mult_cont_df(): Prepares estimates number events, patients median survival times, well hazard ratio estimates, confidence intervals p-values, multiple biomarkers given single data set. variables corresponds names variables found data, passed named list requires elements tte, is_event, biomarkers (vector continuous biomarker variables) optionally subgroups strata. h_tab_surv_one_biomarker(): Prepares single sub-table given df_sub containing results single biomarker.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/h_survival_biomarkers_subgroups.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Helper functions for tabulating biomarker effects on survival by subgroup — h_survival_biomarkers_subgroups","text":"","code":"library(dplyr) library(forcats)  adtte <- tern_ex_adtte  # Save variable labels before data processing steps. adtte_labels <- formatters::var_labels(adtte, fill = FALSE)  adtte_f <- adtte %>%   filter(PARAMCD == \"OS\") %>%   mutate(     AVALU = as.character(AVALU),     is_event = CNSR == 0   ) labels <- c(\"AVALU\" = adtte_labels[[\"AVALU\"]], \"is_event\" = \"Event Flag\") formatters::var_labels(adtte_f)[names(labels)] <- labels  # This is how the variable list is converted internally. h_surv_to_coxreg_variables(   variables = list(     tte = \"AVAL\",     is_event = \"EVNT\",     covariates = c(\"A\", \"B\"),     strata = \"D\"   ),   biomarker = \"AGE\" ) #> $time #> [1] \"AVAL\" #>  #> $event #> [1] \"EVNT\" #>  #> $arm #> [1] \"AGE\" #>  #> $covariates #> [1] \"A\" \"B\" #>  #> $strata #> [1] \"D\" #>   # For a single population, estimate separately the effects # of two biomarkers. df <- h_coxreg_mult_cont_df(   variables = list(     tte = \"AVAL\",     is_event = \"is_event\",     biomarkers = c(\"BMRKR1\", \"AGE\"),     covariates = \"SEX\",     strata = c(\"STRATA1\", \"STRATA2\")   ),   data = adtte_f ) df #>   biomarker              biomarker_label n_tot n_tot_events   median       hr #> 1    BMRKR1 Continuous Level Biomarker 1   200          141 753.5176 1.000189 #> 2       AGE                          Age   200          141 753.5176 1.008267 #>         lcl      ucl conf_level      pval     pval_label #> 1 0.9511092 1.051802       0.95 0.9941244 p-value (Wald) #> 2 0.9845155 1.032591       0.95 0.4984743 p-value (Wald)  # If the data set is empty, still the corresponding rows with missings are returned. h_coxreg_mult_cont_df(   variables = list(     tte = \"AVAL\",     is_event = \"is_event\",     biomarkers = c(\"BMRKR1\", \"AGE\"),     covariates = \"REGION1\",     strata = c(\"STRATA1\", \"STRATA2\")   ),   data = adtte_f[NULL, ] ) #>   biomarker              biomarker_label n_tot n_tot_events median hr lcl ucl #> 1    BMRKR1 Continuous Level Biomarker 1     0            0     NA NA  NA  NA #> 2       AGE                          Age     0            0     NA NA  NA  NA #>   conf_level pval     pval_label #> 1       0.95   NA p-value (Wald) #> 2       0.95   NA p-value (Wald)  # Starting from above `df`, zoom in on one biomarker and add required columns. df1 <- df[1, ] df1$subgroup <- \"All patients\" df1$row_type <- \"content\" df1$var <- \"ALL\" df1$var_label <- \"All patients\" h_tab_surv_one_biomarker(   df1,   vars = c(\"n_tot\", \"n_tot_events\", \"median\", \"hr\", \"ci\", \"pval\"),   time_unit = \"days\" ) #>                Total n   Total Events   Median (days)   Hazard Ratio   95% Wald CI    p-value (Wald) #> ———————————————————————————————————————————————————————————————————————————————————————————————————— #> All patients     200         141            753.5           1.00       (0.95, 1.05)       0.9941"},{"path":"https://insightsengineering.github.io/tern/main/reference/h_survival_duration_subgroups.html","id":null,"dir":"Reference","previous_headings":"","what":"Helper functions for tabulating survival duration by subgroup — h_survival_duration_subgroups","title":"Helper functions for tabulating survival duration by subgroup — h_survival_duration_subgroups","text":"Helper functions tabulate data frame statistics median survival time hazard ratio population subgroups.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/h_survival_duration_subgroups.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Helper functions for tabulating survival duration by subgroup — h_survival_duration_subgroups","text":"","code":"h_survtime_df(tte, is_event, arm)  h_survtime_subgroups_df(   variables,   data,   groups_lists = list(),   label_all = \"All Patients\" )  h_coxph_df(tte, is_event, arm, strata_data = NULL, control = control_coxph())  h_coxph_subgroups_df(   variables,   data,   groups_lists = list(),   control = control_coxph(),   label_all = \"All Patients\" )"},{"path":"https://insightsengineering.github.io/tern/main/reference/h_survival_duration_subgroups.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Helper functions for tabulating survival duration by subgroup — h_survival_duration_subgroups","text":"tte (numeric) vector time--event duration values. is_event (flag)TRUE event, FALSE time event censored. arm (factor) treatment group variable. variables (named list string) list additional analysis variables. data (data.frame) dataset containing variables summarize. groups_lists (named list list) optionally contains subgroups variable list, specifies new group levels via names levels belong character vectors elements list. label_all (string) label total population analysis. strata_data (factor, data.frame, NULL) required stratified analysis performed. control (list) parameters comparison details, specified using helper function control_coxph(). possible parameter options : pval_method (string) p-value method testing null hypothesis hazard ratio = 1. Default method \"log-rank\" comes survival::survdiff(), can also set \"wald\" \"likelihood\" (survival::coxph()). ties (string) specifying method tie handling. Default \"efron\", can also set \"breslow\" \"exact\". See survival::coxph(). conf_level (proportion) confidence level interval HR.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/h_survival_duration_subgroups.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Helper functions for tabulating survival duration by subgroup — h_survival_duration_subgroups","text":"h_survtime_df() returns data.frame columns arm, n, n_events, median. h_survtime_subgroups_df() returns data.frame columns arm, n, n_events, median, subgroup, var, var_label, row_type. h_coxph_df() returns data.frame columns arm, n_tot, n_tot_events, hr, lcl, ucl, conf_level, pval pval_label. h_coxph_subgroups_df() returns data.frame columns arm, n_tot, n_tot_events, hr, lcl, ucl, conf_level, pval, pval_label, subgroup, var, var_label, row_type.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/h_survival_duration_subgroups.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Helper functions for tabulating survival duration by subgroup — h_survival_duration_subgroups","text":"Main functionality prepare data use layout-creating function.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/h_survival_duration_subgroups.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Helper functions for tabulating survival duration by subgroup — h_survival_duration_subgroups","text":"h_survtime_df(): Helper prepare data frame median survival times arm. h_survtime_subgroups_df(): Summarizes median survival times arm across subgroups data frame. variables corresponds names variables found data, passed named list requires elements tte, is_event, arm optionally subgroups. groups_lists optionally specifies groupings subgroups variables. h_coxph_df(): Helper prepare data frame estimates treatment hazard ratio. h_coxph_subgroups_df(): Summarizes estimates treatment hazard ratio across subgroups data frame. variables corresponds names variables found data, passed named list requires elements tte, is_event, arm optionally subgroups strata. groups_lists optionally specifies groupings subgroups variables.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/h_survival_duration_subgroups.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Helper functions for tabulating survival duration by subgroup — h_survival_duration_subgroups","text":"","code":"library(dplyr) library(forcats)  adtte <- tern_ex_adtte  # Save variable labels before data processing steps. adtte_labels <- formatters::var_labels(adtte)  adtte_f <- adtte %>%   filter(     PARAMCD == \"OS\",     ARM %in% c(\"B: Placebo\", \"A: Drug X\"),     SEX %in% c(\"M\", \"F\")   ) %>%   mutate(     # Reorder levels of ARM to display reference arm before treatment arm.     ARM = droplevels(fct_relevel(ARM, \"B: Placebo\")),     SEX = droplevels(SEX),     is_event = CNSR == 0   ) labels <- c(\"ARM\" = adtte_labels[[\"ARM\"]], \"SEX\" = adtte_labels[[\"SEX\"]], \"is_event\" = \"Event Flag\") formatters::var_labels(adtte_f)[names(labels)] <- labels  # Extract median survival time for one group. h_survtime_df(   tte = adtte_f$AVAL,   is_event = adtte_f$is_event,   arm = adtte_f$ARM ) #>          arm  n n_events   median #> 1 B: Placebo 73       57 727.8043 #> 2  A: Drug X 69       44 974.6402  # Extract median survival time for multiple groups. h_survtime_subgroups_df(   variables = list(     tte = \"AVAL\",     is_event = \"is_event\",     arm = \"ARM\",     subgroups = c(\"SEX\", \"BMRKR2\")   ),   data = adtte_f ) #>           arm  n n_events    median     subgroup    var #> 1  B: Placebo 73       57  727.8043 All Patients    ALL #> 2   A: Drug X 69       44  974.6402 All Patients    ALL #> 3  B: Placebo 40       31  599.1772            F    SEX #> 4   A: Drug X 38       24 1016.2982            F    SEX #> 5  B: Placebo 33       26  888.4916            M    SEX #> 6   A: Drug X 31       20  974.6402            M    SEX #> 7  B: Placebo 24       21  735.4722          LOW BMRKR2 #> 8   A: Drug X 26       15  974.6402          LOW BMRKR2 #> 9  B: Placebo 23       14  731.8352       MEDIUM BMRKR2 #> 10  A: Drug X 26       17  964.2197       MEDIUM BMRKR2 #> 11 B: Placebo 26       22  654.8245         HIGH BMRKR2 #> 12  A: Drug X 17       12 1016.2982         HIGH BMRKR2 #>                       var_label row_type #> 1                  All Patients  content #> 2                  All Patients  content #> 3                           Sex analysis #> 4                           Sex analysis #> 5                           Sex analysis #> 6                           Sex analysis #> 7  Continuous Level Biomarker 2 analysis #> 8  Continuous Level Biomarker 2 analysis #> 9  Continuous Level Biomarker 2 analysis #> 10 Continuous Level Biomarker 2 analysis #> 11 Continuous Level Biomarker 2 analysis #> 12 Continuous Level Biomarker 2 analysis  # Define groupings for BMRKR2 levels. h_survtime_subgroups_df(   variables = list(     tte = \"AVAL\",     is_event = \"is_event\",     arm = \"ARM\",     subgroups = c(\"SEX\", \"BMRKR2\")   ),   data = adtte_f,   groups_lists = list(     BMRKR2 = list(       \"low\" = \"LOW\",       \"low/medium\" = c(\"LOW\", \"MEDIUM\"),       \"low/medium/high\" = c(\"LOW\", \"MEDIUM\", \"HIGH\")     )   ) ) #>           arm  n n_events    median        subgroup    var #> 1  B: Placebo 73       57  727.8043    All Patients    ALL #> 2   A: Drug X 69       44  974.6402    All Patients    ALL #> 3  B: Placebo 40       31  599.1772               F    SEX #> 4   A: Drug X 38       24 1016.2982               F    SEX #> 5  B: Placebo 33       26  888.4916               M    SEX #> 6   A: Drug X 31       20  974.6402               M    SEX #> 7  B: Placebo 24       21  735.4722             low BMRKR2 #> 8   A: Drug X 26       15  974.6402             low BMRKR2 #> 9  B: Placebo 47       35  735.4722      low/medium BMRKR2 #> 10  A: Drug X 52       32  964.2197      low/medium BMRKR2 #> 11 B: Placebo 73       57  727.8043 low/medium/high BMRKR2 #> 12  A: Drug X 69       44  974.6402 low/medium/high BMRKR2 #>                       var_label row_type #> 1                  All Patients  content #> 2                  All Patients  content #> 3                           Sex analysis #> 4                           Sex analysis #> 5                           Sex analysis #> 6                           Sex analysis #> 7  Continuous Level Biomarker 2 analysis #> 8  Continuous Level Biomarker 2 analysis #> 9  Continuous Level Biomarker 2 analysis #> 10 Continuous Level Biomarker 2 analysis #> 11 Continuous Level Biomarker 2 analysis #> 12 Continuous Level Biomarker 2 analysis  # Extract hazard ratio for one group. h_coxph_df(adtte_f$AVAL, adtte_f$is_event, adtte_f$ARM) #>   arm n_tot n_tot_events        hr       lcl      ucl conf_level       pval #> 1       142          101 0.7108557 0.4779138 1.057337       0.95 0.09049511 #>           pval_label #> 1 p-value (log-rank)  # Extract hazard ratio for one group with stratification factor. h_coxph_df(adtte_f$AVAL, adtte_f$is_event, adtte_f$ARM, strata_data = adtte_f$STRATA1) #>   arm n_tot n_tot_events        hr       lcl     ucl conf_level       pval #> 1       142          101 0.6646586 0.4399495 1.00414       0.95 0.05089188 #>           pval_label #> 1 p-value (log-rank)  # Extract hazard ratio for multiple groups. h_coxph_subgroups_df(   variables = list(     tte = \"AVAL\",     is_event = \"is_event\",     arm = \"ARM\",     subgroups = c(\"SEX\", \"BMRKR2\")   ),   data = adtte_f ) #>   arm n_tot n_tot_events        hr       lcl       ucl conf_level       pval #> 1       142          101 0.7108557 0.4779138 1.0573368       0.95 0.09049511 #> 2        78           55 0.5595391 0.3246658 0.9643271       0.95 0.03411759 #> 3        64           46 0.9102874 0.5032732 1.6464678       0.95 0.75582028 #> 4        50           36 0.7617717 0.3854349 1.5055617       0.95 0.43236030 #> 5        49           31 0.7651261 0.3641277 1.6077269       0.95 0.47860004 #> 6        43           34 0.6662356 0.3257413 1.3626456       0.95 0.26285846 #>           pval_label     subgroup    var                    var_label row_type #> 1 p-value (log-rank) All Patients    ALL                 All Patients  content #> 2 p-value (log-rank)            F    SEX                          Sex analysis #> 3 p-value (log-rank)            M    SEX                          Sex analysis #> 4 p-value (log-rank)          LOW BMRKR2 Continuous Level Biomarker 2 analysis #> 5 p-value (log-rank)       MEDIUM BMRKR2 Continuous Level Biomarker 2 analysis #> 6 p-value (log-rank)         HIGH BMRKR2 Continuous Level Biomarker 2 analysis  # Define groupings of BMRKR2 levels. h_coxph_subgroups_df(   variables = list(     tte = \"AVAL\",     is_event = \"is_event\",     arm = \"ARM\",     subgroups = c(\"SEX\", \"BMRKR2\")   ),   data = adtte_f,   groups_lists = list(     BMRKR2 = list(       \"low\" = \"LOW\",       \"low/medium\" = c(\"LOW\", \"MEDIUM\"),       \"low/medium/high\" = c(\"LOW\", \"MEDIUM\", \"HIGH\")     )   ) ) #>   arm n_tot n_tot_events        hr       lcl       ucl conf_level       pval #> 1       142          101 0.7108557 0.4779138 1.0573368       0.95 0.09049511 #> 2        78           55 0.5595391 0.3246658 0.9643271       0.95 0.03411759 #> 3        64           46 0.9102874 0.5032732 1.6464678       0.95 0.75582028 #> 4        50           36 0.7617717 0.3854349 1.5055617       0.95 0.43236030 #> 5        99           67 0.7472958 0.4600419 1.2139136       0.95 0.23764314 #> 6       142          101 0.7108557 0.4779138 1.0573368       0.95 0.09049511 #>           pval_label        subgroup    var                    var_label #> 1 p-value (log-rank)    All Patients    ALL                 All Patients #> 2 p-value (log-rank)               F    SEX                          Sex #> 3 p-value (log-rank)               M    SEX                          Sex #> 4 p-value (log-rank)             low BMRKR2 Continuous Level Biomarker 2 #> 5 p-value (log-rank)      low/medium BMRKR2 Continuous Level Biomarker 2 #> 6 p-value (log-rank) low/medium/high BMRKR2 Continuous Level Biomarker 2 #>   row_type #> 1  content #> 2 analysis #> 3 analysis #> 4 analysis #> 5 analysis #> 6 analysis  # Extract hazard ratio for multiple groups with stratification factors. h_coxph_subgroups_df(   variables = list(     tte = \"AVAL\",     is_event = \"is_event\",     arm = \"ARM\",     subgroups = c(\"SEX\", \"BMRKR2\"),     strata = c(\"STRATA1\", \"STRATA2\")   ),   data = adtte_f ) #>   arm n_tot n_tot_events        hr       lcl       ucl conf_level       pval #> 1       142          101 0.6126133 0.3913507 0.9589739       0.95 0.03086774 #> 2        78           55 0.3934024 0.2027682 0.7632630       0.95 0.00469167 #> 3        64           46 0.9501768 0.4730073 1.9087145       0.95 0.88580522 #> 4        50           36 0.7378635 0.3140465 1.7336363       0.95 0.48408079 #> 5        49           31 0.9408062 0.4172095 2.1215148       0.95 0.88305965 #> 6        43           34 0.5125617 0.2125140 1.2362459       0.95 0.13124382 #>           pval_label     subgroup    var                    var_label row_type #> 1 p-value (log-rank) All Patients    ALL                 All Patients  content #> 2 p-value (log-rank)            F    SEX                          Sex analysis #> 3 p-value (log-rank)            M    SEX                          Sex analysis #> 4 p-value (log-rank)          LOW BMRKR2 Continuous Level Biomarker 2 analysis #> 5 p-value (log-rank)       MEDIUM BMRKR2 Continuous Level Biomarker 2 analysis #> 6 p-value (log-rank)         HIGH BMRKR2 Continuous Level Biomarker 2 analysis"},{"path":"https://insightsengineering.github.io/tern/main/reference/h_tab_one_biomarker.html","id":null,"dir":"Reference","previous_headings":"","what":"Helper function for tabulation of a single biomarker result — h_tab_one_biomarker","title":"Helper function for tabulation of a single biomarker result — h_tab_one_biomarker","text":"Please see h_tab_surv_one_biomarker() h_tab_rsp_one_biomarker(), use function examples. function wrapper rtables::summarize_row_groups().","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/h_tab_one_biomarker.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Helper function for tabulation of a single biomarker result — h_tab_one_biomarker","text":"","code":"h_tab_one_biomarker(   df,   afuns,   colvars,   na_str = default_na_str(),   .indent_mods = 0L,   ... )"},{"path":"https://insightsengineering.github.io/tern/main/reference/h_tab_one_biomarker.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Helper function for tabulation of a single biomarker result — h_tab_one_biomarker","text":"df (data.frame) results single biomarker. afuns (named list function) analysis functions. colvars (named list) named list elements vars (variables tabulate) labels (labels). na_str (string) string used replace NA empty values output. .indent_mods (named integer) indent modifiers labels. Defaults 0, corresponds unmodified default behavior. Can negative. ... additional arguments lower level functions.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/h_tab_one_biomarker.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Helper function for tabulation of a single biomarker result — h_tab_one_biomarker","text":"rtables table object statistics columns.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/h_tbl_coxph_pairwise.html","id":null,"dir":"Reference","previous_headings":"","what":"Helper function for generating a pairwise Cox-PH table — h_tbl_coxph_pairwise","title":"Helper function for generating a pairwise Cox-PH table — h_tbl_coxph_pairwise","text":"Create data.frame pairwise stratified unstratified Cox-PH analysis results.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/h_tbl_coxph_pairwise.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Helper function for generating a pairwise Cox-PH table — h_tbl_coxph_pairwise","text":"","code":"h_tbl_coxph_pairwise(   df,   variables,   ref_group_coxph = NULL,   control_coxph_pw = control_coxph(),   annot_coxph_ref_lbls = FALSE )"},{"path":"https://insightsengineering.github.io/tern/main/reference/h_tbl_coxph_pairwise.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Helper function for generating a pairwise Cox-PH table — h_tbl_coxph_pairwise","text":"df (data.frame) data set containing analysis variables. variables (named list) variable names. Details : tte (numeric) variable indicating time--event duration values. is_event (logical) event variable. TRUE event, FALSE time event censored. arm (factor) treatment group variable. strata (character NULL) variable names indicating stratification factors. ref_group_coxph (string NULL) level arm variable use reference group calculations annot_coxph table. NULL (default), uses first level arm variable. control_coxph_pw (list) parameters comparison details, specified using helper function control_coxph(). possible parameter options : pval_method (string) p-value method testing hazard ratio = 1. Default method \"log-rank\", can also set \"wald\" \"likelihood\". ties (string) method tie handling. Default \"efron\", can also set \"breslow\" \"exact\". See survival::coxph() conf_level (proportion) confidence level interval HR. annot_coxph_ref_lbls (flag) whether reference group explicitly printed labels annot_coxph table. FALSE (default), comparison groups printed annot_coxph table labels.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/h_tbl_coxph_pairwise.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Helper function for generating a pairwise Cox-PH table — h_tbl_coxph_pairwise","text":"data.frame containing statistics HR, XX% CI (XX taken control_coxph_pw), p-value (log-rank).","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/h_tbl_coxph_pairwise.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Helper function for generating a pairwise Cox-PH table — h_tbl_coxph_pairwise","text":"","code":"library(dplyr)  adtte <- tern_ex_adtte %>%   filter(PARAMCD == \"OS\") %>%   mutate(is_event = CNSR == 0)  h_tbl_coxph_pairwise(   df = adtte,   variables = list(tte = \"AVAL\", is_event = \"is_event\", arm = \"ARM\"),   control_coxph_pw = control_coxph(conf_level = 0.9) ) #>                  HR       90% CI p-value (log-rank) #> B: Placebo     1.41 (1.01, 1.96)             0.0905 #> C: Combination 1.81 (1.24, 2.64)             0.0086"},{"path":"https://insightsengineering.github.io/tern/main/reference/h_tbl_median_surv.html","id":null,"dir":"Reference","previous_headings":"","what":"Helper function for survival estimations — h_tbl_median_surv","title":"Helper function for survival estimations — h_tbl_median_surv","text":"Transform survival fit table groups rows characterized N, median confidence interval.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/h_tbl_median_surv.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Helper function for survival estimations — h_tbl_median_surv","text":"","code":"h_tbl_median_surv(fit_km, armval = \"All\")"},{"path":"https://insightsengineering.github.io/tern/main/reference/h_tbl_median_surv.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Helper function for survival estimations — h_tbl_median_surv","text":"fit_km (survfit) result survival::survfit(). armval (string) used strata name treatment arm variable one level. Default \"\".","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/h_tbl_median_surv.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Helper function for survival estimations — h_tbl_median_surv","text":"summary table statistics N, Median, XX% CI (XX taken fit_km).","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/h_tbl_median_surv.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Helper function for survival estimations — h_tbl_median_surv","text":"","code":"library(dplyr) library(survival)  adtte <- tern_ex_adtte %>% filter(PARAMCD == \"OS\") fit <- survfit(   formula = Surv(AVAL, 1 - CNSR) ~ ARMCD,   data = adtte ) h_tbl_median_surv(fit_km = fit) #>        N Median        95% CI #> ARM A 69  974.6   (687, 1625) #> ARM B 73  727.8 (555.8, 1156) #> ARM C 58  632.3   (393, 1001)"},{"path":"https://insightsengineering.github.io/tern/main/reference/h_worsen_counter.html","id":null,"dir":"Reference","previous_headings":"","what":"Helper function to analyze patients for s_count_abnormal_lab_worsen_by_baseline() — h_worsen_counter","title":"Helper function to analyze patients for s_count_abnormal_lab_worsen_by_baseline() — h_worsen_counter","text":"Helper function count number patients fraction patients according highest post-baseline lab grade variable .var, baseline lab grade variable baseline_var, direction interest specified direction_var.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/h_worsen_counter.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Helper function to analyze patients for s_count_abnormal_lab_worsen_by_baseline() — h_worsen_counter","text":"","code":"h_worsen_counter(df, id, .var, baseline_var, direction_var)"},{"path":"https://insightsengineering.github.io/tern/main/reference/h_worsen_counter.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Helper function to analyze patients for s_count_abnormal_lab_worsen_by_baseline() — h_worsen_counter","text":"df (data.frame) data set containing analysis variables. id (string) subject variable name. .var (string) single variable name passed rtables requested statistics function. baseline_var (string) name baseline lab grade variable. direction_var (string) name direction variable specifying direction shift table interest. lab records flagged L, H B included shift table. L: low direction H: high direction B: low high directions","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/h_worsen_counter.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Helper function to analyze patients for s_count_abnormal_lab_worsen_by_baseline() — h_worsen_counter","text":"counts fraction patients whose worst post-baseline lab grades worse baseline grades, post-baseline worst grades \"1\", \"2\", \"3\", \"4\" \"\".","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/main/reference/h_worsen_counter.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Helper function to analyze patients for s_count_abnormal_lab_worsen_by_baseline() — h_worsen_counter","text":"","code":"library(dplyr)  # The direction variable, GRADDR, is based on metadata adlb <- tern_ex_adlb %>%   mutate(     GRADDR = case_when(       PARAMCD == \"ALT\" ~ \"B\",       PARAMCD == \"CRP\" ~ \"L\",       PARAMCD == \"IGA\" ~ \"H\"     )   ) %>%   filter(SAFFL == \"Y\" & ONTRTFL == \"Y\" & GRADDR != \"\")  df <- h_adlb_worsen(   adlb,   worst_flag_low = c(\"WGRLOFL\" = \"Y\"),   worst_flag_high = c(\"WGRHIFL\" = \"Y\"),   direction_var = \"GRADDR\" )  # `h_worsen_counter` h_worsen_counter(   df %>% filter(PARAMCD == \"CRP\" & GRADDR == \"Low\"),   id = \"USUBJID\",   .var = \"ATOXGR\",   baseline_var = \"BTOXGR\",   direction_var = \"GRADDR\" ) #> $fraction #> $fraction$`1` #>   num denom  #>    25   180  #>  #> $fraction$`2` #>   num denom  #>    15   186  #>  #> $fraction$`3` #>   num denom  #>    18   191  #>  #> $fraction$`4` #>   num denom  #>    17   196  #>  #> $fraction$Any #>   num denom  #>    75   196  #>  #>"},{"path":"https://insightsengineering.github.io/tern/main/reference/h_xticks.html","id":null,"dir":"Reference","previous_headings":"","what":"Helper function to calculate x-tick positions — h_xticks","title":"Helper function to calculate x-tick positions — h_xticks","text":"Calculate positions ticks x-axis. However, xticks already exists kept . based function ggplot2 relies , required graphic patient--risk annotation table.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/h_xticks.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Helper function to calculate x-tick positions — h_xticks","text":"","code":"h_xticks(data, xticks = NULL, max_time = NULL)"},{"path":"https://insightsengineering.github.io/tern/main/reference/h_xticks.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Helper function to calculate x-tick positions — h_xticks","text":"data (data.frame) survival data pre-processed h_data_plot. xticks (numeric NULL) numeric vector tick positions single number spacing ticks x-axis. NULL (default), labeling::extended() used determine optimal tick positions x-axis. max_time (numeric(1)) maximum value show x-axis. data values less threshold value plotted (defaults NULL).","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/h_xticks.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Helper function to calculate x-tick positions — h_xticks","text":"vector positions use x-axis ticks ggplot object.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/h_xticks.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Helper function to calculate x-tick positions — h_xticks","text":"","code":"library(dplyr) library(survival)  data <- tern_ex_adtte %>%   filter(PARAMCD == \"OS\") %>%   survfit(formula = Surv(AVAL, 1 - CNSR) ~ ARMCD, data = .) %>%   h_data_plot()  h_xticks(data) #> [1]    0 1000 2000 3000 4000 5000 h_xticks(data, xticks = seq(0, 3000, 500)) #> [1]    0  500 1000 1500 2000 2500 3000 h_xticks(data, xticks = 500) #>  [1]    0  500 1000 1500 2000 2500 3000 3500 4000 4500 h_xticks(data, xticks = 500, max_time = 6000) #>  [1]    0  500 1000 1500 2000 2500 3000 3500 4000 4500 5000 5500 6000 h_xticks(data, xticks = c(0, 500), max_time = 300) #> [1]   0 500 h_xticks(data, xticks = 500, max_time = 300) #>  [1]    0  500 1000 1500 2000 2500 3000 3500 4000 4500"},{"path":[]},{"path":"https://insightsengineering.github.io/tern/main/reference/imputation_rule.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Apply 1/3 or 1/2 imputation rule to data — imputation_rule","text":"","code":"imputation_rule(   df,   x_stats,   stat,   imp_rule,   post = FALSE,   avalcat_var = \"AVALCAT1\" )"},{"path":"https://insightsengineering.github.io/tern/main/reference/imputation_rule.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Apply 1/3 or 1/2 imputation rule to data — imputation_rule","text":"df (data.frame) data set containing analysis variables. x_stats (named list) named list statistics, typically results s_summary(). stat (string) statistic return value/NA level according imputation rule applied. imp_rule (string) imputation rule setting. Set \"1/3\" implement 1/3 imputation rule \"1/2\" implement 1/2 imputation rule. post (flag) whether data corresponds post-dose time-point (defaults FALSE). parameter used imp_rule set \"1/3\". avalcat_var (string) name variable indicates whether row df corresponds analysis value category \"BLQ\", \"LTR\", \"<PCLLOQ\", none (defaults \"AVALCAT1\"). Variable avalcat_var must present df.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/imputation_rule.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Apply 1/3 or 1/2 imputation rule to data — imputation_rule","text":"list containing statistic value (val) NA level (na_str) displayed according specified imputation rule.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/main/reference/imputation_rule.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Apply 1/3 or 1/2 imputation rule to data — imputation_rule","text":"","code":"set.seed(1) df <- data.frame(   AVAL = runif(50, 0, 1),   AVALCAT1 = sample(c(1, \"BLQ\"), 50, replace = TRUE) ) x_stats <- s_summary(df$AVAL) imputation_rule(df, x_stats, \"max\", \"1/3\") #> $val #>       max  #> 0.9919061  #>  #> $na_str #> [1] \"ND\" #>  imputation_rule(df, x_stats, \"geom_mean\", \"1/3\") #> $val #> [1] NA #>  #> $na_str #> [1] \"NE\" #>  imputation_rule(df, x_stats, \"mean\", \"1/2\") #> $val #> [1] NA #>  #> $na_str #> [1] \"ND\" #>"},{"path":"https://insightsengineering.github.io/tern/main/reference/incidence_rate.html","id":null,"dir":"Reference","previous_headings":"","what":"Incidence rate estimation — incidence_rate","title":"Incidence rate estimation — incidence_rate","text":"analyze function estimate_incidence_rate() creates layout element estimate event rate adjusted person-years risk, otherwise known incidence rate. primary analysis variable specified via vars person-years risk. addition variable, n_events variable number events observed (value 1 means event observed 0 means event observed) must also specified.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/incidence_rate.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Incidence rate estimation — incidence_rate","text":"","code":"estimate_incidence_rate(   lyt,   vars,   n_events,   id_var = \"USUBJID\",   control = control_incidence_rate(),   na_str = default_na_str(),   nested = TRUE,   summarize = FALSE,   label_fmt = \"%s - %.labels\",   ...,   show_labels = \"hidden\",   table_names = vars,   .stats = c(\"person_years\", \"n_events\", \"rate\", \"rate_ci\"),   .formats = NULL,   .labels = NULL,   .indent_mods = NULL )  s_incidence_rate(   df,   .var,   n_events,   is_event = lifecycle::deprecated(),   id_var = \"USUBJID\",   control = control_incidence_rate() )  a_incidence_rate(   df,   labelstr = \"\",   .var,   .df_row,   n_events,   id_var = \"USUBJID\",   control = control_incidence_rate(),   .stats = NULL,   .formats = c(person_years = \"xx.x\", n_events = \"xx\", rate = \"xx.xx\", rate_ci =     \"(xx.xx, xx.xx)\", n_unique = \"xx\", n_rate = \"xx (xx.x)\"),   .labels = NULL,   .indent_mods = NULL,   na_str = default_na_str(),   label_fmt = \"%s - %.labels\" )"},{"path":"https://insightsengineering.github.io/tern/main/reference/incidence_rate.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Incidence rate estimation — incidence_rate","text":"lyt (PreDataTableLayouts) layout analyses added . vars (character) variable names primary analysis variable iterated . n_events (string) name integer variable indicating whether event observed (1) (0). id_var (string) name variable used patient identifier \"n_unique\" included .stats. Defaults \"USUBJID\". control (list) parameters estimation details, specified using helper function control_incidence_rate(). Possible parameter options : conf_level (proportion) confidence level estimated incidence rate. conf_type (string)normal (default), normal_log, exact, byar confidence interval type. input_time_unit (string)day, week, month, year (default) indicating time unit data input. num_pt_year (numeric) time unit desired output (person-years). na_str (string) string used replace NA empty values output. nested (flag) whether layout instruction applied within existing layout structure _if possible (TRUE, default) new top-level element (FALSE). Ignored nest split. underneath analyses, allowed. summarize (flag) whether function act analyze function (summarize = FALSE), summarize function (summarize = TRUE). Defaults FALSE. label_fmt (string) labels formatted row split occurs summarize = TRUE. string use \"%s\" represent row split levels, \"%.labels\" represent labels supplied .labels argument. Defaults \"%s - %.labels\". ... additional arguments lower level functions. show_labels (string) label visibility: one \"default\", \"visible\" \"hidden\". table_names (character) can customized case vars analyzed multiple times, avoid warnings rtables. .stats (character) statistics select table. Options : 'person_years', 'n_events', 'rate', 'rate_ci', 'n_unique', 'n_rate' .formats (named character list) formats statistics. See Details analyze_vars information \"auto\" setting. .labels (named character) labels statistics (without indent). .indent_mods (named integer) indent modifiers labels. Defaults 0, corresponds unmodified default behavior. Can negative. df (data.frame) data set containing analysis variables. .var (string) single variable name passed rtables requested statistics function. is_event (flag)TRUE event, FALSE time event censored. labelstr (string) label level parent split currently summarized (must present second argument Content Row Functions). See rtables::summarize_row_groups() information. .df_row (data.frame) data frame across columns given row split.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/incidence_rate.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Incidence rate estimation — incidence_rate","text":"estimate_incidence_rate() returns layout object suitable passing layouting functions, rtables::build_table(). Adding function rtable layout add formatted rows containing statistics s_incidence_rate() table layout. s_incidence_rate() returns following statistics: person_years: Total person-years risk. n_events: Total number events observed. rate: Estimated incidence rate. rate_ci: Confidence interval incidence rate. n_unique: Total number patients least one event observed. n_rate: Total number events observed & estimated incidence rate. a_incidence_rate() returns corresponding list formatted rtables::CellValue().","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/incidence_rate.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Incidence rate estimation — incidence_rate","text":"estimate_incidence_rate(): Layout-creating function can take statistics function arguments additional format arguments. function wrapper rtables::analyze(). s_incidence_rate(): Statistics function estimates incidence rate associated confidence interval. a_incidence_rate(): Formatted analysis function used afun estimate_incidence_rate().","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/main/reference/incidence_rate.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Incidence rate estimation — incidence_rate","text":"","code":"df <- data.frame(   USUBJID = as.character(seq(6)),   CNSR = c(0, 1, 1, 0, 0, 0),   AVAL = c(10.1, 20.4, 15.3, 20.8, 18.7, 23.4),   ARM = factor(c(\"A\", \"A\", \"A\", \"B\", \"B\", \"B\")),   STRATA1 = factor(c(\"X\", \"Y\", \"Y\", \"X\", \"X\", \"Y\")) ) df$n_events <- 1 - df$CNSR  basic_table(show_colcounts = TRUE) %>%   split_cols_by(\"ARM\") %>%   estimate_incidence_rate(     vars = \"AVAL\",     n_events = \"n_events\",     control = control_incidence_rate(       input_time_unit = \"month\",       num_pt_year = 100     )   ) %>%   build_table(df) #>                                            A                 B        #>                                          (N=3)             (N=3)      #> ————————————————————————————————————————————————————————————————————— #> Total patient-years at risk               3.8               5.2       #> Number of adverse events observed          1                 3        #> AE rate per 100 patient-years            26.20             57.23      #> 95% CI                              (-25.15, 77.55)   (-7.53, 122.00)  # summarize = TRUE basic_table(show_colcounts = TRUE) %>%   split_cols_by(\"ARM\") %>%   split_rows_by(\"STRATA1\", child_labels = \"visible\") %>%   estimate_incidence_rate(     vars = \"AVAL\",     n_events = \"n_events\",     .stats = c(\"n_unique\", \"n_rate\"),     summarize = TRUE,     label_fmt = \"%.labels\"   ) %>%   build_table(df) #>                                                                          A         B    #>                                                                        (N=3)     (N=3)  #> ——————————————————————————————————————————————————————————————————————————————————————— #> X                                                                                       #>   Total number of patients with at least one adverse event               1         2    #>   Number of adverse events observed (AE rate per 100 patient-years)   1 (9.9)   2 (5.1) #> Y                                                                                       #>   Total number of patients with at least one adverse event               0         1    #>   Number of adverse events observed (AE rate per 100 patient-years)   0 (0.0)   1 (4.3)  a_incidence_rate(   df,   .var = \"AVAL\",   .df_row = df,   n_events = \"n_events\" ) #> RowsVerticalSection (in_rows) object print method: #> ---------------------------- #>       row_name formatted_cell indent_mod #> 1 person_years          108.7          0 #> 2     n_events              4          0 #> 3         rate           3.68          0 #> 4      rate_ci   (0.07, 7.29)          0 #> 5     n_unique              4          0 #> 6       n_rate        4 (3.7)          0 #>                                                           row_label #> 1                                       Total patient-years at risk #> 2                                 Number of adverse events observed #> 3                                     AE rate per 100 patient-years #> 4                                                            95% CI #> 5          Total number of patients with at least one adverse event #> 6 Number of adverse events observed (AE rate per 100 patient-years)"},{"path":"https://insightsengineering.github.io/tern/main/reference/labels_or_names.html","id":null,"dir":"Reference","previous_headings":"","what":"Labels or names of list elements — labels_or_names","title":"Labels or names of list elements — labels_or_names","text":"Internal helper function working nested statistic function results typically labels names can use.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/labels_or_names.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Labels or names of list elements — labels_or_names","text":"","code":"labels_or_names(x)"},{"path":"https://insightsengineering.github.io/tern/main/reference/labels_or_names.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Labels or names of list elements — labels_or_names","text":"x (list) list.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/labels_or_names.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Labels or names of list elements — labels_or_names","text":"character vector labels names list elements.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/labels_use_control.html","id":null,"dir":"Reference","previous_headings":"","what":"Update labels according to control specifications — labels_use_control","title":"Update labels according to control specifications — labels_use_control","text":"Given list statistic labels list control parameters, updates labels relevant control specification. example, control element conf_level set 0.9, default label statistic mean_ci updated \"Mean 90% CI\". labels supplied via labels_custom updated regardless control.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/labels_use_control.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Update labels according to control specifications — labels_use_control","text":"","code":"labels_use_control(labels_default, control, labels_custom = NULL)"},{"path":"https://insightsengineering.github.io/tern/main/reference/labels_use_control.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Update labels according to control specifications — labels_use_control","text":"labels_default (named character) named vector statistic labels modify according control specifications. Labels explicitly defined labels_custom affected. control (named list) list control parameters apply adjust default labels. labels_custom (named character) named vector labels customized user affected control.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/labels_use_control.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Update labels according to control specifications — labels_use_control","text":"named character vector labels control specifications applied relevant labels.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/labels_use_control.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Update labels according to control specifications — labels_use_control","text":"","code":"control <- list(conf_level = 0.80, quantiles = c(0.1, 0.83), test_mean = 0.57) get_labels_from_stats(c(\"mean_ci\", \"quantiles\", \"mean_pval\")) %>%   labels_use_control(control = control) #>                          mean_ci                        quantiles  #>                    \"Mean 80% CI\"                \"10% and 83%-ile\"  #>                        mean_pval  #> \"Mean p-value (H0: mean = 0.57)\""},{"path":"https://insightsengineering.github.io/tern/main/reference/logistic_regression_cols.html","id":null,"dir":"Reference","previous_headings":"","what":"Logistic regression multivariate column layout function — logistic_regression_cols","title":"Logistic regression multivariate column layout function — logistic_regression_cols","text":"Layout-creating function creates multivariate column layout summarizing logistic regression results. function wrapper rtables::split_cols_by_multivar().","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/logistic_regression_cols.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Logistic regression multivariate column layout function — logistic_regression_cols","text":"","code":"logistic_regression_cols(lyt, conf_level = 0.95)"},{"path":"https://insightsengineering.github.io/tern/main/reference/logistic_regression_cols.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Logistic regression multivariate column layout function — logistic_regression_cols","text":"lyt (PreDataTableLayouts) layout analyses added . conf_level (proportion) confidence level interval.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/logistic_regression_cols.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Logistic regression multivariate column layout function — logistic_regression_cols","text":"layout object suitable passing layouting functions. Adding function rtable layout split table columns corresponding statistics df, estimate, std_error, odds_ratio, ci, pvalue.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/logistic_summary_by_flag.html","id":null,"dir":"Reference","previous_headings":"","what":"Logistic regression summary table — logistic_summary_by_flag","title":"Logistic regression summary table — logistic_summary_by_flag","text":"Constructor content functions used summarize_logistic() summarize logistic regression results. function wrapper rtables::summarize_row_groups().","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/logistic_summary_by_flag.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Logistic regression summary table — logistic_summary_by_flag","text":"","code":"logistic_summary_by_flag(   flag_var,   na_str = default_na_str(),   .indent_mods = NULL )"},{"path":"https://insightsengineering.github.io/tern/main/reference/logistic_summary_by_flag.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Logistic regression summary table — logistic_summary_by_flag","text":"flag_var (string) variable name identifying row used content function. na_str (string) string used replace NA empty values output. .indent_mods (named integer) indent modifiers labels. Defaults 0, corresponds unmodified default behavior. Can negative.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/logistic_summary_by_flag.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Logistic regression summary table — logistic_summary_by_flag","text":"content function.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/make_names.html","id":null,"dir":"Reference","previous_headings":"","what":"Make names without dots — make_names","title":"Make names without dots — make_names","text":"Make names without dots","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/make_names.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Make names without dots — make_names","text":"","code":"make_names(nams)"},{"path":"https://insightsengineering.github.io/tern/main/reference/make_names.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Make names without dots — make_names","text":"nams (character) vector original names.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/make_names.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Make names without dots — make_names","text":"character vector proper names, use dots contrast make.names().","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/month2day.html","id":null,"dir":"Reference","previous_headings":"","what":"Conversion of months to days — month2day","title":"Conversion of months to days — month2day","text":"Conversion months days. approximative calculation considers month average 30.4375 days.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/month2day.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Conversion of months to days — month2day","text":"","code":"month2day(x)"},{"path":"https://insightsengineering.github.io/tern/main/reference/month2day.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Conversion of months to days — month2day","text":"x (numeric(1)) time months.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/month2day.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Conversion of months to days — month2day","text":"numeric vector time days.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/month2day.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Conversion of months to days — month2day","text":"","code":"x <- c(13.25, 8.15, 1, 2.834) month2day(x) #> [1] 403.29688 248.06563  30.43750  86.25988"},{"path":"https://insightsengineering.github.io/tern/main/reference/muffled_car_anova.html","id":null,"dir":"Reference","previous_headings":"","what":"Muffled car::Anova — muffled_car_anova","title":"Muffled car::Anova — muffled_car_anova","text":"Applied survival models, car::Anova() signal strata terms dropped model formula present, function deliberately muffles message.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/muffled_car_anova.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Muffled car::Anova — muffled_car_anova","text":"","code":"muffled_car_anova(mod, test_statistic)"},{"path":"https://insightsengineering.github.io/tern/main/reference/muffled_car_anova.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Muffled car::Anova — muffled_car_anova","text":"mod (coxph) Cox regression model fitted survival::coxph(). test_statistic (string) method used estimation p.values; wald (default) likelihood.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/muffled_car_anova.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Muffled car::Anova — muffled_car_anova","text":"output car::Anova(), convergence message muffled.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/n_available.html","id":null,"dir":"Reference","previous_headings":"","what":"Number of available (non-missing entries) in a vector — n_available","title":"Number of available (non-missing entries) in a vector — n_available","text":"Small utility function better readability.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/n_available.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Number of available (non-missing entries) in a vector — n_available","text":"","code":"n_available(x)"},{"path":"https://insightsengineering.github.io/tern/main/reference/n_available.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Number of available (non-missing entries) in a vector — n_available","text":"x (vector) vector count non-missing values.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/n_available.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Number of available (non-missing entries) in a vector — n_available","text":"Number non-missing values.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/odds_ratio.html","id":null,"dir":"Reference","previous_headings":"","what":"Odds ratio estimation — odds_ratio","title":"Odds ratio estimation — odds_ratio","text":"analyze function estimate_odds_ratio() creates layout element compare bivariate responses two groups estimating odds ratio confidence interval. primary analysis variable specified vars group variable. Additional variables can included analysis via variables argument, accepts arm, arm variable, strata, stratification variable. two arm levels present, can combined two groups using groups_list argument.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/odds_ratio.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Odds ratio estimation — odds_ratio","text":"","code":"estimate_odds_ratio(   lyt,   vars,   variables = list(arm = NULL, strata = NULL),   conf_level = 0.95,   groups_list = NULL,   na_str = default_na_str(),   nested = TRUE,   method = \"exact\",   show_labels = \"hidden\",   table_names = vars,   var_labels = vars,   .stats = \"or_ci\",   .formats = NULL,   .labels = NULL,   .indent_mods = NULL )  s_odds_ratio(   df,   .var,   .ref_group,   .in_ref_col,   .df_row,   variables = list(arm = NULL, strata = NULL),   conf_level = 0.95,   groups_list = NULL,   method = \"exact\" )  a_odds_ratio(   df,   .var,   .ref_group,   .in_ref_col,   .df_row,   variables = list(arm = NULL, strata = NULL),   conf_level = 0.95,   groups_list = NULL,   method = \"exact\" )"},{"path":"https://insightsengineering.github.io/tern/main/reference/odds_ratio.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Odds ratio estimation — odds_ratio","text":"lyt (PreDataTableLayouts) layout analyses added . vars (character) variable names primary analysis variable iterated . variables (named list string) list additional analysis variables. conf_level (proportion) confidence level interval. groups_list (named list character) specifies new group levels via names levels belong character vectors elements list. na_str (string) string used replace NA empty values output. nested (flag) whether layout instruction applied within existing layout structure _if possible (TRUE, default) new top-level element (FALSE). Ignored nest split. underneath analyses, allowed. method (string) whether use correct (\"exact\") calculation conditional likelihood one approximations. See survival::clogit() details. show_labels (string) label visibility: one \"default\", \"visible\" \"hidden\". table_names (character) can customized case vars analyzed multiple times, avoid warnings rtables. var_labels (character) variable labels. .stats (character) statistics select table. Options : 'or_ci', 'n_tot' .formats (named character list) formats statistics. See Details analyze_vars information \"auto\" setting. .labels (named character) labels statistics (without indent). .indent_mods (named integer) indent modifiers labels. Defaults 0, corresponds unmodified default behavior. Can negative. df (data.frame) data set containing analysis variables. .var (string) single variable name passed rtables requested statistics function. .ref_group (data.frame vector) data corresponding reference group. .in_ref_col (flag)TRUE working reference level, FALSE otherwise. .df_row (data.frame) data frame across columns given row split.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/odds_ratio.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Odds ratio estimation — odds_ratio","text":"estimate_odds_ratio() returns layout object suitable passing layouting functions, rtables::build_table(). Adding function rtable layout add formatted rows containing statistics s_odds_ratio() table layout. s_odds_ratio() returns named list statistics or_ci (containing est, lcl, ucl) n_tot. a_odds_ratio() returns corresponding list formatted rtables::CellValue().","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/odds_ratio.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Odds ratio estimation — odds_ratio","text":"estimate_odds_ratio(): Layout-creating function can take statistics function arguments additional format arguments. function wrapper rtables::analyze(). s_odds_ratio(): Statistics function estimates odds ratio treatment control. variables list arm strata variable names must passed stratified analysis required. a_odds_ratio(): Formatted analysis function used afun estimate_odds_ratio().","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/odds_ratio.html","id":"note","dir":"Reference","previous_headings":"","what":"Note","title":"Odds ratio estimation — odds_ratio","text":"function uses logistic regression unstratified analyses, conditional logistic regression stratified analyses. Wald confidence interval calculated specified confidence level. stratified analyses, currently implementation conditional likelihood confidence intervals, therefore likelihood confidence interval available option. vars contains responders non-responders odds ratio estimation possible returned values NA.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/main/reference/odds_ratio.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Odds ratio estimation — odds_ratio","text":"","code":"set.seed(12) dta <- data.frame(   rsp = sample(c(TRUE, FALSE), 100, TRUE),   grp = factor(rep(c(\"A\", \"B\"), each = 50), levels = c(\"A\", \"B\")),   strata = factor(sample(c(\"C\", \"D\"), 100, TRUE)) )  l <- basic_table() %>%   split_cols_by(var = \"grp\", ref_group = \"B\") %>%   estimate_odds_ratio(vars = \"rsp\")  build_table(l, df = dta) #>                               A            B #> ———————————————————————————————————————————— #> Odds Ratio (95% CI)   0.85 (0.38 - 1.88)      # Unstratified analysis. s_odds_ratio(   df = subset(dta, grp == \"A\"),   .var = \"rsp\",   .ref_group = subset(dta, grp == \"B\"),   .in_ref_col = FALSE,   .df_row = dta ) #> $or_ci #>       est       lcl       ucl  #> 0.8484848 0.3831831 1.8788053  #> attr(,\"label\") #> [1] \"Odds Ratio (95% CI)\" #>  #> $n_tot #> n_tot  #>   100  #> attr(,\"label\") #> [1] \"Total n\" #>   # Stratified analysis. s_odds_ratio(   df = subset(dta, grp == \"A\"),   .var = \"rsp\",   .ref_group = subset(dta, grp == \"B\"),   .in_ref_col = FALSE,   .df_row = dta,   variables = list(arm = \"grp\", strata = \"strata\") ) #> $or_ci #>       est       lcl       ucl  #> 0.7689750 0.3424155 1.7269154  #> attr(,\"label\") #> [1] \"Odds Ratio (95% CI)\" #>  #> $n_tot #> n_tot  #>   100  #> attr(,\"label\") #> [1] \"Total n\" #>   a_odds_ratio(   df = subset(dta, grp == \"A\"),   .var = \"rsp\",   .ref_group = subset(dta, grp == \"B\"),   .in_ref_col = FALSE,   .df_row = dta ) #> RowsVerticalSection (in_rows) object print method: #> ---------------------------- #>   row_name     formatted_cell indent_mod           row_label #> 1    or_ci 0.85 (0.38 - 1.88)          1 Odds Ratio (95% CI) #> 2    n_tot                100          0             Total n"},{"path":"https://insightsengineering.github.io/tern/main/reference/prop_diff.html","id":null,"dir":"Reference","previous_headings":"","what":"Proportion difference estimation — prop_diff","title":"Proportion difference estimation — prop_diff","text":"analysis function estimate_proportion_diff() creates layout element estimate difference proportion responders within studied population. primary analysis variable, vars, logical variable indicating whether response occurred record. See method parameter options methods use constructing confidence interval proportion difference. stratification variable can supplied via strata element variables argument.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/prop_diff.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Proportion difference estimation — prop_diff","text":"","code":"estimate_proportion_diff(   lyt,   vars,   variables = list(strata = NULL),   conf_level = 0.95,   method = c(\"waldcc\", \"wald\", \"cmh\", \"ha\", \"newcombe\", \"newcombecc\", \"strat_newcombe\",     \"strat_newcombecc\"),   weights_method = \"cmh\",   na_str = default_na_str(),   nested = TRUE,   ...,   var_labels = vars,   show_labels = \"hidden\",   table_names = vars,   .stats = NULL,   .formats = NULL,   .labels = NULL,   .indent_mods = NULL )  s_proportion_diff(   df,   .var,   .ref_group,   .in_ref_col,   variables = list(strata = NULL),   conf_level = 0.95,   method = c(\"waldcc\", \"wald\", \"cmh\", \"ha\", \"newcombe\", \"newcombecc\", \"strat_newcombe\",     \"strat_newcombecc\"),   weights_method = \"cmh\" )  a_proportion_diff(   df,   .var,   .ref_group,   .in_ref_col,   variables = list(strata = NULL),   conf_level = 0.95,   method = c(\"waldcc\", \"wald\", \"cmh\", \"ha\", \"newcombe\", \"newcombecc\", \"strat_newcombe\",     \"strat_newcombecc\"),   weights_method = \"cmh\" )"},{"path":"https://insightsengineering.github.io/tern/main/reference/prop_diff.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Proportion difference estimation — prop_diff","text":"lyt (PreDataTableLayouts) layout analyses added . vars (character) variable names primary analysis variable iterated . variables (named list string) list additional analysis variables. conf_level (proportion) confidence level interval. method (string) method used confidence interval estimation. weights_method (string) weights method. Can either \"cmh\" \"heuristic\" directs way weights estimated. na_str (string) string used replace NA empty values output. nested (flag) whether layout instruction applied within existing layout structure _if possible (TRUE, default) new top-level element (FALSE). Ignored nest split. underneath analyses, allowed. ... additional arguments lower level functions. var_labels (character) variable labels. show_labels (string) label visibility: one \"default\", \"visible\" \"hidden\". table_names (character) can customized case vars analyzed multiple times, avoid warnings rtables. .stats (character) statistics select table. Options : 'diff', 'diff_ci' .formats (named character list) formats statistics. See Details analyze_vars information \"auto\" setting. .labels (named character) labels statistics (without indent). .indent_mods (named integer) indent modifiers labels. Defaults 0, corresponds unmodified default behavior. Can negative. df (data.frame) data set containing analysis variables. .var (string) single variable name passed rtables requested statistics function. .ref_group (data.frame vector) data corresponding reference group. .in_ref_col (flag)TRUE working reference level, FALSE otherwise.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/prop_diff.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Proportion difference estimation — prop_diff","text":"estimate_proportion_diff() returns layout object suitable passing layouting functions, rtables::build_table(). Adding function rtable layout add formatted rows containing statistics s_proportion_diff() table layout. s_proportion_diff() returns named list elements diff diff_ci. a_proportion_diff() returns corresponding list formatted rtables::CellValue().","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/prop_diff.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Proportion difference estimation — prop_diff","text":"estimate_proportion_diff(): Layout-creating function can take statistics function arguments additional format arguments. function wrapper rtables::analyze(). s_proportion_diff(): Statistics function estimating difference terms responder proportion. a_proportion_diff(): Formatted analysis function used afun estimate_proportion_diff().","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/prop_diff.html","id":"note","dir":"Reference","previous_headings":"","what":"Note","title":"Proportion difference estimation — prop_diff","text":"performing unstratified analysis, methods \"cmh\", \"strat_newcombe\", \"strat_newcombecc\" permitted.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/main/reference/prop_diff.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Proportion difference estimation — prop_diff","text":"","code":"## \"Mid\" case: 4/4 respond in group A, 1/2 respond in group B. nex <- 100 # Number of example rows dta <- data.frame(   \"rsp\" = sample(c(TRUE, FALSE), nex, TRUE),   \"grp\" = sample(c(\"A\", \"B\"), nex, TRUE),   \"f1\" = sample(c(\"a1\", \"a2\"), nex, TRUE),   \"f2\" = sample(c(\"x\", \"y\", \"z\"), nex, TRUE),   stringsAsFactors = TRUE )  l <- basic_table() %>%   split_cols_by(var = \"grp\", ref_group = \"B\") %>%   estimate_proportion_diff(     vars = \"rsp\",     conf_level = 0.90,     method = \"ha\"   )  build_table(l, df = dta) #>                                        A         B #> —————————————————————————————————————————————————— #> Difference in Response rate (%)       12.0         #>   90% CI (Anderson-Hauck)         (-5.4, 29.4)      s_proportion_diff(   df = subset(dta, grp == \"A\"),   .var = \"rsp\",   .ref_group = subset(dta, grp == \"B\"),   .in_ref_col = FALSE,   conf_level = 0.90,   method = \"ha\" ) #> $diff #> [1] 12 #> attr(,\"label\") #> [1] \"Difference in Response rate (%)\" #>  #> $diff_ci #> [1] -5.374519 29.374519 #> attr(,\"label\") #> [1] \"90% CI (Anderson-Hauck)\" #>   # CMH example with strata s_proportion_diff(   df = subset(dta, grp == \"A\"),   .var = \"rsp\",   .ref_group = subset(dta, grp == \"B\"),   .in_ref_col = FALSE,   variables = list(strata = c(\"f1\", \"f2\")),   conf_level = 0.90,   method = \"cmh\" ) #> $diff #> [1] 12.05847 #> attr(,\"label\") #> [1] \"Difference in Response rate (%)\" #>  #> $diff_ci #> [1] -2.67057 26.78750 #> attr(,\"label\") #> [1] \"90% CI (CMH, without correction)\" #>   a_proportion_diff(   df = subset(dta, grp == \"A\"),   .var = \"rsp\",   .ref_group = subset(dta, grp == \"B\"),   .in_ref_col = FALSE,   conf_level = 0.90,   method = \"ha\" ) #> RowsVerticalSection (in_rows) object print method: #> ---------------------------- #>   row_name formatted_cell indent_mod                       row_label #> 1     diff           12.0          0 Difference in Response rate (%) #> 2  diff_ci   (-5.4, 29.4)          1         90% CI (Anderson-Hauck)"},{"path":"https://insightsengineering.github.io/tern/main/reference/prop_diff_test.html","id":null,"dir":"Reference","previous_headings":"","what":"Difference test for two proportions — prop_diff_test","title":"Difference test for two proportions — prop_diff_test","text":"analyze function test_proportion_diff() creates layout element test difference two proportions. primary analysis variable, vars, indicates whether response occurred record. See method parameter options methods use calculate p-value. Additionally, stratification variable can supplied via strata element variables argument.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/prop_diff_test.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Difference test for two proportions — prop_diff_test","text":"","code":"test_proportion_diff(   lyt,   vars,   variables = list(strata = NULL),   method = c(\"chisq\", \"schouten\", \"fisher\", \"cmh\"),   na_str = default_na_str(),   nested = TRUE,   ...,   var_labels = vars,   show_labels = \"hidden\",   table_names = vars,   .stats = NULL,   .formats = NULL,   .labels = NULL,   .indent_mods = NULL )  s_test_proportion_diff(   df,   .var,   .ref_group,   .in_ref_col,   variables = list(strata = NULL),   method = c(\"chisq\", \"schouten\", \"fisher\", \"cmh\") )  a_test_proportion_diff(   df,   .var,   .ref_group,   .in_ref_col,   variables = list(strata = NULL),   method = c(\"chisq\", \"schouten\", \"fisher\", \"cmh\") )"},{"path":"https://insightsengineering.github.io/tern/main/reference/prop_diff_test.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Difference test for two proportions — prop_diff_test","text":"lyt (PreDataTableLayouts) layout analyses added . vars (character) variable names primary analysis variable iterated . variables (named list string) list additional analysis variables. method (string) one chisq, cmh, fisher, schouten; specifies test used calculate p-value. na_str (string) string used replace NA empty values output. nested (flag) whether layout instruction applied within existing layout structure _if possible (TRUE, default) new top-level element (FALSE). Ignored nest split. underneath analyses, allowed. ... additional arguments lower level functions. var_labels (character) variable labels. show_labels (string) label visibility: one \"default\", \"visible\" \"hidden\". table_names (character) can customized case vars analyzed multiple times, avoid warnings rtables. .stats (character) statistics select table. Options : 'pval' .formats (named character list) formats statistics. See Details analyze_vars information \"auto\" setting. .labels (named character) labels statistics (without indent). .indent_mods (named integer) indent modifiers labels. Defaults 0, corresponds unmodified default behavior. Can negative. df (data.frame) data set containing analysis variables. .var (string) single variable name passed rtables requested statistics function. .ref_group (data.frame vector) data corresponding reference group. .in_ref_col (flag)TRUE working reference level, FALSE otherwise.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/prop_diff_test.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Difference test for two proportions — prop_diff_test","text":"test_proportion_diff() returns layout object suitable passing layouting functions, rtables::build_table(). Adding function rtable layout add formatted rows containing statistics s_test_proportion_diff() table layout. s_test_proportion_diff() returns named list single item pval attribute label describing method used. p-value tests null hypothesis proportions two groups . a_test_proportion_diff() returns corresponding list formatted rtables::CellValue().","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/prop_diff_test.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Difference test for two proportions — prop_diff_test","text":"test_proportion_diff(): Layout-creating function can take statistics function arguments additional format arguments. function wrapper rtables::analyze(). s_test_proportion_diff(): Statistics function tests difference two proportions. a_test_proportion_diff(): Formatted analysis function used afun test_proportion_diff().","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/main/reference/prop_diff_test.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Difference test for two proportions — prop_diff_test","text":"","code":"dta <- data.frame(   rsp = sample(c(TRUE, FALSE), 100, TRUE),   grp = factor(rep(c(\"A\", \"B\"), each = 50)),   strata = factor(rep(c(\"V\", \"W\", \"X\", \"Y\", \"Z\"), each = 20)) )  # With `rtables` pipelines. l <- basic_table() %>%   split_cols_by(var = \"grp\", ref_group = \"B\") %>%   test_proportion_diff(     vars = \"rsp\",     method = \"cmh\", variables = list(strata = \"strata\")   )  build_table(l, df = dta) #>                                              A      B #> ————————————————————————————————————————————————————— #>   p-value (Cochran-Mantel-Haenszel Test)   1.0000"},{"path":"https://insightsengineering.github.io/tern/main/reference/prune_occurrences.html","id":null,"dir":"Reference","previous_headings":"","what":"Occurrence table pruning — prune_occurrences","title":"Occurrence table pruning — prune_occurrences","text":"Family constructor condition functions flexibly prune occurrence tables. condition functions always return whether row result higher threshold. Since class CombinationFunction() can logically combined condition functions.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/prune_occurrences.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Occurrence table pruning — prune_occurrences","text":"","code":"keep_rows(row_condition)  keep_content_rows(content_row_condition)  has_count_in_cols(atleast, ...)  has_count_in_any_col(atleast, ...)  has_fraction_in_cols(atleast, ...)  has_fraction_in_any_col(atleast, ...)  has_fractions_difference(atleast, ...)  has_counts_difference(atleast, ...)"},{"path":"https://insightsengineering.github.io/tern/main/reference/prune_occurrences.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Occurrence table pruning — prune_occurrences","text":"row_condition (CombinationFunction) condition function works individual analysis rows flags whether kept pruned table. content_row_condition (CombinationFunction) condition function works individual first content rows leaf tables flags whether leaf tables kept pruned table. atleast (numeric(1)) threshold met order keep row. ... arguments row column access, see rtables_access: either col_names (character) including names columns used, alternatively col_indices (integer) giving indices directly instead.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/prune_occurrences.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Occurrence table pruning — prune_occurrences","text":"keep_rows() returns pruning function can used rtables::prune_table() prune rtables table. keep_content_rows() returns pruning function checks condition first content row leaf tables table. has_count_in_cols() returns condition function sums counts specified column. has_count_in_any_col() returns condition function compares counts specified columns threshold. has_fraction_in_cols() returns condition function sums counts specified column, computes fraction dividing total column counts. has_fraction_in_any_col() returns condition function looks fractions specified columns checks whether fulfill threshold. has_fractions_difference() returns condition function extracts fractions specified column, computes difference minimum maximum. has_counts_difference() returns condition function extracts counts specified column, computes difference minimum maximum.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/prune_occurrences.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Occurrence table pruning — prune_occurrences","text":"keep_rows(): Constructor creating pruning functions based row condition function. removes analysis rows (TableRow) pruned, .e., fulfill row condition. removes sub-tree children left. keep_content_rows(): Constructor creating pruning functions based condition (first) content row leaf tables. removes leaf tables first content row fulfill condition. check individual rows. proceeds recursively removing sub tree children left. has_count_in_cols(): Constructor creating condition functions total counts specified columns. has_count_in_any_col(): Constructor creating condition functions counts specified columns satisfying threshold. has_fraction_in_cols(): Constructor creating condition functions total fraction specified columns. has_fraction_in_any_col(): Constructor creating condition functions fraction specified columns. has_fractions_difference(): Constructor creating condition function checks difference fractions reported specified column. has_counts_difference(): Constructor creating condition function checks difference counts reported specified column.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/prune_occurrences.html","id":"note","dir":"Reference","previous_headings":"","what":"Note","title":"Occurrence table pruning — prune_occurrences","text":"Since table specifications worded positively, name constructor condition functions positively, . However, note result keep_rows() says pruned, conform rtables::prune_table() interface.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/prune_occurrences.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Occurrence table pruning — prune_occurrences","text":"","code":"# \\donttest{ tab <- basic_table() %>%   split_cols_by(\"ARM\") %>%   split_rows_by(\"RACE\") %>%   split_rows_by(\"STRATA1\") %>%   summarize_row_groups() %>%   analyze_vars(\"COUNTRY\", .stats = \"count_fraction\") %>%   build_table(DM) # }  # \\donttest{ # `keep_rows` is_non_empty <- !CombinationFunction(all_zero_or_na) prune_table(tab, keep_rows(is_non_empty)) #>                             A: Drug X    B: Placebo   C: Combination #> ———————————————————————————————————————————————————————————————————— #> ASIAN                                                                #>   A                         27 (22.3%)   20 (18.9%)     31 (24.0%)   #>     CHN                     14 (51.9%)    9 (45%)       12 (38.7%)   #>     USA                      2 (7.4%)      1 (5%)       8 (25.8%)    #>     BRA                      1 (3.7%)     4 (20%)        1 (3.2%)    #>     PAK                     3 (11.1%)     2 (10%)        2 (6.5%)    #>     NGA                     3 (11.1%)      1 (5%)        3 (9.7%)    #>     RUS                      2 (7.4%)      1 (5%)        1 (3.2%)    #>     JPN                         0          1 (5%)        2 (6.5%)    #>     GBR                         0          1 (5%)        1 (3.2%)    #>     CAN                      2 (7.4%)        0           1 (3.2%)    #>   B                         24 (19.8%)   29 (27.4%)     22 (17.1%)   #>     CHN                      12 (50%)    13 (44.8%)      11 (50%)    #>     USA                      2 (8.3%)    5 (17.2%)       1 (4.5%)    #>     BRA                     4 (16.7%)    3 (10.3%)       1 (4.5%)    #>     PAK                      2 (8.3%)     2 (6.9%)      4 (18.2%)    #>     NGA                      2 (8.3%)     1 (3.4%)      3 (13.6%)    #>     RUS                      1 (4.2%)     1 (3.4%)       2 (9.1%)    #>     JPN                         0        4 (13.8%)          0        #>     GBR                      1 (4.2%)        0              0        #>   C                         28 (23.1%)   19 (17.9%)     31 (24.0%)   #>     CHN                     13 (46.4%)   10 (52.6%)     16 (51.6%)   #>     USA                     3 (10.7%)    3 (15.8%)      4 (12.9%)    #>     BRA                      1 (3.6%)     1 (5.3%)      4 (12.9%)    #>     PAK                      1 (3.6%)     1 (5.3%)       3 (9.7%)    #>     NGA                     4 (14.3%)     1 (5.3%)       2 (6.5%)    #>     RUS                     4 (14.3%)    2 (10.5%)       1 (3.2%)    #>     JPN                      2 (7.1%)     1 (5.3%)       1 (3.2%)    #> BLACK OR AFRICAN AMERICAN                                            #>   A                          6 (5.0%)     7 (6.6%)       8 (6.2%)    #>     CHN                      3 (50%)     3 (42.9%)      5 (62.5%)    #>     USA                     2 (33.3%)    1 (14.3%)      1 (12.5%)    #>     BRA                         0        1 (14.3%)          0        #>     PAK                         0            0          1 (12.5%)    #>     NGA                         0            0          1 (12.5%)    #>     JPN                     1 (16.7%)        0              0        #>     GBR                         0        2 (28.6%)          0        #>   B                         10 (8.3%)     6 (5.7%)      12 (9.3%)    #>     CHN                      3 (30%)     2 (33.3%)      8 (66.7%)    #>     USA                      1 (10%)         0           1 (8.3%)    #>     BRA                      2 (20%)     1 (16.7%)       1 (8.3%)    #>     PAK                         0        1 (16.7%)          0        #>     RUS                         0        1 (16.7%)          0        #>     JPN                      2 (20%)         0           1 (8.3%)    #>     GBR                      1 (10%)         0           1 (8.3%)    #>     CAN                      1 (10%)     1 (16.7%)          0        #>   C                         12 (9.9%)    11 (10.4%)      7 (5.4%)    #>     CHN                     8 (66.7%)    5 (45.5%)      5 (71.4%)    #>     USA                      1 (8.3%)    2 (18.2%)      1 (14.3%)    #>     BRA                      1 (8.3%)    2 (18.2%)          0        #>     PAK                      1 (8.3%)     1 (9.1%)      1 (14.3%)    #>     NGA                         0         1 (9.1%)          0        #>     RUS                      1 (8.3%)        0              0        #> WHITE                                                                #>   A                          3 (2.5%)     6 (5.7%)       6 (4.7%)    #>     CHN                     2 (66.7%)    2 (33.3%)       3 (50%)     #>     USA                     1 (33.3%)    1 (16.7%)          0        #>     PAK                         0        1 (16.7%)      1 (16.7%)    #>     NGA                         0        1 (16.7%)          0        #>     RUS                         0            0          1 (16.7%)    #>     JPN                         0        1 (16.7%)          0        #>     CAN                         0            0          1 (16.7%)    #>   B                          7 (5.8%)     5 (4.7%)       4 (3.1%)    #>     CHN                     4 (57.1%)     1 (20%)        3 (75%)     #>     USA                         0         1 (20%)           0        #>     BRA                         0         1 (20%)           0        #>     PAK                     1 (14.3%)        0              0        #>     NGA                     1 (14.3%)        0              0        #>     RUS                     1 (14.3%)        0           1 (25%)     #>     JPN                         0         1 (20%)           0        #>     CAN                         0         1 (20%)           0        #>   C                          4 (3.3%)     3 (2.8%)       8 (6.2%)    #>     CHN                      3 (75%)      3 (100%)       6 (75%)     #>     USA                      1 (25%)         0          1 (12.5%)    #>     JPN                         0            0          1 (12.5%)    # }  # `keep_content_rows` # \\donttest{ more_than_twenty <- has_count_in_cols(atleast = 20L, col_names = names(tab)) prune_table(tab, keep_content_rows(more_than_twenty)) #>                             A: Drug X    B: Placebo   C: Combination #> ———————————————————————————————————————————————————————————————————— #> ASIAN                                                                #>   A                         27 (22.3%)   20 (18.9%)     31 (24.0%)   #>     CHN                     14 (51.9%)    9 (45%)       12 (38.7%)   #>     USA                      2 (7.4%)      1 (5%)       8 (25.8%)    #>     BRA                      1 (3.7%)     4 (20%)        1 (3.2%)    #>     PAK                     3 (11.1%)     2 (10%)        2 (6.5%)    #>     NGA                     3 (11.1%)      1 (5%)        3 (9.7%)    #>     RUS                      2 (7.4%)      1 (5%)        1 (3.2%)    #>     JPN                         0          1 (5%)        2 (6.5%)    #>     GBR                         0          1 (5%)        1 (3.2%)    #>     CAN                      2 (7.4%)        0           1 (3.2%)    #>     CHE                         0            0              0        #>   B                         24 (19.8%)   29 (27.4%)     22 (17.1%)   #>     CHN                      12 (50%)    13 (44.8%)      11 (50%)    #>     USA                      2 (8.3%)    5 (17.2%)       1 (4.5%)    #>     BRA                     4 (16.7%)    3 (10.3%)       1 (4.5%)    #>     PAK                      2 (8.3%)     2 (6.9%)      4 (18.2%)    #>     NGA                      2 (8.3%)     1 (3.4%)      3 (13.6%)    #>     RUS                      1 (4.2%)     1 (3.4%)       2 (9.1%)    #>     JPN                         0        4 (13.8%)          0        #>     GBR                      1 (4.2%)        0              0        #>     CAN                         0            0              0        #>     CHE                         0            0              0        #>   C                         28 (23.1%)   19 (17.9%)     31 (24.0%)   #>     CHN                     13 (46.4%)   10 (52.6%)     16 (51.6%)   #>     USA                     3 (10.7%)    3 (15.8%)      4 (12.9%)    #>     BRA                      1 (3.6%)     1 (5.3%)      4 (12.9%)    #>     PAK                      1 (3.6%)     1 (5.3%)       3 (9.7%)    #>     NGA                     4 (14.3%)     1 (5.3%)       2 (6.5%)    #>     RUS                     4 (14.3%)    2 (10.5%)       1 (3.2%)    #>     JPN                      2 (7.1%)     1 (5.3%)       1 (3.2%)    #>     GBR                         0            0              0        #>     CAN                         0            0              0        #>     CHE                         0            0              0        #> BLACK OR AFRICAN AMERICAN                                            #>   A                          6 (5.0%)     7 (6.6%)       8 (6.2%)    #>     CHN                      3 (50%)     3 (42.9%)      5 (62.5%)    #>     USA                     2 (33.3%)    1 (14.3%)      1 (12.5%)    #>     BRA                         0        1 (14.3%)          0        #>     PAK                         0            0          1 (12.5%)    #>     NGA                         0            0          1 (12.5%)    #>     RUS                         0            0              0        #>     JPN                     1 (16.7%)        0              0        #>     GBR                         0        2 (28.6%)          0        #>     CAN                         0            0              0        #>     CHE                         0            0              0        #>   B                         10 (8.3%)     6 (5.7%)      12 (9.3%)    #>     CHN                      3 (30%)     2 (33.3%)      8 (66.7%)    #>     USA                      1 (10%)         0           1 (8.3%)    #>     BRA                      2 (20%)     1 (16.7%)       1 (8.3%)    #>     PAK                         0        1 (16.7%)          0        #>     NGA                         0            0              0        #>     RUS                         0        1 (16.7%)          0        #>     JPN                      2 (20%)         0           1 (8.3%)    #>     GBR                      1 (10%)         0           1 (8.3%)    #>     CAN                      1 (10%)     1 (16.7%)          0        #>     CHE                         0            0              0        #>   C                         12 (9.9%)    11 (10.4%)      7 (5.4%)    #>     CHN                     8 (66.7%)    5 (45.5%)      5 (71.4%)    #>     USA                      1 (8.3%)    2 (18.2%)      1 (14.3%)    #>     BRA                      1 (8.3%)    2 (18.2%)          0        #>     PAK                      1 (8.3%)     1 (9.1%)      1 (14.3%)    #>     NGA                         0         1 (9.1%)          0        #>     RUS                      1 (8.3%)        0              0        #>     JPN                         0            0              0        #>     GBR                         0            0              0        #>     CAN                         0            0              0        #>     CHE                         0            0              0        # }  # \\donttest{ more_than_one <- has_count_in_cols(atleast = 1L, col_names = names(tab)) prune_table(tab, keep_rows(more_than_one)) #>                             A: Drug X    B: Placebo   C: Combination #> ———————————————————————————————————————————————————————————————————— #> ASIAN                                                                #>   A                         27 (22.3%)   20 (18.9%)     31 (24.0%)   #>     CHN                     14 (51.9%)    9 (45%)       12 (38.7%)   #>     USA                      2 (7.4%)      1 (5%)       8 (25.8%)    #>     BRA                      1 (3.7%)     4 (20%)        1 (3.2%)    #>     PAK                     3 (11.1%)     2 (10%)        2 (6.5%)    #>     NGA                     3 (11.1%)      1 (5%)        3 (9.7%)    #>     RUS                      2 (7.4%)      1 (5%)        1 (3.2%)    #>     JPN                         0          1 (5%)        2 (6.5%)    #>     GBR                         0          1 (5%)        1 (3.2%)    #>     CAN                      2 (7.4%)        0           1 (3.2%)    #>   B                         24 (19.8%)   29 (27.4%)     22 (17.1%)   #>     CHN                      12 (50%)    13 (44.8%)      11 (50%)    #>     USA                      2 (8.3%)    5 (17.2%)       1 (4.5%)    #>     BRA                     4 (16.7%)    3 (10.3%)       1 (4.5%)    #>     PAK                      2 (8.3%)     2 (6.9%)      4 (18.2%)    #>     NGA                      2 (8.3%)     1 (3.4%)      3 (13.6%)    #>     RUS                      1 (4.2%)     1 (3.4%)       2 (9.1%)    #>     JPN                         0        4 (13.8%)          0        #>     GBR                      1 (4.2%)        0              0        #>   C                         28 (23.1%)   19 (17.9%)     31 (24.0%)   #>     CHN                     13 (46.4%)   10 (52.6%)     16 (51.6%)   #>     USA                     3 (10.7%)    3 (15.8%)      4 (12.9%)    #>     BRA                      1 (3.6%)     1 (5.3%)      4 (12.9%)    #>     PAK                      1 (3.6%)     1 (5.3%)       3 (9.7%)    #>     NGA                     4 (14.3%)     1 (5.3%)       2 (6.5%)    #>     RUS                     4 (14.3%)    2 (10.5%)       1 (3.2%)    #>     JPN                      2 (7.1%)     1 (5.3%)       1 (3.2%)    #> BLACK OR AFRICAN AMERICAN                                            #>   A                          6 (5.0%)     7 (6.6%)       8 (6.2%)    #>     CHN                      3 (50%)     3 (42.9%)      5 (62.5%)    #>     USA                     2 (33.3%)    1 (14.3%)      1 (12.5%)    #>     BRA                         0        1 (14.3%)          0        #>     PAK                         0            0          1 (12.5%)    #>     NGA                         0            0          1 (12.5%)    #>     JPN                     1 (16.7%)        0              0        #>     GBR                         0        2 (28.6%)          0        #>   B                         10 (8.3%)     6 (5.7%)      12 (9.3%)    #>     CHN                      3 (30%)     2 (33.3%)      8 (66.7%)    #>     USA                      1 (10%)         0           1 (8.3%)    #>     BRA                      2 (20%)     1 (16.7%)       1 (8.3%)    #>     PAK                         0        1 (16.7%)          0        #>     RUS                         0        1 (16.7%)          0        #>     JPN                      2 (20%)         0           1 (8.3%)    #>     GBR                      1 (10%)         0           1 (8.3%)    #>     CAN                      1 (10%)     1 (16.7%)          0        #>   C                         12 (9.9%)    11 (10.4%)      7 (5.4%)    #>     CHN                     8 (66.7%)    5 (45.5%)      5 (71.4%)    #>     USA                      1 (8.3%)    2 (18.2%)      1 (14.3%)    #>     BRA                      1 (8.3%)    2 (18.2%)          0        #>     PAK                      1 (8.3%)     1 (9.1%)      1 (14.3%)    #>     NGA                         0         1 (9.1%)          0        #>     RUS                      1 (8.3%)        0              0        #> WHITE                                                                #>   A                          3 (2.5%)     6 (5.7%)       6 (4.7%)    #>     CHN                     2 (66.7%)    2 (33.3%)       3 (50%)     #>     USA                     1 (33.3%)    1 (16.7%)          0        #>     PAK                         0        1 (16.7%)      1 (16.7%)    #>     NGA                         0        1 (16.7%)          0        #>     RUS                         0            0          1 (16.7%)    #>     JPN                         0        1 (16.7%)          0        #>     CAN                         0            0          1 (16.7%)    #>   B                          7 (5.8%)     5 (4.7%)       4 (3.1%)    #>     CHN                     4 (57.1%)     1 (20%)        3 (75%)     #>     USA                         0         1 (20%)           0        #>     BRA                         0         1 (20%)           0        #>     PAK                     1 (14.3%)        0              0        #>     NGA                     1 (14.3%)        0              0        #>     RUS                     1 (14.3%)        0           1 (25%)     #>     JPN                         0         1 (20%)           0        #>     CAN                         0         1 (20%)           0        #>   C                          4 (3.3%)     3 (2.8%)       8 (6.2%)    #>     CHN                      3 (75%)      3 (100%)       6 (75%)     #>     USA                      1 (25%)         0          1 (12.5%)    #>     JPN                         0            0          1 (12.5%)    # }  # \\donttest{ # `has_count_in_any_col` any_more_than_one <- has_count_in_any_col(atleast = 1L, col_names = names(tab)) prune_table(tab, keep_rows(any_more_than_one)) #>                             A: Drug X    B: Placebo   C: Combination #> ———————————————————————————————————————————————————————————————————— #> ASIAN                                                                #>   A                         27 (22.3%)   20 (18.9%)     31 (24.0%)   #>     CHN                     14 (51.9%)    9 (45%)       12 (38.7%)   #>     USA                      2 (7.4%)      1 (5%)       8 (25.8%)    #>     BRA                      1 (3.7%)     4 (20%)        1 (3.2%)    #>     PAK                     3 (11.1%)     2 (10%)        2 (6.5%)    #>     NGA                     3 (11.1%)      1 (5%)        3 (9.7%)    #>     RUS                      2 (7.4%)      1 (5%)        1 (3.2%)    #>     JPN                         0          1 (5%)        2 (6.5%)    #>     GBR                         0          1 (5%)        1 (3.2%)    #>     CAN                      2 (7.4%)        0           1 (3.2%)    #>   B                         24 (19.8%)   29 (27.4%)     22 (17.1%)   #>     CHN                      12 (50%)    13 (44.8%)      11 (50%)    #>     USA                      2 (8.3%)    5 (17.2%)       1 (4.5%)    #>     BRA                     4 (16.7%)    3 (10.3%)       1 (4.5%)    #>     PAK                      2 (8.3%)     2 (6.9%)      4 (18.2%)    #>     NGA                      2 (8.3%)     1 (3.4%)      3 (13.6%)    #>     RUS                      1 (4.2%)     1 (3.4%)       2 (9.1%)    #>     JPN                         0        4 (13.8%)          0        #>     GBR                      1 (4.2%)        0              0        #>   C                         28 (23.1%)   19 (17.9%)     31 (24.0%)   #>     CHN                     13 (46.4%)   10 (52.6%)     16 (51.6%)   #>     USA                     3 (10.7%)    3 (15.8%)      4 (12.9%)    #>     BRA                      1 (3.6%)     1 (5.3%)      4 (12.9%)    #>     PAK                      1 (3.6%)     1 (5.3%)       3 (9.7%)    #>     NGA                     4 (14.3%)     1 (5.3%)       2 (6.5%)    #>     RUS                     4 (14.3%)    2 (10.5%)       1 (3.2%)    #>     JPN                      2 (7.1%)     1 (5.3%)       1 (3.2%)    #> BLACK OR AFRICAN AMERICAN                                            #>   A                          6 (5.0%)     7 (6.6%)       8 (6.2%)    #>     CHN                      3 (50%)     3 (42.9%)      5 (62.5%)    #>     USA                     2 (33.3%)    1 (14.3%)      1 (12.5%)    #>     BRA                         0        1 (14.3%)          0        #>     PAK                         0            0          1 (12.5%)    #>     NGA                         0            0          1 (12.5%)    #>     JPN                     1 (16.7%)        0              0        #>     GBR                         0        2 (28.6%)          0        #>   B                         10 (8.3%)     6 (5.7%)      12 (9.3%)    #>     CHN                      3 (30%)     2 (33.3%)      8 (66.7%)    #>     USA                      1 (10%)         0           1 (8.3%)    #>     BRA                      2 (20%)     1 (16.7%)       1 (8.3%)    #>     PAK                         0        1 (16.7%)          0        #>     RUS                         0        1 (16.7%)          0        #>     JPN                      2 (20%)         0           1 (8.3%)    #>     GBR                      1 (10%)         0           1 (8.3%)    #>     CAN                      1 (10%)     1 (16.7%)          0        #>   C                         12 (9.9%)    11 (10.4%)      7 (5.4%)    #>     CHN                     8 (66.7%)    5 (45.5%)      5 (71.4%)    #>     USA                      1 (8.3%)    2 (18.2%)      1 (14.3%)    #>     BRA                      1 (8.3%)    2 (18.2%)          0        #>     PAK                      1 (8.3%)     1 (9.1%)      1 (14.3%)    #>     NGA                         0         1 (9.1%)          0        #>     RUS                      1 (8.3%)        0              0        #> WHITE                                                                #>   A                          3 (2.5%)     6 (5.7%)       6 (4.7%)    #>     CHN                     2 (66.7%)    2 (33.3%)       3 (50%)     #>     USA                     1 (33.3%)    1 (16.7%)          0        #>     PAK                         0        1 (16.7%)      1 (16.7%)    #>     NGA                         0        1 (16.7%)          0        #>     RUS                         0            0          1 (16.7%)    #>     JPN                         0        1 (16.7%)          0        #>     CAN                         0            0          1 (16.7%)    #>   B                          7 (5.8%)     5 (4.7%)       4 (3.1%)    #>     CHN                     4 (57.1%)     1 (20%)        3 (75%)     #>     USA                         0         1 (20%)           0        #>     BRA                         0         1 (20%)           0        #>     PAK                     1 (14.3%)        0              0        #>     NGA                     1 (14.3%)        0              0        #>     RUS                     1 (14.3%)        0           1 (25%)     #>     JPN                         0         1 (20%)           0        #>     CAN                         0         1 (20%)           0        #>   C                          4 (3.3%)     3 (2.8%)       8 (6.2%)    #>     CHN                      3 (75%)      3 (100%)       6 (75%)     #>     USA                      1 (25%)         0          1 (12.5%)    #>     JPN                         0            0          1 (12.5%)    # }  # \\donttest{ # `has_fraction_in_cols` more_than_five_percent <- has_fraction_in_cols(atleast = 0.05, col_names = names(tab)) prune_table(tab, keep_rows(more_than_five_percent)) #>                             A: Drug X    B: Placebo   C: Combination #> ———————————————————————————————————————————————————————————————————— #> ASIAN                                                                #>   A                         27 (22.3%)   20 (18.9%)     31 (24.0%)   #>     CHN                     14 (51.9%)    9 (45%)       12 (38.7%)   #>   B                         24 (19.8%)   29 (27.4%)     22 (17.1%)   #>     CHN                      12 (50%)    13 (44.8%)      11 (50%)    #>   C                         28 (23.1%)   19 (17.9%)     31 (24.0%)   #>     CHN                     13 (46.4%)   10 (52.6%)     16 (51.6%)   #> BLACK OR AFRICAN AMERICAN                                            #>   C                         12 (9.9%)    11 (10.4%)      7 (5.4%)    #>     CHN                     8 (66.7%)    5 (45.5%)      5 (71.4%)    # }  # \\donttest{ # `has_fraction_in_any_col` any_atleast_five_percent <- has_fraction_in_any_col(atleast = 0.05, col_names = names(tab)) prune_table(tab, keep_rows(any_atleast_five_percent)) #>                             A: Drug X    B: Placebo   C: Combination #> ———————————————————————————————————————————————————————————————————— #> ASIAN                                                                #>   A                         27 (22.3%)   20 (18.9%)     31 (24.0%)   #>     CHN                     14 (51.9%)    9 (45%)       12 (38.7%)   #>     USA                      2 (7.4%)      1 (5%)       8 (25.8%)    #>     BRA                      1 (3.7%)     4 (20%)        1 (3.2%)    #>     PAK                     3 (11.1%)     2 (10%)        2 (6.5%)    #>     NGA                     3 (11.1%)      1 (5%)        3 (9.7%)    #>     RUS                      2 (7.4%)      1 (5%)        1 (3.2%)    #>     JPN                         0          1 (5%)        2 (6.5%)    #>     GBR                         0          1 (5%)        1 (3.2%)    #>     CAN                      2 (7.4%)        0           1 (3.2%)    #>   B                         24 (19.8%)   29 (27.4%)     22 (17.1%)   #>     CHN                      12 (50%)    13 (44.8%)      11 (50%)    #>     USA                      2 (8.3%)    5 (17.2%)       1 (4.5%)    #>     BRA                     4 (16.7%)    3 (10.3%)       1 (4.5%)    #>     PAK                      2 (8.3%)     2 (6.9%)      4 (18.2%)    #>     NGA                      2 (8.3%)     1 (3.4%)      3 (13.6%)    #>     RUS                      1 (4.2%)     1 (3.4%)       2 (9.1%)    #>     JPN                         0        4 (13.8%)          0        #>   C                         28 (23.1%)   19 (17.9%)     31 (24.0%)   #>     CHN                     13 (46.4%)   10 (52.6%)     16 (51.6%)   #>     USA                     3 (10.7%)    3 (15.8%)      4 (12.9%)    #>     BRA                      1 (3.6%)     1 (5.3%)      4 (12.9%)    #>     PAK                      1 (3.6%)     1 (5.3%)       3 (9.7%)    #>     NGA                     4 (14.3%)     1 (5.3%)       2 (6.5%)    #>     RUS                     4 (14.3%)    2 (10.5%)       1 (3.2%)    #>     JPN                      2 (7.1%)     1 (5.3%)       1 (3.2%)    #> BLACK OR AFRICAN AMERICAN                                            #>   A                          6 (5.0%)     7 (6.6%)       8 (6.2%)    #>     CHN                      3 (50%)     3 (42.9%)      5 (62.5%)    #>     USA                     2 (33.3%)    1 (14.3%)      1 (12.5%)    #>     BRA                         0        1 (14.3%)          0        #>     PAK                         0            0          1 (12.5%)    #>     NGA                         0            0          1 (12.5%)    #>     JPN                     1 (16.7%)        0              0        #>     GBR                         0        2 (28.6%)          0        #>   B                         10 (8.3%)     6 (5.7%)      12 (9.3%)    #>     CHN                      3 (30%)     2 (33.3%)      8 (66.7%)    #>     USA                      1 (10%)         0           1 (8.3%)    #>     BRA                      2 (20%)     1 (16.7%)       1 (8.3%)    #>     PAK                         0        1 (16.7%)          0        #>     RUS                         0        1 (16.7%)          0        #>     JPN                      2 (20%)         0           1 (8.3%)    #>     GBR                      1 (10%)         0           1 (8.3%)    #>     CAN                      1 (10%)     1 (16.7%)          0        #>   C                         12 (9.9%)    11 (10.4%)      7 (5.4%)    #>     CHN                     8 (66.7%)    5 (45.5%)      5 (71.4%)    #>     USA                      1 (8.3%)    2 (18.2%)      1 (14.3%)    #>     BRA                      1 (8.3%)    2 (18.2%)          0        #>     PAK                      1 (8.3%)     1 (9.1%)      1 (14.3%)    #>     NGA                         0         1 (9.1%)          0        #>     RUS                      1 (8.3%)        0              0        #> WHITE                                                                #>   A                          3 (2.5%)     6 (5.7%)       6 (4.7%)    #>     CHN                     2 (66.7%)    2 (33.3%)       3 (50%)     #>     USA                     1 (33.3%)    1 (16.7%)          0        #>     PAK                         0        1 (16.7%)      1 (16.7%)    #>     NGA                         0        1 (16.7%)          0        #>     RUS                         0            0          1 (16.7%)    #>     JPN                         0        1 (16.7%)          0        #>     CAN                         0            0          1 (16.7%)    #>   B                          7 (5.8%)     5 (4.7%)       4 (3.1%)    #>     CHN                     4 (57.1%)     1 (20%)        3 (75%)     #>     USA                         0         1 (20%)           0        #>     BRA                         0         1 (20%)           0        #>     PAK                     1 (14.3%)        0              0        #>     NGA                     1 (14.3%)        0              0        #>     RUS                     1 (14.3%)        0           1 (25%)     #>     JPN                         0         1 (20%)           0        #>     CAN                         0         1 (20%)           0        #>   C                          4 (3.3%)     3 (2.8%)       8 (6.2%)    #>     CHN                      3 (75%)      3 (100%)       6 (75%)     #>     USA                      1 (25%)         0          1 (12.5%)    #>     JPN                         0            0          1 (12.5%)    # }  # \\donttest{ # `has_fractions_difference` more_than_five_percent_diff <- has_fractions_difference(atleast = 0.05, col_names = names(tab)) prune_table(tab, keep_rows(more_than_five_percent_diff)) #>                             A: Drug X    B: Placebo   C: Combination #> ———————————————————————————————————————————————————————————————————— #> ASIAN                                                                #>   A                         27 (22.3%)   20 (18.9%)     31 (24.0%)   #>     CHN                     14 (51.9%)    9 (45%)       12 (38.7%)   #>     USA                      2 (7.4%)      1 (5%)       8 (25.8%)    #>     BRA                      1 (3.7%)     4 (20%)        1 (3.2%)    #>     NGA                     3 (11.1%)      1 (5%)        3 (9.7%)    #>     JPN                         0          1 (5%)        2 (6.5%)    #>     GBR                         0          1 (5%)        1 (3.2%)    #>     CAN                      2 (7.4%)        0           1 (3.2%)    #>   B                         24 (19.8%)   29 (27.4%)     22 (17.1%)   #>     CHN                      12 (50%)    13 (44.8%)      11 (50%)    #>     USA                      2 (8.3%)    5 (17.2%)       1 (4.5%)    #>     BRA                     4 (16.7%)    3 (10.3%)       1 (4.5%)    #>     PAK                      2 (8.3%)     2 (6.9%)      4 (18.2%)    #>     NGA                      2 (8.3%)     1 (3.4%)      3 (13.6%)    #>     RUS                      1 (4.2%)     1 (3.4%)       2 (9.1%)    #>     JPN                         0        4 (13.8%)          0        #>   C                         28 (23.1%)   19 (17.9%)     31 (24.0%)   #>     CHN                     13 (46.4%)   10 (52.6%)     16 (51.6%)   #>     USA                     3 (10.7%)    3 (15.8%)      4 (12.9%)    #>     BRA                      1 (3.6%)     1 (5.3%)      4 (12.9%)    #>     PAK                      1 (3.6%)     1 (5.3%)       3 (9.7%)    #>     NGA                     4 (14.3%)     1 (5.3%)       2 (6.5%)    #>     RUS                     4 (14.3%)    2 (10.5%)       1 (3.2%)    #> BLACK OR AFRICAN AMERICAN                                            #>   A                          6 (5.0%)     7 (6.6%)       8 (6.2%)    #>     CHN                      3 (50%)     3 (42.9%)      5 (62.5%)    #>     USA                     2 (33.3%)    1 (14.3%)      1 (12.5%)    #>     BRA                         0        1 (14.3%)          0        #>     PAK                         0            0          1 (12.5%)    #>     NGA                         0            0          1 (12.5%)    #>     JPN                     1 (16.7%)        0              0        #>     GBR                         0        2 (28.6%)          0        #>   B                         10 (8.3%)     6 (5.7%)      12 (9.3%)    #>     CHN                      3 (30%)     2 (33.3%)      8 (66.7%)    #>     USA                      1 (10%)         0           1 (8.3%)    #>     BRA                      2 (20%)     1 (16.7%)       1 (8.3%)    #>     PAK                         0        1 (16.7%)          0        #>     RUS                         0        1 (16.7%)          0        #>     JPN                      2 (20%)         0           1 (8.3%)    #>     GBR                      1 (10%)         0           1 (8.3%)    #>     CAN                      1 (10%)     1 (16.7%)          0        #>   C                         12 (9.9%)    11 (10.4%)      7 (5.4%)    #>     CHN                     8 (66.7%)    5 (45.5%)      5 (71.4%)    #>     USA                      1 (8.3%)    2 (18.2%)      1 (14.3%)    #>     BRA                      1 (8.3%)    2 (18.2%)          0        #>     PAK                      1 (8.3%)     1 (9.1%)      1 (14.3%)    #>     NGA                         0         1 (9.1%)          0        #>     RUS                      1 (8.3%)        0              0        #> WHITE                                                                #>   A                          3 (2.5%)     6 (5.7%)       6 (4.7%)    #>     CHN                     2 (66.7%)    2 (33.3%)       3 (50%)     #>     USA                     1 (33.3%)    1 (16.7%)          0        #>     PAK                         0        1 (16.7%)      1 (16.7%)    #>     NGA                         0        1 (16.7%)          0        #>     RUS                         0            0          1 (16.7%)    #>     JPN                         0        1 (16.7%)          0        #>     CAN                         0            0          1 (16.7%)    #>   B                          7 (5.8%)     5 (4.7%)       4 (3.1%)    #>     CHN                     4 (57.1%)     1 (20%)        3 (75%)     #>     USA                         0         1 (20%)           0        #>     BRA                         0         1 (20%)           0        #>     PAK                     1 (14.3%)        0              0        #>     NGA                     1 (14.3%)        0              0        #>     RUS                     1 (14.3%)        0           1 (25%)     #>     JPN                         0         1 (20%)           0        #>     CAN                         0         1 (20%)           0        #>   C                          4 (3.3%)     3 (2.8%)       8 (6.2%)    #>     CHN                      3 (75%)      3 (100%)       6 (75%)     #>     USA                      1 (25%)         0          1 (12.5%)    #>     JPN                         0            0          1 (12.5%)    # }  # \\donttest{ more_than_one_diff <- has_counts_difference(atleast = 1L, col_names = names(tab)) prune_table(tab, keep_rows(more_than_one_diff)) #>                             A: Drug X    B: Placebo   C: Combination #> ———————————————————————————————————————————————————————————————————— #> ASIAN                                                                #>   A                         27 (22.3%)   20 (18.9%)     31 (24.0%)   #>     CHN                     14 (51.9%)    9 (45%)       12 (38.7%)   #>     USA                      2 (7.4%)      1 (5%)       8 (25.8%)    #>     BRA                      1 (3.7%)     4 (20%)        1 (3.2%)    #>     PAK                     3 (11.1%)     2 (10%)        2 (6.5%)    #>     NGA                     3 (11.1%)      1 (5%)        3 (9.7%)    #>     RUS                      2 (7.4%)      1 (5%)        1 (3.2%)    #>     JPN                         0          1 (5%)        2 (6.5%)    #>     GBR                         0          1 (5%)        1 (3.2%)    #>     CAN                      2 (7.4%)        0           1 (3.2%)    #>   B                         24 (19.8%)   29 (27.4%)     22 (17.1%)   #>     CHN                      12 (50%)    13 (44.8%)      11 (50%)    #>     USA                      2 (8.3%)    5 (17.2%)       1 (4.5%)    #>     BRA                     4 (16.7%)    3 (10.3%)       1 (4.5%)    #>     PAK                      2 (8.3%)     2 (6.9%)      4 (18.2%)    #>     NGA                      2 (8.3%)     1 (3.4%)      3 (13.6%)    #>     RUS                      1 (4.2%)     1 (3.4%)       2 (9.1%)    #>     JPN                         0        4 (13.8%)          0        #>     GBR                      1 (4.2%)        0              0        #>   C                         28 (23.1%)   19 (17.9%)     31 (24.0%)   #>     CHN                     13 (46.4%)   10 (52.6%)     16 (51.6%)   #>     USA                     3 (10.7%)    3 (15.8%)      4 (12.9%)    #>     BRA                      1 (3.6%)     1 (5.3%)      4 (12.9%)    #>     PAK                      1 (3.6%)     1 (5.3%)       3 (9.7%)    #>     NGA                     4 (14.3%)     1 (5.3%)       2 (6.5%)    #>     RUS                     4 (14.3%)    2 (10.5%)       1 (3.2%)    #>     JPN                      2 (7.1%)     1 (5.3%)       1 (3.2%)    #> BLACK OR AFRICAN AMERICAN                                            #>   A                          6 (5.0%)     7 (6.6%)       8 (6.2%)    #>     CHN                      3 (50%)     3 (42.9%)      5 (62.5%)    #>     USA                     2 (33.3%)    1 (14.3%)      1 (12.5%)    #>     BRA                         0        1 (14.3%)          0        #>     PAK                         0            0          1 (12.5%)    #>     NGA                         0            0          1 (12.5%)    #>     JPN                     1 (16.7%)        0              0        #>     GBR                         0        2 (28.6%)          0        #>   B                         10 (8.3%)     6 (5.7%)      12 (9.3%)    #>     CHN                      3 (30%)     2 (33.3%)      8 (66.7%)    #>     USA                      1 (10%)         0           1 (8.3%)    #>     BRA                      2 (20%)     1 (16.7%)       1 (8.3%)    #>     PAK                         0        1 (16.7%)          0        #>     RUS                         0        1 (16.7%)          0        #>     JPN                      2 (20%)         0           1 (8.3%)    #>     GBR                      1 (10%)         0           1 (8.3%)    #>     CAN                      1 (10%)     1 (16.7%)          0        #>   C                         12 (9.9%)    11 (10.4%)      7 (5.4%)    #>     CHN                     8 (66.7%)    5 (45.5%)      5 (71.4%)    #>     USA                      1 (8.3%)    2 (18.2%)      1 (14.3%)    #>     BRA                      1 (8.3%)    2 (18.2%)          0        #>     NGA                         0         1 (9.1%)          0        #>     RUS                      1 (8.3%)        0              0        #> WHITE                                                                #>   A                          3 (2.5%)     6 (5.7%)       6 (4.7%)    #>     CHN                     2 (66.7%)    2 (33.3%)       3 (50%)     #>     USA                     1 (33.3%)    1 (16.7%)          0        #>     PAK                         0        1 (16.7%)      1 (16.7%)    #>     NGA                         0        1 (16.7%)          0        #>     RUS                         0            0          1 (16.7%)    #>     JPN                         0        1 (16.7%)          0        #>     CAN                         0            0          1 (16.7%)    #>   B                          7 (5.8%)     5 (4.7%)       4 (3.1%)    #>     CHN                     4 (57.1%)     1 (20%)        3 (75%)     #>     USA                         0         1 (20%)           0        #>     BRA                         0         1 (20%)           0        #>     PAK                     1 (14.3%)        0              0        #>     NGA                     1 (14.3%)        0              0        #>     RUS                     1 (14.3%)        0           1 (25%)     #>     JPN                         0         1 (20%)           0        #>     CAN                         0         1 (20%)           0        #>   C                          4 (3.3%)     3 (2.8%)       8 (6.2%)    #>     CHN                      3 (75%)      3 (100%)       6 (75%)     #>     USA                      1 (25%)         0          1 (12.5%)    #>     JPN                         0            0          1 (12.5%)    # }"},{"path":"https://insightsengineering.github.io/tern/main/reference/range_noinf.html","id":null,"dir":"Reference","previous_headings":"","what":"Re-implemented range() default S3 method for numerical objects — range_noinf","title":"Re-implemented range() default S3 method for numerical objects — range_noinf","text":"function returns c(NA, NA) instead c(-Inf, Inf) zero-length data without warnings.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/range_noinf.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Re-implemented range() default S3 method for numerical objects — range_noinf","text":"","code":"range_noinf(x, na.rm = FALSE, finite = FALSE)"},{"path":"https://insightsengineering.github.io/tern/main/reference/range_noinf.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Re-implemented range() default S3 method for numerical objects — range_noinf","text":"x (numeric) sequence numbers range computed. na.rm (flag) flag indicating NA omitted. finite (flag) flag indicating non-finite elements removed.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/range_noinf.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Re-implemented range() default S3 method for numerical objects — range_noinf","text":"2-element vector class numeric.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/reapply_varlabels.html","id":null,"dir":"Reference","previous_headings":"","what":"Reapply variable labels — reapply_varlabels","title":"Reapply variable labels — reapply_varlabels","text":"helper function used tests.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/reapply_varlabels.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Reapply variable labels — reapply_varlabels","text":"","code":"reapply_varlabels(x, varlabels, ...)"},{"path":"https://insightsengineering.github.io/tern/main/reference/reapply_varlabels.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Reapply variable labels — reapply_varlabels","text":"x (vector) vector elements needs new labels. varlabels (character) vector labels x. ... parameters added list.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/reapply_varlabels.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Reapply variable labels — reapply_varlabels","text":"x variable labels reapplied.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/response_biomarkers_subgroups.html","id":null,"dir":"Reference","previous_headings":"","what":"Tabulate biomarker effects on binary response by subgroup — response_biomarkers_subgroups","title":"Tabulate biomarker effects on binary response by subgroup — response_biomarkers_subgroups","text":"tabulate_rsp_biomarkers() function creates layout element tabulate estimated biomarker effects binary response endpoint across subgroups, returning statistics including response rate odds ratio population subgroup. table created df, list data frames returned extract_rsp_biomarkers(), statistics include specified via vars parameter. forest plot can created resulting table using g_forest() function.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/response_biomarkers_subgroups.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Tabulate biomarker effects on binary response by subgroup — response_biomarkers_subgroups","text":"","code":"tabulate_rsp_biomarkers(   df,   vars = c(\"n_tot\", \"n_rsp\", \"prop\", \"or\", \"ci\", \"pval\"),   na_str = default_na_str(),   .indent_mods = 0L )"},{"path":"https://insightsengineering.github.io/tern/main/reference/response_biomarkers_subgroups.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Tabulate biomarker effects on binary response by subgroup — response_biomarkers_subgroups","text":"df (data.frame) containing analysis variables, returned extract_rsp_biomarkers(). vars (character) names statistics reported among: n_tot: Total number patients per group. n_rsp: Total number responses per group. prop: Total response proportion per group. : Odds ratio. ci: Confidence interval odds ratio. pval: p-value effect. Note, statistics n_tot, ci required. na_str (string) string used replace NA empty values output. .indent_mods (named integer) indent modifiers labels. Defaults 0, corresponds unmodified default behavior. Can negative.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/response_biomarkers_subgroups.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Tabulate biomarker effects on binary response by subgroup — response_biomarkers_subgroups","text":"rtables table summarizing biomarker effects binary response subgroup.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/response_biomarkers_subgroups.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Tabulate biomarker effects on binary response by subgroup — response_biomarkers_subgroups","text":"functions create layout starting data frame contains required statistics. tables typically used input forest plots.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/response_biomarkers_subgroups.html","id":"note","dir":"Reference","previous_headings":"","what":"Note","title":"Tabulate biomarker effects on binary response by subgroup — response_biomarkers_subgroups","text":"contrast tabulate_rsp_subgroups() tabulation function start input layout lyt. internally table created combining multiple subtables.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/main/reference/response_biomarkers_subgroups.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Tabulate biomarker effects on binary response by subgroup — response_biomarkers_subgroups","text":"","code":"library(dplyr) library(forcats)  adrs <- tern_ex_adrs adrs_labels <- formatters::var_labels(adrs)  adrs_f <- adrs %>%   filter(PARAMCD == \"BESRSPI\") %>%   mutate(rsp = AVALC == \"CR\") formatters::var_labels(adrs_f) <- c(adrs_labels, \"Response\")  df <- extract_rsp_biomarkers(   variables = list(     rsp = \"rsp\",     biomarkers = c(\"BMRKR1\", \"AGE\"),     covariates = \"SEX\",     subgroups = \"BMRKR2\"   ),   data = adrs_f )  # \\donttest{ ## Table with default columns. tabulate_rsp_biomarkers(df) #>                                  Total n   Responders   Response (%)   Odds Ratio      95% CI      p-value (Wald) #> ————————————————————————————————————————————————————————————————————————————————————————————————————————————————— #> Age                                                                                                               #>   All Patients                     200        164          82.0%          1.00      (0.95, 1.05)       0.8530     #>   Continuous Level Biomarker 2                                                                                    #>     LOW                            70          53          75.7%          0.93      (0.85, 1.01)       0.0845     #>     MEDIUM                         68          58          85.3%          0.99      (0.88, 1.11)       0.8190     #>     HIGH                           62          53          85.5%          1.06      (0.96, 1.18)       0.2419     #> Continuous Level Biomarker 1                                                                                      #>   All Patients                     200        164          82.0%          0.98      (0.88, 1.08)       0.6353     #>   Continuous Level Biomarker 2                                                                                    #>     LOW                            70          53          75.7%          1.15      (0.95, 1.40)       0.1584     #>     MEDIUM                         68          58          85.3%          0.88      (0.73, 1.06)       0.1700     #>     HIGH                           62          53          85.5%          0.88      (0.72, 1.08)       0.2104      ## Table with a manually chosen set of columns: leave out \"pval\", reorder. tab <- tabulate_rsp_biomarkers(   df = df,   vars = c(\"n_rsp\", \"ci\", \"n_tot\", \"prop\", \"or\") )  ## Finally produce the forest plot. g_forest(tab, xlim = c(0.7, 1.4))  # }"},{"path":"https://insightsengineering.github.io/tern/main/reference/response_subgroups.html","id":null,"dir":"Reference","previous_headings":"","what":"Tabulate binary response by subgroup — response_subgroups","title":"Tabulate binary response by subgroup — response_subgroups","text":"tabulate_rsp_subgroups() function creates layout element tabulate binary response subgroup, returning statistics including response rate odds ratio population subgroup. table created df, list data frames returned extract_rsp_subgroups(), statistics include specified via vars parameter. forest plot can created resulting table using g_forest() function.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/response_subgroups.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Tabulate binary response by subgroup — response_subgroups","text":"","code":"tabulate_rsp_subgroups(   lyt,   df,   vars = c(\"n_tot\", \"n\", \"prop\", \"or\", \"ci\"),   groups_lists = list(),   label_all = \"All Patients\",   riskdiff = NULL,   na_str = default_na_str(),   .formats = c(n = \"xx\", n_rsp = \"xx\", prop = \"xx.x%\", n_tot = \"xx\", or =     list(format_extreme_values(2L)), ci = list(format_extreme_values_ci(2L)), pval =     \"x.xxxx | (<0.0001)\") )  a_response_subgroups(   .formats = list(n = \"xx\", n_rsp = \"xx\", prop = \"xx.x%\", n_tot = \"xx\", or =     list(format_extreme_values(2L)), ci = list(format_extreme_values_ci(2L)), pval =     \"x.xxxx | (<0.0001)\", riskdiff = \"xx.x (xx.x - xx.x)\"),   na_str = default_na_str() )"},{"path":"https://insightsengineering.github.io/tern/main/reference/response_subgroups.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Tabulate binary response by subgroup — response_subgroups","text":"lyt (PreDataTableLayouts) layout analyses added . df (list) list data frames containing analysis variables. List created using extract_rsp_subgroups(). vars (character) names statistics reported among: n: Total number observations per group. n_rsp: Number responders per group. prop: Proportion responders. n_tot: Total number observations. : Odds ratio. ci : Confidence interval odds ratio. pval: p-value effect. Note, statistics n_tot, , ci required. groups_lists (named list list) optionally contains subgroups variable list, specifies new group levels via names levels belong character vectors elements list. label_all (string) label total population analysis. riskdiff (list) risk (proportion) difference column added, list settings apply within column. See control_riskdiff() details. NULL, risk difference column added. riskdiff$arm_x riskdiff$arm_y NULL, first level df$prop$arm used arm_x second level arm_y. na_str (string) string used replace NA empty values output. .formats (named character list) formats statistics. See Details analyze_vars information \"auto\" setting.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/response_subgroups.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Tabulate binary response by subgroup — response_subgroups","text":"rtables table summarizing binary response subgroup. a_response_subgroups() returns corresponding list formatted rtables::CellValue().","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/response_subgroups.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Tabulate binary response by subgroup — response_subgroups","text":"functions create layout starting data frame contains required statistics. Tables typically used part forest plot.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/response_subgroups.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Tabulate binary response by subgroup — response_subgroups","text":"tabulate_rsp_subgroups(): Table-creating function creates table summarizing binary response subgroup. function wrapper rtables::analyze_colvars() rtables::summarize_row_groups(). a_response_subgroups(): Formatted analysis function used afun tabulate_rsp_subgroups().","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/main/reference/response_subgroups.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Tabulate binary response by subgroup — response_subgroups","text":"","code":"library(dplyr) library(forcats)  adrs <- tern_ex_adrs adrs_labels <- formatters::var_labels(adrs)  adrs_f <- adrs %>%   filter(PARAMCD == \"BESRSPI\") %>%   filter(ARM %in% c(\"A: Drug X\", \"B: Placebo\")) %>%   droplevels() %>%   mutate(     # Reorder levels of factor to make the placebo group the reference arm.     ARM = fct_relevel(ARM, \"B: Placebo\"),     rsp = AVALC == \"CR\"   ) formatters::var_labels(adrs_f) <- c(adrs_labels, \"Response\")  # Unstratified analysis. df <- extract_rsp_subgroups(   variables = list(rsp = \"rsp\", arm = \"ARM\", subgroups = c(\"SEX\", \"BMRKR2\")),   data = adrs_f ) df #> $prop #>           arm  n n_rsp      prop     subgroup    var #> 1  B: Placebo 73    50 0.6849315 All Patients    ALL #> 2   A: Drug X 69    59 0.8550725 All Patients    ALL #> 3  B: Placebo 40    25 0.6250000            F    SEX #> 4   A: Drug X 38    36 0.9473684            F    SEX #> 5  B: Placebo 33    25 0.7575758            M    SEX #> 6   A: Drug X 31    23 0.7419355            M    SEX #> 7  B: Placebo 24    13 0.5416667          LOW BMRKR2 #> 8   A: Drug X 26    21 0.8076923          LOW BMRKR2 #> 9  B: Placebo 23    17 0.7391304       MEDIUM BMRKR2 #> 10  A: Drug X 26    23 0.8846154       MEDIUM BMRKR2 #> 11 B: Placebo 26    20 0.7692308         HIGH BMRKR2 #> 12  A: Drug X 17    15 0.8823529         HIGH BMRKR2 #>                       var_label row_type #> 1                  All Patients  content #> 2                  All Patients  content #> 3                           Sex analysis #> 4                           Sex analysis #> 5                           Sex analysis #> 6                           Sex analysis #> 7  Continuous Level Biomarker 2 analysis #> 8  Continuous Level Biomarker 2 analysis #> 9  Continuous Level Biomarker 2 analysis #> 10 Continuous Level Biomarker 2 analysis #> 11 Continuous Level Biomarker 2 analysis #> 12 Continuous Level Biomarker 2 analysis #>  #> $or #>   arm n_tot        or       lcl       ucl conf_level     subgroup    var #> 1       142  2.714000 1.1804488  6.239827       0.95 All Patients    ALL #> 2        78 10.800000 2.2669576 51.452218       0.95            F    SEX #> 3        64  0.920000 0.2966470  2.853223       0.95            M    SEX #> 4        50  3.553846 1.0047370 12.570277       0.95          LOW BMRKR2 #> 5        49  2.705882 0.5911718 12.385232       0.95       MEDIUM BMRKR2 #> 6        43  2.250000 0.3970298 12.750933       0.95         HIGH BMRKR2 #>                      var_label row_type #> 1                 All Patients  content #> 2                          Sex analysis #> 3                          Sex analysis #> 4 Continuous Level Biomarker 2 analysis #> 5 Continuous Level Biomarker 2 analysis #> 6 Continuous Level Biomarker 2 analysis #>   # Stratified analysis. df_strat <- extract_rsp_subgroups(   variables = list(rsp = \"rsp\", arm = \"ARM\", subgroups = c(\"SEX\", \"BMRKR2\"), strata = \"STRATA1\"),   data = adrs_f ) df_strat #> $prop #>           arm  n n_rsp      prop     subgroup    var #> 1  B: Placebo 73    50 0.6849315 All Patients    ALL #> 2   A: Drug X 69    59 0.8550725 All Patients    ALL #> 3  B: Placebo 40    25 0.6250000            F    SEX #> 4   A: Drug X 38    36 0.9473684            F    SEX #> 5  B: Placebo 33    25 0.7575758            M    SEX #> 6   A: Drug X 31    23 0.7419355            M    SEX #> 7  B: Placebo 24    13 0.5416667          LOW BMRKR2 #> 8   A: Drug X 26    21 0.8076923          LOW BMRKR2 #> 9  B: Placebo 23    17 0.7391304       MEDIUM BMRKR2 #> 10  A: Drug X 26    23 0.8846154       MEDIUM BMRKR2 #> 11 B: Placebo 26    20 0.7692308         HIGH BMRKR2 #> 12  A: Drug X 17    15 0.8823529         HIGH BMRKR2 #>                       var_label row_type #> 1                  All Patients  content #> 2                  All Patients  content #> 3                           Sex analysis #> 4                           Sex analysis #> 5                           Sex analysis #> 6                           Sex analysis #> 7  Continuous Level Biomarker 2 analysis #> 8  Continuous Level Biomarker 2 analysis #> 9  Continuous Level Biomarker 2 analysis #> 10 Continuous Level Biomarker 2 analysis #> 11 Continuous Level Biomarker 2 analysis #> 12 Continuous Level Biomarker 2 analysis #>  #> $or #>   arm n_tot        or       lcl       ucl conf_level     subgroup    var #> 1       142 2.6343899 1.1537821  6.015009       0.95 All Patients    ALL #> 2        78 9.5946605 2.0379337 45.171985       0.95            F    SEX #> 3        64 0.8947158 0.2936803  2.725809       0.95            M    SEX #> 4        50 3.5976656 1.0101319 12.813374       0.95          LOW BMRKR2 #> 5        49 2.6242168 0.5162572 13.339308       0.95       MEDIUM BMRKR2 #> 6        43 2.2816865 0.4116391 12.647228       0.95         HIGH BMRKR2 #>                      var_label row_type #> 1                 All Patients  content #> 2                          Sex analysis #> 3                          Sex analysis #> 4 Continuous Level Biomarker 2 analysis #> 5 Continuous Level Biomarker 2 analysis #> 6 Continuous Level Biomarker 2 analysis #>   # Grouping of the BMRKR2 levels. df_grouped <- extract_rsp_subgroups(   variables = list(rsp = \"rsp\", arm = \"ARM\", subgroups = c(\"SEX\", \"BMRKR2\")),   data = adrs_f,   groups_lists = list(     BMRKR2 = list(       \"low\" = \"LOW\",       \"low/medium\" = c(\"LOW\", \"MEDIUM\"),       \"low/medium/high\" = c(\"LOW\", \"MEDIUM\", \"HIGH\")     )   ) ) df_grouped #> $prop #>           arm  n n_rsp      prop        subgroup    var #> 1  B: Placebo 73    50 0.6849315    All Patients    ALL #> 2   A: Drug X 69    59 0.8550725    All Patients    ALL #> 3  B: Placebo 40    25 0.6250000               F    SEX #> 4   A: Drug X 38    36 0.9473684               F    SEX #> 5  B: Placebo 33    25 0.7575758               M    SEX #> 6   A: Drug X 31    23 0.7419355               M    SEX #> 7  B: Placebo 24    13 0.5416667             low BMRKR2 #> 8   A: Drug X 26    21 0.8076923             low BMRKR2 #> 9  B: Placebo 47    30 0.6382979      low/medium BMRKR2 #> 10  A: Drug X 52    44 0.8461538      low/medium BMRKR2 #> 11 B: Placebo 73    50 0.6849315 low/medium/high BMRKR2 #> 12  A: Drug X 69    59 0.8550725 low/medium/high BMRKR2 #>                       var_label row_type #> 1                  All Patients  content #> 2                  All Patients  content #> 3                           Sex analysis #> 4                           Sex analysis #> 5                           Sex analysis #> 6                           Sex analysis #> 7  Continuous Level Biomarker 2 analysis #> 8  Continuous Level Biomarker 2 analysis #> 9  Continuous Level Biomarker 2 analysis #> 10 Continuous Level Biomarker 2 analysis #> 11 Continuous Level Biomarker 2 analysis #> 12 Continuous Level Biomarker 2 analysis #>  #> $or #>   arm n_tot        or      lcl       ucl conf_level        subgroup    var #> 1       142  2.714000 1.180449  6.239827       0.95    All Patients    ALL #> 2        78 10.800000 2.266958 51.452218       0.95               F    SEX #> 3        64  0.920000 0.296647  2.853223       0.95               M    SEX #> 4        50  3.553846 1.004737 12.570277       0.95             low BMRKR2 #> 5        99  3.116667 1.193409  8.139385       0.95      low/medium BMRKR2 #> 6       142  2.714000 1.180449  6.239827       0.95 low/medium/high BMRKR2 #>                      var_label row_type #> 1                 All Patients  content #> 2                          Sex analysis #> 3                          Sex analysis #> 4 Continuous Level Biomarker 2 analysis #> 5 Continuous Level Biomarker 2 analysis #> 6 Continuous Level Biomarker 2 analysis #>   # Table with default columns basic_table() %>%   tabulate_rsp_subgroups(df) #>                                             B: Placebo           A: Drug X                                  #> Baseline Risk Factors          Total n   n    Response (%)   n    Response (%)   Odds Ratio      95% CI     #> ——————————————————————————————————————————————————————————————————————————————————————————————————————————— #> All Patients                     142     73      68.5%       69      85.5%          2.71      (1.18, 6.24)  #> Sex                                                                                                         #>   F                              78      40      62.5%       38      94.7%         10.80      (2.27, 51.45) #>   M                              64      33      75.8%       31      74.2%          0.92      (0.30, 2.85)  #> Continuous Level Biomarker 2                                                                                #>   LOW                            50      24      54.2%       26      80.8%          3.55      (1.00, 12.57) #>   MEDIUM                         49      23      73.9%       26      88.5%          2.71      (0.59, 12.39) #>   HIGH                           43      26      76.9%       17      88.2%          2.25      (0.40, 12.75)  # Table with selected columns basic_table() %>%   tabulate_rsp_subgroups(     df = df,     vars = c(\"n_tot\", \"n\", \"n_rsp\", \"prop\", \"or\", \"ci\")   ) #>                                                    B: Placebo                       A: Drug X                                         #> Baseline Risk Factors          Total n   n    Responders   Response (%)   n    Responders   Response (%)   Odds Ratio      95% CI     #> ————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————— #> All Patients                     142     73       50          68.5%       69       59          85.5%          2.71      (1.18, 6.24)  #> Sex                                                                                                                                   #>   F                              78      40       25          62.5%       38       36          94.7%         10.80      (2.27, 51.45) #>   M                              64      33       25          75.8%       31       23          74.2%          0.92      (0.30, 2.85)  #> Continuous Level Biomarker 2                                                                                                          #>   LOW                            50      24       13          54.2%       26       21          80.8%          3.55      (1.00, 12.57) #>   MEDIUM                         49      23       17          73.9%       26       23          88.5%          2.71      (0.59, 12.39) #>   HIGH                           43      26       20          76.9%       17       15          88.2%          2.25      (0.40, 12.75)  # Table with risk difference column added basic_table() %>%   tabulate_rsp_subgroups(     df,     riskdiff = control_riskdiff(       arm_x = levels(df$prop$arm)[1],       arm_y = levels(df$prop$arm)[2]     )   ) #>                                             B: Placebo           A: Drug X                                                                 #> Baseline Risk Factors          Total n   n    Response (%)   n    Response (%)   Odds Ratio      95% CI       Risk Difference (%) (95% CI) #> —————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————— #> All Patients                     142     73      68.5%       69      85.5%          2.71      (1.18, 6.24)        -17.0 (-30.5 - -3.5)     #> Sex                                                                                                                                        #>   F                              78      40      62.5%       38      94.7%         10.80      (2.27, 51.45)      -32.2 (-48.8 - -15.6)     #>   M                              64      33      75.8%       31      74.2%          0.92      (0.30, 2.85)         1.6 (-19.7 - 22.8)      #> Continuous Level Biomarker 2                                                                                                               #>   LOW                            50      24      54.2%       26      80.8%          3.55      (1.00, 12.57)       -26.6 (-51.6 - -1.6)     #>   MEDIUM                         49      23      73.9%       26      88.5%          2.71      (0.59, 12.39)       -14.5 (-36.3 - 7.2)      #>   HIGH                           43      26      76.9%       17      88.2%          2.25      (0.40, 12.75)       -11.3 (-33.6 - 11.0)"},{"path":"https://insightsengineering.github.io/tern/main/reference/rtable2gg.html","id":null,"dir":"Reference","previous_headings":"","what":"Convert rtable objects to ggplot objects — rtable2gg","title":"Convert rtable objects to ggplot objects — rtable2gg","text":"Given rtables::rtable() object, performs basic conversion ggplot2::ggplot() object built using functions ggplot2 package. table titles /footnotes ignored.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/rtable2gg.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Convert rtable objects to ggplot objects — rtable2gg","text":"","code":"rtable2gg(tbl, fontsize = 12, colwidths = NULL, lbl_col_padding = 0)"},{"path":"https://insightsengineering.github.io/tern/main/reference/rtable2gg.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Convert rtable objects to ggplot objects — rtable2gg","text":"tbl (VTableTree)rtables table object. fontsize (numeric(1)) font size. colwidths (numeric NULL) vector column widths. element's position colwidths corresponds column tbl position. NULL, column widths calculated according maximum number characters per column. lbl_col_padding (numeric) additional padding use calculating spacing first (label) column second column tbl. colwidths specified, width first column becomes colwidths[1] + lbl_col_padding. Defaults 0.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/rtable2gg.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Convert rtable objects to ggplot objects — rtable2gg","text":"ggplot object.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/rtable2gg.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Convert rtable objects to ggplot objects — rtable2gg","text":"","code":"dta <- data.frame(   ARM     = rep(LETTERS[1:3], rep(6, 3)),   AVISIT  = rep(paste0(\"V\", 1:3), 6),   AVAL    = c(9:1, rep(NA, 9)) )  lyt <- basic_table() %>%   split_cols_by(var = \"ARM\") %>%   split_rows_by(var = \"AVISIT\") %>%   analyze_vars(vars = \"AVAL\")  tbl <- build_table(lyt, df = dta)  rtable2gg(tbl)   rtable2gg(tbl, fontsize = 15, colwidths = c(2, 1, 1, 1))"},{"path":"https://insightsengineering.github.io/tern/main/reference/rtables_access.html","id":null,"dir":"Reference","previous_headings":"","what":"Helper functions for accessing information from rtables — rtables_access","title":"Helper functions for accessing information from rtables — rtables_access","text":"couple functions help accessing data rtables objects. Currently work occurrence tables, defined count first element fraction second element cell.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/rtables_access.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Helper functions for accessing information from rtables — rtables_access","text":"","code":"h_row_first_values(table_row, col_names = NULL, col_indices = NULL)  h_row_counts(table_row, col_names = NULL, col_indices = NULL)  h_row_fractions(table_row, col_names = NULL, col_indices = NULL)  h_col_counts(table, col_names = NULL, col_indices = NULL)  h_content_first_row(table)  is_leaf_table(table)  check_names_indices(table_row, col_names = NULL, col_indices = NULL)"},{"path":"https://insightsengineering.github.io/tern/main/reference/rtables_access.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Helper functions for accessing information from rtables — rtables_access","text":"table_row (TableRow) analysis row occurrence table. col_names (character) names columns extract . col_indices (integer) indices columns extract . col_names provided, inferred names table_row. Note currently works well single column split. table (VTableNodeInfo) occurrence table row.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/rtables_access.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Helper functions for accessing information from rtables — rtables_access","text":"h_row_first_values() returns vector numeric values. h_row_counts() returns vector numeric values. h_row_fractions() returns vector proportions. h_col_counts() returns vector column counts. h_content_first_row() returns row rtables table. is_leaf_table() returns logical value indicating whether current table leaf. check_names_indices returns column indices.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/rtables_access.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Helper functions for accessing information from rtables — rtables_access","text":"h_row_first_values(): Helper function extract first values content cell specified columns TableRow. Defaults columns. h_row_counts(): Helper function extracts row values checks convertible integers (integerish values). h_row_fractions(): Helper function extract fractions specified columns TableRow. specifically extracts second values content cell checks fraction. h_col_counts(): Helper function extract column counts specified columns table. h_content_first_row(): Helper function get first row content table current table. is_leaf_table(): Helper function says whether current table leaf tree. check_names_indices(): Internal helper function tests standard inputs column indices.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/main/reference/rtables_access.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Helper functions for accessing information from rtables — rtables_access","text":"","code":"tbl <- basic_table() %>%   split_cols_by(\"ARM\") %>%   split_rows_by(\"RACE\") %>%   analyze(\"AGE\", function(x) {     list(       \"mean (sd)\" = rcell(c(mean(x), sd(x)), format = \"xx.x (xx.x)\"),       \"n\" = length(x),       \"frac\" = rcell(c(0.1, 0.1), format = \"xx (xx)\")     )   }) %>%   build_table(tern_ex_adsl) %>%   prune_table() tree_row_elem <- collect_leaves(tbl[2, ])[[1]] result <- max(h_row_first_values(tree_row_elem)) result #> [1] 35.31214  # Row counts (integer values) # h_row_counts(tree_row_elem) # Fails because there are no integers # Using values with integers tree_row_elem <- collect_leaves(tbl[3, ])[[1]] result <- h_row_counts(tree_row_elem) # result  # Row fractions tree_row_elem <- collect_leaves(tbl[4, ])[[1]] h_row_fractions(tree_row_elem) #>      A: Drug X     B: Placebo C: Combination  #>            0.1            0.1            0.1"},{"path":"https://insightsengineering.github.io/tern/main/reference/s_bland_altman.html","id":null,"dir":"Reference","previous_headings":"","what":"Bland-Altman analysis — s_bland_altman","title":"Bland-Altman analysis — s_bland_altman","text":"Statistics function uses Bland-Altman method assess agreement two numerical vectors calculates variety statistics.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/s_bland_altman.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Bland-Altman analysis — s_bland_altman","text":"","code":"s_bland_altman(x, y, conf_level = 0.95)"},{"path":"https://insightsengineering.github.io/tern/main/reference/s_bland_altman.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Bland-Altman analysis — s_bland_altman","text":"x (numeric) vector numbers want analyze. y (numeric) vector numbers want analyze, compared x. conf_level (proportion) confidence level interval.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/s_bland_altman.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Bland-Altman analysis — s_bland_altman","text":"named list following elements: df difference_mean ci_mean difference_sd difference_se upper_agreement_limit lower_agreement_limit agreement_limit_se upper_agreement_limit_ci lower_agreement_limit_ci t_value n","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/s_bland_altman.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Bland-Altman analysis — s_bland_altman","text":"","code":"x <- seq(1, 60, 5) y <- seq(5, 50, 4)  s_bland_altman(x, y, conf_level = 0.9) #> $df #>    average difference #> 1      3.0         -4 #> 2      7.5         -3 #> 3     12.0         -2 #> 4     16.5         -1 #> 5     21.0          0 #> 6     25.5          1 #> 7     30.0          2 #> 8     34.5          3 #> 9     39.0          4 #> 10    43.5          5 #> 11    48.0          6 #> 12    52.5          7 #>  #> $difference_mean #> [1] 1.5 #>  #> $ci_mean #> [1] -0.3692162  3.3692162 #>  #> $difference_sd #> [1] 3.605551 #>  #> $difference_se #> [1] 1.040833 #>  #> $upper_agreement_limit #> [1] 7.430604 #>  #> $lower_agreement_limit #> [1] -4.430604 #>  #> $agreement_limit_se #> [1] 1.802776 #>  #> $upper_agreement_limit_ci #> [1]  4.193027 10.668181 #>  #> $lower_agreement_limit_ci #> [1] -7.668181 -1.193027 #>  #> $t_value #> [1] 1.795885 #>  #> $n #> [1] 12 #>"},{"path":"https://insightsengineering.github.io/tern/main/reference/s_cox_multivariate.html","id":null,"dir":"Reference","previous_headings":"","what":"Multivariate Cox model - summarized results — s_cox_multivariate","title":"Multivariate Cox model - summarized results — s_cox_multivariate","text":"Analyses based multivariate Cox model usually performed Controlled Substance Reporting regulatory documents serve exploratory purposes (e.g., publication). practice, model usually includes main effects (without interaction terms). produces hazard ratio estimates covariates included model. analysis follows principles (e.g., stratified vs. unstratified analysis tie handling) usual Cox model analysis. Since usually pre-specified hypothesis testing analysis, p.values need interpreted caution. (Statistical Analysis Clinical Trials Data R, NEST's bookdown)","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/s_cox_multivariate.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Multivariate Cox model - summarized results — s_cox_multivariate","text":"","code":"s_cox_multivariate(   formula,   data,   conf_level = 0.95,   pval_method = c(\"wald\", \"likelihood\"),   ... )"},{"path":"https://insightsengineering.github.io/tern/main/reference/s_cox_multivariate.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Multivariate Cox model - summarized results — s_cox_multivariate","text":"formula (formula) formula corresponding investigated survival::Surv() survival model including covariates. data (data.frame) data frame includes variable formula covariates. conf_level (proportion) confidence level hazard ratio interval estimations. Default 0.95. pval_method (string) method used estimation p-values, one \"wald\" (default) \"likelihood\". ... optional parameters passed survival::coxph(). Can include ties, character string specifying method tie handling, one exact (default), efron, breslow.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/s_cox_multivariate.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Multivariate Cox model - summarized results — s_cox_multivariate","text":"list elements mod, msum, aov, coef_inter.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/s_cox_multivariate.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Multivariate Cox model - summarized results — s_cox_multivariate","text":"output limited single effect terms. Work ongoing estimation interaction terms scope defined  Global Data Standards Repository (GDS_Standard_TLG_Specs_Tables_2.doc).","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/main/reference/s_cox_multivariate.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Multivariate Cox model - summarized results — s_cox_multivariate","text":"","code":"library(dplyr)  adtte <- tern_ex_adtte adtte_f <- subset(adtte, PARAMCD == \"OS\") # _f: filtered adtte_f <- filter(   adtte_f,   PARAMCD == \"OS\" &     SEX %in% c(\"F\", \"M\") &     RACE %in% c(\"ASIAN\", \"BLACK OR AFRICAN AMERICAN\", \"WHITE\") ) adtte_f$SEX <- droplevels(adtte_f$SEX) adtte_f$RACE <- droplevels(adtte_f$RACE)"},{"path":"https://insightsengineering.github.io/tern/main/reference/sas_na.html","id":null,"dir":"Reference","previous_headings":"","what":"Convert strings to NA — sas_na","title":"Convert strings to NA — sas_na","text":"SAS imports missing data empty strings strings whitespaces . helper function can used convert values NAs.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/sas_na.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Convert strings to NA — sas_na","text":"","code":"sas_na(x, empty = TRUE, whitespaces = TRUE)"},{"path":"https://insightsengineering.github.io/tern/main/reference/sas_na.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Convert strings to NA — sas_na","text":"x (factor character) values missing values substituted. empty (flag) TRUE, empty strings get replaced NA. whitespaces (flag) TRUE, strings made whitespaces get replaced NA.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/sas_na.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Convert strings to NA — sas_na","text":"x \"\" /whitespace-values substituted NA, depending values empty whitespaces.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/sas_na.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Convert strings to NA — sas_na","text":"","code":"sas_na(c(\"1\", \"\", \" \", \"   \", \"b\")) #> [1] \"1\" NA  NA  NA  \"b\" sas_na(factor(c(\"\", \" \", \"b\"))) #> [1] <NA> <NA> b    #> Levels: b  is.na(sas_na(c(\"1\", \"\", \" \", \"   \", \"b\"))) #> [1] FALSE  TRUE  TRUE  TRUE FALSE"},{"path":"https://insightsengineering.github.io/tern/main/reference/score_occurrences.html","id":null,"dir":"Reference","previous_headings":"","what":"Occurrence table sorting — score_occurrences","title":"Occurrence table sorting — score_occurrences","text":"Functions score occurrence table subtables rows can used sorting occurrence tables.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/score_occurrences.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Occurrence table sorting — score_occurrences","text":"","code":"score_occurrences(table_row)  score_occurrences_cols(...)  score_occurrences_subtable(...)  score_occurrences_cont_cols(...)"},{"path":"https://insightsengineering.github.io/tern/main/reference/score_occurrences.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Occurrence table sorting — score_occurrences","text":"table_row (TableRow) analysis row occurrence table. ... arguments row column access, see rtables_access: either col_names (character) including names columns used, alternatively col_indices (integer) giving indices directly instead.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/score_occurrences.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Occurrence table sorting — score_occurrences","text":"score_occurrences() returns sum counts across columns table row. score_occurrences_cols() returns function sums counts across specified columns table row. score_occurrences_subtable() returns function sums counts subtable across specified columns. score_occurrences_cont_cols() returns function sums counts first content row specified columns.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/score_occurrences.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Occurrence table sorting — score_occurrences","text":"score_occurrences(): Scoring function sums counts across columns. fail anything else counts used. score_occurrences_cols(): Scoring functions can produced constructor include specific columns scoring. See h_row_counts() information. score_occurrences_subtable(): Scoring functions produced constructor can used subtables: sum specified column counts subtable. useful available content row summing counts. score_occurrences_cont_cols(): Produces score function sorting table summing first content row specified columns. Note extending rtables::cont_n_onecol() rtables::cont_n_allcols().","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/main/reference/score_occurrences.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Occurrence table sorting — score_occurrences","text":"","code":"lyt <- basic_table() %>%   split_cols_by(\"ARM\") %>%   add_colcounts() %>%   analyze_num_patients(     vars = \"USUBJID\",     .stats = c(\"unique\"),     .labels = c(\"Total number of patients with at least one event\")   ) %>%   split_rows_by(\"AEBODSYS\", child_labels = \"visible\", nested = FALSE) %>%   summarize_num_patients(     var = \"USUBJID\",     .stats = c(\"unique\", \"nonunique\"),     .labels = c(       \"Total number of patients with at least one event\",       \"Total number of events\"     )   ) %>%   count_occurrences(vars = \"AEDECOD\")  tbl <- build_table(lyt, tern_ex_adae, alt_counts_df = tern_ex_adsl) %>%   prune_table()  tbl_sorted <- tbl %>%   sort_at_path(path = c(\"AEBODSYS\", \"*\", \"AEDECOD\"), scorefun = score_occurrences)  tbl_sorted #>                                                      A: Drug X    B: Placebo   C: Combination #>                                                        (N=69)       (N=73)         (N=58)     #> ————————————————————————————————————————————————————————————————————————————————————————————— #> Total number of patients with at least one event     59 (85.5%)   57 (78.1%)     48 (82.8%)   #> cl D.1                                                                                        #>   Total number of patients with at least one event   29 (42.0%)   27 (37.0%)     20 (34.5%)   #>   Total number of events                                 39           35             28       #>     dcd D.1.1.4.2                                    16 (23.2%)   13 (17.8%)     16 (27.6%)   #>     dcd D.1.1.1.1                                    17 (24.6%)   18 (24.7%)     7 (12.1%)    #> cl C.1                                                                                        #>   Total number of patients with at least one event   15 (21.7%)   13 (17.8%)     18 (31.0%)   #>   Total number of events                                 17           15             19       #>     dcd C.1.1.1.3                                    15 (21.7%)   13 (17.8%)     18 (31.0%)   #> cl C.2                                                                                        #>   Total number of patients with at least one event   20 (29.0%)   14 (19.2%)     10 (17.2%)   #>   Total number of events                                 21           15             14       #>     dcd C.2.1.2.1                                    20 (29.0%)   14 (19.2%)     10 (17.2%)   #> cl B.2                                                                                        #>   Total number of patients with at least one event   29 (42.0%)   27 (37.0%)     24 (41.4%)   #>   Total number of events                                 40           38             33       #>     dcd B.2.2.3.1                                    17 (24.6%)   15 (20.5%)     16 (27.6%)   #>     dcd B.2.1.2.1                                    17 (24.6%)   16 (21.9%)     13 (22.4%)   #> cl B.1                                                                                        #>   Total number of patients with at least one event   15 (21.7%)   19 (26.0%)     15 (25.9%)   #>   Total number of events                                 19           19             18       #>     dcd B.1.1.1.1                                    15 (21.7%)   19 (26.0%)     15 (25.9%)   #> cl D.2                                                                                        #>   Total number of patients with at least one event   21 (30.4%)   20 (27.4%)     12 (20.7%)   #>   Total number of events                                 27           22             15       #>     dcd D.2.1.5.3                                    21 (30.4%)   20 (27.4%)     12 (20.7%)   #> cl A.1                                                                                        #>   Total number of patients with at least one event   31 (44.9%)   24 (32.9%)     27 (46.6%)   #>   Total number of events                                 39           33             35       #>     dcd A.1.1.1.1                                    17 (24.6%)   17 (23.3%)     14 (24.1%)   #>     dcd A.1.1.1.2                                    17 (24.6%)   14 (19.2%)     17 (29.3%)    score_cols_a_and_b <- score_occurrences_cols(col_names = c(\"A: Drug X\", \"B: Placebo\"))  # Note that this here just sorts the AEDECOD inside the AEBODSYS. The AEBODSYS are not sorted. # That would require a second pass of `sort_at_path`. tbl_sorted <- tbl %>%   sort_at_path(path = c(\"AEBODSYS\", \"*\", \"AEDECOD\"), scorefun = score_cols_a_and_b)  tbl_sorted #>                                                      A: Drug X    B: Placebo   C: Combination #>                                                        (N=69)       (N=73)         (N=58)     #> ————————————————————————————————————————————————————————————————————————————————————————————— #> Total number of patients with at least one event     59 (85.5%)   57 (78.1%)     48 (82.8%)   #> cl D.1                                                                                        #>   Total number of patients with at least one event   29 (42.0%)   27 (37.0%)     20 (34.5%)   #>   Total number of events                                 39           35             28       #>     dcd D.1.1.1.1                                    17 (24.6%)   18 (24.7%)     7 (12.1%)    #>     dcd D.1.1.4.2                                    16 (23.2%)   13 (17.8%)     16 (27.6%)   #> cl C.1                                                                                        #>   Total number of patients with at least one event   15 (21.7%)   13 (17.8%)     18 (31.0%)   #>   Total number of events                                 17           15             19       #>     dcd C.1.1.1.3                                    15 (21.7%)   13 (17.8%)     18 (31.0%)   #> cl C.2                                                                                        #>   Total number of patients with at least one event   20 (29.0%)   14 (19.2%)     10 (17.2%)   #>   Total number of events                                 21           15             14       #>     dcd C.2.1.2.1                                    20 (29.0%)   14 (19.2%)     10 (17.2%)   #> cl B.2                                                                                        #>   Total number of patients with at least one event   29 (42.0%)   27 (37.0%)     24 (41.4%)   #>   Total number of events                                 40           38             33       #>     dcd B.2.1.2.1                                    17 (24.6%)   16 (21.9%)     13 (22.4%)   #>     dcd B.2.2.3.1                                    17 (24.6%)   15 (20.5%)     16 (27.6%)   #> cl B.1                                                                                        #>   Total number of patients with at least one event   15 (21.7%)   19 (26.0%)     15 (25.9%)   #>   Total number of events                                 19           19             18       #>     dcd B.1.1.1.1                                    15 (21.7%)   19 (26.0%)     15 (25.9%)   #> cl D.2                                                                                        #>   Total number of patients with at least one event   21 (30.4%)   20 (27.4%)     12 (20.7%)   #>   Total number of events                                 27           22             15       #>     dcd D.2.1.5.3                                    21 (30.4%)   20 (27.4%)     12 (20.7%)   #> cl A.1                                                                                        #>   Total number of patients with at least one event   31 (44.9%)   24 (32.9%)     27 (46.6%)   #>   Total number of events                                 39           33             35       #>     dcd A.1.1.1.1                                    17 (24.6%)   17 (23.3%)     14 (24.1%)   #>     dcd A.1.1.1.2                                    17 (24.6%)   14 (19.2%)     17 (29.3%)    score_subtable_all <- score_occurrences_subtable(col_names = names(tbl))  # Note that this code just sorts the AEBODSYS, not the AEDECOD within AEBODSYS. That # would require a second pass of `sort_at_path`. tbl_sorted <- tbl %>%   sort_at_path(path = c(\"AEBODSYS\"), scorefun = score_subtable_all, decreasing = FALSE)  tbl_sorted #>                                                      A: Drug X    B: Placebo   C: Combination #>                                                        (N=69)       (N=73)         (N=58)     #> ————————————————————————————————————————————————————————————————————————————————————————————— #> Total number of patients with at least one event     59 (85.5%)   57 (78.1%)     48 (82.8%)   #> cl C.2                                                                                        #>   Total number of patients with at least one event   20 (29.0%)   14 (19.2%)     10 (17.2%)   #>   Total number of events                                 21           15             14       #>     dcd C.2.1.2.1                                    20 (29.0%)   14 (19.2%)     10 (17.2%)   #> cl C.1                                                                                        #>   Total number of patients with at least one event   15 (21.7%)   13 (17.8%)     18 (31.0%)   #>   Total number of events                                 17           15             19       #>     dcd C.1.1.1.3                                    15 (21.7%)   13 (17.8%)     18 (31.0%)   #> cl B.1                                                                                        #>   Total number of patients with at least one event   15 (21.7%)   19 (26.0%)     15 (25.9%)   #>   Total number of events                                 19           19             18       #>     dcd B.1.1.1.1                                    15 (21.7%)   19 (26.0%)     15 (25.9%)   #> cl D.2                                                                                        #>   Total number of patients with at least one event   21 (30.4%)   20 (27.4%)     12 (20.7%)   #>   Total number of events                                 27           22             15       #>     dcd D.2.1.5.3                                    21 (30.4%)   20 (27.4%)     12 (20.7%)   #> cl D.1                                                                                        #>   Total number of patients with at least one event   29 (42.0%)   27 (37.0%)     20 (34.5%)   #>   Total number of events                                 39           35             28       #>     dcd D.1.1.1.1                                    17 (24.6%)   18 (24.7%)     7 (12.1%)    #>     dcd D.1.1.4.2                                    16 (23.2%)   13 (17.8%)     16 (27.6%)   #> cl B.2                                                                                        #>   Total number of patients with at least one event   29 (42.0%)   27 (37.0%)     24 (41.4%)   #>   Total number of events                                 40           38             33       #>     dcd B.2.1.2.1                                    17 (24.6%)   16 (21.9%)     13 (22.4%)   #>     dcd B.2.2.3.1                                    17 (24.6%)   15 (20.5%)     16 (27.6%)   #> cl A.1                                                                                        #>   Total number of patients with at least one event   31 (44.9%)   24 (32.9%)     27 (46.6%)   #>   Total number of events                                 39           33             35       #>     dcd A.1.1.1.1                                    17 (24.6%)   17 (23.3%)     14 (24.1%)   #>     dcd A.1.1.1.2                                    17 (24.6%)   14 (19.2%)     17 (29.3%)"},{"path":[]},{"path":"https://insightsengineering.github.io/tern/main/reference/split_cols_by_groups.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Split columns by groups of levels — split_cols_by_groups","text":"","code":"split_cols_by_groups(lyt, var, groups_list = NULL, ref_group = NULL, ...)"},{"path":"https://insightsengineering.github.io/tern/main/reference/split_cols_by_groups.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Split columns by groups of levels — split_cols_by_groups","text":"lyt (PreDataTableLayouts) layout analyses added . var (string) single variable name passed rtables requested statistics function. groups_list (named list character) specifies new group levels via names levels belong character vectors elements list. ref_group (data.frame vector) data corresponding reference group. ... additional arguments rtables::split_cols_by() order. instance, control formats (format), add joint column groups (incl_all).","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/split_cols_by_groups.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Split columns by groups of levels — split_cols_by_groups","text":"layout object suitable passing layouting functions. Adding function rtable layout add column split including given groups table layout.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/main/reference/split_cols_by_groups.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Split columns by groups of levels — split_cols_by_groups","text":"","code":"# 1 - Basic use  # Without group combination `split_cols_by_groups` is # equivalent to [rtables::split_cols_by()]. basic_table() %>%   split_cols_by_groups(\"ARM\") %>%   add_colcounts() %>%   analyze(\"AGE\") %>%   build_table(DM) #>        A: Drug X   B: Placebo   C: Combination #>         (N=121)     (N=106)        (N=129)     #> —————————————————————————————————————————————— #> Mean     34.91       33.02          34.57       # Add a reference column. basic_table() %>%   split_cols_by_groups(\"ARM\", ref_group = \"B: Placebo\") %>%   add_colcounts() %>%   analyze(     \"AGE\",     afun = function(x, .ref_group, .in_ref_col) {       if (.in_ref_col) {         in_rows(\"Diff Mean\" = rcell(NULL))       } else {         in_rows(\"Diff Mean\" = rcell(mean(x) - mean(.ref_group), format = \"xx.xx\"))       }     }   ) %>%   build_table(DM) #>             A: Drug X   B: Placebo   C: Combination #>              (N=121)     (N=106)        (N=129)     #> ——————————————————————————————————————————————————— #> Diff Mean     1.89                        1.55       # 2 - Adding group specification  # Manual preparation of the groups. groups <- list(   \"Arms A+B\" = c(\"A: Drug X\", \"B: Placebo\"),   \"Arms A+C\" = c(\"A: Drug X\", \"C: Combination\") )  # Use of split_cols_by_groups without reference column. basic_table() %>%   split_cols_by_groups(\"ARM\", groups) %>%   add_colcounts() %>%   analyze(\"AGE\") %>%   build_table(DM) #>        Arms A+B   Arms A+C #>        (N=227)    (N=250)  #> —————————————————————————— #> Mean    34.03      34.73    # Including differentiated output in the reference column. basic_table() %>%   split_cols_by_groups(\"ARM\", groups_list = groups, ref_group = \"Arms A+B\") %>%   analyze(     \"AGE\",     afun = function(x, .ref_group, .in_ref_col) {       if (.in_ref_col) {         in_rows(\"Diff. of Averages\" = rcell(NULL))       } else {         in_rows(\"Diff. of Averages\" = rcell(mean(x) - mean(.ref_group), format = \"xx.xx\"))       }     }   ) %>%   build_table(DM) #>                     Arms A+B   Arms A+C #> ——————————————————————————————————————— #> Diff. of Averages                0.71    # 3 - Binary list dividing factor levels into reference and treatment  # `combine_groups` defines reference and treatment. groups <- combine_groups(   fct = DM$ARM,   ref = c(\"A: Drug X\", \"B: Placebo\") ) groups #> $`A: Drug X/B: Placebo` #> [1] \"A: Drug X\"  \"B: Placebo\" #>  #> $`C: Combination` #> [1] \"C: Combination\" #>   # Use group definition without reference column. basic_table() %>%   split_cols_by_groups(\"ARM\", groups_list = groups) %>%   add_colcounts() %>%   analyze(\"AGE\") %>%   build_table(DM) #>        A: Drug X/B: Placebo   C: Combination #>              (N=227)             (N=129)     #> ———————————————————————————————————————————— #> Mean          34.03               34.57       # Use group definition with reference column (first item of groups). basic_table() %>%   split_cols_by_groups(\"ARM\", groups, ref_group = names(groups)[1]) %>%   add_colcounts() %>%   analyze(     \"AGE\",     afun = function(x, .ref_group, .in_ref_col) {       if (.in_ref_col) {         in_rows(\"Diff Mean\" = rcell(NULL))       } else {         in_rows(\"Diff Mean\" = rcell(mean(x) - mean(.ref_group), format = \"xx.xx\"))       }     }   ) %>%   build_table(DM) #>             A: Drug X/B: Placebo   C: Combination #>                   (N=227)             (N=129)     #> ————————————————————————————————————————————————— #> Diff Mean                               0.54"},{"path":"https://insightsengineering.github.io/tern/main/reference/split_text_grob.html","id":null,"dir":"Reference","previous_headings":"","what":"Split text according to available text width — split_text_grob","title":"Split text according to available text width — split_text_grob","text":"Dynamically wrap text.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/split_text_grob.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Split text according to available text width — split_text_grob","text":"","code":"split_text_grob(   text,   x = grid::unit(0.5, \"npc\"),   y = grid::unit(0.5, \"npc\"),   width = grid::unit(1, \"npc\"),   just = \"centre\",   hjust = NULL,   vjust = NULL,   default.units = \"npc\",   name = NULL,   gp = grid::gpar(),   vp = NULL )"},{"path":"https://insightsengineering.github.io/tern/main/reference/split_text_grob.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Split text according to available text width — split_text_grob","text":"text (string) text wrap. x numeric vector unit object specifying x-values. y numeric vector unit object specifying y-values. width (grid::unit) unit object specifying maximum width text. just justification text     relative (x, y) location.  two values, first     value specifies horizontal justification second value specifies     vertical justification.  Possible string values : \"left\",     \"right\", \"centre\", \"center\", \"bottom\",     \"top\".  numeric values, 0 means left (bottom) alignment     1 means right (top) alignment. hjust numeric vector specifying horizontal justification.     specified, overrides just setting. vjust numeric vector specifying vertical justification.     specified, overrides just setting. default.units string indicating default units use     x y     given numeric vectors. name character identifier. gp object class \"gpar\", typically output     call function gpar.  basically     list graphical parameter settings. vp Grid viewport object (NULL).","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/split_text_grob.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Split text according to available text width — split_text_grob","text":"text grob.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/split_text_grob.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Split text according to available text width — split_text_grob","text":"code taken R Graphics Paul Murell, 2nd edition","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/stack_grobs.html","id":null,"dir":"Reference","previous_headings":"","what":"Stack multiple grobs — stack_grobs","title":"Stack multiple grobs — stack_grobs","text":"Stack grobs new grob 1 column multiple rows layout.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/stack_grobs.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Stack multiple grobs — stack_grobs","text":"","code":"stack_grobs(   ...,   grobs = list(...),   padding = grid::unit(2, \"line\"),   vp = NULL,   gp = NULL,   name = NULL )"},{"path":"https://insightsengineering.github.io/tern/main/reference/stack_grobs.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Stack multiple grobs — stack_grobs","text":"... grobs. grobs (list grob) list grobs. padding (grid::unit) unit length 1, space grob. vp (viewport NULL) viewport() object (NULL). gp (gpar) gpar() object. name (string) character identifier grob.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/stack_grobs.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Stack multiple grobs — stack_grobs","text":"grob.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/stack_grobs.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Stack multiple grobs — stack_grobs","text":"","code":"library(grid)  g1 <- circleGrob(gp = gpar(col = \"blue\")) g2 <- circleGrob(gp = gpar(col = \"red\")) g3 <- textGrob(\"TEST TEXT\") grid.newpage() grid.draw(stack_grobs(g1, g2, g3))  showViewport()   grid.newpage() pushViewport(viewport(layout = grid.layout(1, 2))) vp1 <- viewport(layout.pos.row = 1, layout.pos.col = 2) grid.draw(stack_grobs(g1, g2, g3, vp = vp1, name = \"test\"))  showViewport()  grid.ls(grobs = TRUE, viewports = TRUE, print = FALSE)"},{"path":"https://insightsengineering.github.io/tern/main/reference/stat_mean_ci.html","id":null,"dir":"Reference","previous_headings":"","what":"Confidence interval for mean — stat_mean_ci","title":"Confidence interval for mean — stat_mean_ci","text":"Convenient function calculating mean confidence interval. calculates arithmetic well geometric mean. can used ggplot helper function plotting.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/stat_mean_ci.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Confidence interval for mean — stat_mean_ci","text":"","code":"stat_mean_ci(   x,   conf_level = 0.95,   na.rm = TRUE,   n_min = 2,   gg_helper = TRUE,   geom_mean = FALSE )"},{"path":"https://insightsengineering.github.io/tern/main/reference/stat_mean_ci.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Confidence interval for mean — stat_mean_ci","text":"x (numeric) vector numbers want analyze. conf_level (proportion) confidence level interval. na.rm (flag) whether NA values removed x prior analysis. n_min (numeric(1)) minimum number non-missing x estimate confidence interval mean. gg_helper (flag) whether output aligned use ggplots. geom_mean (flag) whether geometric mean calculated.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/stat_mean_ci.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Confidence interval for mean — stat_mean_ci","text":"named vector values mean_ci_lwr mean_ci_upr.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/stat_mean_ci.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Confidence interval for mean — stat_mean_ci","text":"","code":"stat_mean_ci(sample(10), gg_helper = FALSE) #> mean_ci_lwr mean_ci_upr  #>    3.334149    7.665851   p <- ggplot2::ggplot(mtcars, ggplot2::aes(cyl, mpg)) +   ggplot2::geom_point()  p + ggplot2::stat_summary(   fun.data = stat_mean_ci,   geom = \"errorbar\" )   p + ggplot2::stat_summary(   fun.data = stat_mean_ci,   fun.args = list(conf_level = 0.5),   geom = \"errorbar\" )   p + ggplot2::stat_summary(   fun.data = stat_mean_ci,   fun.args = list(conf_level = 0.5, geom_mean = TRUE),   geom = \"errorbar\" )"},{"path":"https://insightsengineering.github.io/tern/main/reference/stat_mean_pval.html","id":null,"dir":"Reference","previous_headings":"","what":"p-Value of the mean — stat_mean_pval","title":"p-Value of the mean — stat_mean_pval","text":"Convenient function calculating two-sided p-value mean.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/stat_mean_pval.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"p-Value of the mean — stat_mean_pval","text":"","code":"stat_mean_pval(x, na.rm = TRUE, n_min = 2, test_mean = 0)"},{"path":"https://insightsengineering.github.io/tern/main/reference/stat_mean_pval.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"p-Value of the mean — stat_mean_pval","text":"x (numeric) vector numbers want analyze. na.rm (flag) whether NA values removed x prior analysis. n_min (numeric(1)) minimum number non-missing x estimate p-value mean. test_mean (numeric(1)) mean value test null hypothesis.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/stat_mean_pval.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"p-Value of the mean — stat_mean_pval","text":"p-value.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/stat_mean_pval.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"p-Value of the mean — stat_mean_pval","text":"","code":"stat_mean_pval(sample(10)) #>     p_value  #> 0.000278196   stat_mean_pval(rnorm(10), test_mean = 0.5) #>    p_value  #> 0.04235675"},{"path":"https://insightsengineering.github.io/tern/main/reference/stat_median_ci.html","id":null,"dir":"Reference","previous_headings":"","what":"Confidence interval for median — stat_median_ci","title":"Confidence interval for median — stat_median_ci","text":"Convenient function calculating median confidence interval. can used ggplot helper function plotting.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/stat_median_ci.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Confidence interval for median — stat_median_ci","text":"","code":"stat_median_ci(x, conf_level = 0.95, na.rm = TRUE, gg_helper = TRUE)"},{"path":"https://insightsengineering.github.io/tern/main/reference/stat_median_ci.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Confidence interval for median — stat_median_ci","text":"x (numeric) vector numbers want analyze. conf_level (proportion) confidence level interval. na.rm (flag) whether NA values removed x prior analysis. gg_helper (flag) whether output aligned use ggplots.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/stat_median_ci.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Confidence interval for median — stat_median_ci","text":"named vector values median_ci_lwr median_ci_upr.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/stat_median_ci.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Confidence interval for median — stat_median_ci","text":"function adapted DescTools/versions/0.99.35/source","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/stat_median_ci.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Confidence interval for median — stat_median_ci","text":"","code":"stat_median_ci(sample(10), gg_helper = FALSE) #> median_ci_lwr median_ci_upr  #>             2             9  #> attr(,\"conf_level\") #> [1] 0.9785156  p <- ggplot2::ggplot(mtcars, ggplot2::aes(cyl, mpg)) +   ggplot2::geom_point() p + ggplot2::stat_summary(   fun.data = stat_median_ci,   geom = \"errorbar\" )"},{"path":"https://insightsengineering.github.io/tern/main/reference/stat_propdiff_ci.html","id":null,"dir":"Reference","previous_headings":"","what":"Proportion difference and confidence interval — stat_propdiff_ci","title":"Proportion difference and confidence interval — stat_propdiff_ci","text":"Function calculating proportion (risk) difference confidence interval arm X (reference group) arm Y. Risk difference calculated subtracting cumulative incidence arm Y cumulative incidence arm X.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/stat_propdiff_ci.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Proportion difference and confidence interval — stat_propdiff_ci","text":"","code":"stat_propdiff_ci(   x,   y,   N_x,   N_y,   list_names = NULL,   conf_level = 0.95,   pct = TRUE )"},{"path":"https://insightsengineering.github.io/tern/main/reference/stat_propdiff_ci.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Proportion difference and confidence interval — stat_propdiff_ci","text":"x (list integer) list number occurrences arm X (reference group). y (list integer) list number occurrences arm Y. Must equal length x. N_x (numeric(1)) total number records arm X. N_y (numeric(1)) total number records arm Y. list_names (character) names variable/level corresponding pair proportions x y. Must equal length x y. conf_level (proportion) confidence level interval. pct (flag) whether output returned percentages. Defaults TRUE.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/stat_propdiff_ci.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Proportion difference and confidence interval — stat_propdiff_ci","text":"List proportion differences CIs corresponding pair number occurrences x y. list element consists 3 statistics: proportion difference, CI lower bound, CI upper bound.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/main/reference/stat_propdiff_ci.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Proportion difference and confidence interval — stat_propdiff_ci","text":"","code":"stat_propdiff_ci(   x = list(0.375), y = list(0.01), N_x = 5, N_y = 5, list_names = \"x\", conf_level = 0.9 ) #> $x #> [1]   7.30000 -12.35184  26.95184 #>   stat_propdiff_ci(   x = list(0.5, 0.75, 1), y = list(0.25, 0.05, 0.5), N_x = 10, N_y = 20, pct = FALSE ) #> [[1]] #> [1]  0.0375000 -0.1060891  0.1810891 #>  #> [[2]] #> [1]  0.07250000 -0.09220915  0.23720915 #>  #> [[3]] #> [1]  0.0750000 -0.1231285  0.2731285 #>"},{"path":"https://insightsengineering.github.io/tern/main/reference/strata_normal_quantile.html","id":null,"dir":"Reference","previous_headings":"","what":"Helper function for the estimation of stratified quantiles — strata_normal_quantile","title":"Helper function for the estimation of stratified quantiles — strata_normal_quantile","text":"function wraps estimation stratified percentiles assume approximation large numbers. necessary case proportions strata unequal.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/strata_normal_quantile.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Helper function for the estimation of stratified quantiles — strata_normal_quantile","text":"","code":"strata_normal_quantile(vars, weights, conf_level)"},{"path":"https://insightsengineering.github.io/tern/main/reference/strata_normal_quantile.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Helper function for the estimation of stratified quantiles — strata_normal_quantile","text":"vars (character) variable names primary analysis variable iterated . weights (numeric NULL) weights level strata. NULL, estimated using iterative algorithm proposed Yan2010-jt;textualtern minimizes weighted squared length confidence interval. conf_level (proportion) confidence level interval.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/strata_normal_quantile.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Helper function for the estimation of stratified quantiles — strata_normal_quantile","text":"Stratified quantile.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/main/reference/strata_normal_quantile.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Helper function for the estimation of stratified quantiles — strata_normal_quantile","text":"","code":"strata_data <- table(data.frame(   \"f1\" = sample(c(TRUE, FALSE), 100, TRUE),   \"f2\" = sample(c(\"x\", \"y\", \"z\"), 100, TRUE),   stringsAsFactors = TRUE )) ns <- colSums(strata_data) ests <- strata_data[\"TRUE\", ] / ns vars <- ests * (1 - ests) / ns weights <- rep(1 / length(ns), length(ns))  strata_normal_quantile(vars, weights, 0.95) #> [1] 1.14181"},{"path":"https://insightsengineering.github.io/tern/main/reference/study_arm.html","id":null,"dir":"Reference","previous_headings":"","what":"Indicate study arm variable in formula — study_arm","title":"Indicate study arm variable in formula — study_arm","text":"use study_arm indicate study arm variable tern formulas.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/study_arm.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Indicate study arm variable in formula — study_arm","text":"","code":"study_arm(x)"},{"path":"https://insightsengineering.github.io/tern/main/reference/study_arm.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Indicate study arm variable in formula — study_arm","text":"x arm information","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/study_arm.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Indicate study arm variable in formula — study_arm","text":"x","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/summarize_ancova.html","id":null,"dir":"Reference","previous_headings":"","what":"Summarize analysis of covariance (ANCOVA) results — summarize_ancova","title":"Summarize analysis of covariance (ANCOVA) results — summarize_ancova","text":"analyze function summarize_ancova() creates layout element summarize ANCOVA results. function can used analyze multiple endpoints /multiple timepoints within response variable(s) specified vars. Additional variables analysis, namely arm (grouping) variable covariate variables, can defined via variables argument. See details specify variables. interaction term can implemented model needed. interaction variable interact arm variable specified via interaction_term parameter, specific value interaction_term extract ANCOVA results via interaction_y parameter.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/summarize_ancova.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Summarize analysis of covariance (ANCOVA) results — summarize_ancova","text":"","code":"summarize_ancova(   lyt,   vars,   variables,   conf_level,   interaction_y = FALSE,   interaction_item = NULL,   var_labels,   na_str = default_na_str(),   nested = TRUE,   ...,   show_labels = \"visible\",   table_names = vars,   .stats = NULL,   .formats = NULL,   .labels = NULL,   .indent_mods = NULL )  s_ancova(   df,   .var,   .df_row,   variables,   .ref_group,   .in_ref_col,   conf_level,   interaction_y = FALSE,   interaction_item = NULL )  a_ancova(   df,   .var,   .df_row,   variables,   .ref_group,   .in_ref_col,   conf_level,   interaction_y = FALSE,   interaction_item = NULL )"},{"path":"https://insightsengineering.github.io/tern/main/reference/summarize_ancova.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Summarize analysis of covariance (ANCOVA) results — summarize_ancova","text":"lyt (PreDataTableLayouts) layout analyses added . vars (character) variable names primary analysis variable iterated . variables (named list string) list additional analysis variables, expected elements: arm (string) group variable, covariate adjusted means multiple groups summarized. Specifically, first level arm variable taken reference group. covariates (character) vector can contain single variable names (\"X1\"), /interaction terms indicated \"X1 * X2\". conf_level (proportion) confidence level interval. interaction_y (string flag) selected item inside interaction_item variable used select specific ANCOVA results. interaction needed, default option FALSE. interaction_item (string NULL) name variable interactions arm. interaction needed, default option NULL. var_labels (character) variable labels. na_str (string) string used replace NA empty values output. nested (flag) whether layout instruction applied within existing layout structure _if possible (TRUE, default) new top-level element (FALSE). Ignored nest split. underneath analyses, allowed. ... additional arguments lower level functions. show_labels (string) label visibility: one \"default\", \"visible\" \"hidden\". table_names (character) can customized case vars analyzed multiple times, avoid warnings rtables. .stats (character) statistics select table. Options : 'n', 'lsmean', 'lsmean_diff', 'lsmean_diff_ci', 'pval' .formats (named character list) formats statistics. See Details analyze_vars information \"auto\" setting. .labels (named character) labels statistics (without indent). .indent_mods (named integer) indent modifiers labels. Defaults 0, corresponds unmodified default behavior. Can negative. df (data.frame) data set containing analysis variables. .var (string) single variable name passed rtables requested statistics function. .df_row (data.frame) data set includes variables called .var variables. .ref_group (data.frame vector) data corresponding reference group. .in_ref_col (flag)TRUE working reference level, FALSE otherwise.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/summarize_ancova.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Summarize analysis of covariance (ANCOVA) results — summarize_ancova","text":"summarize_ancova() returns layout object suitable passing layouting functions, rtables::build_table(). Adding function rtable layout add formatted rows containing statistics s_ancova() table layout. s_ancova() returns named list 5 statistics: n: Count complete sample size group. lsmean: Estimated marginal means group. lsmean_diff: Difference estimated marginal means comparison reference group. working reference group, empty. lsmean_diff_ci: Confidence level difference estimated marginal means comparison reference group. pval: p-value (adjusted multiple comparisons). a_ancova() returns corresponding list formatted rtables::CellValue().","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/summarize_ancova.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Summarize analysis of covariance (ANCOVA) results — summarize_ancova","text":"summarize_ancova(): Layout-creating function can take statistics function arguments additional format arguments. function wrapper rtables::analyze(). s_ancova(): Statistics function produces named list results investigated linear model. a_ancova(): Formatted analysis function used afun summarize_ancova().","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/summarize_ancova.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Summarize analysis of covariance (ANCOVA) results — summarize_ancova","text":"","code":"basic_table() %>%   split_cols_by(\"Species\", ref_group = \"setosa\") %>%   add_colcounts() %>%   summarize_ancova(     vars = \"Petal.Length\",     variables = list(arm = \"Species\", covariates = NULL),     table_names = \"unadj\",     conf_level = 0.95, var_labels = \"Unadjusted comparison\",     .labels = c(lsmean = \"Mean\", lsmean_diff = \"Difference in Means\")   ) %>%   summarize_ancova(     vars = \"Petal.Length\",     variables = list(arm = \"Species\", covariates = c(\"Sepal.Length\", \"Sepal.Width\")),     table_names = \"adj\",     conf_level = 0.95, var_labels = \"Adjusted comparison (covariates: Sepal.Length and Sepal.Width)\"   ) %>%   build_table(iris) #>                                                                  setosa    versicolor     virginica   #>                                                                  (N=50)      (N=50)         (N=50)    #> ————————————————————————————————————————————————————————————————————————————————————————————————————— #> Unadjusted comparison                                                                                 #>   n                                                                50          50             50      #>   Mean                                                            1.46        4.26           5.55     #>   Difference in Means                                                         2.80           4.09     #>     95% CI                                                                (2.63, 2.97)   (3.92, 4.26) #>     p-value                                                                 <0.0001        <0.0001    #> Adjusted comparison (covariates: Sepal.Length and Sepal.Width)                                        #>   n                                                                50          50             50      #>   Adjusted Mean                                                   2.02        4.19           5.07     #>   Difference in Adjusted Means                                                2.17           3.05     #>     95% CI                                                                (1.96, 2.38)   (2.81, 3.29) #>     p-value                                                                 <0.0001        <0.0001"},{"path":"https://insightsengineering.github.io/tern/main/reference/summarize_change.html","id":null,"dir":"Reference","previous_headings":"","what":"Summarize change from baseline values or absolute baseline values — summarize_change","title":"Summarize change from baseline values or absolute baseline values — summarize_change","text":"analyze function summarize_change() creates layout element summarize change baseline absolute baseline values. primary analysis variable vars indicates numerical change baseline results. Required secondary analysis variables value baseline_flag can supplied function via variables argument. value element name analysis value variable, baseline_flag element name flag variable indicates whether records contain baseline values. Depending baseline flag given, either absolute baseline values (baseline) change baseline values (post-baseline) summarized.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/summarize_change.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Summarize change from baseline values or absolute baseline values — summarize_change","text":"","code":"summarize_change(   lyt,   vars,   variables,   var_labels = vars,   na_str = default_na_str(),   na_rm = TRUE,   nested = TRUE,   show_labels = \"default\",   table_names = vars,   section_div = NA_character_,   ...,   .stats = c(\"n\", \"mean_sd\", \"median\", \"range\"),   .formats = c(n = \"xx\", mean_sd = \"xx.xx (xx.xx)\", mean_se = \"xx.xx (xx.xx)\", median =     \"xx.xx\", range = \"xx.xx - xx.xx\", mean_ci = \"(xx.xx, xx.xx)\", median_ci =     \"(xx.xx, xx.xx)\", mean_pval = \"xx.xx\"),   .labels = c(mean_sd = \"Mean (SD)\", mean_se = \"Mean (SE)\", median = \"Median\", range =     \"Min - Max\"),   .indent_mods = NULL )  s_change_from_baseline(df, ...)  a_change_from_baseline(   df,   ...,   .stats = NULL,   .formats = NULL,   .labels = NULL,   .indent_mods = NULL )"},{"path":"https://insightsengineering.github.io/tern/main/reference/summarize_change.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Summarize change from baseline values or absolute baseline values — summarize_change","text":"lyt (PreDataTableLayouts) layout analyses added . vars (character) variable names primary analysis variable iterated . variables (named list string) list additional analysis variables. var_labels (character) variable labels. na_str (string) string used replace NA empty values output. nested (flag) whether layout instruction applied within existing layout structure _if possible (TRUE, default) new top-level element (FALSE). Ignored nest split. underneath analyses, allowed. show_labels (string) label visibility: one \"default\", \"visible\" \"hidden\". table_names (character) can customized case vars analyzed multiple times, avoid warnings rtables. section_div (string) string repeated section divider group defined split instruction, NA_character_ (default) section divider. ... additional arguments lower level functions. .stats (character) statistics select table. Options : 'n', 'sum', 'mean', 'sd', 'se', 'mean_sd', 'mean_se', 'mean_ci', 'mean_sei', 'mean_sdi', 'mean_pval', 'median', 'mad', 'median_ci', 'quantiles', 'iqr', 'range', 'min', 'max', 'median_range', 'cv', 'geom_mean', 'geom_mean_ci', 'geom_cv', 'median_ci_3d', 'mean_ci_3d', 'geom_mean_ci_3d' .formats (named character list) formats statistics. See Details analyze_vars information \"auto\" setting. .labels (named character) labels statistics (without indent). .indent_mods (named integer) indent modifiers labels. Defaults 0, corresponds unmodified default behavior. Can negative. df (data.frame) data set containing analysis variables.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/summarize_change.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Summarize change from baseline values or absolute baseline values — summarize_change","text":"summarize_change() returns layout object suitable passing layouting functions, rtables::build_table(). Adding function rtable layout add formatted rows containing statistics s_change_from_baseline() table layout. s_change_from_baseline() returns values returned s_summary.numeric(). a_change_from_baseline() returns corresponding list formatted rtables::CellValue().","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/summarize_change.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Summarize change from baseline values or absolute baseline values — summarize_change","text":"summarize_change(): Layout-creating function can take statistics function arguments additional format arguments. function wrapper rtables::analyze(). s_change_from_baseline(): Statistics function summarizes baseline post-baseline visits. a_change_from_baseline(): Formatted analysis function used afun summarize_change().","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/summarize_change.html","id":"note","dir":"Reference","previous_headings":"","what":"Note","title":"Summarize change from baseline values or absolute baseline values — summarize_change","text":"used split visits layout, data subset contains either baseline post-baseline data. data df must either baseline post-baseline visits. Otherwise error thrown.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/summarize_change.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Summarize change from baseline values or absolute baseline values — summarize_change","text":"","code":"library(dplyr)  # Fabricate dataset dta_test <- data.frame(   USUBJID = rep(1:6, each = 3),   AVISIT = rep(paste0(\"V\", 1:3), 6),   ARM = rep(LETTERS[1:3], rep(6, 3)),   AVAL = c(9:1, rep(NA, 9)) ) %>%   mutate(ABLFLL = AVISIT == \"V1\") %>%   group_by(USUBJID) %>%   mutate(     BLVAL = AVAL[ABLFLL],     CHG = AVAL - BLVAL   ) %>%   ungroup()  results <- basic_table() %>%   split_cols_by(\"ARM\") %>%   split_rows_by(\"AVISIT\") %>%   summarize_change(\"CHG\", variables = list(value = \"AVAL\", baseline_flag = \"ABLFLL\")) %>%   build_table(dta_test)  results #>                     A                 B               C     #> ——————————————————————————————————————————————————————————— #> V1                                                          #>   n                 2                 1               0     #>   Mean (SD)    7.50 (2.12)    3.00 (<Missing>)    <Missing> #>   Median          7.50              3.00          <Missing> #>   Min - Max    6.00 - 9.00       3.00 - 3.00      <Missing> #> V2                                                          #>   n                 2                 1               0     #>   Mean (SD)   -1.00 (0.00)    -1.00 (<Missing>)   <Missing> #>   Median          -1.00             -1.00         <Missing> #>   Min - Max   -1.00 - -1.00     -1.00 - -1.00     <Missing> #> V3                                                          #>   n                 2                 1               0     #>   Mean (SD)   -2.00 (0.00)    -2.00 (<Missing>)   <Missing> #>   Median          -2.00             -2.00         <Missing> #>   Min - Max   -2.00 - -2.00     -2.00 - -2.00     <Missing>"},{"path":"https://insightsengineering.github.io/tern/main/reference/summarize_colvars.html","id":null,"dir":"Reference","previous_headings":"","what":"Summarize variables in columns — summarize_colvars","title":"Summarize variables in columns — summarize_colvars","text":"analyze function summarize_colvars() uses statistics function s_summary() analyze variables arranged columns. variables analyze specified table layout via column splits (see rtables::split_cols_by() rtables::split_cols_by_multivar()) prior using summarize_colvars(). function minimal wrapper rtables::analyze_colvars(), function typically used apply different analysis methods rows column variable. use analysis methods column labels, please refer analyze_vars_in_cols() function.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/summarize_colvars.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Summarize variables in columns — summarize_colvars","text":"","code":"summarize_colvars(   lyt,   ...,   na_str = default_na_str(),   .stats = c(\"n\", \"mean_sd\", \"median\", \"range\", \"count_fraction\"),   .formats = NULL,   .labels = NULL,   .indent_mods = NULL )"},{"path":"https://insightsengineering.github.io/tern/main/reference/summarize_colvars.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Summarize variables in columns — summarize_colvars","text":"lyt (PreDataTableLayouts) layout analyses added . ... arguments passed s_summary(). na_str (string) string used replace NA empty values output. .stats (character) statistics select table. .formats (named character list) formats statistics. See Details analyze_vars information \"auto\" setting. .labels (named character) labels statistics (without indent). .indent_mods (named vector integer) indent modifiers labels. element vector name-value pair name corresponding statistic specified .stats value indentation statistic's row label.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/summarize_colvars.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Summarize variables in columns — summarize_colvars","text":"layout object suitable passing layouting functions, rtables::build_table(). Adding function rtable layout summarize given variables, arrange output columns, add table layout.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/main/reference/summarize_colvars.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Summarize variables in columns — summarize_colvars","text":"","code":"dta_test <- data.frame(   USUBJID = rep(1:6, each = 3),   PARAMCD = rep(\"lab\", 6 * 3),   AVISIT = rep(paste0(\"V\", 1:3), 6),   ARM = rep(LETTERS[1:3], rep(6, 3)),   AVAL = c(9:1, rep(NA, 9)),   CHG = c(1:9, rep(NA, 9)) )  ## Default output within a `rtables` pipeline. basic_table() %>%   split_cols_by(\"ARM\") %>%   split_rows_by(\"AVISIT\") %>%   split_cols_by_multivar(vars = c(\"AVAL\", \"CHG\")) %>%   summarize_colvars() %>%   build_table(dta_test) #>                         A                             B                             C           #>                 AVAL         CHG           AVAL               CHG           AVAL         CHG    #> ——————————————————————————————————————————————————————————————————————————————————————————————— #> V1                                                                                              #>   n               2           2              1                 1              0           0     #>   Mean (SD)   7.5 (2.1)   2.5 (2.1)   3.0 (<Missing>)   7.0 (<Missing>)   <Missing>   <Missing> #>   Median         7.5         2.5            3.0               7.0         <Missing>   <Missing> #>   Min - Max   6.0 - 9.0   1.0 - 4.0      3.0 - 3.0         7.0 - 7.0      <Missing>   <Missing> #> V2                                                                                              #>   n               2           2              1                 1              0           0     #>   Mean (SD)   6.5 (2.1)   3.5 (2.1)   2.0 (<Missing>)   8.0 (<Missing>)   <Missing>   <Missing> #>   Median         6.5         3.5            2.0               8.0         <Missing>   <Missing> #>   Min - Max   5.0 - 8.0   2.0 - 5.0      2.0 - 2.0         8.0 - 8.0      <Missing>   <Missing> #> V3                                                                                              #>   n               2           2              1                 1              0           0     #>   Mean (SD)   5.5 (2.1)   4.5 (2.1)   1.0 (<Missing>)   9.0 (<Missing>)   <Missing>   <Missing> #>   Median         5.5         4.5            1.0               9.0         <Missing>   <Missing> #>   Min - Max   4.0 - 7.0   3.0 - 6.0      1.0 - 1.0         9.0 - 9.0      <Missing>   <Missing>  ## Selection of statistics, formats and labels also work. basic_table() %>%   split_cols_by(\"ARM\") %>%   split_rows_by(\"AVISIT\") %>%   split_cols_by_multivar(vars = c(\"AVAL\", \"CHG\")) %>%   summarize_colvars(     .stats = c(\"n\", \"mean_sd\"),     .formats = c(\"mean_sd\" = \"xx.x, xx.x\"),     .labels = c(n = \"n\", mean_sd = \"Mean, SD\")   ) %>%   build_table(dta_test) #>                       A                           B                            C           #>                AVAL       CHG           AVAL             CHG           AVAL         CHG    #> —————————————————————————————————————————————————————————————————————————————————————————— #> V1                                                                                         #>   n             2          2             1                1              0           0     #>   Mean, SD   7.5, 2.1   2.5, 2.1   3.0, <Missing>   7.0, <Missing>   <Missing>   <Missing> #> V2                                                                                         #>   n             2          2             1                1              0           0     #>   Mean, SD   6.5, 2.1   3.5, 2.1   2.0, <Missing>   8.0, <Missing>   <Missing>   <Missing> #> V3                                                                                         #>   n             2          2             1                1              0           0     #>   Mean, SD   5.5, 2.1   4.5, 2.1   1.0, <Missing>   9.0, <Missing>   <Missing>   <Missing>  ## Use arguments interpreted by `s_summary`. basic_table() %>%   split_cols_by(\"ARM\") %>%   split_rows_by(\"AVISIT\") %>%   split_cols_by_multivar(vars = c(\"AVAL\", \"CHG\")) %>%   summarize_colvars(na.rm = FALSE) %>%   build_table(dta_test) #>                         A                             B                             C           #>                 AVAL         CHG           AVAL               CHG           AVAL         CHG    #> ——————————————————————————————————————————————————————————————————————————————————————————————— #> V1                                                                                              #>   n               2           2              1                 1              0           0     #>   Mean (SD)   7.5 (2.1)   2.5 (2.1)   3.0 (<Missing>)   7.0 (<Missing>)   <Missing>   <Missing> #>   Median         7.5         2.5            3.0               7.0         <Missing>   <Missing> #>   Min - Max   6.0 - 9.0   1.0 - 4.0      3.0 - 3.0         7.0 - 7.0      <Missing>   <Missing> #> V2                                                                                              #>   n               2           2              1                 1              0           0     #>   Mean (SD)   6.5 (2.1)   3.5 (2.1)   2.0 (<Missing>)   8.0 (<Missing>)   <Missing>   <Missing> #>   Median         6.5         3.5            2.0               8.0         <Missing>   <Missing> #>   Min - Max   5.0 - 8.0   2.0 - 5.0      2.0 - 2.0         8.0 - 8.0      <Missing>   <Missing> #> V3                                                                                              #>   n               2           2              1                 1              0           0     #>   Mean (SD)   5.5 (2.1)   4.5 (2.1)   1.0 (<Missing>)   9.0 (<Missing>)   <Missing>   <Missing> #>   Median         5.5         4.5            1.0               9.0         <Missing>   <Missing> #>   Min - Max   4.0 - 7.0   3.0 - 6.0      1.0 - 1.0         9.0 - 9.0      <Missing>   <Missing>"},{"path":"https://insightsengineering.github.io/tern/main/reference/summarize_functions.html","id":null,"dir":"Reference","previous_headings":"","what":"Summarize functions — summarize_functions","title":"Summarize functions — summarize_functions","text":"functions wrappers rtables::summarize_row_groups(), applying corresponding tern content functions add summary rows given table layout:","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/summarize_functions.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Summarize functions — summarize_functions","text":"add_rowcounts() estimate_multinomial_response() (rtables::analyze()) h_tab_one_biomarker() (probably deprecate) logistic_summary_by_flag() summarize_num_patients() summarize_occurrences() summarize_occurrences_by_grade() summarize_patients_events_in_cols() summarize_patients_exposure_in_cols() Additionally, summarize_coxreg() function utilizes rtables::summarize_row_groups() (combination several rtables functions like rtables::analyze_colvars()) output Cox regression summary table.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/main/reference/summarize_glm_count.html","id":null,"dir":"Reference","previous_headings":"","what":"Summarize Poisson negative binomial regression — summarize_glm_count","title":"Summarize Poisson negative binomial regression — summarize_glm_count","text":"Summarize results Poisson negative binomial regression. can used analyze count /frequency data using linear model. specifically useful analyzing count data (using Poisson Negative Binomial distribution) result generalized linear model one (e.g. arm) covariates.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/summarize_glm_count.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Summarize Poisson negative binomial regression — summarize_glm_count","text":"","code":"summarize_glm_count(   lyt,   vars,   variables,   distribution,   conf_level,   rate_mean_method = c(\"emmeans\", \"ppmeans\")[1],   weights = stats::weights,   scale = 1,   var_labels,   na_str = default_na_str(),   nested = TRUE,   ...,   show_labels = \"visible\",   table_names = vars,   .stats = get_stats(\"summarize_glm_count\"),   .formats = NULL,   .labels = NULL,   .indent_mods = c(n = 0L, rate = 0L, rate_ci = 1L, rate_ratio = 0L, rate_ratio_ci = 1L,     pval = 1L) )  s_glm_count(   df,   .var,   .df_row,   variables,   .ref_group,   .in_ref_col,   distribution,   conf_level,   rate_mean_method,   weights,   scale = 1 )"},{"path":"https://insightsengineering.github.io/tern/main/reference/summarize_glm_count.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Summarize Poisson negative binomial regression — summarize_glm_count","text":"lyt (PreDataTableLayouts) layout analyses added . vars (character) variable names primary analysis variable iterated . variables (named list string) list additional analysis variables, expected elements: arm (string) group variable, covariate adjusted means multiple groups summarized. Specifically, first level arm variable taken reference group. covariates (character) vector can contain single variable names (\"X1\"), /interaction terms indicated \"X1 * X2\". offset (numeric) numeric vector scalar adding offset. distribution (character) character value specifying distribution used regression (Poisson, Quasi-Poisson, negative binomial). conf_level (proportion) confidence level interval. rate_mean_method (character(1)) method used estimate mean odds ratio. Defaults emmeans. see details information. weights (character) character vector specifying weights used averaging predictions. Number weights must equal number levels included covariates. Weights option passed emmeans::emmeans(). scale (numeric(1)) linear scaling factor rate confidence intervals. Defaults 1. var_labels (character) variable labels. na_str (string) string used replace NA empty values output. nested (flag) whether layout instruction applied within existing layout structure _if possible (TRUE, default) new top-level element (FALSE). Ignored nest split. underneath analyses, allowed. ... additional arguments lower level functions. show_labels (string) label visibility: one \"default\", \"visible\" \"hidden\". table_names (character) can customized case vars analyzed multiple times, avoid warnings rtables. .stats (character) statistics select table. Options : 'n', 'rate', 'rate_ci', 'rate_ratio', 'rate_ratio_ci', 'pval' .formats (named character list) formats statistics. See Details analyze_vars information \"auto\" setting. .labels (named character) labels statistics (without indent). .indent_mods (named integer) indent modifiers labels. Defaults 0, corresponds unmodified default behavior. Can negative. df (data.frame) data set containing analysis variables. .var (string) single variable name passed rtables requested statistics function. .df_row (data.frame) dataset includes variables called .var variables. .ref_group (data.frame vector) data corresponding reference group. .in_ref_col (flag)TRUE working reference level, FALSE otherwise.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/summarize_glm_count.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Summarize Poisson negative binomial regression — summarize_glm_count","text":"summarize_glm_count() returns layout object suitable passing layouting functions, rtables::build_table(). Adding function rtable layout add formatted rows containing statistics s_glm_count() table layout. s_glm_count() returns named list 5 statistics: n: Count complete sample size group. rate: Estimated event rate per follow-time. rate_ci: Confidence level estimated rate per follow-time. rate_ratio: Ratio event rates treatment arm reference arm. rate_ratio_ci: Confidence level rate ratio. pval: p-value.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/summarize_glm_count.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Summarize Poisson negative binomial regression — summarize_glm_count","text":"summarize_glm_count() uses s_glm_count() calculate statistics table. analysis function uses h_glm_count() estimate GLM stats::glm() Poisson Quasi-Poisson distributions MASS::glm.nb() Negative Binomial distribution. methods assume logarithmic link function. point, rates confidence intervals estimated model using either emmeans::emmeans() rate_mean_method = \"emmeans\" h_ppmeans() rate_mean_method = \"ppmeans\". reference group specified building table split_cols_by(ref_group), rate ratio p-value calculated. Otherwise, use emmeans::contrast() calculate rate ratio p-value reference group. Values always estimated method = \"trt.vs.ctrl\" ref equal first arm value.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/summarize_glm_count.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Summarize Poisson negative binomial regression — summarize_glm_count","text":"summarize_glm_count(): Layout-creating function can take statistics function arguments additional format arguments. function wrapper rtables::analyze(). s_glm_count(): Statistics function produces named list results investigated Poisson model.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/summarize_glm_count.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Summarize Poisson negative binomial regression — summarize_glm_count","text":"","code":"library(dplyr)  anl <- tern_ex_adtte %>% filter(PARAMCD == \"TNE\") anl$AVAL_f <- as.factor(anl$AVAL)  lyt <- basic_table() %>%   split_cols_by(\"ARM\", ref_group = \"B: Placebo\") %>%   add_colcounts() %>%   analyze_vars(     \"AVAL_f\",     var_labels = \"Number of exacerbations per patient\",     .stats = c(\"count_fraction\"),     .formats = c(\"count_fraction\" = \"xx (xx.xx%)\"),     .labels = c(\"Number of exacerbations per patient\")   ) %>%   summarize_glm_count(     vars = \"AVAL\",     variables = list(arm = \"ARM\", offset = \"lgTMATRSK\", covariates = NULL),     conf_level = 0.95,     distribution = \"poisson\",     rate_mean_method = \"emmeans\",     var_labels = \"Adjusted (P) exacerbation rate (per year)\",     table_names = \"adjP\",     .stats = c(\"rate\"),     .labels = c(rate = \"Rate\")   ) %>%   summarize_glm_count(     vars = \"AVAL\",     variables = list(arm = \"ARM\", offset = \"lgTMATRSK\", covariates = c(\"REGION1\")),     conf_level = 0.95,     distribution = \"quasipoisson\",     rate_mean_method = \"ppmeans\",     var_labels = \"Adjusted (QP) exacerbation rate (per year)\",     table_names = \"adjQP\",     .stats = c(\"rate\", \"rate_ci\", \"rate_ratio\", \"rate_ratio_ci\", \"pval\"),     .labels = c(       rate = \"Rate\", rate_ci = \"Rate CI\", rate_ratio = \"Rate Ratio\",       rate_ratio_ci = \"Rate Ratio CI\", pval = \"p value\"     )   ) %>%   summarize_glm_count(     vars = \"AVAL\",     variables = list(arm = \"ARM\", offset = \"lgTMATRSK\", covariates = c(\"REGION1\")),     conf_level = 0.95,     distribution = \"negbin\",     rate_mean_method = \"emmeans\",     var_labels = \"Adjusted (NB) exacerbation rate (per year)\",     table_names = \"adjNB\",     .stats = c(\"rate\", \"rate_ci\", \"rate_ratio\", \"rate_ratio_ci\", \"pval\"),     .labels = c(       rate = \"Rate\", rate_ci = \"Rate CI\", rate_ratio = \"Rate Ratio\",       rate_ratio_ci = \"Rate Ratio CI\", pval = \"p value\"     )   )  build_table(lyt = lyt, df = anl) #>                                                  A: Drug X            B: Placebo         C: Combination   #>                                                    (N=69)               (N=73)               (N=58)       #> ————————————————————————————————————————————————————————————————————————————————————————————————————————— #> Number of exacerbations per patient                                                                       #>   0                                              3 (4.35%)            8 (10.96%)           6 (10.34%)     #>   1                                             11 (15.94%)           9 (12.33%)           6 (10.34%)     #>   2                                             18 (26.09%)          15 (20.55%)           9 (15.52%)     #>   3                                             14 (20.29%)          11 (15.07%)          15 (25.86%)     #>   4                                             10 (14.49%)           9 (12.33%)           9 (15.52%)     #>   5                                              7 (10.14%)           9 (12.33%)           8 (13.79%)     #>   6                                              4 (5.80%)            4 (5.48%)            4 (6.90%)      #>   7                                              2 (2.90%)            8 (10.96%)           0 (0.00%)      #>   10                                             0 (0.00%)            0 (0.00%)            1 (1.72%)      #> Adjusted (P) exacerbation rate (per year)                                                                 #>   Rate                                             8.2061               9.1554               7.8551       #> Adjusted (QP) exacerbation rate (per year)                                                                #>   Rate                                             3.1214               3.4860               2.6152       #>     Rate CI                                   (1.7307, 5.6294)     (1.9833, 6.1272)     (1.3661, 5.0065)  #>   Rate Ratio                                       0.8954                                    0.7502       #>     Rate Ratio CI                             (0.3975, 2.0170)                          (0.3067, 1.8348)  #>     p value                                        0.7897                                    0.5288       #> Adjusted (NB) exacerbation rate (per year)                                                                #>   Rate                                            33.0138              37.3569              34.9046       #>     Rate CI                                  (21.6999, 50.2266)   (24.5906, 56.7507)   (23.0925, 52.7587) #>   Rate Ratio                                       0.8837                                    0.9344       #>     Rate Ratio CI                             (0.5872, 1.3300)                          (0.6063, 1.4400)  #>     p value                                        0.5534                                    0.7583"},{"path":"https://insightsengineering.github.io/tern/main/reference/summarize_logistic.html","id":null,"dir":"Reference","previous_headings":"","what":"Multivariate logistic regression table — summarize_logistic","title":"Multivariate logistic regression table — summarize_logistic","text":"Layout-creating function summarizes logistic variable regression binary outcome categorical/continuous covariates model statement. covariate category (categorical) specified values (continuous), present degrees freedom, regression parameter estimate standard error (SE) relative reference group category. Report odds ratios covariate category specified values corresponding Wald confidence intervals default allow user specify confidence levels. Report p-value Wald chi-square test null hypothesis covariate effect response model containing specified covariates. Allow option include one two-way interaction present similar output interaction degree freedom.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/summarize_logistic.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Multivariate logistic regression table — summarize_logistic","text":"","code":"summarize_logistic(   lyt,   conf_level,   drop_and_remove_str = \"\",   .indent_mods = NULL )"},{"path":"https://insightsengineering.github.io/tern/main/reference/summarize_logistic.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Multivariate logistic regression table — summarize_logistic","text":"lyt (PreDataTableLayouts) layout analyses added . conf_level (proportion) confidence level interval. drop_and_remove_str (string) string dropped removed. .indent_mods (named integer) indent modifiers labels. Defaults 0, corresponds unmodified default behavior. Can negative.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/summarize_logistic.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Multivariate logistic regression table — summarize_logistic","text":"layout object suitable passing layouting functions, rtables::build_table(). Adding function rtable layout add logistic regression variable summary table layout.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/summarize_logistic.html","id":"note","dir":"Reference","previous_headings":"","what":"Note","title":"Multivariate logistic regression table — summarize_logistic","text":"formula, variable names need standard data.frame column names without special characters.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/summarize_logistic.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Multivariate logistic regression table — summarize_logistic","text":"","code":"library(dplyr) library(broom)  adrs_f <- tern_ex_adrs %>%   filter(PARAMCD == \"BESRSPI\") %>%   filter(RACE %in% c(\"ASIAN\", \"WHITE\", \"BLACK OR AFRICAN AMERICAN\")) %>%   mutate(     Response = case_when(AVALC %in% c(\"PR\", \"CR\") ~ 1, TRUE ~ 0),     RACE = factor(RACE),     SEX = factor(SEX)   ) formatters::var_labels(adrs_f) <- c(formatters::var_labels(tern_ex_adrs), Response = \"Response\") mod1 <- fit_logistic(   data = adrs_f,   variables = list(     response = \"Response\",     arm = \"ARMCD\",     covariates = c(\"AGE\", \"RACE\")   ) ) #> Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred mod2 <- fit_logistic(   data = adrs_f,   variables = list(     response = \"Response\",     arm = \"ARMCD\",     covariates = c(\"AGE\", \"RACE\"),     interaction = \"AGE\"   ) ) #> Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred  df <- tidy(mod1, conf_level = 0.99) df2 <- tidy(mod2, conf_level = 0.99)  # flagging empty strings with \"_\" df <- df_explicit_na(df, na_level = \"_\") df2 <- df_explicit_na(df2, na_level = \"_\")  result1 <- basic_table() %>%   summarize_logistic(     conf_level = 0.95,     drop_and_remove_str = \"_\"   ) %>%   build_table(df = df) result1 #>                                       Degrees of Freedom   Parameter Estimate   Standard Error   Odds Ratio     Wald 95% CI     p-value #> ——————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————— #> Planned Arm Code                              2                                                                                 0.3004  #>   Reference ARM A, n = 64                                                                                                               #>   ARM B, n = 68                               1                  -1.775             1.144           0.17       (<0.01, 3.23)    0.1209  #>   ARM C, n = 52                               1                  17.192            3626.588       >999.99     (0.00, >999.99)   0.9962  #> Age                                                                                                                                     #>   Age                                         1                  0.170              0.095           1.19       (0.93, 1.51)     0.0746  #> Race                                          2                                                                                 0.7967  #>   Reference ASIAN, n = 110                                                                                                              #>   BLACK OR AFRICAN AMERICAN, n = 40           1                  17.923            4001.705       >999.99     (0.00, >999.99)   0.9964  #>   WHITE, n = 34                               1                  -0.656             0.974           0.52       (0.04, 6.37)     0.5002   result2 <- basic_table() %>%   summarize_logistic(     conf_level = 0.95,     drop_and_remove_str = \"_\"   ) %>%   build_table(df = df2) result2 #>                                         Degrees of Freedom   Parameter Estimate   Standard Error   Odds Ratio     Wald 95% CI     p-value #> ————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————— #> Race                                            2                                                                                 0.9361  #>   Reference ASIAN, n = 110                                                                                                                #>   BLACK OR AFRICAN AMERICAN, n = 40             1                  18.150            3944.701       >999.99     (0.00, >999.99)   0.9963  #>   WHITE, n = 34                                 1                  -0.373             1.026           0.69       (0.05, 9.68)     0.7164  #> Planned Arm Code                                2                                                                                 0.2539  #>   Reference ARM A, n = 64                                                                                                                 #>   ARM B, n = 68                                 1                 -11.527             6.962                                       0.0978  #>     Age                                                                                                                                   #>       35                                                                                              0.48       (0.01, 15.48)            #>   ARM C, n = 52                                 1                  16.333           20278.387                                     0.9994  #>     Age                                                                                                                                   #>       35                                                                                            >999.99     (0.00, >999.99)           #> Age                                                                                                                                       #>   Age                                           1                  -0.039             0.151                                       0.7981  #>     Planned Arm Code                                                                                                                      #>       ARM A                                                                                           0.96       (0.65, 1.42)             #>       ARM B                                                                                           1.31       (0.92, 1.86)             #>       ARM C                                                                                           0.99      (0.00, >999.99)           #> Interaction of Planned Arm Code * Age           2                                                                                 0.3276  #>   Reference ARM A, n = 64                                                                                                                 #>   ARM B, n = 68                                 1                  0.308              0.206                                       0.1352  #>   ARM C, n = 52                                 1                  0.029             548.592                                      1.0000"},{"path":"https://insightsengineering.github.io/tern/main/reference/summarize_num_patients.html","id":null,"dir":"Reference","previous_headings":"","what":"Count number of patients — summarize_num_patients","title":"Count number of patients — summarize_num_patients","text":"analyze function analyze_num_patients() creates layout element count total numbers unique non-unique patients. primary analysis variable vars used uniquely identify patients. count_by variable can used identify non-unique patients number patients unique combination values vars count_by returned instead nonunique statistic. required variable can used specify variable required non-missing record included counts. summarize function summarize_num_patients() performs function analyze_num_patients() except creates content rows, data rows, summarize current table row/column context operates level latest row split root table row splits occurred.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/summarize_num_patients.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Count number of patients — summarize_num_patients","text":"","code":"analyze_num_patients(   lyt,   vars,   required = NULL,   count_by = NULL,   unique_count_suffix = TRUE,   na_str = default_na_str(),   nested = TRUE,   .stats = NULL,   .formats = NULL,   .labels = c(unique = \"Number of patients with at least one event\", nonunique =     \"Number of events\"),   show_labels = c(\"default\", \"visible\", \"hidden\"),   .indent_mods = 0L,   riskdiff = FALSE,   ... )  summarize_num_patients(   lyt,   var,   required = NULL,   count_by = NULL,   unique_count_suffix = TRUE,   na_str = default_na_str(),   .stats = NULL,   .formats = NULL,   .labels = c(unique = \"Number of patients with at least one event\", nonunique =     \"Number of events\"),   .indent_mods = 0L,   riskdiff = FALSE,   ... )  s_num_patients(   x,   labelstr,   .N_col,   count_by = NULL,   unique_count_suffix = TRUE )  s_num_patients_content(   df,   labelstr = \"\",   .N_col,   .var,   required = NULL,   count_by = NULL,   unique_count_suffix = TRUE )"},{"path":"https://insightsengineering.github.io/tern/main/reference/summarize_num_patients.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Count number of patients — summarize_num_patients","text":"lyt (PreDataTableLayouts) layout analyses added . vars (character) variable names primary analysis variable iterated . required (character NULL) name variable required non-missing. count_by (character NULL) name variable combined vars counting nonunique records. unique_count_suffix (flag) whether \"(n)\" suffix added unique_count labels. Defaults TRUE. na_str (string) string used replace NA empty values output. nested (flag) whether layout instruction applied within existing layout structure _if possible (TRUE, default) new top-level element (FALSE). Ignored nest split. underneath analyses, allowed. .stats (character) statistics select table. Options : 'unique', 'nonunique', 'unique_count' .formats (named character list) formats statistics. See Details analyze_vars information \"auto\" setting. .labels (named character) labels statistics (without indent). show_labels (string) label visibility: one \"default\", \"visible\" \"hidden\". .indent_mods (named integer) indent modifiers labels. Defaults 0, corresponds unmodified default behavior. Can negative. riskdiff (flag) whether risk difference column present. set TRUE, add_riskdiff() must used split_fun prior column split table layout, specifying columns compared. See stat_propdiff_ci() details risk difference calculation. ... additional arguments lower level functions. x (character factor) vector patient IDs. labelstr (string) label level parent split currently summarized (must present second argument Content Row Functions). See rtables::summarize_row_groups() information. .N_col (integer(1)) column-wise N (column count) full column analyzed typically passed rtables. df (data.frame) data set containing analysis variables. .var, var (string) single variable name passed rtables requested statistics function.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/summarize_num_patients.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Count number of patients — summarize_num_patients","text":"analyze_num_patients() returns layout object suitable passing layouting functions, rtables::build_table(). Adding function rtable layout add formatted rows containing statistics s_num_patients_content() table layout. summarize_num_patients() returns layout object suitable passing layouting functions, rtables::build_table(). Adding function rtable layout add formatted rows containing statistics s_num_patients_content() table layout. s_num_patients() returns named list 3 statistics: unique: Vector counts percentages. nonunique: Vector counts. unique_count: Counts. s_num_patients_content() returns values s_num_patients().","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/summarize_num_patients.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Count number of patients — summarize_num_patients","text":"general, functions starts analyze* expected work like rtables::analyze(), functions starts summarize* based upon rtables::summarize_row_groups(). latter provides value dividing split row column space, , bound fundamental splits, repeated design every page pagination involved.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/summarize_num_patients.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Count number of patients — summarize_num_patients","text":"analyze_num_patients(): Layout-creating function can take statistics function arguments additional format arguments. function wrapper rtables::analyze(). summarize_num_patients(): Layout-creating function can take statistics function arguments additional format arguments. function wrapper rtables::summarize_row_groups(). s_num_patients(): Statistics function counts number unique patients, corresponding percentage taken respect total number patients, number non-unique patients. s_num_patients_content(): Statistics function counts number unique patients column (variable), corresponding percentage taken respect total number patients, number non-unique patients column.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/summarize_num_patients.html","id":"note","dir":"Reference","previous_headings":"","what":"Note","title":"Count number of patients — summarize_num_patients","text":"opposed summarize_num_patients(), function repeat produced rows.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/summarize_num_patients.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Count number of patients — summarize_num_patients","text":"","code":"df <- data.frame(   USUBJID = as.character(c(1, 2, 1, 4, NA, 6, 6, 8, 9)),   ARM = c(\"A\", \"A\", \"A\", \"A\", \"A\", \"B\", \"B\", \"B\", \"B\"),   AGE = c(10, 15, 10, 17, 8, 11, 11, 19, 17),   SEX = c(\"M\", \"M\", \"M\", \"F\", \"F\", \"F\", \"M\", \"F\", \"M\") )  # analyze_num_patients tbl <- basic_table() %>%   split_cols_by(\"ARM\") %>%   add_colcounts() %>%   analyze_num_patients(\"USUBJID\", .stats = c(\"unique\")) %>%   build_table(df)  tbl #>                                                  A           B     #>                                                (N=5)       (N=4)   #> —————————————————————————————————————————————————————————————————— #> Number of patients with at least one event   3 (60.0%)   3 (75.0%)  # summarize_num_patients tbl <- basic_table() %>%   split_cols_by(\"ARM\") %>%   split_rows_by(\"SEX\") %>%   summarize_num_patients(\"USUBJID\", .stats = \"unique_count\") %>%   build_table(df)  tbl #>         A   B #> ————————————— #> M (n)   2   2 #> F (n)   1   2  # Use the statistics function to count number of unique and nonunique patients. s_num_patients(x = as.character(c(1, 1, 1, 2, 4, NA)), labelstr = \"\", .N_col = 6L) #> $unique #> [1] 3.0 0.5 #> attr(,\"label\") #> [1] \"\" #>  #> $nonunique #> [1] 5 #> attr(,\"label\") #> [1] \"\" #>  #> $unique_count #> [1] 3 #> attr(,\"label\") #> [1] \"(n)\" #>  s_num_patients(   x = as.character(c(1, 1, 1, 2, 4, NA)),   labelstr = \"\",   .N_col = 6L,   count_by = c(1, 1, 2, 1, 1, 1) ) #> $unique #> [1] 3.0 0.5 #> attr(,\"label\") #> [1] \"\" #>  #> $nonunique #> [1] 4 #> attr(,\"label\") #> [1] \"\" #>  #> $unique_count #> [1] 3 #> attr(,\"label\") #> [1] \"(n)\" #>   # Count number of unique and non-unique patients.  df <- data.frame(   USUBJID = as.character(c(1, 2, 1, 4, NA)),   EVENT = as.character(c(10, 15, 10, 17, 8)) ) s_num_patients_content(df, .N_col = 5, .var = \"USUBJID\") #> $unique #> [1] 3.0 0.6 #> attr(,\"label\") #> [1] \"\" #>  #> $nonunique #> [1] 4 #> attr(,\"label\") #> [1] \"\" #>  #> $unique_count #> [1] 3 #> attr(,\"label\") #> [1] \"(n)\" #>   df_by_event <- data.frame(   USUBJID = as.character(c(1, 2, 1, 4, NA)),   EVENT = c(10, 15, 10, 17, 8) ) s_num_patients_content(df_by_event, .N_col = 5, .var = \"USUBJID\", count_by = \"EVENT\") #> $unique #> [1] 3.0 0.6 #> attr(,\"label\") #> [1] \"\" #>  #> $nonunique #> [1] 3 #> attr(,\"label\") #> [1] \"\" #>  #> $unique_count #> [1] 3 #> attr(,\"label\") #> [1] \"(n)\" #>"},{"path":"https://insightsengineering.github.io/tern/main/reference/summarize_patients_exposure_in_cols.html","id":null,"dir":"Reference","previous_headings":"","what":"Count number of patients and sum exposure across all patients in columns — summarize_patients_exposure_in_cols","title":"Count number of patients and sum exposure across all patients in columns — summarize_patients_exposure_in_cols","text":"analyze function analyze_patients_exposure_in_cols() creates layout element count total numbers patients sum analysis value (.e. exposure) across patients columns. primary analysis variable ex_var exposure variable used calculate sum_exposure statistic. id variable used uniquely identify patients data unique patients counted n_patients statistic, var variable used create row split needed. percentage returned part n_patients statistic proportion records correspond unique patient. summarize function summarize_patients_exposure_in_cols() performs function analyze_patients_exposure_in_cols() except creates content rows, data rows, summarize current table row/column context operates level latest row split root table row splits occurred. column split yet performed table, col_split must set TRUE first call analyze_patients_exposure_in_cols() summarize_patients_exposure_in_cols().","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/summarize_patients_exposure_in_cols.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Count number of patients and sum exposure across all patients in columns — summarize_patients_exposure_in_cols","text":"","code":"analyze_patients_exposure_in_cols(   lyt,   var = NULL,   ex_var = \"AVAL\",   id = \"USUBJID\",   add_total_level = FALSE,   custom_label = NULL,   col_split = TRUE,   na_str = default_na_str(),   .stats = c(\"n_patients\", \"sum_exposure\"),   .labels = c(n_patients = \"Patients\", sum_exposure = \"Person time\"),   .indent_mods = 0L,   ... )  summarize_patients_exposure_in_cols(   lyt,   var,   ex_var = \"AVAL\",   id = \"USUBJID\",   add_total_level = FALSE,   custom_label = NULL,   col_split = TRUE,   na_str = default_na_str(),   ...,   .stats = c(\"n_patients\", \"sum_exposure\"),   .labels = c(n_patients = \"Patients\", sum_exposure = \"Person time\"),   .indent_mods = NULL )  s_count_patients_sum_exposure(   df,   ex_var = \"AVAL\",   id = \"USUBJID\",   labelstr = \"\",   .stats = c(\"n_patients\", \"sum_exposure\"),   .N_col,   custom_label = NULL )  a_count_patients_sum_exposure(   df,   var = NULL,   ex_var = \"AVAL\",   id = \"USUBJID\",   add_total_level = FALSE,   custom_label = NULL,   labelstr = \"\",   .N_col,   .stats,   .formats = list(n_patients = \"xx (xx.x%)\", sum_exposure = \"xx\") )"},{"path":"https://insightsengineering.github.io/tern/main/reference/summarize_patients_exposure_in_cols.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Count number of patients and sum exposure across all patients in columns — summarize_patients_exposure_in_cols","text":"lyt (PreDataTableLayouts) layout analyses added . var (string) single variable name passed rtables requested statistics function. ex_var (string) name variable df containing exposure values. id (string) subject variable name. add_total_level (flag) adds \"total\" level others includes levels constitute split. custom label can set level via custom_label argument. custom_label (string NULL) provided labelstr empty, used label. col_split (flag) whether columns split. Set FALSE required column split done already earlier layout pipe. na_str (string) string used replace NA empty values output. .stats (character) statistics select table. Options : 'n_patients', 'sum_exposure' .labels (named character) labels statistics (without indent). .indent_mods (named integer) indent modifiers labels. Defaults 0, corresponds unmodified default behavior. Can negative. ... additional arguments lower level functions. df (data.frame) data set containing analysis variables. labelstr (string) label level parent split currently summarized (must present second argument Content Row Functions). See rtables::summarize_row_groups() information. .N_col (integer(1)) column-wise N (column count) full column analyzed typically passed rtables. .formats (named character list) formats statistics. See Details analyze_vars information \"auto\" setting.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/summarize_patients_exposure_in_cols.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Count number of patients and sum exposure across all patients in columns — summarize_patients_exposure_in_cols","text":"analyze_patients_exposure_in_cols() returns layout object suitable passing layouting functions, rtables::build_table(). Adding function rtable layout add formatted data rows, statistics s_count_patients_sum_exposure() arranged columns, table layout. summarize_patients_exposure_in_cols() returns layout object suitable passing layouting functions, rtables::build_table(). Adding function rtable layout add formatted content rows, statistics s_count_patients_sum_exposure() arranged columns, table layout. s_count_patients_sum_exposure() returns named list statistics: n_patients: Number unique patients df. sum_exposure: Sum ex_var across patients df. a_count_patients_sum_exposure() returns formatted rtables::CellValue().","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/summarize_patients_exposure_in_cols.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Count number of patients and sum exposure across all patients in columns — summarize_patients_exposure_in_cols","text":"analyze_patients_exposure_in_cols(): Layout-creating function can take statistics function arguments additional format arguments. function wrapper rtables::split_cols_by_multivar() rtables::analyze_colvars(). summarize_patients_exposure_in_cols(): Layout-creating function can take statistics function arguments additional format arguments. function wrapper rtables::split_cols_by_multivar() rtables::summarize_row_groups(). s_count_patients_sum_exposure(): Statistics function counts numbers patients sum exposure across patients. a_count_patients_sum_exposure(): Analysis function used afun rtables::analyze_colvars() within analyze_patients_exposure_in_cols() cfun rtables::summarize_row_groups() within summarize_patients_exposure_in_cols().","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/summarize_patients_exposure_in_cols.html","id":"note","dir":"Reference","previous_headings":"","what":"Note","title":"Count number of patients and sum exposure across all patients in columns — summarize_patients_exposure_in_cols","text":"opposed summarize_patients_exposure_in_cols() generates content rows, analyze_patients_exposure_in_cols() generates data rows repeated multiple pages pagination used.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/summarize_patients_exposure_in_cols.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Count number of patients and sum exposure across all patients in columns — summarize_patients_exposure_in_cols","text":"","code":"set.seed(1) df <- data.frame(   USUBJID = c(paste(\"id\", seq(1, 12), sep = \"\")),   ARMCD = c(rep(\"ARM A\", 6), rep(\"ARM B\", 6)),   SEX = c(rep(\"Female\", 6), rep(\"Male\", 6)),   AVAL = as.numeric(sample(seq(1, 20), 12)),   stringsAsFactors = TRUE ) adsl <- data.frame(   USUBJID = c(paste(\"id\", seq(1, 12), sep = \"\")),   ARMCD = c(rep(\"ARM A\", 2), rep(\"ARM B\", 2)),   SEX = c(rep(\"Female\", 2), rep(\"Male\", 2)),   stringsAsFactors = TRUE )  lyt <- basic_table() %>%   split_cols_by(\"ARMCD\", split_fun = add_overall_level(\"Total\", first = FALSE)) %>%   summarize_patients_exposure_in_cols(var = \"AVAL\", col_split = TRUE) %>%   analyze_patients_exposure_in_cols(var = \"SEX\", col_split = FALSE) result <- build_table(lyt, df = df, alt_counts_df = adsl) result #>                                               ARM A                      ARM B                       Total           #>                                       Patients    Person time    Patients    Person time    Patients     Person time #> ———————————————————————————————————————————————————————————————————————————————————————————————————————————————————— #> Total patients numbers/person time   6 (100.0%)       46        6 (100.0%)       68        12 (100.0%)       114     #>   Female                             6 (100.0%)       46         0 (0.0%)         0         6 (50.0%)        46      #>   Male                                0 (0.0%)         0        6 (100.0%)       68         6 (50.0%)        68       lyt2 <- basic_table() %>%   split_cols_by(\"ARMCD\", split_fun = add_overall_level(\"Total\", first = FALSE)) %>%   summarize_patients_exposure_in_cols(     var = \"AVAL\", col_split = TRUE,     .stats = \"n_patients\", custom_label = \"some custom label\"   ) %>%   analyze_patients_exposure_in_cols(var = \"SEX\", col_split = FALSE, ex_var = \"AVAL\") result2 <- build_table(lyt2, df = df, alt_counts_df = adsl) result2 #>                       ARM A        ARM B         Total    #>                      Patients     Patients     Patients   #> ————————————————————————————————————————————————————————— #> some custom label   6 (100.0%)   6 (100.0%)   12 (100.0%) #>   Female            6 (100.0%)    0 (0.0%)     6 (50.0%)  #>   Male               0 (0.0%)    6 (100.0%)    6 (50.0%)   lyt3 <- basic_table() %>%   analyze_patients_exposure_in_cols(var = \"SEX\", col_split = TRUE, ex_var = \"AVAL\") result3 <- build_table(lyt3, df = df, alt_counts_df = adsl) result3 #>          Patients    Person time #> ———————————————————————————————— #> Female   6 (50.0%)       46      #> Male     6 (50.0%)       68       # Adding total levels and custom label lyt4 <- basic_table(   show_colcounts = TRUE ) %>%   analyze_patients_exposure_in_cols(     var = \"ARMCD\",     col_split = TRUE,     add_total_level = TRUE,     custom_label = \"TOTAL\"   ) %>%   append_topleft(c(\"\", \"Sex\"))  result4 <- build_table(lyt4, df = df, alt_counts_df = adsl) result4 #>          Patients     Person time #> Sex       (N=12)        (N=12)    #> ————————————————————————————————— #> ARM A    6 (50.0%)        46      #> ARM B    6 (50.0%)        68      #> TOTAL   12 (100.0%)       114      lyt5 <- basic_table() %>%   summarize_patients_exposure_in_cols(var = \"AVAL\", col_split = TRUE)  result5 <- build_table(lyt5, df = df, alt_counts_df = adsl) result5 #>                                       Patients     Person time #> —————————————————————————————————————————————————————————————— #> Total patients numbers/person time   12 (100.0%)       114      lyt6 <- basic_table() %>%   summarize_patients_exposure_in_cols(var = \"AVAL\", col_split = TRUE, .stats = \"sum_exposure\")  result6 <- build_table(lyt6, df = df, alt_counts_df = adsl) result6 #>                                      Person time #> ———————————————————————————————————————————————— #> Total patients numbers/person time       114      a_count_patients_sum_exposure(   df = df,   var = \"SEX\",   .N_col = nrow(df),   .stats = \"n_patients\" ) #> RowsVerticalSection (in_rows) object print method: #> ---------------------------- #>   row_name formatted_cell indent_mod row_label #> 1   Female      6 (50.0%)          0    Female #> 2     Male      6 (50.0%)          0      Male"},{"path":"https://insightsengineering.github.io/tern/main/reference/survival_biomarkers_subgroups.html","id":null,"dir":"Reference","previous_headings":"","what":"Tabulate biomarker effects on survival by subgroup — survival_biomarkers_subgroups","title":"Tabulate biomarker effects on survival by subgroup — survival_biomarkers_subgroups","text":"tabulate_survival_biomarkers() function creates layout element tabulate estimated effects multiple continuous biomarker variables survival across subgroups, returning statistics including median survival time hazard ratio population subgroup. table created df, list data frames returned extract_survival_biomarkers(), statistics include specified via vars parameter. forest plot can created resulting table using g_forest() function.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/survival_biomarkers_subgroups.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Tabulate biomarker effects on survival by subgroup — survival_biomarkers_subgroups","text":"","code":"tabulate_survival_biomarkers(   df,   vars = c(\"n_tot\", \"n_tot_events\", \"median\", \"hr\", \"ci\", \"pval\"),   groups_lists = list(),   control = control_coxreg(),   label_all = lifecycle::deprecated(),   time_unit = NULL,   na_str = default_na_str(),   .indent_mods = 0L )"},{"path":"https://insightsengineering.github.io/tern/main/reference/survival_biomarkers_subgroups.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Tabulate biomarker effects on survival by subgroup — survival_biomarkers_subgroups","text":"df (data.frame) containing analysis variables, returned extract_survival_biomarkers(). vars (character) names statistics reported among: n_tot_events: Total number events per group. n_tot: Total number observations per group. median: Median survival time. hr: Hazard ratio. ci: Confidence interval hazard ratio. pval: p-value effect. Note, one statistics n_tot n_tot_events, well hr ci required. groups_lists (named list list) optionally contains subgroups variable list, specifies new group levels via names levels belong character vectors elements list. control (list) list parameters returned helper function control_coxreg(). label_all please assign label_all parameter within extract_survival_biomarkers() function creating df. time_unit (string) label unit median survival time. Default NULL skips displaying unit. na_str (string) string used replace NA empty values output. .indent_mods (named integer) indent modifiers labels. Defaults 0, corresponds unmodified default behavior. Can negative.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/survival_biomarkers_subgroups.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Tabulate biomarker effects on survival by subgroup — survival_biomarkers_subgroups","text":"rtables table summarizing biomarker effects survival subgroup.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/survival_biomarkers_subgroups.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Tabulate biomarker effects on survival by subgroup — survival_biomarkers_subgroups","text":"functions create layout starting data frame contains required statistics. tables typically used input forest plots.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/survival_biomarkers_subgroups.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Tabulate biomarker effects on survival by subgroup — survival_biomarkers_subgroups","text":"tabulate_survival_biomarkers(): Table-creating function creates table summarizing biomarker effects survival subgroup.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/survival_biomarkers_subgroups.html","id":"note","dir":"Reference","previous_headings":"","what":"Note","title":"Tabulate biomarker effects on survival by subgroup — survival_biomarkers_subgroups","text":"contrast tabulate_survival_subgroups() tabulation function start input layout lyt. internally table created combining multiple subtables.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/main/reference/survival_biomarkers_subgroups.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Tabulate biomarker effects on survival by subgroup — survival_biomarkers_subgroups","text":"","code":"library(dplyr)  adtte <- tern_ex_adtte  # Save variable labels before data processing steps. adtte_labels <- formatters::var_labels(adtte)  adtte_f <- adtte %>%   filter(PARAMCD == \"OS\") %>%   mutate(     AVALU = as.character(AVALU),     is_event = CNSR == 0   ) labels <- c(\"AVALU\" = adtte_labels[[\"AVALU\"]], \"is_event\" = \"Event Flag\") formatters::var_labels(adtte_f)[names(labels)] <- labels  # Typical analysis of two continuous biomarkers `BMRKR1` and `AGE`, # in multiple regression models containing one covariate `RACE`, # as well as one stratification variable `STRATA1`. The subgroups # are defined by the levels of `BMRKR2`.  df <- extract_survival_biomarkers(   variables = list(     tte = \"AVAL\",     is_event = \"is_event\",     biomarkers = c(\"BMRKR1\", \"AGE\"),     strata = \"STRATA1\",     covariates = \"SEX\",     subgroups = \"BMRKR2\"   ),   label_all = \"Total Patients\",   data = adtte_f ) df #>   biomarker              biomarker_label n_tot n_tot_events   median        hr #> 1    BMRKR1 Continuous Level Biomarker 1   200          141 753.5176 1.0010939 #> 2       AGE                          Age   200          141 753.5176 1.0106406 #> 3    BMRKR1 Continuous Level Biomarker 1    70           52 735.4722 0.9905065 #> 4       AGE                          Age    70           52 735.4722 1.0106279 #> 5    BMRKR1 Continuous Level Biomarker 1    68           42 858.9952 0.9623210 #> 6       AGE                          Age    68           42 858.9952 1.0360765 #> 7    BMRKR1 Continuous Level Biomarker 1    62           47 727.8043 1.0770946 #> 8       AGE                          Age    62           47 727.8043 1.0009890 #>         lcl      ucl conf_level      pval     pval_label       subgroup    var #> 1 0.9538978 1.050625       0.95 0.9646086 p-value (Wald) Total Patients    ALL #> 2 0.9871004 1.034742       0.95 0.3787395 p-value (Wald) Total Patients    ALL #> 3 0.9142220 1.073156       0.95 0.8155443 p-value (Wald)            LOW BMRKR2 #> 4 0.9621192 1.061582       0.95 0.6735773 p-value (Wald)            LOW BMRKR2 #> 5 0.8708694 1.063376       0.95 0.4509368 p-value (Wald)         MEDIUM BMRKR2 #> 6 0.9727439 1.103532       0.95 0.2707796 p-value (Wald)         MEDIUM BMRKR2 #> 7 0.9756250 1.189118       0.95 0.1412524 p-value (Wald)           HIGH BMRKR2 #> 8 0.9678535 1.035259       0.95 0.9541048 p-value (Wald)           HIGH BMRKR2 #>                      var_label row_type #> 1               Total Patients  content #> 2               Total Patients  content #> 3 Continuous Level Biomarker 2 analysis #> 4 Continuous Level Biomarker 2 analysis #> 5 Continuous Level Biomarker 2 analysis #> 6 Continuous Level Biomarker 2 analysis #> 7 Continuous Level Biomarker 2 analysis #> 8 Continuous Level Biomarker 2 analysis  # Here we group the levels of `BMRKR2` manually. df_grouped <- extract_survival_biomarkers(   variables = list(     tte = \"AVAL\",     is_event = \"is_event\",     biomarkers = c(\"BMRKR1\", \"AGE\"),     strata = \"STRATA1\",     covariates = \"SEX\",     subgroups = \"BMRKR2\"   ),   data = adtte_f,   groups_lists = list(     BMRKR2 = list(       \"low\" = \"LOW\",       \"low/medium\" = c(\"LOW\", \"MEDIUM\"),       \"low/medium/high\" = c(\"LOW\", \"MEDIUM\", \"HIGH\")     )   ) ) df_grouped #>   biomarker              biomarker_label n_tot n_tot_events   median        hr #> 1    BMRKR1 Continuous Level Biomarker 1   200          141 753.5176 1.0010939 #> 2       AGE                          Age   200          141 753.5176 1.0106406 #> 3    BMRKR1 Continuous Level Biomarker 1    70           52 735.4722 0.9905065 #> 4       AGE                          Age    70           52 735.4722 1.0106279 #> 5    BMRKR1 Continuous Level Biomarker 1   138           94 777.8929 0.9801709 #> 6       AGE                          Age   138           94 777.8929 1.0236283 #> 7    BMRKR1 Continuous Level Biomarker 1   200          141 753.5176 1.0010939 #> 8       AGE                          Age   200          141 753.5176 1.0106406 #>         lcl      ucl conf_level      pval     pval_label        subgroup    var #> 1 0.9538978 1.050625       0.95 0.9646086 p-value (Wald)    All Patients    ALL #> 2 0.9871004 1.034742       0.95 0.3787395 p-value (Wald)    All Patients    ALL #> 3 0.9142220 1.073156       0.95 0.8155443 p-value (Wald)             low BMRKR2 #> 4 0.9621192 1.061582       0.95 0.6735773 p-value (Wald)             low BMRKR2 #> 5 0.9235465 1.040267       0.95 0.5094582 p-value (Wald)      low/medium BMRKR2 #> 6 0.9859367 1.062761       0.95 0.2224475 p-value (Wald)      low/medium BMRKR2 #> 7 0.9538978 1.050625       0.95 0.9646086 p-value (Wald) low/medium/high BMRKR2 #> 8 0.9871004 1.034742       0.95 0.3787395 p-value (Wald) low/medium/high BMRKR2 #>                      var_label row_type #> 1                 All Patients  content #> 2                 All Patients  content #> 3 Continuous Level Biomarker 2 analysis #> 4 Continuous Level Biomarker 2 analysis #> 5 Continuous Level Biomarker 2 analysis #> 6 Continuous Level Biomarker 2 analysis #> 7 Continuous Level Biomarker 2 analysis #> 8 Continuous Level Biomarker 2 analysis  ## Table with default columns. tabulate_survival_biomarkers(df) #>                                  Total n   Total Events   Median   Hazard Ratio   95% Wald CI    p-value (Wald) #> ——————————————————————————————————————————————————————————————————————————————————————————————————————————————— #> Age                                                                                                             #>   Total Patients                   200         141        753.5        1.01       (0.99, 1.03)       0.3787     #>   Continuous Level Biomarker 2                                                                                  #>     LOW                            70           52        735.5        1.01       (0.96, 1.06)       0.6736     #>     MEDIUM                         68           42        859.0        1.04       (0.97, 1.10)       0.2708     #>     HIGH                           62           47        727.8        1.00       (0.97, 1.04)       0.9541     #> Continuous Level Biomarker 1                                                                                    #>   Total Patients                   200         141        753.5        1.00       (0.95, 1.05)       0.9646     #>   Continuous Level Biomarker 2                                                                                  #>     LOW                            70           52        735.5        0.99       (0.91, 1.07)       0.8155     #>     MEDIUM                         68           42        859.0        0.96       (0.87, 1.06)       0.4509     #>     HIGH                           62           47        727.8        1.08       (0.98, 1.19)       0.1413      ## Table with a manually chosen set of columns: leave out \"pval\", reorder. tab <- tabulate_survival_biomarkers(   df = df,   vars = c(\"n_tot_events\", \"ci\", \"n_tot\", \"median\", \"hr\"),   time_unit = as.character(adtte_f$AVALU[1]) )  ## Finally produce the forest plot. # \\donttest{ g_forest(tab, xlim = c(0.8, 1.2))  # }"},{"path":"https://insightsengineering.github.io/tern/main/reference/survival_coxph_pairwise.html","id":null,"dir":"Reference","previous_headings":"","what":"Analyze a pairwise Cox-PH model — survival_coxph_pairwise","title":"Analyze a pairwise Cox-PH model — survival_coxph_pairwise","text":"analyze function coxph_pairwise() creates layout element analyze pairwise Cox-PH model. function can return statistics including p-value, hazard ratio (HR), HR confidence intervals stratified unstratified Cox-PH models. variable(s) analyzed specified via vars argument stratification factors via strata argument.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/survival_coxph_pairwise.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Analyze a pairwise Cox-PH model — survival_coxph_pairwise","text":"","code":"coxph_pairwise(   lyt,   vars,   strata = NULL,   control = control_coxph(),   na_str = default_na_str(),   nested = TRUE,   ...,   var_labels = \"CoxPH\",   show_labels = \"visible\",   table_names = vars,   .stats = c(\"pvalue\", \"hr\", \"hr_ci\"),   .formats = NULL,   .labels = NULL,   .indent_mods = NULL )  s_coxph_pairwise(   df,   .ref_group,   .in_ref_col,   .var,   is_event,   strata = NULL,   strat = lifecycle::deprecated(),   control = control_coxph() )  a_coxph_pairwise(   df,   .ref_group,   .in_ref_col,   .var,   is_event,   strata = NULL,   strat = lifecycle::deprecated(),   control = control_coxph() )"},{"path":"https://insightsengineering.github.io/tern/main/reference/survival_coxph_pairwise.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Analyze a pairwise Cox-PH model — survival_coxph_pairwise","text":"lyt (PreDataTableLayouts) layout analyses added . vars (character) variable names primary analysis variable iterated . strata (character NULL) variable names indicating stratification factors. control (list) parameters comparison details, specified using helper function control_coxph(). possible parameter options : pval_method (string) p-value method testing null hypothesis hazard ratio = 1. Default method \"log-rank\" comes survival::survdiff(), can also set \"wald\" \"likelihood\" (survival::coxph()). ties (string) specifying method tie handling. Default \"efron\", can also set \"breslow\" \"exact\". See survival::coxph(). conf_level (proportion) confidence level interval HR. na_str (string) string used replace NA empty values output. nested (flag) whether layout instruction applied within existing layout structure _if possible (TRUE, default) new top-level element (FALSE). Ignored nest split. underneath analyses, allowed. ... additional arguments lower level functions. var_labels (character) variable labels. show_labels (string) label visibility: one \"default\", \"visible\" \"hidden\". table_names (character) can customized case vars analyzed multiple times, avoid warnings rtables. .stats (character) statistics select table. Options : 'pvalue', 'hr', 'hr_ci', 'n_tot', 'n_tot_events' .formats (named character list) formats statistics. See Details analyze_vars information \"auto\" setting. .labels (named character) labels statistics (without indent). .indent_mods (named integer) indent modifiers labels. Defaults 0, corresponds unmodified default behavior. Can negative. df (data.frame) data set containing analysis variables. .ref_group (data.frame vector) data corresponding reference group. .in_ref_col (flag)TRUE working reference level, FALSE otherwise. .var (string) single variable name passed rtables requested statistics function. is_event (flag)TRUE event, FALSE time event censored. strat Please use strata argument instead.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/survival_coxph_pairwise.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Analyze a pairwise Cox-PH model — survival_coxph_pairwise","text":"coxph_pairwise() returns layout object suitable passing layouting functions, rtables::build_table(). Adding function rtable layout add formatted rows containing statistics s_coxph_pairwise() table layout. s_coxph_pairwise() returns statistics: pvalue: p-value test null hypothesis hazard ratio = 1. hr: Hazard ratio. hr_ci: Confidence interval hazard ratio. n_tot: Total number observations. n_tot_events: Total number events. a_coxph_pairwise() returns corresponding list formatted rtables::CellValue().","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/survival_coxph_pairwise.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Analyze a pairwise Cox-PH model — survival_coxph_pairwise","text":"coxph_pairwise(): Layout-creating function can take statistics function arguments additional format arguments. function wrapper rtables::analyze(). s_coxph_pairwise(): Statistics function analyzes HR, CIs HR, p-value Cox-PH model. a_coxph_pairwise(): Formatted analysis function used afun coxph_pairwise().","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/survival_coxph_pairwise.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Analyze a pairwise Cox-PH model — survival_coxph_pairwise","text":"","code":"library(dplyr)  adtte_f <- tern_ex_adtte %>%   filter(PARAMCD == \"OS\") %>%   mutate(is_event = CNSR == 0)  df <- adtte_f %>% filter(ARMCD == \"ARM A\") df_ref_group <- adtte_f %>% filter(ARMCD == \"ARM B\")  basic_table() %>%   split_cols_by(var = \"ARMCD\", ref_group = \"ARM A\") %>%   add_colcounts() %>%   coxph_pairwise(     vars = \"AVAL\",     is_event = \"is_event\",     var_labels = \"Unstratified Analysis\"   ) %>%   build_table(df = adtte_f) #>                         ARM A       ARM B          ARM C     #>                         (N=69)      (N=73)         (N=58)    #> ———————————————————————————————————————————————————————————— #> Unstratified Analysis                                        #>   p-value (log-rank)                0.0905         0.0086    #>   Hazard Ratio                       1.41           1.81     #>   95% CI                         (0.95, 2.09)   (1.16, 2.84)  basic_table() %>%   split_cols_by(var = \"ARMCD\", ref_group = \"ARM A\") %>%   add_colcounts() %>%   coxph_pairwise(     vars = \"AVAL\",     is_event = \"is_event\",     var_labels = \"Stratified Analysis\",     strata = \"SEX\",     control = control_coxph(pval_method = \"wald\")   ) %>%   build_table(df = adtte_f) #>                       ARM A       ARM B          ARM C     #>                       (N=69)      (N=73)         (N=58)    #> —————————————————————————————————————————————————————————— #> Stratified Analysis                                        #>   p-value (wald)                  0.0784         0.0066    #>   Hazard Ratio                     1.44           1.89     #>   95% CI                       (0.96, 2.15)   (1.19, 2.98)"},{"path":"https://insightsengineering.github.io/tern/main/reference/survival_duration_subgroups.html","id":null,"dir":"Reference","previous_headings":"","what":"Tabulate survival duration by subgroup — survival_duration_subgroups","title":"Tabulate survival duration by subgroup — survival_duration_subgroups","text":"tabulate_survival_subgroups() function creates layout element tabulate survival duration subgroup, returning statistics including median survival time hazard ratio population subgroup. table created df, list data frames returned extract_survival_subgroups(), statistics include specified via vars parameter. forest plot can created resulting table using g_forest() function.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/survival_duration_subgroups.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Tabulate survival duration by subgroup — survival_duration_subgroups","text":"","code":"tabulate_survival_subgroups(   lyt,   df,   vars = c(\"n_tot_events\", \"n_events\", \"median\", \"hr\", \"ci\"),   groups_lists = list(),   label_all = lifecycle::deprecated(),   time_unit = NULL,   riskdiff = NULL,   na_str = default_na_str(),   .formats = c(n = \"xx\", n_events = \"xx\", n_tot_events = \"xx\", median = \"xx.x\", n_tot =     \"xx\", hr = list(format_extreme_values(2L)), ci = list(format_extreme_values_ci(2L)),     pval = \"x.xxxx | (<0.0001)\") )  a_survival_subgroups(   .formats = list(n = \"xx\", n_events = \"xx\", n_tot_events = \"xx\", median = \"xx.x\", n_tot     = \"xx\", hr = list(format_extreme_values(2L)), ci =     list(format_extreme_values_ci(2L)), pval = \"x.xxxx | (<0.0001)\"),   na_str = default_na_str() )"},{"path":"https://insightsengineering.github.io/tern/main/reference/survival_duration_subgroups.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Tabulate survival duration by subgroup — survival_duration_subgroups","text":"lyt (PreDataTableLayouts) layout analyses added . df (list) list data frames containing analysis variables. List created using extract_survival_subgroups(). vars (character) names statistics reported among: n_tot_events: Total number events per group. n_events: Number events per group. n_tot: Total number observations per group. n: Number observations per group. median: Median survival time. hr: Hazard ratio. ci: Confidence interval hazard ratio. pval: p-value effect. Note, one statistics n_tot n_tot_events, well hr ci required. groups_lists (named list list) optionally contains subgroups variable list, specifies new group levels via names levels belong character vectors elements list. label_all please assign label_all parameter within extract_survival_subgroups() function creating df. time_unit (string) label unit median survival time. Default NULL skips displaying unit. riskdiff (list) risk (proportion) difference column added, list settings apply within column. See control_riskdiff() details. NULL, risk difference column added. riskdiff$arm_x riskdiff$arm_y NULL, first level df$survtime$arm used arm_x second level arm_y. na_str (string) string used replace NA empty values output. .formats (named character list) formats statistics. See Details analyze_vars information \"auto\" setting.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/survival_duration_subgroups.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Tabulate survival duration by subgroup — survival_duration_subgroups","text":"rtables table summarizing survival subgroup. a_survival_subgroups() returns corresponding list formatted rtables::CellValue().","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/survival_duration_subgroups.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Tabulate survival duration by subgroup — survival_duration_subgroups","text":"functions create layout starting data frame contains required statistics. Tables typically used part forest plot.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/survival_duration_subgroups.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Tabulate survival duration by subgroup — survival_duration_subgroups","text":"tabulate_survival_subgroups(): Table-creating function creates table summarizing survival subgroup. function wrapper rtables::analyze_colvars() rtables::summarize_row_groups(). a_survival_subgroups(): Formatted analysis function used afun tabulate_survival_subgroups().","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/main/reference/survival_duration_subgroups.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Tabulate survival duration by subgroup — survival_duration_subgroups","text":"","code":"library(dplyr)  adtte <- tern_ex_adtte  # Save variable labels before data processing steps. adtte_labels <- formatters::var_labels(adtte)  adtte_f <- adtte %>%   filter(     PARAMCD == \"OS\",     ARM %in% c(\"B: Placebo\", \"A: Drug X\"),     SEX %in% c(\"M\", \"F\")   ) %>%   mutate(     # Reorder levels of ARM to display reference arm before treatment arm.     ARM = droplevels(forcats::fct_relevel(ARM, \"B: Placebo\")),     SEX = droplevels(SEX),     AVALU = as.character(AVALU),     is_event = CNSR == 0   ) labels <- c(   \"ARM\" = adtte_labels[[\"ARM\"]],   \"SEX\" = adtte_labels[[\"SEX\"]],   \"AVALU\" = adtte_labels[[\"AVALU\"]],   \"is_event\" = \"Event Flag\" ) formatters::var_labels(adtte_f)[names(labels)] <- labels  df <- extract_survival_subgroups(   variables = list(     tte = \"AVAL\",     is_event = \"is_event\",     arm = \"ARM\", subgroups = c(\"SEX\", \"BMRKR2\")   ),   label_all = \"Total Patients\",   data = adtte_f ) df #> $survtime #>           arm  n n_events    median       subgroup    var #> 1  B: Placebo 73       57  727.8043 Total Patients    ALL #> 2   A: Drug X 69       44  974.6402 Total Patients    ALL #> 3  B: Placebo 40       31  599.1772              F    SEX #> 4   A: Drug X 38       24 1016.2982              F    SEX #> 5  B: Placebo 33       26  888.4916              M    SEX #> 6   A: Drug X 31       20  974.6402              M    SEX #> 7  B: Placebo 24       21  735.4722            LOW BMRKR2 #> 8   A: Drug X 26       15  974.6402            LOW BMRKR2 #> 9  B: Placebo 23       14  731.8352         MEDIUM BMRKR2 #> 10  A: Drug X 26       17  964.2197         MEDIUM BMRKR2 #> 11 B: Placebo 26       22  654.8245           HIGH BMRKR2 #> 12  A: Drug X 17       12 1016.2982           HIGH BMRKR2 #>                       var_label row_type #> 1                Total Patients  content #> 2                Total Patients  content #> 3                           Sex analysis #> 4                           Sex analysis #> 5                           Sex analysis #> 6                           Sex analysis #> 7  Continuous Level Biomarker 2 analysis #> 8  Continuous Level Biomarker 2 analysis #> 9  Continuous Level Biomarker 2 analysis #> 10 Continuous Level Biomarker 2 analysis #> 11 Continuous Level Biomarker 2 analysis #> 12 Continuous Level Biomarker 2 analysis #>  #> $hr #>   arm n_tot n_tot_events        hr       lcl       ucl conf_level       pval #> 1       142          101 0.7108557 0.4779138 1.0573368       0.95 0.09049511 #> 2        78           55 0.5595391 0.3246658 0.9643271       0.95 0.03411759 #> 3        64           46 0.9102874 0.5032732 1.6464678       0.95 0.75582028 #> 4        50           36 0.7617717 0.3854349 1.5055617       0.95 0.43236030 #> 5        49           31 0.7651261 0.3641277 1.6077269       0.95 0.47860004 #> 6        43           34 0.6662356 0.3257413 1.3626456       0.95 0.26285846 #>           pval_label       subgroup    var                    var_label #> 1 p-value (log-rank) Total Patients    ALL               Total Patients #> 2 p-value (log-rank)              F    SEX                          Sex #> 3 p-value (log-rank)              M    SEX                          Sex #> 4 p-value (log-rank)            LOW BMRKR2 Continuous Level Biomarker 2 #> 5 p-value (log-rank)         MEDIUM BMRKR2 Continuous Level Biomarker 2 #> 6 p-value (log-rank)           HIGH BMRKR2 Continuous Level Biomarker 2 #>   row_type #> 1  content #> 2 analysis #> 3 analysis #> 4 analysis #> 5 analysis #> 6 analysis #>   df_grouped <- extract_survival_subgroups(   variables = list(     tte = \"AVAL\",     is_event = \"is_event\",     arm = \"ARM\", subgroups = c(\"SEX\", \"BMRKR2\")   ),   data = adtte_f,   groups_lists = list(     BMRKR2 = list(       \"low\" = \"LOW\",       \"low/medium\" = c(\"LOW\", \"MEDIUM\"),       \"low/medium/high\" = c(\"LOW\", \"MEDIUM\", \"HIGH\")     )   ) ) df_grouped #> $survtime #>           arm  n n_events    median        subgroup    var #> 1  B: Placebo 73       57  727.8043    All Patients    ALL #> 2   A: Drug X 69       44  974.6402    All Patients    ALL #> 3  B: Placebo 40       31  599.1772               F    SEX #> 4   A: Drug X 38       24 1016.2982               F    SEX #> 5  B: Placebo 33       26  888.4916               M    SEX #> 6   A: Drug X 31       20  974.6402               M    SEX #> 7  B: Placebo 24       21  735.4722             low BMRKR2 #> 8   A: Drug X 26       15  974.6402             low BMRKR2 #> 9  B: Placebo 47       35  735.4722      low/medium BMRKR2 #> 10  A: Drug X 52       32  964.2197      low/medium BMRKR2 #> 11 B: Placebo 73       57  727.8043 low/medium/high BMRKR2 #> 12  A: Drug X 69       44  974.6402 low/medium/high BMRKR2 #>                       var_label row_type #> 1                  All Patients  content #> 2                  All Patients  content #> 3                           Sex analysis #> 4                           Sex analysis #> 5                           Sex analysis #> 6                           Sex analysis #> 7  Continuous Level Biomarker 2 analysis #> 8  Continuous Level Biomarker 2 analysis #> 9  Continuous Level Biomarker 2 analysis #> 10 Continuous Level Biomarker 2 analysis #> 11 Continuous Level Biomarker 2 analysis #> 12 Continuous Level Biomarker 2 analysis #>  #> $hr #>   arm n_tot n_tot_events        hr       lcl       ucl conf_level       pval #> 1       142          101 0.7108557 0.4779138 1.0573368       0.95 0.09049511 #> 2        78           55 0.5595391 0.3246658 0.9643271       0.95 0.03411759 #> 3        64           46 0.9102874 0.5032732 1.6464678       0.95 0.75582028 #> 4        50           36 0.7617717 0.3854349 1.5055617       0.95 0.43236030 #> 5        99           67 0.7472958 0.4600419 1.2139136       0.95 0.23764314 #> 6       142          101 0.7108557 0.4779138 1.0573368       0.95 0.09049511 #>           pval_label        subgroup    var                    var_label #> 1 p-value (log-rank)    All Patients    ALL                 All Patients #> 2 p-value (log-rank)               F    SEX                          Sex #> 3 p-value (log-rank)               M    SEX                          Sex #> 4 p-value (log-rank)             low BMRKR2 Continuous Level Biomarker 2 #> 5 p-value (log-rank)      low/medium BMRKR2 Continuous Level Biomarker 2 #> 6 p-value (log-rank) low/medium/high BMRKR2 Continuous Level Biomarker 2 #>   row_type #> 1  content #> 2 analysis #> 3 analysis #> 4 analysis #> 5 analysis #> 6 analysis #>   ## Table with default columns. basic_table() %>%   tabulate_survival_subgroups(df, time_unit = adtte_f$AVALU[1]) #>                                                     B: Placebo               A: Drug X                                      #> Baseline Risk Factors          Total Events   Events   Median (DAYS)   Events   Median (DAYS)   Hazard Ratio   95% Wald CI  #> ——————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————— #> Total Patients                     101          57         727.8         44         974.6           0.71       (0.48, 1.06) #> Sex                                                                                                                         #>   F                                 55          31         599.2         24        1016.3           0.56       (0.32, 0.96) #>   M                                 46          26         888.5         20         974.6           0.91       (0.50, 1.65) #> Continuous Level Biomarker 2                                                                                                #>   LOW                               36          21         735.5         15         974.6           0.76       (0.39, 1.51) #>   MEDIUM                            31          14         731.8         17         964.2           0.77       (0.36, 1.61) #>   HIGH                              34          22         654.8         12        1016.3           0.67       (0.33, 1.36)  ## Table with a manually chosen set of columns: adding \"pval\". basic_table() %>%   tabulate_survival_subgroups(     df = df,     vars = c(\"n_tot_events\", \"n_events\", \"median\", \"hr\", \"ci\", \"pval\"),     time_unit = adtte_f$AVALU[1]   ) #>                                                     B: Placebo               A: Drug X                                                           #> Baseline Risk Factors          Total Events   Events   Median (DAYS)   Events   Median (DAYS)   Hazard Ratio   95% Wald CI    p-value (log-rank) #> ———————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————— #> Total Patients                     101          57         727.8         44         974.6           0.71       (0.48, 1.06)         0.0905       #> Sex                                                                                                                                              #>   F                                 55          31         599.2         24        1016.3           0.56       (0.32, 0.96)         0.0341       #>   M                                 46          26         888.5         20         974.6           0.91       (0.50, 1.65)         0.7558       #> Continuous Level Biomarker 2                                                                                                                     #>   LOW                               36          21         735.5         15         974.6           0.76       (0.39, 1.51)         0.4324       #>   MEDIUM                            31          14         731.8         17         964.2           0.77       (0.36, 1.61)         0.4786       #>   HIGH                              34          22         654.8         12        1016.3           0.67       (0.33, 1.36)         0.2629"},{"path":"https://insightsengineering.github.io/tern/main/reference/survival_time.html","id":null,"dir":"Reference","previous_headings":"","what":"Survival time analysis — survival_time","title":"Survival time analysis — survival_time","text":"analyze function surv_time() creates layout element analyze survival time calculating survival time median, median confidence interval, quantiles, range (, censored, event patients). primary analysis variable vars time variable secondary analysis variable is_event indicates whether event occurred.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/survival_time.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Survival time analysis — survival_time","text":"","code":"surv_time(   lyt,   vars,   is_event,   control = control_surv_time(),   ref_fn_censor = TRUE,   na_str = default_na_str(),   nested = TRUE,   ...,   var_labels = \"Time to Event\",   show_labels = \"visible\",   table_names = vars,   .stats = c(\"median\", \"median_ci\", \"quantiles\", \"range\"),   .formats = NULL,   .labels = NULL,   .indent_mods = c(median_ci = 1L) )  s_surv_time(df, .var, is_event, control = control_surv_time())  a_surv_time(   df,   labelstr = \"\",   .var = NULL,   .df_row = NULL,   is_event,   control = control_surv_time(),   ref_fn_censor = TRUE,   .stats = NULL,   .formats = NULL,   .labels = NULL,   .indent_mods = NULL,   na_str = default_na_str() )"},{"path":"https://insightsengineering.github.io/tern/main/reference/survival_time.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Survival time analysis — survival_time","text":"lyt (PreDataTableLayouts) layout analyses added . vars (character) variable names primary analysis variable iterated . is_event (flag)TRUE event, FALSE time event censored. control (list) parameters comparison details, specified using helper function control_surv_time(). possible parameter options : conf_level (proportion) confidence level interval survival time. conf_type (string) confidence interval type. Options \"plain\" (default), \"log\", \"log-log\", see survival::survfit(). Note option \"none\" supported. quantiles (numeric) vector length two specify quantiles survival time. ref_fn_censor (flag) whether referential footnotes indicating censored observations printed range statistic included. na_str (string) string used replace NA empty values output. nested (flag) whether layout instruction applied within existing layout structure _if possible (TRUE, default) new top-level element (FALSE). Ignored nest split. underneath analyses, allowed. ... additional arguments lower level functions. var_labels (character) variable labels. show_labels (string) label visibility: one \"default\", \"visible\" \"hidden\". table_names (character) can customized case vars analyzed multiple times, avoid warnings rtables. .stats (character) statistics select table. Options : 'median', 'median_ci', 'median_ci_3d', 'quantiles', 'quantiles_lower', 'quantiles_upper', 'range_censor', 'range_event', 'range' .formats (named character list) formats statistics. See Details analyze_vars information \"auto\" setting. .labels (named character) labels statistics (without indent). .indent_mods (named integer) indent modifiers labels. element vector name-value pair name corresponding statistic specified .stats value indentation statistic's row label. df (data.frame) data set containing analysis variables. .var (string) single variable name passed rtables requested statistics function. labelstr (string) label level parent split currently summarized (must present second argument Content Row Functions). See rtables::summarize_row_groups() information. .df_row (data.frame) data frame across columns given row split.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/survival_time.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Survival time analysis — survival_time","text":"surv_time() returns layout object suitable passing layouting functions, rtables::build_table(). Adding function rtable layout add formatted rows containing statistics s_surv_time() table layout. s_surv_time() returns statistics: median: Median survival time. median_ci: Confidence interval median time. median_ci_3d: Median confidence interval median time. quantiles: Survival time two specified quantiles. quantiles_lower: quantile confidence interval first specified quantile. quantiles_upper: quantile confidence interval second specified quantile. range_censor: Survival time range censored observations. range_event: Survival time range observations events. range: Survival time range observations. a_surv_time() returns corresponding list formatted rtables::CellValue().","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/survival_time.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Survival time analysis — survival_time","text":"surv_time(): Layout-creating function can take statistics function arguments additional format arguments. function wrapper rtables::analyze(). s_surv_time(): Statistics function analyzes survival times. a_surv_time(): Formatted analysis function used afun surv_time().","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/survival_time.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Survival time analysis — survival_time","text":"","code":"library(dplyr)  adtte_f <- tern_ex_adtte %>%   filter(PARAMCD == \"OS\") %>%   mutate(     AVAL = day2month(AVAL),     is_event = CNSR == 0   ) df <- adtte_f %>% filter(ARMCD == \"ARM A\")  basic_table() %>%   split_cols_by(var = \"ARMCD\") %>%   add_colcounts() %>%   surv_time(     vars = \"AVAL\",     var_labels = \"Survival Time (Months)\",     is_event = \"is_event\",     control = control_surv_time(conf_level = 0.9, conf_type = \"log-log\")   ) %>%   build_table(df = adtte_f) #>                             ARM A          ARM B          ARM C     #>                             (N=69)         (N=73)         (N=58)    #> ——————————————————————————————————————————————————————————————————— #> Survival Time (Months)                                              #>   Median                     32.0           23.9           20.8     #>     90% CI               (22.6, 46.5)   (18.3, 29.2)   (12.9, 25.9) #>   25% and 75%-ile         17.4, 65.3     9.8, 42.0      7.3, 37.1   #>   Range                  0.3 to 155.5   0.1 to 154.1   0.6 to 80.7   a_surv_time(   df,   .df_row = df,   .var = \"AVAL\",   is_event = \"is_event\" ) #> RowsVerticalSection (in_rows) object print method: #> ---------------------------- #>           row_name     formatted_cell indent_mod        row_label #> 1           Median               32.0          0           Median #> 2           95% CI       (22.5, 49.3)          0           95% CI #> 3  Median (95% CI) 32.0 (22.5 - 49.3)          0  Median (95% CI) #> 4  25% and 75%-ile         17.4, 65.3          0  25% and 75%-ile #> 5 25%-ile (95% CI) 17.4 (10.1 - 22.5)          0 25%-ile (95% CI) #> 6 75%-ile (95% CI) 65.3 (49.3 - 87.2)          0 75%-ile (95% CI) #> 7 Range (censored)        0.8 to 63.5          0 Range (censored) #> 8    Range (event)       0.3 to 155.5          0    Range (event) #> 9            Range       0.3 to 155.5          0            Range"},{"path":"https://insightsengineering.github.io/tern/main/reference/survival_timepoint.html","id":null,"dir":"Reference","previous_headings":"","what":"Survival time point analysis — survival_timepoint","title":"Survival time point analysis — survival_timepoint","text":"analyze function surv_timepoint() creates layout element analyze patient survival rates difference survival rates groups given time point. primary analysis variable vars time variable. required inputs time_point, numeric time point interest, is_event, variable indicates whether event occurred. method argument used specify whether want analyze survival estimations (\"surv\"), difference survival control (\"surv_diff\"), (\"\").","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/survival_timepoint.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Survival time point analysis — survival_timepoint","text":"","code":"surv_timepoint(   lyt,   vars,   time_point,   is_event,   control = control_surv_timepoint(),   method = c(\"surv\", \"surv_diff\", \"both\"),   na_str = default_na_str(),   nested = TRUE,   ...,   table_names_suffix = \"\",   var_labels = \"Time\",   show_labels = \"visible\",   .stats = c(\"pt_at_risk\", \"event_free_rate\", \"rate_ci\", \"rate_diff\", \"rate_diff_ci\",     \"ztest_pval\"),   .formats = NULL,   .labels = NULL,   .indent_mods = if (method == \"both\") {      c(rate_diff = 1L, rate_diff_ci = 2L,     ztest_pval = 2L)  } else {      c(rate_diff_ci = 1L, ztest_pval = 1L)  } )  s_surv_timepoint(   df,   .var,   time_point,   is_event,   control = control_surv_timepoint() )  a_surv_timepoint(   df,   .var,   time_point,   is_event,   control = control_surv_timepoint() )  s_surv_timepoint_diff(   df,   .var,   .ref_group,   .in_ref_col,   time_point,   control = control_surv_timepoint(),   ... )  a_surv_timepoint_diff(   df,   .var,   .ref_group,   .in_ref_col,   time_point,   control = control_surv_timepoint(),   ... )"},{"path":"https://insightsengineering.github.io/tern/main/reference/survival_timepoint.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Survival time point analysis — survival_timepoint","text":"lyt (PreDataTableLayouts) layout analyses added . vars (character) variable names primary analysis variable iterated . time_point (numeric(1)) survival time point interest. is_event (flag)TRUE event, FALSE time event censored. control (list) parameters comparison details, specified using helper function control_surv_timepoint(). possible parameter options : conf_level (proportion) confidence level interval survival rate. conf_type (string) confidence interval type. Options \"plain\" (default), \"log\", \"log-log\", see survival::survfit(). Note option \"none\" longer supported. method (string)\"surv\" (survival estimations), \"surv_diff\" (difference survival control), \"\". na_str (string) string used replace NA empty values output. nested (flag) whether layout instruction applied within existing layout structure _if possible (TRUE, default) new top-level element (FALSE). Ignored nest split. underneath analyses, allowed. ... additional arguments lower level functions. table_names_suffix (string) optional suffix table_names used rtables avoid warnings duplicate table names. var_labels (character) variable labels. show_labels (string) label visibility: one \"default\", \"visible\" \"hidden\". .stats (character) statistics select table. Options : 'pt_at_risk', 'event_free_rate', 'rate_se', 'rate_ci', 'rate_diff', 'rate_diff_ci', 'ztest_pval', 'event_free_rate_3d' .formats (named character list) formats statistics. See Details analyze_vars information \"auto\" setting. .labels (named character) labels statistics (without indent). .indent_mods (named integer) indent modifiers labels. element vector name-value pair name corresponding statistic specified .stats value indentation statistic's row label. df (data.frame) data set containing analysis variables. .var (string) single variable name passed rtables requested statistics function. .ref_group (data.frame vector) data corresponding reference group. .in_ref_col (flag)TRUE working reference level, FALSE otherwise.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/survival_timepoint.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Survival time point analysis — survival_timepoint","text":"surv_timepoint() returns layout object suitable passing layouting functions, rtables::build_table(). Adding function rtable layout add formatted rows containing statistics s_surv_timepoint() /s_surv_timepoint_diff() table layout depending value method. s_surv_timepoint() returns statistics: pt_at_risk: Patients remaining risk. event_free_rate: Event-free rate (%). rate_se: Standard error event free rate. rate_ci: Confidence interval event free rate. event_free_rate_3d: Event-free rate (%) Confidence interval. a_surv_timepoint() returns corresponding list formatted rtables::CellValue(). s_surv_timepoint_diff() returns statistics: rate_diff: Event-free rate difference two groups. rate_diff_ci: Confidence interval difference. rate_diff_ci_3d: Event-free rate difference confidence interval two groups. ztest_pval: p-value test difference 0. a_surv_timepoint_diff() returns corresponding list formatted rtables::CellValue().","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/survival_timepoint.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Survival time point analysis — survival_timepoint","text":"surv_timepoint(): Layout-creating function can take statistics function arguments additional format arguments. function wrapper rtables::analyze(). s_surv_timepoint(): Statistics function analyzes survival rate. a_surv_timepoint(): Formatted analysis function used afun surv_timepoint() method = \"surv\". s_surv_timepoint_diff(): Statistics function analyzes difference two survival rates. a_surv_timepoint_diff(): Formatted analysis function used afun surv_timepoint() method = \"surv_diff\".","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/survival_timepoint.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Survival time point analysis — survival_timepoint","text":"","code":"library(dplyr)  adtte_f <- tern_ex_adtte %>%   filter(PARAMCD == \"OS\") %>%   mutate(     AVAL = day2month(AVAL),     is_event = CNSR == 0   )  # Survival at given time points. basic_table() %>%   split_cols_by(var = \"ARMCD\", ref_group = \"ARM A\") %>%   add_colcounts() %>%   surv_timepoint(     vars = \"AVAL\",     var_labels = \"Months\",     is_event = \"is_event\",     time_point = 7   ) %>%   build_table(df = adtte_f) #>                                    ARM A            ARM B            ARM C      #>                                    (N=69)           (N=73)           (N=58)     #> ——————————————————————————————————————————————————————————————————————————————— #> 7 Months                                                                        #>   Patients remaining at risk         54               57               42       #>   Event Free Rate (%)              84.89            79.43            75.50      #>   95% CI                       (76.24, 93.53)   (70.15, 88.71)   (64.33, 86.67)  # Difference in survival at given time points. basic_table() %>%   split_cols_by(var = \"ARMCD\", ref_group = \"ARM A\") %>%   add_colcounts() %>%   surv_timepoint(     vars = \"AVAL\",     var_labels = \"Months\",     is_event = \"is_event\",     time_point = 9,     method = \"surv_diff\",     .indent_mods = c(\"rate_diff\" = 0L, \"rate_diff_ci\" = 2L, \"ztest_pval\" = 2L)   ) %>%   build_table(df = adtte_f) #>                                   ARM A        ARM B            ARM C      #>                                   (N=69)       (N=73)           (N=58)     #> —————————————————————————————————————————————————————————————————————————— #> 9 Months                                                                   #>   Difference in Event Free Rate                -9.64            -13.03     #>       95% CI                               (-22.80, 3.52)   (-27.59, 1.53) #>       p-value (Z-test)                         0.1511           0.0794      # Survival and difference in survival at given time points. basic_table() %>%   split_cols_by(var = \"ARMCD\", ref_group = \"ARM A\") %>%   add_colcounts() %>%   surv_timepoint(     vars = \"AVAL\",     var_labels = \"Months\",     is_event = \"is_event\",     time_point = 9,     method = \"both\"   ) %>%   build_table(df = adtte_f) #>                                       ARM A            ARM B            ARM C      #>                                       (N=69)           (N=73)           (N=58)     #> —————————————————————————————————————————————————————————————————————————————————— #> 9 Months                                                                           #>   Patients remaining at risk            53               53               39       #>   Event Free Rate (%)                 84.89            75.25            71.86      #>   95% CI                          (76.24, 93.53)   (65.32, 85.17)   (60.14, 83.57) #>   Difference in Event Free Rate                        -9.64            -13.03     #>     95% CI                                         (-22.80, 3.52)   (-27.59, 1.53) #>     p-value (Z-test)                                   0.1511           0.0794"},{"path":"https://insightsengineering.github.io/tern/main/reference/tern-package.html","id":null,"dir":"Reference","previous_headings":"","what":"tern Package — tern-package","title":"tern Package — tern-package","text":"Package create tables, listings graphs analyze clinical trials data.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/main/reference/tern-package.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"tern Package — tern-package","text":"Maintainer: Joe Zhu joe.zhu@roche.com Authors: Daniel Sabanés Bové daniel.sabanes_bove@roche.com Jana Stoilova jana.stoilova@roche.com Davide Garolini davide.garolini@roche.com Emily de la Rua emily.de_la_rua@contractors.roche.com Abinaya Yogasekaram abinaya.yogasekaram@contractors.roche.com Heng Wang wang.heng@gene.com Francois Collin Adrian Waddell adrian.waddell@gene.com Pawel Rucki pawel.rucki@roche.com Chendi Liao chendi.liao@roche.com Jennifer Li li.jing@gene.com contributors: F. Hoffmann-La Roche AG [copyright holder, funder]","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/tidy.glm.html","id":null,"dir":"Reference","previous_headings":"","what":"Custom tidy method for binomial GLM results — tidy.glm","title":"Custom tidy method for binomial GLM results — tidy.glm","text":"Helper method (broom::tidy()) prepare data frame glm object binomial family.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/tidy.glm.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Custom tidy method for binomial GLM results — tidy.glm","text":"","code":"# S3 method for class 'glm' tidy(x, conf_level = 0.95, at = NULL, ...)"},{"path":"https://insightsengineering.github.io/tern/main/reference/tidy.glm.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Custom tidy method for binomial GLM results — tidy.glm","text":"x (glm) logistic regression model fitted stats::glm() \"binomial\" family. conf_level (proportion) confidence level interval. (numeric NULL) optional values interaction variable. Otherwise median used. ... additional arguments lower level functions.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/tidy.glm.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Custom tidy method for binomial GLM results — tidy.glm","text":"data.frame containing tidied model.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/main/reference/tidy.glm.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Custom tidy method for binomial GLM results — tidy.glm","text":"","code":"library(dplyr) library(broom)  adrs_f <- tern_ex_adrs %>%   filter(PARAMCD == \"BESRSPI\") %>%   filter(RACE %in% c(\"ASIAN\", \"WHITE\", \"BLACK OR AFRICAN AMERICAN\")) %>%   mutate(     Response = case_when(AVALC %in% c(\"PR\", \"CR\") ~ 1, TRUE ~ 0),     RACE = factor(RACE),     SEX = factor(SEX)   ) formatters::var_labels(adrs_f) <- c(formatters::var_labels(tern_ex_adrs), Response = \"Response\") mod1 <- fit_logistic(   data = adrs_f,   variables = list(     response = \"Response\",     arm = \"ARMCD\",     covariates = c(\"AGE\", \"RACE\")   ) ) #> Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred mod2 <- fit_logistic(   data = adrs_f,   variables = list(     response = \"Response\",     arm = \"ARMCD\",     covariates = c(\"AGE\", \"RACE\"),     interaction = \"AGE\"   ) ) #> Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred  df <- tidy(mod1, conf_level = 0.99) df2 <- tidy(mod2, conf_level = 0.99)"},{"path":"https://insightsengineering.github.io/tern/main/reference/tidy.step.html","id":null,"dir":"Reference","previous_headings":"","what":"Custom tidy method for STEP results — tidy.step","title":"Custom tidy method for STEP results — tidy.step","text":"Tidy STEP results tibble format ready plotting.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/tidy.step.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Custom tidy method for STEP results — tidy.step","text":"","code":"# S3 method for class 'step' tidy(x, ...)"},{"path":"https://insightsengineering.github.io/tern/main/reference/tidy.step.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Custom tidy method for STEP results — tidy.step","text":"x (matrix) results fit_survival_step(). ... used.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/tidy.step.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Custom tidy method for STEP results — tidy.step","text":"tibble one row per STEP subgroup. estimates CIs HR scale, respectively. Additional attributes carry metadata also used plotting.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/main/reference/tidy.step.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Custom tidy method for STEP results — tidy.step","text":"","code":"library(survival) lung$sex <- factor(lung$sex) vars <- list(   time = \"time\",   event = \"status\",   arm = \"sex\",   biomarker = \"age\" ) step_matrix <- fit_survival_step(   variables = vars,   data = lung,   control = c(control_coxph(), control_step(num_points = 10, degree = 2)) ) broom::tidy(step_matrix) #> # A tibble: 10 × 12 #>    `Percentile Center` `Percentile Lower` `Percentile Upper` `Interval Center` #>  *               <dbl>              <dbl>              <dbl>             <dbl> #>  1              0.0909             0                   0.341              50   #>  2              0.182              0                   0.432              54   #>  3              0.273              0.0227              0.523              57   #>  4              0.364              0.114               0.614              59.5 #>  5              0.455              0.205               0.705              62   #>  6              0.545              0.295               0.795              64   #>  7              0.636              0.386               0.886              67   #>  8              0.727              0.477               0.977              69   #>  9              0.818              0.568               1                  71   #> 10              0.909              0.659               1                  74   #> # ℹ 8 more variables: `Interval Lower` <dbl>, `Interval Upper` <dbl>, n <dbl>, #> #   events <dbl>, `Hazard Ratio` <dbl>, se <dbl>, ci_lower <dbl>, #> #   ci_upper <dbl>"},{"path":[]},{"path":"https://insightsengineering.github.io/tern/main/reference/tidy_coxreg.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Custom tidy methods for Cox regression — tidy_coxreg","text":"","code":"# S3 method for class 'summary.coxph' tidy(x, ...)  # S3 method for class 'coxreg.univar' tidy(x, ...)  # S3 method for class 'coxreg.multivar' tidy(x, ...)"},{"path":"https://insightsengineering.github.io/tern/main/reference/tidy_coxreg.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Custom tidy methods for Cox regression — tidy_coxreg","text":"x (list) result Cox regression model fitted fit_coxreg_univar() (univariate models) fit_coxreg_multivar() (multivariate models). ... additional arguments lower level functions.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/tidy_coxreg.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Custom tidy methods for Cox regression — tidy_coxreg","text":"broom::tidy() returns: summary.coxph objects,  data.frame columns: Pr(>|z|), exp(coef), exp(-coef), lower .95, upper .95, level, n. coxreg.univar objects, data.frame columns: effect, term, term_label, level, n, hr, lcl, ucl, pval, ci. coxreg.multivar objects, data.frame columns: term, pval, term_label, hr, lcl, ucl, level, ci.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/tidy_coxreg.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Custom tidy methods for Cox regression — tidy_coxreg","text":"tidy(summary.coxph): Custom tidy method survival::coxph() summary results. Tidy survival::coxph() results data.frame extract model results. tidy(coxreg.univar): Custom tidy method univariate Cox regression. Tidy result Cox regression model fitted fit_coxreg_univar(). tidy(coxreg.multivar): Custom tidy method multivariate Cox regression. Tidy result Cox regression model fitted fit_coxreg_multivar().","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/main/reference/tidy_coxreg.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Custom tidy methods for Cox regression — tidy_coxreg","text":"","code":"library(survival) library(broom)  set.seed(1, kind = \"Mersenne-Twister\")  dta_bladder <- with(   data = bladder[bladder$enum < 5, ],   data.frame(     time = stop,     status = event,     armcd = as.factor(rx),     covar1 = as.factor(enum),     covar2 = factor(       sample(as.factor(enum)),       levels = 1:4, labels = c(\"F\", \"F\", \"M\", \"M\")     )   ) ) labels <- c(\"armcd\" = \"ARM\", \"covar1\" = \"A Covariate Label\", \"covar2\" = \"Sex (F/M)\") formatters::var_labels(dta_bladder)[names(labels)] <- labels dta_bladder$age <- sample(20:60, size = nrow(dta_bladder), replace = TRUE)  formula <- \"survival::Surv(time, status) ~ armcd + covar1\" msum <- summary(coxph(stats::as.formula(formula), data = dta_bladder)) tidy(msum) #>       Pr(>|z|) exp(coef) exp(-coef)  lower .95 upper .95   level   n #> 1 1.287954e-02 0.6110123   1.636628 0.41442417 0.9008549  armcd2 340 #> 2 6.407916e-04 0.4460731   2.241785 0.28061816 0.7090818 covar12 340 #> 3 5.272933e-06 0.3075864   3.251119 0.18517346 0.5109230 covar13 340 #> 4 2.125359e-08 0.1808795   5.528541 0.09943722 0.3290258 covar14 340  ## Cox regression: arm + 1 covariate. mod1 <- fit_coxreg_univar(   variables = list(     time = \"time\", event = \"status\", arm = \"armcd\",     covariates = \"covar1\"   ),   data = dta_bladder,   control = control_coxreg(conf_level = 0.91) )  ## Cox regression: arm + 1 covariate + interaction, 2 candidate covariates. mod2 <- fit_coxreg_univar(   variables = list(     time = \"time\", event = \"status\", arm = \"armcd\",     covariates = c(\"covar1\", \"covar2\")   ),   data = dta_bladder,   control = control_coxreg(conf_level = 0.91, interaction = TRUE) )  tidy(mod1) #>            effect   term        term_label level   n        hr       lcl #> ref    Treatment:  armcd  2 vs control (1)     2 340 0.6386426 0.4557586 #> covar1 Covariate: covar1 A Covariate Label     2 340  0.607037 0.4324571 #>              ucl       pval                   ci #> ref    0.8949131 0.02423805 0.4557586, 0.8949131 #> covar1 0.8520935 0.01257339 0.4324571, 0.8520935 tidy(mod2) #>                           effect   term        term_label level   n        hr #> ref                   Treatment:  armcd  2 vs control (1)     2 340 0.6386426 #> covar1.1              Covariate: covar1 A Covariate Label       340           #> covar1.armcd2/covar11 Covariate: covar1                 1     1     0.6284569 #> covar1.armcd2/covar12 Covariate: covar1                 2     2     0.5806499 #> covar1.armcd2/covar13 Covariate: covar1                 3     3     0.5486103 #> covar1.armcd2/covar14 Covariate: covar1                 4     4     0.6910725 #> covar2.1              Covariate: covar2         Sex (F/M)       340           #> covar2.armcd2/covar2F Covariate: covar2                 F     F     0.6678243 #> covar2.armcd2/covar2M Covariate: covar2                 M     M     0.5954021 #>                             lcl       ucl       pval pval_inter #> ref                   0.4557586 0.8949131 0.02423805            #> covar1.1                     NA        NA             0.9883021 #> covar1.armcd2/covar11 0.3450471 1.1446499                       #> covar1.armcd2/covar12 0.2684726 1.2558239                       #> covar1.armcd2/covar13 0.2226814 1.3515868                       #> covar1.armcd2/covar14 0.2308006 2.0692373                       #> covar2.1                     NA        NA             0.7759013 #> covar2.armcd2/covar2F 0.3649842 1.2219413                       #> covar2.armcd2/covar2M 0.3572772 0.9922368                       #>                                         ci #> ref                   0.4557586, 0.8949131 #> covar1.1                                   #> covar1.armcd2/covar11 0.3450471, 1.1446499 #> covar1.armcd2/covar12 0.2684726, 1.2558239 #> covar1.armcd2/covar13 0.2226814, 1.3515868 #> covar1.armcd2/covar14 0.2308006, 2.0692373 #> covar2.1                                   #> covar2.armcd2/covar2F 0.3649842, 1.2219413 #> covar2.armcd2/covar2M 0.3572772, 0.9922368  multivar_model <- fit_coxreg_multivar(   variables = list(     time = \"time\", event = \"status\", arm = \"armcd\",     covariates = c(\"covar1\", \"covar2\")   ),   data = dta_bladder ) broom::tidy(multivar_model) #>                       term         pval                        term_label #> armcd.1              armcd                            ARM (reference = 1) #> armcd.2                ARM   0.01232761                                 2 #> covar1.1            covar1 7.209956e-09 A Covariate Label (reference = 1) #> covar1.2 A Covariate Label  0.001120332                                 2 #> covar1.3 A Covariate Label 6.293725e-06                                 3 #> covar1.4 A Covariate Label 3.013875e-08                                 4 #> covar2.1            covar2                      Sex (F/M) (reference = F) #> covar2.2         Sex (F/M)    0.1910521                                 M #>                 hr        lcl       ucl level                     ci #> armcd.1                    NA        NA  <NA>                        #> armcd.2  0.6062777 0.40970194 0.8971710     2   0.4097019, 0.8971710 #> covar1.1                   NA        NA  <NA>                        #> covar1.2 0.4564763 0.28481052 0.7316115     2   0.2848105, 0.7316115 #> covar1.3 0.3069612 0.18386073 0.5124813     3   0.1838607, 0.5124813 #> covar1.4 0.1817017 0.09939435 0.3321668     4 0.09939435, 0.33216684 #> covar2.1                   NA        NA  <NA>                        #> covar2.2  1.289373 0.88087820 1.8873019     M   0.8808782, 1.8873019"},{"path":"https://insightsengineering.github.io/tern/main/reference/to_n.html","id":null,"dir":"Reference","previous_headings":"","what":"Replicate entries of a vector if required — to_n","title":"Replicate entries of a vector if required — to_n","text":"Replicate entries vector required.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/to_n.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Replicate entries of a vector if required — to_n","text":"","code":"to_n(x, n)"},{"path":"https://insightsengineering.github.io/tern/main/reference/to_n.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Replicate entries of a vector if required — to_n","text":"x (numeric) vector numbers want analyze. n (integer(1)) number entries needed.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/to_n.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Replicate entries of a vector if required — to_n","text":"x required length already NULL, otherwise scalar replicated version n entries.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/to_n.html","id":"note","dir":"Reference","previous_headings":"","what":"Note","title":"Replicate entries of a vector if required — to_n","text":"function fail x length n /scalar.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/to_string_matrix.html","id":null,"dir":"Reference","previous_headings":"","what":"Convert table into matrix of strings — to_string_matrix","title":"Convert table into matrix of strings — to_string_matrix","text":"Helper function use mostly within tests. with_spacesparameter allows test content also indentation table structure. print_txt_to_copy instead facilitate testing development returning well formatted text needs copied pasted expected output.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/to_string_matrix.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Convert table into matrix of strings — to_string_matrix","text":"","code":"to_string_matrix(   x,   widths = NULL,   max_width = NULL,   hsep = formatters::default_hsep(),   with_spaces = TRUE,   print_txt_to_copy = FALSE )"},{"path":"https://insightsengineering.github.io/tern/main/reference/to_string_matrix.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Convert table into matrix of strings — to_string_matrix","text":"x (VTableTree)rtables table object. widths (numeric  NULL) Proposed widths columns x. expected length numeric vector can retrieved ncol(x) + 1 column row names must also considered. max_width (integer(1), string NULL) width title footer (including footnotes) materials word-wrapped . NULL, set current print width session (getOption(\"width\")). set \"auto\", width table (plus table inset) used. Parameter ignored tf_wrap = FALSE. hsep (string) character repeat create header/body separator line. NULL, object value used. \" \", empty separator printed. See default_hsep() information. with_spaces (flag) whether tested table keep indentation relevant spaces. print_txt_to_copy (flag) utility way copy input table directly expected variable instead copying manually.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/to_string_matrix.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Convert table into matrix of strings — to_string_matrix","text":"matrix strings. print_txt_to_copy = TRUE well formatted printout table printed console, ready copied expected value.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/to_string_matrix.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Convert table into matrix of strings — to_string_matrix","text":"","code":"tbl <- basic_table() %>%   split_rows_by(\"SEX\") %>%   split_cols_by(\"ARM\") %>%   analyze(\"AGE\") %>%   build_table(tern_ex_adsl)  to_string_matrix(tbl, widths = ceiling(propose_column_widths(tbl) / 2)) #>  [1] \"       A:                    \" \"      Drug    B: Pl   C: Comb\" #>  [3] \"        X     acebo   ination\" \"—————————————————————————————\" #>  [5] \"F                            \" \"  M   33.68   35.98    36.02 \" #>  [7] \"  e                          \" \"  a                          \" #>  [9] \"  n                          \" \"M                            \" #> [11] \"  M   34.70   35.68    36.28 \" \"  e                          \" #> [13] \"  a                          \" \"  n                          \""},{"path":"https://insightsengineering.github.io/tern/main/reference/try_car_anova.html","id":null,"dir":"Reference","previous_headings":"","what":"tryCatch around car::Anova — try_car_anova","title":"tryCatch around car::Anova — try_car_anova","text":"Captures warnings executing car::Anova.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/try_car_anova.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"tryCatch around car::Anova — try_car_anova","text":"","code":"try_car_anova(mod, test.statistic)"},{"path":"https://insightsengineering.github.io/tern/main/reference/try_car_anova.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"tryCatch around car::Anova — try_car_anova","text":"mod lm, aov, glm, multinom, polr     mlm, coxph, coxme, lme, mer, merMod, svyglm, svycoxph,     rlm, clm, clmm, suitable model object. test.statistic generalized linear model, whether calculate     \"LR\" (likelihood-ratio), \"Wald\", \"F\" tests; Cox     Cox mixed-effects model, whether calculate \"LR\" (partial-likelihood ratio)     \"Wald\" tests (\"LR\" tests unavailable Cox models using tt argument); default case linear mixed models fit     lmer, whether calculate Wald \"Chisq\" Kenward-Roger     \"F\" tests Satterthwaite degrees freedom (warning: KR F-tests     can time-consuming).     multivariate linear model, multivariate test statistic compute — one     \"Pillai\", \"Wilks\", \"Hotelling-Lawley\", \"Roy\",     \"Pillai\" default. summary method Anova.mlm     objects permits specification one multivariate     test statistic, default report four.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/try_car_anova.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"tryCatch around car::Anova — try_car_anova","text":"list item aov result model error_text captured warnings.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/try_car_anova.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"tryCatch around car::Anova — try_car_anova","text":"","code":"# `car::Anova` on cox regression model including strata and expected # a likelihood ratio test triggers a warning as only Wald method is # accepted.  library(survival)  mod <- coxph(   formula = Surv(time = futime, event = fustat) ~ factor(rx) + strata(ecog.ps),   data = ovarian )"},{"path":"https://insightsengineering.github.io/tern/main/reference/ungroup_stats.html","id":null,"dir":"Reference","previous_headings":"","what":"Ungroup non-numeric statistics — ungroup_stats","title":"Ungroup non-numeric statistics — ungroup_stats","text":"Ungroups grouped non-numeric statistics within input vectors .formats, .labels, .indent_mods.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/ungroup_stats.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Ungroup non-numeric statistics — ungroup_stats","text":"","code":"ungroup_stats(x, .formats, .labels, .indent_mods)"},{"path":"https://insightsengineering.github.io/tern/main/reference/ungroup_stats.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Ungroup non-numeric statistics — ungroup_stats","text":"x (named list numeric) list numeric statistics containing statistics ungroup. .formats (named character list) formats statistics. See Details analyze_vars information \"auto\" setting. .labels (named character) labels statistics (without indent). .indent_mods (named integer) indent modifiers labels. Defaults 0, corresponds unmodified default behavior. Can negative.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/ungroup_stats.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Ungroup non-numeric statistics — ungroup_stats","text":"list modified elements x, .formats, .labels, .indent_mods.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/main/reference/univariate.html","id":null,"dir":"Reference","previous_headings":"","what":"Univariate formula special term — univariate","title":"Univariate formula special term — univariate","text":"special term univariate indicate model fitted individually every variable included univariate.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/univariate.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Univariate formula special term — univariate","text":"","code":"univariate(x)"},{"path":"https://insightsengineering.github.io/tern/main/reference/univariate.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Univariate formula special term — univariate","text":"x (character) vector variable names separated commas.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/univariate.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Univariate formula special term — univariate","text":"used within model formula, produces univariate models variable provided.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/univariate.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Univariate formula special term — univariate","text":"provided alongside pairwise specification, model y ~ ARM + univariate(SEX, AGE, RACE) lead study comparison models y ~ ARM y ~ ARM + SEX y ~ ARM + AGE y ~ ARM + RACE","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/unlist_and_blank_na.html","id":null,"dir":"Reference","previous_headings":"","what":"Blank for missing input — unlist_and_blank_na","title":"Blank for missing input — unlist_and_blank_na","text":"Helper function use tabulating model results.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/unlist_and_blank_na.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Blank for missing input — unlist_and_blank_na","text":"","code":"unlist_and_blank_na(x)"},{"path":"https://insightsengineering.github.io/tern/main/reference/unlist_and_blank_na.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Blank for missing input — unlist_and_blank_na","text":"x (vector) input cell.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/unlist_and_blank_na.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Blank for missing input — unlist_and_blank_na","text":"empty character vector entries x missing (NA), otherwise unlisted version x.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/update_weights_strat_wilson.html","id":null,"dir":"Reference","previous_headings":"","what":"Helper function for the estimation of weights for prop_strat_wilson() — update_weights_strat_wilson","title":"Helper function for the estimation of weights for prop_strat_wilson() — update_weights_strat_wilson","text":"function wraps iteration procedure allows estimate weights proportional strata. assumes minimize weighted squared length confidence interval.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/update_weights_strat_wilson.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Helper function for the estimation of weights for prop_strat_wilson() — update_weights_strat_wilson","text":"","code":"update_weights_strat_wilson(   vars,   strata_qnorm,   initial_weights,   n_per_strata,   max_iterations = 50,   conf_level = 0.95,   tol = 0.001 )"},{"path":"https://insightsengineering.github.io/tern/main/reference/update_weights_strat_wilson.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Helper function for the estimation of weights for prop_strat_wilson() — update_weights_strat_wilson","text":"vars (numeric) normalized proportions strata. strata_qnorm (numeric(1)) initial estimation identical weights quantiles. initial_weights (numeric) initial weights used calculate strata_qnorm. can optimized future need estimate better initial weights. n_per_strata (numeric) number elements strata. max_iterations (integer(1)) maximum number iterations tried. Convergence always checked. conf_level (proportion) confidence level interval. tol (numeric(1)) tolerance threshold convergence.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/update_weights_strat_wilson.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Helper function for the estimation of weights for prop_strat_wilson() — update_weights_strat_wilson","text":"list 3 elements: n_it, weights, diff_v.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/main/reference/update_weights_strat_wilson.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Helper function for the estimation of weights for prop_strat_wilson() — update_weights_strat_wilson","text":"","code":"vs <- c(0.011, 0.013, 0.012, 0.014, 0.017, 0.018) sq <- 0.674 ws <- rep(1 / length(vs), length(vs)) ns <- c(22, 18, 17, 17, 14, 12)  update_weights_strat_wilson(vs, sq, ws, ns, 100, 0.95, 0.001) #> $n_it #> [1] 3 #>  #> $weights #> [1] 0.2067191 0.1757727 0.1896962 0.1636346 0.1357615 0.1284160 #>  #> $diff_v #> [1] 1.458717e-01 1.497223e-03 1.442189e-06 #>"},{"path":"https://insightsengineering.github.io/tern/main/reference/util_handling_additional_fun_params.html","id":null,"dir":"Reference","previous_headings":"","what":"Utilities to handle extra arguments in analysis functions — util_handling_additional_fun_params","title":"Utilities to handle extra arguments in analysis functions — util_handling_additional_fun_params","text":"Important additional parameters, useful modify behavior analysis summary functions listed rtables::additional_fun_params. utility functions can retrieve curated list parameters environment, pass analysis functions dedicated ...; notice final s_* function get argument matching.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/util_handling_additional_fun_params.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Utilities to handle extra arguments in analysis functions — util_handling_additional_fun_params","text":"","code":"retrieve_extra_afun_params(extra_afun_params)  get_additional_afun_params(add_alt_df = FALSE)"},{"path":"https://insightsengineering.github.io/tern/main/reference/util_handling_additional_fun_params.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Utilities to handle extra arguments in analysis functions — util_handling_additional_fun_params","text":"extra_afun_params (list) list additional parameters (character) retrieved environment. Curated list present rtables::additional_fun_params. add_alt_df (logical) TRUE, function also add .alt_df .alt_df_row parameters.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/util_handling_additional_fun_params.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Utilities to handle extra arguments in analysis functions — util_handling_additional_fun_params","text":"retrieve_extra_afun_params returns list values parameters environment. get_additional_afun_params returns list additional parameters.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/util_handling_additional_fun_params.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Utilities to handle extra arguments in analysis functions — util_handling_additional_fun_params","text":"retrieve_extra_afun_params(): Retrieve additional parameters environment. get_additional_afun_params(): Curated list additional parameters analysis functions. Please check rtables::additional_fun_params precise descriptions.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/utils_split_funs.html","id":null,"dir":"Reference","previous_headings":"","what":"Custom split functions — utils_split_funs","title":"Custom split functions — utils_split_funs","text":"Collection useful functions expanding core list functions provided rtables. See rtables::custom_split_funs rtables::make_split_fun() information make custom split function. functions work rtables::split_rows_by() argument split_fun modify way split happens. split functions, consider consulting rtables::split_funcs.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/utils_split_funs.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Custom split functions — utils_split_funs","text":"","code":"ref_group_position(position = \"first\")  level_order(order)"},{"path":"https://insightsengineering.github.io/tern/main/reference/utils_split_funs.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Custom split functions — utils_split_funs","text":"position (string integer) position use reference group facet. Can \"first\", \"last\", specific position. order (character numeric) vector ordering indices split facets.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/utils_split_funs.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Custom split functions — utils_split_funs","text":"ref_group_position() returns utility function puts reference group first, last certain position needs assigned split_fun. level_order() returns utility function changes original levels' order, depending input order split levels.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/utils_split_funs.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Custom split functions — utils_split_funs","text":"ref_group_position(): Split function place reference group facet specific position post-processing stage. level_order(): Split function change level order based integer vector character vector represent split variable's factor levels.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/main/reference/utils_split_funs.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Custom split functions — utils_split_funs","text":"","code":"library(dplyr)  dat <- data.frame(   x = factor(letters[1:5], levels = letters[5:1]),   y = 1:5 )  # With rtables layout functions basic_table() %>%   split_cols_by(\"x\", ref_group = \"c\", split_fun = ref_group_position(\"last\")) %>%   analyze(\"y\") %>%   build_table(dat) #>         e      d      b      a      c   #> ——————————————————————————————————————— #> Mean   5.00   4.00   2.00   1.00   3.00  # With tern layout funcitons adtte_f <- tern_ex_adtte %>%   filter(PARAMCD == \"OS\") %>%   mutate(     AVAL = day2month(AVAL),     is_event = CNSR == 0   )  basic_table() %>%   split_cols_by(var = \"ARMCD\", ref_group = \"ARM B\", split_fun = ref_group_position(\"first\")) %>%   add_colcounts() %>%   surv_time(     vars = \"AVAL\",     var_labels = \"Survival Time (Months)\",     is_event = \"is_event\",   ) %>%   build_table(df = adtte_f) #>                             ARM B          ARM A          ARM C     #>                             (N=73)         (N=69)         (N=58)    #> ——————————————————————————————————————————————————————————————————— #> Survival Time (Months)                                              #>   Median                     23.9           32.0           20.8     #>     95% CI               (18.3, 32.9)   (22.5, 49.3)   (12.9, 26.0) #>   25% and 75%-ile         9.8, 42.0      17.4, 65.3     7.3, 37.1   #>   Range                  0.1 to 154.1   0.3 to 155.5   0.6 to 80.7   basic_table() %>%   split_cols_by(var = \"ARMCD\", ref_group = \"ARM B\", split_fun = ref_group_position(2)) %>%   add_colcounts() %>%   surv_time(     vars = \"AVAL\",     var_labels = \"Survival Time (Months)\",     is_event = \"is_event\",   ) %>%   build_table(df = adtte_f) #>                             ARM A          ARM B          ARM C     #>                             (N=69)         (N=73)         (N=58)    #> ——————————————————————————————————————————————————————————————————— #> Survival Time (Months)                                              #>   Median                     32.0           23.9           20.8     #>     95% CI               (22.5, 49.3)   (18.3, 32.9)   (12.9, 26.0) #>   25% and 75%-ile         17.4, 65.3     9.8, 42.0      7.3, 37.1   #>   Range                  0.3 to 155.5   0.1 to 154.1   0.6 to 80.7   # level_order -------- # Even if default would bring ref_group first, the original order puts it last basic_table() %>%   split_cols_by(\"Species\", split_fun = level_order(c(1, 3, 2))) %>%   analyze(\"Sepal.Length\") %>%   build_table(iris) #>        setosa   virginica   versicolor #> —————————————————————————————————————— #> Mean    5.01      6.59         5.94     # character vector new_order <- level_order(levels(iris$Species)[c(1, 3, 2)]) basic_table() %>%   split_cols_by(\"Species\", ref_group = \"virginica\", split_fun = new_order) %>%   analyze(\"Sepal.Length\") %>%   build_table(iris) #>        setosa   virginica   versicolor #> —————————————————————————————————————— #> Mean    5.01      6.59         5.94"},{"path":[]},{"path":"https://insightsengineering.github.io/tern/main/news/index.html","id":"enhancements-0-9-6-9016","dir":"Changelog","previous_headings":"","what":"Enhancements","title":"tern 0.9.6.9016","text":"Added denom parameter s_count_cumulative(), s_count_missed_doses(), s_count_occurrences_by_grade(). Added \"N_row\" optional input denom s_count_occurrences(). Refactored a_count_occurrences_by_grade(), a_count_patients_with_event(), a_count_patients_with_flags() longer use make_afun(). Added rel_height_plot parameter g_lineplot() control line plot height relative annotation table height. Updated table_font_size parameter g_lineplot() control size text annotation table, including labels. Added as_list parameter g_lineplot() allow users return line plot annotation table elements list instead stacked complex customization. Refactored summarize_change() work without make_afun() access additional function parameter. Added vignette “Understanding tern functions” future reference.","code":""},{"path":"https://insightsengineering.github.io/tern/main/news/index.html","id":"bug-fixes-0-9-6-9016","dir":"Changelog","previous_headings":"","what":"Bug Fixes","title":"tern 0.9.6.9016","text":"Fixed bug a_summary() causing non-unique row_name values occur multiple statistics selected count variables.","code":""},{"path":"https://insightsengineering.github.io/tern/main/news/index.html","id":"miscellaneous-0-9-6-9016","dir":"Changelog","previous_headings":"","what":"Miscellaneous","title":"tern 0.9.6.9016","text":"Reverted deprecation quick get functions summary_formats() summary_labels(). Added disclaimer underlying use get_stats. Corrected handling extra arguments NA summarize_change().","code":""},{"path":"https://insightsengineering.github.io/tern/main/news/index.html","id":"tern-096","dir":"Changelog","previous_headings":"","what":"tern 0.9.6","title":"tern 0.9.6","text":"CRAN release: 2024-09-24","code":""},{"path":"https://insightsengineering.github.io/tern/main/news/index.html","id":"enhancements-0-9-6","dir":"Changelog","previous_headings":"","what":"Enhancements","title":"tern 0.9.6","text":"Added median_ci_3d s_summary includes estimate confidence interval one statistic. Added median_ci_3d, quantiles_lower quantiles_upper s_surv_time includes estimate confidence interval one statistic. Added hr_ci_3d s_coxph_pairwise includes estimate confidence interval one statistic. Added event_free_rate_3d s_surv_timepoint includes estimate confidence interval one statistic. Added rate_diff_ci_3d s_surv_timepoint_diff includes estimate confidence interval one statistic. Added errorbar_width linetype parameters g_lineplot. Added .formats argument tabulate_rsp_subgroups tabulate_survival_subgroups allow users specify formats. Added riskdiff argument tabulate_rsp_subgroups tabulate_survival_subgroups allow users add risk difference table column, function control_riskdiff specify settings risk difference column. Added warning tabulate_rsp_subgroups pval statistic selected df correctly generated add p-values output table. Added n_rate statistic non-default option estimate_incidence_rate returns number events observed estimated incidence rate. Added n_unique statistic non-default option estimate_incidence_rate returns total number patients least one event observed. Refactored estimate_incidence_rate work analyze function summarize function, controlled added summarize parameter. summarize = TRUE, labels can fine-tuned via new label_fmt argument function. Added fraction statistic analyze_var_count method group. Improved summarize_glm_count() documentation associated functions better describe results functions’ purpose. Added method argument s_odds_ratio() estimate_odds_ratio() control whether exact approximate conditional likelihood calculations used.","code":""},{"path":"https://insightsengineering.github.io/tern/main/news/index.html","id":"bug-fixes-0-9-6","dir":"Changelog","previous_headings":"","what":"Bug Fixes","title":"tern 0.9.6","text":"Added defaults d_count_cumulative parameters described documentation. Fixed bug empty levels g_lineplot x-axis shown either plots. Fixed bug a_surv_time threw error split \"is_event\". Fixed disappearing line g_lineplot using one group strata level. Fixed defaults formats labels get_formats_from_stats get_labels_from_stats. Fixed bug linear scaling factor (scale parameter) applied response rate h_glm_count distributions logarithmic link function. Fixed bug decorate_grob handle well empty strings NULL values title footers. Fixed bug g_km caused error multiple records data estimates max time. Fixed issue wrong wrapping due different \\n vector behavior cope well split_string().","code":""},{"path":"https://insightsengineering.github.io/tern/main/news/index.html","id":"miscellaneous-0-9-6","dir":"Changelog","previous_headings":"","what":"Miscellaneous","title":"tern 0.9.6","text":"Began deprecation confusing functions summary_formats summary_labels. Enhanced general descriptions analyze summarize functions throughout package documentation. Finalized deprecation strata cohort_id arguments g_lineplot. Moved incidence rate helper functions separate h_incidence_rate.R file.","code":""},{"path":"https://insightsengineering.github.io/tern/main/news/index.html","id":"tern-095","dir":"Changelog","previous_headings":"","what":"tern 0.9.5","title":"tern 0.9.5","text":"CRAN release: 2024-06-21","code":""},{"path":"https://insightsengineering.github.io/tern/main/news/index.html","id":"enhancements-0-9-5","dir":"Changelog","previous_headings":"","what":"Enhancements","title":"tern 0.9.5","text":"Added facet_var g_lineplot allow plot faceting factor variable. Added examples tests label_all parameter extract_survival_biomarkers extract_survival_subgroups. Added xticks, xlim, ylim arguments g_lineplot allow customization x y axes. Updated g_lineplot legend follow factor levels set users.","code":""},{"path":"https://insightsengineering.github.io/tern/main/news/index.html","id":"bug-fixes-0-9-5","dir":"Changelog","previous_headings":"","what":"Bug Fixes","title":"tern 0.9.5","text":"Fixed bug s_ancova prevented statistics printed arm levels include special characters. Fixed bug decorate_grob prevented right margins respected adding title footers decorations.","code":""},{"path":"https://insightsengineering.github.io/tern/main/news/index.html","id":"miscellaneous-0-9-5","dir":"Changelog","previous_headings":"","what":"Miscellaneous","title":"tern 0.9.5","text":"Began deprecation unused label_all parameter tabulate_survival_biomarkers tabulate_survival_subgroups, redirection parameter associated extract_* functions.","code":""},{"path":"https://insightsengineering.github.io/tern/main/news/index.html","id":"tern-094","dir":"Changelog","previous_headings":"","what":"tern 0.9.4","title":"tern 0.9.4","text":"CRAN release: 2024-04-17","code":""},{"path":"https://insightsengineering.github.io/tern/main/news/index.html","id":"new-features-0-9-4","dir":"Changelog","previous_headings":"","what":"New Features","title":"tern 0.9.4","text":"Added h_glm_negbin h_glm_count enable count data analysis using negative binomial model. Added argument grade_groups_only count_occurrences_by_grade allow users display rows specified grade groups. Added internal function df2gg converts data.frame objects ggplot objects. Added functions control_surv_med_annot control_coxph_annot configure g_km annotation table sizes/positions. Refactored g_km output ggplot object instead grob object. Refactored g_forest output ggplot object instead grob object.","code":""},{"path":"https://insightsengineering.github.io/tern/main/news/index.html","id":"enhancements-0-9-4","dir":"Changelog","previous_headings":"","what":"Enhancements","title":"tern 0.9.4","text":"Default format mean p-values (mean_pval) updated \"xx.xx\" \"x.xxxx | (<0.0001)\".","code":""},{"path":"https://insightsengineering.github.io/tern/main/news/index.html","id":"bug-fixes-0-9-4","dir":"Changelog","previous_headings":"","what":"Bug Fixes","title":"tern 0.9.4","text":"Fixed nested column split label overlay issue rtable2gg clean appearance text labels. Fixed bug s_ancova causing incorrect difference calculations arm variables irregular levels. Fixed bug format_count_fraction_fixed_dp print fraction 1 (100%). Fixed bug g_lineplot causing default labels update according specified control settings. Fixed bug causing error automatic value formatting applied NA values.","code":""},{"path":"https://insightsengineering.github.io/tern/main/news/index.html","id":"miscellaneous-0-9-4","dir":"Changelog","previous_headings":"","what":"Miscellaneous","title":"tern 0.9.4","text":"Added function expect_snapshot_ggplot test setup file process plot snapshot tests allow plot dimensions set. Adapted argument renames introduced ggplot2 3.5.0. Renamed individual_patient_plot.R g_ipp.R. Removed instances deprecated parameters time_unit_input, time_unit_output, na_level indent_mod. Removed deprecated functions summarize_vars, control_summarize_vars, a_compare, create_afun_summary, create_afun_compare, summary_custom. Removed vdiffr package Suggests DESCRIPTION file. Began deprecation named element strat, renamed strata, within variables argument h_rsp_to_logistic_variables, h_logistic_mult_cont_df, h_odds_ratio_subgroups_df, h_coxreg_mult_cont_df, h_coxph_subgroups_df, h_tbl_coxph_pairwise, extract_rsp_biomarkers, extract_rsp_subgroups, extract_survival_biomarkers, extract_survival_subgroups. Began deprecation strat argument s_coxph_pairwise replaced strata argument. Began deprecation forest_grob, forest_dot_line, forest_viewport, vp_forest_table_part, grid.forest functions. Began deprecation longer used Kaplan-Meier helper functions h_ggkm, h_decompose_gg, h_km_layout, h_grob_tbl_at_risk, h_grob_median_surv, h_grob_y_annot, h_grob_coxph. Began deprecation grob/grid related functions stack_grobs, arrange_grobs, draw_grob longer used tern.","code":""},{"path":"https://insightsengineering.github.io/tern/main/news/index.html","id":"tern-093","dir":"Changelog","previous_headings":"","what":"tern 0.9.3","title":"tern 0.9.3","text":"CRAN release: 2023-12-08","code":""},{"path":"https://insightsengineering.github.io/tern/main/news/index.html","id":"new-features-0-9-3","dir":"Changelog","previous_headings":"","what":"New Features","title":"tern 0.9.3","text":"Added ref_group_position function place reference group facet last, first certain position. Added keep_level_order split function retain original order levels split. Added level_order split function reorder manually levels. Added function get_indents_from_stats format return indent modifiers given set statistics. Added internal utility function apply_auto_formatting check \"auto\" formats replace implementation format_auto analyze functions. Added utility function labels_use_control modify labels control specifications. Added list containing default statistics method group, tern_default_stats. Added summarize function version count_occurrences analyze function, summarize_occurrences. Added referential footnotes surv_time censored range observations, controlled via ref_fn_censor parameter. Added helper function h_adlb_abnormal_by_worst_grade prepare ADLB data use input count_abnormal_by_worst_grade. Added s_bland_altman function assess agreement two numerical vectors. Added function rtable2gg converts rtable objects ggplot objects. Added helper function set default na_str globally set_default_na_str() added default_na_str() interested functions.","code":""},{"path":"https://insightsengineering.github.io/tern/main/news/index.html","id":"enhancements-0-9-3","dir":"Changelog","previous_headings":"","what":"Enhancements","title":"tern 0.9.3","text":"Added ref_group_coxph parameter g_km specify reference group used pairwise Cox-PH calculations annot_coxph = TRUE. Added annot_coxph_ref_lbls parameter g_km enable printing reference group table labels annot_coxph = TRUE. Added x_lab parameter g_lineplot customize x-axis label. Remove 25% padding y-axis g_lineplot. Added support creating multiple risk difference columns, comparing single comparison group. Multiple comparison groups can specified vector via arm_y argument. Allowed numeric vector count_by input analyze_num_patients summarize_num_patients. Aligned plot table vertically g_lineplot.","code":""},{"path":"https://insightsengineering.github.io/tern/main/news/index.html","id":"bug-fixes-0-9-3","dir":"Changelog","previous_headings":"","what":"Bug Fixes","title":"tern 0.9.3","text":"Fixed bug decorate_grob preventing text wrapping accounting font size. Fixed implementation na_str argument column-wise analysis tabulation functions.","code":""},{"path":"https://insightsengineering.github.io/tern/main/news/index.html","id":"miscellaneous-0-9-3","dir":"Changelog","previous_headings":"","what":"Miscellaneous","title":"tern 0.9.3","text":"Specified minimal version package dependencies. Upgraded to_string_matrix take account widths printing parameters.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/main/news/index.html","id":"new-features-0-9-2","dir":"Changelog","previous_headings":"","what":"New Features","title":"tern 0.9.2","text":"Added na_str argument analyze & summarize_row_groups wrapper functions count_abnormal, count_abnormal_by_baseline, count_abnormal_by_marked, count_abnormal_by_worst_grade, count_abnormal_lab_worsen_by_baseline, count_cumulative, count_missed_doses, count_occurrences, count_occurrences_by_grade, summarize_occurrences_by_grade, summarize_patients_events_in_cols, count_patients_with_event, count_patients_with_flags, count_values, estimate_multinomial_response, estimate_proportion, h_tab_one_biomarker, estimate_incidence_rate, logistic_summary_by_flag, estimate_odds_ratio, estimate_proportion_diff, test_proportion_diff, summarize_ancova, summarize_change, summarize_glm_count, summarize_num_patients, analyze_num_patients, summarize_patients_exposure_in_cols, coxph_pairwise, tabulate_survival_subgroups, surv_time, surv_timepoint.","code":""},{"path":"https://insightsengineering.github.io/tern/main/news/index.html","id":"enhancements-0-9-2","dir":"Changelog","previous_headings":"","what":"Enhancements","title":"tern 0.9.2","text":"Added formatting function format_count_fraction_lt10 formatting count_fraction special consideration count less 10. Updated s_summary.logical output count_fraction denominator zero display NA instead 0 tables. Updated analyze_vars_in_cols allow character input indicate whether nominal time point post-dose pre-dose applying 1/3 imputation rule.","code":""},{"path":"https://insightsengineering.github.io/tern/main/news/index.html","id":"bug-fixes-0-9-2","dir":"Changelog","previous_headings":"","what":"Bug Fixes","title":"tern 0.9.2","text":"Fixed bug g_km causing error converting certain annotation width units.","code":""},{"path":"https://insightsengineering.github.io/tern/main/news/index.html","id":"miscellaneous-0-9-2","dir":"Changelog","previous_headings":"","what":"Miscellaneous","title":"tern 0.9.2","text":"Began deprecation na_level argument s_count_abnormal_by_baseline, a_summary, analyze_vars, analyze_vars_in_cols, compare_vars, h_map_for_count_abnormal, h_stack_by_baskets, summarize_colvars, a_coxreg, summarize_coxreg replaced na_str argument. strata cohort_id parameters renamed group_var subject_var respectively g_lineplot control_lineplot_vars .","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/main/news/index.html","id":"new-features-0-9-1","dir":"Changelog","previous_headings":"","what":"New Features","title":"tern 0.9.1","text":"Added imputation_rule function apply imputation rule data. Added new format function format_sigfig allow numeric value formatting specified number significant figures. Added vectors containing default statistic formats labels tern_default_formats tern_default_labels, respectively. Added function get_stats return methods given statistical method groups. Added function get_formats_from_stats return formats get_labels_from_stats return labels given set statistics. Added \"auto\" option .formats. uses format_auto determine automatically number digits. Added title argument h_grob_tbl_at_risk annot_at_risk_title argument g_km h_km_layout allows user add “Patients Risk” title Kaplan-Meier risk annotation table.","code":""},{"path":"https://insightsengineering.github.io/tern/main/news/index.html","id":"enhancements-0-9-1","dir":"Changelog","previous_headings":"","what":"Enhancements","title":"tern 0.9.1","text":"Refactored tabulate_rsp_subgroups pass sanitation checks preventing creation degenerate subtables. Updated analyze_vars_in_cols use caching, allow implementation imputation rule via imp_rule argument, allow user specify cell alignment via .aligns argument. Updated add_rowcounts allow addition row counts alt_counts_df using alt_counts argument. Added gp argument g_forest control graphical parameters font size.","code":""},{"path":"https://insightsengineering.github.io/tern/main/news/index.html","id":"miscellaneous-0-9-1","dir":"Changelog","previous_headings":"","what":"Miscellaneous","title":"tern 0.9.1","text":"Grouped functions relating valid method names default formats labels new source file utils_defaults_handling.R. Started deprecation summary_custom() a_summary() S3 method. Renamed statistical method p-value discrete case pval_counts. Removed a_summary_internal() favor one main a_summary().","code":""},{"path":"https://insightsengineering.github.io/tern/main/news/index.html","id":"tern-090","dir":"Changelog","previous_headings":"","what":"tern 0.9.0","title":"tern 0.9.0","text":"CRAN release: 2023-09-01","code":""},{"path":"https://insightsengineering.github.io/tern/main/news/index.html","id":"new-features-0-9-0","dir":"Changelog","previous_headings":"","what":"New Features","title":"tern 0.9.0","text":"Added stat_propdiff_ci function calculate proportion/risk difference CI. Added risk difference column functionality via riskdiff argument functions count_occurrences, count_occurrences_by_grade, count_patients_with_event, count_patients_with_flags, analyze_num_patients, summarize_num_patients.","code":""},{"path":"https://insightsengineering.github.io/tern/main/news/index.html","id":"enhancements-0-9-0","dir":"Changelog","previous_headings":"","what":"Enhancements","title":"tern 0.9.0","text":"Refactored function a_summary longer use helper function create_afun_summary. Refactored functions summarize_vars compare_vars use refactored a_summary function. Created new internal helper functions ungroup_stats ungroup statistics calculated factor variables, a_summary_internal perform calculations a_summary.","code":""},{"path":"https://insightsengineering.github.io/tern/main/news/index.html","id":"bug-fixes-0-9-0","dir":"Changelog","previous_headings":"","what":"Bug Fixes","title":"tern 0.9.0","text":"Fixed bug s_count_occurrences_by_grade “missing” grade always appears final level. Fixed bug analyze_vars_in_cols categorical data used. Fixed bug s_count_occurrences_by_grade levels relabeled reordering account “missing” grades.","code":""},{"path":"https://insightsengineering.github.io/tern/main/news/index.html","id":"miscellaneous-0-9-0","dir":"Changelog","previous_headings":"","what":"Miscellaneous","title":"tern 0.9.0","text":"Fixed swapped descriptions .N_row .N_col parameters. Removed internal calls df_explicit_na. Changes NA values happen externally tern functions, depending users’ needs. Reinstated correct soft deprecation create_afun_summary create_afun_compare.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/main/news/index.html","id":"enhancements-0-8-5","dir":"Changelog","previous_headings":"","what":"Enhancements","title":"tern 0.8.5","text":"Added ylim argument g_km allow user set custom limits y-axis. Added assertion g_km checks whether one arm present data annot_coxph true. Added flag_labels argument s_count_patients_with_flags enable label handling options count_patients_by_flags. Added nested argument analyze wrapper functions count_abnormal, count_abnormal_by_baseline, count_abnormal_by_marked, count_abnormal_by_worst_grade, count_abnormal_lab_worsen_by_baseline, count_cumulative, count_missed_doses, count_occurrences, count_occurrences_by_grade, count_patients_with_event, count_patients_with_flags, count_values, estimate_multinomial_response, estimate_proportion, estimate_incidence_rate, estimate_odds_ratio, estimate_proportion_diff, test_proportion_diff, summarize_ancova, summarize_change, summarize_glm_count, analyze_num_patients, coxph_pairwise, surv_time, surv_timepoint.","code":""},{"path":"https://insightsengineering.github.io/tern/main/news/index.html","id":"miscellaneous-0-8-5","dir":"Changelog","previous_headings":"","what":"Miscellaneous","title":"tern 0.8.5","text":"Started deprecation cycle summarize_vars control_summarize_vars. Renamed analyze_vars control_analyze_vars reflect underlying rtables machinery keeping backward compatibility aliases.","code":""},{"path":"https://insightsengineering.github.io/tern/main/news/index.html","id":"tern-084","dir":"Changelog","previous_headings":"","what":"tern 0.8.4","title":"tern 0.8.4","text":"CRAN release: 2023-06-27","code":""},{"path":"https://insightsengineering.github.io/tern/main/news/index.html","id":"enhancements-0-8-4","dir":"Changelog","previous_headings":"","what":"Enhancements","title":"tern 0.8.4","text":"Added method character class h_coxreg_inter_effect enabling character covariates summarize_coxreg.","code":""},{"path":"https://insightsengineering.github.io/tern/main/news/index.html","id":"miscellaneous-0-8-4","dir":"Changelog","previous_headings":"","what":"Miscellaneous","title":"tern 0.8.4","text":"Began deprecation time_unit_input time_unit_output arguments replaced input_time_unit num_pt_year, respectively, control_incidence_rate. Removed deprecated pairwise function. Deprecated a_compare replaced a_summary argument compare = TRUE. Deprecated helper functions create_afun_summary create_afun_compare longer used a_summary a_compare respectively.","code":""},{"path":"https://insightsengineering.github.io/tern/main/news/index.html","id":"bug-fixes-0-8-4","dir":"Changelog","previous_headings":"","what":"Bug Fixes","title":"tern 0.8.4","text":"Fixed long double assertion check sum(weights) M1mac installation.","code":""},{"path":"https://insightsengineering.github.io/tern/main/news/index.html","id":"tern-083","dir":"Changelog","previous_headings":"","what":"tern 0.8.3","title":"tern 0.8.3","text":"CRAN release: 2023-06-19","code":""},{"path":"https://insightsengineering.github.io/tern/main/news/index.html","id":"enhancements-0-8-3","dir":"Changelog","previous_headings":"","what":"Enhancements","title":"tern 0.8.3","text":"Added explicit zero counts g_km plot “risk” annotation tables. Added flag total level split analyze_patients_exposure_in_cols. Implemented .indent_mods argument functions h_tab_one_biomarker, h_tab_rsp_one_biomarker, h_tab_surv_one_biomarker, summarize_logistic, logistic_summary_by_flag, tabulate_rsp_biomarkers, a_coxreg, summarize_coxreg, tabulate_survival_biomarkers, surv_time, surv_timepoint, cfun_by_flag. Updated summarize_coxreg print covariates data rows univariate Cox regression interactions content rows otherwise. Removed “baseline status” text d_count_abnormal_by_baseline labels. Improved default sizing annotation tables g_km added dynamic scaling surv_med coxph annotation tables, customization via width_annots argument.","code":""},{"path":"https://insightsengineering.github.io/tern/main/news/index.html","id":"bug-fixes-0-8-3","dir":"Changelog","previous_headings":"","what":"Bug Fixes","title":"tern 0.8.3","text":"Fixed bug split_text_grob preventing titles footnotes properly formatted printed decorate_grob. Fixed bug g_lineplot preventing addition lines plot midpoint statistic calculations result NA value(s). Fixed tern:::tidy.glm formals respect broom:::tidy.default formals.","code":""},{"path":"https://insightsengineering.github.io/tern/main/news/index.html","id":"miscellaneous-0-8-3","dir":"Changelog","previous_headings":"","what":"Miscellaneous","title":"tern 0.8.3","text":"Updated README include installation instructions CRAN. Remove examples unexported functions. Export functions has_count_in_cols, has_counts_difference, combine_counts, h_tab_rsp_one_biomarker, arrange_grobs, a_count_patients_sum_exposure, a_coxreg, groups_list_to_df, forest_viewport. Updated README include installation instructions CRAN. Began deprecation indent_mod argument replaced .indent_mods argument summarize_num_patients analyze_num_patients.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/main/news/index.html","id":"breaking-changes-0-8-2","dir":"Changelog","previous_headings":"","what":"Breaking Changes","title":"tern 0.8.2","text":"Refactored s_coxreg summarize_coxregto work new analysis function a_coxreg.","code":""},{"path":"https://insightsengineering.github.io/tern/main/news/index.html","id":"enhancements-0-8-2","dir":"Changelog","previous_headings":"","what":"Enhancements","title":"tern 0.8.2","text":"Added section_div na_level arguments summarize_vars. Added median_range numeric variable statistic option summarize_vars. Corrected ordering factor levels d_onco_rsp_label. Added new “Analyze Functions”, “Summarize Functions”, “Analyze Functions Columns” overview pages. Consolidated KM plot documentation within g_km function. Added a_count_patients_sum_exposure summarize_patients_exposure_in_cols new analyze function analyze_patients_exposure_in_cols. Added informative error user selects invalid method unstratified analyses s_proportion_diff. Updated s_summary s_compare allow NA values input variables. factor variables NAs, na.rm = FALSE explicit NA level automatically added. na.rm = TRUE also consider \"<Missing>\" values exclude . Updated purpose na_level parameter s_summary s_compare align tern functions. Instead string consider NA setting na.rm = TRUE, now defines string print place NA values output table.","code":""},{"path":"https://insightsengineering.github.io/tern/main/news/index.html","id":"bug-fixes-0-8-2","dir":"Changelog","previous_headings":"","what":"Bug Fixes","title":"tern 0.8.2","text":"Fixed missing label TRTEDTM tern datasets. Fixed improper implementation na_level argument summarize_vars preventing effect.","code":""},{"path":"https://insightsengineering.github.io/tern/main/news/index.html","id":"miscellaneous-0-8-2","dir":"Changelog","previous_headings":"","what":"Miscellaneous","title":"tern 0.8.2","text":"Implemented lubridate package date variables tern datasets. Organized .gitignore .Rbuildignore files. Removed deprecated footnotes functions related files. Started deprecation cycle pairwise function. Moved count_patients_with_flags functions count_patients_with_event.R count_patients_with_flags.R.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/main/news/index.html","id":"enhancements-0-8-0","dir":"Changelog","previous_headings":"","what":"Enhancements","title":"tern 0.8.0","text":"Added summarize_glm_count function analyze count data using linear model. Added legend g_step. Added formatting functions format_fraction_fixed_dp format_count_fraction_fixed_dp fixed single decimal place percentages. Added na_level labelstr arguments summarize_vars_in_cols. Added analyze_num_patients include summary beginning repeat paginating. Added h_row_first_values function general helper function retrieve first values specific rows. Added option remove \"(n)\" suffix unique_count labels s_num_patients. Added options g_km annotate statistics (annot_stats) add corresponding vertical lines (annot_stats_lines).","code":""},{"path":"https://insightsengineering.github.io/tern/main/news/index.html","id":"bug-fixes-0-8-0","dir":"Changelog","previous_headings":"","what":"Bug Fixes","title":"tern 0.8.0","text":"Fixed bug causing incorrect ordering numeric grade levels missing grades present s_count_occurrences_by_grade. Refactored summarize_vars_in_cols work pagination machinery. Fixed bug allow passing conf_level argument emmeans::contrast() s_ancova. Fixed bugs rtables_access.R caused checking specific combinations (also standard values never used) column indices names. Fixed single applicable record bug count_abnormal_by_grade. Fixed bug add_rowcounts caused row count row values count zero. Fixed bug h_col_indices causing error pruning combination columns. Fixed bug test_proportion_diff missing argument var_labels.","code":""},{"path":"https://insightsengineering.github.io/tern/main/news/index.html","id":"documentation-and-tests-0-8-0","dir":"Changelog","previous_headings":"","what":"Documentation and Tests","title":"tern 0.8.0","text":"Added tests increase code coverage. Created separate documentation files functions different sections pkgdown reference. Created separate .R files logistic regression cox regression helper functions. Fixed table tests using analyze_num_patients generate initial summary repetition paginating. Updated tests use testthat 3rd edition replaced applicable tests snapshot testing. Updated summarize_ancova examples use iris dataset instead scda data. Created vignette saves cached synthetic CDISC dataset files data/ folder generated cached synthetic datasets. Updated examples/tests use datasets data/ folder instead scda datasets. Removed template tests tern. tests internal repo scda.test.","code":""},{"path":"https://insightsengineering.github.io/tern/main/news/index.html","id":"miscellaneous-0-8-0","dir":"Changelog","previous_headings":"","what":"Miscellaneous","title":"tern 0.8.0","text":"Renamed summarize_vars_in_cols analyze_vars_in_cols reflect appropriate analyze logic. Removed redundant summary_in_cols helper functions. Exported function format_xx. Replaced deprecated ggplot2 functions/arguments fix warnings. Replaced deprecated function forcats::fct_explicit_na forcats::fct_na_value_to_level. Removed deprecated wrap_text function related files. Started deprecation cycle footnotes functions.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/main/news/index.html","id":"new-features-0-7-10","dir":"Changelog","previous_headings":"","what":"New Features","title":"tern 0.7.10","text":"Added stratified Newcombe stratified Wilson statistics estimate_proportion estimate_proportion_diff relative tests. Added stat_mean_pval, new summary statistic calculate p-value mean. Added statistic mean_se (mean standard error) summarize_variables related functions. Introduced Rdpack references.","code":""},{"path":"https://insightsengineering.github.io/tern/main/news/index.html","id":"enhancements-0-7-10","dir":"Changelog","previous_headings":"","what":"Enhancements","title":"tern 0.7.10","text":"Redesign data handling tests removing repetitive data loads library calls. Added DescTools::BinomDiffCI function within tern. Added new parameter summarize_logistic specify pivoted value use analysis. Updated s_coxph_pairwise generate log-rank p-value using original log-rank test instead Cox Proportional-Hazards Model. Implemented nestcolor examples adapting g_km, g_ipp, g_waterfall, g_step, g_lineplot, g_forest. Added parameters interaction_y interaction_item ANCOVA make interaction calculations available. Added new parameter footnotes add footnotes g_km.","code":""},{"path":"https://insightsengineering.github.io/tern/main/news/index.html","id":"migration-from-assertthat-to-checkmate-0-7-10","dir":"Changelog","previous_headings":"","what":"Migration from assertthat to checkmate","title":"tern 0.7.10","text":"Implemented checkmate::assert_vector, checkmate::assert_set_equal, checkmate::assert_int check vector type, length, values. Replaced standard assertions checkmate following functions: all_elements_in_ref, is_df_with_nlevels_factor, is_df_with_no_na_level, is_proportion_vector, is_quantiles_vector, is_character_or_factor, is_nonnegative_count, is_valid_character, assert_character_or_factor, assert_equal_length has_tabletree_colnames. Modified is_proportion, is_equal_length, is_df_with_no_na_level, is_df_with_nlevels_factor, is_variables, is_df_with_variables, is_df_with_factors, is_valid_factor use assertion logic. Added verbose warnings as_factor_keep_attributes. Made assert_df_with_factors assert_proportion_value internal functions. Renamed assertthat.R test-assertthat.R utils_checkmate.R test-utils_checkmate.R.","code":""},{"path":"https://insightsengineering.github.io/tern/main/news/index.html","id":"documentation-and-namespace-polishing-0-7-10","dir":"Changelog","previous_headings":"","what":"Documentation and NAMESPACE Polishing","title":"tern 0.7.10","text":"count_abnormal_by_marked (reference abnormal_by_marked), count_abnormal_lab_worsen_by_baseline h_adlb_worsen (reference abnormal_by_worst_grade_worsen_from_baseline), count_abnormal_by_worst_grade (reference abnormal_by_worst_grade), to_string_matrix, tidy.summary.coxph, tidy.step, surv_timepoint, (reference survival_timepoint), surv_time (reference survival_time), coxph_pairwise (reference survival_coxph_pairwise), extract_survival_subgroups tabulate_survival_subgroups (reference survival_duration_subgroups), extract_survival_biomarkers tabulate_survival_biomarkers (reference survival_biomarkers_subgroups), control_summarize_vars, s_summary a_summary (reference summarize_variables) kept S3 method tree. summarize_patients_exposure_in_cols, summarize_num_patients s_num_patients, s_num_patients_content, summarize_num_patients. count_cumulative, count_missed_doses, count_patients_events_in_cols, summarize_colvars, summarize_change, summarize_ancova,.rtable, color_palette, add_footnotes. (statistical function controls) control_coxreg, control_coxph, control_incidence_rate, control_lineplot_vars, control_surv_time, control_surv_timepoint, control_logisitic, control_step. stat_mean_ci, stat_median_ci, split_cols_by_groups, explicit_na, sas_na, extract_rsp_subgroups, tabulate_rsp_subgroups, extract_rsp_biomarkers, tabulate_rsp_biomarkers, keep_rows, keep_content_rows, has_count_in_any_col, has_fraction_in_cols, has_fraction_in_any_col, has_fractions_difference, test_proportion_diff, pairwise, logistic_regression, estimate_incidence_rate, control_incidence_rate (reference incidence_rate), cut_quantile_bins, estimate_multinomial_rsp, decorate_grob_set, extreme_format, fit_rsp_step, fit_survival_step, footnotes, footnotes-set, format_count_fraction, format_fraction_threshold, formatting_functions, format_fraction, combination_function (S4 method), compare_variables (S3 method), kaplan_meier. (chain functions, reference abnormal_by_marked) s_count_abnormal_by_marked, a_count_abnormal_by_marked. (chain functions, reference abnormal_by_worst_grade_worsen_from_baseline) a_count_abnormal_lab_worsen_by_baseline, s_count_abnormal_lab_worsen_by_baseline. (chain functions, reference abnormal_by_worst_grade) s_count_abnormal_by_worst_grade, a_count_abnormal_by_worst_grade. (chain functions, reference survival_timepoint) s_surv_timepoint, s_surv_timepoint_diff, a_surv_timepoint, a_surv_timepoint_diff. (chain functions, reference survival_time) s_surv_time, a_surv_time. (chain functions, reference survival_coxph_pairwise) s_coxph_pairwise, a_coxph_pairwise. (chain functions, reference survival_duration_subgroups) a_survival_subgroups. (chain functions, reference count_cumulative) s_count_cumulative, a_count_cumulative. (chain functions, reference count_missed_doses) s_count_nonmissing, s_count_missed_doses, a_count_missed_doses. (chain functions, reference count_patients_events_in_cols) s_count_patients_and_multiple_events, summarize_patients_events_in_cols. (chain functions, reference incidence_rate) s_incidence_rate, a_incidence_rate. (cox regression helper) cox_regression_inter, decorate_grob_factory, draw_grob, estimate_coef. summary_labels, summary_formats, s_count_patients_sum_exposure, a_change_from_baseline s_change_from_baseline, a_ancova, s_ancova, arrange_grobs, as_factor_keep_attributes, combine_levels, split_text_grob, groups_list_to_df, s_cox_multivariate, is_leaf_table, a_response_subgroups, range_noinf, has_count_in_cols, has_counts_difference, prop_chisq, prop_cmh, prop_schouten, prop_fisher, s_test_proportion_diff, a_test_proportion_diff, fct_discard, fct_explicit_na_if.","code":""},{"path":"https://insightsengineering.github.io/tern/main/news/index.html","id":"bug-fixes-0-7-10","dir":"Changelog","previous_headings":"","what":"Bug Fixes","title":"tern 0.7.10","text":"Fixed retrieval method stats::ancova output due version inconsistency. Fixed tests respect new standard print NA coming rtables. Fixed error tests coming changes formatters::var_labels. Fixed prop_diff functions respect success responses (TRUE values). Fixed error coming comparing factors vector characters vector. Fixed empty vector exception cut_quantile_bins. Fixed exception error empty strings present pivoted columns (rtables split functions) Fixed bug s_ancova causing error first level arm factor control arm. Fixed bug s_abnormal_by_worst_grade one PARAM level. Fixed bug prop_diff_wald selecting responders, updated tests accordingly. Fixed bug h_ancova caused error deselecting covariates.","code":""},{"path":"https://insightsengineering.github.io/tern/main/news/index.html","id":"miscellaneous-0-7-10","dir":"Changelog","previous_headings":"","what":"Miscellaneous","title":"tern 0.7.10","text":"Added deprecated badge g_mmrm. Removed internal function calls examples (tern:::) added dontrun internal function examples. Removed warnings messages console occurring examples tests. Deprecated functions color_palette h_set_nest_theme favor nestcolor::color_palette nestcolor::theme_nest, respectively. Removed deprecated functions: color_palette, color_palette_core, h_set_nest_theme, s_cox_univariate. Removed deprecated MMRM functions: fit_mmrm, g_mmrm_diagnostic, g_mmrm_lsmeans, .rtable.mmrm, h_mmrm_fixed, h_mmrm_cov, h_mmrm_diagnostic, tidy.mmrm, s_mmrm_lsmeans, s_mmrm_lsmeans_single, summarize_lsmeans. Renamed functions arm study_arm extract extract_by_name. Renamed rtables.R utils_rtables.R. Extracted cox_regression_inter separate file cox_regression. Renamed estimate_incidence_rate.R incidence_rate.R match documentation grouping name. Extracted control_incidence_rate separate file produces separate documentation file. Added @md removed @order incidence_rate.R. Modified examples accordingly. Removed hyperlink prop_schouten function documentation. Exported draw_grob function.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/main/news/index.html","id":"fix-0-7-8","dir":"Changelog","previous_headings":"","what":"Fix","title":"tern 0.7.8","text":"h_split_by_subgroups documentation warning fix wrong placing example block","code":""},{"path":"https://insightsengineering.github.io/tern/main/news/index.html","id":"documentation-and-namespace-polishing-0-7-8","dir":"Changelog","previous_headings":"","what":"Documentation and NAMESPACE polishing","title":"tern 0.7.8","text":"Adopting standard badges @description instead every @descriptionIn function. Corrected accordingly summarize_variables_in_cols Added stable badge g_lineplot, g_step, g_waterfall, cox_regression, score_occurrences, add_rowcounts, odds_ratio, count_occurrences, count_occurrences_by_grade, explicit_na, df_explicit_na, count_patients_with_event, decorate_grob, combine_groups, append_varlabels, univariate, stack_grobs, count_abnormal (reference abnormal), count_abnormal_by_baseline (reference abnormal_by_baseline). (helper functions) h_format_row, h_map_for_count_abnormal (utils functions) make_names, month2day, day2month empty_vector_if_na, aesi_label, n_available, format_xx, arm. count_values_funs, prop_difference, combine_counts. (chain functions) s_count_abnormal, a_count_abnormal. (chain functions) s_count_abnormal_by_baseline, a_count_abnormal_by_baseline, d_count_abnormal_by_baseline. Deprecated s_cox_univariate function now deprecated badge.","code":""},{"path":"https://insightsengineering.github.io/tern/main/news/index.html","id":"enhancements-0-7-8","dir":"Changelog","previous_headings":"","what":"Enhancements","title":"tern 0.7.8","text":"Enhanced g_lineplot table automatically scale table height return ggplot object. Enhanced g_ipp caption argument adjust position. Enhanced prop_diff, tern function related functions able apply continuity correction Newcombe method. Enhanced summarize_numeric_in_columns summarize_variables allow factor/character summary able summarize number BLQs AVALC ADPC dataset. Updated order summarize variables stats manual order consistency. Added sum option summarize_variables. Use consistent color palette plotting (stream default). Enhanced h_pkparam_sort function argument key_var allow data different column names.","code":""},{"path":"https://insightsengineering.github.io/tern/main/news/index.html","id":"miscellaneous-0-7-8","dir":"Changelog","previous_headings":"","what":"Miscellaneous","title":"tern 0.7.8","text":"Updated test-table_aet02.R variant 12. Changed scda data version ‘2022-02-28’. Added template pkgdown site. Removed package dependencies grDevices, stringr, viridisLite. Renaming summarize_numeric_in_columns summarize_variables_in_columns. Renaming summarize_vars_numeric_in_cols summarize_vars_in_cols. Fixed bug points g_lineplot plot connected missing values. Updated package authors.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/main/news/index.html","id":"breaking-changes-0-7-7","dir":"Changelog","previous_headings":"","what":"Breaking changes","title":"tern 0.7.7","text":"Move MMRM separate package tern.mmrm.","code":""},{"path":"https://insightsengineering.github.io/tern/main/news/index.html","id":"new-features-0-7-7","dir":"Changelog","previous_headings":"","what":"New features","title":"tern 0.7.7","text":"Added h_pkparam_sort order PK PARAM value based order dataset generated d_pkparam(). Added d_pkparam generate PK parameter map sorting.","code":""},{"path":"https://insightsengineering.github.io/tern/main/news/index.html","id":"enhancements-0-7-7","dir":"Changelog","previous_headings":"","what":"Enhancements","title":"tern 0.7.7","text":"Changed nudge_y argument h_g_ipp dependent data, fixing issue whereby baseline labels offset incorrectly. Enhanced stat_mean_ci s_summary.numeric calculate geometric mean confidence intervals.","code":""},{"path":"https://insightsengineering.github.io/tern/main/news/index.html","id":"miscellaneous-0-7-7","dir":"Changelog","previous_headings":"","what":"Miscellaneous","title":"tern 0.7.7","text":"Updated dependencies internal adjustments rtables package refactor. Removed with_label, var_labels, var_labels<- resolve conflict formatters package, new dependency. Added new “Introduction tern” “tern tabulation” vignettes.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/main/news/index.html","id":"new-features-0-7-6","dir":"Changelog","previous_headings":"","what":"New features","title":"tern 0.7.6","text":"Added h_map_for_count_abnormal create map used trim_levels_to_map split function calling helper function. supports two methods: one observed mapping, one least low limit zero least one non missing high limit. Added s_summary_numeric_in_cols summarize_vars_numeric_in_cols functions generate summary statistics columns, mainly used PK datasets. Added five statistics s_summary.numeric use s_summary_numeric_in_cols.","code":""},{"path":"https://insightsengineering.github.io/tern/main/news/index.html","id":"enhancements-0-7-6","dir":"Changelog","previous_headings":"","what":"Enhancements","title":"tern 0.7.6","text":"Enhanced functions tabulate_survival_subgroups tabulate_rsp_subgroups (Survival Duration Best Response analyses) calculate N-s based records considered create model. Enhanced function estimate_proportion related functions able apply continuity correction Wilson method. Refactored count_abnormal_by_marked related statistics formatting functions use efficient layout .spl_context argument used determining denominators trim_levels_to_map split function split_rows_by show desired levels table. breaking change. Refactored count_abnormal_by_worst_grade related statistics formatting functions use efficient layout .spl_context argument used determining denominators trim_levels_to_map split function split_rows_by show desired levels table. breaking change. Refactored count_abnormal function related statistics formatting functions use efficient layout trim_levels_to_map split function split_rows_by show desired levels table. Also updated abnormal argument able consider one level direction. breaking change. Enhanced function estimate_incidence_rate related functions consider week time unit data input.","code":""},{"path":"https://insightsengineering.github.io/tern/main/news/index.html","id":"bug-fixes-0-7-6","dir":"Changelog","previous_headings":"","what":"Bug fixes","title":"tern 0.7.6","text":"Fixed bug assertthat functions output wrong data frame names limited length failure message outputs.","code":""},{"path":"https://insightsengineering.github.io/tern/main/news/index.html","id":"miscellaneous-0-7-6","dir":"Changelog","previous_headings":"","what":"Miscellaneous","title":"tern 0.7.6","text":"Removed dependency utils.nest using checkmate purrr packages validation moved get_free_cores skip_if_too_deep functions utils.nest tern.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/main/news/index.html","id":"new-features-0-7-5","dir":"Changelog","previous_headings":"","what":"New features","title":"tern 0.7.5","text":"Added functions estimate continuous biomarker effects across subgroups survival binary response endpoints, used produce corresponding forest plots, see survival_biomarkers_subgroups response_biomarkers_subgroups. Added g_lineplot plot function, including new h_format_row helper function control_lineplot_vars function. Removed g_summary_by. Added new safety helper function h_stack_by_baskets stack events SMQ /CQ basket flag ADAE data set.","code":""},{"path":"https://insightsengineering.github.io/tern/main/news/index.html","id":"enhancements-0-7-5","dir":"Changelog","previous_headings":"","what":"Enhancements","title":"tern 0.7.5","text":"Added couple new statistics s_summary.numeric. Added names attribute element final list returned s_summary.numeric function. Added summary_formats summary_labels helper functions. Added option also convert logical variables factor variables df_explicit_na. Refactored h_append_grade_groups improve flexibility, robustness clearness, make sure result ordering according order grade_groups. Also, added remove_single argument controls whether elements one-element grade groups output removed. Added var_labels show_labels arguments count_occurrences count_patients_with_flags allow creation title row. Added na_level argument count_abnormal_by_baseline. Updated h_append_grade_groups longer fill-empty grade groups zeros.","code":""},{"path":"https://insightsengineering.github.io/tern/main/news/index.html","id":"bug-fixes-0-7-5","dir":"Changelog","previous_headings":"","what":"Bug Fixes","title":"tern 0.7.5","text":"Fixed prop_diff_cmh handle edge case FALSE (TRUE) responses. Enhanced g_mmrm_diagnostic improve error handling data amenable Locally Weighted Scatterplot Smoothing. Plot can now display combination annotation tables number patients risk, median survival time, Cox-PH summary. Function return warning instead error arm variable includes single level annot_coxph = TRUE. Lines plot now start time 0 probability 1. Category labels can include equals sign.","code":""},{"path":"https://insightsengineering.github.io/tern/main/news/index.html","id":"miscellaneous-0-7-5","dir":"Changelog","previous_headings":"","what":"Miscellaneous","title":"tern 0.7.5","text":"Fixed day2month month2day work NA data. Added parameters stat_mean_ci stat_median_ci may return different outputs. Added functionality h_row_counts handle analysis rows NULL cells. Updated LICENCE README new package references. Added error_on_lint: TRUE .lintr.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/main/news/index.html","id":"new-features-0-7-4","dir":"Changelog","previous_headings":"","what":"New features","title":"tern 0.7.4","text":"count_abnormal_by_marked tabulates marked laboratory abnormalities. summarize_patients_exposure_in_cols tabulates patient counts sum exposure across patients.","code":""},{"path":"https://insightsengineering.github.io/tern/main/news/index.html","id":"enhancements-0-7-4","dir":"Changelog","previous_headings":"","what":"Enhancements","title":"tern 0.7.4","text":"Enhanced MMRM-related functions fitting models without arm variable. Updated cox_regression work without covariates. Also case interaction model summary, p-values main effect coefficients longer displayed. Descriptive statistics returned summarize_vars now include quantiles. summarize_vars now accepts control function control_summarize_vars specify details confidence level mean median quantile details. control argument replaces conf_level. Added var_labels show_labels arguments count_occurrences_by_grade. Changed indent argument append_varlabels accept non-negative integer represent indent space defined user. Previous calls Boolean indent integer conversion produce warning.","code":""},{"path":"https://insightsengineering.github.io/tern/main/news/index.html","id":"bug-fixes-0-7-4","dir":"Changelog","previous_headings":"","what":"Bug Fixes","title":"tern 0.7.4","text":"Corrected tabulate_survival_subgroups related survival forest plot functions use total number events, instead observations, default scaling symbol sizes plot. (user might still use total number observations manually wish .) Helper function h_adsl_adlb_merge_using_worst_flag now impute BTOXGR missing visits.","code":""},{"path":"https://insightsengineering.github.io/tern/main/news/index.html","id":"miscellaneous-0-7-4","dir":"Changelog","previous_headings":"","what":"Miscellaneous","title":"tern 0.7.4","text":"Deleted count_abnormal_by_worst_grade_by_baseline related statistic analysis functions simpler design create lab abnormality tables. Switched data examples use scda instead random.cdisc.data package.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/main/news/index.html","id":"new-features-0-7-3","dir":"Changelog","previous_headings":"","what":"New Features","title":"tern 0.7.3","text":"Added Subgroup Treatment Effect Pattern (STEP) model fitting functions fit_rsp_step fit_survival_step, corresponding tidy method tidy.step well graph function g_step. Added new layout function compare_vars compares variables different types columns produces p-value comparison reference column. Function built top summarize_vars functionality. cut_quantile_bins cuts numeric vector quantile bins. fct_collapse_only collapses levels factor keeps order provided. fct_explicit_na_if inserts explicit missings factor based condition. range_noinf kind wrapper function base::range. returns c(NA, NA) instead c(-Inf, Inf) zero-length data.","code":""},{"path":"https://insightsengineering.github.io/tern/main/news/index.html","id":"enhancements-0-7-3","dir":"Changelog","previous_headings":"","what":"Enhancements","title":"tern 0.7.3","text":"Cox regression via fit_coxreg_univar fit_coxreg_multivar now also possible without treatment arm. univariate case means fits separate univariate models provided covariates tabulation corresponding effect estimates can later occur. Added fraction result returned s_count_occurrences. contains list numerators denominators one element per occurrence. Updated sum_num_patients count_occurrences result unique count_fraction return (0, 0) input empty. Added new argument groups_lists extract_survival_subgroups, extract_rsp_subgroups associated helper functions allows group factor levels subgroup variables manually defined groups, enhancing flexibility resulting forest graphs. Forest graph function g_forest now extracts default arguments attributes input table produced tabulate_rsp_subgroups tabulate_survival_subgroups user manually anymore. Remove arm variable name arm labels plot legend annotation tables. Show symbol used mark censored cases match order arm variable factor levels legend. Display hazard ratio confidence interval two decimal places. Updated default position hazard ratio table stay left bottom corner x-axis. Use arm value strata name treatment arm variable single level. Updated s_surv_time function use newly created function range_noinf instead base::range. New argument no_fillin_visits added h_adsl_adlb_merge_using_worst_flag specify excluded visits post-baseline worst toxicity grade output. Improved h_adsl_adlb_merge_using_worst_flag include variables shared adsl adlb, along PARAM, PARAMCD, ATOXGR, BTOXGR optionally AVISIT, AVISITN by_visit = TRUE. Prior output contained USUBJID, ARMCD, PARAMCD, ATOXGR, BTOXGR.","code":""},{"path":"https://insightsengineering.github.io/tern/main/news/index.html","id":"bug-fixes-0-7-3","dir":"Changelog","previous_headings":"","what":"Bug Fixes","title":"tern 0.7.3","text":"Fix bug s_surv_timepoint cases zero patients risk. Modified stat_median_ci function passing empty var empty name, row names contain missing values error show.","code":""},{"path":"https://insightsengineering.github.io/tern/main/news/index.html","id":"miscellaneous-0-7-3","dir":"Changelog","previous_headings":"","what":"Miscellaneous","title":"tern 0.7.3","text":"Deprecated s_cox_univariate function, use fit_coxreg_univar function instead. Updated default formats hr hr_ci a_coxph_pairwise median s_surv_time align STREAM. Updated pre-processing code files test-table_ttet01.R test-table_dort01.R make sure analysis variable EVNT1 levels factor defined. Improved error message number levels factor variable data frame expected.","code":""},{"path":"https://insightsengineering.github.io/tern/main/news/index.html","id":"tern-072","dir":"Changelog","previous_headings":"","what":"tern 0.7.2","title":"tern 0.7.2","text":"Fixed column label internal test errors.","code":""},{"path":"https://insightsengineering.github.io/tern/main/news/index.html","id":"tern-071","dir":"Changelog","previous_headings":"","what":"tern 0.7.1","title":"tern 0.7.1","text":"New argument position_surv_med added g_km move position annotation table median survival times. Fixed bug g_km related ignored arguments pch size passed helper function h_ggkm. Updated xticks max_time arguments g_km greater functionality. max_time added argument h_xticks allow . Fixed bug prop_diff_cmh led NaN weighted proportion difference estimates missing confidence intervals. change, including patients one treatment arm least one stratum estimation lead numeric results. Fixed bug prop_cmh giving error case least one stratum containing less two observations. New argument n_events added estimate_incidence_rate. New argument denom added count_occurrences. New arguments yval ci_ribbon added g_km. Add new individual patient plot function g_ipp along helpers h_g_ipp h_set_nest_theme. Fixed bug count_patients_with_events, now shows zero counts without percentage. Fixed bug get_mmrm_lsmeans allow MMRM analysis 3000 observations. Updated stat_mean_ci stat_median_ci handle edge cases number elements input series equal 1. cases, NA_real_ now returned, instead NA +/-Inf confidence interval (CI) estimates. Rename n_lim argument stat_mean_ci n_min better reflect desired meaning.","code":""},{"path":"https://insightsengineering.github.io/tern/main/news/index.html","id":"tern-070","dir":"Changelog","previous_headings":"","what":"tern 0.7.0","title":"tern 0.7.0","text":"version tern introduces major rewriting tern due change layout based tabulation rtables. tern now build tables directly anymore, instead provides analysis functions build tables, see examples. * Counting patients abnormal values post-baseline count_abnormal. * Counting patients graded abnormal values count_abnormal_by_worst_grade. * Counting patients abnormal values baseline status count_abnormal_by_baseline. * Counting patients missed doses s_count_missed_doses count_missed_doses. * Counting patients event flags count_patients_with_event count_patients_with_flags. * Summarizing variables summarize_vars (supports numeric, factor, character logical variables). Note factors need NAs converted na_level use. * Summarizing change baseline summarize_change. * Summarizing variables columns summarize_colvars. * Estimating difference responder proportions estimate_proportion_diff. * Estimating difference Odds Ratio estimate_odds_ratio. * Testing difference responder proportions test_proportion_diff. * Estimating responder proportion level factor estimate_multinomial_response. * Fitting tabulating results Cox regressions fit_coxreg_univar, fit_coxreg_multivar summarize_coxreg, respectively. * Pruning occurrence tables (tables counts fractions) flexible rules, see ?prune_occurrences details. * Sorting occurrence tables using different options, see ?score_occurrences details. * Fitting tabulating MMRM models fit_mmrm .rtable summarize_lsmeans, see ?tabulate_mmrm details. * Counting number unique non-unique patients summarize_num_patients. * Counting occurrences count_occurrences. * Counting occurrences grade summarize_occurrences_by_grade count_occurrences_by_grade. * Counting patients events columns summarize_patients_events_in_cols. * Tabulating binary outcome response subgroup extract_rsp_subgroups tabulate_rsp_subgroups. * Tabulating survival duration subgroup extract_survival_subgroups tabulate_survival_subgroups.","code":""},{"path":"https://insightsengineering.github.io/tern/main/news/index.html","id":"tern-069","dir":"Changelog","previous_headings":"","what":"tern 0.6.9","title":"tern 0.6.9","text":"Removing used imports.","code":""},{"path":"https://insightsengineering.github.io/tern/main/news/index.html","id":"tern-068","dir":"Changelog","previous_headings":"","what":"tern 0.6.8","title":"tern 0.6.8","text":"Improved handling missing data aggregation functions: a_mean_sd, a_median, a_n_true_and_freq, a_count, a_q1q3, a_iqr, a_range. New default p-value method s_test_proportion_diff: Chi-Squared Test Schouten Correction. Add new function t_contingency contingency tables. Renamed class splitText dynamicSplitText resolve name conflict package ggpubr. Add rreplace_format tabulation post-processing. Add new tern function t_ancova create ANCOVA tables, well corresponding elementary table function t_el_ancova summary function s_ancova. Add new tern function s_odds_ratio estimate Odds Ratio response categories, well corresponding elementary table function t_el_odds_ratio. Added new CI methods (agresti-coull, jeffreys) s_proportion. Added new CI methods anderson-hauck newcombe s_proportion_diff. Added new p-value methods (Fisher’s Exact, Chi-Squared Test Schouten Correction) s_test_proportion_diff. binary summary table function t_binary_outcome takes now lists (instead character vectors) specified helper function control_binary_comparison arguments strat_analysis unstrat_analysis. Odds Ratio estimates CIs now removable included default, similarly subsections arm comparison analyses. Also added argument rsp_multinomial. Add new table function t_el_multinomial_proportion. Add new table function t_abn_shift. Add new MMRM analysis function s_mmrm, well corresponding table functions t_mmrm_lsmeans, t_mmrm_cov, t_mmrm_diagnostic, t_mmrm_fixed, plot functions g_mmrm_lsmeans, g_mmrm_diagnostic. results match SAS results (numeric precision). Deprecated old MMRM functions a_mmrm t_mmrm (give deprecation warning still work) remove next release. reason results functions don’t match SAS results. Fix bug g_km related numbers patients risk table correct numbers integer time--event variable inputs.","code":""},{"path":"https://insightsengineering.github.io/tern/main/news/index.html","id":"tern-067","dir":"Changelog","previous_headings":"","what":"tern 0.6.7","title":"tern 0.6.7","text":"functions row_by argument, inputs longer require use nested_by. Add stat_mean_ci stat_median_ci error bars ggplot2. Add new tern function t_coxreg single interface diverse cox regression types. Add compound table binary endpoint: t_binary_endpoint elementary functions: t_el_proportion, t_el_proportion_diff t_el_test_proportion_diff. supporting summary functions added : s_proportion, s_adj_proportion_diff, s_proportion_diff s_test_proportion_diff. Added new tern function t_events_patyear create event table adjusted person-years. Added new tern function t_abnormality elementary table function t_el_abnormality. Removed grade_levels argument t_events_term_grade_id functions. Post-processing reordering leaves table tree creates different ordering rows required. Creating helper function occur later time. Added prune_zero_rows argument t_events_per_term_grade_id t_max_grade_per_id show rows zeros can clutter visualization Shiny app make slower. Fixed position (N=xx) t_summary_by output summarizing numeric columns parallel compare_in_header. Rename t_coxph t_coxph_pairwise reflect model process, add details documentation. Remove test.nest dependency. Keep column labels splitting data tree.","code":""},{"path":"https://insightsengineering.github.io/tern/main/news/index.html","id":"tern-066","dir":"Changelog","previous_headings":"","what":"tern 0.6.6","title":"tern 0.6.6","text":"Remove test.nest dependency.","code":""},{"path":"https://insightsengineering.github.io/tern/main/news/index.html","id":"tern-065","dir":"Changelog","previous_headings":"","what":"tern 0.6.5","title":"tern 0.6.5","text":"Change default option denominator N t_summary. Fix IQR bug: IQR Q3 minus Q1. Add new function t_logistic multi-variable logistic regression table. Add new function df_explicit_na replace NA explicit values. Added possibility t_tte specify confidence level independent survfit, coxph, ztest, see manual. Fixed bug t_rsp showing p-value, odds ratio CIs strata_data NULL. Added stratified analysis t_forest_rsp t_forest_tte, footnotes g_forest. Added footnotes, footnotes<- add_footnotes<- functions deal footnotes. Added argument conf_int confidence interval level t_el_forest_rps, t_forest_rsp, t_el_forest_tte, t_forest_tte. Added argument col_symbol_size g_forest control relative size symbols used plot. Added s_coxph_pairwise function perform pairwise testing, used t_tte t_coxph. Added methods t_count_true replacing t_summary_true. Updated t_count_unique create analysis subsets, added t_el_count_unique vectors. Fixed bug t_events_term_id table sort order decreasing frequency instead alphabetical. Added function color_palette new nest color palette.","code":""},{"path":"https://insightsengineering.github.io/tern/main/news/index.html","id":"tern-064","dir":"Changelog","previous_headings":"","what":"tern 0.6.4","title":"tern 0.6.4","text":"Refactored renaming functions utils.nest. Added event_type argument t_events_per_term_grade_id. Added one/two-arm t-test functions. Improvements t_summary_by. Internal code refactoring.","code":""},{"path":"https://insightsengineering.github.io/tern/main/news/index.html","id":"tern-063","dir":"Changelog","previous_headings":"","what":"tern 0.6.3","title":"tern 0.6.3","text":"related tree functions see reference trees. Moved label functions rtables. Deleted keys keys<- functions. Exported tabulate_pairwise. get_N, col_N_add_total, check_id. na_as_level. as_factor_keep_attributes. r_by. Disposition elementary table t_el_disposition. t_el_forest_tte, t_el_forest_rsp. Added table_tree argument returns node object. Added f_numeric choose statistics calculate. denominator now also allows omit wanting omit percentages. Renamed row_by. Changed functionality group_data using row_by_list. Removed na_omit_group. Removed indent argument, use indent function rtables. instead","code":""},{"path":"https://insightsengineering.github.io/tern/main/news/index.html","id":"tern-062","dir":"Changelog","previous_headings":"","what":"tern 0.6.2","title":"tern 0.6.2","text":"Use cached data random.cdisc.data speed testing. Added t_summary.Date method. Added save_join.","code":""},{"path":"https://insightsengineering.github.io/tern/main/news/index.html","id":"tern-061","dir":"Changelog","previous_headings":"","what":"tern 0.6.1","title":"tern 0.6.1","text":"Fixed colors Kaplan-Meier Plot Changed width_row.names argument g_forest function width_row_names. Changed censor.show argument g_km function censor_show. Changed col.legend.title argument g_waterfall function col_legend_title. Changed na.rm argument t_count_unique function na_rm. Changed row.name argument t_count_unique function row_name. Changed na.omit.group argument t_forest_rsp function na_omit_group. Changed na.omit.group argument t_forest_tte function na_omit_group. Changed row.name.TRUE row.name.FALSE arguments t_summary.logical row_name_true row_name_false respectively. Rename splotTextGrob split_text_grob. Fix examples. Refactor internal functions code.","code":""},{"path":"https://insightsengineering.github.io/tern/main/news/index.html","id":"tern-060","dir":"Changelog","previous_headings":"","what":"tern 0.6.0","title":"tern 0.6.0","text":"Removed functions addTable, t_summarize_by_visit, t_summarize_variables. Added t_summary_by function. Refactor g_km function, renamed kmGrob kmCurveGrob. Refactor t_events_* family functions. Updated examples.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/main/news/index.html","id":"new-tlgs-0-5-0-3","dir":"Changelog","previous_headings":"","what":"New TLGs","title":"tern 0.5.0.3","text":"t_summary methods data.frame, numeric, logical, character, factor, Date objects. t_events_per_term_id, t_events_per_term_grade_id: Adverse Events & Concomitant Treatment Tables. t_max_grade_per_id, t_count_unique, t_events_summary elementary tables used Adverse Events & Concomitant Treatment Tables. g_waterfall: Horizontal Waterfall Plot.","code":""},{"path":"https://insightsengineering.github.io/tern/main/news/index.html","id":"new-helper-functions-0-5-0-3","dir":"Changelog","previous_headings":"","what":"New Helper Functions","title":"tern 0.5.0.3","text":"decorate_grob, decorate_grob_set, decorate_grob_factory, splitTextGrob. stack_grobs, arrange_grobs, draw_grob.","code":""},{"path":"https://insightsengineering.github.io/tern/main/news/index.html","id":"tlg-changes-0-5-0-3","dir":"Changelog","previous_headings":"","what":"TLG changes","title":"tern 0.5.0.3","text":"t_tte now shows two rows ranges event censored times, respectively. g_km works one arm survfit objects. forest plot functions, added formatting display extreme values “>999.9”. t_summarise_variables uses now n instead N denominator calculating percentages factors default. t_rsp now works response values TRUE FALSE.","code":""},{"path":"https://insightsengineering.github.io/tern/main/news/index.html","id":"deprecated-functions-0-5-0-3","dir":"Changelog","previous_headings":"","what":"Deprecated Functions","title":"tern 0.5.0.3","text":"Deprecated t_summarize_variables t_summary powerful. Replacing t_summarize_by_visit t_summary_by occur upcoming release.","code":""},{"path":"https://insightsengineering.github.io/tern/main/news/index.html","id":"tern-050","dir":"Changelog","previous_headings":"","what":"tern 0.5.0","title":"tern 0.5.0","text":"First version harmonized analysis functions names arguments.","code":""}]