From 16a3b1111cc6d63d211ae266fecbd7af340cd8bb Mon Sep 17 00:00:00 2001
From: Emily de la Rua <emily.de_la_rua@contractors.roche.com>
Date: Thu, 2 Nov 2023 17:00:06 -0400
Subject: [PATCH 01/16] Add tern_default_stats, improve documentation

---
 R/utils_default_stats_formats_labels.R | 154 +++++++++++++++++++------
 man/default_stats_formats_labels.Rd    |  56 +++++----
 2 files changed, 151 insertions(+), 59 deletions(-)

diff --git a/R/utils_default_stats_formats_labels.R b/R/utils_default_stats_formats_labels.R
index 5adda079fa..88d7aa8c5a 100644
--- a/R/utils_default_stats_formats_labels.R
+++ b/R/utils_default_stats_formats_labels.R
@@ -1,13 +1,11 @@
-#' Defaults for statistical method names and their associated formats & labels
+#' Get default statistical methods and their associated formats, labels, and indent modifiers
 #'
 #' @description `r lifecycle::badge("experimental")`
 #'
 #' Utility functions to get valid statistic methods for different method groups
-#' (`.stats`) and their associated formats (`.formats`) and labels (`.labels`). 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.
-#'
-#' @param stats (`character`)\cr statistical methods to get defaults formats or labels for.
+#' (`.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.
 #'
 #' @details
 #' Current choices for `type` are `counts` and `numeric` for [analyze_vars()] and affect `get_stats()`.
@@ -19,18 +17,18 @@
 #' @name default_stats_formats_labels
 NULL
 
-#' @describeIn default_stats_formats_labels Get defaults statistical methods for different
-#'   groups of methods.
+#' @describeIn default_stats_formats_labels Get statistics available for a given method
+#'   group (analyze function).
 #'
-#' @param method_groups (`character`)\cr indicates the group of statistical methods that
-#'   we need the defaults from. A character vector can be used to collect more than one group of statistical
-#'   methods.
-#' @param stats_in (`character`)\cr desired stats to be picked out from the selected method group.
-#' @param add_pval (`flag`)\cr should `"pval"` or `"pval_counts"` (if `method_groups` contains
+#' @param method_groups (`character`)\cr indicates the statistical method group (`tern` analyze function)
+#'   to retrieve default statistics for. A character vector can be used to specify more than one statistical
+#'   method group.
+#' @param stats_in (`character`)\cr statistics to retrieve for the selected method group.
+#' @param add_pval (`flag`)\cr should `"pval"` (or `"pval_counts"` if `method_groups` contains
 #'   `"analyze_vars_counts"`) be added to the statistical methods?
 #'
 #' @return
-#' * `get_stats()` returns a character vector with all default statistical methods.
+#' * `get_stats()` returns a `character` vector of statistical methods.
 #'
 #' @examples
 #' # analyze_vars is numeric
@@ -67,19 +65,10 @@ get_stats <- function(method_groups = "analyze_vars_numeric", stats_in = NULL, a
   # Loop for multiple method groups
   for (mgi in method_groups) {
     # Main switcher
-    out_tmp <- switch(mgi,
-      "count_occurrences" = c("count", "count_fraction", "count_fraction_fixed_dp", "fraction"),
-      "summarize_num_patients" = c("unique", "nonunique", "unique_count"),
-      "analyze_vars_counts" = c("n", "count", "count_fraction", "n_blq"),
-      "analyze_vars_numeric" = c(
-        "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"
-      ),
-      stop(
-        "The selected method group (", mgi, ") has no default statistical method."
-      )
+    out_tmp <- switch(
+      mgi,
+      tern_default_stats,
+      stop("The selected method group (", mgi, ") has no default statistical method.")
     )
     out <- unique(c(out, out_tmp))
   }
@@ -131,14 +120,14 @@ get_stats <- function(method_groups = "analyze_vars_numeric", stats_in = NULL, a
   out
 }
 
-#' @describeIn default_stats_formats_labels Get formats from vector of statistical methods. If not
-#'   present `NULL` is returned.
+#' @describeIn default_stats_formats_labels Get formats corresponding to a list of statistics.
 #'
 #' @param formats_in (named `vector`) \cr inserted formats to replace defaults. It can be a
 #'   character vector from [formatters::list_valid_format_labels()] or a custom format function.
 #'
 #' @return
-#' * `get_formats_from_stats()` returns a named list of formats, they being a value from
+#' * `get_formats_from_stats()` returns a named vector of formats (if present in either
+#'   `tern_default_formats` or `formats_in`, otherwise `NULL`). Values can be taken from
 #'   [formatters::list_valid_format_labels()] or a custom function (e.g. [formatting_functions]).
 #'
 #' @note Formats in `tern` and `rtables` can be functions that take in the table cell value and
@@ -187,9 +176,9 @@ get_formats_from_stats <- function(stats, formats_in = NULL) {
   out
 }
 
-#' @describeIn default_stats_formats_labels Get labels from vector of statistical methods.
+#' @describeIn default_stats_formats_labels Get labels corresponding to a list of statistics.
 #'
-#' @param labels_in (named `vector`)\cr inserted labels to replace defaults.
+#' @param labels_in (named `vector` of `character`)\cr inserted labels to replace defaults.
 #' @param row_nms (`character`)\cr row names. Levels of a `factor` or `character` variable, each
 #'   of which the statistics in `.stats` 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
@@ -197,8 +186,8 @@ get_formats_from_stats <- function(stats, formats_in = NULL) {
 #'   variable names if rows correspond to different variables instead of levels. Defaults to `NULL`.
 #'
 #' @return
-#' * `get_labels_from_stats()` returns a named character vector of default labels (if present
-#'   otherwise `NULL`).
+#' * `get_labels_from_stats()` returns a named `character` vector of labels (if present in either
+#'   `tern_default_labels` or `labels_in`, otherwise `NULL`).
 #'
 #' @examples
 #' # Defaults labels
@@ -306,7 +295,102 @@ get_indents_from_stats <- function(stats, indents_in = NULL, row_nms = NULL) {
   out
 }
 
-#' @describeIn default_stats_formats_labels Named list of default formats for `tern`.
+#' Update Labels According to Control Specifications
+#'
+#' @description `r lifecycle::badge("stable")`
+#'
+#' 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`.
+#'
+#' @param labels_default (named `vector` of `character`)\cr a named vector of statistic labels to modify
+#'   according to the control specifications. Labels that are explicitly defined in `labels_custom` will
+#'   not be affected.
+#' @param labels_custom (named `vector` of `character`)\cr named vector of labels that are customized by
+#'   the user and should not be affected by `control`.
+#' @param control (named `list`)\cr list of control parameters to apply to adjust default labels.
+#'
+#' @return A named character vector of labels with control specifications applied to relevant labels.
+#'
+#' @examples
+#' 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_apply_control(control = control)
+#'
+labels_apply_control <- function(labels_default, control, labels_custom = NULL) {
+  if ("conf_level" %in% names(control)) {
+    labels_default <- sapply(
+      names(labels_default),
+      function(x) {
+        if (!x %in% names(labels_custom)) {
+          gsub(labels_default[[x]], pattern = "[0-9]+% CI", replacement = f_conf_level(control[["conf_level"]]))
+        } else {
+          labels_default[[x]]
+        }
+      }
+    )
+  }
+  if ("quantiles" %in% names(control) && !"quantiles" %in% names(labels_custom)) {
+    labels_default["quantiles"] <- gsub(
+      "[0-9]+% and [0-9]+", paste0(control[["quantiles"]][1] * 100, "% and ", control[["quantiles"]][2] * 100, ""),
+      labels_default["quantiles"]
+    )
+  }
+  if ("test_mean" %in% names(control) && !"mean_pval" %in% names(labels_custom)) {
+    labels_default["mean_pval"] <- gsub(
+      "p-value \\(H0: mean = [0-9\\.]+\\)", f_pval(control[["test_mean"]]), labels_default["mean_pval"]
+    )
+  }
+
+  labels_default
+}
+
+#' @describeIn default_stats_formats_labels Named list of available statistics by method group for `tern`.
+#'
+#' @format
+#' * `tern_default_stats` is a named list of available statistics, with each element
+#'   named for their corresponding statistical method group.
+#'
+#' @export
+tern_default_stats <- list(
+  abnormal = c("fraction"),
+  abnormal_by_baseline = c("fraction"),
+  abnormal_by_marked = c("count_fraction"),
+  abnormal_by_worst_grade = c("count_fraction"),
+  abnormal_by_worst_grade_worsen = c("fraction"),
+  analyze_patients_exposure_in_cols = c("n_patients", "sum_exposure"),
+  analyze_vars_counts = c("n", "count", "count_fraction", "n_blq"),
+  analyze_vars_numeric = c(
+    "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"
+  ),
+  count_cumulative = c("count_fraction"),
+  count_missed_doses = c("n", "count_fraction"),
+  count_occurrences = c("count", "count_fraction", "count_fraction_fixed_dp", "fraction"),
+  count_occurrences_by_grade = c("count_fraction"),
+  count_patients_with_event = c("n", "count", "count_fraction", "n_blq"),
+  count_patients_with_flags = c("n", "count", "count_fraction", "n_blq"),
+  count_values = c("n", "count", "count_fraction", "n_blq"),
+  coxph_pairwise = c("pvalue", "hr", "hr_ci", "n_tot", "n_tot_events"),
+  estimate_incidence_rate = c("person_years", "n_events", "rate", "rate_ci"),
+  estimate_multinomial_response = c("n_prop", "prop_ci"),
+  estimate_odds_ratio = c("or_ci", "n_tot"),
+  estimate_proportion = c("n_prop", "prop_ci"),
+  estimate_proportion_diff = c("diff", "diff_ci"),
+  summarize_ancova = c("n", "lsmean", "lsmean_diff", "lsmean_diff_ci", "pval"),
+  summarize_coxreg = c("n", "hr", "ci", "pval", "pval_inter"),
+  summarize_glm_count = c("n", "rate", "rate_ci", "rate_ratio", "rate_ratio_ci", "pval"),
+  summarize_num_patients = c("unique", "nonunique", "unique_count"),
+  summarize_patients_events_in_cols = c("unique", "all"),
+  surv_time = c("median", "median_ci", "quantiles", "range_censor", "range_event", "range"),
+  surv_timepoint = c("pt_at_risk", "event_free_rate", "rate_se", "rate_ci", "rate_diff", "rate_diff_ci", "ztest_pval"),
+  test_proportion_diff = c("pval")
+)
+
+#' @describeIn default_stats_formats_labels Named vector of default formats for `tern`.
+#'
 #' @format
 #' * `tern_default_formats` is a list of available formats, named after their relevant
 #'   statistic.
diff --git a/man/default_stats_formats_labels.Rd b/man/default_stats_formats_labels.Rd
index 84997cbde5..ab40c29664 100644
--- a/man/default_stats_formats_labels.Rd
+++ b/man/default_stats_formats_labels.Rd
@@ -7,16 +7,22 @@
 \alias{get_formats_from_stats}
 \alias{get_labels_from_stats}
 \alias{get_indents_from_stats}
+\alias{tern_default_stats}
 \alias{tern_default_formats}
 \alias{tern_default_labels}
 \alias{summary_formats}
 \alias{summary_labels}
 \alias{summary_custom}
-\title{Defaults for statistical method names and their associated formats & labels}
+\title{Get default statistical methods and their associated formats, labels, and indent modifiers}
 \format{
 \itemize{
-\item \code{tern_default_formats} is a list of available formats, named after their relevant
-statistic.
+\item \code{tern_default_stats} is a named list of available statistics, with each element
+named for their corresponding statistical method group.
+}
+
+\itemize{
+\item \code{tern_default_formats} is a named vector of available default formats, with each element
+named for their corresponding statistic.
 }
 
 \itemize{
@@ -37,6 +43,8 @@ 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
@@ -55,21 +63,19 @@ summary_custom(
 )
 }
 \arguments{
-\item{method_groups}{(\code{character})\cr indicates the group of statistical methods that
-we need the defaults from. A character vector can be used to collect more than one group of statistical
-methods.}
+\item{method_groups}{(\code{character})\cr indicates the statistical method group (\code{tern} analyze function)
+to retrieve default statistics for. A character vector can be used to specify more than one statistical
+method group.}
 
-\item{stats_in}{(\code{character})\cr desired stats to be picked out from the selected method group.}
+\item{stats_in}{(\code{character})\cr statistics to retrieve for the selected method group.}
 
-\item{add_pval}{(\code{flag})\cr should \code{"pval"} or \code{"pval_counts"} (if \code{method_groups} contains
+\item{add_pval}{(\code{flag})\cr should \code{"pval"} (or \code{"pval_counts"} if \code{method_groups} contains
 \code{"analyze_vars_counts"}) be added to the statistical methods?}
 
-\item{stats}{(\code{character})\cr statistical methods to get defaults formats or labels for.}
-
 \item{formats_in}{(named \code{vector}) \cr inserted formats to replace defaults. It can be a
 character vector from \code{\link[formatters:list_formats]{formatters::list_valid_format_labels()}} or a custom format function.}
 
-\item{labels_in}{(named \code{vector})\cr inserted labels to replace defaults.}
+\item{labels_in}{(named \code{vector} of \code{character})\cr inserted labels to replace defaults.}
 
 \item{row_nms}{(\code{character})\cr row names. Levels of a \code{factor} or \code{character} variable, each
 of which the statistics in \code{.stats} will be calculated for. If this parameter is set, these
@@ -103,17 +109,18 @@ statistics by setting \code{indent_mods_custom} to a single integer value.}
 }
 \value{
 \itemize{
-\item \code{get_stats()} returns a character vector with all default statistical methods.
+\item \code{get_stats()} returns a \code{character} vector of statistical methods.
 }
 
 \itemize{
-\item \code{get_formats_from_stats()} returns a named list of formats, they being a value from
+\item \code{get_formats_from_stats()} returns a named vector of formats (if present in either
+\code{tern_default_formats} or \code{formats_in}, otherwise \code{NULL}). Values can be taken from
 \code{\link[formatters:list_formats]{formatters::list_valid_format_labels()}} or a custom function (e.g. \link{formatting_functions}).
 }
 
 \itemize{
-\item \code{get_labels_from_stats()} returns a named character vector of default labels (if present
-otherwise \code{NULL}).
+\item \code{get_labels_from_stats()} returns a named \code{character} vector of labels (if present in either
+\code{tern_default_labels} or \code{labels_in}, otherwise \code{NULL}).
 }
 
 \itemize{
@@ -138,26 +145,27 @@ and \code{indent_mods}.
 \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#experimental}{\figure{lifecycle-experimental.svg}{options: alt='[Experimental]'}}}{\strong{[Experimental]}}
 
 Utility functions to get valid statistic methods for different method groups
-(\code{.stats}) and their associated formats (\code{.formats}) and labels (\code{.labels}). This utility
-is used across \code{tern}, but some of its working principles can be seen in \code{\link[=analyze_vars]{analyze_vars()}}.
-See notes to understand why this is experimental.
+(\code{.stats}) and their associated formats (\code{.formats}), labels (\code{.labels}), and indent modifiers
+(\code{.indent_mods}). This utility is used across \code{tern}, but some of its working principles can be
+seen in \code{\link[=analyze_vars]{analyze_vars()}}. See notes to understand why this is experimental.
 }
 \details{
 Current choices for \code{type} are \code{counts} and \code{numeric} for \code{\link[=analyze_vars]{analyze_vars()}} and affect \code{get_stats()}.
 }
 \section{Functions}{
 \itemize{
-\item \code{get_stats()}: Get defaults statistical methods for different
-groups of methods.
+\item \code{get_stats()}: Get statistics available for a given method
+group (analyze function).
 
-\item \code{get_formats_from_stats()}: Get formats from vector of statistical methods. If not
-present \code{NULL} is returned.
+\item \code{get_formats_from_stats()}: Get formats corresponding to a list of statistics.
 
-\item \code{get_labels_from_stats()}: Get labels from vector of statistical methods.
+\item \code{get_labels_from_stats()}: Get labels corresponding to a list of statistics.
 
 \item \code{get_indents_from_stats()}: Format indent modifiers for a given vector/list of statistics.
 
-\item \code{tern_default_formats}: Named list of default formats for \code{tern}.
+\item \code{tern_default_stats}: Named list of available statistics by method group for \code{tern}.
+
+\item \code{tern_default_formats}: Named vector of default formats for \code{tern}.
 
 \item \code{tern_default_labels}: \code{character} vector that contains default labels
 for \code{tern}.

From caef29e215d1c4f304b0908ea289a5dbfa3036cc Mon Sep 17 00:00:00 2001
From: Emily de la Rua <emily.de_la_rua@contractors.roche.com>
Date: Thu, 2 Nov 2023 17:00:24 -0400
Subject: [PATCH 02/16] Update NAMESPACE

---
 NAMESPACE | 1 +
 1 file changed, 1 insertion(+)

diff --git a/NAMESPACE b/NAMESPACE
index c6396b4d69..6bcc4bb4b7 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -287,6 +287,7 @@ export(tabulate_survival_biomarkers)
 export(tabulate_survival_subgroups)
 export(tern_default_formats)
 export(tern_default_labels)
+export(tern_default_stats)
 export(test_proportion_diff)
 export(to_n)
 export(to_string_matrix)

From 6fb59af3b8ff36e62338a707a6b9bc8ad7c6fc42 Mon Sep 17 00:00:00 2001
From: Emily de la Rua <emily.de_la_rua@contractors.roche.com>
Date: Thu, 2 Nov 2023 17:01:47 -0400
Subject: [PATCH 03/16] Remove control function

---
 R/utils_default_stats_formats_labels.R | 51 --------------------------
 1 file changed, 51 deletions(-)

diff --git a/R/utils_default_stats_formats_labels.R b/R/utils_default_stats_formats_labels.R
index 88d7aa8c5a..f311c52323 100644
--- a/R/utils_default_stats_formats_labels.R
+++ b/R/utils_default_stats_formats_labels.R
@@ -295,57 +295,6 @@ get_indents_from_stats <- function(stats, indents_in = NULL, row_nms = NULL) {
   out
 }
 
-#' Update Labels According to Control Specifications
-#'
-#' @description `r lifecycle::badge("stable")`
-#'
-#' 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`.
-#'
-#' @param labels_default (named `vector` of `character`)\cr a named vector of statistic labels to modify
-#'   according to the control specifications. Labels that are explicitly defined in `labels_custom` will
-#'   not be affected.
-#' @param labels_custom (named `vector` of `character`)\cr named vector of labels that are customized by
-#'   the user and should not be affected by `control`.
-#' @param control (named `list`)\cr list of control parameters to apply to adjust default labels.
-#'
-#' @return A named character vector of labels with control specifications applied to relevant labels.
-#'
-#' @examples
-#' 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_apply_control(control = control)
-#'
-labels_apply_control <- function(labels_default, control, labels_custom = NULL) {
-  if ("conf_level" %in% names(control)) {
-    labels_default <- sapply(
-      names(labels_default),
-      function(x) {
-        if (!x %in% names(labels_custom)) {
-          gsub(labels_default[[x]], pattern = "[0-9]+% CI", replacement = f_conf_level(control[["conf_level"]]))
-        } else {
-          labels_default[[x]]
-        }
-      }
-    )
-  }
-  if ("quantiles" %in% names(control) && !"quantiles" %in% names(labels_custom)) {
-    labels_default["quantiles"] <- gsub(
-      "[0-9]+% and [0-9]+", paste0(control[["quantiles"]][1] * 100, "% and ", control[["quantiles"]][2] * 100, ""),
-      labels_default["quantiles"]
-    )
-  }
-  if ("test_mean" %in% names(control) && !"mean_pval" %in% names(labels_custom)) {
-    labels_default["mean_pval"] <- gsub(
-      "p-value \\(H0: mean = [0-9\\.]+\\)", f_pval(control[["test_mean"]]), labels_default["mean_pval"]
-    )
-  }
-
-  labels_default
-}
-
 #' @describeIn default_stats_formats_labels Named list of available statistics by method group for `tern`.
 #'
 #' @format

From 6636eb1792c9f11d8cac308ae2436b67354683c7 Mon Sep 17 00:00:00 2001
From: Emily de la Rua <emily.de_la_rua@contractors.roche.com>
Date: Thu, 2 Nov 2023 18:01:33 -0400
Subject: [PATCH 04/16] Update NEWS

---
 NEWS.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/NEWS.md b/NEWS.md
index bd197f3432..2030b40e85 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -4,6 +4,7 @@
 * Added `ref_group_position` function to place the reference group facet last, first or at a certain position.
 * Added `keep_level_order` split function to retain original order of levels in a split.
 * Added `level_order` split function to reorder manually the levels.
+* Added list containing default statistics for each method group, `tern_default_stats`.
 
 ### Enhancements
 * Added `ref_group_coxph` parameter to `g_km` to specify the reference group used for pairwise Cox-PH calculations when `annot_coxph = TRUE`.

From 2dd73c34e198bef4e6aa5ea44da0dcb3fc9f400d Mon Sep 17 00:00:00 2001
From: Emily de la Rua <emily.de_la_rua@contractors.roche.com>
Date: Thu, 2 Nov 2023 18:08:25 -0400
Subject: [PATCH 05/16] Refactor switcher

---
 R/utils_default_stats_formats_labels.R | 9 ++++-----
 1 file changed, 4 insertions(+), 5 deletions(-)

diff --git a/R/utils_default_stats_formats_labels.R b/R/utils_default_stats_formats_labels.R
index f311c52323..47861a1878 100644
--- a/R/utils_default_stats_formats_labels.R
+++ b/R/utils_default_stats_formats_labels.R
@@ -64,12 +64,11 @@ get_stats <- function(method_groups = "analyze_vars_numeric", stats_in = NULL, a
 
   # Loop for multiple method groups
   for (mgi in method_groups) {
-    # Main switcher
-    out_tmp <- switch(
-      mgi,
-      tern_default_stats,
+    out_tmp <- if (mgi %in% names(tern_default_stats)) {
+      tern_default_stats[[mgi]]
+    } else {
       stop("The selected method group (", mgi, ") has no default statistical method.")
-    )
+    }
     out <- unique(c(out, out_tmp))
   }
 

From 19b7ead7808340137ecc9decec1679fdff644766 Mon Sep 17 00:00:00 2001
From: "27856297+dependabot-preview[bot]@users.noreply.github.com"
 <27856297+dependabot-preview[bot]@users.noreply.github.com>
Date: Thu, 2 Nov 2023 22:12:06 +0000
Subject: [PATCH 06/16] [skip actions] Roxygen Man Pages Auto Update

---
 man/default_stats_formats_labels.Rd | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/man/default_stats_formats_labels.Rd b/man/default_stats_formats_labels.Rd
index ab40c29664..f336c14791 100644
--- a/man/default_stats_formats_labels.Rd
+++ b/man/default_stats_formats_labels.Rd
@@ -21,8 +21,8 @@ named for their corresponding statistical method group.
 }
 
 \itemize{
-\item \code{tern_default_formats} is a named vector of available default formats, with each element
-named for their corresponding statistic.
+\item \code{tern_default_formats} is a list of available formats, named after their relevant
+statistic.
 }
 
 \itemize{

From d30659a585027e6ed42c40c0a0c10fd7676b96a5 Mon Sep 17 00:00:00 2001
From: Emily de la Rua <emily.de_la_rua@contractors.roche.com>
Date: Thu, 2 Nov 2023 18:19:51 -0400
Subject: [PATCH 07/16] Empty commit


From c96d0e916bd0a8916bd3ef29784e4dcd6be50bc7 Mon Sep 17 00:00:00 2001
From: Emily de la Rua <emily.de_la_rua@contractors.roche.com>
Date: Thu, 2 Nov 2023 18:37:13 -0400
Subject: [PATCH 08/16] Fix docs

---
 R/utils_default_stats_formats_labels.R | 2 ++
 man/default_stats_formats_labels.Rd    | 2 ++
 2 files changed, 4 insertions(+)

diff --git a/R/utils_default_stats_formats_labels.R b/R/utils_default_stats_formats_labels.R
index 47861a1878..3c30dcc7bb 100644
--- a/R/utils_default_stats_formats_labels.R
+++ b/R/utils_default_stats_formats_labels.R
@@ -7,6 +7,8 @@
 #' (`.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.
 #'
+#' @param stats (`character`)\cr statistical methods to get defaults for.
+#'
 #' @details
 #' Current choices for `type` are `counts` and `numeric` for [analyze_vars()] and affect `get_stats()`.
 #'
diff --git a/man/default_stats_formats_labels.Rd b/man/default_stats_formats_labels.Rd
index f336c14791..e8dd196eb9 100644
--- a/man/default_stats_formats_labels.Rd
+++ b/man/default_stats_formats_labels.Rd
@@ -72,6 +72,8 @@ method group.}
 \item{add_pval}{(\code{flag})\cr should \code{"pval"} (or \code{"pval_counts"} if \code{method_groups} contains
 \code{"analyze_vars_counts"}) be added to the statistical methods?}
 
+\item{stats}{(\code{character})\cr statistical methods to get defaults for.}
+
 \item{formats_in}{(named \code{vector}) \cr inserted formats to replace defaults. It can be a
 character vector from \code{\link[formatters:list_formats]{formatters::list_valid_format_labels()}} or a custom format function.}
 

From a173ff97cf3298572e1a00dfaa9da34e813b21e0 Mon Sep 17 00:00:00 2001
From: Emily de la Rua <emily.de_la_rua@contractors.roche.com>
Date: Mon, 6 Nov 2023 15:26:05 -0500
Subject: [PATCH 09/16] Add "count_fraction_fixed_dp" for all methods that
 allow "count_fraction"

---
 R/utils_default_stats_formats_labels.R | 18 +++++++++---------
 1 file changed, 9 insertions(+), 9 deletions(-)

diff --git a/R/utils_default_stats_formats_labels.R b/R/utils_default_stats_formats_labels.R
index 3c30dcc7bb..00b72c35bf 100644
--- a/R/utils_default_stats_formats_labels.R
+++ b/R/utils_default_stats_formats_labels.R
@@ -306,23 +306,23 @@ get_indents_from_stats <- function(stats, indents_in = NULL, row_nms = NULL) {
 tern_default_stats <- list(
   abnormal = c("fraction"),
   abnormal_by_baseline = c("fraction"),
-  abnormal_by_marked = c("count_fraction"),
-  abnormal_by_worst_grade = c("count_fraction"),
+  abnormal_by_marked = c("count_fraction", "count_fraction_fixed_dp"),
+  abnormal_by_worst_grade = c("count_fraction", "count_fraction_fixed_dp"),
   abnormal_by_worst_grade_worsen = c("fraction"),
   analyze_patients_exposure_in_cols = c("n_patients", "sum_exposure"),
-  analyze_vars_counts = c("n", "count", "count_fraction", "n_blq"),
+  analyze_vars_counts = c("n", "count", "count_fraction", "count_fraction_fixed_dp", "n_blq"),
   analyze_vars_numeric = c(
     "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"
   ),
-  count_cumulative = c("count_fraction"),
-  count_missed_doses = c("n", "count_fraction"),
+  count_cumulative = c("count_fraction", "count_fraction_fixed_dp"),
+  count_missed_doses = c("n", "count_fraction", "count_fraction_fixed_dp"),
   count_occurrences = c("count", "count_fraction", "count_fraction_fixed_dp", "fraction"),
-  count_occurrences_by_grade = c("count_fraction"),
-  count_patients_with_event = c("n", "count", "count_fraction", "n_blq"),
-  count_patients_with_flags = c("n", "count", "count_fraction", "n_blq"),
-  count_values = c("n", "count", "count_fraction", "n_blq"),
+  count_occurrences_by_grade = c("count_fraction", "count_fraction_fixed_dp"),
+  count_patients_with_event = c("n", "count", "count_fraction", "count_fraction_fixed_dp", "n_blq"),
+  count_patients_with_flags = c("n", "count", "count_fraction", "count_fraction_fixed_dp", "n_blq"),
+  count_values = c("n", "count", "count_fraction", "count_fraction_fixed_dp", "n_blq"),
   coxph_pairwise = c("pvalue", "hr", "hr_ci", "n_tot", "n_tot_events"),
   estimate_incidence_rate = c("person_years", "n_events", "rate", "rate_ci"),
   estimate_multinomial_response = c("n_prop", "prop_ci"),

From 4e81efd55fb6a77a2c811fc3e2cf77f798612575 Mon Sep 17 00:00:00 2001
From: Emily de la Rua <emily.de_la_rua@contractors.roche.com>
Date: Mon, 6 Nov 2023 16:36:16 -0500
Subject: [PATCH 10/16] Deprecate `vars` argument in tabulate functions to
 replace with `.stats`

---
 NEWS.md                           |  1 +
 R/response_biomarkers_subgroups.R | 10 ++++++++--
 R/response_subgroups.R            | 10 ++++++++--
 R/survival_biomarkers_subgroups.R | 10 ++++++++--
 R/survival_duration_subgroups.R   | 10 ++++++++--
 5 files changed, 33 insertions(+), 8 deletions(-)

diff --git a/NEWS.md b/NEWS.md
index 820eaa5ba7..87d9c9a7c0 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -13,6 +13,7 @@
 
 ### Miscellaneous
 * Specified minimal version of package dependencies.
+* Began deprecation of `vars` argument in `tabulate_rsp_biomarkers`, `tabulate_rsp_subgroups`, `tabulate_survival_biomarkers`, and `tabulate_survival_subgroups` and replaced it with the `.stats` argument.
 
 # tern 0.9.2
 
diff --git a/R/response_biomarkers_subgroups.R b/R/response_biomarkers_subgroups.R
index e66fc32f4e..37259a072e 100644
--- a/R/response_biomarkers_subgroups.R
+++ b/R/response_biomarkers_subgroups.R
@@ -8,7 +8,7 @@
 #' @inheritParams argument_convention
 #' @param df (`data.frame`)\cr containing all analysis variables, as returned by
 #'   [extract_rsp_biomarkers()].
-#' @param vars (`character`)\cr the names of statistics to be reported among:
+#' @param .stats (`character`)\cr the names of statistics to be reported among:
 #'   * `n_tot`: Total number of patients per group.
 #'   * `n_rsp`: Total number of responses per group.
 #'   * `prop`: Total response proportion per group.
@@ -67,8 +67,14 @@
 #' @export
 #' @name response_biomarkers_subgroups
 tabulate_rsp_biomarkers <- function(df,
-                                    vars = c("n_tot", "n_rsp", "prop", "or", "ci", "pval"),
+                                    vars = lifecycle::deprecated(),
+                                    .stats = c("n_tot", "n_rsp", "prop", "or", "ci", "pval"),
                                     .indent_mods = 0L) {
+  if (lifecycle::is_present(vars)) {
+    lifecycle::deprecate_warn("0.9.3", "tabulate_rsp_biomarkers(vars)", "tabulate_rsp_biomarkers(.stats)")
+    .stats <- vars
+  }
+
   checkmate::assert_data_frame(df)
   checkmate::assert_character(df$biomarker)
   checkmate::assert_character(df$biomarker_label)
diff --git a/R/response_subgroups.R b/R/response_subgroups.R
index e194b1542d..7ea3c467bc 100644
--- a/R/response_subgroups.R
+++ b/R/response_subgroups.R
@@ -178,7 +178,7 @@ a_response_subgroups <- function(.formats = list(
 #'
 #' @param df (`list`)\cr of data frames containing all analysis variables. List should be
 #'   created using [extract_rsp_subgroups()].
-#' @param vars (`character`)\cr the names of statistics to be reported among:
+#' @param .stats (`character`)\cr the names of statistics to be reported among:
 #'   * `n`: Total number of observations per group.
 #'   * `n_rsp`: Number of responders per group.
 #'   * `prop`: Proportion of responders.
@@ -205,7 +205,13 @@ a_response_subgroups <- function(.formats = list(
 #' @export
 tabulate_rsp_subgroups <- function(lyt,
                                    df,
-                                   vars = c("n_tot", "n", "prop", "or", "ci")) {
+                                   vars = lifecycle::deprecated(),
+                                   .stats = c("n_tot", "n", "prop", "or", "ci")) {
+  if (lifecycle::is_present(vars)) {
+    lifecycle::deprecate_warn("0.9.3", "tabulate_rsp_subgroups(vars)", "tabulate_rsp_subgroups(.stats)")
+    .stats <- vars
+  }
+
   conf_level <- df$or$conf_level[1]
   method <- if ("pval_label" %in% names(df$or)) {
     df$or$pval_label[1]
diff --git a/R/survival_biomarkers_subgroups.R b/R/survival_biomarkers_subgroups.R
index b3bfc67ed7..6bef780835 100644
--- a/R/survival_biomarkers_subgroups.R
+++ b/R/survival_biomarkers_subgroups.R
@@ -172,7 +172,7 @@ extract_survival_biomarkers <- function(variables,
 #'
 #' @param df (`data.frame`)\cr containing all analysis variables, as returned by
 #'   [extract_survival_biomarkers()].
-#' @param vars (`character`)\cr the names of statistics to be reported among:
+#' @param .stats (`character`)\cr the names of statistics to be reported among:
 #'   * `n_tot_events`: Total number of events per group.
 #'   * `n_tot`: Total number of observations per group.
 #'   * `median`: Median survival time.
@@ -207,9 +207,15 @@ extract_survival_biomarkers <- function(variables,
 #'
 #' @export
 tabulate_survival_biomarkers <- function(df,
-                                         vars = c("n_tot", "n_tot_events", "median", "hr", "ci", "pval"),
+                                         vars = lifecycle::deprecated(),
                                          time_unit = NULL,
+                                         .stats = c("n_tot", "n_tot_events", "median", "hr", "ci", "pval"),
                                          .indent_mods = 0L) {
+  if (lifecycle::is_present(vars)) {
+    lifecycle::deprecate_warn("0.9.3", "tabulate_survival_biomarkers(vars)", "tabulate_survival_biomarkers(.stats)")
+    .stats <- vars
+  }
+
   checkmate::assert_data_frame(df)
   checkmate::assert_character(df$biomarker)
   checkmate::assert_character(df$biomarker_label)
diff --git a/R/survival_duration_subgroups.R b/R/survival_duration_subgroups.R
index 4f50bd466c..2a4f2a365d 100644
--- a/R/survival_duration_subgroups.R
+++ b/R/survival_duration_subgroups.R
@@ -212,7 +212,7 @@ a_survival_subgroups <- function(.formats = list( # nolint start
 #'
 #' @param df (`list`)\cr of data frames containing all analysis variables. List should be
 #'   created using [extract_survival_subgroups()].
-#' @param vars (`character`)\cr the name of statistics to be reported among:
+#' @param .stats (`character`)\cr the name of statistics to be reported among:
 #'   * `n_tot_events`: Total number of events per group.
 #'   * `n_events`: Number of events per group.
 #'   * `n_tot`: Total number of observations per group.
@@ -242,9 +242,15 @@ a_survival_subgroups <- function(.formats = list( # nolint start
 #' @export
 tabulate_survival_subgroups <- function(lyt,
                                         df,
-                                        vars = c("n_tot_events", "n_events", "median", "hr", "ci"),
+                                        vars = lifecycle::deprecated(),
                                         time_unit = NULL,
+                                        .stats = c("n_tot_events", "n_events", "median", "hr", "ci"),
                                         na_str = NA_character_) {
+  if (lifecycle::is_present(vars)) {
+    lifecycle::deprecate_warn("0.9.3", "tabulate_survival_subgroups(vars)", "tabulate_survival_subgroups(.stats)")
+    .stats <- vars
+  }
+
   conf_level <- df$hr$conf_level[1]
   method <- df$hr$pval_label[1]
 

From ce083dcc78a1e074609138bd77e850ede8a95548 Mon Sep 17 00:00:00 2001
From: Emily de la Rua <emily.de_la_rua@contractors.roche.com>
Date: Mon, 6 Nov 2023 16:37:29 -0500
Subject: [PATCH 11/16] Add `get_stats` calls to `.stats` param descriptions

---
 R/abnormal.R                            | 2 ++
 R/abnormal_by_baseline.R                | 2 ++
 R/abnormal_by_marked.R                  | 2 ++
 R/abnormal_by_worst_grade.R             | 2 ++
 R/abnormal_by_worst_grade_worsen.R      | 2 ++
 R/analyze_variables.R                   | 4 +++-
 R/count_cumulative.R                    | 2 ++
 R/count_missed_doses.R                  | 2 ++
 R/count_occurrences.R                   | 2 ++
 R/count_occurrences_by_grade.R          | 2 ++
 R/count_patients_events_in_cols.R       | 3 +++
 R/count_patients_with_event.R           | 2 ++
 R/count_patients_with_flags.R           | 2 ++
 R/count_values.R                        | 2 ++
 R/estimate_multinomial_rsp.R            | 2 ++
 R/estimate_proportion.R                 | 2 ++
 R/incidence_rate.R                      | 2 ++
 R/odds_ratio.R                          | 2 ++
 R/prop_diff.R                           | 2 ++
 R/prop_diff_test.R                      | 2 ++
 R/response_biomarkers_subgroups.R       | 2 +-
 R/summarize_ancova.R                    | 2 ++
 R/summarize_change.R                    | 2 ++
 R/summarize_coxreg.R                    | 2 ++
 R/summarize_glm_count.R                 | 2 ++
 R/summarize_num_patients.R              | 2 ++
 R/summarize_patients_exposure_in_cols.R | 2 ++
 R/survival_biomarkers_subgroups.R       | 2 +-
 R/survival_coxph_pairwise.R             | 2 ++
 R/survival_time.R                       | 2 ++
 R/survival_timepoint.R                  | 2 ++
 R/utils_default_stats_formats_labels.R  | 4 ++++
 32 files changed, 66 insertions(+), 3 deletions(-)

diff --git a/R/abnormal.R b/R/abnormal.R
index ec337dd3ee..947fd93d59 100644
--- a/R/abnormal.R
+++ b/R/abnormal.R
@@ -13,6 +13,8 @@
 #' @param abnormal (named `list`)\cr list identifying the abnormal range level(s) in `var`. Defaults to
 #'   `list(Low = "LOW", High = "HIGH")` but you can also group different levels into the named list,
 #'   for example, `abnormal = list(Low = c("LOW", "LOW LOW"), High = c("HIGH", "HIGH HIGH"))`.
+#' @param .stats (`character`)\cr statistics to select for the table. Run `get_stats("abnormal")`
+#'   to see available statistics for this function.
 #'
 #' @note
 #' * `count_abnormal()` only works with a single variable containing multiple abnormal levels.
diff --git a/R/abnormal_by_baseline.R b/R/abnormal_by_baseline.R
index b308a74162..191e1e8bec 100644
--- a/R/abnormal_by_baseline.R
+++ b/R/abnormal_by_baseline.R
@@ -18,6 +18,8 @@
 #'
 #' @inheritParams argument_convention
 #' @param abnormal (`character`)\cr identifying the abnormal range level(s) in `.var`.
+#' @param .stats (`character`)\cr statistics to select for the table. Run `get_stats("abnormal_by_baseline")`
+#'   to see available statistics for this function.
 #'
 #' @note
 #' * `df` should be filtered to include only post-baseline records.
diff --git a/R/abnormal_by_marked.R b/R/abnormal_by_marked.R
index ffcaee38ba..c2bf670215 100644
--- a/R/abnormal_by_marked.R
+++ b/R/abnormal_by_marked.R
@@ -14,6 +14,8 @@
 #' @inheritParams argument_convention
 #' @param category (`list`)\cr with different marked category names for single
 #'   and last or replicated.
+#' @param .stats (`character`)\cr statistics to select for the table. Run `get_stats("abnormal_by_marked")`
+#'   to see available statistics for this function.
 #'
 #' @note `Single, not last` and `Last or replicated` levels are mutually exclusive. If a patient has
 #'   abnormalities that meet both the `Single, not last` and `Last or replicated` criteria, then the
diff --git a/R/abnormal_by_worst_grade.R b/R/abnormal_by_worst_grade.R
index d6f7ee59fc..e4deb22784 100644
--- a/R/abnormal_by_worst_grade.R
+++ b/R/abnormal_by_worst_grade.R
@@ -12,6 +12,8 @@
 #'   * `Any`: Numerator is number of patients with at least one abnormality, which means grade is different from 0.
 #'
 #' @inheritParams argument_convention
+#' @param .stats (`character`)\cr statistics to select for the table. Run `get_stats("abnormal_by_worst_grade")`
+#'   to see available statistics for this function.
 #'
 #' @details The pre-processing steps are crucial when using this function. From the standard lab grade variable
 #'   `ATOXGR`, derive the following two variables:
diff --git a/R/abnormal_by_worst_grade_worsen.R b/R/abnormal_by_worst_grade_worsen.R
index 120dc107a2..8c47944ce7 100644
--- a/R/abnormal_by_worst_grade_worsen.R
+++ b/R/abnormal_by_worst_grade_worsen.R
@@ -5,6 +5,8 @@
 #' Patient count and fraction for laboratory events (worsen from baseline) shift table.
 #'
 #' @inheritParams argument_convention
+#' @param .stats (`character`)\cr statistics to select for the table. Run `get_stats("abnormal_by_worst_grade_worsen")`
+#'   to see all available statistics.
 #'
 #' @seealso Relevant helper functions [h_adlb_worsen()] and [h_worsen_counter()]
 #'
diff --git a/R/analyze_variables.R b/R/analyze_variables.R
index b44e4c16a5..0ca9abee55 100644
--- a/R/analyze_variables.R
+++ b/R/analyze_variables.R
@@ -46,6 +46,9 @@ control_summarize_vars <- control_analyze_vars
 #' functions; in this case [rtables::analyze()].
 #'
 #' @inheritParams argument_convention
+#' @param .stats (`character`)\cr statistics to select for the table. Run `get_stats("analyze_vars_numeric")` to see
+#'   statistics available for numeric variables, and `get_stats("analyze_vars_counts")` for statistics available
+#'   for non-numeric variables.
 #'
 #' @name analyze_variables
 NULL
@@ -454,7 +457,6 @@ s_summary.logical <- function(x,
 #' a_summary(rnorm(10), .N_col = 10, .N_row = 20, .var = "bla")
 #' a_summary(rnorm(10, 5, 1), .ref_group = rnorm(20, -5, 1), .var = "bla", compare = TRUE)
 #'
-
 #' @export
 a_summary <- function(x,
                       .N_col, # nolint
diff --git a/R/count_cumulative.R b/R/count_cumulative.R
index 4f94ba5d86..3928560dab 100644
--- a/R/count_cumulative.R
+++ b/R/count_cumulative.R
@@ -7,6 +7,8 @@
 #'
 #' @inheritParams h_count_cumulative
 #' @inheritParams argument_convention
+#' @param .stats (`character`)\cr statistics to select for the table. Run `get_stats("count_cumulative")`
+#'   to see available statistics for this function.
 #'
 #' @seealso Relevant helper function [h_count_cumulative()], and descriptive function [d_count_cumulative()].
 #'
diff --git a/R/count_missed_doses.R b/R/count_missed_doses.R
index 735acb5460..55f57dcd9f 100644
--- a/R/count_missed_doses.R
+++ b/R/count_missed_doses.R
@@ -6,6 +6,8 @@
 #' mainly the special labels.
 #'
 #' @inheritParams argument_convention
+#' @param .stats (`character`)\cr statistics to select for the table. Run `get_stats("count_missed_doses")`
+#'   to see available statistics for this function.
 #'
 #' @seealso Relevant description function [d_count_missed_doses()].
 #'
diff --git a/R/count_occurrences.R b/R/count_occurrences.R
index 677458f416..09b9873ccd 100644
--- a/R/count_occurrences.R
+++ b/R/count_occurrences.R
@@ -8,6 +8,8 @@
 #' counted only once.
 #'
 #' @inheritParams argument_convention
+#' @param .stats (`character`)\cr statistics to select for the table. Run `get_stats("count_occurrences")`
+#'   to see available statistics for this function.
 #'
 #' @note 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
diff --git a/R/count_occurrences_by_grade.R b/R/count_occurrences_by_grade.R
index 9b67fc7278..785aff4256 100644
--- a/R/count_occurrences_by_grade.R
+++ b/R/count_occurrences_by_grade.R
@@ -10,6 +10,8 @@
 #' @param grade_groups (named `list` of `character`)\cr containing groupings of grades.
 #' @param remove_single (`logical`)\cr `TRUE` 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.
+#' @param .stats (`character`)\cr statistics to select for the table. Run `get_stats("count_occurrences_by_grade")`
+#'   to see available statistics for this function.
 #'
 #' @seealso Relevant helper function [h_append_grade_groups()].
 #'
diff --git a/R/count_patients_events_in_cols.R b/R/count_patients_events_in_cols.R
index 5eb601aaf4..135e0018d4 100644
--- a/R/count_patients_events_in_cols.R
+++ b/R/count_patients_events_in_cols.R
@@ -6,6 +6,9 @@
 #' when a column table layout is required.
 #'
 #' @inheritParams argument_convention
+#' @param .stats (`character`)\cr statistics to select for the table. Run
+#'   `get_stats("summarize_patients_events_in_cols")` to see available statistics for this function, in addition to any
+#'   added using `filters_list`.
 #'
 #' @name count_patients_events_in_cols
 NULL
diff --git a/R/count_patients_with_event.R b/R/count_patients_with_event.R
index 92cc42edba..9b6d1bc91e 100644
--- a/R/count_patients_with_event.R
+++ b/R/count_patients_with_event.R
@@ -5,6 +5,8 @@
 #' The primary analysis variable `.var` denotes the unique patient identifier.
 #'
 #' @inheritParams argument_convention
+#' @param .stats (`character`)\cr statistics to select for the table. Run `get_stats("count_patients_with_event")`
+#'   to see available statistics for this function.
 #'
 #' @seealso [count_patients_with_flags]
 #'
diff --git a/R/count_patients_with_flags.R b/R/count_patients_with_flags.R
index e7580b34cf..1b3edf3354 100644
--- a/R/count_patients_with_flags.R
+++ b/R/count_patients_with_flags.R
@@ -5,6 +5,8 @@
 #' The primary analysis variable `.var` denotes the unique patient identifier.
 #'
 #' @inheritParams argument_convention
+#' @param .stats (`character`)\cr statistics to select for the table. Run `get_stats("count_patients_with_flags")`
+#'   to see available statistics for this function.
 #'
 #' @seealso [count_patients_with_event]
 #'
diff --git a/R/count_values.R b/R/count_values.R
index ebbf8068dd..428e80159a 100644
--- a/R/count_values.R
+++ b/R/count_values.R
@@ -5,6 +5,8 @@
 #' We can count the occurrence of specific values in a variable of interest.
 #'
 #' @inheritParams argument_convention
+#' @param .stats (`character`)\cr statistics to select for the table. Run `get_stats("count_values")`
+#'   to see available statistics for this function.
 #'
 #' @note
 #' * For `factor` variables, `s_count_values` checks whether `values` are all included in the levels of `x`
diff --git a/R/estimate_multinomial_rsp.R b/R/estimate_multinomial_rsp.R
index fb3fafff16..5c003ffd26 100644
--- a/R/estimate_multinomial_rsp.R
+++ b/R/estimate_multinomial_rsp.R
@@ -6,6 +6,8 @@
 #' regarding the level of a factor.
 #'
 #' @inheritParams argument_convention
+#' @param .stats (`character`)\cr statistics to select for the table. Run `get_stats("estimate_multinomial_response")`
+#'   to see available statistics for this function.
 #'
 #' @seealso Relevant description function [d_onco_rsp_label()].
 #'
diff --git a/R/estimate_proportion.R b/R/estimate_proportion.R
index d7d88f1525..8552aaab8d 100644
--- a/R/estimate_proportion.R
+++ b/R/estimate_proportion.R
@@ -5,6 +5,8 @@
 #' Estimate the proportion of responders within a studied population.
 #'
 #' @inheritParams argument_convention
+#' @param .stats (`character`)\cr statistics to select for the table. Run `get_stats("estimate_proportion")`
+#'   to see available statistics for this function.
 #'
 #' @seealso [h_proportions]
 #'
diff --git a/R/incidence_rate.R b/R/incidence_rate.R
index ddf0410ebc..91c8946021 100644
--- a/R/incidence_rate.R
+++ b/R/incidence_rate.R
@@ -15,6 +15,8 @@
 #'     indicating time unit for data input.
 #'   * `num_pt_year` (`numeric`)\cr time unit for desired output (in person-years).
 #' @param n_events (`integer`)\cr number of events observed.
+#' @param .stats (`character`)\cr statistics to select for the table. Run `get_stats("estimate_incidence_rate")`
+#'   to see available statistics for this function.
 #'
 #' @seealso [control_incidence_rate()] and helper functions [h_incidence_rate].
 #'
diff --git a/R/odds_ratio.R b/R/odds_ratio.R
index dac3c1cba7..cc9ea9754f 100644
--- a/R/odds_ratio.R
+++ b/R/odds_ratio.R
@@ -6,6 +6,8 @@
 #' along with a confidence interval.
 #'
 #' @inheritParams argument_convention
+#' @param .stats (`character`)\cr statistics to select for the table. Run `get_stats("estimate_odds_ratio")`
+#'   to see available statistics for this function.
 #'
 #' @details This function uses either logistic regression for unstratified
 #'   analyses, or conditional logistic regression for stratified analyses.
diff --git a/R/prop_diff.R b/R/prop_diff.R
index 27a27c8c06..b82ac4ff1a 100644
--- a/R/prop_diff.R
+++ b/R/prop_diff.R
@@ -3,6 +3,8 @@
 #' @description `r lifecycle::badge("stable")`
 #'
 #' @inheritParams argument_convention
+#' @param .stats (`character`)\cr statistics to select for the table. Run `get_stats("estimate_proportion_diff")`
+#'   to see available statistics for this function.
 #'
 #' @seealso [d_proportion_diff()]
 #'
diff --git a/R/prop_diff_test.R b/R/prop_diff_test.R
index c8b65343f9..2f77dfabd5 100644
--- a/R/prop_diff_test.R
+++ b/R/prop_diff_test.R
@@ -5,6 +5,8 @@
 #' Various tests were implemented to test the difference between two proportions.
 #'
 #' @inheritParams argument_convention
+#' @param .stats (`character`)\cr statistics to select for the table. Run `get_stats("test_proportion_diff")`
+#'   to see available statistics for this function.
 #'
 #' @seealso [h_prop_diff_test]
 #'
diff --git a/R/response_biomarkers_subgroups.R b/R/response_biomarkers_subgroups.R
index 37259a072e..ca87a298b4 100644
--- a/R/response_biomarkers_subgroups.R
+++ b/R/response_biomarkers_subgroups.R
@@ -78,7 +78,7 @@ tabulate_rsp_biomarkers <- function(df,
   checkmate::assert_data_frame(df)
   checkmate::assert_character(df$biomarker)
   checkmate::assert_character(df$biomarker_label)
-  checkmate::assert_subset(vars, c("n_tot", "n_rsp", "prop", "or", "ci", "pval"))
+  checkmate::assert_subset(vars, get_stats("tabulate_rsp_biomarkers"))
 
   df_subs <- split(df, f = df$biomarker)
   tabs <- lapply(df_subs, FUN = function(df_sub) {
diff --git a/R/summarize_ancova.R b/R/summarize_ancova.R
index 8af0627940..6033c88aa9 100644
--- a/R/summarize_ancova.R
+++ b/R/summarize_ancova.R
@@ -6,6 +6,8 @@
 #' multiple timepoints within the same response variable `.var`.
 #'
 #' @inheritParams argument_convention
+#' @param .stats (`character`)\cr statistics to select for the table. Run `get_stats("summarize_ancova")`
+#'   to see available statistics for this function.
 #'
 #' @name summarize_ancova
 NULL
diff --git a/R/summarize_change.R b/R/summarize_change.R
index 0c3d66a217..a57c9a46aa 100644
--- a/R/summarize_change.R
+++ b/R/summarize_change.R
@@ -8,6 +8,8 @@
 #' or the change from baseline values (post-baseline) are then summarized.
 #'
 #' @inheritParams argument_convention
+#' @param .stats (`character`)\cr statistics to select for the table. Run `get_stats("analyze_vars_numeric)`
+#'   to see available statistics for this function.
 #'
 #' @name summarize_change
 NULL
diff --git a/R/summarize_coxreg.R b/R/summarize_coxreg.R
index 0e19cdb554..a0f112c935 100644
--- a/R/summarize_coxreg.R
+++ b/R/summarize_coxreg.R
@@ -5,6 +5,8 @@
 #' Fits a Cox regression model and estimates hazard ratio to describe the effect size in a survival analysis.
 #'
 #' @inheritParams argument_convention
+#' @param .stats (`character`)\cr statistics to select for the table. Run `get_stats("summarize_coxreg")`
+#'   to see available statistics for this function.
 #'
 #' @details Cox models are the most commonly used methods to estimate the magnitude of
 #'   the effect in survival analysis. It assumes proportional hazards: the ratio
diff --git a/R/summarize_glm_count.R b/R/summarize_glm_count.R
index ca6544e950..2d03024d53 100644
--- a/R/summarize_glm_count.R
+++ b/R/summarize_glm_count.R
@@ -6,6 +6,8 @@
 #' This can be used to analyze count and/or frequency data using a linear model.
 #'
 #' @inheritParams argument_convention
+#' @param .stats (`character`)\cr statistics to select for the table. Run `get_stats("summarize_glm_count")`
+#'   to see available statistics for this function.
 #'
 #' @name summarize_glm_count
 NULL
diff --git a/R/summarize_num_patients.R b/R/summarize_num_patients.R
index 8883eb2f1b..01f3644d28 100644
--- a/R/summarize_num_patients.R
+++ b/R/summarize_num_patients.R
@@ -10,6 +10,8 @@
 #'   `nonunique` records.
 #' @param unique_count_suffix (`logical`)\cr should `"(n)"` suffix be added to `unique_count` labels.
 #'   Defaults to `TRUE`.
+#' @param .stats (`character`)\cr statistics to select for the table. Run `get_stats("summarize_num_patients")`
+#'   to see available statistics for this function.
 #'
 #' @name summarize_num_patients
 NULL
diff --git a/R/summarize_patients_exposure_in_cols.R b/R/summarize_patients_exposure_in_cols.R
index d83672db3a..5ad66ba14d 100644
--- a/R/summarize_patients_exposure_in_cols.R
+++ b/R/summarize_patients_exposure_in_cols.R
@@ -6,6 +6,8 @@
 #' when a column table layout is required.
 #'
 #' @inheritParams argument_convention
+#' @param .stats (`character`)\cr statistics to select for the table. Run
+#' `get_stats("analyze_patients_exposure_in_cols")` to see available statistics for this function.
 #'
 #' @name summarize_patients_exposure_in_cols
 NULL
diff --git a/R/survival_biomarkers_subgroups.R b/R/survival_biomarkers_subgroups.R
index 6bef780835..c14184b5ff 100644
--- a/R/survival_biomarkers_subgroups.R
+++ b/R/survival_biomarkers_subgroups.R
@@ -219,7 +219,7 @@ tabulate_survival_biomarkers <- function(df,
   checkmate::assert_data_frame(df)
   checkmate::assert_character(df$biomarker)
   checkmate::assert_character(df$biomarker_label)
-  checkmate::assert_subset(vars, c("n_tot", "n_tot_events", "median", "hr", "ci", "pval"))
+  checkmate::assert_subset(vars, get_stats("tabulate_survival_biomarkers"))
 
   df_subs <- split(df, f = df$biomarker)
   tabs <- lapply(df_subs, FUN = function(df_sub) {
diff --git a/R/survival_coxph_pairwise.R b/R/survival_coxph_pairwise.R
index bdf9092fe1..3c4b682eaa 100644
--- a/R/survival_coxph_pairwise.R
+++ b/R/survival_coxph_pairwise.R
@@ -14,6 +14,8 @@
 #'   * `ties` (`string`)\cr specifying the method for tie handling. Default is `"efron"`,
 #'     can also be set to `"breslow"` or `"exact"`. See more in [survival::coxph()]
 #'   * `conf_level` (`proportion`)\cr confidence level of the interval for HR.
+#' @param .stats (`character`)\cr statistics to select for the table. Run `get_stats("coxph_pairwise")`
+#'   to see available statistics for this function.
 #'
 #' @name survival_coxph_pairwise
 NULL
diff --git a/R/survival_time.R b/R/survival_time.R
index e7d96d1d47..7457e5eab2 100644
--- a/R/survival_time.R
+++ b/R/survival_time.R
@@ -12,6 +12,8 @@
 #'   * `conf_type` (`string`)\cr confidence interval type. Options are "plain" (default), "log", or "log-log",
 #'     see more in [survival::survfit()]. Note option "none" is not supported.
 #'   * `quantiles` (`numeric`)\cr vector of length two to specify the quantiles of survival time.
+#' @param .stats (`character`)\cr statistics to select for the table. Run `get_stats("surv_time")`
+#'   to see available statistics for this function.
 #'
 #' @name survival_time
 NULL
diff --git a/R/survival_timepoint.R b/R/survival_timepoint.R
index e32fda1113..4f42239d2f 100644
--- a/R/survival_timepoint.R
+++ b/R/survival_timepoint.R
@@ -13,6 +13,8 @@
 #'   * `conf_type` (`string`)\cr confidence interval type. Options are "plain" (default), "log", "log-log",
 #'     see more in [survival::survfit()]. Note option "none" is no longer supported.
 #'   * `time_point` (`number`)\cr survival time point of interest.
+#' @param .stats (`character`)\cr statistics to select for the table. Run `get_stats("surv_timepoint")`
+#'   to see available statistics for this function.
 #'
 #' @name survival_timepoint
 NULL
diff --git a/R/utils_default_stats_formats_labels.R b/R/utils_default_stats_formats_labels.R
index 00b72c35bf..02415faad6 100644
--- a/R/utils_default_stats_formats_labels.R
+++ b/R/utils_default_stats_formats_labels.R
@@ -336,6 +336,10 @@ tern_default_stats <- list(
   summarize_patients_events_in_cols = c("unique", "all"),
   surv_time = c("median", "median_ci", "quantiles", "range_censor", "range_event", "range"),
   surv_timepoint = c("pt_at_risk", "event_free_rate", "rate_se", "rate_ci", "rate_diff", "rate_diff_ci", "ztest_pval"),
+  tabulate_rsp_biomarkers = c("n_tot", "n_rsp", "prop", "or", "ci", "pval"),
+  tabulate_rsp_subgroups = c("n", "n_rsp", "prop", "n_tot", "or", "ci", "pval"),
+  tabulate_survival_biomarkers = c("n_tot", "n_tot_events", "median", "hr", "ci", "pval"),
+  tabulate_survival_subgroups = c("n_tot_events", "n_events", "n_tot", "n", "median", "hr", "ci", "pval"),
   test_proportion_diff = c("pval")
 )
 

From 42d695b9ee18fc2cbee4002e25b727b67c59f3af Mon Sep 17 00:00:00 2001
From: Emily de la Rua <emily.de_la_rua@contractors.roche.com>
Date: Mon, 6 Nov 2023 16:40:29 -0500
Subject: [PATCH 12/16] Update docs

---
 R/compare_variables.R                      |  3 +++
 man/abnormal.Rd                            |  3 ++-
 man/abnormal_by_baseline.Rd                |  3 ++-
 man/abnormal_by_marked.Rd                  |  3 ++-
 man/abnormal_by_worst_grade.Rd             |  3 ++-
 man/abnormal_by_worst_grade_worsen.Rd      |  3 ++-
 man/analyze_variables.Rd                   |  4 +++-
 man/compare_variables.Rd                   |  4 +++-
 man/count_cumulative.Rd                    |  3 ++-
 man/count_missed_doses.Rd                  |  3 ++-
 man/count_occurrences.Rd                   |  3 ++-
 man/count_occurrences_by_grade.Rd          |  3 ++-
 man/count_patients_events_in_cols.Rd       |  4 +++-
 man/count_patients_with_event.Rd           |  3 ++-
 man/count_patients_with_flags.Rd           |  3 ++-
 man/count_values_funs.Rd                   |  3 ++-
 man/d_survival_subgroups_colvars.Rd        | 14 +-------------
 man/estimate_multinomial_rsp.Rd            |  3 ++-
 man/estimate_proportions.Rd                |  3 ++-
 man/h_response_biomarkers_subgroups.Rd     | 11 +----------
 man/h_survival_biomarkers_subgroups.Rd     | 11 +----------
 man/incidence_rate.Rd                      |  3 ++-
 man/odds_ratio.Rd                          |  3 ++-
 man/prop_diff.Rd                           |  3 ++-
 man/prop_diff_test.Rd                      |  3 ++-
 man/response_biomarkers_subgroups.Rd       |  7 +++++--
 man/response_subgroups.Rd                  | 11 +++++++++--
 man/summarize_ancova.Rd                    |  3 ++-
 man/summarize_change.Rd                    |  3 ++-
 man/summarize_glm_count.Rd                 |  3 ++-
 man/summarize_num_patients.Rd              |  3 ++-
 man/summarize_patients_exposure_in_cols.Rd |  3 ++-
 man/survival_biomarkers_subgroups.Rd       | 11 +++++++----
 man/survival_coxph_pairwise.Rd             |  3 ++-
 man/survival_duration_subgroups.Rd         | 11 +++++++----
 man/survival_time.Rd                       |  3 ++-
 man/survival_timepoint.Rd                  |  3 ++-
 37 files changed, 95 insertions(+), 74 deletions(-)

diff --git a/R/compare_variables.R b/R/compare_variables.R
index e82eda8459..20b8deb3d1 100644
--- a/R/compare_variables.R
+++ b/R/compare_variables.R
@@ -5,6 +5,9 @@
 #' Comparison with a reference group for different `x` objects.
 #'
 #' @inheritParams argument_convention
+#' @param .stats (`character`)\cr statistics to select for the table. Run `get_stats("analyze_vars_numeric")` to see
+#'   statistics available for numeric variables, and `get_stats("analyze_vars_counts")` for statistics available
+#'   for non-numeric variables.
 #'
 #' @note
 #' * For factor variables, `denom` for factor proportions can only be `n` since the purpose is to compare proportions
diff --git a/man/abnormal.Rd b/man/abnormal.Rd
index 0e50726669..623676559a 100644
--- a/man/abnormal.Rd
+++ b/man/abnormal.Rd
@@ -64,7 +64,8 @@ underneath analyses, which is not allowed.}
 \item{table_names}{(\code{character})\cr this can be customized in case that the same \code{vars} are analyzed multiple times,
 to avoid warnings from \code{rtables}.}
 
-\item{.stats}{(\code{character})\cr statistics to select for the table.}
+\item{.stats}{(\code{character})\cr statistics to select for the table. Run \code{get_stats("abnormal")}
+to see available statistics for this function.}
 
 \item{.formats}{(named \code{character} or \code{list})\cr formats for the statistics. See Details in \code{analyze_vars} for more
 information on the \code{"auto"} setting.}
diff --git a/man/abnormal_by_baseline.Rd b/man/abnormal_by_baseline.Rd
index 312721849c..4c9cfa0462 100644
--- a/man/abnormal_by_baseline.Rd
+++ b/man/abnormal_by_baseline.Rd
@@ -65,7 +65,8 @@ underneath analyses, which is not allowed.}
 \item{table_names}{(\code{character})\cr this can be customized in case that the same \code{vars} are analyzed multiple times,
 to avoid warnings from \code{rtables}.}
 
-\item{.stats}{(\code{character})\cr statistics to select for the table.}
+\item{.stats}{(\code{character})\cr statistics to select for the table. Run \code{get_stats("abnormal_by_baseline")}
+to see available statistics for this function.}
 
 \item{.formats}{(named \code{character} or \code{list})\cr formats for the statistics. See Details in \code{analyze_vars} for more
 information on the \code{"auto"} setting.}
diff --git a/man/abnormal_by_marked.Rd b/man/abnormal_by_marked.Rd
index 73a2ca8e54..4129bf5f54 100644
--- a/man/abnormal_by_marked.Rd
+++ b/man/abnormal_by_marked.Rd
@@ -59,7 +59,8 @@ underneath analyses, which is not allowed.}
 
 \item{...}{additional arguments for the lower level functions.}
 
-\item{.stats}{(\code{character})\cr statistics to select for the table.}
+\item{.stats}{(\code{character})\cr statistics to select for the table. Run \code{get_stats("abnormal_by_marked")}
+to see available statistics for this function.}
 
 \item{.formats}{(named \code{character} or \code{list})\cr formats for the statistics. See Details in \code{analyze_vars} for more
 information on the \code{"auto"} setting.}
diff --git a/man/abnormal_by_worst_grade.Rd b/man/abnormal_by_worst_grade.Rd
index e9afd5d467..04d01e6769 100644
--- a/man/abnormal_by_worst_grade.Rd
+++ b/man/abnormal_by_worst_grade.Rd
@@ -54,7 +54,8 @@ underneath analyses, which is not allowed.}
 
 \item{...}{additional arguments for the lower level functions.}
 
-\item{.stats}{(\code{character})\cr statistics to select for the table.}
+\item{.stats}{(\code{character})\cr statistics to select for the table. Run \code{get_stats("abnormal_by_worst_grade")}
+to see available statistics for this function.}
 
 \item{.formats}{(named \code{character} or \code{list})\cr formats for the statistics. See Details in \code{analyze_vars} for more
 information on the \code{"auto"} setting.}
diff --git a/man/abnormal_by_worst_grade_worsen.Rd b/man/abnormal_by_worst_grade_worsen.Rd
index 6e6254c234..96db79332a 100644
--- a/man/abnormal_by_worst_grade_worsen.Rd
+++ b/man/abnormal_by_worst_grade_worsen.Rd
@@ -58,7 +58,8 @@ underneath analyses, which is not allowed.}
 \item{table_names}{(\code{character})\cr this can be customized in case that the same \code{vars} are analyzed multiple times,
 to avoid warnings from \code{rtables}.}
 
-\item{.stats}{(\code{character})\cr statistics to select for the table.}
+\item{.stats}{(\code{character})\cr statistics to select for the table. Run \code{get_stats("abnormal_by_worst_grade_worsen")}
+to see all available statistics.}
 
 \item{.formats}{(named \code{character} or \code{list})\cr formats for the statistics. See Details in \code{analyze_vars} for more
 information on the \code{"auto"} setting.}
diff --git a/man/analyze_variables.Rd b/man/analyze_variables.Rd
index 29cf623b9c..45f30d9a67 100644
--- a/man/analyze_variables.Rd
+++ b/man/analyze_variables.Rd
@@ -138,7 +138,9 @@ to print out information about factor casting.}
 \item{compare}{(\code{logical})\cr Whether comparison statistics should be analyzed instead of summary statistics
 (\code{compare = TRUE} adds \code{pval} statistic comparing against reference group).}
 
-\item{.stats}{(\code{character})\cr statistics to select for the table.}
+\item{.stats}{(\code{character})\cr statistics to select for the table. Run \code{get_stats("analyze_vars_numeric")} to see
+statistics available for numeric variables, and \code{get_stats("analyze_vars_counts")} for statistics available
+for non-numeric variables.}
 
 \item{.formats}{(named \code{character} or \code{list})\cr formats for the statistics. See Details in \code{analyze_vars} for more
 information on the \code{"auto"} setting.}
diff --git a/man/compare_variables.Rd b/man/compare_variables.Rd
index c937b6ceb8..750a8e1d27 100644
--- a/man/compare_variables.Rd
+++ b/man/compare_variables.Rd
@@ -109,7 +109,9 @@ to avoid warnings from \code{rtables}.}
 \item{section_div}{(\code{string})\cr string which should be repeated as a section divider after each group
 defined by this split instruction, or \code{NA_character_} (the default) for no section divider.}
 
-\item{.stats}{(\code{character})\cr statistics to select for the table.}
+\item{.stats}{(\code{character})\cr statistics to select for the table. Run \code{get_stats("analyze_vars_numeric")} to see
+statistics available for numeric variables, and \code{get_stats("analyze_vars_counts")} for statistics available
+for non-numeric variables.}
 
 \item{.formats}{(named \code{character} or \code{list})\cr formats for the statistics. See Details in \code{analyze_vars} for more
 information on the \code{"auto"} setting.}
diff --git a/man/count_cumulative.Rd b/man/count_cumulative.Rd
index f4a986a167..32b20fef79 100644
--- a/man/count_cumulative.Rd
+++ b/man/count_cumulative.Rd
@@ -70,7 +70,8 @@ underneath analyses, which is not allowed.}
 \item{table_names}{(\code{character})\cr this can be customized in case that the same \code{vars} are analyzed multiple times,
 to avoid warnings from \code{rtables}.}
 
-\item{.stats}{(\code{character})\cr statistics to select for the table.}
+\item{.stats}{(\code{character})\cr statistics to select for the table. Run \code{get_stats("count_cumulative")}
+to see available statistics for this function.}
 
 \item{.formats}{(named \code{character} or \code{list})\cr formats for the statistics. See Details in \code{analyze_vars} for more
 information on the \code{"auto"} setting.}
diff --git a/man/count_missed_doses.Rd b/man/count_missed_doses.Rd
index a4e02a3963..5757ac8fc5 100644
--- a/man/count_missed_doses.Rd
+++ b/man/count_missed_doses.Rd
@@ -55,7 +55,8 @@ underneath analyses, which is not allowed.}
 \item{table_names}{(\code{character})\cr this can be customized in case that the same \code{vars} are analyzed multiple times,
 to avoid warnings from \code{rtables}.}
 
-\item{.stats}{(\code{character})\cr statistics to select for the table.}
+\item{.stats}{(\code{character})\cr statistics to select for the table. Run \code{get_stats("count_missed_doses")}
+to see available statistics for this function.}
 
 \item{.formats}{(named \code{character} or \code{list})\cr formats for the statistics. See Details in \code{analyze_vars} for more
 information on the \code{"auto"} setting.}
diff --git a/man/count_occurrences.Rd b/man/count_occurrences.Rd
index f7c5f5d156..91328fc06b 100644
--- a/man/count_occurrences.Rd
+++ b/man/count_occurrences.Rd
@@ -87,7 +87,8 @@ by a statistics function.}
 (must be present as second argument in Content Row Functions). See \code{\link[rtables:summarize_row_groups]{rtables::summarize_row_groups()}}
 for more information.}
 
-\item{.stats}{(\code{character})\cr statistics to select for the table.}
+\item{.stats}{(\code{character})\cr statistics to select for the table. Run \code{get_stats("count_occurrences")}
+to see available statistics for this function.}
 
 \item{.formats}{(named \code{character} or \code{list})\cr formats for the statistics. See Details in \code{analyze_vars} for more
 information on the \code{"auto"} setting.}
diff --git a/man/count_occurrences_by_grade.Rd b/man/count_occurrences_by_grade.Rd
index 3222c09ead..3ab336c87c 100644
--- a/man/count_occurrences_by_grade.Rd
+++ b/man/count_occurrences_by_grade.Rd
@@ -95,7 +95,8 @@ underneath analyses, which is not allowed.}
 \item{table_names}{(\code{character})\cr this can be customized in case that the same \code{vars} are analyzed multiple times,
 to avoid warnings from \code{rtables}.}
 
-\item{.stats}{(\code{character})\cr statistics to select for the table.}
+\item{.stats}{(\code{character})\cr statistics to select for the table. Run \code{get_stats("count_occurrences_by_grade")}
+to see available statistics for this function.}
 
 \item{.formats}{(named \code{character} or \code{list})\cr formats for the statistics. See Details in \code{analyze_vars} for more
 information on the \code{"auto"} setting.}
diff --git a/man/count_patients_events_in_cols.Rd b/man/count_patients_events_in_cols.Rd
index 84011b90ce..78e1abcea5 100644
--- a/man/count_patients_events_in_cols.Rd
+++ b/man/count_patients_events_in_cols.Rd
@@ -52,7 +52,9 @@ be used as label.}
 
 \item{...}{additional arguments for the lower level functions.}
 
-\item{.stats}{(\code{character})\cr statistics to select for the table.}
+\item{.stats}{(\code{character})\cr statistics to select for the table. Run
+\code{get_stats("summarize_patients_events_in_cols")} to see available statistics for this function, in addition to any
+added using \code{filters_list}.}
 
 \item{.labels}{(named \code{character})\cr labels for the statistics (without indent).}
 
diff --git a/man/count_patients_with_event.Rd b/man/count_patients_with_event.Rd
index 173780583e..882abfe795 100644
--- a/man/count_patients_with_event.Rd
+++ b/man/count_patients_with_event.Rd
@@ -81,7 +81,8 @@ underneath analyses, which is not allowed.}
 \item{table_names}{(\code{character})\cr this can be customized in case that the same \code{vars} are analyzed multiple times,
 to avoid warnings from \code{rtables}.}
 
-\item{.stats}{(\code{character})\cr statistics to select for the table.}
+\item{.stats}{(\code{character})\cr statistics to select for the table. Run \code{get_stats("count_patients_with_event")}
+to see available statistics for this function.}
 
 \item{.formats}{(named \code{character} or \code{list})\cr formats for the statistics. See Details in \code{analyze_vars} for more
 information on the \code{"auto"} setting.}
diff --git a/man/count_patients_with_flags.Rd b/man/count_patients_with_flags.Rd
index 0464e49820..19981fcc13 100644
--- a/man/count_patients_with_flags.Rd
+++ b/man/count_patients_with_flags.Rd
@@ -88,7 +88,8 @@ underneath analyses, which is not allowed.}
 \item{table_names}{(\code{character})\cr this can be customized in case that the same \code{vars} are analyzed multiple times,
 to avoid warnings from \code{rtables}.}
 
-\item{.stats}{(\code{character})\cr statistics to select for the table.}
+\item{.stats}{(\code{character})\cr statistics to select for the table. Run \code{get_stats("count_patients_with_flags")}
+to see available statistics for this function.}
 
 \item{.formats}{(named \code{character} or \code{list})\cr formats for the statistics. See Details in \code{analyze_vars} for more
 information on the \code{"auto"} setting.}
diff --git a/man/count_values_funs.Rd b/man/count_values_funs.Rd
index 33d0d3b0e8..4a500b1723 100644
--- a/man/count_values_funs.Rd
+++ b/man/count_values_funs.Rd
@@ -83,7 +83,8 @@ underneath analyses, which is not allowed.}
 \item{table_names}{(\code{character})\cr this can be customized in case that the same \code{vars} are analyzed multiple times,
 to avoid warnings from \code{rtables}.}
 
-\item{.stats}{(\code{character})\cr statistics to select for the table.}
+\item{.stats}{(\code{character})\cr statistics to select for the table. Run \code{get_stats("count_values")}
+to see available statistics for this function.}
 
 \item{.formats}{(named \code{character} or \code{list})\cr formats for the statistics. See Details in \code{analyze_vars} for more
 information on the \code{"auto"} setting.}
diff --git a/man/d_survival_subgroups_colvars.Rd b/man/d_survival_subgroups_colvars.Rd
index c336aeb858..8eb00bafda 100644
--- a/man/d_survival_subgroups_colvars.Rd
+++ b/man/d_survival_subgroups_colvars.Rd
@@ -7,19 +7,7 @@
 d_survival_subgroups_colvars(vars, conf_level, method, time_unit = NULL)
 }
 \arguments{
-\item{vars}{(\code{character})\cr the name of statistics to be reported among:
-\itemize{
-\item \code{n_tot_events}: Total number of events per group.
-\item \code{n_events}: Number of events per group.
-\item \code{n_tot}: Total number of observations per group.
-\item \code{n}: Number of observations per group.
-\item \code{median}: Median survival time.
-\item \code{hr}: Hazard ratio.
-\item \code{ci}: Confidence interval of hazard ratio.
-\item \code{pval}: p-value of the effect.
-Note, one of the statistics \code{n_tot} and \code{n_tot_events}, as well as both \code{hr} and \code{ci}
-are required.
-}}
+\item{vars}{(\code{character})\cr variable names for the primary analysis variable to be iterated over.}
 
 \item{conf_level}{(\code{proportion})\cr confidence level of the interval.}
 
diff --git a/man/estimate_multinomial_rsp.Rd b/man/estimate_multinomial_rsp.Rd
index b3cff3fb4d..9767dcba74 100644
--- a/man/estimate_multinomial_rsp.Rd
+++ b/man/estimate_multinomial_rsp.Rd
@@ -49,7 +49,8 @@ underneath analyses, which is not allowed.}
 \item{table_names}{(\code{character})\cr this can be customized in case that the same \code{vars} are analyzed multiple times,
 to avoid warnings from \code{rtables}.}
 
-\item{.stats}{(\code{character})\cr statistics to select for the table.}
+\item{.stats}{(\code{character})\cr statistics to select for the table. Run \code{get_stats("estimate_multinomial_response")}
+to see available statistics for this function.}
 
 \item{.formats}{(named \code{character} or \code{list})\cr formats for the statistics. See Details in \code{analyze_vars} for more
 information on the \code{"auto"} setting.}
diff --git a/man/estimate_proportions.Rd b/man/estimate_proportions.Rd
index 7fce15b0ec..e785b535f9 100644
--- a/man/estimate_proportions.Rd
+++ b/man/estimate_proportions.Rd
@@ -90,7 +90,8 @@ underneath analyses, which is not allowed.}
 \item{table_names}{(\code{character})\cr this can be customized in case that the same \code{vars} are analyzed multiple times,
 to avoid warnings from \code{rtables}.}
 
-\item{.stats}{(\code{character})\cr statistics to select for the table.}
+\item{.stats}{(\code{character})\cr statistics to select for the table. Run \code{get_stats("estimate_proportion")}
+to see available statistics for this function.}
 
 \item{.formats}{(named \code{character} or \code{list})\cr formats for the statistics. See Details in \code{analyze_vars} for more
 information on the \code{"auto"} setting.}
diff --git a/man/h_response_biomarkers_subgroups.Rd b/man/h_response_biomarkers_subgroups.Rd
index 04ae098657..a270b3df8e 100644
--- a/man/h_response_biomarkers_subgroups.Rd
+++ b/man/h_response_biomarkers_subgroups.Rd
@@ -28,16 +28,7 @@ returned by \code{\link[=extract_rsp_biomarkers]{extract_rsp_biomarkers()}} (it
 added by that high-level function relative to what is returned by \code{\link[=h_logistic_mult_cont_df]{h_logistic_mult_cont_df()}},
 see the example).}
 
-\item{vars}{(\code{character})\cr the names of statistics to be reported among:
-\itemize{
-\item \code{n_tot}: Total number of patients per group.
-\item \code{n_rsp}: Total number of responses per group.
-\item \code{prop}: Total response proportion per group.
-\item \code{or}: Odds ratio.
-\item \code{ci}: Confidence interval of odds ratio.
-\item \code{pval}: p-value of the effect.
-Note, the statistics \code{n_tot}, \code{or} and \code{ci} are required.
-}}
+\item{vars}{(\code{character})\cr variable names for the primary analysis variable to be iterated over.}
 
 \item{.indent_mods}{(named \code{integer})\cr indent modifiers for the labels. Defaults to 0, which corresponds to the
 unmodified default behavior. Can be negative.}
diff --git a/man/h_survival_biomarkers_subgroups.Rd b/man/h_survival_biomarkers_subgroups.Rd
index f88dba3596..385afd7d6e 100644
--- a/man/h_survival_biomarkers_subgroups.Rd
+++ b/man/h_survival_biomarkers_subgroups.Rd
@@ -27,16 +27,7 @@ returned by \code{\link[=extract_survival_biomarkers]{extract_survival_biomarker
 added by that high-level function relative to what is returned by \code{\link[=h_coxreg_mult_cont_df]{h_coxreg_mult_cont_df()}},
 see the example).}
 
-\item{vars}{(\code{character})\cr the names of statistics to be reported among:
-\itemize{
-\item \code{n_tot_events}: Total number of events per group.
-\item \code{n_tot}: Total number of observations per group.
-\item \code{median}: Median survival time.
-\item \code{hr}: Hazard ratio.
-\item \code{ci}: Confidence interval of hazard ratio.
-\item \code{pval}: p-value of the effect.
-Note, one of the statistics \code{n_tot} and \code{n_tot_events}, as well as both \code{hr} and \code{ci} are required.
-}}
+\item{vars}{(\code{character})\cr variable names for the primary analysis variable to be iterated over.}
 
 \item{time_unit}{(\code{string})\cr label with unit of median survival time. Default \code{NULL} skips displaying unit.}
 
diff --git a/man/incidence_rate.Rd b/man/incidence_rate.Rd
index 16db00037a..961e83c6db 100644
--- a/man/incidence_rate.Rd
+++ b/man/incidence_rate.Rd
@@ -75,7 +75,8 @@ underneath analyses, which is not allowed.}
 \item{table_names}{(\code{character})\cr this can be customized in case that the same \code{vars} are analyzed multiple times,
 to avoid warnings from \code{rtables}.}
 
-\item{.stats}{(\code{character})\cr statistics to select for the table.}
+\item{.stats}{(\code{character})\cr statistics to select for the table. Run \code{get_stats("estimate_incidence_rate")}
+to see available statistics for this function.}
 
 \item{.formats}{(named \code{character} or \code{list})\cr formats for the statistics. See Details in \code{analyze_vars} for more
 information on the \code{"auto"} setting.}
diff --git a/man/odds_ratio.Rd b/man/odds_ratio.Rd
index 6ab700ead7..d01e6082c7 100644
--- a/man/odds_ratio.Rd
+++ b/man/odds_ratio.Rd
@@ -79,7 +79,8 @@ underneath analyses, which is not allowed.}
 \item{table_names}{(\code{character})\cr this can be customized in case that the same \code{vars} are analyzed multiple times,
 to avoid warnings from \code{rtables}.}
 
-\item{.stats}{(\code{character})\cr statistics to select for the table.}
+\item{.stats}{(\code{character})\cr statistics to select for the table. Run \code{get_stats("estimate_odds_ratio")}
+to see available statistics for this function.}
 
 \item{.formats}{(named \code{character} or \code{list})\cr formats for the statistics. See Details in \code{analyze_vars} for more
 information on the \code{"auto"} setting.}
diff --git a/man/prop_diff.Rd b/man/prop_diff.Rd
index f6a60c42b4..880dffd42b 100644
--- a/man/prop_diff.Rd
+++ b/man/prop_diff.Rd
@@ -84,7 +84,8 @@ underneath analyses, which is not allowed.}
 \item{table_names}{(\code{character})\cr this can be customized in case that the same \code{vars} are analyzed multiple times,
 to avoid warnings from \code{rtables}.}
 
-\item{.stats}{(\code{character})\cr statistics to select for the table.}
+\item{.stats}{(\code{character})\cr statistics to select for the table. Run \code{get_stats("estimate_proportion_diff")}
+to see available statistics for this function.}
 
 \item{.formats}{(named \code{character} or \code{list})\cr formats for the statistics. See Details in \code{analyze_vars} for more
 information on the \code{"auto"} setting.}
diff --git a/man/prop_diff_test.Rd b/man/prop_diff_test.Rd
index 2babe8f7c4..af4a86a21b 100644
--- a/man/prop_diff_test.Rd
+++ b/man/prop_diff_test.Rd
@@ -74,7 +74,8 @@ underneath analyses, which is not allowed.}
 \item{table_names}{(\code{character})\cr this can be customized in case that the same \code{vars} are analyzed multiple times,
 to avoid warnings from \code{rtables}.}
 
-\item{.stats}{(\code{character})\cr statistics to select for the table.}
+\item{.stats}{(\code{character})\cr statistics to select for the table. Run \code{get_stats("test_proportion_diff")}
+to see available statistics for this function.}
 
 \item{.formats}{(named \code{character} or \code{list})\cr formats for the statistics. See Details in \code{analyze_vars} for more
 information on the \code{"auto"} setting.}
diff --git a/man/response_biomarkers_subgroups.Rd b/man/response_biomarkers_subgroups.Rd
index b43185f9a7..3f3027a559 100644
--- a/man/response_biomarkers_subgroups.Rd
+++ b/man/response_biomarkers_subgroups.Rd
@@ -7,7 +7,8 @@
 \usage{
 tabulate_rsp_biomarkers(
   df,
-  vars = c("n_tot", "n_rsp", "prop", "or", "ci", "pval"),
+  vars = lifecycle::deprecated(),
+  .stats = c("n_tot", "n_rsp", "prop", "or", "ci", "pval"),
   .indent_mods = 0L
 )
 }
@@ -15,7 +16,9 @@ tabulate_rsp_biomarkers(
 \item{df}{(\code{data.frame})\cr containing all analysis variables, as returned by
 \code{\link[=extract_rsp_biomarkers]{extract_rsp_biomarkers()}}.}
 
-\item{vars}{(\code{character})\cr the names of statistics to be reported among:
+\item{vars}{(\code{character})\cr variable names for the primary analysis variable to be iterated over.}
+
+\item{.stats}{(\code{character})\cr the names of statistics to be reported among:
 \itemize{
 \item \code{n_tot}: Total number of patients per group.
 \item \code{n_rsp}: Total number of responses per group.
diff --git a/man/response_subgroups.Rd b/man/response_subgroups.Rd
index e03ee9dd70..77b748c3b0 100644
--- a/man/response_subgroups.Rd
+++ b/man/response_subgroups.Rd
@@ -12,7 +12,12 @@ a_response_subgroups(
     "x.xxxx | (<0.0001)")
 )
 
-tabulate_rsp_subgroups(lyt, df, vars = c("n_tot", "n", "prop", "or", "ci"))
+tabulate_rsp_subgroups(
+  lyt,
+  df,
+  vars = lifecycle::deprecated(),
+  .stats = c("n_tot", "n", "prop", "or", "ci")
+)
 }
 \arguments{
 \item{.formats}{(named \code{character} or \code{list})\cr formats for the statistics. See Details in \code{analyze_vars} for more
@@ -23,7 +28,9 @@ information on the \code{"auto"} setting.}
 \item{df}{(\code{list})\cr of data frames containing all analysis variables. List should be
 created using \code{\link[=extract_rsp_subgroups]{extract_rsp_subgroups()}}.}
 
-\item{vars}{(\code{character})\cr the names of statistics to be reported among:
+\item{vars}{(\code{character})\cr variable names for the primary analysis variable to be iterated over.}
+
+\item{.stats}{(\code{character})\cr the names of statistics to be reported among:
 \itemize{
 \item \code{n}: Total number of observations per group.
 \item \code{n_rsp}: Number of responders per group.
diff --git a/man/summarize_ancova.Rd b/man/summarize_ancova.Rd
index 4405cdac5d..8e40ef601a 100644
--- a/man/summarize_ancova.Rd
+++ b/man/summarize_ancova.Rd
@@ -88,7 +88,8 @@ underneath analyses, which is not allowed.}
 \item{table_names}{(\code{character})\cr this can be customized in case that the same \code{vars} are analyzed multiple times,
 to avoid warnings from \code{rtables}.}
 
-\item{.stats}{(\code{character})\cr statistics to select for the table.}
+\item{.stats}{(\code{character})\cr statistics to select for the table. Run \code{get_stats("summarize_ancova")}
+to see available statistics for this function.}
 
 \item{.formats}{(named \code{character} or \code{list})\cr formats for the statistics. See Details in \code{analyze_vars} for more
 information on the \code{"auto"} setting.}
diff --git a/man/summarize_change.Rd b/man/summarize_change.Rd
index fa056f3665..9bd064f942 100644
--- a/man/summarize_change.Rd
+++ b/man/summarize_change.Rd
@@ -48,7 +48,8 @@ underneath analyses, which is not allowed.}
 \item{table_names}{(\code{character})\cr this can be customized in case that the same \code{vars} are analyzed multiple times,
 to avoid warnings from \code{rtables}.}
 
-\item{.stats}{(\code{character})\cr statistics to select for the table.}
+\item{.stats}{(\code{character})\cr statistics to select for the table. Run \verb{get_stats("analyze_vars_numeric)}
+to see available statistics for this function.}
 
 \item{.formats}{(named \code{character} or \code{list})\cr formats for the statistics. See Details in \code{analyze_vars} for more
 information on the \code{"auto"} setting.}
diff --git a/man/summarize_glm_count.Rd b/man/summarize_glm_count.Rd
index 33c5f841dd..8704187af3 100644
--- a/man/summarize_glm_count.Rd
+++ b/man/summarize_glm_count.Rd
@@ -91,7 +91,8 @@ underneath analyses, which is not allowed.}
 \item{table_names}{(\code{character})\cr this can be customized in case that the same \code{vars} are analyzed multiple times,
 to avoid warnings from \code{rtables}.}
 
-\item{.stats}{(\code{character})\cr statistics to select for the table.}
+\item{.stats}{(\code{character})\cr statistics to select for the table. Run \code{get_stats("summarize_glm_count")}
+to see available statistics for this function.}
 
 \item{.formats}{(named \code{character} or \code{list})\cr formats for the statistics. See Details in \code{analyze_vars} for more
 information on the \code{"auto"} setting.}
diff --git a/man/summarize_num_patients.Rd b/man/summarize_num_patients.Rd
index 22ae0c0c0b..d6d0cdf86c 100644
--- a/man/summarize_num_patients.Rd
+++ b/man/summarize_num_patients.Rd
@@ -82,7 +82,8 @@ by a statistics function.}
 
 \item{na_str}{(\code{string})\cr string used to replace all \code{NA} or empty values in the output.}
 
-\item{.stats}{(\code{character})\cr statistics to select for the table.}
+\item{.stats}{(\code{character})\cr statistics to select for the table. Run \code{get_stats("summarize_num_patients")}
+to see available statistics for this function.}
 
 \item{.formats}{(named \code{character} or \code{list})\cr formats for the statistics. See Details in \code{analyze_vars} for more
 information on the \code{"auto"} setting.}
diff --git a/man/summarize_patients_exposure_in_cols.Rd b/man/summarize_patients_exposure_in_cols.Rd
index 0d15ebfed3..5559c08f71 100644
--- a/man/summarize_patients_exposure_in_cols.Rd
+++ b/man/summarize_patients_exposure_in_cols.Rd
@@ -64,7 +64,8 @@ analyze_patients_exposure_in_cols(
 (must be present as second argument in Content Row Functions). See \code{\link[rtables:summarize_row_groups]{rtables::summarize_row_groups()}}
 for more information.}
 
-\item{.stats}{(\code{character})\cr statistics to select for the table.}
+\item{.stats}{(\code{character})\cr statistics to select for the table. Run
+\code{get_stats("analyze_patients_exposure_in_cols")} to see available statistics for this function.}
 
 \item{.N_col}{(\code{integer})\cr column-wise N (column count) for the full column being analyzed that is typically
 passed by \code{rtables}.}
diff --git a/man/survival_biomarkers_subgroups.Rd b/man/survival_biomarkers_subgroups.Rd
index 6c35fd44ad..a6cdfc9478 100644
--- a/man/survival_biomarkers_subgroups.Rd
+++ b/man/survival_biomarkers_subgroups.Rd
@@ -7,8 +7,9 @@
 \usage{
 tabulate_survival_biomarkers(
   df,
-  vars = c("n_tot", "n_tot_events", "median", "hr", "ci", "pval"),
+  vars = lifecycle::deprecated(),
   time_unit = NULL,
+  .stats = c("n_tot", "n_tot_events", "median", "hr", "ci", "pval"),
   .indent_mods = 0L
 )
 }
@@ -16,7 +17,11 @@ tabulate_survival_biomarkers(
 \item{df}{(\code{data.frame})\cr containing all analysis variables, as returned by
 \code{\link[=extract_survival_biomarkers]{extract_survival_biomarkers()}}.}
 
-\item{vars}{(\code{character})\cr the names of statistics to be reported among:
+\item{vars}{(\code{character})\cr variable names for the primary analysis variable to be iterated over.}
+
+\item{time_unit}{(\code{string})\cr label with unit of median survival time. Default \code{NULL} skips displaying unit.}
+
+\item{.stats}{(\code{character})\cr the names of statistics to be reported among:
 \itemize{
 \item \code{n_tot_events}: Total number of events per group.
 \item \code{n_tot}: Total number of observations per group.
@@ -27,8 +32,6 @@ tabulate_survival_biomarkers(
 Note, one of the statistics \code{n_tot} and \code{n_tot_events}, as well as both \code{hr} and \code{ci} are required.
 }}
 
-\item{time_unit}{(\code{string})\cr label with unit of median survival time. Default \code{NULL} skips displaying unit.}
-
 \item{.indent_mods}{(named \code{integer})\cr indent modifiers for the labels. Defaults to 0, which corresponds to the
 unmodified default behavior. Can be negative.}
 }
diff --git a/man/survival_coxph_pairwise.Rd b/man/survival_coxph_pairwise.Rd
index 272d6e0f95..b3acb2b678 100644
--- a/man/survival_coxph_pairwise.Rd
+++ b/man/survival_coxph_pairwise.Rd
@@ -85,7 +85,8 @@ underneath analyses, which is not allowed.}
 \item{table_names}{(\code{character})\cr this can be customized in case that the same \code{vars} are analyzed multiple times,
 to avoid warnings from \code{rtables}.}
 
-\item{.stats}{(\code{character})\cr statistics to select for the table.}
+\item{.stats}{(\code{character})\cr statistics to select for the table. Run \code{get_stats("coxph_pairwise")}
+to see available statistics for this function.}
 
 \item{.formats}{(named \code{character} or \code{list})\cr formats for the statistics. See Details in \code{analyze_vars} for more
 information on the \code{"auto"} setting.}
diff --git a/man/survival_duration_subgroups.Rd b/man/survival_duration_subgroups.Rd
index 4dad3e1ece..2c7edc456e 100644
--- a/man/survival_duration_subgroups.Rd
+++ b/man/survival_duration_subgroups.Rd
@@ -15,8 +15,9 @@ a_survival_subgroups(
 tabulate_survival_subgroups(
   lyt,
   df,
-  vars = c("n_tot_events", "n_events", "median", "hr", "ci"),
+  vars = lifecycle::deprecated(),
   time_unit = NULL,
+  .stats = c("n_tot_events", "n_events", "median", "hr", "ci"),
   na_str = NA_character_
 )
 }
@@ -29,7 +30,11 @@ information on the \code{"auto"} setting.}
 \item{df}{(\code{list})\cr of data frames containing all analysis variables. List should be
 created using \code{\link[=extract_survival_subgroups]{extract_survival_subgroups()}}.}
 
-\item{vars}{(\code{character})\cr the name of statistics to be reported among:
+\item{vars}{(\code{character})\cr variable names for the primary analysis variable to be iterated over.}
+
+\item{time_unit}{(\code{string})\cr label with unit of median survival time. Default \code{NULL} skips displaying unit.}
+
+\item{.stats}{(\code{character})\cr the name of statistics to be reported among:
 \itemize{
 \item \code{n_tot_events}: Total number of events per group.
 \item \code{n_events}: Number of events per group.
@@ -43,8 +48,6 @@ Note, one of the statistics \code{n_tot} and \code{n_tot_events}, as well as bot
 are required.
 }}
 
-\item{time_unit}{(\code{string})\cr label with unit of median survival time. Default \code{NULL} skips displaying unit.}
-
 \item{na_str}{(\code{string})\cr string used to replace all \code{NA} or empty values in the output.}
 }
 \value{
diff --git a/man/survival_time.Rd b/man/survival_time.Rd
index 8a72bca3b2..175af2dd53 100644
--- a/man/survival_time.Rd
+++ b/man/survival_time.Rd
@@ -60,7 +60,8 @@ underneath analyses, which is not allowed.}
 \item{table_names}{(\code{character})\cr this can be customized in case that the same \code{vars} are analyzed multiple times,
 to avoid warnings from \code{rtables}.}
 
-\item{.stats}{(\code{character})\cr statistics to select for the table.}
+\item{.stats}{(\code{character})\cr statistics to select for the table. Run \code{get_stats("surv_time")}
+to see available statistics for this function.}
 
 \item{.formats}{(named \code{character} or \code{list})\cr formats for the statistics. See Details in \code{analyze_vars} for more
 information on the \code{"auto"} setting.}
diff --git a/man/survival_timepoint.Rd b/man/survival_timepoint.Rd
index 5160962dee..743fb427cc 100644
--- a/man/survival_timepoint.Rd
+++ b/man/survival_timepoint.Rd
@@ -112,7 +112,8 @@ avoid warnings from duplicate table names.}
 \item{method}{(\code{string})\cr either \code{surv} (survival estimations),
 \code{surv_diff} (difference in survival with the control) or \code{both}.}
 
-\item{.stats}{(\code{character})\cr statistics to select for the table.}
+\item{.stats}{(\code{character})\cr statistics to select for the table. Run \code{get_stats("surv_timepoint")}
+to see available statistics for this function.}
 
 \item{.formats}{(named \code{character} or \code{list})\cr formats for the statistics. See Details in \code{analyze_vars} for more
 information on the \code{"auto"} setting.}

From 0857820dc4da4e73b2b0c9c18ed88975eda22560 Mon Sep 17 00:00:00 2001
From: Emily de la Rua <emily.de_la_rua@contractors.roche.com>
Date: Mon, 6 Nov 2023 16:51:08 -0500
Subject: [PATCH 13/16] Sync docs

---
 man/default_stats_formats_labels.Rd | 7 +++----
 1 file changed, 3 insertions(+), 4 deletions(-)

diff --git a/man/default_stats_formats_labels.Rd b/man/default_stats_formats_labels.Rd
index 899602794a..1c84fbea96 100644
--- a/man/default_stats_formats_labels.Rd
+++ b/man/default_stats_formats_labels.Rd
@@ -21,8 +21,8 @@ named for their corresponding statistical method group.
 }
 
 \itemize{
-\item \code{tern_default_formats} is a list of available formats, named after their relevant
-statistic.
+\item \code{tern_default_formats} is a named vector of available default formats, with each element
+named for their corresponding statistic.
 }
 
 \itemize{
@@ -169,8 +169,7 @@ group (analyze function).
 
 \item \code{tern_default_formats}: Named vector of default formats for \code{tern}.
 
-\item \code{tern_default_labels}: \code{character} vector that contains default labels
-for \code{tern}.
+\item \code{tern_default_labels}: Named \code{character} vector of default labels for \code{tern}.
 
 \item \code{summary_formats()}: Quick function to retrieve default formats for summary statistics:
 \code{\link[=analyze_vars]{analyze_vars()}} and \code{\link[=analyze_vars_in_cols]{analyze_vars_in_cols()}} principally.

From 4d70e97d2eac38db551e68b3f17aaf17aad71232 Mon Sep 17 00:00:00 2001
From: Emily de la Rua <emily.de_la_rua@contractors.roche.com>
Date: Mon, 6 Nov 2023 17:09:45 -0500
Subject: [PATCH 14/16] Revert deprecation of arg name

---
 NEWS.md                           |  1 -
 R/response_biomarkers_subgroups.R | 10 ++--------
 R/response_subgroups.R            | 10 ++--------
 R/survival_biomarkers_subgroups.R | 10 ++--------
 R/survival_duration_subgroups.R   | 10 ++--------
 5 files changed, 8 insertions(+), 33 deletions(-)

diff --git a/NEWS.md b/NEWS.md
index b2a35131e4..4e8b1fa3a1 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -19,7 +19,6 @@
 
 ### Miscellaneous
 * Specified minimal version of package dependencies.
-* Began deprecation of `vars` argument in `tabulate_rsp_biomarkers`, `tabulate_rsp_subgroups`, `tabulate_survival_biomarkers`, and `tabulate_survival_subgroups` and replaced it with the `.stats` argument.
 
 # tern 0.9.2
 
diff --git a/R/response_biomarkers_subgroups.R b/R/response_biomarkers_subgroups.R
index ca87a298b4..b22034b894 100644
--- a/R/response_biomarkers_subgroups.R
+++ b/R/response_biomarkers_subgroups.R
@@ -8,7 +8,7 @@
 #' @inheritParams argument_convention
 #' @param df (`data.frame`)\cr containing all analysis variables, as returned by
 #'   [extract_rsp_biomarkers()].
-#' @param .stats (`character`)\cr the names of statistics to be reported among:
+#' @param vars (`character`)\cr the names of statistics to be reported among:
 #'   * `n_tot`: Total number of patients per group.
 #'   * `n_rsp`: Total number of responses per group.
 #'   * `prop`: Total response proportion per group.
@@ -67,14 +67,8 @@
 #' @export
 #' @name response_biomarkers_subgroups
 tabulate_rsp_biomarkers <- function(df,
-                                    vars = lifecycle::deprecated(),
-                                    .stats = c("n_tot", "n_rsp", "prop", "or", "ci", "pval"),
+                                    vars = c("n_tot", "n_rsp", "prop", "or", "ci", "pval"),
                                     .indent_mods = 0L) {
-  if (lifecycle::is_present(vars)) {
-    lifecycle::deprecate_warn("0.9.3", "tabulate_rsp_biomarkers(vars)", "tabulate_rsp_biomarkers(.stats)")
-    .stats <- vars
-  }
-
   checkmate::assert_data_frame(df)
   checkmate::assert_character(df$biomarker)
   checkmate::assert_character(df$biomarker_label)
diff --git a/R/response_subgroups.R b/R/response_subgroups.R
index 7ea3c467bc..e194b1542d 100644
--- a/R/response_subgroups.R
+++ b/R/response_subgroups.R
@@ -178,7 +178,7 @@ a_response_subgroups <- function(.formats = list(
 #'
 #' @param df (`list`)\cr of data frames containing all analysis variables. List should be
 #'   created using [extract_rsp_subgroups()].
-#' @param .stats (`character`)\cr the names of statistics to be reported among:
+#' @param vars (`character`)\cr the names of statistics to be reported among:
 #'   * `n`: Total number of observations per group.
 #'   * `n_rsp`: Number of responders per group.
 #'   * `prop`: Proportion of responders.
@@ -205,13 +205,7 @@ a_response_subgroups <- function(.formats = list(
 #' @export
 tabulate_rsp_subgroups <- function(lyt,
                                    df,
-                                   vars = lifecycle::deprecated(),
-                                   .stats = c("n_tot", "n", "prop", "or", "ci")) {
-  if (lifecycle::is_present(vars)) {
-    lifecycle::deprecate_warn("0.9.3", "tabulate_rsp_subgroups(vars)", "tabulate_rsp_subgroups(.stats)")
-    .stats <- vars
-  }
-
+                                   vars = c("n_tot", "n", "prop", "or", "ci")) {
   conf_level <- df$or$conf_level[1]
   method <- if ("pval_label" %in% names(df$or)) {
     df$or$pval_label[1]
diff --git a/R/survival_biomarkers_subgroups.R b/R/survival_biomarkers_subgroups.R
index c14184b5ff..3c59f0204f 100644
--- a/R/survival_biomarkers_subgroups.R
+++ b/R/survival_biomarkers_subgroups.R
@@ -172,7 +172,7 @@ extract_survival_biomarkers <- function(variables,
 #'
 #' @param df (`data.frame`)\cr containing all analysis variables, as returned by
 #'   [extract_survival_biomarkers()].
-#' @param .stats (`character`)\cr the names of statistics to be reported among:
+#' @param vars (`character`)\cr the names of statistics to be reported among:
 #'   * `n_tot_events`: Total number of events per group.
 #'   * `n_tot`: Total number of observations per group.
 #'   * `median`: Median survival time.
@@ -207,15 +207,9 @@ extract_survival_biomarkers <- function(variables,
 #'
 #' @export
 tabulate_survival_biomarkers <- function(df,
-                                         vars = lifecycle::deprecated(),
+                                         vars = c("n_tot", "n_tot_events", "median", "hr", "ci", "pval"),
                                          time_unit = NULL,
-                                         .stats = c("n_tot", "n_tot_events", "median", "hr", "ci", "pval"),
                                          .indent_mods = 0L) {
-  if (lifecycle::is_present(vars)) {
-    lifecycle::deprecate_warn("0.9.3", "tabulate_survival_biomarkers(vars)", "tabulate_survival_biomarkers(.stats)")
-    .stats <- vars
-  }
-
   checkmate::assert_data_frame(df)
   checkmate::assert_character(df$biomarker)
   checkmate::assert_character(df$biomarker_label)
diff --git a/R/survival_duration_subgroups.R b/R/survival_duration_subgroups.R
index 2a4f2a365d..4f50bd466c 100644
--- a/R/survival_duration_subgroups.R
+++ b/R/survival_duration_subgroups.R
@@ -212,7 +212,7 @@ a_survival_subgroups <- function(.formats = list( # nolint start
 #'
 #' @param df (`list`)\cr of data frames containing all analysis variables. List should be
 #'   created using [extract_survival_subgroups()].
-#' @param .stats (`character`)\cr the name of statistics to be reported among:
+#' @param vars (`character`)\cr the name of statistics to be reported among:
 #'   * `n_tot_events`: Total number of events per group.
 #'   * `n_events`: Number of events per group.
 #'   * `n_tot`: Total number of observations per group.
@@ -242,15 +242,9 @@ a_survival_subgroups <- function(.formats = list( # nolint start
 #' @export
 tabulate_survival_subgroups <- function(lyt,
                                         df,
-                                        vars = lifecycle::deprecated(),
+                                        vars = c("n_tot_events", "n_events", "median", "hr", "ci"),
                                         time_unit = NULL,
-                                        .stats = c("n_tot_events", "n_events", "median", "hr", "ci"),
                                         na_str = NA_character_) {
-  if (lifecycle::is_present(vars)) {
-    lifecycle::deprecate_warn("0.9.3", "tabulate_survival_subgroups(vars)", "tabulate_survival_subgroups(.stats)")
-    .stats <- vars
-  }
-
   conf_level <- df$hr$conf_level[1]
   method <- df$hr$pval_label[1]
 

From 9b8695b1f3de353fcf79e2dfaf6f3d920a902970 Mon Sep 17 00:00:00 2001
From: "27856297+dependabot-preview[bot]@users.noreply.github.com"
 <27856297+dependabot-preview[bot]@users.noreply.github.com>
Date: Mon, 6 Nov 2023 22:12:19 +0000
Subject: [PATCH 15/16] [skip actions] Roxygen Man Pages Auto Update

---
 man/d_survival_subgroups_colvars.Rd    | 14 +++++++++++++-
 man/h_response_biomarkers_subgroups.Rd | 11 ++++++++++-
 man/h_survival_biomarkers_subgroups.Rd | 11 ++++++++++-
 man/response_biomarkers_subgroups.Rd   |  7 ++-----
 man/response_subgroups.Rd              | 11 ++---------
 man/survival_biomarkers_subgroups.Rd   | 11 ++++-------
 man/survival_duration_subgroups.Rd     | 11 ++++-------
 7 files changed, 45 insertions(+), 31 deletions(-)

diff --git a/man/d_survival_subgroups_colvars.Rd b/man/d_survival_subgroups_colvars.Rd
index 8eb00bafda..c336aeb858 100644
--- a/man/d_survival_subgroups_colvars.Rd
+++ b/man/d_survival_subgroups_colvars.Rd
@@ -7,7 +7,19 @@
 d_survival_subgroups_colvars(vars, conf_level, method, time_unit = NULL)
 }
 \arguments{
-\item{vars}{(\code{character})\cr variable names for the primary analysis variable to be iterated over.}
+\item{vars}{(\code{character})\cr the name of statistics to be reported among:
+\itemize{
+\item \code{n_tot_events}: Total number of events per group.
+\item \code{n_events}: Number of events per group.
+\item \code{n_tot}: Total number of observations per group.
+\item \code{n}: Number of observations per group.
+\item \code{median}: Median survival time.
+\item \code{hr}: Hazard ratio.
+\item \code{ci}: Confidence interval of hazard ratio.
+\item \code{pval}: p-value of the effect.
+Note, one of the statistics \code{n_tot} and \code{n_tot_events}, as well as both \code{hr} and \code{ci}
+are required.
+}}
 
 \item{conf_level}{(\code{proportion})\cr confidence level of the interval.}
 
diff --git a/man/h_response_biomarkers_subgroups.Rd b/man/h_response_biomarkers_subgroups.Rd
index a270b3df8e..04ae098657 100644
--- a/man/h_response_biomarkers_subgroups.Rd
+++ b/man/h_response_biomarkers_subgroups.Rd
@@ -28,7 +28,16 @@ returned by \code{\link[=extract_rsp_biomarkers]{extract_rsp_biomarkers()}} (it
 added by that high-level function relative to what is returned by \code{\link[=h_logistic_mult_cont_df]{h_logistic_mult_cont_df()}},
 see the example).}
 
-\item{vars}{(\code{character})\cr variable names for the primary analysis variable to be iterated over.}
+\item{vars}{(\code{character})\cr the names of statistics to be reported among:
+\itemize{
+\item \code{n_tot}: Total number of patients per group.
+\item \code{n_rsp}: Total number of responses per group.
+\item \code{prop}: Total response proportion per group.
+\item \code{or}: Odds ratio.
+\item \code{ci}: Confidence interval of odds ratio.
+\item \code{pval}: p-value of the effect.
+Note, the statistics \code{n_tot}, \code{or} and \code{ci} are required.
+}}
 
 \item{.indent_mods}{(named \code{integer})\cr indent modifiers for the labels. Defaults to 0, which corresponds to the
 unmodified default behavior. Can be negative.}
diff --git a/man/h_survival_biomarkers_subgroups.Rd b/man/h_survival_biomarkers_subgroups.Rd
index 385afd7d6e..f88dba3596 100644
--- a/man/h_survival_biomarkers_subgroups.Rd
+++ b/man/h_survival_biomarkers_subgroups.Rd
@@ -27,7 +27,16 @@ returned by \code{\link[=extract_survival_biomarkers]{extract_survival_biomarker
 added by that high-level function relative to what is returned by \code{\link[=h_coxreg_mult_cont_df]{h_coxreg_mult_cont_df()}},
 see the example).}
 
-\item{vars}{(\code{character})\cr variable names for the primary analysis variable to be iterated over.}
+\item{vars}{(\code{character})\cr the names of statistics to be reported among:
+\itemize{
+\item \code{n_tot_events}: Total number of events per group.
+\item \code{n_tot}: Total number of observations per group.
+\item \code{median}: Median survival time.
+\item \code{hr}: Hazard ratio.
+\item \code{ci}: Confidence interval of hazard ratio.
+\item \code{pval}: p-value of the effect.
+Note, one of the statistics \code{n_tot} and \code{n_tot_events}, as well as both \code{hr} and \code{ci} are required.
+}}
 
 \item{time_unit}{(\code{string})\cr label with unit of median survival time. Default \code{NULL} skips displaying unit.}
 
diff --git a/man/response_biomarkers_subgroups.Rd b/man/response_biomarkers_subgroups.Rd
index 3f3027a559..b43185f9a7 100644
--- a/man/response_biomarkers_subgroups.Rd
+++ b/man/response_biomarkers_subgroups.Rd
@@ -7,8 +7,7 @@
 \usage{
 tabulate_rsp_biomarkers(
   df,
-  vars = lifecycle::deprecated(),
-  .stats = c("n_tot", "n_rsp", "prop", "or", "ci", "pval"),
+  vars = c("n_tot", "n_rsp", "prop", "or", "ci", "pval"),
   .indent_mods = 0L
 )
 }
@@ -16,9 +15,7 @@ tabulate_rsp_biomarkers(
 \item{df}{(\code{data.frame})\cr containing all analysis variables, as returned by
 \code{\link[=extract_rsp_biomarkers]{extract_rsp_biomarkers()}}.}
 
-\item{vars}{(\code{character})\cr variable names for the primary analysis variable to be iterated over.}
-
-\item{.stats}{(\code{character})\cr the names of statistics to be reported among:
+\item{vars}{(\code{character})\cr the names of statistics to be reported among:
 \itemize{
 \item \code{n_tot}: Total number of patients per group.
 \item \code{n_rsp}: Total number of responses per group.
diff --git a/man/response_subgroups.Rd b/man/response_subgroups.Rd
index 77b748c3b0..e03ee9dd70 100644
--- a/man/response_subgroups.Rd
+++ b/man/response_subgroups.Rd
@@ -12,12 +12,7 @@ a_response_subgroups(
     "x.xxxx | (<0.0001)")
 )
 
-tabulate_rsp_subgroups(
-  lyt,
-  df,
-  vars = lifecycle::deprecated(),
-  .stats = c("n_tot", "n", "prop", "or", "ci")
-)
+tabulate_rsp_subgroups(lyt, df, vars = c("n_tot", "n", "prop", "or", "ci"))
 }
 \arguments{
 \item{.formats}{(named \code{character} or \code{list})\cr formats for the statistics. See Details in \code{analyze_vars} for more
@@ -28,9 +23,7 @@ information on the \code{"auto"} setting.}
 \item{df}{(\code{list})\cr of data frames containing all analysis variables. List should be
 created using \code{\link[=extract_rsp_subgroups]{extract_rsp_subgroups()}}.}
 
-\item{vars}{(\code{character})\cr variable names for the primary analysis variable to be iterated over.}
-
-\item{.stats}{(\code{character})\cr the names of statistics to be reported among:
+\item{vars}{(\code{character})\cr the names of statistics to be reported among:
 \itemize{
 \item \code{n}: Total number of observations per group.
 \item \code{n_rsp}: Number of responders per group.
diff --git a/man/survival_biomarkers_subgroups.Rd b/man/survival_biomarkers_subgroups.Rd
index a6cdfc9478..6c35fd44ad 100644
--- a/man/survival_biomarkers_subgroups.Rd
+++ b/man/survival_biomarkers_subgroups.Rd
@@ -7,9 +7,8 @@
 \usage{
 tabulate_survival_biomarkers(
   df,
-  vars = lifecycle::deprecated(),
+  vars = c("n_tot", "n_tot_events", "median", "hr", "ci", "pval"),
   time_unit = NULL,
-  .stats = c("n_tot", "n_tot_events", "median", "hr", "ci", "pval"),
   .indent_mods = 0L
 )
 }
@@ -17,11 +16,7 @@ tabulate_survival_biomarkers(
 \item{df}{(\code{data.frame})\cr containing all analysis variables, as returned by
 \code{\link[=extract_survival_biomarkers]{extract_survival_biomarkers()}}.}
 
-\item{vars}{(\code{character})\cr variable names for the primary analysis variable to be iterated over.}
-
-\item{time_unit}{(\code{string})\cr label with unit of median survival time. Default \code{NULL} skips displaying unit.}
-
-\item{.stats}{(\code{character})\cr the names of statistics to be reported among:
+\item{vars}{(\code{character})\cr the names of statistics to be reported among:
 \itemize{
 \item \code{n_tot_events}: Total number of events per group.
 \item \code{n_tot}: Total number of observations per group.
@@ -32,6 +27,8 @@ tabulate_survival_biomarkers(
 Note, one of the statistics \code{n_tot} and \code{n_tot_events}, as well as both \code{hr} and \code{ci} are required.
 }}
 
+\item{time_unit}{(\code{string})\cr label with unit of median survival time. Default \code{NULL} skips displaying unit.}
+
 \item{.indent_mods}{(named \code{integer})\cr indent modifiers for the labels. Defaults to 0, which corresponds to the
 unmodified default behavior. Can be negative.}
 }
diff --git a/man/survival_duration_subgroups.Rd b/man/survival_duration_subgroups.Rd
index 2c7edc456e..4dad3e1ece 100644
--- a/man/survival_duration_subgroups.Rd
+++ b/man/survival_duration_subgroups.Rd
@@ -15,9 +15,8 @@ a_survival_subgroups(
 tabulate_survival_subgroups(
   lyt,
   df,
-  vars = lifecycle::deprecated(),
+  vars = c("n_tot_events", "n_events", "median", "hr", "ci"),
   time_unit = NULL,
-  .stats = c("n_tot_events", "n_events", "median", "hr", "ci"),
   na_str = NA_character_
 )
 }
@@ -30,11 +29,7 @@ information on the \code{"auto"} setting.}
 \item{df}{(\code{list})\cr of data frames containing all analysis variables. List should be
 created using \code{\link[=extract_survival_subgroups]{extract_survival_subgroups()}}.}
 
-\item{vars}{(\code{character})\cr variable names for the primary analysis variable to be iterated over.}
-
-\item{time_unit}{(\code{string})\cr label with unit of median survival time. Default \code{NULL} skips displaying unit.}
-
-\item{.stats}{(\code{character})\cr the name of statistics to be reported among:
+\item{vars}{(\code{character})\cr the name of statistics to be reported among:
 \itemize{
 \item \code{n_tot_events}: Total number of events per group.
 \item \code{n_events}: Number of events per group.
@@ -48,6 +43,8 @@ Note, one of the statistics \code{n_tot} and \code{n_tot_events}, as well as bot
 are required.
 }}
 
+\item{time_unit}{(\code{string})\cr label with unit of median survival time. Default \code{NULL} skips displaying unit.}
+
 \item{na_str}{(\code{string})\cr string used to replace all \code{NA} or empty values in the output.}
 }
 \value{

From 6db1432399666c173b1adfd4cca1da3ae23a6aaf Mon Sep 17 00:00:00 2001
From: Emily de la Rua <emily.de_la_rua@contractors.roche.com>
Date: Mon, 6 Nov 2023 17:21:27 -0500
Subject: [PATCH 16/16] Empty commit