fix lint checks + merge from main

Merge remote-tracking branch 'refs/remotes/origin/1301-feature-request-add-confidence-intervals-for-quantiles-in-surv_time' into 1301-feature-request-add-confidence-intervals-for-quantiles-in-surv_time

# Conflicts:
#	R/survival_time.R

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: tern
 Title: Create Common TLGs Used in Clinical Trials
-Version: 0.9.5.9020
-Date: 2024-09-05
+Version: 0.9.5.9021
+Date: 2024-09-06
 Authors@R: c(
     person("Joe", "Zhu", , "[email protected]", role = c("aut", "cre")),
     person("Daniel", "Sabanés Bové", , "[email protected]", role = "aut"),

NEWS.md

@@ -1,4 +1,4 @@
-# tern 0.9.5.9020
+# tern 0.9.5.9021
 ### Enhancements
 * Added `errorbar_width` and `linetype` parameters to `g_lineplot`.
 * Reworking of `summarize_glm_count()` documentation and all its associated functions to better describe the results and the functions' purpose.
@@ -20,6 +20,7 @@
 ### Miscellaneous
 * Began deprecation of the confusing functions `summary_formats` and `summary_labels`.
 * Enhanced general descriptions of analyze and summarize functions throughout package documentation.
+* Finalized deprecation of the `strata` and `cohort_id` arguments to `g_lineplot`.
 
 # tern 0.9.5
 

R/argument_convention.R

@@ -31,7 +31,6 @@
 #' @param conf_level (`proportion`)\cr confidence level of the interval.
 #' @param data (`data.frame`)\cr the dataset containing the variables to summarize.
 #' @param df (`data.frame`)\cr data set containing all analysis variables.
-#' @param draw (`flag`)\cr whether the plot should be drawn.
 #' @param groups_lists (named `list` of `list`)\cr optionally contains for each `subgroups` variable a
 #'   list, which specifies the new group levels via the names and the
 #'   levels that belong to it in the character vectors that are elements of the list.
@@ -49,8 +48,6 @@
 #' @param nested (`flag`)\cr whether this layout instruction should be applied within the existing layout structure _if
 #'   possible (`TRUE`, the default) or as a new top-level element (`FALSE`). Ignored if it would nest a split.
 #'   underneath analyses, which is not allowed.
-#' @param newpage (`flag`)\cr whether the plot should be drawn on a new page.
-#'   Only considered if `draw = TRUE` is used.
 #' @param prune_zero_rows (`flag`)\cr whether to prune all zero rows.
 #' @param riskdiff (`flag`)\cr whether a risk difference column is present. When set to `TRUE`, [add_riskdiff()] must be
 #'   used as `split_fun` in the prior column split of the table layout, specifying which columns should be compared.
@@ -72,7 +69,6 @@
 #' @param ylim (`numeric(2)`)\cr vector containing lower and upper limits for the y-axis, respectively.
 #'   If `NULL` (default), the default scale range is used.
 #'
-#'
 #' @details Although this function just returns `NULL` it has two uses, for
 #'   the `tern` users it provides a documentation of arguments that are
 #'   commonly and consistently used in the framework. For the developer it adds a

R/g_forest.R

@@ -182,19 +182,19 @@ g_forest <- function(tbl,
   # Deprecated argument warnings
   if (lifecycle::is_present(width_row_names)) {
     lifecycle::deprecate_warn(
-      "0.9.3", "g_forest(width_row_names)", "g_forest(lbl_col_padding)",
+      "0.9.4", "g_forest(width_row_names)", "g_forest(lbl_col_padding)",
       details = "The width of the row label column can be adjusted via the `lbl_col_padding` parameter."
     )
   }
   if (lifecycle::is_present(width_forest)) {
     lifecycle::deprecate_warn(
-      "0.9.3", "g_forest(width_forest)", "g_forest(rel_width_forest)",
+      "0.9.4", "g_forest(width_forest)", "g_forest(rel_width_forest)",
       details = "Relative width of the forest plot (as a proportion) can be set via the `rel_width_forest` parameter."
     )
   }
   if (lifecycle::is_present(gp)) {
     lifecycle::deprecate_warn(
-      "0.9.3", "g_forest(gp)", "g_forest(ggtheme)",
+      "0.9.4", "g_forest(gp)", "g_forest(ggtheme)",
       details = paste(
         "`g_forest` is now generated as a `ggplot` object.",
         "Additional display settings should be supplied via the `ggtheme` parameter."
@@ -203,13 +203,13 @@ g_forest <- function(tbl,
   }
   if (lifecycle::is_present(draw)) {
     lifecycle::deprecate_warn(
-      "0.9.3", "g_forest(draw)",
+      "0.9.4", "g_forest(draw)",
       details = "`g_forest` now generates `ggplot` objects. This parameter has no effect."
     )
   }
   if (lifecycle::is_present(newpage)) {
     lifecycle::deprecate_warn(
-      "0.9.3", "g_forest(newpage)",
+      "0.9.4", "g_forest(newpage)",
       details = "`g_forest` now generates `ggplot` objects. This parameter has no effect."
     )
   }

R/g_lineplot.R

@@ -548,9 +548,7 @@ h_format_row <- function(x, format, labels = NULL) {
 #' @param x (`string`)\cr x-variable name.
 #' @param y (`string`)\cr y-variable name.
 #' @param group_var (`string` or `NA`)\cr group variable name.
-#' @param strata `r lifecycle::badge("deprecated")` use the `group_var` parameter instead.
 #' @param subject_var (`string` or `NA`)\cr subject variable name.
-#' @param cohort_id `r lifecycle::badge("deprecated")` use the `subject_var` parameter instead.
 #' @param facet_var (`string` or `NA`)\cr faceting variable name.
 #' @param paramcd (`string` or `NA`)\cr parameter code variable name.
 #' @param y_unit (`string` or `NA`)\cr y-axis unit variable name.
@@ -568,19 +566,7 @@ control_lineplot_vars <- function(x = "AVISIT",
                                   facet_var = NA,
                                   paramcd = "PARAMCD",
                                   y_unit = "AVALU",
-                                  subject_var = "USUBJID",
-                                  strata = lifecycle::deprecated(),
-                                  cohort_id = lifecycle::deprecated()) {
-  if (lifecycle::is_present(strata)) {
-    lifecycle::deprecate_warn("0.9.2", "control_lineplot_vars(strata)", "control_lineplot_vars(group_var)")
-    group_var <- strata
-  }
-
-  if (lifecycle::is_present(cohort_id)) {
-    lifecycle::deprecate_warn("0.9.2", "control_lineplot_vars(cohort_id)", "control_lineplot_vars(subject_id)")
-    subject_id <- cohort_id
-  }
-
+                                  subject_var = "USUBJID") {
   checkmate::assert_string(x)
   checkmate::assert_string(y)
   checkmate::assert_string(group_var, na.ok = TRUE, null.ok = TRUE)

R/h_km.R

@@ -188,7 +188,7 @@ h_tbl_coxph_pairwise <- function(df,
   if ("strat" %in% names(variables)) {
     warning(
       "Warning: the `strat` element name of the `variables` list argument to `h_tbl_coxph_pairwise() ",
-      "was deprecated in tern 0.9.3.\n  ",
+      "was deprecated in tern 0.9.4.\n  ",
       "Please use the name `strata` instead of `strat` in the `variables` argument."
     )
     variables[["strata"]] <- variables[["strat"]]

R/h_response_biomarkers_subgroups.R

@@ -49,7 +49,7 @@ h_rsp_to_logistic_variables <- function(variables, biomarker) {
   if ("strat" %in% names(variables)) {
     warning(
       "Warning: the `strat` element name of the `variables` list argument to `h_rsp_to_logistic_variables() ",
-      "was deprecated in tern 0.9.3.\n  ",
+      "was deprecated in tern 0.9.4.\n  ",
       "Please use the name `strata` instead of `strat` in the `variables` argument."
     )
     variables[["strata"]] <- variables[["strat"]]
@@ -106,7 +106,7 @@ h_logistic_mult_cont_df <- function(variables,
   if ("strat" %in% names(variables)) {
     warning(
       "Warning: the `strat` element name of the `variables` list argument to `h_logistic_mult_cont_df() ",
-      "was deprecated in tern 0.9.3.\n  ",
+      "was deprecated in tern 0.9.4.\n  ",
       "Please use the name `strata` instead of `strat` in the `variables` argument."
     )
     variables[["strata"]] <- variables[["strat"]]

R/h_response_subgroups.R

@@ -328,7 +328,7 @@ h_odds_ratio_subgroups_df <- function(variables,
   if ("strat" %in% names(variables)) {
     warning(
       "Warning: the `strat` element name of the `variables` list argument to `h_odds_ratio_subgroups_df() ",
-      "was deprecated in tern 0.9.3.\n  ",
+      "was deprecated in tern 0.9.4.\n  ",
       "Please use the name `strata` instead of `strat` in the `variables` argument."
     )
     variables[["strata"]] <- variables[["strat"]]

R/h_survival_biomarkers_subgroups.R

@@ -110,7 +110,7 @@ h_coxreg_mult_cont_df <- function(variables,
   if ("strat" %in% names(variables)) {
     warning(
       "Warning: the `strat` element name of the `variables` list argument to `h_coxreg_mult_cont_df() ",
-      "was deprecated in tern 0.9.3.\n  ",
+      "was deprecated in tern 0.9.4.\n  ",
       "Please use the name `strata` instead of `strat` in the `variables` argument."
     )
     variables[["strata"]] <- variables[["strat"]]

R/h_survival_duration_subgroups.R

@@ -335,7 +335,7 @@ h_coxph_subgroups_df <- function(variables,
   if ("strat" %in% names(variables)) {
     warning(
       "Warning: the `strat` element name of the `variables` list argument to `h_coxph_subgroups_df() ",
-      "was deprecated in tern 0.9.3.\n  ",
+      "was deprecated in tern 0.9.4.\n  ",
       "Please use the name `strata` instead of `strat` in the `variables` argument."
     )
     variables[["strata"]] <- variables[["strat"]]

R/response_biomarkers_subgroups.R

@@ -195,7 +195,7 @@ extract_rsp_biomarkers <- function(variables,
   if ("strat" %in% names(variables)) {
     warning(
       "Warning: the `strat` element name of the `variables` list argument to `extract_rsp_biomarkers() ",
-      "was deprecated in tern 0.9.3.\n  ",
+      "was deprecated in tern 0.9.4.\n  ",
       "Please use the name `strata` instead of `strat` in the `variables` argument."
     )
     variables[["strata"]] <- variables[["strat"]]

R/response_subgroups.R

@@ -99,7 +99,7 @@ extract_rsp_subgroups <- function(variables,
   if ("strat" %in% names(variables)) {
     warning(
       "Warning: the `strat` element name of the `variables` list argument to `extract_rsp_subgroups() ",
-      "was deprecated in tern 0.9.3.\n  ",
+      "was deprecated in tern 0.9.4.\n  ",
       "Please use the name `strata` instead of `strat` in the `variables` argument."
     )
     variables[["strata"]] <- variables[["strat"]]

R/survival_biomarkers_subgroups.R

@@ -116,7 +116,7 @@ extract_survival_biomarkers <- function(variables,
   if ("strat" %in% names(variables)) {
     warning(
       "Warning: the `strat` element name of the `variables` list argument to `extract_survival_biomarkers() ",
-      "was deprecated in tern 0.9.3.\n  ",
+      "was deprecated in tern 0.9.4.\n  ",
       "Please use the name `strata` instead of `strat` in the `variables` argument."
     )
     variables[["strata"]] <- variables[["strat"]]

R/survival_coxph_pairwise.R

@@ -47,7 +47,7 @@ s_coxph_pairwise <- function(df,
                              strat = lifecycle::deprecated(),
                              control = control_coxph()) {
   if (lifecycle::is_present(strat)) {
-    lifecycle::deprecate_warn("0.9.3", "s_coxph_pairwise(strat)", "s_coxph_pairwise(strata)")
+    lifecycle::deprecate_warn("0.9.4", "s_coxph_pairwise(strat)", "s_coxph_pairwise(strata)")
     strata <- strat
   }
 

R/survival_duration_subgroups.R

@@ -123,7 +123,7 @@ extract_survival_subgroups <- function(variables,
   if ("strat" %in% names(variables)) {
     warning(
       "Warning: the `strat` element name of the `variables` list argument to `extract_survival_subgroups() ",
-      "was deprecated in tern 0.9.3.\n  ",
+      "was deprecated in tern 0.9.4.\n  ",
       "Please use the name `strata` instead of `strat` in the `variables` argument."
     )
     variables[["strata"]] <- variables[["strat"]]

R/survival_time.R

@@ -81,9 +81,11 @@ s_surv_time <- function(df,
   srv_qt_ci <- lapply(quantiles, function(x) {
     name <- as.character(100 * x)
 
-    c(srv_qt_tab_pre[[paste0("quantile.", name)]],
+    c(
+      srv_qt_tab_pre[[paste0("quantile.", name)]],
       srv_qt_tab_pre[[paste0("lower.", name)]],
-      srv_qt_tab_pre[[paste0("upper.", name)]])
+      srv_qt_tab_pre[[paste0("upper.", name)]]
+    )
   })
 
   list(
@@ -107,7 +109,6 @@ s_surv_time <- function(df,
     quantiles_ci_2 = formatters::with_label(
       unname(srv_qt_ci[[2]]), paste0(quantiles[2] * 100, "%-ile with ", f_conf_level(conf_level))
     )
-
   )
 }
 
@@ -144,13 +145,17 @@ a_surv_time <- function(df,
   rng_censor_upr <- x_stats[["range_censor"]][2]
 
   # Use method-specific defaults
-  fmts <- c(median_ci = "(xx.x, xx.x)", quantiles = "xx.x, xx.x", range = "xx.x to xx.x",
-            median_ci_1_line = "xx.x (xx.x - xx.x)",
-            quantiles_ci_1 = "xx.x (xx.x - xx.x)", quantiles_ci_2 = "xx.x (xx.x - xx.x)")
-  lbls <- c(median_ci = "95% CI", range = "Range", range_censor = "Range (censored)", range_event = "Range (event)",
-            median_ci_1_line = "Median 95% CI",
-            quantiles_ci_1 = "25%-ile with 95% CI",
-            quantiles_ci_2 = "75%-ile with 95% CI")
+  fmts <- c(
+    median_ci = "(xx.x, xx.x)", quantiles = "xx.x, xx.x", range = "xx.x to xx.x",
+    median_ci_1_line = "xx.x (xx.x - xx.x)",
+    quantiles_ci_1 = "xx.x (xx.x - xx.x)", quantiles_ci_2 = "xx.x (xx.x - xx.x)"
+  )
+  lbls <- c(
+    median_ci = "95% CI", range = "Range", range_censor = "Range (censored)", range_event = "Range (event)",
+    median_ci_1_line = "Median 95% CI",
+    quantiles_ci_1 = "25%-ile with 95% CI",
+    quantiles_ci_2 = "75%-ile with 95% CI"
+  )
   lbls_custom <- .labels
   .formats <- c(.formats, fmts[setdiff(names(fmts), names(.formats))])
   .labels <- c(.labels, lbls[setdiff(names(lbls), names(lbls_custom))])

R/utils_default_stats_formats_labels.R

@@ -345,14 +345,14 @@ labels_use_control <- function(labels_default, control, labels_custom = NULL) {
     )
   }
   if ("quantiles" %in% names(control) && "quantiles_ci_1" %in% names(labels_default) &&
-      !"quantiles_ci_1" %in% names(labels_custom)) { # nolint
+    !"quantiles_ci_1" %in% names(labels_custom)) { # nolint
     labels_default["quantiles_ci_1"] <- gsub(
       "[0-9]+%-ile", paste0(control[["quantiles"]][1] * 100, "%-ile", ""),
       labels_default["quantiles_ci_1"]
     )
   }
   if ("quantiles" %in% names(control) && "quantiles_ci_2" %in% names(labels_default) &&
-      !"quantiles_ci_2" %in% names(labels_custom)) { # nolint
+    !"quantiles_ci_2" %in% names(labels_custom)) { # nolint
     labels_default["quantiles_ci_2"] <- gsub(
       "[0-9]+%-ile", paste0(control[["quantiles"]][2] * 100, "%-ile", ""),
       labels_default["quantiles_ci_2"]
@@ -536,7 +536,7 @@ tern_default_labels <- c(
 #' @export
 summary_formats <- function(type = "numeric", include_pval = FALSE) {
   lifecycle::deprecate_warn(
-    "0.9.5.9005", "summary_formats()",
+    "0.9.6", "summary_formats()",
     details = 'Use get_formats_from_stats(get_stats("analyze_vars_numeric", add_pval = include_pval)) instead'
   )
   met_grp <- paste0(c("analyze_vars", type), collapse = "_")
@@ -559,7 +559,7 @@ summary_formats <- function(type = "numeric", include_pval = FALSE) {
 #' @export
 summary_labels <- function(type = "numeric", include_pval = FALSE) {
   lifecycle::deprecate_warn(
-    "0.9.5.9005", "summary_formats()",
+    "0.9.6", "summary_formats()",
     details = 'Use get_labels_from_stats(get_stats("analyze_vars_numeric", add_pval = include_pval)) instead'
   )
   met_grp <- paste0(c("analyze_vars", type), collapse = "_")

tests/testthat/test-g_lineplot.R

@@ -138,9 +138,6 @@ testthat::test_that("g_lineplot xticks, xlim, and ylim arguments work", {
 
 testthat::test_that("control_lineplot_vars works", {
   testthat::expect_silent(control_lineplot_vars(group_var = NA))
-
-  # Deprecation warnings work
-  lifecycle::expect_deprecated(lifecycle::expect_deprecated(control_lineplot_vars(strata = NA, cohort_id = NA)))
 })
 
 testthat::test_that("g_lineplot works with no strata (group_var) and allows points when only one strata is provided", {