Finalize deprecation of <0.9.4 arguments (#1304)

Fixes #1303

NEWS.md

@@ -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/utils_default_stats_formats_labels.R

@@ -514,7 +514,7 @@ 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 = "_")
@@ -537,7 +537,7 @@ 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", {