Update lifecycle badges (#1412)

Part of insightsengineering/coredev-tasks#649

Removed stable badges.
Changed `depracate_warn/soft` -> `depracate_stop` for parameters
deprecated before 0.9.1. On CRAN we have 0.10.0, so next one is 0.10.1
or higher.

---------

Signed-off-by: Marcin <[email protected]>
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
Co-authored-by: Dawid Kałędkowski <[email protected]>

Author: 3 people

R/arm_ref_comp.R

@@ -1,6 +1,6 @@
 #' Observer for Treatment reference variable
 #'
-#' @description `r lifecycle::badge("stable")`
+#' @description
 #' Updates the reference and comparison Treatments when the selected Treatment variable changes
 #'
 #' @param session (`environment`)\cr shiny session
@@ -93,7 +93,7 @@ arm_ref_comp_observer <- function(session,
 
 #' Check if the Treatment variable is reference or compare
 #'
-#' @description `r lifecycle::badge("stable")`
+#' @description Check Treatment variable type.
 #' @param x (`character`)\cr Name of the variable
 #' @param df_to_check (`data.frame`)\cr table to check
 #' @param module (`character`)\cr teal module the ref and comp are called in

R/facet_grid_formula.R

@@ -2,7 +2,7 @@
 
 #' Facetting formula `x_facet ~ y_facet`
 #'
-#' @description `r lifecycle::badge("stable")`
+#' @description
 #' Replaces `x_facet` or `y_facet` by . when empty character
 #'
 #' @md

R/tm_g_ipp.R

@@ -35,21 +35,12 @@ template_g_ipp <- function(dataname = "ANL",
                            avalu_var = "AVALU",
                            id_var = "USUBJID",
                            visit_var = "AVISIT",
-                           base_var = lifecycle::deprecated(),
                            baseline_var = "BASE",
                            add_baseline_hline = FALSE,
                            separate_by_obs = FALSE,
                            ggplot2_args = teal.widgets::ggplot2_args(),
                            suppress_legend = FALSE,
                            add_avalu = TRUE) {
-  if (lifecycle::is_present(base_var)) {
-    baseline_var <- base_var
-    warning(
-      "The `base_var` argument of `template_g_ipp()` is deprecated as of teal.modules.clinical 0.8.16. ",
-      "Please use the `baseline_var` argument instead.",
-      call. = FALSE
-    )
-  }
 
   checkmate::assert_string(dataname)
   checkmate::assert_string(paramcd)
@@ -175,6 +166,7 @@ template_g_ipp <- function(dataname = "ANL",
 #' @inheritParams module_arguments
 #' @inheritParams teal::module
 #' @inheritParams template_g_ipp
+#' @inheritParams template_arguments
 #' @param arm_var ([teal.transform::choices_selected()])\cr object with
 #'   all available choices and preselected option for variable values that can be used as arm variable.
 #'
@@ -324,14 +316,11 @@ tm_g_ipp <- function(label,
                      transformators = list(),
                      decorators = list()) {
   if (lifecycle::is_present(base_var)) {
-    baseline_var <- base_var
-    warning(
-      "The `base_var` argument of `tm_g_ipp()` is deprecated as of teal.modules.clinical 0.8.16. ",
-      "Please use the `baseline_var` argument instead.",
-      call. = FALSE
+    lifecycle::deprecate_stop(
+      when = "0.8.16",
+      what = "tm_g_ipp(base_var)",
+      details = "Please use the `baseline_var` argument instead."
     )
-  } else {
-    base_var <- baseline_var # resolves missing argument error
   }
 
   message("Initializing tm_g_ipp")

R/tm_g_km.R

@@ -40,32 +40,10 @@ template_g_km <- function(dataname = "ANL",
                           control_annot_surv_med = control_surv_med_annot(),
                           control_annot_coxph = tern::control_coxph_annot(x = 0.27, y = 0.35, w = 0.3),
                           legend_pos = NULL,
-                          position_coxph = lifecycle::deprecated(),
-                          width_annots = lifecycle::deprecated(),
                           rel_height_plot = 0.80,
                           ci_ribbon = FALSE,
                           title = "KM Plot") {
-  if (lifecycle::is_present(position_coxph)) {
-    control_annot_coxph[["x"]] <- position_coxph[1]
-    control_annot_coxph[["y"]] <- position_coxph[2]
-    lifecycle::deprecate_warn(
-      "0.8.17",
-      "template_g_km(position_coxph)",
-      details = "Please use the 'x' and 'y' elements of the `control_annot_coxph` argument instead."
-    )
-  }
-  if (lifecycle::is_present(width_annots)) {
-    control_annot_surv_med[["w"]] <- width_annots[["surv_med"]]
-    control_annot_coxph[["w"]] <- width_annots[["coxph"]]
-    lifecycle::deprecate_warn(
-      "0.8.17",
-      "template_g_km(width_annots)",
-      details = paste(
-        "Please use the 'w' element of the `control_annot_surv_med`",
-        "and `control_annot_coxph` arguments instead."
-      )
-    )
-  }
+
   checkmate::assert_string(dataname)
   checkmate::assert_string(arm_var)
   checkmate::assert_string(aval_var)

R/tm_g_lineplot.R

@@ -5,7 +5,6 @@
 #' @inheritParams tern::g_lineplot
 #' @inheritParams tern::control_lineplot_vars
 #' @inheritParams template_arguments
-#' @param strata `r lifecycle::badge("deprecated")` Please use the `group_var` argument instead.
 #' @param group_var (`string` or `NA`)\cr group variable name.
 #' @param param (`character`)\cr parameter to filter the data by.
 #' @param incl_screen (`logical`)\cr whether the screening visit should be included.
@@ -23,7 +22,6 @@
 #'
 #' @keywords internal
 template_g_lineplot <- function(dataname = "ANL",
-                                strata = lifecycle::deprecated(),
                                 group_var = "ARM",
                                 x = "AVISIT",
                                 y = "AVAL",
@@ -42,14 +40,6 @@ template_g_lineplot <- function(dataname = "ANL",
                                 title = "Line Plot",
                                 y_lab = "",
                                 ggplot2_args = teal.widgets::ggplot2_args()) {
-  if (lifecycle::is_present(strata)) {
-    warning(
-      "The `strata` argument of `template_g_lineplot()` is deprecated as of teal.modules.clinical 0.9.1. ",
-      "Please use the `group_var` argument instead.",
-      call. = FALSE
-    )
-    group_var <- strata
-  }
 
   checkmate::assert_string(dataname)
   checkmate::assert_string(group_var)
@@ -212,6 +202,7 @@ template_g_lineplot <- function(dataname = "ANL",
 #' @inheritParams module_arguments
 #' @inheritParams teal::module
 #' @inheritParams template_g_lineplot
+#' @param strata `r lifecycle::badge("deprecated")` Please use the `group_var` argument instead.
 #'
 #' @inherit module_arguments return seealso
 #'
@@ -327,14 +318,11 @@ tm_g_lineplot <- function(label,
                           transformators = list(),
                           decorators = list()) {
   if (lifecycle::is_present(strata)) {
-    warning(
-      "The `strata` argument of `tm_g_lineplot()` is deprecated as of teal.modules.clinical 0.9.1. ",
-      "Please use the `group_var` argument instead.",
-      call. = FALSE
+    lifecycle::deprecate_stop(
+      when = "0.9.1",
+      what = "tm_g_lineplot(strata)",
+      with = "tm_g_lineplot(group_var)"
     )
-    group_var <- strata
-  } else {
-    strata <- group_var # resolves missing argument error
   }
 
   # Now handle 'parentname' calculation based on 'group_var'

R/tm_g_pp_vitals.R

@@ -15,19 +15,10 @@ template_vitals <- function(dataname = "ANL",
                             paramcd = "PARAMCD",
                             paramcd_levels = c("SYSBP", "DIABP", "PUL", "RESP", "OXYSAT", "WGHT", "TEMP"),
                             xaxis = "ADY",
-                            aval = lifecycle::deprecated(),
                             aval_var = "AVAL",
                             patient_id,
                             font_size = 12L,
                             ggplot2_args = teal.widgets::ggplot2_args()) {
-  if (lifecycle::is_present(aval)) {
-    aval_var <- aval
-    warning(
-      "The `aval` argument of `template_vitals()` is deprecated as of teal.modules.clinical 0.8.16. ",
-      "Please use the `aval_var` argument instead.",
-      call. = FALSE
-    )
-  }
 
   checkmate::assert_string(dataname)
   checkmate::assert_string(paramcd)
@@ -205,6 +196,7 @@ template_vitals <- function(dataname = "ANL",
 #' @inheritParams module_arguments
 #' @inheritParams teal::module
 #' @inheritParams template_vitals
+#' @inheritParams template_arguments
 #' @param xaxis ([teal.transform::choices_selected()])\cr object with all
 #'   available choices and preselected option for the time variable from `dataname` to be put on the plot x-axis.
 #'
@@ -299,14 +291,11 @@ tm_g_pp_vitals <- function(label,
                            transformators = list(),
                            decorators = list()) {
   if (lifecycle::is_present(aval)) {
-    aval_var <- aval
-    warning(
-      "The `aval` argument of `tm_g_pp_vitals()` is deprecated as of teal.modules.clinical 0.8.16. ",
-      "Please use the `aval_var` argument instead.",
-      call. = FALSE
+    lifecycle::deprecate_stop(
+      when = "0.8.16",
+      what = "tm_g_pp_vitals(aval)",
+      with = "tm_g_pp_vitals(aval_var)"
     )
-  } else {
-    aval <- aval_var # resolves missing argument error
   }
 
   message("Initializing tm_g_pp_vitals")

R/tm_t_logistic.R

@@ -9,7 +9,6 @@
 #' @param topleft (`character`)\cr text to use as top-left annotation in the table.
 #' @param interaction_var (`character`)\cr names of the variables that can be used for interaction variable selection.
 #' @param responder_val (`character`)\cr values of the responder variable corresponding with a successful response.
-#' @param paramcd `r lifecycle::badge("deprecated")` The `paramcd` argument is not used in this function.
 #' @param label_paramcd (`character`)\cr label of response parameter value to print in the table title.
 #'
 #' @inherit template_arguments return
@@ -20,7 +19,6 @@
 template_logistic <- function(dataname,
                               arm_var,
                               aval_var,
-                              paramcd = lifecycle::deprecated(),
                               label_paramcd,
                               cov_var,
                               interaction_var,
@@ -32,9 +30,6 @@ template_logistic <- function(dataname,
                               responder_val = c("CR", "PR"),
                               at = NULL,
                               basic_table_args = teal.widgets::basic_table_args()) {
-  if (lifecycle::is_present(paramcd)) {
-    lifecycle::deprecate_warn("0.8.16", "template_logistic(paramcd)")
-  }
 
   # Common assertion no matter if arm_var is NULL or not.
   checkmate::assert_string(dataname)

R/tm_t_pp_laboratory.R

@@ -19,30 +19,10 @@ template_laboratory <- function(dataname = "ANL",
                                 param = "PARAM",
                                 anrind = "ANRIND",
                                 timepoints = "ADY",
-                                aval = lifecycle::deprecated(),
                                 aval_var = "AVAL",
-                                avalu = lifecycle::deprecated(),
                                 avalu_var = "AVALU",
                                 patient_id = NULL,
                                 round_value = 0L) {
-  if (lifecycle::is_present(aval)) {
-    aval_var <- aval
-    warning(
-      "The `aval` argument of `template_laboratory()` is deprecated as of teal.modules.clinical 0.8.16. ",
-      "Please use the `aval_var` argument instead.",
-      call. = FALSE
-    )
-  }
-
-  if (lifecycle::is_present(avalu)) {
-    avalu_var <- avalu
-    warning(
-      "The `avalu` argument of `template_laboratory()` is deprecated as of teal.modules.clinical 0.8.16. ",
-      "Please use the `avalu_var` argument instead.",
-      call. = FALSE
-    )
-  }
-
   checkmate::assert_string(dataname)
   checkmate::assert_string(paramcd)
   checkmate::assert_string(param)
@@ -133,6 +113,7 @@ template_laboratory <- function(dataname = "ANL",
 #' @inheritParams module_arguments
 #' @inheritParams teal::module
 #' @inheritParams template_laboratory
+#' @inheritParams template_arguments
 #' @param param ([teal.transform::choices_selected()])\cr object with all
 #'   available choices and preselected option for the `PARAM` variable from `dataname`.
 #' @param timepoints ([teal.transform::choices_selected()])\cr object with all
@@ -223,25 +204,19 @@ tm_t_pp_laboratory <- function(label,
   }
 
   if (lifecycle::is_present(aval)) {
-    aval_var <- aval
-    warning(
-      "The `aval` argument of `tm_t_pp_laboratory()` is deprecated as of teal.modules.clinical 0.8.16. ",
-      "Please use the `aval_var` argument instead.",
-      call. = FALSE
+    lifecycle::deprecate_stop(
+      when = "0.8.16",
+      what = "tm_t_pp_laboratory(aval)",
+      with = "tm_t_pp_laboratory(aval_var)"
     )
-  } else {
-    aval <- aval_var # resolves missing argument error
   }
 
   if (lifecycle::is_present(avalu)) {
-    avalu_var <- avalu
-    warning(
-      "The `avalu` argument of `tm_t_pp_laboratory()` is deprecated as of teal.modules.clinical 0.8.16. ",
-      "Please use the `avalu_var` argument instead.",
-      call. = FALSE
+    lifecycle::deprecate_stop(
+      when = "0.8.16",
+      what = "tm_t_pp_laboratory(avalu)",
+      with = "tm_t_pp_laboratory(avalu_var)"
     )
-  } else {
-    avalu <- avalu_var # resolves missing argument error
   }
 
   message("Initializing tm_t_pp_laboratory")

R/tm_t_shift_by_arm.R

@@ -20,21 +20,12 @@ template_shift_by_arm <- function(dataname,
                                   treatment_flag_var = "ONTRTFL",
                                   treatment_flag = "Y",
                                   aval_var = "ANRIND",
-                                  base_var = lifecycle::deprecated(),
                                   baseline_var = "BNRIND",
                                   na.rm = FALSE, # nolint: object_name.
                                   na_level = tern::default_na_str(),
                                   add_total = FALSE,
                                   total_label = default_total_label(),
                                   basic_table_args = teal.widgets::basic_table_args()) {
-  if (lifecycle::is_present(base_var)) {
-    baseline_var <- base_var
-    warning(
-      "The `base_var` argument of `template_shift_by_arm()` is deprecated as of teal.modules.clinical 0.8.16. ",
-      "Please use the `baseline_var` argument instead.",
-      call. = FALSE
-    )
-  }
 
   checkmate::assert_string(dataname)
   checkmate::assert_string(parentname)
@@ -192,6 +183,7 @@ template_shift_by_arm <- function(dataname,
 #' @inheritParams module_arguments
 #' @inheritParams teal::module
 #' @inheritParams template_shift_by_arm
+#' @inheritParams template_arguments
 #'
 #' @inherit module_arguments return seealso
 #'
@@ -300,14 +292,12 @@ tm_t_shift_by_arm <- function(label,
                               transformators = list(),
                               decorators = list()) {
   if (lifecycle::is_present(base_var)) {
-    baseline_var <- base_var
-    warning(
-      "The `base_var` argument of `tm_t_shift_by_arm()` is deprecated as of teal.modules.clinical 0.8.16. ",
-      "Please use the `baseline_var` argument instead.",
-      call. = FALSE
+    lifecycle::deprecate_stop( 
+      when = "0.8.16",
+      what = "tm_t_shift_by_arm(base_var)",
+      details = "Please use the `baseline_var` argument instead."
     )
-  } else {
-    base_var <- baseline_var # resolves missing argument error
+    baseline_var <- base_var
   }
 
   message("Initializing tm_t_shift_by_arm")