Add more labelling options to count_patients_with_flags

NEWS.md

@@ -5,6 +5,7 @@
 * Started deprecation cycle for `summarize_vars` and `control_summarize_vars`. Renamed into `analyze_vars` and `control_analyze_vars` to reflect underlying `rtables` machinery while keeping backward compatibility with aliases.
 * Added `ylim` argument to `g_km` to allow the user to set custom limits for the y-axis.
 * Added assertion to `g_km` which checks whether there is one arm present in the data when `annot_coxph` is true.
+* Added `flag_labels` argument to `s_count_patients_with_flags` to enable more label handling options in `count_patients_by_flags`. 
 
 ### Miscellaneous
 * Began deprecation of `time_unit_input` and `time_unit_output` arguments and replaced them with the `input_time_unit` and `num_pt_year`, respectively, in `control_incidence_rate`.

R/count_patients_with_flags.R

@@ -18,6 +18,12 @@ NULL
 #' @param .var (`character`)\cr name of the column that contains the unique identifier.
 #' @param flag_variables (`character`)\cr a character vector specifying the names of `logical`
 #'   variables from analysis dataset used for counting the number of unique identifiers.
+#' @param flag_labels (`character`)\cr vector of labels to use for flag variables.
+#'
+#' @note If `flag_labels` is not specified, variables labels will be extracted from `df`. If variables are not
+#'   labelled, variable names will be used instead. Alternatively, a named `vector` can be supplied to
+#'   `flag_variables` such that within each name-value pair the name corresponds to the variable name and the value is
+#'   the label to use for this variable.
 #'
 #' @return
 #' * `s_count_patients_with_flags()` returns the count and the fraction of unique identifiers with each particular
@@ -56,12 +62,22 @@ NULL
 s_count_patients_with_flags <- function(df,
                                         .var,
                                         flag_variables,
+                                        flag_labels = NULL,
                                         .N_col, # nolint
                                         .N_row, # nolint
                                         denom = c("n", "N_row", "N_col")) {
-  if (is.null(names(flag_variables))) flag_variables <- stats::setNames(flag_variables, flag_variables)
-  flag_names <- unname(flag_variables)
-  flag_variables <- names(flag_variables)
+  checkmate::assert_character(flag_variables)
+  if (!is.null(flag_labels)) {
+    checkmate::assert_character(flag_labels, len = length(flag_variables), any.missing = FALSE)
+    flag_names <- flag_labels
+  } else {
+    if (is.null(names(flag_variables))) {
+      flag_names <- var_labels(df[flag_variables], fill = TRUE)
+    } else {
+      flag_names <- unname(flag_variables)
+      flag_variables <- names(flag_variables)
+    }
+  }
 
   checkmate::assert_subset(flag_variables, colnames(df))
   temp <- sapply(flag_variables, function(x) {

tests/testthat/test-count_patients_with_flags.R

@@ -159,3 +159,81 @@ testthat::test_that("count_patients_with_flags works with label row specified",
   res <- testthat::expect_silent(result)
   testthat::expect_snapshot(res)
 })
+
+testthat::test_that("Custom variable label behaviour works", {
+  adae_local <- tern_ex_adae %>%
+    dplyr::mutate(
+      SER = AESER == "Y",
+      REL = AEREL == "Y",
+      CTC35 = AETOXGR %in% c("3", "4", "5"),
+      CTC45 = AETOXGR %in% c("4", "5")
+    )
+  columns <- c("SER", "REL", "CTC35", "CTC45")
+
+  # No variable labels (variable names used)
+  lyt <- basic_table() %>%
+    split_cols_by("ACTARM") %>%
+    count_patients_with_flags(
+      "USUBJID",
+      flag_variables = aesi_vars,
+      denom = "N_col",
+      var_labels = "Total number of patients with at least one",
+      show_labels = "visible"
+    )
+  result <- build_table(lyt, df = adae_local, alt_counts_df = tern_ex_adsl)
+
+  res <- testthat::expect_silent(result)
+  testthat::expect_snapshot(res)
+
+  labels <- c("Serious AE", "Related AE", "Grade 3-5 AE", "Grade 4/5 AE")
+  for (i in seq_along(columns)) {
+    attr(adae_local[[columns[i]]], "label") <- labels[i]
+  }
+  aesi_vars <- c("SER", "REL", "CTC35", "CTC45")
+
+  # Variable labels from df
+  lyt <- basic_table() %>%
+    split_cols_by("ACTARM") %>%
+    count_patients_with_flags(
+      "USUBJID",
+      flag_variables = aesi_vars,
+      denom = "N_col",
+      var_labels = "Total number of patients with at least one",
+      show_labels = "visible"
+    )
+  result <- build_table(lyt, df = adae_local, alt_counts_df = tern_ex_adsl)
+
+  res <- testthat::expect_silent(result)
+  testthat::expect_snapshot(res)
+
+  # Custom labels via flag_labels argument
+  lyt <- basic_table() %>%
+    split_cols_by("ACTARM") %>%
+    count_patients_with_flags(
+      "USUBJID",
+      flag_variables = aesi_vars,
+      flag_labels = c("Category 1", "Category 2", "Category 3", "Category 4"),
+      denom = "N_col",
+      var_labels = "Total number of patients with at least one",
+      show_labels = "visible"
+    )
+  result <- build_table(lyt, df = adae_local, alt_counts_df = tern_ex_adsl)
+
+  res <- testthat::expect_silent(result)
+  testthat::expect_snapshot(res)
+
+  # Labels supplied within flag_variables argument
+  lyt <- basic_table() %>%
+    split_cols_by("ACTARM") %>%
+    count_patients_with_flags(
+      "USUBJID",
+      flag_variables = formatters::var_labels(adae_local[, aesi_vars]),
+      denom = "N_col",
+      var_labels = "Total number of patients with at least one",
+      show_labels = "visible"
+    )
+  result <- build_table(lyt, df = adae_local, alt_counts_df = tern_ex_adsl)
+
+  res <- testthat::expect_silent(result)
+  testthat::expect_snapshot(res)
+})