Fix indent modifier bug in count_patients_with_flags() (#1350)

Fixes #1349
insightsengineering · Nov 6, 2024 · a7b7523 · a7b7523
1 parent 435fd51
commit a7b7523
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Showing 3 changed files with 62 additions and 7 deletions.
diff --git a/R/count_patients_with_flags.R b/R/count_patients_with_flags.R
@@ -155,13 +155,15 @@ a_count_patients_with_flags <- function(df,
     NULL
   }
   .indent_mods <- get_indents_from_stats(.stats, .indent_mods, row_nms = flag_variables)
-  .indent_mods <- sapply(names(.indent_mods), function(x) {
-    if (.indent_mods[x] == 0 && !is.null(length(indent_stat_def))) {
-      idx <- which(names(indent_stat_def) == gsub("\\..*", "", x))
-      if (length(idx) > 0) .indent_mods[[x]] <- indent_stat_def[[idx]]
-    }
-    .indent_mods[x]
-  })
+  if (!is.null(names(.indent_mods))) {
+    .indent_mods <- sapply(names(.indent_mods), function(x) {
+      if (.indent_mods[x] == 0 && !is.null(length(indent_stat_def))) {
+        idx <- which(names(indent_stat_def) == gsub("\\..*", "", x))
+        if (length(idx) > 0) .indent_mods[[x]] <- indent_stat_def[[idx]]
+      }
+      .indent_mods[x]
+    })
+  }
 
   if ("count_fraction_fixed_dp" %in% .stats) x_stats[["count_fraction_fixed_dp"]] <- x_stats[["count_fraction"]]
   x_stats <- x_stats[.stats]

diff --git a/tests/testthat/_snaps/count_patients_with_flags.md b/tests/testthat/_snaps/count_patients_with_flags.md
@@ -467,3 +467,14 @@
       SAE                      53 (26.2%)   49 (27.7%)     39 (24.1%)          -1.4 (-10.4 - 7.5)     
       SAE with fatal outcome   50 (24.8%)   47 (26.6%)     42 (25.9%)          -1.8 (-10.6 - 7.0)     
 
+# count_patients_with_flags works with single indent mod value
+
+    Code
+      res
+    Output
+                                                                           A           B    
+                                                                         (N=6)       (N=4)  
+      ——————————————————————————————————————————————————————————————————————————————————————
+            Total number of patients with at least one adverse event   1 (16.7%)   1 (25.0%)
+            Total number of patients with fatal AEs                        0       1 (25.0%)
+
diff --git a/tests/testthat/test-count_patients_with_flags.R b/tests/testthat/test-count_patients_with_flags.R
@@ -386,3 +386,45 @@ testthat::test_that("count_patients_with_flags works as expected with risk diffe
   res <- testthat::expect_silent(result)
   testthat::expect_snapshot(res)
 })
+
+testthat::test_that("count_patients_with_flags works with single indent mod value", {
+  test_data <- tibble::tibble(
+    SUBJID = c("1001", "1001", "1001", "1002", "1002", "1002", "1003", "1003", "1003"),
+    ARM = factor(c("A", "A", "A", "A", "A", "A", "B", "B", "B"), levels = c("A", "B")),
+    TRTEMFL = c("Y", "", "", "NA", "", "", "Y", "", ""),
+    AEOUT = c("", "", "", "", "", "", "FATAL", "", "FATAL")
+  ) %>%
+    dplyr::mutate(
+      flag1 = TRTEMFL == "Y",
+      flag2 = TRTEMFL == "Y" & AEOUT == "FATAL",
+    )
+  labels <- c(
+    "A",
+    "B",
+    "C",
+    "D",
+    "Total number of patients with at least one adverse event",
+    "Total number of patients with fatal AEs"
+  )
+  formatters::var_labels(test_data) <- labels
+
+  test_adsl_like <- tibble::tibble(
+    SUBJID = as.character(1001:1010),
+    ARM = factor(c("A", "A", "B", "B", "A", "A", "A", "B", "B", "A"), levels = c("A", "B")),
+    stringsAsFactors = FALSE
+  )
+
+  lyt <- basic_table() %>%
+    split_cols_by("ARM") %>%
+    add_colcounts() %>%
+    count_patients_with_flags(
+      "SUBJID",
+      flag_variables = formatters::var_labels(test_data[, c("flag1", "flag2")]),
+      denom = "N_col",
+      .indent_mods = 3L
+    )
+  result <- build_table(lyt, df = test_data, alt_counts_df = test_adsl_like)
+
+  res <- testthat::expect_silent(result)
+  testthat::expect_snapshot(res)
+})