Merge branch 'main' into 1062_numeric_count_by@main

Signed-off-by: Emily de la Rua <59304861+edelarua@users.noreply.github.com>

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: tern
 Title: Create Common TLGs Used in Clinical Trials
-Version: 0.9.2.9018
+Version: 0.9.2.9019
 Date: 2023-11-27
 Authors@R: c(
     person("Joe", "Zhu", , "joe.zhu@roche.com", role = c("aut", "cre")),

NEWS.md

@@ -1,4 +1,4 @@
-# tern 0.9.2.9018
+# tern 0.9.2.9019
 
 ### New Features
 * Added `ref_group_position` function to place the reference group facet last, first or at a certain position.
@@ -18,6 +18,7 @@
 * Added `annot_coxph_ref_lbls` parameter to `g_km` to enable printing the reference group in table labels when `annot_coxph = TRUE`.
 * Added `x_lab` parameter to `g_lineplot` to customize x-axis label.
 * Remove 25% padding of y-axis in `g_lineplot`.
+* Added support for creating multiple risk difference columns, each comparing to a single comparison group. Multiple comparison groups can be specified as a vector via the `arm_y` argument.
 * Allowed numeric vector as `count_by` input in `analyze_num_patients` and `summarize_num_patients`.
 
 ### Bug Fixes

R/riskdiff.R

@@ -8,8 +8,11 @@
 #' `riskdiff` to `TRUE` in all following analyze function calls.
 #'
 #' @param arm_x (`character`)\cr Name of reference arm to use in risk difference calculations.
-#' @param arm_y (`character`)\cr Name of arm to compare to reference arm in risk difference calculations.
-#' @param col_label (`character`)\cr Label to use when rendering the risk difference column within the table.
+#' @param arm_y (`character`)\cr Names of one or more arms to compare to reference arm in risk difference
+#'   calculations. A new column will be added for each value of `arm_y`.
+#' @param col_label (`character`)\cr Labels to use when rendering the risk difference column within the table.
+#'   If more than one comparison arm is specified in `arm_y`, default labels will specify which two arms are
+#'   being compared (reference arm vs. comparison arm).
 #' @param pct (`flag`)\cr whether output should be returned as percentages. Defaults to `TRUE`.
 #'
 #' @return A closure suitable for use as a split function (`split_fun`) within [rtables::split_cols_by()]
@@ -22,7 +25,7 @@
 #' adae$AESEV <- factor(adae$AESEV)
 #'
 #' lyt <- basic_table() %>%
-#'   split_cols_by("ARMCD", split_fun = add_riskdiff(arm_x = "ARM A", arm_y = "ARM B")) %>%
+#'   split_cols_by("ARMCD", split_fun = add_riskdiff(arm_x = "ARM A", arm_y = c("ARM B", "ARM C"))) %>%
 #'   count_occurrences_by_grade(
 #'     var = "AESEV",
 #'     riskdiff = TRUE
@@ -34,13 +37,24 @@
 #' @export
 add_riskdiff <- function(arm_x,
                          arm_y,
-                         col_label = "Risk Difference (%) (95% CI)",
+                         col_label = paste0(
+                           "Risk Difference (%) (95% CI)", if (length(arm_y) > 1) paste0("\n", arm_x, " vs. ", arm_y)
+                         ),
                          pct = TRUE) {
-  sapply(c(arm_x, arm_y, col_label), checkmate::assert_character, len = 1)
-  combodf <- tibble::tribble(
-    ~valname, ~label, ~levelcombo, ~exargs,
-    paste("riskdiff", arm_x, arm_y, sep = "_"), col_label, c(arm_x, arm_y), list()
-  )
+  checkmate::assert_character(arm_x, len = 1)
+  checkmate::assert_character(arm_y, min.len = 1)
+  checkmate::assert_character(col_label, len = length(arm_y))
+
+  combodf <- tibble::tribble(~valname, ~label, ~levelcombo, ~exargs)
+  for (i in seq_len(length(arm_y))) {
+    combodf <- rbind(
+      combodf,
+      tibble::tribble(
+        ~valname, ~label, ~levelcombo, ~exargs,
+        paste("riskdiff", arm_x, arm_y[i], sep = "_"), col_label[i], c(arm_x, arm_y[i]), list()
+      )
+    )
+  }
   if (pct) combodf$valname <- paste0(combodf$valname, "_pct")
   add_combo_levels(combodf)
 }

tests/testthat/_snaps/count_occurrences.md

@@ -283,3 +283,21 @@
         MEDIUM   5 (7.8%)     2 (3.0%)       1 (1.6%)           4.8 (-2.9 - 12.6)         2 (2.6%)     3 (4.7%)       2 (4.4%)           -2.1 (-8.4 - 4.1)         3 (5.0%)     4 (8.7%)       1 (1.8%)           -3.7 (-13.5 - 6.1)     
         HIGH     2 (3.1%)     5 (7.5%)       5 (8.1%)           -4.3 (-11.9 - 3.3)        2 (2.6%)     5 (7.8%)       3 (6.7%)           -5.2 (-12.7 - 2.2)            0        2 (4.3%)       3 (5.5%)           -4.3 (-10.2 - 1.5)     
 
+---
+
+    Code
+      res
+    Output
+                                                           Risk Difference (%) (95% CI)   Risk Difference (%) (95% CI)
+                 A: Drug X   B: Placebo   C: Combination     A: Drug X vs. B: Placebo     A: Drug X vs. C: Combination
+                  (N=202)     (N=177)        (N=162)                 (N=379)                        (N=364)           
+      ————————————————————————————————————————————————————————————————————————————————————————————————————————————————
+      F                                                                                                               
+        LOW      12 (5.9%)   11 (6.2%)      10 (6.2%)           -0.3 (-5.1 - 4.6)              -0.2 (-5.2 - 4.7)      
+        MEDIUM   11 (5.4%)   13 (7.3%)      10 (6.2%)           -1.9 (-6.9 - 3.1)              -0.7 (-5.6 - 4.1)      
+        HIGH     10 (5.0%)    7 (4.0%)       7 (4.3%)            1.0 (-3.2 - 5.1)               0.6 (-3.7 - 5.0)      
+      M                                                                                                               
+        LOW      12 (5.9%)    5 (2.8%)       6 (3.7%)            3.1 (-1.0 - 7.2)               2.2 (-2.1 - 6.6)      
+        MEDIUM   10 (5.0%)    9 (5.1%)       4 (2.5%)           -0.1 (-4.5 - 4.3)               2.5 (-1.3 - 6.3)      
+        HIGH     4 (2.0%)    12 (6.8%)      11 (6.8%)           -4.8 (-9.0 - -0.6)             -4.8 (-9.1 - -0.5)     
+

tests/testthat/test-count_occurrences.R

@@ -272,4 +272,17 @@ testthat::test_that("summarize_occurrences works as expected with risk differenc
 
   res <- testthat::expect_silent(result)
   testthat::expect_snapshot(res)
+
+  # Multiple comparison groups
+  result <- basic_table(show_colcounts = TRUE) %>%
+    split_cols_by("ARM", split_fun = add_riskdiff("A: Drug X", c("B: Placebo", "C: Combination"))) %>%
+    split_rows_by("SEX", child_labels = "visible") %>%
+    summarize_occurrences(
+      var = "BMRKR2",
+      riskdiff = TRUE
+    ) %>%
+    build_table(tern_ex_adae)
+
+  res <- testthat::expect_silent(result)
+  testthat::expect_snapshot(res)
 })