Merge branch 'main' into 898_s_summary_na@main

insightsengineering · Jun 6, 2023 · c9bb68a · c9bb68a
2 parents 943821e + 4980e32
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: tern
 Title: Create Common TLGs Used in Clinical Trials
-Version: 0.8.2.9005
+Version: 0.8.2.9006
 Date: 2023-06-06
 Authors@R: c(
     person("Joe", "Zhu", , "[email protected]", role = c("aut", "cre")),

diff --git a/NEWS.md b/NEWS.md
@@ -1,7 +1,8 @@
-# tern 0.8.2.9005
+# tern 0.8.2.9006
 
 ### Enhancements
 * Added explicit zero counts to `g_km` plot "at risk" annotation tables.
+* Added a flag for total level split in `analyze_patients_exposure_in_cols`.
 * Implemented `.indent_mods` argument in functions `h_tab_one_biomarker`, `h_tab_rsp_one_biomarker`, `h_tab_surv_one_biomarker`, `summarize_logistic`, `logistic_summary_by_flag`, `tabulate_rsp_biomarkers`, a_coxreg, `summarize_coxreg`, `tabulate_survival_biomarkers`, `surv_time`, `surv_timepoint`, and `cfun_by_flag`.
 
 ### Miscellaneous

diff --git a/R/argument_convention.R b/R/argument_convention.R
@@ -19,6 +19,8 @@
 #'   by a statistics function.
 #' @param .spl_context (`data.frame`)\cr gives information about ancestor split states
 #'   that is passed by `rtables`.
+#' @param add_total_level (`flag`)\cr adds a "total" level after the others which includes all the levels
+#'   that constitute the split. A custom label can be set for this level via the `custom_label` argument.
 #' @param col_by (`factor`)\cr defining column groups.
 #' @param conf_level (`proportion`)\cr confidence level of the interval.
 #' @param data (`data.frame`)\cr the dataset containing the variables to summarize.

diff --git a/R/summarize_patients_exposure_in_cols.R b/R/summarize_patients_exposure_in_cols.R
@@ -112,10 +112,13 @@ a_count_patients_sum_exposure <- function(df,
                                           ex_var = "AVAL",
                                           id = "USUBJID",
                                           labelstr = "",
+                                          add_total_level = FALSE,
                                           .N_col, # nolint
                                           .stats,
                                           .formats = list(n_patients = "xx (xx.x%)", sum_exposure = "xx"),
                                           custom_label = NULL) {
+  checkmate::assert_flag(add_total_level)
+
   if (!is.null(var)) {
     assert_df_with_variables(df, list(var = var))
     df[[var]] <- as.factor(df[[var]])
@@ -144,6 +147,17 @@ a_count_patients_sum_exposure <- function(df,
         custom_label = lvl
       )[[.stats]]
     }
+    if (add_total_level) {
+      y[[.stats]][["Total"]] <- s_count_patients_sum_exposure(
+        df = df,
+        ex_var = ex_var,
+        id = id,
+        labelstr = labelstr,
+        .N_col = .N_col,
+        .stats = .stats,
+        custom_label = custom_label
+      )[[.stats]]
+    }
   }
 
   in_rows(.list = y[[.stats]], .formats = .formats[[.stats]])
@@ -234,14 +248,31 @@ summarize_patients_exposure_in_cols <- function(lyt, # nolint
 #' result5 <- build_table(lyt5, df = df, alt_counts_df = adsl)
 #' result5
 #'
+#' # Adding total levels and custom label
+#' lyt <- basic_table(
+#'   show_colcounts = TRUE
+#' ) %>%
+#'   analyze_patients_exposure_in_cols(
+#'     var = "ARMCD",
+#'     col_split = TRUE,
+#'     add_total_level = TRUE,
+#'     custom_label = "TOTAL"
+#'   ) %>%
+#'   append_topleft(c("", "Sex"))
+#'
+#' tbl <- build_table(lyt, df = df, alt_counts_df = adsl)
+#' tbl
+#'
 #' @export
 analyze_patients_exposure_in_cols <- function(lyt, # nolint
                                               var = NULL,
                                               ex_var = "AVAL",
                                               col_split = TRUE,
+                                              add_total_level = FALSE,
                                               .stats = c("n_patients", "sum_exposure"),
                                               .labels = c(n_patients = "Patients", sum_exposure = "Person time"),
-                                              .indent_mods = 0L) {
+                                              .indent_mods = 0L,
+                                              ...) {
   if (col_split) {
     lyt <- split_cols_by_multivar(
       lyt = lyt,
@@ -253,7 +284,14 @@ analyze_patients_exposure_in_cols <- function(lyt, # nolint
   lyt <- lyt %>% analyze_colvars(
     afun = a_count_patients_sum_exposure,
     indent_mod = .indent_mods,
-    extra_args = list(var = var, ex_var = ex_var)
+    extra_args = c(
+      list(
+        var = var,
+        ex_var = ex_var,
+        add_total_level = add_total_level
+      ),
+      ...
+    )
   )
   lyt
 }
diff --git a/man/argument_convention.Rd b/man/argument_convention.Rd
diff --git a/man/summarize_patients_exposure_in_cols.Rd b/man/summarize_patients_exposure_in_cols.Rd
diff --git a/tests/testthat/_snaps/summarize_patients_exposure_in_cols.md b/tests/testthat/_snaps/summarize_patients_exposure_in_cols.md
@@ -87,3 +87,21 @@
       ————————————————————————————————————————————————
       Total patients numbers/person time   12 (100.0%)
 
+# patients_exposure_in_cols works with totals after the row split
+
+    Code
+      res
+    Output
+      Extent of Exposure
+      
+      ——————————————————————————————————————
+                    Patients     Person time
+      Sex            (N=12)        (N=12)   
+      ——————————————————————————————————————
+      Female        6 (50.0%)        16     
+      Male          6 (50.0%)        19     
+      REAL TOTAL   12 (100.0%)       35     
+      ——————————————————————————————————————
+      
+      * Patient Time is the sum of patients and times
+
diff --git a/tests/testthat/test-summarize_patients_exposure_in_cols.R b/tests/testthat/test-summarize_patients_exposure_in_cols.R
@@ -42,8 +42,7 @@ testthat::test_that("summarize_patients_exposure_in_cols works well with default
   result <- basic_table() %>%
     split_cols_by("ARMCD", split_fun = add_overall_level("Total", first = FALSE)) %>%
     summarize_patients_exposure_in_cols(var = "AVAL", col_split = TRUE) %>%
-    split_rows_by("SEX") %>%
-    summarize_patients_exposure_in_cols(var = "AVAL", col_split = FALSE) %>%
+    analyze_patients_exposure_in_cols(var = "SEX", col_split = FALSE) %>%
     build_table(df = df, alt_counts_df = adsl)
 
   res <- testthat::expect_silent(result)
@@ -62,9 +61,8 @@ testthat::test_that("summarize_patients_exposure_in_cols works well with custom
       custom_label = "xyz",
       .stats = "sum_exposure"
     ) %>%
-    split_rows_by("SEX") %>%
-    summarize_patients_exposure_in_cols(
-      var = "AVAL",
+    analyze_patients_exposure_in_cols(
+      var = "SEX",
       col_split = FALSE,
       .stats = "sum_exposure"
     ) %>%
@@ -146,3 +144,24 @@ testthat::test_that(
     testthat::expect_snapshot(res)
   }
 )
+
+testthat::test_that("patients_exposure_in_cols works with totals after the row split", {
+  # Fixes adding total as last analyze level, issue #950
+  lyt <- basic_table(
+    title = "Extent of Exposure",
+    main_footer = "* Patient Time is the sum of patients and times",
+    show_colcounts = TRUE
+  ) %>%
+    analyze_patients_exposure_in_cols(
+      var = "SEX",
+      col_split = TRUE,
+      add_total_level = TRUE,
+      custom_label = "REAL TOTAL"
+    ) %>%
+    append_topleft(c("", "Sex"))
+
+  tbl <- build_table(lyt, anl_local)
+
+  res <- testthat::expect_silent(tbl)
+  testthat::expect_snapshot(res)
+})