Add nested argument to all analyze wrapper functions (#1009)

Closes #999
insightsengineering · Jul 24, 2023 · 4a2675b · 4a2675b
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Showing 56 changed files with 187 additions and 10 deletions.
diff --git a/NEWS.md b/NEWS.md
@@ -6,6 +6,7 @@
 * 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`. 
+* Added the `nested` argument to `analyze` wrapper functions `count_abnormal`, `count_abnormal_by_baseline`, `count_abnormal_by_marked`, `count_abnormal_by_worst_grade`, `count_abnormal_lab_worsen_by_baseline`, `count_cumulative`, `count_missed_doses`, `count_occurrences`, `count_occurrences_by_grade`, `count_patients_with_event`, `count_patients_with_flags`, `count_values`, `estimate_multinomial_response`, `estimate_proportion`, `estimate_incidence_rate`, `estimate_odds_ratio`, `estimate_proportion_diff`, `test_proportion_diff`, `summarize_ancova`, `summarize_change`, `summarize_glm_count`, `analyze_num_patients`, `coxph_pairwise`, `surv_time`, and `surv_timepoint`.
 
 ### Miscellaneous
 * 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.

diff --git a/R/abnormal.R b/R/abnormal.R
@@ -140,6 +140,7 @@ a_count_abnormal <- make_afun(
 #' @export
 count_abnormal <- function(lyt,
                            var,
+                           nested = TRUE,
                            ...,
                            table_names = var,
                            .stats = NULL,
@@ -161,6 +162,7 @@ count_abnormal <- function(lyt,
     lyt = lyt,
     vars = var,
     afun = afun,
+    nested = nested,
     table_names = table_names,
     extra_args = list(...),
     show_labels = "hidden"

diff --git a/R/abnormal_by_baseline.R b/R/abnormal_by_baseline.R
@@ -183,6 +183,7 @@ a_count_abnormal_by_baseline <- make_afun(
 count_abnormal_by_baseline <- function(lyt,
                                        var,
                                        abnormal,
+                                       nested = TRUE,
                                        ...,
                                        table_names = abnormal,
                                        .stats = NULL,
@@ -206,6 +207,7 @@ count_abnormal_by_baseline <- function(lyt,
       vars = var,
       var_labels = names(abn),
       afun = afun,
+      nested = nested,
       table_names = table_names[i],
       extra_args = c(list(abnormal = abn), list(...)),
       show_labels = "visible"

diff --git a/R/abnormal_by_marked.R b/R/abnormal_by_marked.R
@@ -196,6 +196,7 @@ a_count_abnormal_by_marked <- make_afun(
 #' @export
 count_abnormal_by_marked <- function(lyt,
                                      var,
+                                     nested = TRUE,
                                      ...,
                                      .stats = NULL,
                                      .formats = NULL,
@@ -216,6 +217,7 @@ count_abnormal_by_marked <- function(lyt,
     lyt = lyt,
     vars = var,
     afun = afun,
+    nested = nested,
     show_labels = "hidden",
     extra_args = c(list(...))
   )

diff --git a/R/abnormal_by_worst_grade.R b/R/abnormal_by_worst_grade.R
@@ -164,6 +164,7 @@ a_count_abnormal_by_worst_grade <- make_afun( # nolint
 #' @export
 count_abnormal_by_worst_grade <- function(lyt,
                                           var,
+                                          nested = TRUE,
                                           ...,
                                           .stats = NULL,
                                           .formats = NULL,
@@ -181,6 +182,7 @@ count_abnormal_by_worst_grade <- function(lyt,
     lyt = lyt,
     vars = var,
     afun = afun,
+    nested = nested,
     extra_args = list(...),
     show_labels = "hidden"
   )

diff --git a/R/abnormal_by_worst_grade_worsen.R b/R/abnormal_by_worst_grade_worsen.R
@@ -356,6 +356,7 @@ a_count_abnormal_lab_worsen_by_baseline <- make_afun( # nolint
 #' @export
 count_abnormal_lab_worsen_by_baseline <- function(lyt, # nolint
                                                   var,
+                                                  nested = TRUE,
                                                   ...,
                                                   table_names = NULL,
                                                   .stats = NULL,
@@ -376,6 +377,7 @@ count_abnormal_lab_worsen_by_baseline <- function(lyt, # nolint
     lyt = lyt,
     vars = var,
     afun = afun,
+    nested = nested,
     extra_args = list(...),
     show_labels = "hidden"
   )

diff --git a/R/argument_convention.R b/R/argument_convention.R
@@ -37,8 +37,8 @@
 #' @param lyt (`layout`)\cr input layout where analyses will be added to.
 #' @param na.rm (`flag`)\cr whether `NA` values should be removed from `x` prior to analysis.
 #' @param na_level (`string`)\cr string used to replace all `NA` or empty values in the output.
-#' @param nested (`flag`)\cr whether this layout instruction be applied within the existing layout structure _if
-#'   possible_ (`TRUE`, the default) or as a new top-level element (`FALSE`). Ignored if it would nest a split
+#' @param nested (`flag`)\cr whether this layout instruction should be applied within the existing layout structure _if
+#'   possible_ (`TRUE`, the default) or as a new top-level element (`FALSE`). Ignored if it would nest a split.
 #'   underneath analyses, which is not allowed.
 #' @param newpage (`flag`)\cr whether the plot should be drawn on a new page.
 #'   Only considered if `draw = TRUE` is used.

diff --git a/R/count_cumulative.R b/R/count_cumulative.R
@@ -151,6 +151,7 @@ count_cumulative <- function(lyt,
                              vars,
                              var_labels = vars,
                              show_labels = "visible",
+                             nested = TRUE,
                              ...,
                              table_names = vars,
                              .stats = NULL,
@@ -172,6 +173,7 @@ count_cumulative <- function(lyt,
     table_names = table_names,
     var_labels = var_labels,
     show_labels = show_labels,
+    nested = nested,
     extra_args = list(...)
   )
 }
diff --git a/R/count_missed_doses.R b/R/count_missed_doses.R
@@ -112,6 +112,7 @@ count_missed_doses <- function(lyt,
                                vars,
                                var_labels = vars,
                                show_labels = "visible",
+                               nested = TRUE,
                                ...,
                                table_names = vars,
                                .stats = NULL,
@@ -133,6 +134,7 @@ count_missed_doses <- function(lyt,
     var_labels = var_labels,
     table_names = table_names,
     show_labels = show_labels,
+    nested = nested,
     extra_args = list(...)
   )
 }
diff --git a/R/count_occurrences.R b/R/count_occurrences.R
@@ -169,6 +169,7 @@ count_occurrences <- function(lyt,
                               vars,
                               var_labels = vars,
                               show_labels = "hidden",
+                              nested = TRUE,
                               ...,
                               table_names = vars,
                               .stats = "count_fraction",
@@ -191,6 +192,7 @@ count_occurrences <- function(lyt,
     var_labels = var_labels,
     show_labels = show_labels,
     table_names = table_names,
+    nested = nested,
     extra_args = list(...)
   )
 }
diff --git a/R/count_occurrences_by_grade.R b/R/count_occurrences_by_grade.R
@@ -260,6 +260,7 @@ count_occurrences_by_grade <- function(lyt,
                                        var,
                                        var_labels = var,
                                        show_labels = "default",
+                                       nested = TRUE,
                                        ...,
                                        table_names = var,
                                        .stats = NULL,
@@ -281,6 +282,7 @@ count_occurrences_by_grade <- function(lyt,
     show_labels = show_labels,
     afun = afun,
     table_names = table_names,
+    nested = nested,
     extra_args = list(...)
   )
 }

diff --git a/R/count_patients_with_event.R b/R/count_patients_with_event.R
@@ -144,6 +144,7 @@ a_count_patients_with_event <- make_afun(
 #' @export
 count_patients_with_event <- function(lyt,
                                       vars,
+                                      nested = TRUE,
                                       ...,
                                       table_names = vars,
                                       .stats = "count_fraction",
@@ -162,6 +163,7 @@ count_patients_with_event <- function(lyt,
     lyt,
     vars,
     afun = afun,
+    nested = nested,
     extra_args = list(...),
     show_labels = ifelse(length(vars) > 1, "visible", "hidden"),
     table_names = table_names

diff --git a/R/count_patients_with_flags.R b/R/count_patients_with_flags.R
@@ -157,6 +157,7 @@ count_patients_with_flags <- function(lyt,
                                       var,
                                       var_labels = var,
                                       show_labels = "hidden",
+                                      nested = TRUE,
                                       ...,
                                       table_names = paste0("tbl_flags_", var),
                                       .stats = "count_fraction",
@@ -177,6 +178,7 @@ count_patients_with_flags <- function(lyt,
     show_labels = show_labels,
     afun = afun,
     table_names = table_names,
+    nested = nested,
     extra_args = list(...)
   )
 

diff --git a/R/count_values.R b/R/count_values.R
@@ -122,6 +122,7 @@ a_count_values <- make_afun(
 count_values <- function(lyt,
                          vars,
                          values,
+                         nested = TRUE,
                          ...,
                          table_names = vars,
                          .stats = "count_fraction",
@@ -139,6 +140,7 @@ count_values <- function(lyt,
     lyt,
     vars,
     afun = afun,
+    nested = nested,
     extra_args = c(list(values = values), list(...)),
     show_labels = ifelse(length(vars) > 1, "visible", "hidden"),
     table_names = table_names

diff --git a/R/estimate_multinomial_rsp.R b/R/estimate_multinomial_rsp.R
@@ -146,6 +146,7 @@ a_length_proportion <- make_afun(
 #' @export
 estimate_multinomial_response <- function(lyt,
                                           var,
+                                          nested = TRUE,
                                           ...,
                                           show_labels = "hidden",
                                           table_names = var,
@@ -169,6 +170,7 @@ estimate_multinomial_response <- function(lyt,
     afun = afun,
     show_labels = show_labels,
     table_names = table_names,
+    nested = nested,
     extra_args = list(...)
   )
 }
diff --git a/R/estimate_proportion.R b/R/estimate_proportion.R
@@ -162,6 +162,7 @@ a_proportion <- make_afun(
 #' @export
 estimate_proportion <- function(lyt,
                                 vars,
+                                nested = TRUE,
                                 ...,
                                 show_labels = "hidden",
                                 table_names = vars,
@@ -180,6 +181,7 @@ estimate_proportion <- function(lyt,
     lyt,
     vars,
     afun = afun,
+    nested = nested,
     extra_args = list(...),
     show_labels = show_labels,
     table_names = table_names

diff --git a/R/incidence_rate.R b/R/incidence_rate.R
@@ -135,6 +135,7 @@ a_incidence_rate <- make_afun(
 #' @export
 estimate_incidence_rate <- function(lyt,
                                     vars,
+                                    nested = TRUE,
                                     ...,
                                     show_labels = "hidden",
                                     table_names = vars,
@@ -156,6 +157,7 @@ estimate_incidence_rate <- function(lyt,
     show_labels = show_labels,
     table_names = table_names,
     afun = afun,
+    nested = nested,
     extra_args = list(...)
   )
 }

diff --git a/R/odds_ratio.R b/R/odds_ratio.R
@@ -188,6 +188,7 @@ a_odds_ratio <- make_afun(
 #' @export
 estimate_odds_ratio <- function(lyt,
                                 vars,
+                                nested = TRUE,
                                 ...,
                                 show_labels = "hidden",
                                 table_names = vars,
@@ -207,6 +208,7 @@ estimate_odds_ratio <- function(lyt,
     lyt,
     vars,
     afun = afun,
+    nested = nested,
     extra_args = list(...),
     show_labels = show_labels,
     table_names = table_names

diff --git a/R/prop_diff.R b/R/prop_diff.R
@@ -191,6 +191,7 @@ a_proportion_diff <- make_afun(
 #' @export
 estimate_proportion_diff <- function(lyt,
                                      vars,
+                                     nested = TRUE,
                                      ...,
                                      var_labels = vars,
                                      show_labels = "hidden",
@@ -212,6 +213,7 @@ estimate_proportion_diff <- function(lyt,
     vars,
     afun = afun,
     var_labels = var_labels,
+    nested = nested,
     extra_args = list(...),
     show_labels = show_labels,
     table_names = table_names

diff --git a/R/prop_diff_test.R b/R/prop_diff_test.R
@@ -136,6 +136,7 @@ a_test_proportion_diff <- make_afun(
 #' @export
 test_proportion_diff <- function(lyt,
                                  vars,
+                                 nested = TRUE,
                                  ...,
                                  var_labels = vars,
                                  show_labels = "hidden",
@@ -156,6 +157,7 @@ test_proportion_diff <- function(lyt,
     vars,
     afun = afun,
     var_labels = var_labels,
+    nested = nested,
     extra_args = list(...),
     show_labels = show_labels,
     table_names = table_names

diff --git a/R/summarize_ancova.R b/R/summarize_ancova.R
@@ -244,6 +244,7 @@ a_ancova <- make_afun(
 summarize_ancova <- function(lyt,
                              vars,
                              var_labels,
+                             nested = TRUE,
                              ...,
                              show_labels = "visible",
                              table_names = vars,
@@ -270,6 +271,7 @@ summarize_ancova <- function(lyt,
     show_labels = show_labels,
     table_names = table_names,
     afun = afun,
+    nested = nested,
     extra_args = list(...)
   )
 }
diff --git a/R/summarize_change.R b/R/summarize_change.R
@@ -120,6 +120,7 @@ a_change_from_baseline <- make_afun(
 #' @export
 summarize_change <- function(lyt,
                              vars,
+                             nested = TRUE,
                              ...,
                              table_names = vars,
                              .stats = c("n", "mean_sd", "median", "range"),
@@ -138,6 +139,7 @@ summarize_change <- function(lyt,
     lyt,
     vars,
     afun = afun,
+    nested = nested,
     extra_args = list(...),
     table_names = table_names
   )

diff --git a/R/summarize_glm_count.R b/R/summarize_glm_count.R
@@ -400,6 +400,7 @@ a_glm_count <- make_afun(
 summarize_glm_count <- function(lyt,
                                 vars,
                                 var_labels,
+                                nested = TRUE,
                                 ...,
                                 show_labels = "visible",
                                 table_names = vars,
@@ -422,6 +423,7 @@ summarize_glm_count <- function(lyt,
     show_labels = show_labels,
     table_names = table_names,
     afun = afun,
+    nested = nested,
     extra_args = list(...)
   )
 }
diff --git a/R/summarize_num_patients.R b/R/summarize_num_patients.R
@@ -203,6 +203,7 @@ summarize_num_patients <- function(lyt,
 #' @export
 analyze_num_patients <- function(lyt,
                                  vars,
+                                 nested = TRUE,
                                  .stats = NULL,
                                  .formats = NULL,
                                  .labels = c(
@@ -232,6 +233,7 @@ analyze_num_patients <- function(lyt,
     afun = afun,
     lyt = lyt,
     vars = vars,
+    nested = nested,
     extra_args = list(...),
     show_labels = show_labels,
     indent_mod = .indent_mods

diff --git a/R/survival_coxph_pairwise.R b/R/survival_coxph_pairwise.R
@@ -165,6 +165,7 @@ a_coxph_pairwise <- make_afun(
 #' @export
 coxph_pairwise <- function(lyt,
                            vars,
+                           nested = TRUE,
                            ...,
                            var_labels = "CoxPH",
                            show_labels = "visible",
@@ -187,6 +188,7 @@ coxph_pairwise <- function(lyt,
     show_labels = show_labels,
     table_names = table_names,
     afun = afun,
+    nested = nested,
     extra_args = list(...)
   )
 }