Update defaults

NEWS.md

@@ -4,7 +4,7 @@
 * Reworking of `summarize_glm_count()` documentation and all its associated functions to better describe the results and the functions' purpose.
 * Added the `.formats` argument to `tabulate_rsp_subgroups` and `tabulate_survival_subgroups` to allow users to specify formats.
 * Added the `riskdiff` argument to `tabulate_rsp_subgroups` and `tabulate_survival_subgroups` to allow users to add a risk difference table column, and function `control_riskdiff` to specify settings for the risk difference column.
-* Added `"chisq"` as default `method` parameter value to `extract_rsp_subgroups`, `h_odds_ratio_df`, and `h_odds_ratio_subgroups_df`.
+* Added `"chisq"` as default `method` parameter value to `extract_rsp_subgroups`.
 * Added warning to `tabulate_rsp_subgroups` when `pval` statistic is selected but `df` has not been correctly generated to add p-values to the output table.
 
 ### Bug Fixes

R/argument_convention.R

@@ -43,7 +43,7 @@
 #'   for more information.
 #' @param lyt (`PreDataTableLayouts`)\cr layout that analyses will be added to.
 #' @param method (`string` or `NULL`)\cr specifies the test used to calculate the p-value for the difference between
-#'   two proportions. For options, see [test_proportion_diff()]. Defaults to `"chisq"`. If `NULL`, no test is performed.
+#'   two proportions. For options, see [test_proportion_diff()]. Default is `NULL` so no test is performed.
 #' @param na.rm (`flag`)\cr whether `NA` values should be removed from `x` prior to analysis.
 #' @param na_str (`string`)\cr string used to replace all `NA` or empty values in the output.
 #' @param nested (`flag`)\cr whether this layout instruction should be applied within the existing layout structure _if

R/h_response_subgroups.R

@@ -175,7 +175,7 @@ h_proportion_subgroups_df <- function(variables,
 #' )
 #'
 #' @export
-h_odds_ratio_df <- function(rsp, arm, strata_data = NULL, conf_level = 0.95, method = "chisq") {
+h_odds_ratio_df <- function(rsp, arm, strata_data = NULL, conf_level = 0.95, method = NULL) {
   assert_valid_factor(arm, n.levels = 2, len = length(rsp))
 
   df_rsp <- data.frame(
@@ -323,7 +323,7 @@ h_odds_ratio_subgroups_df <- function(variables,
                                       data,
                                       groups_lists = list(),
                                       conf_level = 0.95,
-                                      method = "chisq",
+                                      method = NULL,
                                       label_all = "All Patients") {
   if ("strat" %in% names(variables)) {
     warning(

R/response_subgroups.R

@@ -74,6 +74,8 @@ NULL
 #'
 #' @inheritParams argument_convention
 #' @inheritParams response_subgroups
+#' @param method (`string` or `NULL`)\cr specifies the test used to calculate the p-value for the difference between
+#'   two proportions. For options, see [test_proportion_diff()]. Defaults to `"chisq"`. If `NULL`, no test is performed.
 #' @param label_all (`string`)\cr label for the total population analysis.
 #'
 #' @return A named list of two elements:
@@ -411,7 +413,7 @@ tabulate_rsp_subgroups <- function(lyt,
 #' @export
 d_rsp_subgroups_colvars <- function(vars,
                                     conf_level = NULL,
-                                    method = "p-value (Chi-Squared Test)") {
+                                    method = NULL) {
   checkmate::assert_character(vars)
   checkmate::assert_subset(c("n_tot", "or", "ci"), vars)
   checkmate::assert_subset(

tests/testthat/test-h_response_subgroups.R

@@ -211,6 +211,7 @@ testthat::test_that("h_odds_ratio_subgroups_df works as expected with groups_lis
       subgroups = c("SEX", "BMRKR2")
     ),
     data = adrs,
+    method = NULL,
     groups_lists = list(
       BMRKR2 = list(
         "low" = "LOW",