Merge branch 'main' into 903_check_tests@96_exporter_pagination_migra…

…tion

NEWS.md

@@ -5,6 +5,7 @@
 
 ### Bug Fixes
 * Fixed missing label for `TRTEDTM` in `tern` datasets.
+* Fixed improper implementation of `na_level` argument in `summarize_vars` preventing it from having an effect.
 
 ### Enhancements
 * Added `section_div` and `na_level` (`na_str`) to `summarize_vars`.
@@ -13,6 +14,7 @@
 * Added new "Analyze Functions" and "Summarize Functions" overview pages.
 * Moved all KM plot documentation to the `g_km` function.
 * Added `a_count_patients_sum_exposure` for new analyze function `analyze_patients_exposure_in_cols` and `summarize_patients_exposure_in_cols`.
+* Added more informative error when the user selects an invalid method for unstratified analyses in `s_proportion_diff`.
 
 ### Miscellaneous
 * Implemented the `lubridate` package for date variables in `tern` datasets.

R/prop_diff.R

@@ -18,6 +18,9 @@ NULL
 #' @return
 #' * `s_proportion_diff()` returns a named list of elements `diff` and `diff_ci`.
 #'
+#' @note When performing an unstratified analysis, methods `"cmh"`, `"strat_newcombe"`, and `"strat_newcombecc"` are
+#'   not permitted.
+#'
 #' @examples
 #' # Summary
 #'
@@ -65,6 +68,12 @@ s_proportion_diff <- function(df,
                               ),
                               weights_method = "cmh") {
   method <- match.arg(method)
+  if (is.null(variables$strata) && checkmate::test_subset(method, c("cmh", "strat_newcombe", "strat_newcombecc"))) {
+    stop(paste(
+      "When performing an unstratified analysis, methods 'cmh', 'strat_newcombe', and 'strat_newcombecc' are not",
+      "permitted. Please choose a different method."
+    ))
+  }
   y <- list(diff = "", diff_ci = "")
 
   if (!.in_ref_col) {

R/summarize_variables.R

@@ -380,7 +380,8 @@ s_summary.factor <- function(x,
 #' @param verbose (`logical`)\cr Defaults to `TRUE`, which prints out warnings and messages. It is mainly used
 #'   to print out information about factor casting.
 #'
-#' @note Automatic conversion of character to factor does not guarantee that the table
+#' @note
+#' * Automatic conversion of character to factor does not guarantee that the table
 #'   can be generated correctly. In particular for sparse tables this very likely can fail.
 #'   It is therefore better to always pre-process the dataset such that factors are manually
 #'   created from character variables before passing the dataset to [rtables::build_table()].
@@ -722,7 +723,6 @@ create_afun_summary <- function(.stats, .formats, .labels, .indent_mods) {
 summarize_vars <- function(lyt,
                            vars,
                            var_labels = vars,
-                           na_level = NA_character_,
                            nested = TRUE,
                            ...,
                            show_labels = "default",
@@ -739,7 +739,6 @@ summarize_vars <- function(lyt,
     vars = vars,
     var_labels = var_labels,
     afun = afun,
-    na_str = na_level,
     nested = nested,
     extra_args = list(...),
     inclNAs = TRUE,

tests/testthat/_snaps/summarize_coxreg.md

@@ -43,7 +43,7 @@
         row_name formatted_cell indent_mod row_label
       1  Label 1            340          0   Label 1
 
-# summarize_coxreg adds the univariable Cox regression layer to rtables
+# summarize_coxreg adds the univariate Cox regression layer to rtables
 
     Code
       res
@@ -97,7 +97,7 @@
        * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * 
         Sex (F/M)           340       0.62       (0.42, 0.92)   0.0182 
 
-# summarize_coxreg works with interactions in univariable case
+# summarize_coxreg works with interactions in univariate case
 
     Code
       res
@@ -118,7 +118,7 @@
           F                           0.67       (0.36, 1.22)                                
           M                           0.60       (0.36, 0.99)                                
 
-# summarize_coxreg 'at' argument works in univariable case
+# summarize_coxreg 'at' argument works in univariate case
 
     Code
       res
@@ -155,7 +155,7 @@
           F                           0.67       (0.36, 1.22)                     ---        
           M                           0.60       (0.36, 0.99)                     ---        
 
-# summarize_coxreg works without treatment arm in univariable case
+# summarize_coxreg works without treatment arm in univariate case
 
     Code
       res
@@ -170,7 +170,7 @@
         Sex (F/M) (reference = F)                                                
           M                                     1.33       (0.97, 1.82)   0.1414 
 
-# summarize_coxreg works with numeric covariate without treatment arm in univariable case
+# summarize_coxreg works with numeric covariate without treatment arm in univariate case
 
     Code
       res

tests/testthat/_snaps/summarize_variables.md

@@ -1128,3 +1128,26 @@
       Median      NA      3.5         5.5   
       Min - Max   NA   3.0 - 4.0   5.0 - 6.0
 
+# `summarize_vars` na_level argument works with non-default input
+
+    Code
+      res
+    Output
+          all obs
+      ———————————
+      n      4   
+      a   2 (50%)
+      b   2 (50%)
+
+---
+
+    Code
+      res
+    Output
+           all obs 
+      —————————————
+      n       6    
+      a   2 (33.3%)
+      b   2 (33.3%)
+      c   2 (33.3%)
+

tests/testthat/test-summarize_variables.R

@@ -345,3 +345,23 @@ testthat::test_that("`summarize_vars` works with empty named numeric variables",
   res <- testthat::expect_silent(result)
   testthat::expect_snapshot(res)
 })
+
+testthat::test_that("`summarize_vars` na_level argument works with non-default input", {
+  dta <- tibble::tibble(
+    foo = factor(c("a", "a", "b", "b", "c", "c"), levels = c("a", "b", "c"))
+  )
+
+  result <- basic_table() %>%
+    summarize_vars(vars = "foo", na_level = "c") %>%
+    build_table(dta)
+
+  res <- testthat::expect_silent(result)
+  testthat::expect_snapshot(res)
+
+  result <- basic_table() %>%
+    summarize_vars(vars = "foo", na_level = "c", na.rm = FALSE) %>%
+    build_table(dta)
+
+  res <- testthat::expect_silent(result)
+  testthat::expect_snapshot(res)
+})