Fix na_level bug in summarize_vars

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`.

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_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)
+})