Correct ordering of grade levels in s_count_occurences_by_grade (#1040

)

Closes #1018

NEWS.md

@@ -5,9 +5,12 @@
 * Refactored `summarize_vars` and `compare_vars` to use refactored `a_summary`.
 * Created new internal helper functions `ungroup_stats` to ungroup statistics calculated for factor variables, and `a_summary_internal` to perform calculations for `a_summary`.
 
+### Bug Fixes
+* Fixed bug in `s_count_occurrences_by_grade` so that "missing" grade always appears as the final level.
+* Fix bug in `analyze_vars_in_cols` when categorical data was used.
+
 ### Miscellaneous
 * Fix swapped descriptions for the `.N_row` and `.N_col` parameters.
-* Fix bug in `analyze_vars_in_cols` when categorical data was used.
 * Removal of internal calls to `df_explicit_na`. Changes in `NA` values should happen externally to `tern` functions, depending on users' needs.
 * Reinstated correct soft deprecation for `create_afun_summary` and `create_afun_compare`.
 

R/count_occurrences_by_grade.R

@@ -179,6 +179,10 @@ s_count_occurrences_by_grade <- function(df,
       grade <- formatters::with_label(factor(grade, levels = lvl_ord, ordered = TRUE), grade_lbl)
     }
 
+    missing_lvl <- grepl("missing", tolower(levels(grade)))
+    if (any(missing_lvl)) {
+      levels(grade) <- c(levels(grade)[!missing_lvl], levels(grade)[missing_lvl])
+    }
     df_max <- stats::aggregate(grade ~ id, FUN = max, drop = FALSE)
     l_count <- as.list(table(df_max$grade))
   }

tests/testthat/_snaps/count_occurrences_by_grade.md

@@ -101,6 +101,32 @@
       
       
 
+# s_count_occurrences_by_grade sorts grade levels so that 'missing' level appears last
+
+    Code
+      res
+    Output
+      $count_fraction
+      $count_fraction$`1`
+      [1] 0 0
+      
+      $count_fraction$`2`
+      [1] 2.0 0.2
+      
+      $count_fraction$`3`
+      [1] 2.0 0.2
+      
+      $count_fraction$`4`
+      [1] 2.0 0.2
+      
+      $count_fraction$`5`
+      [1] 0 0
+      
+      $count_fraction$Missing
+      [1] 0 0
+      
+      
+
 # s_count_occurrences_by_grade works with valid input for grade grouping
 
     Code

tests/testthat/test-count_occurrences_by_grade.R

@@ -57,6 +57,16 @@ testthat::test_that("s_count_occurrences_by_grade works with valid input and def
   testthat::expect_snapshot(res)
 })
 
+testthat::test_that("s_count_occurrences_by_grade sorts grade levels so that 'missing' level appears last", {
+  df <- raw_data
+  df$AETOXGR <- factor(c("Missing", 2, 3, 1, 1, 2, 3), levels = c("Missing", 1:5))
+
+  result <- s_count_occurrences_by_grade(df = df, .var = "AETOXGR", .N_col = 10)
+
+  res <- testthat::expect_silent(result)
+  testthat::expect_snapshot(res)
+})
+
 testthat::test_that("s_count_occurrences_by_grade works with valid input for grade grouping", {
   df <- raw_data
   result <- s_count_occurrences_by_grade(