Closes #2468 fix_derive_vars_crit_flag: create integer flag (#2618)

* #2468 fix_derive_vars_crit_flag: create correct numeric flag (CRITyFN instead of CRITyFLN) * #2468 fix_derive_vars_crit_flag: update vignettes * #2468 fix_derive_vars_crit_flag: style files * #2468 fix_derive_vars_crit_flag: fix typo in variable names * #2468 fix_derive_vars_crit_flag: create integer flag
pharmaverse · Dec 20, 2024 · 187c977 · 187c977
1 parent ebb8beb
commit 187c977
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Showing 2 changed files with 11 additions and 13 deletions.
diff --git a/R/derive_vars_crit_flag.R b/R/derive_vars_crit_flag.R
@@ -110,10 +110,8 @@ derive_vars_crit_flag <- function(dataset,
 
   if (values_yn) {
     crityfl_no <- "N"
-    crityfn_no <- 0L
   } else {
     crityfl_no <- NA_character_
-    crityfn_no <- NA_integer_
   }
 
   tryCatch(
@@ -156,7 +154,7 @@ derive_vars_crit_flag <- function(dataset,
   if (create_numeric_flag) {
     new_critfnvar <- paste0("CRIT", as.character(crit_nr), "FN")
     dataset <- dataset %>% mutate(
-      !!new_critfnvar := yn_to_numeric(!!sym(new_critflvar))
+      !!new_critfnvar := as.integer(yn_to_numeric(!!sym(new_critflvar)))
     )
   }
   dataset

diff --git a/tests/testthat/test-derive_vars_crit_flag.R b/tests/testthat/test-derive_vars_crit_flag.R
@@ -21,10 +21,10 @@ test_that("derive_vars_crit_flag Test 1: works with defaults", {
 ## Test 2: create numeric flag ----
 test_that("derive_vars_crit_flag Test 2: create numeric flag", {
   expected <- tibble::tribble(
-    ~AVAL, ~CRIT1FL,      ~CRIT1FN, ~CRIT1,
-    23,    NA_character_, NA_real_, NA_character_,
-    42,    "Y",           1,        "AVAL > 40",
-    NA,    NA_character_, NA_real_, NA_character_
+    ~AVAL, ~CRIT1FL,      ~CRIT1FN,    ~CRIT1,
+    23,    NA_character_, NA_integer_, NA_character_,
+    42,    "Y",           1L,          "AVAL > 40",
+    NA,    NA_character_, NA_integer_, NA_character_
   )
 
   expect_dfs_equal(
@@ -42,12 +42,12 @@ test_that("derive_vars_crit_flag Test 2: create numeric flag", {
 ## Test 3: using values Y and N ----
 test_that("derive_vars_crit_flag Test 3: using values Y and N", {
   expected <- tibble::tribble(
-    ~PARAMCD, ~AVAL, ~CRIT2FL,      ~CRIT2FN, ~CRIT2,
-    "AST",    23,    "N",           0,        "AST > 40",
-    "AST",    42,    "Y",           1,        "AST > 40",
-    "AST",    NA,    NA_character_, NA_real_, "AST > 40",
-    "ALT",    26,    "N",           0,        "ALT > 40",
-    "ALT",    56,    "Y",           1,        "ALT > 40",
+    ~PARAMCD, ~AVAL, ~CRIT2FL,      ~CRIT2FN,    ~CRIT2,
+    "AST",    23,    "N",           0L,          "AST > 40",
+    "AST",    42,    "Y",           1L,          "AST > 40",
+    "AST",    NA,    NA_character_, NA_integer_, "AST > 40",
+    "ALT",    26,    "N",           0L,          "ALT > 40",
+    "ALT",    56,    "Y",           1L,          "ALT > 40"
   )
 
   expect_dfs_equal(