Closes #2468 fix_derive_vars_crit_flag: create correct numeric flag (#…

…2616) * #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
pharmaverse · Dec 19, 2024 · 06c1bbe · 06c1bbe
1 parent ef04a31
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diff --git a/NEWS.md b/NEWS.md
@@ -5,7 +5,7 @@
 - New function `derive_vars_cat()` for deriving pairs of variables or more, e.g. 
 `AVALCATy` & `AVALCAyN`. (#2480)
 - New function `derive_vars_crit_flag()` for deriving criterion flag variables
-(`CRITy`, `CRITyFL`, `CRITyFLN`). (#2468)
+(`CRITy`, `CRITyFL`, `CRITyFN`). (#2468)
 - New function `transform_range()`  to transform values from a source range to a
 target range. (#2571)
 - Replace use of `data("sdtm")` with `sdtm <- pharmaverse::sdtm` in templates and vignettes. (#2498)

diff --git a/R/derive_vars_crit_flag.R b/R/derive_vars_crit_flag.R
@@ -1,4 +1,4 @@
-#' Derive Criterion Flag Variables `CRITy`, `CRITyFL`, and `CRITyFLN`
+#' Derive Criterion Flag Variables `CRITy`, `CRITyFL`, and `CRITyFN`
 #'
 #' @description
 #'
@@ -49,12 +49,12 @@
 #'   *Permitted Values*: `TRUE`, `FALSE`
 #' @param create_numeric_flag Create a numeric flag?
 #'
-#'   If set to `TRUE`, the `CRITyFLN` variable is created. It is set to `1` if
+#'   If set to `TRUE`, the `CRITyFN` variable is created. It is set to `1` if
 #'   `CRITyFL == "Y"`, it set to `0` if `CRITyFL == "N"`, and to `NA` otherwise.
 #'
 #'   *Permitted Values*: `TRUE`, `FALSE`
 #' @return The input dataset with the variables `CRITy`, `CRITyFL`, and
-#'   optionally `CRITyFLN` added.
+#'   optionally `CRITyFN` added.
 #'
 #' @family der_bds_findings
 #' @keywords der_bds_findings
@@ -110,10 +110,10 @@ derive_vars_crit_flag <- function(dataset,
 
   if (values_yn) {
     crityfl_no <- "N"
-    crityfln_no <- 0L
+    crityfn_no <- 0L
   } else {
     crityfl_no <- NA_character_
-    crityfln_no <- NA_integer_
+    crityfn_no <- NA_integer_
   }
 
   tryCatch(
@@ -154,9 +154,9 @@ derive_vars_crit_flag <- function(dataset,
   )
 
   if (create_numeric_flag) {
-    new_critflnvar <- paste0("CRIT", as.character(crit_nr), "FLN")
+    new_critfnvar <- paste0("CRIT", as.character(crit_nr), "FN")
     dataset <- dataset %>% mutate(
-      !!new_critflnvar := yn_to_numeric(!!sym(new_critflvar))
+      !!new_critfnvar := yn_to_numeric(!!sym(new_critflvar))
     )
   }
   dataset

diff --git a/man/derive_vars_crit_flag.Rd b/man/derive_vars_crit_flag.Rd
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,      ~CRIT1FLN, ~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_real_, NA_character_,
+    42,    "Y",           1,        "AVAL > 40",
+    NA,    NA_character_, NA_real_, 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,      ~CRIT2FLN, ~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",           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",
   )
 
   expect_dfs_equal(

diff --git a/vignettes/bds_finding.Rmd b/vignettes/bds_finding.Rmd
@@ -45,7 +45,7 @@ otherwise specified.*
 * [Assign Treatment (`TRTA`, `TRTP`)](#treatment)
 * [Assign `ASEQ`](#aseq)
 * [Derive Categorization Variables (`AVALCATy`)](#cat)
-* [Derive Criterion Variables (`CRITy`, `CRITyFL`, `CRITyFLN`)](#crit_vars)
+* [Derive Criterion Variables (`CRITy`, `CRITyFL`, `CRITyFN`)](#crit_vars)
 * [Add ADSL variables](#adsl_vars)
 * [Derive New Rows](#additional)
 * [Add Labels and Attributes](#attributes)
@@ -879,9 +879,9 @@ dataset_vignette(
 )
 ```
 
-## Derive Criterion Variables (`CRITy`, `CRITyFL`, `CRITyFLN`) {#crit_vars}
+## Derive Criterion Variables (`CRITy`, `CRITyFL`, `CRITyFN`) {#crit_vars}
 
-For deriving criterion variables (`CRITy`, `CRITyFL`, `CRITyFLN`) `{admiral}`
+For deriving criterion variables (`CRITy`, `CRITyFL`, `CRITyFN`) `{admiral}`
 provides `derive_vars_crit_flag()`. It ensures that they are derived in an
 ADaM-compliant way (see documentation of the function for details).
 
@@ -921,7 +921,7 @@ advs <- advs %>%
 ```{r, eval=TRUE, echo=FALSE}
 dataset_vignette(
   arrange(advs, USUBJID, AVISITN, ATPTN, PARAMCD),
-  display_vars = exprs(USUBJID, PARAMCD, AVAL, CHG, CRIT1, CRIT1FL, CRIT1FLN),
+  display_vars = exprs(USUBJID, PARAMCD, AVAL, CHG, CRIT1, CRIT1FL, CRIT1FN),
   filter = PARAMCD %in% c("DIABP", "SYSBP")
 )
 ```
@@ -946,7 +946,7 @@ advs <- advs %>%
 ```{r, eval=TRUE, echo=FALSE}
 dataset_vignette(
   arrange(advs, USUBJID, AVISITN, ATPTN),
-  display_vars = exprs(USUBJID, PARAMCD, AVAL, CHG, CRIT2, CRIT2FL, CRIT2FLN),
+  display_vars = exprs(USUBJID, PARAMCD, AVAL, CHG, CRIT2, CRIT2FL, CRIT2FN),
   filter = PARAMCD == "SYSBP"
 )
 ```