Merge branch 'main' into main

DESCRIPTION

@@ -1,7 +1,7 @@
 Type: Package
 Package: admiral
 Title: ADaM in R Asset Library
-Version: 1.1.1.9041
+Version: 1.1.1.9045
 Authors@R: c(
     person("Ben", "Straub", , "[email protected]", role = c("aut", "cre")),
     person("Stefan", "Bundfuss", role = "aut",

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)

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 +110,8 @@ derive_vars_crit_flag <- function(dataset,
 
   if (values_yn) {
     crityfl_no <- "N"
-    crityfln_no <- 0L
   } else {
     crityfl_no <- NA_character_
-    crityfln_no <- NA_integer_
   }
 
   tryCatch(
@@ -154,9 +152,9 @@ 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 := as.integer(yn_to_numeric(!!sym(new_critflvar)))
     )
   }
   dataset

R/derive_vars_transposed.R

@@ -118,6 +118,8 @@ derive_vars_transposed <- function(dataset,
     optional = TRUE
   )
 
+  dataset_merge <- filter_if(dataset_merge, filter)
+
   # check for duplicates in dataset_merge as these will create list columns,
   # which is not acceptable for ADaM datasets
   signal_duplicate_records(
@@ -134,7 +136,6 @@ derive_vars_transposed <- function(dataset,
   )
 
   dataset_transposed <- dataset_merge %>%
-    filter_if(filter) %>%
     pivot_wider(
       names_from = !!key_var,
       values_from = !!value_var,

tests/testthat/_snaps/compute_scale.md

@@ -7,7 +7,7 @@
       ! Argument `target_range` is missing with no default and `source_range` is not missing.
       i Either both or neither arguments should be specified.
 
----
+# compute_scale Test 7: error if target_range is supplied, but not source_range
 
     Code
       compute_scale(input, target_range = c(0, 100), min_n = 2)

tests/testthat/_snaps/derive_var_trtemfl.md

@@ -34,3 +34,12 @@
       ! `intensity` argument was specified but not `initial_intensity`
       Either both or none of them must be specified.
 
+# derive_var_trtemfl Test 11: error if `group_var` without `subject_keys`
+
+    Code
+      derive_var_trtemfl(adae, group_var = AEGRPID, subject_keys = NULL)
+    Condition
+      Error in `derive_var_trtemfl()`:
+      ! `group_var` argument was specified but not `subject_keys`
+      `subject_keys` argument must be provided when `group_var` is specified.
+

tests/testthat/test-derive_var_trtemfl.R

@@ -194,7 +194,7 @@ test_that("derive_var_trtemfl Test 9: error if `intensity` without `initial_inte
 })
 
 ## Test 10: warning if both `initial_intensity` and `group_var` are specified ----
-test_that("derive_var_trtemfl Test 9: error if `intensity` without `initial_intensity`", {
+test_that("derive_var_trtemfl Test 10: error if `intensity` without `initial_intensity`", {
   expect_warning(
     derive_var_trtemfl(
       adae2,
@@ -204,3 +204,15 @@ test_that("derive_var_trtemfl Test 9: error if `intensity` without `initial_inte
     "`initial_intensity` argument is ignored when `group_var` is specified"
   )
 })
+
+## Test 11: error if `group_var` are specified without `subject_keys` ----
+test_that("derive_var_trtemfl Test 11: error if `group_var` without `subject_keys`", {
+  expect_snapshot(
+    derive_var_trtemfl(
+      adae,
+      group_var = AEGRPID,
+      subject_keys = NULL
+    ),
+    error = TRUE
+  )
+})

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_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,      ~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",           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(

tests/testthat/test-derive_vars_transposed.R

@@ -40,6 +40,15 @@ test_that("derive_vars_transposed Test 2: filtering the merge dataset works", {
     "STUDY01", "P02",       31,    3,
     "STUDY01", "P03",       42,   NA
   )
+
+  dataset_merge <- tibble::tribble(
+    ~STUDYID,  ~USUBJID, ~TESTCD, ~VALUE,
+    "STUDY01", "P01",    "T01",       31,
+    "STUDY01", "P01",    "T02",        5,
+    "STUDY01", "P02",    "T01",        3,
+    "STUDY01", "P01",    "T02",        9
+  )
+
   actual_output <- derive_vars_transposed(
     dataset,
     dataset_merge,

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"
 )
 ```