Merge branch '2595-deprecation@466-deprecation-20' of https://github.…

…com/pharmaverse/admiral into 2595-deprecation@466-deprecation-20

DESCRIPTION

@@ -1,7 +1,7 @@
 Type: Package
 Package: admiral
 Title: ADaM in R Asset Library
-Version: 1.1.1.9043
+Version: 1.1.1.9045
 Authors@R: c(
     person("Ben", "Straub", , "[email protected]", role = c("aut", "cre")),
     person("Stefan", "Bundfuss", role = "aut",

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

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,      ~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(