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Closes #2468 fix_derive_vars_crit_flag: create integer flag #2618

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merged 6 commits into from
Dec 20, 2024
Merged

Closes #2468 fix_derive_vars_crit_flag: create integer flag #2618

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93483fa
#2468 fix_derive_vars_crit_flag: create correct numeric flag (CRITyFN…
bundfussr Dec 19, 2024
166f1a7
#2468 fix_derive_vars_crit_flag: update vignettes
bundfussr Dec 19, 2024
b4cb124
#2468 fix_derive_vars_crit_flag: style files
bundfussr Dec 19, 2024
c8f34c5
#2468 fix_derive_vars_crit_flag: fix typo in variable names
bundfussr Dec 19, 2024
34859c2
#2468 fix_derive_vars_crit_flag: create integer flag
bundfussr Dec 20, 2024
a68ee0c
Merge branch 'main' into 2468_fix_derive_vars_crit_flag
bundfussr Dec 20, 2024
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4 changes: 1 addition & 3 deletions R/derive_vars_crit_flag.R
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Original file line number Diff line number Diff line change
Expand Up @@ -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(
Expand Down Expand Up @@ -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
Expand Down
20 changes: 10 additions & 10 deletions tests/testthat/test-derive_vars_crit_flag.R
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Original file line number Diff line number Diff line change
Expand Up @@ -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(
Expand All @@ -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(
Expand Down
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