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unit tests

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This commit is contained in:
dr. M.S. (Matthijs) Berends
2023-02-12 17:10:48 +01:00
parent 68abb00c59
commit 45a9697c84
23 changed files with 438 additions and 406 deletions
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10
R/first_isolate.R
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@ -480,7 +480,7 @@ first_isolate <- function(x = NULL,
),
use.names = FALSE
)
if (!is.null(col_keyantimicrobials)) {
# with key antibiotics
x$other_key_ab <- !antimicrobials_equal(
@ -501,20 +501,20 @@ first_isolate <- function(x = NULL,
x$newvar_genus_species != "" &
(x$other_pat_or_mo | x$more_than_episode_ago)
}
# first one as TRUE
x[row.start, "newvar_first_isolate"] <- TRUE
# no tests that should be included, or ICU
if (!is.null(col_testcode)) {
x[which(x[, col_testcode] %in% tolower(testcodes_exclude)), "newvar_first_isolate"] <- FALSE
}
if (!is.null(col_icu)) {
if (icu_exclude == TRUE) {
if (isTRUE(info)) {
message_("Excluding ", format(sum(col_icu, na.rm = TRUE), big.mark = " "), " isolates from ICU.",
add_fn = font_black,
as_note = FALSE
add_fn = font_black,
as_note = FALSE
)
}
x[which(col_icu), "newvar_first_isolate"] <- FALSE