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unit test fix

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This commit is contained in:
dr. M.S. (Matthijs) Berends
2022-08-28 19:17:12 +02:00
parent 0d67db4f32
commit 71db246d5c
27 changed files with 51 additions and 74 deletions
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2
R/first_isolate.R
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@ -529,7 +529,7 @@ first_isolate <- function(x = NULL,
}
if (!is.null(col_icu)) {
if (icu_exclude == TRUE) {
message_("Excluding ", format(sum(!col_icu, na.rm = TRUE), big.mark = ","), " isolates from ICU.",
message_("Excluding ", format(sum(col_icu, na.rm = TRUE), big.mark = ","), " isolates from ICU.",
add_fn = font_black,
as_note = FALSE
)

12
R/mo.R
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@ -204,12 +204,12 @@ as.mo <- function(x,
))
}
reference_df <- repair_reference_df(reference_df)
if (!is.null(reference_df) &&
check_validity_mo_source(reference_df) &&
isFALSE(Becker) &&
isFALSE(Lancefield) &&
all(x %in% unlist(reference_df), na.rm = TRUE)) {
reference_df <- repair_reference_df(reference_df)
all(x %in% reference_df[, 1, drop = TRUE], na.rm = TRUE)) {
suppressWarnings(
y <- data.frame(x = x, stringsAsFactors = FALSE) %pm>%
pm_left_join(reference_df, by = "x") %pm>%
@ -221,6 +221,7 @@ as.mo <- function(x,
y <- x
} else {
# will be checked for mo class in validation and uses exec_as.mo internally if necessary
y <- mo_validate(
x = x, property = "mo",
Becker = Becker, Lancefield = Lancefield,
@ -420,7 +421,7 @@ exec_as.mo <- function(x,
}
# all empty
if (all(identical(trimws(x_input), "") | is.na(x_input) | length(x) == 0)) {
if (all(identical(trimws(x_input), "") | is.na(x_input) | length(x) == 0, na.rm = TRUE)) {
if (property == "mo") {
return(set_clean_class(rep(NA_character_, length(x_input)),
new_class = c("mo", "character")
@ -428,7 +429,7 @@ exec_as.mo <- function(x,
} else {
return(rep(NA_character_, length(x_input)))
}
} else if (all(x %in% reference_df[, 1, drop = TRUE][[1]])) {
} else if (all(x %in% reference_df[, 1, drop = TRUE], na.rm = TRUE)) {
# all in reference df
colnames(reference_df)[1] <- "x"
suppressWarnings(
@ -2357,6 +2358,9 @@ replace_ignore_pattern <- function(x, ignore_pattern) {
}
repair_reference_df <- function(reference_df) {
if (is.null(reference_df)) {
return(NULL)
}
# has valid own reference_df
reference_df <- reference_df %pm>%
pm_filter(!is.na(mo))