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(v2.1.1.9125) replace 'antibiotic selectors' with 'antimicrobial selectors'

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dr. M.S. (Matthijs) Berends
2025-01-17 12:09:39 +01:00
parent 1697ad37ce
commit 92c4fc0f94
33 changed files with 1029 additions and 807 deletions
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76
R/guess_ab_col.R
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@ -105,7 +105,8 @@ get_column_abx <- function(x,
only_sir_columns = FALSE,
sort = TRUE,
reuse_previous_result = TRUE,
fn = NULL) {
fn = NULL,
return_all = FALSE) {
# check if retrieved before, then get it from package environment
if (isTRUE(reuse_previous_result) && identical(
unique_call_id(
@ -253,47 +254,50 @@ get_column_abx <- function(x,
if (sort == TRUE) {
out <- out[order(names(out), out)]
}
# only keep the first hits, no duplicates
duplicates <- c(out[duplicated(names(out))], out[duplicated(unname(out))])
if (length(duplicates) > 0) {
all_okay <- FALSE
}
if (isTRUE(info)) {
if (all_okay == TRUE) {
message_(" OK.", add_fn = list(font_green, font_bold), as_note = FALSE)
} else {
message_(" WARNING.", add_fn = list(font_yellow, font_bold), as_note = FALSE)
if (return_all == FALSE) {
# only keep the first hits, no duplicates
duplicates <- c(out[duplicated(names(out))], out[duplicated(unname(out))])
if (length(duplicates) > 0) {
all_okay <- FALSE
}
for (i in seq_len(length(out))) {
if (isTRUE(verbose) && !names(out[i]) %in% names(duplicates)) {
message_(
"Using column '", font_bold(out[i]), "' as input for ", names(out)[i],
" (", ab_name(names(out)[i], tolower = TRUE, language = NULL), ")."
)
if (isTRUE(info)) {
if (all_okay == TRUE) {
message_(" OK.", add_fn = list(font_green, font_bold), as_note = FALSE)
} else {
message_(" WARNING.", add_fn = list(font_yellow, font_bold), as_note = FALSE)
}
if (names(out[i]) %in% names(duplicates)) {
already_set_as <- out[unname(out) == unname(out[i])][1L]
if (names(out)[i] != names(already_set_as)) {
warning_(
paste0(
"Column '", font_bold(out[i]), "' will not be used for ",
names(out)[i], " (", ab_name(names(out)[i], tolower = TRUE, language = NULL), ")",
", as it is already set for ",
names(already_set_as), " (", ab_name(names(already_set_as), tolower = TRUE, language = NULL), ")"
),
add_fn = font_red,
immediate = verbose
for (i in seq_len(length(out))) {
if (isTRUE(verbose) && !names(out[i]) %in% names(duplicates)) {
message_(
"Using column '", font_bold(out[i]), "' as input for ", names(out)[i],
" (", ab_name(names(out)[i], tolower = TRUE, language = NULL), ")."
)
}
if (names(out[i]) %in% names(duplicates)) {
already_set_as <- out[unname(out) == unname(out[i])][1L]
if (names(out)[i] != names(already_set_as)) {
warning_(
paste0(
"Column '", font_bold(out[i]), "' will not be used for ",
names(out)[i], " (", ab_name(names(out)[i], tolower = TRUE, language = NULL), ")",
", as it is already set for ",
names(already_set_as), " (", ab_name(names(already_set_as), tolower = TRUE, language = NULL), ")"
),
add_fn = font_red,
immediate = verbose
)
}
}
}
}
}
out <- out[!duplicated(names(out))]
out <- out[!duplicated(unname(out))]
if (sort == TRUE) {
out <- out[order(names(out), out)]
out <- out[!duplicated(names(out))]
out <- out[!duplicated(unname(out))]
if (sort == TRUE) {
out <- out[order(names(out), out)]
}
}
if (!is.null(hard_dependencies)) {