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(v0.7.1.9057) get_column_abx() improvement

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dr. M.S. (Matthijs) Berends
2019-08-15 17:09:27 +02:00
parent 920212e815
commit 04d49a62af
12 changed files with 31 additions and 35 deletions
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28
R/guess_ab_col.R
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@ -148,27 +148,21 @@ get_column_abx <- function(x,
}
# sort on name
x <- x[sort(names(x))]
dupes <- x[base::duplicated(x)]
x <- x[order(names(x), x)]
duplicates <- x[base::duplicated(x)]
x <- x[!names(x) %in% names(duplicates)]
if (verbose == TRUE) {
for (i in 1:length(x)) {
if (x[i] %in% dupes) {
message(red(paste0("NOTE: Using column `", bold(x[i]), "` as input for `", names(x)[i],
"` (", ab_name(names(x)[i], language = "en", tolower = TRUE), ") [DUPLICATED USE].")))
} else {
message(blue(paste0("NOTE: Using column `", bold(x[i]), "` as input for `", names(x)[i],
"` (", ab_name(names(x)[i], language = "en", tolower = TRUE), ").")))
}
message(blue(paste0("NOTE: Using column `", bold(x[i]), "` as input for `", names(x)[i],
"` (", ab_name(names(x)[i], tolower = TRUE), ").")))
}
}
if (n_distinct(x) != length(x)) {
msg_txt <- paste("Column(s)", paste0("`", dupes, "`", collapse = " and "), "used for more than one antibiotic.")
if (verbose == FALSE) {
msg_txt <- paste(msg_txt, "Use verbose = TRUE to see which antibiotics are used by which columns.")
} else if (length(duplicates) > 0) {
for (i in 1:length(duplicates)) {
warning(red(paste0("Using column `", bold(duplicates[i]), "` as input for `", names(x[which(x == duplicates[i])]),
"` (", ab_name(names(x[names(which(x == duplicates))[i]]), tolower = TRUE),
"), although it was matched for multiple antibiotics or columns.")), call. = FALSE)
}
stop(msg_txt, call. = FALSE)
}
if (!is.null(hard_dependencies)) {