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(v1.4.0.9015) bugfix

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This commit is contained in:
dr. M.S. (Matthijs) Berends
2020-11-10 16:35:56 +01:00
parent dd5a0319ef
commit 15c732703d
35 changed files with 224 additions and 161 deletions
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24
R/guess_ab_col.R
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@ -167,8 +167,9 @@ get_column_abx <- function(x,
if (length(dots) > 0) {
newnames <- suppressWarnings(as.ab(names(dots), info = FALSE))
if (any(is.na(newnames))) {
warning("Invalid antibiotic reference(s): ", toString(names(dots)[is.na(newnames)]),
call. = FALSE, immediate. = TRUE)
warning_("Invalid antibiotic reference(s): ", toString(names(dots)[is.na(newnames)]),
call = FALSE,
immediate = TRUE)
}
# turn all NULLs to NAs
dots <- unlist(lapply(dots, function(x) if (is.null(x)) NA else x))
@ -205,11 +206,12 @@ get_column_abx <- function(x,
"` (", ab_name(names(x)[i], tolower = TRUE, language = NULL), ").")
}
if (info == TRUE & names(x[i]) %in% names(duplicates)) {
warning(font_red(paste0("Using column `", font_bold(x[i]), "` as input for `", names(x)[i],
"` (", ab_name(names(x)[i], tolower = TRUE, language = NULL),
"), although it was matched for multiple antibiotics or columns.")),
call. = FALSE,
immediate. = verbose)
warning_(paste0("Using column `", font_bold(x[i]), "` as input for `", names(x)[i],
"` (", ab_name(names(x)[i], tolower = TRUE, language = NULL),
"), although it was matched for multiple antibiotics or columns."),
add_fn = font_red,
call = FALSE,
immediate = verbose)
}
}
@ -245,8 +247,8 @@ generate_warning_abs_missing <- function(missing, any = FALSE) {
} else {
any_txt <- c("", "are")
}
warning(paste0("Introducing NAs since", any_txt[1], " these antimicrobials ", any_txt[2], " required: ",
paste(missing, collapse = ", ")),
immediate. = TRUE,
call. = FALSE)
warning_(paste0("Introducing NAs since", any_txt[1], " these antimicrobials ", any_txt[2], " required: ",
paste(missing, collapse = ", ")),
immediate = TRUE,
call = FALSE)
}