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This commit is contained in:
dr. M.S. (Matthijs) Berends
2023-01-23 15:01:21 +01:00
parent af139a3c82
commit 19fd0ef121
57 changed files with 2864 additions and 2739 deletions
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39
R/guess_ab_col.R
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@ -274,14 +274,15 @@ get_column_abx <- function(x,
}
if (names(out[i]) %in% names(duplicates)) {
already_set_as <- out[unname(out) == unname(out[i])][1L]
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
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
)
}
}
@ -307,11 +308,12 @@ get_column_abx <- function(x,
if (isTRUE(info) && !all(soft_dependencies %in% names(out))) {
# missing a soft dependency may lower the reliability
missing <- soft_dependencies[!soft_dependencies %in% names(out)]
missing_msg <- vector_and(paste0(
ab_name(missing, tolower = TRUE, language = NULL),
" (", font_bold(missing, collapse = NULL), ")"
),
quotes = FALSE
missing_msg <- vector_and(
paste0(
ab_name(missing, tolower = TRUE, language = NULL),
" (", font_bold(missing, collapse = NULL), ")"
),
quotes = FALSE
)
message_(
"Reliability would be improved if these antimicrobial results would be available too: ",
@ -355,10 +357,11 @@ 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: ",
vector_and(missing, quotes = FALSE)
),
immediate = TRUE
warning_(
paste0(
"Introducing NAs since", any_txt[1], " these antimicrobials ", any_txt[2], " required: ",
vector_and(missing, quotes = FALSE)
),
immediate = TRUE
)
}