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(v3.0.1.9001) fix antibiogram

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dr. M.S. (Matthijs) Berends
2025-09-30 10:54:07 +02:00
parent adee419f1c
commit 0b24967b23
8 changed files with 28 additions and 15 deletions
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6
R/antibiogram.R
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@@ -453,7 +453,7 @@ antibiogram.default <- function(x,
deprecation_warning("antibiotics", "antimicrobials", fn = "antibiogram", is_argument = TRUE)
antimicrobials <- list(...)$antibiotics
}
meet_criteria(antimicrobials, allow_class = c("character", "numeric", "integer"), allow_NA = FALSE, allow_NULL = FALSE)
meet_criteria(antimicrobials, allow_class = c("character", "numeric", "integer", "function"), allow_NA = FALSE, allow_NULL = FALSE)
if (!is.function(mo_transform)) {
meet_criteria(mo_transform, allow_class = "character", has_length = 1, is_in = c("name", "shortname", "gramstain", colnames(AMR::microorganisms)), allow_NULL = TRUE, allow_NA = TRUE)
}
@@ -518,6 +518,10 @@ antibiogram.default <- function(x,
# get antimicrobials
ab_trycatch <- tryCatch(colnames(suppressWarnings(x[, antimicrobials, drop = FALSE])), error = function(e) NULL)
if (is.null(ab_trycatch)) {
# try with tidyverse
ab_trycatch <- tryCatch(colnames(dplyr::select(x, {{ antimicrobials }})), error = function(e) NULL)
}
if (is.null(ab_trycatch)) {
stop_ifnot(is.character(suppressMessages(antimicrobials)), "`antimicrobials` must be an antimicrobial selector, or a character vector.")
antimicrobials.bak <- antimicrobials