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(v2.1.1.9157) improved as.ab(), fixed knit_print of antibiogram

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dr. M.S. (Matthijs) Berends
2025-02-26 13:27:20 +01:00
parent b10989f431
commit 195dfb4b91
20 changed files with 107 additions and 42 deletions
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14
R/antibiogram.R
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@ -441,7 +441,7 @@ antibiogram.default <- function(x,
x <- ascertain_sir_classes(x, "x")
meet_criteria(wisca, allow_class = "logical", has_length = 1)
if (isTRUE(wisca)) {
if (!is.null(mo_transform)) {
if (!is.null(mo_transform) && !missing(mo_transform)) {
warning_("WISCA must be based on the species level as WISCA parameters are based on this. For that reason, `mo_transform` will be ignored.")
}
mo_transform <- function(x) suppressMessages(suppressWarnings(paste(mo_genus(x, keep_synonyms = TRUE, language = NULL), mo_species(x, keep_synonyms = TRUE, language = NULL))))
@ -1245,10 +1245,14 @@ knit_print.antibiogram <- function(x, italicise = TRUE, na = getOption("knitr.ka
meet_criteria(italicise, allow_class = "logical", has_length = 1)
meet_criteria(na, allow_class = "character", has_length = 1, allow_NA = TRUE)
if (!isTRUE(attributes(x)$wisca) && isTRUE(italicise) && "mo" %in% colnames(attributes(x)$long_numeric)) {
# make all microorganism names italic, according to nomenclature
names_col <- ifelse(isTRUE(attributes(x)$has_syndromic_group), 2, 1)
x[[names_col]] <- italicise_taxonomy(x[[names_col]], type = "markdown")
add_MO_lookup_to_AMR_env()
cols_with_mo_names <- vapply(FUN.VALUE = logical(1), x, function(x) any(x %in% AMR_env$MO_lookup$fullname, na.rm = TRUE))
if (any(cols_with_mo_names)) {
for (i in which(cols_with_mo_names)) {
# make all microorganism names italic, according to nomenclature
x[[i]] <- italicise_taxonomy(x[[i]], type = "markdown")
}
}
old_option <- getOption("knitr.kable.NA")