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add fn

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dr. M.S. (Matthijs) Berends
2026-05-05 12:41:45 +02:00
parent cead31bed0
commit 155c2707ce
4 changed files with 24 additions and 4 deletions
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11
R/mo_property.R
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@@ -102,8 +102,10 @@
#'
#' # other properties ---------------------------------------------------------
#'
#' mo_pathogenicity("Klebsiella pneumoniae")
#' mo_morphology("Klebsiella pneumoniae")
#' mo_gramstain("Klebsiella pneumoniae")
#' mo_gramstain("Klebsiella pneumoniae", add_morphology = TRUE)
#' mo_pathogenicity("Klebsiella pneumoniae")
#' mo_snomed("Klebsiella pneumoniae")
#' mo_type("Klebsiella pneumoniae")
#' mo_rank("Klebsiella pneumoniae")
@@ -472,6 +474,7 @@ mo_gramstain <- function(x, language = get_AMR_locale(), keep_synonyms = getOpti
meet_criteria(x, allow_NA = TRUE)
language <- validate_language(language)
meet_criteria(keep_synonyms, allow_class = "logical", has_length = 1)
meet_criteria(add_morphology, allow_class = "logical", has_length = 1)
x.mo <- as.mo(x, language = language, keep_synonyms = keep_synonyms, ...)
metadata <- get_mo_uncertainties()
@@ -497,6 +500,12 @@ mo_gramstain <- function(x, language = get_AMR_locale(), keep_synonyms = getOpti
# and of course our own ID for Gram-positives
| x.mo %in% c("B_GRAMP", "B_ANAER-POS")] <- "Gram-positive"
if (isTRUE(add_morphology)) {
morphs <- mo_morphology(x.mo, language = NULL)
morphs[is.na(x)] <- ""
x[!is.na(x)] <- paste(x[!is.na(x)], tolower(morphs[!is.na(x)]))
}
load_mo_uncertainties(metadata)
translate_into_language(x, language = language, only_unknown = FALSE)
}