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new mo_group_members()

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dr. M.S. (Matthijs) Berends
2024-04-19 10:18:21 +02:00
parent 7e7bc9d56e
commit 2899b3c840
10 changed files with 86 additions and 26 deletions
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41
R/mo_property.R
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@ -106,7 +106,12 @@
#' mo_rank("Klebsiella pneumoniae")
#' mo_url("Klebsiella pneumoniae")
#' mo_is_yeast(c("Candida", "Trichophyton", "Klebsiella"))
#'
#'
#' mo_group_members("Streptococcus group A")
#' mo_group_members(c("Streptococcus group C",
#' "Streptococcus group G",
#' "Streptococcus group L"))
#'
#'
#' # scientific reference -----------------------------------------------------
#'
@ -796,6 +801,37 @@ mo_current <- function(x, language = get_AMR_locale(), ...) {
mo_name(out, language = language)
}
#' @rdname mo_property
#' @export
mo_group_members <- function(x, language = get_AMR_locale(), keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...) {
if (missing(x)) {
# this tries to find the data and an 'mo' column
x <- find_mo_col(fn = "mo_synonyms")
}
meet_criteria(x, allow_NA = TRUE)
language <- validate_language(language)
meet_criteria(keep_synonyms, allow_class = "logical", has_length = 1)
add_MO_lookup_to_AMR_env()
x.mo <- as.mo(x, language = language, keep_synonyms = keep_synonyms, ...)
metadata <- get_mo_uncertainties()
members <- lapply(x.mo, function(y) {
AMR::microorganisms.groups$mo_name[which(AMR::microorganisms.groups$mo_group == y)]
})
names(members) <- mo_name(x, keep_synonyms = TRUE, language = language)
if (length(members) == 1) {
members <- unname(unlist(members))
}
load_mo_uncertainties(metadata)
members
}
#' @rdname mo_property
#' @export
mo_info <- function(x, language = get_AMR_locale(), keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...) {
@ -823,7 +859,8 @@ mo_info <- function(x, language = get_AMR_locale(), keep_synonyms = getOption("A
ref = mo_ref(y, keep_synonyms = keep_synonyms),
snomed = unlist(mo_snomed(y, keep_synonyms = keep_synonyms)),
lpsn = mo_lpsn(y, language = language, keep_synonyms = keep_synonyms),
gbif = mo_gbif(y, language = language, keep_synonyms = keep_synonyms)
gbif = mo_gbif(y, language = language, keep_synonyms = keep_synonyms),
group_members = mo_group_members(y, language = language, keep_synonyms = keep_synonyms)
)
)
})