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make rsi work in more cases, documentation update

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dr. M.S. (Matthijs) Berends
2023-02-22 14:38:57 +01:00
parent 380cbec0e8
commit dad25302f2
87 changed files with 401 additions and 327 deletions
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38
R/mo_property.R
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@ -58,7 +58,7 @@
#'
#' SNOMED codes ([mo_snomed()]) are from the version of `r documentation_date(TAXONOMY_VERSION$SNOMED$accessed_date)`. See *Source* and the [microorganisms] data set for more info.
#'
#' Old taxonomic names (so-called 'synonyms') can be retrieved with [mo_synonyms()], the current taxonomic name can be retrieved with [mo_current()]. Both functions return full names.
#' Old taxonomic names (so-called 'synonyms') can be retrieved with [mo_synonyms()] (which will have the scientific reference as [name][base::names()]), the current taxonomic name can be retrieved with [mo_current()]. Both functions return full names.
#'
#' All output [will be translated][translate] where possible.
#' @section Matching Score for Microorganisms:
@ -108,13 +108,13 @@
#'
#' # scientific reference -----------------------------------------------------
#'
#' mo_ref("Klebsiella pneumoniae")
#' mo_authors("Klebsiella pneumoniae")
#' mo_year("Klebsiella pneumoniae")
#' mo_lpsn("Klebsiella pneumoniae")
#' mo_gbif("Klebsiella pneumoniae")
#' mo_synonyms("Klebsiella pneumoniae")
#'
#' mo_ref("Klebsiella aerogenes")
#' mo_authors("Klebsiella aerogenes")
#' mo_year("Klebsiella aerogenes")
#' mo_lpsn("Klebsiella aerogenes")
#' mo_gbif("Klebsiella aerogenes")
#' mo_synonyms("Klebsiella aerogenes")
#'
#'
#' # abbreviations known in the field -----------------------------------------
#'
@ -124,7 +124,8 @@
#' mo_gramstain("VISA")
#'
#' mo_genus("EHEC")
#' mo_species("EHEC")
#' mo_species("EIEC")
#' mo_name("UPEC")
#'
#'
#' # known subspecies ---------------------------------------------------------
@ -740,23 +741,22 @@ mo_synonyms <- function(x, language = get_AMR_locale(), keep_synonyms = getOptio
syns <- lapply(x.mo, function(y) {
gbif <- AMR_env$MO_lookup$gbif[match(y, AMR_env$MO_lookup$mo)]
lpsn <- AMR_env$MO_lookup$lpsn[match(y, AMR_env$MO_lookup$mo)]
out <- AMR_env$MO_lookup[which(AMR_env$MO_lookup$lpsn_renamed_to == lpsn | AMR_env$MO_lookup$gbif_renamed_to == gbif), "fullname", drop = TRUE]
if (length(out) == 0) {
fullname <- AMR_env$MO_lookup[which(AMR_env$MO_lookup$lpsn_renamed_to == lpsn | AMR_env$MO_lookup$gbif_renamed_to == gbif), "fullname", drop = TRUE]
if (length(fullname) == 0) {
NULL
} else {
out
ref <- AMR_env$MO_lookup[which(AMR_env$MO_lookup$lpsn_renamed_to == lpsn | AMR_env$MO_lookup$gbif_renamed_to == gbif), "ref", drop = TRUE]
names(fullname) <- ref
fullname
}
})
if (length(syns) > 1) {
names(syns) <- mo_name(x, language = language)
result <- syns
} else {
result <- unlist(syns)
if (length(syns) == 1) {
syns <- unlist(syns)
}
load_mo_uncertainties(metadata)
result
syns
}
#' @rdname mo_property