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(v1.5.0.9041) SNOMED update
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@ -51,6 +51,8 @@
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#' All output [will be translated][translate] where possible.
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#'
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#' The function [mo_url()] will return the direct URL to the online database entry, which also shows the scientific reference of the concerned species.
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#'
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#' SNOMED codes - [mo_snomed()] - are from the `r SNOMED_VERSION$current_source`. See the [microorganisms] data set for more info.
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#' @inheritSection mo_matching_score Matching Score for Microorganisms
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#' @inheritSection catalogue_of_life Catalogue of Life
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#' @inheritSection as.mo Source
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@ -60,7 +62,7 @@
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#' - An [integer] in case of [mo_year()]
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#' - A [list] in case of [mo_taxonomy()] and [mo_info()]
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#' - A named [character] in case of [mo_url()]
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#' - A [double] in case of [mo_snomed()]
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#' - A [numeric] in case of [mo_snomed()]
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#' - A [character] in all other cases
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#' @export
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#' @seealso [microorganisms]
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@ -161,7 +163,8 @@
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#'
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#' # get a list with the complete taxonomy (from kingdom to subspecies)
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#' mo_taxonomy("E. coli")
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#' # get a list with the taxonomy, the authors, Gram-stain and URL to the online database
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#' # get a list with the taxonomy, the authors, Gram-stain,
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#' # SNOMED codes, and URL to the online database
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#' mo_info("E. coli")
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#' }
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mo_name <- function(x, language = get_locale(), ...) {
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@ -629,7 +632,8 @@ mo_info <- function(x, language = get_locale(), ...) {
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list(synonyms = mo_synonyms(y),
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gramstain = mo_gramstain(y, language = language),
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url = unname(mo_url(y, open = FALSE)),
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ref = mo_ref(y))))
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ref = mo_ref(y),
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snomed = unlist(mo_snomed(y)))))
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if (length(info) > 1) {
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names(info) <- mo_name(x)
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result <- info
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@ -659,10 +663,10 @@ mo_url <- function(x, open = FALSE, language = get_locale(), ...) {
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df <- data.frame(mo, stringsAsFactors = FALSE) %pm>%
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pm_left_join(pm_select(microorganisms, mo, source, species_id), by = "mo")
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df$url <- ifelse(df$source == "CoL",
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paste0(catalogue_of_life$url_CoL, "details/species/id/", df$species_id, "/"),
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paste0(CATALOGUE_OF_LIFE$url_CoL, "details/species/id/", df$species_id, "/"),
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NA_character_)
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u <- df$url
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u[mo_kingdom(mo) == "Bacteria"] <- paste0(catalogue_of_life$url_LPSN, "/species/", gsub(" ", "-", tolower(mo_names), fixed = TRUE))
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u[mo_kingdom(mo) == "Bacteria"] <- paste0(CATALOGUE_OF_LIFE$url_LPSN, "/species/", gsub(" ", "-", tolower(mo_names), fixed = TRUE))
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u[mo_kingdom(mo) == "Bacteria" & mo_rank(mo) == "genus"] <- gsub("/species/",
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"/genus/",
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u[mo_kingdom(mo) == "Bacteria" & mo_rank(mo) == "genus"],
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