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(v1.5.0.9041) SNOMED update

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dr. M.S. (Matthijs) Berends
2021-03-11 21:42:30 +01:00
parent 8d6ceb6a15
commit 4e0a9533ad
65 changed files with 86943 additions and 67626 deletions
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14
R/mo_property.R
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@ -51,6 +51,8 @@
#' All output [will be translated][translate] where possible.
#'
#' The function [mo_url()] will return the direct URL to the online database entry, which also shows the scientific reference of the concerned species.
#'
#' SNOMED codes - [mo_snomed()] - are from the `r SNOMED_VERSION$current_source`. See the [microorganisms] data set for more info.
#' @inheritSection mo_matching_score Matching Score for Microorganisms
#' @inheritSection catalogue_of_life Catalogue of Life
#' @inheritSection as.mo Source
@ -60,7 +62,7 @@
#' - An [integer] in case of [mo_year()]
#' - A [list] in case of [mo_taxonomy()] and [mo_info()]
#' - A named [character] in case of [mo_url()]
#' - A [double] in case of [mo_snomed()]
#' - A [numeric] in case of [mo_snomed()]
#' - A [character] in all other cases
#' @export
#' @seealso [microorganisms]
@ -161,7 +163,8 @@
#'
#' # get a list with the complete taxonomy (from kingdom to subspecies)
#' mo_taxonomy("E. coli")
#' # get a list with the taxonomy, the authors, Gram-stain and URL to the online database
#' # get a list with the taxonomy, the authors, Gram-stain,
#' # SNOMED codes, and URL to the online database
#' mo_info("E. coli")
#' }
mo_name <- function(x, language = get_locale(), ...) {
@ -629,7 +632,8 @@ mo_info <- function(x, language = get_locale(), ...) {
list(synonyms = mo_synonyms(y),
gramstain = mo_gramstain(y, language = language),
url = unname(mo_url(y, open = FALSE)),
ref = mo_ref(y))))
ref = mo_ref(y),
snomed = unlist(mo_snomed(y)))))
if (length(info) > 1) {
names(info) <- mo_name(x)
result <- info
@ -659,10 +663,10 @@ mo_url <- function(x, open = FALSE, language = get_locale(), ...) {
df <- data.frame(mo, stringsAsFactors = FALSE) %pm>%
pm_left_join(pm_select(microorganisms, mo, source, species_id), by = "mo")
df$url <- ifelse(df$source == "CoL",
paste0(catalogue_of_life$url_CoL, "details/species/id/", df$species_id, "/"),
paste0(CATALOGUE_OF_LIFE$url_CoL, "details/species/id/", df$species_id, "/"),
NA_character_)
u <- df$url
u[mo_kingdom(mo) == "Bacteria"] <- paste0(catalogue_of_life$url_LPSN, "/species/", gsub(" ", "-", tolower(mo_names), fixed = TRUE))
u[mo_kingdom(mo) == "Bacteria"] <- paste0(CATALOGUE_OF_LIFE$url_LPSN, "/species/", gsub(" ", "-", tolower(mo_names), fixed = TRUE))
u[mo_kingdom(mo) == "Bacteria" & mo_rank(mo) == "genus"] <- gsub("/species/",
"/genus/",
u[mo_kingdom(mo) == "Bacteria" & mo_rank(mo) == "genus"],