P281424/AMR
1
0
Fork 0
mirror of https://github.com/msberends/AMR.git synced 2025-07-08 07:51:57 +02:00
Code Releases Activity

(v0.9.0.9016) Support SNOMED codes

Browse Source
This commit is contained in:
dr. M.S. (Matthijs) Berends
2020-01-27 19:14:23 +01:00
parent 42b079cdb7
commit a13c62e6e8
31 changed files with 456 additions and 342 deletions
Download Patch File Download Diff File Expand all files Collapse all files

12
R/mo_property.R
View File

@ -45,6 +45,7 @@
#' - 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 [`character`] in all other cases
#' @export
#' @seealso [microorganisms]
@ -62,11 +63,12 @@
#'
#' # colloquial properties ----------------------------------------------------
#' mo_name("E. coli") # "Escherichia coli"
#' mo_fullname("E. coli") # "Escherichia coli", same as mo_name()
#' mo_fullname("E. coli") # "Escherichia coli" - same as mo_name()
#' mo_shortname("E. coli") # "E. coli"
#'
#' # other properties ---------------------------------------------------------
#' mo_gramstain("E. coli") # "Gram-negative"
#' mo_snomed("E. coli") # 112283007, 116395006, ... (SNOMED codes)
#' mo_type("E. coli") # "Bacteria" (equal to kingdom, but may be translated)
#' mo_rank("E. coli") # "species"
#' mo_url("E. coli") # get the direct url to the online database entry
@ -249,6 +251,12 @@ mo_gramstain <- function(x, language = get_locale(), ...) {
translate_AMR(x, language = language, only_unknown = FALSE)
}
#' @rdname mo_property
#' @export
mo_snomed <- function(x, ...) {
mo_validate(x = x, property = "snomed", ...)
}
#' @rdname mo_property
#' @export
mo_ref <- function(x, ...) {
@ -428,6 +436,8 @@ mo_validate <- function(x, property, ...) {
return(to_class_mo(x))
} else if (property == "col_id") {
return(as.integer(x))
} else if (property == "snomed") {
return(as.double(eval(parse(text = x))))
} else {
return(x)
}