P281424/AMR
1
0
Fork 0
mirror of https://github.com/msberends/AMR.git synced 2025-07-11 12:22:01 +02:00
Code Releases Activity

(v1.7.1.9067) Support for Swedish and Russian

Browse Source
This commit is contained in:
dr. M.S. (Matthijs) Berends
2021-12-12 09:42:03 +01:00
parent 5b5f70a103
commit 56f1ce328a
81 changed files with 1588 additions and 530 deletions
Download Patch File Download Diff File Expand all files Collapse all files

56
R/mo_property.R
View File

@ -29,7 +29,7 @@
#' @inheritSection lifecycle Stable Lifecycle
#' @param x any [character] (vector) that can be coerced to a valid microorganism code with [as.mo()]. Can be left blank for auto-guessing the column containing microorganism codes if used in a data set, see *Examples*.
#' @param property one of the column names of the [microorganisms] data set: `r vector_or(colnames(microorganisms), sort = FALSE, quotes = TRUE)`, or must be `"shortname"`
#' @param language language of the returned text, defaults to system language (see [get_locale()]) and can be overwritten by setting the option `AMR_locale`, e.g. `options(AMR_locale = "de")`, see [translate]. Also used to translate text like "no growth". Use `language = NULL` or `language = ""` to prevent translation.
#' @param language language of the returned text, defaults to system language (see [get_AMR_locale()]) and can be overwritten by setting the option `AMR_locale`, e.g. `options(AMR_locale = "de")`, see [translate]. Also used to translate text like "no growth". Use `language = NULL` or `language = ""` to prevent translation.
#' @param ... other arguments passed on to [as.mo()], such as 'allow_uncertain' and 'ignore_pattern'
#' @param ab any (vector of) text that can be coerced to a valid antibiotic code with [as.ab()]
#' @param open browse the URL using [`browseURL()`][utils::browseURL()]
@ -170,7 +170,7 @@
#' mo_info("E. coli")
#' }
#' }
mo_name <- function(x, language = get_locale(), ...) {
mo_name <- function(x, language = get_AMR_locale(), ...) {
if (missing(x)) {
# this tries to find the data and an <mo> column
x <- find_mo_col(fn = "mo_name")
@ -190,7 +190,7 @@ mo_fullname <- mo_name
#' @rdname mo_property
#' @export
mo_shortname <- function(x, language = get_locale(), ...) {
mo_shortname <- function(x, language = get_AMR_locale(), ...) {
if (missing(x)) {
# this tries to find the data and an <mo> column
x <- find_mo_col(fn = "mo_shortname")
@ -230,7 +230,7 @@ mo_shortname <- function(x, language = get_locale(), ...) {
#' @rdname mo_property
#' @export
mo_subspecies <- function(x, language = get_locale(), ...) {
mo_subspecies <- function(x, language = get_AMR_locale(), ...) {
if (missing(x)) {
# this tries to find the data and an <mo> column
x <- find_mo_col(fn = "mo_subspecies")
@ -243,7 +243,7 @@ mo_subspecies <- function(x, language = get_locale(), ...) {
#' @rdname mo_property
#' @export
mo_species <- function(x, language = get_locale(), ...) {
mo_species <- function(x, language = get_AMR_locale(), ...) {
if (missing(x)) {
# this tries to find the data and an <mo> column
x <- find_mo_col(fn = "mo_species")
@ -256,7 +256,7 @@ mo_species <- function(x, language = get_locale(), ...) {
#' @rdname mo_property
#' @export
mo_genus <- function(x, language = get_locale(), ...) {
mo_genus <- function(x, language = get_AMR_locale(), ...) {
if (missing(x)) {
# this tries to find the data and an <mo> column
x <- find_mo_col(fn = "mo_genus")
@ -269,7 +269,7 @@ mo_genus <- function(x, language = get_locale(), ...) {
#' @rdname mo_property
#' @export
mo_family <- function(x, language = get_locale(), ...) {
mo_family <- function(x, language = get_AMR_locale(), ...) {
if (missing(x)) {
# this tries to find the data and an <mo> column
x <- find_mo_col(fn = "mo_family")
@ -282,7 +282,7 @@ mo_family <- function(x, language = get_locale(), ...) {
#' @rdname mo_property
#' @export
mo_order <- function(x, language = get_locale(), ...) {
mo_order <- function(x, language = get_AMR_locale(), ...) {
if (missing(x)) {
# this tries to find the data and an <mo> column
x <- find_mo_col(fn = "mo_order")
@ -295,7 +295,7 @@ mo_order <- function(x, language = get_locale(), ...) {
#' @rdname mo_property
#' @export
mo_class <- function(x, language = get_locale(), ...) {
mo_class <- function(x, language = get_AMR_locale(), ...) {
if (missing(x)) {
# this tries to find the data and an <mo> column
x <- find_mo_col(fn = "mo_class")
@ -308,7 +308,7 @@ mo_class <- function(x, language = get_locale(), ...) {
#' @rdname mo_property
#' @export
mo_phylum <- function(x, language = get_locale(), ...) {
mo_phylum <- function(x, language = get_AMR_locale(), ...) {
if (missing(x)) {
# this tries to find the data and an <mo> column
x <- find_mo_col(fn = "mo_phylum")
@ -321,7 +321,7 @@ mo_phylum <- function(x, language = get_locale(), ...) {
#' @rdname mo_property
#' @export
mo_kingdom <- function(x, language = get_locale(), ...) {
mo_kingdom <- function(x, language = get_AMR_locale(), ...) {
if (missing(x)) {
# this tries to find the data and an <mo> column
x <- find_mo_col(fn = "mo_kingdom")
@ -338,7 +338,7 @@ mo_domain <- mo_kingdom
#' @rdname mo_property
#' @export
mo_type <- function(x, language = get_locale(), ...) {
mo_type <- function(x, language = get_AMR_locale(), ...) {
if (missing(x)) {
# this tries to find the data and an <mo> column
x <- find_mo_col(fn = "mo_type")
@ -354,7 +354,7 @@ mo_type <- function(x, language = get_locale(), ...) {
#' @rdname mo_property
#' @export
mo_gramstain <- function(x, language = get_locale(), ...) {
mo_gramstain <- function(x, language = get_AMR_locale(), ...) {
if (missing(x)) {
# this tries to find the data and an <mo> column
x <- find_mo_col(fn = "mo_gramstain")
@ -385,7 +385,7 @@ mo_gramstain <- function(x, language = get_locale(), ...) {
#' @rdname mo_property
#' @export
mo_is_gram_negative <- function(x, language = get_locale(), ...) {
mo_is_gram_negative <- function(x, language = get_AMR_locale(), ...) {
if (missing(x)) {
# this tries to find the data and an <mo> column
x <- find_mo_col(fn = "mo_is_gram_negative")
@ -404,7 +404,7 @@ mo_is_gram_negative <- function(x, language = get_locale(), ...) {
#' @rdname mo_property
#' @export
mo_is_gram_positive <- function(x, language = get_locale(), ...) {
mo_is_gram_positive <- function(x, language = get_AMR_locale(), ...) {
if (missing(x)) {
# this tries to find the data and an <mo> column
x <- find_mo_col(fn = "mo_is_gram_positive")
@ -423,7 +423,7 @@ mo_is_gram_positive <- function(x, language = get_locale(), ...) {
#' @rdname mo_property
#' @export
mo_is_yeast <- function(x, language = get_locale(), ...) {
mo_is_yeast <- function(x, language = get_AMR_locale(), ...) {
if (missing(x)) {
# this tries to find the data and an <mo> column
x <- find_mo_col(fn = "mo_is_yeast")
@ -449,7 +449,7 @@ mo_is_yeast <- function(x, language = get_locale(), ...) {
#' @rdname mo_property
#' @export
mo_is_intrinsic_resistant <- function(x, ab, language = get_locale(), ...) {
mo_is_intrinsic_resistant <- function(x, ab, language = get_AMR_locale(), ...) {
if (missing(x)) {
# this tries to find the data and an <mo> column
x <- find_mo_col(fn = "mo_is_intrinsic_resistant")
@ -483,7 +483,7 @@ mo_is_intrinsic_resistant <- function(x, ab, language = get_locale(), ...) {
#' @rdname mo_property
#' @export
mo_snomed <- function(x, language = get_locale(), ...) {
mo_snomed <- function(x, language = get_AMR_locale(), ...) {
if (missing(x)) {
# this tries to find the data and an <mo> column
x <- find_mo_col(fn = "mo_snomed")
@ -496,7 +496,7 @@ mo_snomed <- function(x, language = get_locale(), ...) {
#' @rdname mo_property
#' @export
mo_ref <- function(x, language = get_locale(), ...) {
mo_ref <- function(x, language = get_AMR_locale(), ...) {
if (missing(x)) {
# this tries to find the data and an <mo> column
x <- find_mo_col(fn = "mo_ref")
@ -509,7 +509,7 @@ mo_ref <- function(x, language = get_locale(), ...) {
#' @rdname mo_property
#' @export
mo_authors <- function(x, language = get_locale(), ...) {
mo_authors <- function(x, language = get_AMR_locale(), ...) {
if (missing(x)) {
# this tries to find the data and an <mo> column
x <- find_mo_col(fn = "mo_authors")
@ -525,7 +525,7 @@ mo_authors <- function(x, language = get_locale(), ...) {
#' @rdname mo_property
#' @export
mo_year <- function(x, language = get_locale(), ...) {
mo_year <- function(x, language = get_AMR_locale(), ...) {
if (missing(x)) {
# this tries to find the data and an <mo> column
x <- find_mo_col(fn = "mo_year")
@ -541,7 +541,7 @@ mo_year <- function(x, language = get_locale(), ...) {
#' @rdname mo_property
#' @export
mo_lpsn <- function(x, language = get_locale(), ...) {
mo_lpsn <- function(x, language = get_AMR_locale(), ...) {
if (missing(x)) {
# this tries to find the data and an <mo> column
x <- find_mo_col(fn = "mo_rank")
@ -554,7 +554,7 @@ mo_lpsn <- function(x, language = get_locale(), ...) {
#' @rdname mo_property
#' @export
mo_rank <- function(x, language = get_locale(), ...) {
mo_rank <- function(x, language = get_AMR_locale(), ...) {
if (missing(x)) {
# this tries to find the data and an <mo> column
x <- find_mo_col(fn = "mo_rank")
@ -567,7 +567,7 @@ mo_rank <- function(x, language = get_locale(), ...) {
#' @rdname mo_property
#' @export
mo_taxonomy <- function(x, language = get_locale(), ...) {
mo_taxonomy <- function(x, language = get_AMR_locale(), ...) {
if (missing(x)) {
# this tries to find the data and an <mo> column
x <- find_mo_col(fn = "mo_taxonomy")
@ -593,7 +593,7 @@ mo_taxonomy <- function(x, language = get_locale(), ...) {
#' @rdname mo_property
#' @export
mo_synonyms <- function(x, language = get_locale(), ...) {
mo_synonyms <- function(x, language = get_AMR_locale(), ...) {
if (missing(x)) {
# this tries to find the data and an <mo> column
x <- find_mo_col(fn = "mo_synonyms")
@ -626,7 +626,7 @@ mo_synonyms <- function(x, language = get_locale(), ...) {
#' @rdname mo_property
#' @export
mo_info <- function(x, language = get_locale(), ...) {
mo_info <- function(x, language = get_AMR_locale(), ...) {
if (missing(x)) {
# this tries to find the data and an <mo> column
x <- find_mo_col(fn = "mo_info")
@ -657,7 +657,7 @@ mo_info <- function(x, language = get_locale(), ...) {
#' @rdname mo_property
#' @export
mo_url <- function(x, open = FALSE, language = get_locale(), ...) {
mo_url <- function(x, open = FALSE, language = get_AMR_locale(), ...) {
if (missing(x)) {
# this tries to find the data and an <mo> column
x <- find_mo_col(fn = "mo_url")
@ -696,7 +696,7 @@ mo_url <- function(x, open = FALSE, language = get_locale(), ...) {
#' @rdname mo_property
#' @export
mo_property <- function(x, property = "fullname", language = get_locale(), ...) {
mo_property <- function(x, property = "fullname", language = get_AMR_locale(), ...) {
if (missing(x)) {
# this tries to find the data and an <mo> column
x <- find_mo_col(fn = "mo_property")