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(v2.1.1.9186) replace antibiotics with antimicrobials!

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dr. M.S. (Matthijs) Berends
2025-03-07 20:43:26 +01:00
parent f2b2a450cb
commit f7938289eb
140 changed files with 4870 additions and 4702 deletions
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10
R/ab_property.R
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@ -29,10 +29,10 @@
#' Get Properties of an Antibiotic
#'
#' Use these functions to return a specific property of an antibiotic from the [antibiotics] data set. All input values will be evaluated internally with [as.ab()].
#' Use these functions to return a specific property of an antibiotic from the [antimicrobials] data set. All input values will be evaluated internally with [as.ab()].
#' @param x any (vector of) text that can be coerced to a valid antibiotic drug code with [as.ab()]
#' @param tolower a [logical] to indicate whether the first [character] of every output should be transformed to a lower case [character]. This will lead to e.g. "polymyxin B" and not "polymyxin b".
#' @param property one of the column names of one of the [antibiotics] data set: `vector_or(colnames(antibiotics), sort = FALSE)`.
#' @param property one of the column names of one of the [antimicrobials] data set: `vector_or(colnames(antimicrobials), sort = FALSE)`.
#' @param language language of the returned text - the default is the current system language (see [get_AMR_locale()]) and can also be set with the package option [`AMR_locale`][AMR-options]. Use `language = NULL` or `language = ""` to prevent translation.
#' @param administration way of administration, either `"oral"` or `"iv"`
#' @param open browse the URL using [utils::browseURL()]
@ -55,7 +55,7 @@
#' - A [data.frame] in case of [set_ab_names()]
#' - A [character] in all other cases
#' @export
#' @seealso [antibiotics]
#' @seealso [antimicrobials]
#' @inheritSection AMR Reference Data Publicly Available
#' @examples
#' # all properties:
@ -337,7 +337,7 @@ ab_url <- function(x, open = FALSE, ...) {
#' @export
ab_property <- function(x, property = "name", language = get_AMR_locale(), ...) {
meet_criteria(x, allow_NA = TRUE)
meet_criteria(property, is_in = colnames(AMR::antibiotics), has_length = 1)
meet_criteria(property, is_in = colnames(AMR::antimicrobials), has_length = 1)
language <- validate_language(language)
translate_into_language(ab_validate(x = x, property = property, ...), language = language)
}
@ -347,7 +347,7 @@ ab_property <- function(x, property = "name", language = get_AMR_locale(), ...)
#' @export
set_ab_names <- function(data, ..., property = "name", language = get_AMR_locale(), snake_case = NULL) {
meet_criteria(data, allow_class = c("data.frame", "character"))
meet_criteria(property, is_in = colnames(AMR::antibiotics), has_length = 1, ignore.case = TRUE)
meet_criteria(property, is_in = colnames(AMR::antimicrobials), has_length = 1, ignore.case = TRUE)
language <- validate_language(language)
meet_criteria(snake_case, allow_class = "logical", has_length = 1, allow_NULL = TRUE)