mirror of https://github.com/msberends/AMR.git
108 lines
4.2 KiB
R
Executable File
108 lines
4.2 KiB
R
Executable File
# ==================================================================== #
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# TITLE #
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# Antimicrobial Resistance (AMR) Analysis #
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# #
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# SOURCE #
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# https://gitlab.com/msberends/AMR #
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# #
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# LICENCE #
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# (c) 2019 Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
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# #
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# This R package is free software; you can freely use and distribute #
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# it for both personal and commercial purposes under the terms of the #
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# GNU General Public License version 2.0 (GNU GPL-2), as published by #
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# the Free Software Foundation. #
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# #
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# This R package was created for academic research and was publicly #
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# released in the hope that it will be useful, but it comes WITHOUT #
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# ANY WARRANTY OR LIABILITY. #
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# Visit our website for more info: https://msberends.gitlab.io/AMR. #
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# ==================================================================== #
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#' Property of an antibiotic
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#'
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#' Use these functions to return a specific property of an antibiotic from the \code{\link{antibiotics}} data set, based on their ATC code. Get such a code with \code{\link{as.atc}}.
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#' @param x a (vector of a) valid \code{\link{atc}} code or any text that can be coerced to a valid atc with \code{\link{as.atc}}
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#' @param property one of the column names of one of the \code{\link{antibiotics}} data set, like \code{"atc"} and \code{"official"}
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#' @param language language of the returned text, defaults to English (\code{"en"}) and can be set with \code{\link{getOption}("AMR_locale")}. Either one of \code{"en"} (English) or \code{"nl"} (Dutch).
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#' @rdname atc_property
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#' @return A vector of values. In case of \code{atc_tradenames}, if \code{x} is of length one, a vector will be returned. Otherwise a \code{\link{list}}, with \code{x} as names.
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#' @export
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#' @importFrom dplyr %>% left_join pull
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#' @seealso \code{\link{antibiotics}}
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#' @inheritSection AMR Read more on our website!
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#' @examples
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#' as.atc("amcl") # J01CR02
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#' atc_name("amcl") # Amoxicillin and beta-lactamase inhibitor
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#' atc_name("amcl", "nl") # Amoxicilline met enzymremmer
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#' atc_trivial_nl("amcl") # Amoxicilline/clavulaanzuur
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#' atc_certe("amcl") # amcl
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#' atc_umcg("amcl") # AMCL
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atc_property <- function(x, property = 'official') {
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property <- property[1]
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if (!property %in% colnames(AMR::antibiotics)) {
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stop("invalid property: ", property, " - use a column name of the `antibiotics` data set")
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}
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if (!is.atc(x)) {
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x <- as.atc(x) # this will give a warning if x cannot be coerced
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}
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suppressWarnings(
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data.frame(atc = x, stringsAsFactors = FALSE) %>%
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left_join(AMR::antibiotics, by = "atc") %>%
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pull(property)
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)
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}
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#' @rdname atc_property
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#' @export
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atc_official <- function(x, language = NULL) {
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if (is.null(language)) {
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language <- getOption("AMR_locale", default = "en")[1L]
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} else {
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language <- tolower(language[1])
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}
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if (language %in% c("en", "")) {
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atc_property(x, "official")
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} else if (language == "nl") {
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atc_property(x, "official_nl")
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} else {
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stop("Unsupported language: '", language, "' - use one of: 'en', 'nl'", call. = FALSE)
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}
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}
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#' @rdname atc_property
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#' @export
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atc_name <- atc_official
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#' @rdname atc_property
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#' @export
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atc_trivial_nl <- function(x) {
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atc_property(x, "trivial_nl")
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}
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#' @rdname atc_property
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#' @export
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atc_certe <- function(x) {
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atc_property(x, "certe")
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}
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#' @rdname atc_property
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#' @export
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atc_umcg <- function(x) {
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atc_property(x, "umcg")
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}
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#' @rdname atc_property
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#' @export
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atc_tradenames <- function(x) {
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res <- atc_property(x, "trade_name")
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res <- strsplit(res, "|", fixed = TRUE)
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if (length(x) == 1) {
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res <- unlist(res)
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} else {
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names(res) <- x
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}
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res
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}
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