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110 lines
4.0 KiB
R
110 lines
4.0 KiB
R
# ==================================================================== #
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# TITLE #
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# Antimicrobial Resistance (AMR) Analysis #
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# #
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# AUTHORS #
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# Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
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# #
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# LICENCE #
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# This program is free software; you can redistribute it and/or modify #
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# it under the terms of the GNU General Public License version 2.0, #
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# as published by the Free Software Foundation. #
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# #
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# This program is distributed in the hope that it will be useful, #
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# but WITHOUT ANY WARRANTY; without even the implied warranty of #
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# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the #
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# GNU General Public License for more details. #
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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 ab_property
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#' @return A vector of values. In case of \code{ab_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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#' @examples
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#' ab_atc("amcl") # J01CR02
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#' ab_name("amcl") # Amoxicillin and beta-lactamase inhibitor
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#' ab_name("amcl", "nl") # Amoxicilline met enzymremmer
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#' ab_trivial_nl("amcl") # Amoxicilline/clavulaanzuur
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#' ab_certe("amcl") # amcl
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#' ab_umcg("amcl") # AMCL
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ab_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 ab_property
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#' @export
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ab_atc <- function(x) {
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as.character(as.atc(x))
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}
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#' @rdname ab_property
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#' @export
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ab_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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ab_property(x, "official")
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} else if (language == "nl") {
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ab_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 ab_property
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#' @export
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ab_name <- ab_official
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#' @rdname ab_property
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#' @export
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ab_trivial_nl <- function(x) {
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ab_property(x, "trivial_nl")
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}
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#' @rdname ab_property
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#' @export
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ab_certe <- function(x) {
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ab_property(x, "certe")
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}
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#' @rdname ab_property
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#' @export
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ab_umcg <- function(x) {
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ab_property(x, "umcg")
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}
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#' @rdname ab_property
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#' @export
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ab_tradenames <- function(x) {
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res <- ab_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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