AMR/R/ab_property.R

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# ==================================================================== #
# TITLE #
# Antimicrobial Resistance (AMR) Analysis #
# #
# AUTHORS #
# Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
# #
# LICENCE #
# This program is free software; you can redistribute it and/or modify #
# it under the terms of the GNU General Public License version 2.0, #
# as published by the Free Software Foundation. #
# #
# This program is distributed in the hope that it will be useful, #
# but WITHOUT ANY WARRANTY; without even the implied warranty of #
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the #
# GNU General Public License for more details. #
# ==================================================================== #
#' Property of an antibiotic
#'
#' 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}}.
#' @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}}
#' @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).
#' @rdname ab_property
#' @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.
#' @export
#' @importFrom dplyr %>% left_join pull
#' @seealso \code{\link{antibiotics}}
#' @examples
#' ab_atc("amcl") # J01CR02
#' ab_name("amcl") # Amoxicillin and beta-lactamase inhibitor
#' ab_name("amcl", "nl") # Amoxicilline met enzymremmer
#' ab_trivial_nl("amcl") # Amoxicilline/clavulaanzuur
#' ab_certe("amcl") # amcl
#' ab_umcg("amcl") # AMCL
ab_property <- function(x, property = 'official') {
property <- property[1]
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if (!property %in% colnames(AMR::antibiotics)) {
stop("invalid property: ", property, " - use a column name of the `antibiotics` data set")
}
if (!is.atc(x)) {
x <- as.atc(x) # this will give a warning if x cannot be coerced
}
suppressWarnings(
data.frame(atc = x, stringsAsFactors = FALSE) %>%
left_join(AMR::antibiotics, by = "atc") %>%
pull(property)
)
}
#' @rdname ab_property
#' @export
ab_atc <- function(x) {
as.character(as.atc(x))
}
#' @rdname ab_property
#' @export
ab_official <- function(x, language = NULL) {
if (is.null(language)) {
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language <- getOption("AMR_locale", default = "en")[1L]
} else {
language <- tolower(language[1])
}
if (language %in% c("en", "")) {
ab_property(x, "official")
} else if (language == "nl") {
ab_property(x, "official_nl")
} else {
stop("Unsupported language: '", language, "' - use one of: 'en', 'nl'", call. = FALSE)
}
}
#' @rdname ab_property
#' @export
ab_name <- ab_official
#' @rdname ab_property
#' @export
ab_trivial_nl <- function(x) {
ab_property(x, "trivial_nl")
}
#' @rdname ab_property
#' @export
ab_certe <- function(x) {
ab_property(x, "certe")
}
#' @rdname ab_property
#' @export
ab_umcg <- function(x) {
ab_property(x, "umcg")
}
#' @rdname ab_property
#' @export
ab_tradenames <- function(x) {
res <- ab_property(x, "trade_name")
res <- strsplit(res, "|", fixed = TRUE)
if (length(x) == 1) {
res <- unlist(res)
} else {
names(res) <- x
}
res
}