mirror of https://github.com/msberends/AMR.git
248 lines
9.4 KiB
R
248 lines
9.4 KiB
R
# ==================================================================== #
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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://github.com/msberends/AMR #
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# #
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# LICENCE #
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# (c) 2018-2020 Berends MS, Luz CF et al. #
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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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# We created this package for both routine data analysis and academic #
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# research and it was publicly released in the hope that it will be #
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# useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY. #
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# Visit our website for more info: https://msberends.github.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 [antibiotics] data set. All input values will be evaluated internally with [as.ab()].
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#' @inheritSection lifecycle Stable lifecycle
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#' @param x any (vector of) text that can be coerced to a valid microorganism code with [as.ab()]
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#' @param tolower 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".
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#' @param property one of the column names of one of the [antibiotics] data set
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#' @param language language of the returned text, defaults to system language (see [get_locale()]) and can also be set with `getOption("AMR_locale")`. Use `language = NULL` or `language = ""` to prevent translation.
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#' @param administration way of administration, either `"oral"` or `"iv"`
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#' @param units a logical to indicate whether the units instead of the DDDs itself must be returned, see Examples
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#' @param open browse the URL using [utils::browseURL()]
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#' @param ... other parameters passed on to [as.ab()]
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#' @details All output will be [translate]d where possible.
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#'
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#' The function [ab_url()] will return the direct URL to the official WHO website. A warning will be returned if the required ATC code is not available.
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#' @inheritSection as.ab Source
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#' @rdname ab_property
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#' @name ab_property
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#' @return
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#' - An [`integer`] in case of [ab_cid()]
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#' - A named [`list`] in case of [ab_info()] and multiple [ab_synonyms()]/[ab_tradenames()]
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#' - A [`double`] in case of [ab_ddd()]
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#' - A [`character`] in all other cases
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#' @export
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#' @seealso [antibiotics]
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#' @inheritSection AMR Read more on our website!
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#' @examples
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#' # all properties:
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#' ab_name("AMX") # "Amoxicillin"
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#' ab_atc("AMX") # J01CA04 (ATC code from the WHO)
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#' ab_cid("AMX") # 33613 (Compound ID from PubChem)
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#' ab_synonyms("AMX") # a list with brand names of amoxicillin
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#' ab_tradenames("AMX") # same
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#' ab_group("AMX") # "Beta-lactams/penicillins"
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#' ab_atc_group1("AMX") # "Beta-lactam antibacterials, penicillins"
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#' ab_atc_group2("AMX") # "Penicillins with extended spectrum"
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#' ab_url("AMX") # link to the official WHO page
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#'
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#' # smart lowercase tranformation
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#' ab_name(x = c("AMC", "PLB")) # "Amoxicillin/clavulanic acid" "Polymyxin B"
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#' ab_name(x = c("AMC", "PLB"),
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#' tolower = TRUE) # "amoxicillin/clavulanic acid" "polymyxin B"
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#'
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#' # defined daily doses (DDD)
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#' ab_ddd("AMX", "oral") # 1
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#' ab_ddd("AMX", "oral", units = TRUE) # "g"
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#' ab_ddd("AMX", "iv") # 1
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#' ab_ddd("AMX", "iv", units = TRUE) # "g"
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#'
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#' ab_info("AMX") # all properties as a list
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#'
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#' # all ab_* functions use as.ab() internally, so you can go from 'any' to 'any':
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#' ab_atc("AMP") # ATC code of AMP (ampicillin)
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#' ab_group("J01CA01") # Drug group of ampicillins ATC code
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#' ab_loinc("ampicillin") # LOINC codes of ampicillin
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#' ab_name("21066-6") # "Ampicillin" (using LOINC)
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#' ab_name(6249) # "Ampicillin" (using CID)
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#' ab_name("J01CA01") # "Ampicillin" (using ATC)
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#'
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#' # spelling from different languages and dyslexia are no problem
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#' ab_atc("ceftriaxon")
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#' ab_atc("cephtriaxone")
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#' ab_atc("cephthriaxone")
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#' ab_atc("seephthriaaksone")
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ab_name <- function(x, language = get_locale(), tolower = FALSE, ...) {
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x <- translate_AMR(ab_validate(x = x, property = "name", ...), language = language)
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if (tolower == TRUE) {
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# use perl to only transform the first character
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# as we want "polymyxin B", not "polymyxin b"
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x <- gsub("^([A-Z])", "\\L\\1", x, perl = TRUE)
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}
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x
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}
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#' @rdname ab_property
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#' @aliases ATC
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#' @export
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ab_atc <- function(x, ...) {
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ab_validate(x = x, property = "atc", ...)
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}
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#' @rdname ab_property
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#' @export
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ab_cid <- function(x, ...) {
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ab_validate(x = x, property = "cid", ...)
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}
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#' @rdname ab_property
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#' @export
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ab_synonyms <- function(x, ...) {
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syns <- ab_validate(x = x, property = "synonyms", ...)
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names(syns) <- x
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if (length(syns) == 1) {
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unname(unlist(syns))
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} else {
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syns
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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_tradenames <- function(x, ...) {
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ab_synonyms(x, ...)
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}
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#' @rdname ab_property
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#' @export
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ab_group <- function(x, language = get_locale(), ...) {
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translate_AMR(ab_validate(x = x, property = "group", ...), language = language)
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}
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#' @rdname ab_property
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#' @export
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ab_atc_group1 <- function(x, language = get_locale(), ...) {
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translate_AMR(ab_validate(x = x, property = "atc_group1", ...), language = language)
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}
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#' @rdname ab_property
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#' @export
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ab_atc_group2 <- function(x, language = get_locale(), ...) {
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translate_AMR(ab_validate(x = x, property = "atc_group2", ...), language = language)
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}
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#' @rdname ab_property
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#' @export
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ab_loinc <- function(x, ...) {
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loincs <- ab_validate(x = x, property = "loinc", ...)
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names(loincs) <- x
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if (length(loincs) == 1) {
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unname(unlist(loincs))
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} else {
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loincs
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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_ddd <- function(x, administration = "oral", units = FALSE, ...) {
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stop_ifnot(administration %in% c("oral", "iv"), "`administration` must be 'oral' or 'iv'")
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ddd_prop <- administration
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if (units == TRUE) {
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ddd_prop <- paste0(ddd_prop, "_units")
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} else {
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ddd_prop <- paste0(ddd_prop, "_ddd")
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}
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ab_validate(x = x, property = ddd_prop, ...)
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}
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#' @rdname ab_property
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#' @export
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ab_info <- function(x, language = get_locale(), ...) {
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x <- as.ab(x, ...)
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base::list(ab = as.character(x),
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atc = ab_atc(x),
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cid = ab_cid(x),
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name = ab_name(x, language = language),
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group = ab_group(x, language = language),
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atc_group1 = ab_atc_group1(x, language = language),
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atc_group2 = ab_atc_group2(x, language = language),
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tradenames = ab_tradenames(x),
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ddd = list(oral = list(amount = ab_ddd(x, administration = "oral", units = FALSE),
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units = ab_ddd(x, administration = "oral", units = TRUE)),
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iv = list(amount = ab_ddd(x, administration = "iv", units = FALSE),
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units = ab_ddd(x, administration = "iv", units = TRUE))))
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}
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#' @rdname ab_property
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#' @export
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ab_url <- function(x, open = FALSE, ...) {
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ab <- as.ab(x = x, ... = ...)
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u <- paste0("https://www.whocc.no/atc_ddd_index/?code=", ab_atc(ab), "&showdescription=no")
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u[is.na(ab_atc(ab))] <- NA_character_
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names(u) <- ab_name(ab)
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NAs <- ab_name(ab, tolower = TRUE, language = NULL)[!is.na(ab) & is.na(ab_atc(ab))]
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if (length(NAs) > 0) {
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warning("No ATC code available for ", paste0(NAs, collapse = ", "), ".")
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}
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if (open == TRUE) {
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if (length(u) > 1 & !is.na(u[1L])) {
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warning("only the first URL will be opened, as `browseURL()` only suports one string.")
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}
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if (!is.na(u[1L])) {
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utils::browseURL(u[1L])
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}
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}
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u
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}
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#' @rdname ab_property
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#' @export
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ab_property <- function(x, property = "name", language = get_locale(), ...) {
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stop_if(length(property) != 1L, "'property' must be of length 1.")
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stop_ifnot(property %in% colnames(antibiotics),
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"invalid property: '", property, "' - use a column name of the `antibiotics` data set")
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translate_AMR(ab_validate(x = x, property = property, ...), language = language)
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}
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ab_validate <- function(x, property, ...) {
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check_dataset_integrity()
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# try to catch an error when inputting an invalid parameter
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# so the 'call.' can be set to FALSE
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tryCatch(x[1L] %in% antibiotics[1, property],
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error = function(e) stop(e$message, call. = FALSE))
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x_bak <- x
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if (!all(x %in% antibiotics[, property])) {
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x <- data.frame(ab = as.ab(x, ...), stringsAsFactors = FALSE) %>%
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left_join(antibiotics, by = "ab") %>%
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pull(property)
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}
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if (property == "ab") {
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return(structure(x, class = property))
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} else if (property == "cid") {
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return(as.integer(x))
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} else if (property %like% "ddd") {
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return(as.double(x))
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} else {
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x[is.na(x) & !is.na(x_bak)] <- NA
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return(x)
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}
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}
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