mirror of https://github.com/msberends/AMR.git
163 lines
6.1 KiB
R
Executable File
163 lines
6.1 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.gitab.io/AMR. #
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# ==================================================================== #
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#' Name of an antibiotic
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#'
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#' Convert antibiotic codes to a (trivial) antibiotic name or ATC code, or vice versa. This uses the data from \code{\link{antibiotics}}.
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#' @param abcode a code or name, like \code{"AMOX"}, \code{"AMCL"} or \code{"J01CA04"}
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#' @param from,to type to transform from and to. See \code{\link{antibiotics}} for its column names. WIth \code{from = "guess"} the from will be guessed from \code{"atc"}, \code{"certe"} and \code{"umcg"}. When using \code{to = "atc"}, the ATC code will be searched using \code{\link{as.atc}}.
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#' @param textbetween text to put between multiple returned texts
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#' @param tolower return output as lower case with function \code{\link{tolower}}.
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#' @details \strong{The \code{\link{ab_property}} functions are faster and more concise}, but do not support concatenated strings, like \code{abname("AMCL+GENT"}.
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#' @keywords ab antibiotics
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#' @source \code{\link{antibiotics}}
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#' @inheritSection WHOCC WHOCC
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#' @export
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#' @importFrom dplyr %>% pull
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#' @inheritSection AMR Read more on our website!
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#' @examples
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#' abname("AMCL")
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#' # "Amoxicillin and beta-lactamase inhibitor"
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#'
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#' # It is quite flexible at default (having `from = "guess"`)
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#' abname(c("amox", "J01CA04", "Trimox", "dispermox", "Amoxil"))
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#' # "Amoxicillin" "Amoxicillin" "Amoxicillin" "Amoxicillin" "Amoxicillin"
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#'
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#' # Multiple antibiotics can be combined with "+".
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#' # The second antibiotic will be set to lower case when `tolower` was not set:
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#' abname("AMCL+GENT", textbetween = "/")
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#' # "amoxicillin and enzyme inhibitor/gentamicin"
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#'
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#' abname(c("AMCL", "GENT"))
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#' # "Amoxicillin and beta-lactamase inhibitor" "Gentamicin"
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#'
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#' abname("AMCL", to = "trivial_nl")
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#' # "Amoxicilline/clavulaanzuur"
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#'
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#' abname("AMCL", to = "atc")
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#' # "J01CR02"
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#'
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#' # specific codes for University Medical Center Groningen (UMCG):
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#' abname("J01CR02", from = "atc", to = "umcg")
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#' # "AMCL"
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#'
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#' # specific codes for Certe:
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#' abname("J01CR02", from = "atc", to = "certe")
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#' # "amcl"
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abname <- function(abcode,
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from = c("guess", "atc", "certe", "umcg"),
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to = 'official',
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textbetween = ' + ',
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tolower = FALSE) {
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if (length(to) != 1L) {
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stop('`to` must be of length 1', call. = FALSE)
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}
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if (to == "atc") {
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return(as.character(as.atc(abcode)))
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}
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abx <- AMR::antibiotics
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from <- from[1]
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colnames(abx) <- colnames(abx) %>% tolower()
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from <- from %>% tolower()
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to <- to %>% tolower()
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if (!(from %in% colnames(abx) | from == "guess") |
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!to %in% colnames(abx)) {
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stop(paste0('Invalid `from` or `to`. Choose one of ',
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colnames(abx) %>% paste(collapse = ", "), '.'), call. = FALSE)
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}
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abcode <- as.character(abcode)
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abcode.bak <- abcode
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for (i in 1:length(abcode)) {
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if (abcode[i] %like% "[+]") {
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# support for multiple ab's with +
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parts <- trimws(strsplit(abcode[i], split = "+", fixed = TRUE)[[1]])
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ab1 <- abname(parts[1], from = from, to = to)
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ab2 <- abname(parts[2], from = from, to = to)
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if (missing(tolower)) {
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ab2 <- tolower(ab2)
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}
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abcode[i] <- paste0(ab1, textbetween, ab2)
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next
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}
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if (from %in% c("atc", "guess")) {
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if (abcode[i] %in% abx$atc) {
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abcode[i] <- abx[which(abx$atc == abcode[i]),] %>% pull(to) %>% .[1]
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next
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}
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}
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if (from %in% c("certe", "guess")) {
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if (abcode[i] %in% abx$certe) {
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abcode[i] <- abx[which(abx$certe == abcode[i]),] %>% pull(to) %>% .[1]
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next
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}
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}
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if (from %in% c("umcg", "guess")) {
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if (abcode[i] %in% abx$umcg) {
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abcode[i] <- abx[which(abx$umcg == abcode[i]),] %>% pull(to) %>% .[1]
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next
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}
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}
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if (from %in% c("trade_name", "guess")) {
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if (abcode[i] %in% abx$trade_name) {
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abcode[i] <- abx[which(abx$trade_name == abcode[i]),] %>% pull(to) %>% .[1]
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next
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}
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if (sum(abx$trade_name %like% abcode[i]) > 0) {
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abcode[i] <- abx[which(abx$trade_name %like% abcode[i]),] %>% pull(to) %>% .[1]
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next
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}
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}
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if (from != "guess") {
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# when not found, try any `from`
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abcode[i] <- abx[which(abx[,from] == abcode[i]),] %>% pull(to) %>% .[1]
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}
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if (is.na(abcode[i]) | length(abcode[i] == 0)) {
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# try as.atc
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try(suppressWarnings(
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abcode[i] <- as.atc(abcode[i])
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), silent = TRUE)
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if (is.na(abcode[i])) {
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# still not found
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abcode[i] <- abcode.bak[i]
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warning('Code "', abcode.bak[i], '" not found in antibiotics list.', call. = FALSE)
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} else {
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# fill in the found ATC code
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abcode[i] <- abname(abcode[i], from = "atc", to = to)
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}
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}
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}
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if (tolower == TRUE) {
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abcode <- abcode %>% tolower()
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}
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abcode
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}
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