mirror of https://github.com/msberends/AMR.git
520 lines
20 KiB
R
Executable File
520 lines
20 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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#' Determine multidrug-resistant organisms (MDRO)
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#'
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#' Determine which isolates are multidrug-resistant organisms (MDRO) according to (country-specific) guidelines.
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#' @param x table with antibiotic columns, like e.g. \code{AMX} and \code{AMC}
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#' @param guideline a specific guideline to mention, see Details. EUCAST guidelines will be used when left empty, see Details.
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#' @param info print progress
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#' @inheritParams eucast_rules
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#' @param verbose print additional info: missing antibiotic columns per parameter
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#' @inheritSection eucast_rules Antibiotics
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#' @details Currently supported guidelines are:
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#' \itemize{
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#' \item{\code{guideline = "EUCAST"}: EUCAST Expert Rules Version 3.1 "Intrinsic Resistance and Exceptional Phenotypes Tables" (\href{http://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Expert_Rules/Expert_rules_intrinsic_exceptional_V3.1.pdf}{link})}
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#' \item{\code{guideline = "TB"}: World Health Organization "Companion handbook to the WHO guidelines for the programmatic management of drug-resistant tuberculosis" (\href{https://www.who.int/tb/publications/pmdt_companionhandbook/en/}{link})}
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#' \item{\code{guideline = "MRGN"}: (work in progress)}
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#' \item{\code{guideline = "BRMO"}: Rijksinstituut voor Volksgezondheid en Milieu "WIP-richtlijn BRMO (Bijzonder Resistente Micro-Organismen) [ZKH]" (\href{https://www.rivm.nl/Documenten_en_publicaties/Professioneel_Praktisch/Richtlijnen/Infectieziekten/WIP_Richtlijnen/WIP_Richtlijnen/Ziekenhuizen/WIP_richtlijn_BRMO_Bijzonder_Resistente_Micro_Organismen_ZKH}{link})}
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#' }
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#'
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#' Please suggest your own (country-specific) guidelines by letting us know: \url{https://gitlab.com/msberends/AMR/issues/new}.
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#' @return For TB (\code{mdr_tb()}): Ordered factor with levels \code{Negative < Mono-resistance < Poly-resistance < Multidrug resistance < Extensive drug resistance}.
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#'
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#' For everything else: Ordered factor with levels \code{Negative < Positive, unconfirmed < Positive}. The value \code{"Positive, unconfirmed"} means that, according to the guideline, it is not entirely sure if the isolate is multi-drug resistant and this should be confirmed with additional (e.g. molecular) tests.
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#' @rdname mdro
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#' @importFrom dplyr %>%
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#' @importFrom crayon red blue bold
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#' @export
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#' @inheritSection AMR Read more on our website!
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#' @source
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#' EUCAST Expert Rules Version 3.1 "Intrinsic Resistance and Exceptional Phenotypes Tables" (\href{http://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Expert_Rules/Expert_rules_intrinsic_exceptional_V3.1.pdf}{link})
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#'
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#' World Health Organization "Companion handbook to the WHO guidelines for the programmatic management of drug-resistant tuberculosis" (\href{https://www.who.int/tb/publications/pmdt_companionhandbook/en/}{link})
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#'
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#' Rijksinstituut voor Volksgezondheid en Milieu "WIP-richtlijn BRMO (Bijzonder Resistente Micro-Organismen) [ZKH]" (\href{https://www.rivm.nl/Documenten_en_publicaties/Professioneel_Praktisch/Richtlijnen/Infectieziekten/WIP_Richtlijnen/WIP_Richtlijnen/Ziekenhuizen/WIP_richtlijn_BRMO_Bijzonder_Resistente_Micro_Organismen_ZKH}{link})
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#' @examples
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#' library(dplyr)
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#'
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#' example_isolates %>%
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#' mutate(EUCAST = mdro(.),
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#' BRMO = brmo(.))
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mdro <- function(x,
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guideline = NULL,
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col_mo = NULL,
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info = TRUE,
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verbose = FALSE,
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...) {
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if (!is.data.frame(x)) {
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stop("`x` must be a data frame.", call. = FALSE)
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}
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if (!is.null(list(...)$country)) {
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warning("Using `country` is deprecated, use `guideline` instead. Please see ?mdro.", call. = FALSE)
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guideline <- list(...)$country
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}
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if (length(guideline) > 1) {
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stop("`guideline` must be a length one character string.", call. = FALSE)
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}
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if (is.null(guideline)) {
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guideline <- "eucast"
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}
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if (tolower(guideline) == "nl") {
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guideline <- "BRMO"
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}
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if (tolower(guideline) == "de") {
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guideline <- "MRGN"
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}
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if (!tolower(guideline) %in% c("brmo", "mrgn", "eucast", "tb")) {
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stop("invalid guideline: ", guideline, call. = FALSE)
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}
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guideline <- list(code = tolower(guideline))
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# try to find columns based on type
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# -- mo
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if (is.null(col_mo)) {
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col_mo <- search_type_in_df(x = x, type = "mo")
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}
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if (is.null(col_mo) & guideline$code == "tb") {
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message(blue("NOTE: No column found as input for `col_mo`,",
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bold("assuming all records contain", italic("Mycobacterium tuberculosis.\n"))))
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x$mo <- AMR::as.mo("Mycobacterium tuberculosis")
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col_mo <- "mo"
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}
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if (is.null(col_mo)) {
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stop("`col_mo` must be set.", call. = FALSE)
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}
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if (guideline$code == "eucast") {
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guideline$name <- "EUCAST Expert Rules, \"Intrinsic Resistance and Exceptional Phenotypes Tables\""
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guideline$author <- "EUCAST (European Committee on Antimicrobial Susceptibility Testing)"
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guideline$version <- "3.1"
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guideline$source <- "http://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Expert_Rules/Expert_rules_intrinsic_exceptional_V3.1.pdf"
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} else if (guideline$code == "tb") {
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guideline$name <- "Companion handbook to the WHO guidelines for the programmatic management of drug-resistant tuberculosis"
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guideline$author <- "WHO (World Health Organization)"
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guideline$version <- "WHO/HTM/TB/2014.11"
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guideline$source <- "https://www.who.int/tb/publications/pmdt_companionhandbook/en/"
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# support per country:
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} else if (guideline$code == "mrgn") {
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guideline$name <- "Germany"
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guideline$name <- ""
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guideline$version <- ""
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guideline$source <- ""
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} else if (guideline$code == "brmo") {
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guideline$name <- "WIP-Richtlijn Bijzonder Resistente Micro-organismen (BRMO)"
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guideline$author <- "RIVM (Rijksinstituut voor de Volksgezondheid)"
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guideline$version <- "Revision as of December 2017"
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guideline$source <- "https://www.rivm.nl/Documenten_en_publicaties/Professioneel_Praktisch/Richtlijnen/Infectieziekten/WIP_Richtlijnen/WIP_Richtlijnen/Ziekenhuizen/WIP_richtlijn_BRMO_Bijzonder_Resistente_Micro_Organismen_ZKH"
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} else {
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stop("This guideline is currently unsupported: ", guideline$code, call. = FALSE)
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}
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if (info == TRUE) {
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cat("Determining multidrug-resistant organisms (MDRO), according to:\n",
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"Guideline: ", red(guideline$name), "\n",
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"Version: ", red(guideline$version), "\n",
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"Author: ", red(guideline$author), "\n",
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"Source: ", blue(guideline$source), "\n",
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"\n", sep = "")
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}
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if (guideline$code == "tb") {
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cols_ab <- get_column_abx(x = x,
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soft_dependencies = c("CAP",
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"ETH",
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"GAT",
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"INH",
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"PZA",
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"RIF",
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"RIB",
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"RFP"),
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verbose = verbose, ...)
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} else {
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cols_ab <- get_column_abx(x = x, verbose = verbose, ...)
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}
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AMC <- cols_ab["AMC"]
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AMK <- cols_ab["AMK"]
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AMP <- cols_ab["AMP"]
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AMX <- cols_ab["AMX"]
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ATM <- cols_ab["ATM"]
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AZL <- cols_ab["AZL"]
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AZM <- cols_ab["AZM"]
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CAZ <- cols_ab["CAZ"]
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CED <- cols_ab["CED"]
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CHL <- cols_ab["CHL"]
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CIP <- cols_ab["CIP"]
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CLI <- cols_ab["CLI"]
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CLR <- cols_ab["CLR"]
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COL <- cols_ab["COL"]
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CRO <- cols_ab["CRO"]
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CTX <- cols_ab["CTX"]
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CXM <- cols_ab["CXM"]
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CZO <- cols_ab["CZO"]
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DAP <- cols_ab["DAP"]
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DOX <- cols_ab["DOX"]
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ERY <- cols_ab["ERY"]
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ETP <- cols_ab["ETP"]
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FEP <- cols_ab["FEP"]
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FLC <- cols_ab["FLC"]
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FOS <- cols_ab["FOS"]
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FOX <- cols_ab["FOX"]
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FUS <- cols_ab["FUS"]
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GEN <- cols_ab["GEN"]
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IPM <- cols_ab["IPM"]
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KAN <- cols_ab["KAN"]
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LIN <- cols_ab["LIN"]
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LNZ <- cols_ab["LNZ"]
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LVX <- cols_ab["LVX"]
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MEM <- cols_ab["MEM"]
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MEZ <- cols_ab["MEZ"]
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MTR <- cols_ab["MTR"]
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MFX <- cols_ab["MFX"]
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MNO <- cols_ab["MNO"]
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NAL <- cols_ab["NAL"]
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NEO <- cols_ab["NEO"]
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NET <- cols_ab["NET"]
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NIT <- cols_ab["NIT"]
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NOR <- cols_ab["NOR"]
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NOV <- cols_ab["NOV"]
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OFX <- cols_ab["OFX"]
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PEN <- cols_ab["PEN"]
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PIP <- cols_ab["PIP"]
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PLB <- cols_ab["PLB"]
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PRI <- cols_ab["PRI"]
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QDA <- cols_ab["QDA"]
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RID <- cols_ab["RID"]
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RIF <- cols_ab["RIF"]
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RXT <- cols_ab["RXT"]
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SIS <- cols_ab["SIS"]
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SXT <- cols_ab["SXT"]
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TCY <- cols_ab["TCY"]
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TEC <- cols_ab["TEC"]
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TGC <- cols_ab["TGC"]
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TIC <- cols_ab["TIC"]
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TMP <- cols_ab["TMP"]
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TOB <- cols_ab["TOB"]
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TZP <- cols_ab["TZP"]
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VAN <- cols_ab["VAN"]
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# additional for TB
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CAP <- cols_ab["CAP"]
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ETH <- cols_ab["ETH"]
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GAT <- cols_ab["GAT"]
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INH <- cols_ab["INH"]
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PZA <- cols_ab["PZA"]
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RIF <- cols_ab["RIF"]
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RIB <- cols_ab["RIB"]
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RFP <- cols_ab["RFP"]
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abx_tb <- c(CAP, ETH, GAT, INH, PZA, RIF, RIB, RFP)
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abx_tb <- abx_tb[!is.na(abx_tb)]
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if (guideline$code == "tb" & length(abx_tb) == 0) {
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stop("No antimycobacterials found in data set.", call. = FALSE)
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}
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ab_missing <- function(ab) {
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isTRUE(ab %in% c(NULL, NA)) | length(ab) == 0
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}
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# antibiotic classes
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aminoglycosides <- c(TOB, GEN)
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cephalosporins <- c(FEP, CTX, FOX, CED, CAZ, CRO, CXM, CZO)
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cephalosporins_3rd <- c(CTX, CRO, CAZ)
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carbapenems <- c(ETP, IPM, MEM)
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fluoroquinolones <- c(OFX, CIP, LVX, MFX)
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# helper function for editing the table
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trans_tbl <- function(to, rows, cols, any_all) {
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cols <- cols[!ab_missing(cols)]
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cols <- cols[!is.na(cols)]
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if (length(rows) > 0 & length(cols) > 0) {
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if (any_all == "any") {
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row_filter <- which(x[, cols] == "R")
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} else if (any_all == "all") {
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row_filter <- x %>%
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mutate(index = 1:nrow(.)) %>%
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filter_at(vars(cols), all_vars(. == "R")) %>%
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pull((index))
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}
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rows <- rows[rows %in% row_filter]
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x[rows, "MDRO"] <<- to
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}
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}
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x <- x %>%
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mutate_at(vars(col_mo), as.mo) %>%
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# join to microorganisms data set
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left_join_microorganisms(by = col_mo) %>%
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# add unconfirmed to where genus is available
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mutate(MDRO = ifelse(!is.na(genus), 1, NA_integer_))
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if (guideline$code == "eucast") {
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# EUCAST ------------------------------------------------------------------
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# Table 5
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trans_tbl(3,
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which(x$family == "Enterobacteriaceae"
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| x$fullname %like% "^Pseudomonas aeruginosa"
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| x$genus == "Acinetobacter"),
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COL,
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"all")
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trans_tbl(3,
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which(x$fullname %like% "^Salmonella Typhi"),
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c(carbapenems, fluoroquinolones),
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"any")
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trans_tbl(3,
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which(x$fullname %like% "^Haemophilus influenzae"),
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c(cephalosporins_3rd, carbapenems, fluoroquinolones),
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"any")
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trans_tbl(3,
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which(x$fullname %like% "^Moraxella catarrhalis"),
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c(cephalosporins_3rd, fluoroquinolones),
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"any")
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trans_tbl(3,
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which(x$fullname %like% "^Neisseria meningitidis"),
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c(cephalosporins_3rd, fluoroquinolones),
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"any")
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trans_tbl(3,
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which(x$fullname %like% "^Neisseria gonorrhoeae"),
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AZM,
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"any")
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# Table 6
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trans_tbl(3,
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which(x$fullname %like% "^Staphylococcus (aureus|epidermidis|coagulase negatief|hominis|haemolyticus|intermedius|pseudointermedius)"),
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c(VAN, TEC, DAP, LNZ, QDA, TGC),
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"any")
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trans_tbl(3,
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which(x$genus == "Corynebacterium"),
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c(VAN, TEC, DAP, LNZ, QDA, TGC),
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"any")
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trans_tbl(3,
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which(x$fullname %like% "^Streptococcus pneumoniae"),
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c(carbapenems, VAN, TEC, DAP, LNZ, QDA, TGC, RIF),
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"any")
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trans_tbl(3, # Sr. groups A/B/C/G
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which(x$fullname %like% "^Streptococcus (pyogenes|agalactiae|equisimilis|equi|zooepidemicus|dysgalactiae|anginosus)"),
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c(PEN, cephalosporins, VAN, TEC, DAP, LNZ, QDA, TGC),
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"any")
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trans_tbl(3,
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which(x$genus == "Enterococcus"),
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c(DAP, LNZ, TGC, TEC),
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"any")
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trans_tbl(3,
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which(x$fullname %like% "^Enterococcus faecalis"),
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c(AMP, AMX),
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"any")
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# Table 7
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trans_tbl(3,
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which(x$genus == "Bacteroides"),
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MTR,
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"any")
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trans_tbl(3,
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which(x$fullname %like% "^Clostridium difficile"),
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c(MTR, VAN),
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"any")
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}
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if (guideline$code == "mrgn") {
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# Germany -----------------------------------------------------------------
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stop("We are still working on German guidelines in this beta version.", call. = FALSE)
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}
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if (guideline$code == "brmo") {
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# Netherlands -------------------------------------------------------------
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aminoglycosides <- aminoglycosides[!is.na(aminoglycosides)]
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fluoroquinolones <- fluoroquinolones[!is.na(fluoroquinolones)]
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carbapenems <- carbapenems[!is.na(carbapenems)]
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amino <- AMX %or% AMP
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third <- CAZ %or% CTX
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ESBLs <- c(amino, third)
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ESBLs <- ESBLs[!is.na(ESBLs)]
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if (length(ESBLs) != 2) {
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ESBLs <- character(0)
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}
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# Table 1
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trans_tbl(3,
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which(x$family == "Enterobacteriaceae"),
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c(aminoglycosides, fluoroquinolones),
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"all")
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trans_tbl(2,
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which(x$family == "Enterobacteriaceae"),
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carbapenems,
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"any")
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trans_tbl(2,
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which(x$family == "Enterobacteriaceae"),
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ESBLs,
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"all")
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# Table 2
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trans_tbl(2,
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which(x$genus == "Acinetobacter"),
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c(carbapenems),
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"any")
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trans_tbl(3,
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which(x$genus == "Acinetobacter"),
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c(aminoglycosides, fluoroquinolones),
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"all")
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trans_tbl(3,
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which(x$fullname %like% "^Stenotrophomonas maltophilia"),
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SXT,
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"all")
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if (!ab_missing(MEM) & !ab_missing(IPM)
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& !ab_missing(GEN) & !ab_missing(TOB)
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& !ab_missing(CIP)
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& !ab_missing(CAZ)
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& !ab_missing(TZP) ) {
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x$psae <- 0
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x[which(x[, MEM] == "R" | x[, IPM] == "R"), "psae"] <- 1 + x[which(x[, MEM] == "R" | x[, IPM] == "R"), "psae"]
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x[which(x[, GEN] == "R" & x[, TOB] == "R"), "psae"] <- 1 + x[which(x[, GEN] == "R" & x[, TOB] == "R"), "psae"]
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x[which(x[, CIP] == "R"), "psae"] <- 1 + x[which(x[, CIP] == "R"), "psae"]
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x[which(x[, CAZ] == "R"), "psae"] <- 1 + x[which(x[, CAZ] == "R"), "psae"]
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x[which(x[, TZP] == "R"), "psae"] <- 1 + x[which(x[, TZP] == "R"), "psae"]
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} else {
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x$psae <- 0
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}
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x[which(
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x$fullname %like% "Pseudomonas aeruginosa"
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& x$psae >= 3
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), "MDRO"] <- 3
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# Table 3
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trans_tbl(3,
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which(x$fullname %like% "Streptococcus pneumoniae"),
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PEN,
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"all")
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trans_tbl(3,
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which(x$fullname %like% "Streptococcus pneumoniae"),
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VAN,
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"all")
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trans_tbl(3,
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which(x$fullname %like% "Enterococcus faecium"),
|
|
c(PEN, VAN),
|
|
"all")
|
|
}
|
|
|
|
prepare_drug <- function(ab) {
|
|
# returns vector values of drug
|
|
# if `ab` is a column name, looks up the values in `x`
|
|
if (length(ab) == 1 & is.character(ab)) {
|
|
if (ab %in% colnames(x)) {
|
|
ab <- as.data.frame(x)[, ab]
|
|
}
|
|
}
|
|
ab <- as.character(as.rsi(ab))
|
|
ab[is.na(ab)] <- ""
|
|
ab
|
|
}
|
|
drug_is_R <- function(ab) {
|
|
# returns logical vector
|
|
ab <- prepare_drug(ab)
|
|
if (length(ab) == 1) {
|
|
rep(ab, NROW(x)) == "R"
|
|
} else {
|
|
ab == "R"
|
|
}
|
|
}
|
|
drug_is_not_R <- function(ab) {
|
|
# returns logical vector
|
|
ab <- prepare_drug(ab)
|
|
if (length(ab) == 1) {
|
|
rep(ab, NROW(x)) != "R"
|
|
} else {
|
|
ab != "R"
|
|
}
|
|
}
|
|
|
|
if (guideline$code == "tb") {
|
|
# Tuberculosis ------------------------------------------------------------
|
|
x <- x %>%
|
|
mutate(mono_count = 0,
|
|
mono_count = ifelse(drug_is_R(INH), mono_count + 1, mono_count),
|
|
mono_count = ifelse(drug_is_R(RIF), mono_count + 1, mono_count),
|
|
mono_count = ifelse(drug_is_R(ETH), mono_count + 1, mono_count),
|
|
mono_count = ifelse(drug_is_R(PZA), mono_count + 1, mono_count),
|
|
mono_count = ifelse(drug_is_R(RIB), mono_count + 1, mono_count),
|
|
mono_count = ifelse(drug_is_R(RFP), mono_count + 1, mono_count),
|
|
# from here on logicals
|
|
mono = mono_count > 0,
|
|
poly = ifelse(mono_count > 1 & drug_is_not_R(RIF) & drug_is_not_R(INH),
|
|
TRUE, FALSE),
|
|
mdr = ifelse(drug_is_R(RIF) & drug_is_R(INH),
|
|
TRUE, FALSE),
|
|
xdr = ifelse(drug_is_R(LVX) | drug_is_R(MFX) | drug_is_R(GAT),
|
|
TRUE, FALSE),
|
|
second = ifelse(drug_is_R(CAP) | drug_is_R(KAN) | drug_is_R(AMK),
|
|
TRUE, FALSE),
|
|
xdr = ifelse(mdr & xdr & second, TRUE, FALSE)) %>%
|
|
mutate(mdr_tb = case_when(xdr ~ 5,
|
|
mdr ~ 4,
|
|
poly ~ 3,
|
|
mono ~ 2,
|
|
TRUE ~ 1),
|
|
# keep all real TB, make other species NA
|
|
mdr_tb = ifelse(x$fullname == "Mycobacterium tuberculosis", mdr_tb, NA_real_))
|
|
}
|
|
|
|
# return results
|
|
if (guideline$code == "tb") {
|
|
factor(x = x$mdr_tb,
|
|
levels = 1:5,
|
|
labels = c("Negative", "Mono-resistance", "Poly-resistance", "Multidrug resistance", "Extensive drug resistance"),
|
|
ordered = TRUE)
|
|
} else {
|
|
factor(x = x$MDRO,
|
|
levels = 1:3,
|
|
labels = c("Negative", "Positive, unconfirmed", "Positive"),
|
|
ordered = TRUE)
|
|
}
|
|
}
|
|
|
|
#' @rdname mdro
|
|
#' @export
|
|
brmo <- function(x, guideline = "BRMO", ...) {
|
|
mdro(x, guideline = "BRMO", ...)
|
|
}
|
|
|
|
#' @rdname mdro
|
|
#' @export
|
|
mrgn <- function(x, guideline = "MRGN", ...) {
|
|
mdro(x = x, guideline = "MRGN", ...)
|
|
}
|
|
|
|
#' @rdname mdro
|
|
#' @export
|
|
mdr_tb <- function(x, guideline = "TB", ...) {
|
|
mdro(x = x, guideline = "TB", ...)
|
|
}
|
|
|
|
#' @rdname mdro
|
|
#' @export
|
|
eucast_exceptional_phenotypes <- function(x, guideline = "EUCAST", ...) {
|
|
mdro(x = x, guideline = "EUCAST", ...)
|
|
}
|