mirror of https://github.com/msberends/AMR.git
498 lines
22 KiB
R
Executable File
498 lines
22 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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#' 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 tbl table with antibiotic columns, like e.g. \code{amox} and \code{amcl}
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#' @param country country code to determine guidelines. EUCAST rules will be used when left empty, see Details. Should be or a code from the \href{https://en.wikipedia.org/wiki/ISO_3166-1_alpha-2#Officially_assigned_code_elements}{list of ISO 3166-1 alpha-2 country codes}. Case-insensitive. Currently supported are \code{de} (Germany) and \code{nl} (the Netherlands).
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#' @param info print progress
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#' @inheritParams eucast_rules
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#' @param metr column name of an antibiotic, see Antibiotics
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#' @param ... parameters that are passed on to methods
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#' @inheritSection eucast_rules Antibiotics
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#' @details When \code{country} will be left blank, guidelines will be taken from EUCAST Expert Rules Version 3.1 "Intrinsic Resistance and Exceptional Phenotypes Tables" (\url{http://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Expert_Rules/Expert_rules_intrinsic_exceptional_V3.1.pdf}).
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#' @return Ordered factor with levels \code{Negative < Positive, unconfirmed < Positive}.
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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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#' @examples
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#' library(dplyr)
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#'
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#' septic_patients %>%
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#' mutate(EUCAST = mdro(.),
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#' BRMO = brmo(.))
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mdro <- function(tbl,
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country = NULL,
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col_mo = NULL,
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info = TRUE,
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amcl = guess_ab_col(),
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amik = guess_ab_col(),
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amox = guess_ab_col(),
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ampi = guess_ab_col(),
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azit = guess_ab_col(),
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aztr = guess_ab_col(),
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cefa = guess_ab_col(),
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cfra = guess_ab_col(),
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cfep = guess_ab_col(),
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cfot = guess_ab_col(),
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cfox = guess_ab_col(),
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cfta = guess_ab_col(),
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cftr = guess_ab_col(),
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cfur = guess_ab_col(),
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chlo = guess_ab_col(),
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cipr = guess_ab_col(),
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clar = guess_ab_col(),
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clin = guess_ab_col(),
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clox = guess_ab_col(),
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coli = guess_ab_col(),
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czol = guess_ab_col(),
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dapt = guess_ab_col(),
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doxy = guess_ab_col(),
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erta = guess_ab_col(),
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eryt = guess_ab_col(),
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fosf = guess_ab_col(),
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fusi = guess_ab_col(),
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gent = guess_ab_col(),
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imip = guess_ab_col(),
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kana = guess_ab_col(),
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levo = guess_ab_col(),
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linc = guess_ab_col(),
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line = guess_ab_col(),
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mero = guess_ab_col(),
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metr = guess_ab_col(),
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mino = guess_ab_col(),
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moxi = guess_ab_col(),
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nali = guess_ab_col(),
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neom = guess_ab_col(),
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neti = guess_ab_col(),
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nitr = guess_ab_col(),
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novo = guess_ab_col(),
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norf = guess_ab_col(),
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oflo = guess_ab_col(),
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peni = guess_ab_col(),
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pipe = guess_ab_col(),
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pita = guess_ab_col(),
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poly = guess_ab_col(),
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qida = guess_ab_col(),
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rifa = guess_ab_col(),
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roxi = guess_ab_col(),
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siso = guess_ab_col(),
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teic = guess_ab_col(),
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tetr = guess_ab_col(),
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tica = guess_ab_col(),
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tige = guess_ab_col(),
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tobr = guess_ab_col(),
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trim = guess_ab_col(),
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trsu = guess_ab_col(),
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vanc = guess_ab_col()) {
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if (!is.data.frame(tbl)) {
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stop("`tbl` must be a data frame.", call. = FALSE)
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}
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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) & "mo" %in% lapply(tbl, class)) {
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col_mo <- colnames(tbl)[lapply(tbl, class) == "mo"][1]
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message(blue(paste0("NOTE: Using column `", bold(col_mo), "` as input for `col_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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# strip whitespaces
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if (length(country) > 1) {
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stop('`country` must be a length one character string.', call. = FALSE)
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}
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if (is.null(country)) {
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country <- 'EUCAST'
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}
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country <- trimws(country)
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if (tolower(country) != 'eucast' & !country %like% '^[a-z]{2}$') {
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stop('This is not a valid ISO 3166-1 alpha-2 country code: "', country, '". Please see ?mdro.', call. = FALSE)
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}
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# create list and make country code case-independent
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guideline <- list(country = list(code = tolower(country)))
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if (guideline$country$code == 'eucast') {
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guideline$country$name <- '(European guidelines)'
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guideline$name <- 'EUCAST Expert Rules, "Intrinsic Resistance and Exceptional Phenotypes Tables"'
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guideline$version <- 'Version 3.1'
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guideline$source <- 'http://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Expert_Rules/Expert_rules_intrinsic_exceptional_V3.1.pdf'
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# support per country:
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} else if (guideline$country$code == 'de') {
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guideline$country$name <- 'Germany'
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guideline$name <- ''
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guideline$version <- ''
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guideline$source <- ''
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} else if (guideline$country$code == 'nl') {
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guideline$country$name <- 'The Netherlands'
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guideline$name <- 'WIP-Richtlijn BRMO'
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guideline$version <- 'Revision of December 2017'
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guideline$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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# add here more countries like this:
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# } else if (country$code == 'xx') {
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# country$name <- 'country name'
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} else {
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stop('This country code is currently unsupported: ', guideline$country$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(paste0(guideline$name, ", ", guideline$version, "\n")),
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"Country : ", red(paste0(guideline$country$name, "\n")),
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"Source : ", blue(paste0(guideline$source, "\n")),
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"\n", sep = "")
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}
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# check columns
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if (identical(amcl, as.name("guess_ab_col"))) { amcl <- guess_ab_col(tbl, "amcl", verbose = info) }
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if (identical(amik, as.name("guess_ab_col"))) { amik <- guess_ab_col(tbl, "amik", verbose = info) }
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if (identical(amox, as.name("guess_ab_col"))) { amox <- guess_ab_col(tbl, "amox", verbose = info) }
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if (identical(ampi, as.name("guess_ab_col"))) { ampi <- guess_ab_col(tbl, "ampi", verbose = info) }
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if (identical(azit, as.name("guess_ab_col"))) { azit <- guess_ab_col(tbl, "azit", verbose = info) }
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if (identical(aztr, as.name("guess_ab_col"))) { aztr <- guess_ab_col(tbl, "aztr", verbose = info) }
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if (identical(cefa, as.name("guess_ab_col"))) { cefa <- guess_ab_col(tbl, "cefa", verbose = info) }
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if (identical(cfra, as.name("guess_ab_col"))) { cfra <- guess_ab_col(tbl, "cfra", verbose = info) }
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if (identical(cfep, as.name("guess_ab_col"))) { cfep <- guess_ab_col(tbl, "cfep", verbose = info) }
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if (identical(cfot, as.name("guess_ab_col"))) { cfot <- guess_ab_col(tbl, "cfot", verbose = info) }
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if (identical(cfox, as.name("guess_ab_col"))) { cfox <- guess_ab_col(tbl, "cfox", verbose = info) }
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if (identical(cfta, as.name("guess_ab_col"))) { cfta <- guess_ab_col(tbl, "cfta", verbose = info) }
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if (identical(cftr, as.name("guess_ab_col"))) { cftr <- guess_ab_col(tbl, "cftr", verbose = info) }
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if (identical(cfur, as.name("guess_ab_col"))) { cfur <- guess_ab_col(tbl, "cfur", verbose = info) }
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if (identical(chlo, as.name("guess_ab_col"))) { chlo <- guess_ab_col(tbl, "chlo", verbose = info) }
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if (identical(cipr, as.name("guess_ab_col"))) { cipr <- guess_ab_col(tbl, "cipr", verbose = info) }
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if (identical(clar, as.name("guess_ab_col"))) { clar <- guess_ab_col(tbl, "clar", verbose = info) }
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if (identical(clin, as.name("guess_ab_col"))) { clin <- guess_ab_col(tbl, "clin", verbose = info) }
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if (identical(clox, as.name("guess_ab_col"))) { clox <- guess_ab_col(tbl, "clox", verbose = info) }
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if (identical(coli, as.name("guess_ab_col"))) { coli <- guess_ab_col(tbl, "coli", verbose = info) }
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if (identical(czol, as.name("guess_ab_col"))) { czol <- guess_ab_col(tbl, "czol", verbose = info) }
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if (identical(dapt, as.name("guess_ab_col"))) { dapt <- guess_ab_col(tbl, "dapt", verbose = info) }
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if (identical(doxy, as.name("guess_ab_col"))) { doxy <- guess_ab_col(tbl, "doxy", verbose = info) }
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if (identical(erta, as.name("guess_ab_col"))) { erta <- guess_ab_col(tbl, "erta", verbose = info) }
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if (identical(eryt, as.name("guess_ab_col"))) { eryt <- guess_ab_col(tbl, "eryt", verbose = info) }
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if (identical(fosf, as.name("guess_ab_col"))) { fosf <- guess_ab_col(tbl, "fosf", verbose = info) }
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if (identical(fusi, as.name("guess_ab_col"))) { fusi <- guess_ab_col(tbl, "fusi", verbose = info) }
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if (identical(gent, as.name("guess_ab_col"))) { gent <- guess_ab_col(tbl, "gent", verbose = info) }
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if (identical(imip, as.name("guess_ab_col"))) { imip <- guess_ab_col(tbl, "imip", verbose = info) }
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if (identical(kana, as.name("guess_ab_col"))) { kana <- guess_ab_col(tbl, "kana", verbose = info) }
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if (identical(levo, as.name("guess_ab_col"))) { levo <- guess_ab_col(tbl, "levo", verbose = info) }
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if (identical(linc, as.name("guess_ab_col"))) { linc <- guess_ab_col(tbl, "linc", verbose = info) }
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if (identical(line, as.name("guess_ab_col"))) { line <- guess_ab_col(tbl, "line", verbose = info) }
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if (identical(mero, as.name("guess_ab_col"))) { mero <- guess_ab_col(tbl, "mero", verbose = info) }
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if (identical(metr, as.name("guess_ab_col"))) { metr <- guess_ab_col(tbl, "metr", verbose = info) }
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if (identical(mino, as.name("guess_ab_col"))) { mino <- guess_ab_col(tbl, "mino", verbose = info) }
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if (identical(moxi, as.name("guess_ab_col"))) { moxi <- guess_ab_col(tbl, "moxi", verbose = info) }
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if (identical(nali, as.name("guess_ab_col"))) { nali <- guess_ab_col(tbl, "nali", verbose = info) }
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if (identical(neom, as.name("guess_ab_col"))) { neom <- guess_ab_col(tbl, "neom", verbose = info) }
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if (identical(neti, as.name("guess_ab_col"))) { neti <- guess_ab_col(tbl, "neti", verbose = info) }
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if (identical(nitr, as.name("guess_ab_col"))) { nitr <- guess_ab_col(tbl, "nitr", verbose = info) }
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if (identical(novo, as.name("guess_ab_col"))) { novo <- guess_ab_col(tbl, "novo", verbose = info) }
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if (identical(norf, as.name("guess_ab_col"))) { norf <- guess_ab_col(tbl, "norf", verbose = info) }
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if (identical(oflo, as.name("guess_ab_col"))) { oflo <- guess_ab_col(tbl, "oflo", verbose = info) }
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if (identical(peni, as.name("guess_ab_col"))) { peni <- guess_ab_col(tbl, "peni", verbose = info) }
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if (identical(pipe, as.name("guess_ab_col"))) { pipe <- guess_ab_col(tbl, "pipe", verbose = info) }
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if (identical(pita, as.name("guess_ab_col"))) { pita <- guess_ab_col(tbl, "pita", verbose = info) }
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if (identical(poly, as.name("guess_ab_col"))) { poly <- guess_ab_col(tbl, "poly", verbose = info) }
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if (identical(qida, as.name("guess_ab_col"))) { qida <- guess_ab_col(tbl, "qida", verbose = info) }
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if (identical(rifa, as.name("guess_ab_col"))) { rifa <- guess_ab_col(tbl, "rifa", verbose = info) }
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if (identical(roxi, as.name("guess_ab_col"))) { roxi <- guess_ab_col(tbl, "roxi", verbose = info) }
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if (identical(siso, as.name("guess_ab_col"))) { siso <- guess_ab_col(tbl, "siso", verbose = info) }
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if (identical(teic, as.name("guess_ab_col"))) { teic <- guess_ab_col(tbl, "teic", verbose = info) }
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if (identical(tetr, as.name("guess_ab_col"))) { tetr <- guess_ab_col(tbl, "tetr", verbose = info) }
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if (identical(tica, as.name("guess_ab_col"))) { tica <- guess_ab_col(tbl, "tica", verbose = info) }
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if (identical(tige, as.name("guess_ab_col"))) { tige <- guess_ab_col(tbl, "tige", verbose = info) }
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if (identical(tobr, as.name("guess_ab_col"))) { tobr <- guess_ab_col(tbl, "tobr", verbose = info) }
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if (identical(trim, as.name("guess_ab_col"))) { trim <- guess_ab_col(tbl, "trim", verbose = info) }
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if (identical(trsu, as.name("guess_ab_col"))) { trsu <- guess_ab_col(tbl, "trsu", verbose = info) }
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if (identical(vanc, as.name("guess_ab_col"))) { vanc <- guess_ab_col(tbl, "vanc", verbose = info) }
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col.list <- c(amcl, amik, amox, ampi, azit, aztr, cefa, cfra, cfep, cfot,
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cfox, cfta, cftr, cfur, chlo, cipr, clar, clin, clox, coli,
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czol, dapt, doxy, erta, eryt, fosf, fusi, gent, imip, kana,
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levo, linc, line, mero, metr, mino, moxi, nali, neom, neti,
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nitr, novo, norf, oflo, peni, pipe, pita, poly, qida, rifa,
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roxi, siso, teic, tetr, tica, tige, tobr, trim, trsu, vanc)
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if (length(col.list) < 60) {
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warning('Some columns do not exist -- THIS MAY STRONGLY INFLUENCE THE OUTCOME.',
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immediate. = TRUE,
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call. = FALSE)
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}
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col.list <- check_available_columns(tbl = tbl, col.list = col.list, info = info)
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amcl <- col.list[amcl]
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amik <- col.list[amik]
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amox <- col.list[amox]
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ampi <- col.list[ampi]
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azit <- col.list[azit]
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aztr <- col.list[aztr]
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cefa <- col.list[cefa]
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cfra <- col.list[cfra]
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cfep <- col.list[cfep]
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cfot <- col.list[cfot]
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cfox <- col.list[cfox]
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cfta <- col.list[cfta]
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cftr <- col.list[cftr]
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cfur <- col.list[cfur]
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chlo <- col.list[chlo]
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cipr <- col.list[cipr]
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clar <- col.list[clar]
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clin <- col.list[clin]
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clox <- col.list[clox]
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coli <- col.list[coli]
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czol <- col.list[czol]
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dapt <- col.list[dapt]
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doxy <- col.list[doxy]
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erta <- col.list[erta]
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eryt <- col.list[eryt]
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fosf <- col.list[fosf]
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fusi <- col.list[fusi]
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gent <- col.list[gent]
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imip <- col.list[imip]
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kana <- col.list[kana]
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levo <- col.list[levo]
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linc <- col.list[linc]
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line <- col.list[line]
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mero <- col.list[mero]
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metr <- col.list[metr]
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mino <- col.list[mino]
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moxi <- col.list[moxi]
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nali <- col.list[nali]
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neom <- col.list[neom]
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neti <- col.list[neti]
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nitr <- col.list[nitr]
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novo <- col.list[novo]
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norf <- col.list[norf]
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oflo <- col.list[oflo]
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peni <- col.list[peni]
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pipe <- col.list[pipe]
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pita <- col.list[pita]
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poly <- col.list[poly]
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qida <- col.list[qida]
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rifa <- col.list[rifa]
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roxi <- col.list[roxi]
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siso <- col.list[siso]
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teic <- col.list[teic]
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tetr <- col.list[tetr]
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tica <- col.list[tica]
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tige <- col.list[tige]
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tobr <- col.list[tobr]
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trim <- col.list[trim]
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trsu <- col.list[trsu]
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vanc <- col.list[vanc]
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# antibiotic classes
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aminoglycosides <- c(tobr, gent) # can also be kana but that one is often intrinsic R
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cephalosporins <- c(cfep, cfot, cfox, cfra, cfta, cftr, cfur, czol)
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cephalosporins_3rd <- c(cfot, cftr, cfta)
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carbapenems <- c(erta, imip, mero)
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fluoroquinolones <- c(oflo, cipr, levo, moxi)
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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[!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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col_filter <- which(tbl[, cols] == 'R')
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} else if (any_all == "all") {
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col_filter <- tbl %>%
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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% col_filter]
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tbl[rows, 'MDRO'] <<- to
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}
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}
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tbl <- tbl %>%
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mutate_at(vars(col_mo), as.mo) %>%
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|
# join to microorganisms data set
|
|
left_join_microorganisms(by = col_mo) %>%
|
|
# add unconfirmed to where genus is available
|
|
mutate(MDRO = ifelse(!is.na(genus), 1, NA_integer_))
|
|
|
|
if (guideline$country$code == 'eucast') {
|
|
# EUCAST ------------------------------------------------------------------
|
|
# Table 5
|
|
trans_tbl(3,
|
|
which(tbl$family == 'Enterobacteriaceae'
|
|
| tbl$fullname %like% '^Pseudomonas aeruginosa'
|
|
| tbl$genus == 'Acinetobacter'),
|
|
coli,
|
|
"all")
|
|
trans_tbl(3,
|
|
which(tbl$fullname %like% '^Salmonella Typhi'),
|
|
c(carbapenems, fluoroquinolones),
|
|
"any")
|
|
trans_tbl(3,
|
|
which(tbl$fullname %like% '^Haemophilus influenzae'),
|
|
c(cephalosporins_3rd, carbapenems, fluoroquinolones),
|
|
"any")
|
|
trans_tbl(3,
|
|
which(tbl$fullname %like% '^Moraxella catarrhalis'),
|
|
c(cephalosporins_3rd, fluoroquinolones),
|
|
"any")
|
|
trans_tbl(3,
|
|
which(tbl$fullname %like% '^Neisseria meningitidis'),
|
|
c(cephalosporins_3rd, fluoroquinolones),
|
|
"any")
|
|
trans_tbl(3,
|
|
which(tbl$fullname %like% '^Neisseria gonorrhoeae'),
|
|
azit,
|
|
"any")
|
|
# Table 6
|
|
trans_tbl(3,
|
|
which(tbl$fullname %like% '^Staphylococcus (aureus|epidermidis|coagulase negatief|hominis|haemolyticus|intermedius|pseudointermedius)'),
|
|
c(vanc, teic, dapt, line, qida, tige),
|
|
"any")
|
|
trans_tbl(3,
|
|
which(tbl$genus == 'Corynebacterium'),
|
|
c(vanc, teic, dapt, line, qida, tige),
|
|
"any")
|
|
trans_tbl(3,
|
|
which(tbl$fullname %like% '^Streptococcus pneumoniae'),
|
|
c(carbapenems, vanc, teic, dapt, line, qida, tige, rifa),
|
|
"any")
|
|
trans_tbl(3, # Sr. groups A/B/C/G
|
|
which(tbl$fullname %like% '^Streptococcus (pyogenes|agalactiae|equisimilis|equi|zooepidemicus|dysgalactiae|anginosus)'),
|
|
c(peni, cephalosporins, vanc, teic, dapt, line, qida, tige),
|
|
"any")
|
|
trans_tbl(3,
|
|
which(tbl$genus == 'Enterococcus'),
|
|
c(dapt, line, tige, teic),
|
|
"any")
|
|
trans_tbl(3,
|
|
which(tbl$fullname %like% '^Enterococcus faecalis'),
|
|
c(ampi, amox),
|
|
"any")
|
|
# Table 7
|
|
trans_tbl(3,
|
|
which(tbl$genus == 'Bacteroides'),
|
|
metr,
|
|
"any")
|
|
trans_tbl(3,
|
|
which(tbl$fullname %like% '^Clostridium difficile'),
|
|
c(metr, vanc),
|
|
"any")
|
|
}
|
|
|
|
if (guideline$country$code == 'de') {
|
|
# Germany -----------------------------------------------------------------
|
|
stop("We are still working on German guidelines in this beta version.", call. = FALSE)
|
|
}
|
|
|
|
if (guideline$country$code == 'nl') {
|
|
# Netherlands -------------------------------------------------------------
|
|
aminoglycosides <- aminoglycosides[!is.na(aminoglycosides)]
|
|
fluoroquinolones <- fluoroquinolones[!is.na(fluoroquinolones)]
|
|
carbapenems <- carbapenems[!is.na(carbapenems)]
|
|
|
|
# Table 1
|
|
trans_tbl(3,
|
|
which(tbl$family == 'Enterobacteriaceae'),
|
|
c(aminoglycosides, fluoroquinolones),
|
|
"all")
|
|
|
|
trans_tbl(2,
|
|
which(tbl$family == 'Enterobacteriaceae'),
|
|
c(carbapenems),
|
|
"any")
|
|
|
|
# Table 2
|
|
trans_tbl(2,
|
|
which(tbl$genus == 'Acinetobacter'),
|
|
c(carbapenems),
|
|
"any")
|
|
trans_tbl(3,
|
|
which(tbl$genus == 'Acinetobacter'),
|
|
c(aminoglycosides, fluoroquinolones),
|
|
"all")
|
|
|
|
trans_tbl(3,
|
|
which(tbl$fullname %like% '^Stenotrophomonas maltophilia'),
|
|
trsu,
|
|
"all")
|
|
|
|
if (!is.na(mero) & !is.na(imip)
|
|
& !is.na(gent) & !is.na(tobr)
|
|
& !is.na(cipr)
|
|
& !is.na(cfta)
|
|
& !is.na(pita) ) {
|
|
tbl <- tbl %>% mutate(
|
|
psae = 0,
|
|
psae = ifelse(mero == "R" | imip == "R", psae + 1, psae),
|
|
psae = ifelse(gent == "R" & tobr == "R", psae + 1, psae),
|
|
psae = ifelse(cipr == "R", psae + 1, psae),
|
|
psae = ifelse(cfta == "R", psae + 1, psae),
|
|
psae = ifelse(pita == "R", psae + 1, psae),
|
|
psae = ifelse(is.na(psae), 0, psae)
|
|
)
|
|
} else {
|
|
tbl$psae <- 0
|
|
}
|
|
tbl[which(
|
|
tbl$fullname %like% 'Pseudomonas aeruginosa'
|
|
& tbl$psae >= 3
|
|
), 'MDRO'] <- 3
|
|
|
|
# Table 3
|
|
trans_tbl(3,
|
|
which(tbl$fullname %like% 'Streptococcus pneumoniae'),
|
|
peni,
|
|
"all")
|
|
trans_tbl(3,
|
|
which(tbl$fullname %like% 'Streptococcus pneumoniae'),
|
|
vanc,
|
|
"all")
|
|
trans_tbl(3,
|
|
which(tbl$fullname %like% 'Enterococcus faecium'),
|
|
c(peni, vanc),
|
|
"all")
|
|
}
|
|
|
|
factor(x = tbl$MDRO,
|
|
levels = 1:3,
|
|
labels = c('Negative', 'Positive, unconfirmed', 'Positive'),
|
|
ordered = TRUE)
|
|
}
|
|
|
|
#' @rdname mdro
|
|
#' @export
|
|
brmo <- function(..., country = "nl") {
|
|
mdro(..., country = "nl")
|
|
}
|
|
|
|
#' @rdname mdro
|
|
#' @export
|
|
mrgn <- function(tbl, country = "de", ...) {
|
|
mdro(tbl = tbl, country = "de", ...)
|
|
}
|
|
|
|
#' @rdname mdro
|
|
#' @export
|
|
eucast_exceptional_phenotypes <- function(tbl, country = "EUCAST", ...) {
|
|
mdro(tbl = tbl, country = "EUCAST", ...)
|
|
}
|