mirror of https://github.com/msberends/AMR.git
652 lines
26 KiB
R
652 lines
26 KiB
R
# ==================================================================== #
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# TITLE #
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# Antimicrobial Resistance (AMR) Analysis #
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# #
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# AUTHORS #
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# Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
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# #
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# LICENCE #
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# This program is free software; you can redistribute it and/or modify #
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# it under the terms of the GNU General Public License version 2.0, #
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# as published by the Free Software Foundation. #
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# #
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# This program is distributed in the hope that it will be useful, #
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# but WITHOUT ANY WARRANTY; without even the implied warranty of #
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# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the #
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# GNU General Public License for more details. #
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# ==================================================================== #
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#' EUCAST expert rules
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#'
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#' Apply expert rules (like intrinsic resistance), as defined by the European Committee on Antimicrobial Susceptibility Testing (EUCAST, \url{http://eucast.org}), see \emph{Source}.
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#' @param tbl table with antibiotic columns, like e.g. \code{amox} and \code{amcl}
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#' @param col_bactcode column name of the bacteria ID in \code{tbl} - should also be present in \code{bactlist$bactid}, see \code{\link{bactlist}}.
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#' @param info print progress
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#' @param amcl,amik,amox,ampi,azit,aztr,cefa,cfra,cfep,cfot,cfox,cfta,cftr,cfur,chlo,cipr,clar,clin,clox,coli,czol,dapt,doxy,erta,eryt,fosf,fusi,gent,imip,kana,levo,linc,line,mero,mino,moxi,nali,neom,neti,nitr,novo,norf,oflo,peni,pita,poly,qida,rifa,roxi,siso,teic,tetr,tica,tige,tobr,trim,trsu,vanc column names of antibiotics. Use \code{NA} to skip a column, like \code{tica = NA}. Non-existing column will be skipped.
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#' @param ... parameters that are passed on to \code{EUCAST_rules}
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#' @rdname EUCAST
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#' @export
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#' @importFrom dplyr %>% left_join select
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#' @return table with edited variables of antibiotics.
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#' @source
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#' EUCAST Expert Rules Version 2.0: \cr
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#' Leclercq et al. \strong{EUCAST expert rules in antimicrobial susceptibility testing.} \emph{Clin Microbiol Infect.} 2013;19(2):141-60. \cr
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#' \url{https://doi.org/10.1111/j.1469-0691.2011.03703.x} \cr
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#' \cr
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#' EUCAST Expert Rules Version 3.1: \cr
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#' \url{http://www.eucast.org/expert_rules_and_intrinsic_resistance}
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#' @examples
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#' a <- data.frame(bactid = c("STAAUR", "ESCCOL", "KLEPNE", "PSEAER"),
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#' vanc = "-",
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#' amox = "-",
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#' coli = "-",
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#' cfta = "-",
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#' cfur = "-",
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#' stringsAsFactors = FALSE)
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#' a
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#'
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#' b <- EUCAST_rules(a)
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#' b
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EUCAST_rules <- function(tbl,
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col_bactcode = 'bactid',
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info = TRUE,
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amcl = 'amcl',
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amik = 'amik',
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amox = 'amox',
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ampi = 'ampi',
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azit = 'azit',
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aztr = 'aztr',
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cefa = 'cefa',
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cfra = 'cfra',
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cfep = 'cfep',
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cfot = 'cfot',
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cfox = 'cfox',
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cfta = 'cfta',
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cftr = 'cftr',
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cfur = 'cfur',
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chlo = 'chlo',
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cipr = 'cipr',
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clar = 'clar',
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clin = 'clin',
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clox = 'clox',
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coli = 'coli',
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czol = 'czol',
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dapt = 'dapt',
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doxy = 'doxy',
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erta = 'erta',
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eryt = 'eryt',
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fosf = 'fosf',
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fusi = 'fusi',
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gent = 'gent',
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imip = 'imip',
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kana = 'kana',
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levo = 'levo',
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linc = 'linc',
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line = 'line',
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mero = 'mero',
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mino = 'mino',
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moxi = 'moxi',
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nali = 'nali',
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neom = 'neom',
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neti = 'neti',
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nitr = 'nitr',
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novo = 'novo',
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norf = 'norf',
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oflo = 'oflo',
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peni = 'peni',
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pita = 'pita',
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poly = 'poly',
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qida = 'qida',
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rifa = 'rifa',
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roxi = 'roxi',
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siso = 'siso',
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teic = 'teic',
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tetr = 'tetr',
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tica = 'tica',
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tige = 'tige',
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tobr = 'tobr',
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trim = 'trim',
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trsu = 'trsu',
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vanc = 'vanc') {
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if (!col_bactcode %in% colnames(tbl)) {
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stop('Column ', col_bactcode, ' not found.')
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}
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# kolommen controleren
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col.list <- c(amcl, amik, amox, ampi, azit, aztr, cefa, cfra, cfep,
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cfot, cfox, cfta, cftr, cfur, cipr, clar, clin, clox, coli, czol,
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dapt, doxy, erta, eryt, fusi, gent, imip, kana, levo, linc, line,
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mero, mino, moxi, nali, neom, neti, nitr, novo, norf, oflo, peni,
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pita, poly, qida, rifa, roxi, siso, teic, tetr, tica, tige, tobr,
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trim, trsu, vanc)
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col.list <- col.list[!is.na(col.list)]
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if (!all(col.list %in% colnames(tbl))) {
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if (info == TRUE) {
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cat('\n')
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}
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if (info == TRUE) {
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warning('These columns do not exist and will be ignored:\n',
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col.list[!(col.list %in% colnames(tbl))] %>% toString(),
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immediate. = TRUE,
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call. = FALSE)
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}
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if (!amcl %in% colnames(tbl)) { amcl <- NA }
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if (!amik %in% colnames(tbl)) { amik <- NA }
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if (!amox %in% colnames(tbl)) { amox <- NA }
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if (!ampi %in% colnames(tbl)) { ampi <- NA }
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if (!azit %in% colnames(tbl)) { azit <- NA }
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if (!aztr %in% colnames(tbl)) { aztr <- NA }
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if (!cefa %in% colnames(tbl)) { cefa <- NA }
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if (!cfra %in% colnames(tbl)) { cfra <- NA }
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if (!cfep %in% colnames(tbl)) { cfep <- NA }
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if (!cfot %in% colnames(tbl)) { cfot <- NA }
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if (!cfox %in% colnames(tbl)) { cfox <- NA }
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if (!cfta %in% colnames(tbl)) { cfta <- NA }
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if (!cftr %in% colnames(tbl)) { cftr <- NA }
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if (!cfur %in% colnames(tbl)) { cfur <- NA }
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if (!chlo %in% colnames(tbl)) { chlo <- NA }
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if (!cipr %in% colnames(tbl)) { cipr <- NA }
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if (!clar %in% colnames(tbl)) { clar <- NA }
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if (!clin %in% colnames(tbl)) { clin <- NA }
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if (!clox %in% colnames(tbl)) { clox <- NA }
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if (!coli %in% colnames(tbl)) { coli <- NA }
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if (!czol %in% colnames(tbl)) { czol <- NA }
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if (!dapt %in% colnames(tbl)) { dapt <- NA }
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if (!doxy %in% colnames(tbl)) { doxy <- NA }
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if (!erta %in% colnames(tbl)) { erta <- NA }
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if (!eryt %in% colnames(tbl)) { eryt <- NA }
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if (!fosf %in% colnames(tbl)) { fosf <- NA }
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if (!fusi %in% colnames(tbl)) { fusi <- NA }
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if (!gent %in% colnames(tbl)) { gent <- NA }
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if (!imip %in% colnames(tbl)) { imip <- NA }
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if (!kana %in% colnames(tbl)) { kana <- NA }
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if (!levo %in% colnames(tbl)) { levo <- NA }
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if (!linc %in% colnames(tbl)) { linc <- NA }
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if (!line %in% colnames(tbl)) { line <- NA }
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if (!mero %in% colnames(tbl)) { mero <- NA }
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if (!mino %in% colnames(tbl)) { mino <- NA }
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if (!moxi %in% colnames(tbl)) { moxi <- NA }
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if (!nali %in% colnames(tbl)) { nali <- NA }
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if (!neom %in% colnames(tbl)) { neom <- NA }
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if (!neti %in% colnames(tbl)) { neti <- NA }
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if (!nitr %in% colnames(tbl)) { nitr <- NA }
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if (!novo %in% colnames(tbl)) { novo <- NA }
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if (!norf %in% colnames(tbl)) { norf <- NA }
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if (!oflo %in% colnames(tbl)) { oflo <- NA }
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if (!peni %in% colnames(tbl)) { peni <- NA }
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if (!pita %in% colnames(tbl)) { pita <- NA }
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if (!poly %in% colnames(tbl)) { poly <- NA }
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if (!qida %in% colnames(tbl)) { qida <- NA }
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if (!rifa %in% colnames(tbl)) { rifa <- NA }
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if (!roxi %in% colnames(tbl)) { roxi <- NA }
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if (!siso %in% colnames(tbl)) { siso <- NA }
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if (!teic %in% colnames(tbl)) { teic <- NA }
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if (!tetr %in% colnames(tbl)) { tetr <- NA }
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if (!tica %in% colnames(tbl)) { tica <- NA }
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if (!tige %in% colnames(tbl)) { tige <- NA }
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if (!tobr %in% colnames(tbl)) { tobr <- NA }
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if (!trim %in% colnames(tbl)) { trim <- NA }
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if (!trsu %in% colnames(tbl)) { trsu <- NA }
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if (!vanc %in% colnames(tbl)) { vanc <- NA }
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}
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total <- 0
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# functie voor uitvoeren
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edit_rsi <- function(to, rows, cols) {
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#voortgang$tick()$print()
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cols <- cols[!is.na(cols)]
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if (length(rows) > 0 & length(cols) > 0) {
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tbl[rows, cols] <<- to
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total <<- total + (length(rows) * length(cols))
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}
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}
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# bactlist aan vastknopen (bestaande kolommen krijgen extra suffix)
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joinby <- colnames(AMR::bactlist)[1]
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names(joinby) <- col_bactcode
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tbl <- tbl %>% left_join(y = AMR::bactlist, by = joinby, suffix = c("_tempbactlist", ""))
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# antibioticagroepen
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aminoglycosiden <- c(tobr, gent, kana, neom, neti, siso)
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tetracyclines <- c(doxy, mino, tetr) # sinds EUCAST v3.1 is tige(cycline) apart
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polymyxines <- c(poly, coli)
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macroliden <- c(eryt, azit, roxi, clar) # sinds EUCAST v3.1 is clinda apart
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glycopeptiden <- c(vanc, teic)
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streptogramines <- qida # eigenlijk pristinamycine en quinupristine/dalfopristine
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cefalosporines <- c(cfep, cfot, cfox, cfra, cfta, cftr, cfur, czol)
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carbapenems <- c(erta, imip, mero)
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aminopenicillines <- c(ampi, amox)
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ureidopenicillines <- pita # eigenlijk ook azlo en mezlo
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fluorochinolonen <- c(oflo, cipr, norf, levo, moxi)
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if (info == TRUE) {
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cat('\nApplying EUCAST expert rules on',
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tbl[!is.na(tbl$genus),] %>% nrow(),
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'isolates according to "EUCAST Expert Rules Version 3.1"\n\n')
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}
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# Table 1: Intrinsic resistance in Enterobacteriaceae ----
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if (info == TRUE) {
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cat('...Table 1: Intrinsic resistance in Enterobacteriaceae\n')
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}
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#voortgang <- progress_estimated(17)
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# Intrisiek R voor groep
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edit_rsi(to = 'R',
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rows = which(tbl$family == 'Enterobacteriaceae'),
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cols = c(peni, glycopeptiden, fusi, macroliden, linc, streptogramines, rifa, dapt, line))
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# Citrobacter
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edit_rsi(to = 'R',
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rows = which(tbl$fullname %like% '^Citrobacter (koseri|amalonaticus|sedlakii|farmeri|rodentium)'),
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cols = c(aminopenicillines, tica))
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edit_rsi(to = 'R',
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rows = which(tbl$fullname %like% '^Citrobacter (freundii|braakii|murliniae|werkmanii|youngae)'),
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cols = c(aminopenicillines, amcl, czol, cfox))
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# Enterobacter
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edit_rsi(to = 'R',
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rows = which(tbl$fullname %like% '^Enterobacter cloacae'),
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cols = c(aminopenicillines, amcl, czol, cfox))
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edit_rsi(to = 'R',
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rows = which(tbl$fullname %like% '^Enterobacter aerogenes'),
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cols = c(aminopenicillines, amcl, czol, cfox))
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# Escherichia
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edit_rsi(to = 'R',
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rows = which(tbl$fullname %like% '^Escherichia hermanni'),
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cols = c(aminopenicillines, tica))
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# Hafnia
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edit_rsi(to = 'R',
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rows = which(tbl$fullname %like% '^Hafnia alvei'),
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cols = c(aminopenicillines, amcl, czol, cfox))
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# Klebsiella
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edit_rsi(to = 'R',
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rows = which(tbl$fullname %like% '^Klebsiella'),
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cols = c(aminopenicillines, tica))
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# Morganella / Proteus
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edit_rsi(to = 'R',
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rows = which(tbl$fullname %like% '^Morganella morganii'),
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cols = c(aminopenicillines, amcl, czol, tetracyclines, polymyxines, nitr))
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edit_rsi(to = 'R',
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rows = which(tbl$fullname %like% '^Proteus mirabilis'),
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cols = c(tetracyclines, tige, polymyxines, nitr))
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edit_rsi(to = 'R',
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rows = which(tbl$fullname %like% '^Proteus penneri'),
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cols = c(aminopenicillines, czol, cfur, tetracyclines, tige, polymyxines, nitr))
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edit_rsi(to = 'R',
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rows = which(tbl$fullname %like% '^Proteus vulgaris'),
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cols = c(aminopenicillines, czol, cfur, tetracyclines, tige, polymyxines, nitr))
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# Providencia
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edit_rsi(to = 'R',
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rows = which(tbl$fullname %like% '^Providencia rettgeri'),
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cols = c(aminopenicillines, amcl, czol, cfur, tetracyclines, tige, polymyxines, nitr))
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edit_rsi(to = 'R',
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rows = which(tbl$fullname %like% '^Providencia stuartii'),
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cols = c(aminopenicillines, amcl, czol, cfur, tetracyclines, tige, polymyxines, nitr))
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# Raoultella
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edit_rsi(to = 'R',
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rows = which(tbl$fullname %like% '^Raoultella'),
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cols = c(aminopenicillines, tica))
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# Serratia
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edit_rsi(to = 'R',
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rows = which(tbl$fullname %like% '^Serratia marcescens'),
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cols = c(aminopenicillines, amcl, czol, cfox, cfur, tetracyclines[tetracyclines != 'mino'], polymyxines, nitr))
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# Yersinia
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edit_rsi(to = 'R',
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rows = which(tbl$fullname %like% '^Yersinia enterocolitica'),
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cols = c(aminopenicillines, amcl, tica, czol, cfox))
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edit_rsi(to = 'R',
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rows = which(tbl$fullname %like% '^Yersinia pseudotuberculosis'),
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cols = c(poly, coli))
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# Table 2: Intrinsic resistance in non-fermentative Gram-negative bacteria ----
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if (info == TRUE) {
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cat('...Table 2: Intrinsic resistance in non-fermentative Gram-negative bacteria\n')
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}
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#voortgang <- progress_estimated(8)
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# Intrisiek R voor groep
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edit_rsi(to = 'R',
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rows = which(tbl$genus %in% c('Achromobacter',
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'Acinetobacter',
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'Alcaligenes',
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'Bordatella',
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'Burkholderia',
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'Elizabethkingia',
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'Flavobacterium',
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'Ochrobactrum',
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'Pseudomonas',
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'Stenotrophomonas')),
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cols = c(peni, cfox, cfur, glycopeptiden, fusi, macroliden, linc, streptogramines, rifa, dapt, line))
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# Acinetobacter
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edit_rsi(to = 'R',
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rows = which(tbl$fullname %like% '^Acinetobacter (baumannii|pittii|nosocomialis|calcoaceticus)'),
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cols = c(aminopenicillines, amcl, czol, cfot, cftr, aztr, erta, trim, fosf, tetracyclines[tetracyclines != 'mino']))
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# Achromobacter
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edit_rsi(to = 'R',
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rows = which(tbl$fullname %like% '^Achromobacter (xylosoxydans|xylosoxidans)'),
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cols = c(aminopenicillines, czol, cfot, cftr, erta))
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# Burkholderia
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edit_rsi(to = 'R',
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# onder 'Burkholderia cepacia complex' vallen deze species allemaal: PMID 16217180.
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rows = which(tbl$fullname %like% '^Burkholderia (cepacia|multivorans|cenocepacia|stabilis|vietnamiensis|dolosa|ambifaria|anthina|pyrrocinia|ubonensis)'),
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cols = c(aminopenicillines, amcl, tica, pita, czol, cfot, cftr, aztr, erta, cipr, chlo, aminoglycosiden, trim, fosf, polymyxines))
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# Elizabethkingia
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edit_rsi(to = 'R',
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rows = which(tbl$fullname %like% '^Elizabethkingia meningoseptic(a|um)'),
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cols = c(aminopenicillines, amcl, tica, czol, cfot, cftr, cfta, cfep, aztr, erta, imip, mero, polymyxines))
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# Ochrobactrum
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edit_rsi(to = 'R',
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rows = which(tbl$fullname %like% '^Ochrobactrum anthropi'),
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cols = c(aminopenicillines, amcl, tica, pita, czol, cfot, cftr, cfta, cfep, aztr, erta))
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# Pseudomonas
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edit_rsi(to = 'R',
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rows = which(tbl$fullname %like% '^Pseudomonas aeruginosa'),
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cols = c(aminopenicillines, amcl, czol, cfot, cftr, erta, chlo, kana, neom, trim, trsu, tetracyclines, tige))
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# Stenotrophomonas
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edit_rsi(to = 'R',
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rows = which(tbl$fullname %like% '^Stenotrophomonas maltophilia'),
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cols = c(aminopenicillines, amcl, tica, pita, czol, cfot, cftr, cfta, aztr, erta, imip, mero, aminoglycosiden, trim, fosf, tetr))
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# Table 3: Intrinsic resistance in other Gram-negative bacteria ----
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if (info == TRUE) {
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cat('...Table 3: Intrinsic resistance in other Gram-negative bacteria\n')
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}
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#voortgang <- progress_estimated(7)
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# Intrisiek R voor groep
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edit_rsi(to = 'R',
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rows = which(tbl$genus %in% c('Haemophilus',
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'Moraxella',
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'Neisseria',
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'Campylobacter')),
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cols = c(glycopeptiden, linc, dapt, line))
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# Haemophilus
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edit_rsi(to = 'R',
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rows = which(tbl$fullname %like% '^Haemophilus influenzae'),
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cols = c(fusi, streptogramines))
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# Moraxella
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edit_rsi(to = 'R',
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rows = which(tbl$fullname %like% '^Moraxella catarrhalis'),
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cols = trim)
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# Neisseria
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edit_rsi(to = 'R',
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rows = which(tbl$genus == 'Neisseria'),
|
|
cols = trim)
|
|
# Campylobacter
|
|
edit_rsi(to = 'R',
|
|
rows = which(tbl$fullname %like% '^Campylobacter fetus'),
|
|
cols = c(fusi, streptogramines, trim, nali))
|
|
edit_rsi(to = 'R',
|
|
rows = which(tbl$fullname %like% '^Campylobacter (jejuni|coli)'),
|
|
cols = c(fusi, streptogramines, trim))
|
|
|
|
|
|
# Table 4: Intrinsic resistance in Gram-positive bacteria ----
|
|
if (info == TRUE) {
|
|
cat('...Table 4: Intrinsic resistance in Gram-positive bacteria\n')
|
|
}
|
|
#voortgang <- progress_estimated(14)
|
|
# Intrisiek R voor groep
|
|
edit_rsi(to = 'R',
|
|
rows = which(tbl$gramstain %like% 'Positi(e|)(v|f)'),
|
|
cols = c(aztr, polymyxines, nali))
|
|
# Staphylococcus
|
|
edit_rsi(to = 'R',
|
|
rows = which(tbl$fullname %like% '^Staphylococcus saprophyticus'),
|
|
cols = c(fusi, cfta, fosf, novo))
|
|
edit_rsi(to = 'R',
|
|
rows = which(tbl$fullname %like% '^Staphylococcus (cohnii|xylosus)'),
|
|
cols = c(cfta, novo))
|
|
edit_rsi(to = 'R',
|
|
rows = which(tbl$fullname %like% '^Staphylococcus capitis'),
|
|
cols = c(cfta, fosf))
|
|
edit_rsi(to = 'R',
|
|
rows = which(tbl$fullname %like% '^Staphylococcus (aureus|epidermidis|coagulase negatief|hominis|haemolyticus|intermedius|pseudointermedius)'),
|
|
cols = cfta)
|
|
# Streptococcus
|
|
edit_rsi(to = 'R',
|
|
rows = which(tbl$genus == 'Streptococcus'),
|
|
cols = c(fusi, cfta, aminoglycosiden))
|
|
# Enterococcus
|
|
edit_rsi(to = 'R',
|
|
rows = which(tbl$fullname %like% '^Enterococcus faecalis'),
|
|
cols = c(fusi, cfta, cefalosporines[cefalosporines != cfta], aminoglycosiden, macroliden, clin, qida, trim, trsu))
|
|
edit_rsi(to = 'R',
|
|
rows = which(tbl$fullname %like% '^Enterococcus (gallinarum|casseliflavus)'),
|
|
cols = c(fusi, cfta, cefalosporines[cefalosporines != cfta], aminoglycosiden, macroliden, clin, qida, vanc, trim, trsu))
|
|
edit_rsi(to = 'R',
|
|
rows = which(tbl$fullname %like% '^Enterococcus faecium'),
|
|
cols = c(fusi, cfta, cefalosporines[cefalosporines != cfta], aminoglycosiden, macroliden, trim, trsu))
|
|
# Corynebacterium
|
|
edit_rsi(to = 'R',
|
|
rows = which(tbl$genus == 'Corynebacterium'),
|
|
cols = fosf)
|
|
# Listeria
|
|
edit_rsi(to = 'R',
|
|
rows = which(tbl$fullname %like% '^Listeria monocytogenes'),
|
|
cols = c(cfta, cefalosporines[cefalosporines != cfta]))
|
|
# overig
|
|
edit_rsi(to = 'R',
|
|
rows = which(tbl$genus %in% c('Leuconostoc', 'Pediococcus')),
|
|
cols = c(vanc, teic))
|
|
edit_rsi(to = 'R',
|
|
rows = which(tbl$genus == 'Lactobacillus'),
|
|
cols = c(vanc, teic))
|
|
edit_rsi(to = 'R',
|
|
rows = which(tbl$fullname %like% '^Clostridium (ramosum|innocuum)'),
|
|
cols = vanc)
|
|
|
|
# Table 8: Interpretive rules for B-lactam agents and Gram-positive cocci ----
|
|
if (info == TRUE) {
|
|
cat('...Table 8: Interpretive rules for B-lactam agents and Gram-positive cocci\n')
|
|
}
|
|
#voortgang <- progress_estimated(2)
|
|
# regel 8.3
|
|
if (!is.na(peni)) {
|
|
edit_rsi(to = 'S',
|
|
rows = which(tbl$fullname %like% '^Streptococcus (pyogenes|agalactiae|dysgalactiae|groep A|groep B|groep C|groep G)'
|
|
& tbl[, peni] == 'S'),
|
|
cols = c(aminopenicillines, cefalosporines, carbapenems))
|
|
}
|
|
# regel 8.6
|
|
if (!is.na(ampi)) {
|
|
edit_rsi(to = 'R',
|
|
rows = which(tbl$genus == 'Enterococcus'
|
|
& tbl[, ampi] == 'R'),
|
|
cols = c(ureidopenicillines, carbapenems))
|
|
}
|
|
if (!is.na(amox)) {
|
|
edit_rsi(to = 'R',
|
|
rows = which(tbl$genus == 'Enterococcus'
|
|
& tbl[, amox] == 'R'),
|
|
cols = c(ureidopenicillines, carbapenems))
|
|
}
|
|
|
|
# Table 9: Interpretive rules for B-lactam agents and Gram-negative rods ----
|
|
if (info == TRUE) {
|
|
cat('...Table 9: Interpretive rules for B-lactam agents and Gram-negative rods\n')
|
|
}
|
|
#voortgang <- progress_estimated(1)
|
|
# regel 9.3
|
|
if (!is.na(tica) & !is.na(pita)) {
|
|
edit_rsi(to = 'R',
|
|
rows = which(tbl$family == 'Enterobacteriaceae'
|
|
& tbl[, tica] == 'R'
|
|
& tbl[, pita] == 'S'),
|
|
cols = pita)
|
|
}
|
|
|
|
# Table 10: Interpretive rules for B-lactam agents and other Gram-negative bacteria ----
|
|
if (info == TRUE) {
|
|
cat('...Table 10: Interpretive rules for B-lactam agents and other Gram-negative bacteria\n')
|
|
}
|
|
#voortgang <- progress_estimated(1)
|
|
# regel 10.2
|
|
if (!is.na(ampi)) {
|
|
# hiervoor moeten we eerst weten of ze B-lactamase-positief zijn
|
|
# edit_rsi(to = 'R',
|
|
# rows = which(tbl$fullname %like% '^Haemophilus influenza'
|
|
# & tbl[, ampi] == 'R'),
|
|
# cols = c(ampi, amox, amcl, pita, cfur))
|
|
}
|
|
|
|
# Table 11: Interpretive rules for macrolides, lincosamides, and streptogramins ----
|
|
if (info == TRUE) {
|
|
cat('...Table 11: Interpretive rules for macrolides, lincosamides, and streptogramins\n')
|
|
}
|
|
# regel 11.1
|
|
if (!is.na(eryt)) {
|
|
if (!is.na(azit)) {
|
|
tbl[, azit] <- tbl[, eryt]
|
|
}
|
|
if (!is.na(clar)) {
|
|
tbl[, clar] <- tbl[, eryt]
|
|
}
|
|
}
|
|
|
|
# Table 12: Interpretive rules for aminoglycosides ----
|
|
if (info == TRUE) {
|
|
cat('...Table 12: Interpretive rules for aminoglycosides\n')
|
|
}
|
|
#voortgang <- progress_estimated(4)
|
|
# regel 12.2
|
|
if (!is.na(tobr)) {
|
|
edit_rsi(to = 'R',
|
|
rows = which(tbl$genus == 'Staphylococcus'
|
|
& tbl[, tobr] == 'R'),
|
|
cols = c(kana, amik))
|
|
}
|
|
# regel 12.3
|
|
if (!is.na(gent)) {
|
|
edit_rsi(to = 'R',
|
|
rows = which(tbl$genus == 'Staphylococcus'
|
|
& tbl[, gent] == 'R'),
|
|
cols = aminoglycosiden)
|
|
}
|
|
# regel 12.8
|
|
if (!is.na(gent) & !is.na(tobr)) {
|
|
edit_rsi(to = 'R',
|
|
rows = which(tbl$family == 'Enterobacteriaceae'
|
|
& tbl[, gent] == 'I'
|
|
& tbl[, tobr] == 'S'),
|
|
cols = gent)
|
|
}
|
|
# regel 12.9
|
|
if (!is.na(gent) & !is.na(tobr)) {
|
|
edit_rsi(to = 'R',
|
|
rows = which(tbl$family == 'Enterobacteriaceae'
|
|
& tbl[, tobr] == 'I'
|
|
& tbl[, gent] == 'R'),
|
|
cols = tobr)
|
|
}
|
|
|
|
|
|
# Table 13: Interpretive rules for quinolones ----
|
|
if (info == TRUE) {
|
|
cat('...Table 13: Interpretive rules for quinolones\n')
|
|
}
|
|
#voortgang <- progress_estimated(4)
|
|
# regel 13.2
|
|
if (!is.na(moxi)) {
|
|
edit_rsi(to = 'R',
|
|
rows = which(tbl$genus == 'Staphylococcus'
|
|
& tbl[, moxi] == 'R'),
|
|
cols = fluorochinolonen)
|
|
}
|
|
# regel 13.4
|
|
if (!is.na(moxi)) {
|
|
edit_rsi(to = 'R',
|
|
rows = which(tbl$fullname %like% '^Streptococcus pneumoniae'
|
|
& tbl[, moxi] == 'R'),
|
|
cols = fluorochinolonen)
|
|
}
|
|
# regel 13.5
|
|
if (!is.na(cipr)) {
|
|
edit_rsi(to = 'R',
|
|
rows = which(tbl$family == 'Enterobacteriaceae'
|
|
& tbl[, cipr] == 'R'),
|
|
cols = fluorochinolonen)
|
|
}
|
|
# regel 13.8
|
|
if (!is.na(cipr)) {
|
|
edit_rsi(to = 'R',
|
|
rows = which(tbl$fullname %like% '^Neisseria gonorrhoeae'
|
|
& tbl[, cipr] == 'R'),
|
|
cols = fluorochinolonen)
|
|
}
|
|
|
|
|
|
# Other ----
|
|
if (info == TRUE) {
|
|
cat('...Other\n')
|
|
}
|
|
#voortgang <- progress_estimated(2)
|
|
if (!is.na(amcl)) {
|
|
edit_rsi(to = 'R',
|
|
rows = which(tbl[, amcl] == 'R'),
|
|
cols = ampi)
|
|
}
|
|
if (!is.na(trsu)) {
|
|
edit_rsi(to = 'R',
|
|
rows = which(tbl[, trsu] == 'R'),
|
|
cols = trim)
|
|
}
|
|
if (!is.na(ampi) & !is.na(amox)) {
|
|
tbl[, amox] <- tbl %>% pull(ampi)
|
|
}
|
|
|
|
# Toegevoegde kolommen weer verwijderen
|
|
bactlist.ncol <- ncol(AMR::bactlist) - 2
|
|
tbl.ncol <- ncol(tbl)
|
|
tbl <- tbl %>% select(-c((tbl.ncol - bactlist.ncol):tbl.ncol))
|
|
# en eventueel toegevoegde suffix aan bestaande kolommen weer verwijderen
|
|
colnames(tbl) <- gsub("_tempbactlist", "", colnames(tbl))
|
|
|
|
if (info == TRUE) {
|
|
cat('\nDone.\nExpert rules applied to', total, 'test results.\n')
|
|
}
|
|
|
|
tbl
|
|
}
|
|
|
|
#' @rdname EUCAST
|
|
#' @export
|
|
interpretive_reading <- function(...) {
|
|
EUCAST_rules(...)
|
|
}
|
|
|
|
#' Poperties of a microorganism
|
|
#'
|
|
#' @param bactcode ID of a microorganisme, like \code{"STAAUR} and \code{"ESCCOL}
|
|
#' @param property One of the values \code{bactid}, \code{bactsys}, \code{family}, \code{genus}, \code{species}, \code{subspecies}, \code{fullname}, \code{type}, \code{gramstain}, \code{aerobic}
|
|
#' @export
|
|
#' @importFrom dplyr %>% filter select
|
|
#' @seealso \code{\link{bactlist}}
|
|
mo_property <- function(bactcode, property = 'fullname') {
|
|
|
|
mocode <- as.character(bactcode)
|
|
|
|
for (i in 1:length(mocode)) {
|
|
bug <- mocode[i]
|
|
|
|
if (!is.na(bug)) {
|
|
result = tryCatch({
|
|
mocode[i] <-
|
|
AMR::bactlist %>%
|
|
filter(bactid == bactcode) %>%
|
|
select(property) %>%
|
|
unlist() %>%
|
|
as.character()
|
|
}, error = function(error_condition) {
|
|
warning('Code ', bug, ' not found in bacteria list.')
|
|
}, finally = {
|
|
if (mocode[i] == bug & !property %in% c('bactid', 'bactsys')) {
|
|
mocode[i] <- NA
|
|
}
|
|
})
|
|
}
|
|
|
|
}
|
|
mocode
|
|
}
|