AMR/R/EUCAST.R

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# ==================================================================== #
# TITLE #
# Antimicrobial Resistance (AMR) Analysis #
# #
# AUTHORS #
# Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
# #
# LICENCE #
# This program is free software; you can redistribute it and/or modify #
# it under the terms of the GNU General Public License version 2.0, #
# as published by the Free Software Foundation. #
# #
# This program is distributed in the hope that it will be useful, #
# but WITHOUT ANY WARRANTY; without even the implied warranty of #
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the #
# GNU General Public License for more details. #
# ==================================================================== #
#' EUCAST expert rules
#'
#' Apply expert rules (like intrinsic resistance), as defined by the European Committee on Antimicrobial Susceptibility Testing (EUCAST, \url{http://eucast.org}), see \emph{Source}.
#' @param tbl table with antibiotic columns, like e.g. \code{amox} and \code{amcl}
#' @param col_bactcode column name of the bacteria ID in \code{tbl} - should also be present in \code{bactlist$bactid}, see \code{\link{bactlist}}.
#' @param info print progress
#' @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.
#' @param ... parameters that are passed on to \code{EUCAST_rules}
#' @rdname EUCAST
#' @export
#' @importFrom dplyr %>% left_join select
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#' @return table with edited variables of antibiotics.
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#' @source
#' EUCAST Expert Rules Version 2.0: \cr
#' Leclercq et al. \strong{EUCAST expert rules in antimicrobial susceptibility testing.} \emph{Clin Microbiol Infect.} 2013;19(2):141-60. \cr
#' \url{https://doi.org/10.1111/j.1469-0691.2011.03703.x} \cr
#' \cr
#' EUCAST Expert Rules Version 3.1: \cr
#' \url{http://www.eucast.org/expert_rules_and_intrinsic_resistance}
#' @examples
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#' a <- data.frame(bactid = c("STAAUR", "ESCCOL", "KLEPNE", "PSEAER"),
#' vanc = "-",
#' amox = "-",
#' coli = "-",
#' cfta = "-",
#' cfur = "-",
#' stringsAsFactors = FALSE)
#' a
#'
#' b <- EUCAST_rules(a)
#' b
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EUCAST_rules <- function(tbl,
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col_bactcode = 'bactid',
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info = TRUE,
amcl = 'amcl',
amik = 'amik',
amox = 'amox',
ampi = 'ampi',
azit = 'azit',
aztr = 'aztr',
cefa = 'cefa',
cfra = 'cfra',
cfep = 'cfep',
cfot = 'cfot',
cfox = 'cfox',
cfta = 'cfta',
cftr = 'cftr',
cfur = 'cfur',
chlo = 'chlo',
cipr = 'cipr',
clar = 'clar',
clin = 'clin',
clox = 'clox',
coli = 'coli',
czol = 'czol',
dapt = 'dapt',
doxy = 'doxy',
erta = 'erta',
eryt = 'eryt',
fosf = 'fosf',
fusi = 'fusi',
gent = 'gent',
imip = 'imip',
kana = 'kana',
levo = 'levo',
linc = 'linc',
line = 'line',
mero = 'mero',
mino = 'mino',
moxi = 'moxi',
nali = 'nali',
neom = 'neom',
neti = 'neti',
nitr = 'nitr',
novo = 'novo',
norf = 'norf',
oflo = 'oflo',
peni = 'peni',
pita = 'pita',
poly = 'poly',
qida = 'qida',
rifa = 'rifa',
roxi = 'roxi',
siso = 'siso',
teic = 'teic',
tetr = 'tetr',
tica = 'tica',
tige = 'tige',
tobr = 'tobr',
trim = 'trim',
trsu = 'trsu',
vanc = 'vanc') {
if (!col_bactcode %in% colnames(tbl)) {
stop('Column ', col_bactcode, ' not found.')
}
# kolommen controleren
col.list <- c(amcl, amik, amox, ampi, azit, aztr, cefa, cfra, cfep,
cfot, cfox, cfta, cftr, cfur, cipr, clar, clin, clox, coli, czol,
dapt, doxy, erta, eryt, 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)
col.list <- col.list[!is.na(col.list)]
if (!all(col.list %in% colnames(tbl))) {
if (info == TRUE) {
cat('\n')
}
if (info == TRUE) {
warning('These columns do not exist and will be ignored:\n',
col.list[!(col.list %in% colnames(tbl))] %>% toString(),
immediate. = TRUE,
call. = FALSE)
}
if (!amcl %in% colnames(tbl)) { amcl <- NA }
if (!amik %in% colnames(tbl)) { amik <- NA }
if (!amox %in% colnames(tbl)) { amox <- NA }
if (!ampi %in% colnames(tbl)) { ampi <- NA }
if (!azit %in% colnames(tbl)) { azit <- NA }
if (!aztr %in% colnames(tbl)) { aztr <- NA }
if (!cefa %in% colnames(tbl)) { cefa <- NA }
if (!cfra %in% colnames(tbl)) { cfra <- NA }
if (!cfep %in% colnames(tbl)) { cfep <- NA }
if (!cfot %in% colnames(tbl)) { cfot <- NA }
if (!cfox %in% colnames(tbl)) { cfox <- NA }
if (!cfta %in% colnames(tbl)) { cfta <- NA }
if (!cftr %in% colnames(tbl)) { cftr <- NA }
if (!cfur %in% colnames(tbl)) { cfur <- NA }
if (!chlo %in% colnames(tbl)) { chlo <- NA }
if (!cipr %in% colnames(tbl)) { cipr <- NA }
if (!clar %in% colnames(tbl)) { clar <- NA }
if (!clin %in% colnames(tbl)) { clin <- NA }
if (!clox %in% colnames(tbl)) { clox <- NA }
if (!coli %in% colnames(tbl)) { coli <- NA }
if (!czol %in% colnames(tbl)) { czol <- NA }
if (!dapt %in% colnames(tbl)) { dapt <- NA }
if (!doxy %in% colnames(tbl)) { doxy <- NA }
if (!erta %in% colnames(tbl)) { erta <- NA }
if (!eryt %in% colnames(tbl)) { eryt <- NA }
if (!fosf %in% colnames(tbl)) { fosf <- NA }
if (!fusi %in% colnames(tbl)) { fusi <- NA }
if (!gent %in% colnames(tbl)) { gent <- NA }
if (!imip %in% colnames(tbl)) { imip <- NA }
if (!kana %in% colnames(tbl)) { kana <- NA }
if (!levo %in% colnames(tbl)) { levo <- NA }
if (!linc %in% colnames(tbl)) { linc <- NA }
if (!line %in% colnames(tbl)) { line <- NA }
if (!mero %in% colnames(tbl)) { mero <- NA }
if (!mino %in% colnames(tbl)) { mino <- NA }
if (!moxi %in% colnames(tbl)) { moxi <- NA }
if (!nali %in% colnames(tbl)) { nali <- NA }
if (!neom %in% colnames(tbl)) { neom <- NA }
if (!neti %in% colnames(tbl)) { neti <- NA }
if (!nitr %in% colnames(tbl)) { nitr <- NA }
if (!novo %in% colnames(tbl)) { novo <- NA }
if (!norf %in% colnames(tbl)) { norf <- NA }
if (!oflo %in% colnames(tbl)) { oflo <- NA }
if (!peni %in% colnames(tbl)) { peni <- NA }
if (!pita %in% colnames(tbl)) { pita <- NA }
if (!poly %in% colnames(tbl)) { poly <- NA }
if (!qida %in% colnames(tbl)) { qida <- NA }
if (!rifa %in% colnames(tbl)) { rifa <- NA }
if (!roxi %in% colnames(tbl)) { roxi <- NA }
if (!siso %in% colnames(tbl)) { siso <- NA }
if (!teic %in% colnames(tbl)) { teic <- NA }
if (!tetr %in% colnames(tbl)) { tetr <- NA }
if (!tica %in% colnames(tbl)) { tica <- NA }
if (!tige %in% colnames(tbl)) { tige <- NA }
if (!tobr %in% colnames(tbl)) { tobr <- NA }
if (!trim %in% colnames(tbl)) { trim <- NA }
if (!trsu %in% colnames(tbl)) { trsu <- NA }
if (!vanc %in% colnames(tbl)) { vanc <- NA }
}
total <- 0
# functie voor uitvoeren
edit_rsi <- function(to, rows, cols) {
#voortgang$tick()$print()
cols <- cols[!is.na(cols)]
if (length(rows) > 0 & length(cols) > 0) {
tbl[rows, cols] <<- to
total <<- total + (length(rows) * length(cols))
}
}
# bactlist aan vastknopen (bestaande kolommen krijgen extra suffix)
joinby <- colnames(AMR::bactlist)[1]
names(joinby) <- col_bactcode
tbl <- tbl %>% left_join(y = AMR::bactlist, by = joinby, suffix = c("_tempbactlist", ""))
# antibioticagroepen
aminoglycosiden <- c(tobr, gent, kana, neom, neti, siso)
tetracyclines <- c(doxy, mino, tetr) # sinds EUCAST v3.1 is tige(cycline) apart
polymyxines <- c(poly, coli)
macroliden <- c(eryt, azit, roxi, clar) # sinds EUCAST v3.1 is clinda apart
glycopeptiden <- c(vanc, teic)
streptogramines <- qida # eigenlijk pristinamycine en quinupristine/dalfopristine
cefalosporines <- c(cfep, cfot, cfox, cfra, cfta, cftr, cfur, czol)
carbapenems <- c(erta, imip, mero)
aminopenicillines <- c(ampi, amox)
ureidopenicillines <- pita # eigenlijk ook azlo en mezlo
fluorochinolonen <- c(oflo, cipr, norf, levo, moxi)
if (info == TRUE) {
cat('\nApplying EUCAST expert rules on',
tbl[!is.na(tbl$genus),] %>% nrow(),
'isolates according to "EUCAST Expert Rules Version 3.1"\n\n')
}
# Table 1: Intrinsic resistance in Enterobacteriaceae ----
if (info == TRUE) {
cat('...Table 1: Intrinsic resistance in Enterobacteriaceae\n')
}
#voortgang <- progress_estimated(17)
# Intrisiek R voor groep
edit_rsi(to = 'R',
rows = which(tbl$family == 'Enterobacteriaceae'),
cols = c(peni, glycopeptiden, fusi, macroliden, linc, streptogramines, rifa, dapt, line))
# Citrobacter
edit_rsi(to = 'R',
rows = which(tbl$fullname %like% '^Citrobacter (koseri|amalonaticus|sedlakii|farmeri|rodentium)'),
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cols = c(aminopenicillines, tica))
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edit_rsi(to = 'R',
rows = which(tbl$fullname %like% '^Citrobacter (freundii|braakii|murliniae|werkmanii|youngae)'),
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cols = c(aminopenicillines, amcl, czol, cfox))
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# Enterobacter
edit_rsi(to = 'R',
rows = which(tbl$fullname %like% '^Enterobacter cloacae'),
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cols = c(aminopenicillines, amcl, czol, cfox))
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edit_rsi(to = 'R',
rows = which(tbl$fullname %like% '^Enterobacter aerogenes'),
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cols = c(aminopenicillines, amcl, czol, cfox))
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# Escherichia
edit_rsi(to = 'R',
rows = which(tbl$fullname %like% '^Escherichia hermanni'),
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cols = c(aminopenicillines, tica))
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# Hafnia
edit_rsi(to = 'R',
rows = which(tbl$fullname %like% '^Hafnia alvei'),
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cols = c(aminopenicillines, amcl, czol, cfox))
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# Klebsiella
edit_rsi(to = 'R',
rows = which(tbl$fullname %like% '^Klebsiella'),
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cols = c(aminopenicillines, tica))
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# Morganella / Proteus
edit_rsi(to = 'R',
rows = which(tbl$fullname %like% '^Morganella morganii'),
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cols = c(aminopenicillines, amcl, czol, tetracyclines, polymyxines, nitr))
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edit_rsi(to = 'R',
rows = which(tbl$fullname %like% '^Proteus mirabilis'),
cols = c(tetracyclines, tige, polymyxines, nitr))
edit_rsi(to = 'R',
rows = which(tbl$fullname %like% '^Proteus penneri'),
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cols = c(aminopenicillines, czol, cfur, tetracyclines, tige, polymyxines, nitr))
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edit_rsi(to = 'R',
rows = which(tbl$fullname %like% '^Proteus vulgaris'),
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cols = c(aminopenicillines, czol, cfur, tetracyclines, tige, polymyxines, nitr))
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# Providencia
edit_rsi(to = 'R',
rows = which(tbl$fullname %like% '^Providencia rettgeri'),
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cols = c(aminopenicillines, amcl, czol, cfur, tetracyclines, tige, polymyxines, nitr))
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edit_rsi(to = 'R',
rows = which(tbl$fullname %like% '^Providencia stuartii'),
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cols = c(aminopenicillines, amcl, czol, cfur, tetracyclines, tige, polymyxines, nitr))
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# Raoultella
edit_rsi(to = 'R',
rows = which(tbl$fullname %like% '^Raoultella'),
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cols = c(aminopenicillines, tica))
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# Serratia
edit_rsi(to = 'R',
rows = which(tbl$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
edit_rsi(to = 'R',
rows = which(tbl$fullname %like% '^Yersinia enterocolitica'),
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cols = c(aminopenicillines, amcl, tica, czol, cfox))
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edit_rsi(to = 'R',
rows = which(tbl$fullname %like% '^Yersinia pseudotuberculosis'),
cols = c(poly, coli))
# Table 2: Intrinsic resistance in non-fermentative Gram-negative bacteria ----
if (info == TRUE) {
cat('...Table 2: Intrinsic resistance in non-fermentative Gram-negative bacteria\n')
}
#voortgang <- progress_estimated(8)
# Intrisiek R voor groep
edit_rsi(to = 'R',
rows = which(tbl$genus %in% c('Achromobacter',
'Acinetobacter',
'Alcaligenes',
'Bordatella',
'Burkholderia',
'Elizabethkingia',
'Flavobacterium',
'Ochrobactrum',
'Pseudomonas',
'Stenotrophomonas')),
cols = c(peni, cfox, cfur, glycopeptiden, fusi, macroliden, linc, streptogramines, rifa, dapt, line))
# Acinetobacter
edit_rsi(to = 'R',
rows = which(tbl$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
edit_rsi(to = 'R',
rows = which(tbl$fullname %like% '^Achromobacter (xylosoxydans|xylosoxidans)'),
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cols = c(aminopenicillines, czol, cfot, cftr, erta))
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# Burkholderia
edit_rsi(to = 'R',
# onder 'Burkholderia cepacia complex' vallen deze species allemaal: PMID 16217180.
rows = which(tbl$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
edit_rsi(to = 'R',
rows = which(tbl$fullname %like% '^Elizabethkingia meningoseptic(a|um)'),
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cols = c(aminopenicillines, amcl, tica, czol, cfot, cftr, cfta, cfep, aztr, erta, imip, mero, polymyxines))
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# Ochrobactrum
edit_rsi(to = 'R',
rows = which(tbl$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
edit_rsi(to = 'R',
rows = which(tbl$fullname %like% '^Pseudomonas aeruginosa'),
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cols = c(aminopenicillines, amcl, czol, cfot, cftr, erta, chlo, kana, neom, trim, trsu, tetracyclines, tige))
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# Stenotrophomonas
edit_rsi(to = 'R',
rows = which(tbl$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 ----
if (info == TRUE) {
cat('...Table 3: Intrinsic resistance in other Gram-negative bacteria\n')
}
#voortgang <- progress_estimated(7)
# Intrisiek R voor groep
edit_rsi(to = 'R',
rows = which(tbl$genus %in% c('Haemophilus',
'Moraxella',
'Neisseria',
'Campylobacter')),
cols = c(glycopeptiden, linc, dapt, line))
# Haemophilus
edit_rsi(to = 'R',
rows = which(tbl$fullname %like% '^Haemophilus influenzae'),
cols = c(fusi, streptogramines))
# Moraxella
edit_rsi(to = 'R',
rows = which(tbl$fullname %like% '^Moraxella catarrhalis'),
cols = trim)
# Neisseria
edit_rsi(to = 'R',
rows = which(tbl$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))
}
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if (!is.na(amox)) {
edit_rsi(to = 'R',
rows = which(tbl$genus == 'Enterococcus'
& tbl[, amox] == 'R'),
cols = c(ureidopenicillines, carbapenems))
}
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# Table 9: Interpretive rules for B-lactam agents and Gram-negative rods ----
if (info == TRUE) {
cat('...Table 9: Interpretive rules for B-lactam agents and Gram-negative rods\n')
}
#voortgang <- progress_estimated(1)
# regel 9.3
if (!is.na(tica) & !is.na(pita)) {
edit_rsi(to = 'R',
rows = which(tbl$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)) {
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tbl[, amox] <- tbl %>% pull(ampi)
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}
# 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
}