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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_bactid column name of the bacteria ID in \code{tbl} - values of this column should be present in \code{microorganisms$bactid}, see \code{\link{microorganisms}}
#' @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
#' @return table with edited variables of antibiotics.
#' @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 (Intrinsic Resistance and Exceptional Phenotypes Tables): \cr
#' \url{http://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Expert_Rules/Expert_rules_intrinsic_exceptional_V3.1.pdf}
#' @examples
#' a <- data.frame(bactid = c("STAAUR", # Staphylococcus aureus
#' "ENCFAE", # Enterococcus faecalis
#' "ESCCOL", # Escherichia coli
#' "KLEPNE", # Klebsiella pneumoniae
#' "PSEAER"), # Pseudomonas aeruginosa
#' vanc = "-", # Vancomycin
#' amox = "-", # Amoxicillin
#' coli = "-", # Colistin
#' cfta = "-", # Ceftazidime
#' cfur = "-", # Cefuroxime
#' stringsAsFactors = FALSE)
#' a
#'
#' b <- EUCAST_rules(a)
#' b
EUCAST_rules <- function(tbl,
col_bactid = 'bactid',
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') {
EUCAST_VERSION <- "3.1"
if (!col_bactid %in% colnames(tbl)) {
stop('Column ', col_bactid, ' not found.')
}
# check columns
col.list <- c(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)
col.list <- col.list[!is.na(col.list)]
col.list.bak <- col.list
# are they available as upper case or lower case then?
for (i in 1:length(col.list)) {
if (toupper(col.list[i]) %in% colnames(tbl)) {
col.list[i] <- toupper(col.list[i])
} else if (tolower(col.list[i]) %in% colnames(tbl)) {
col.list[i] <- tolower(col.list[i])
} else if (!col.list[i] %in% colnames(tbl)) {
col.list[i] <- NA
}
}
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: ',
col.list.bak[!(col.list %in% colnames(tbl))] %>% toString(),
immediate. = TRUE,
call. = FALSE)
}
}
amcl <- col.list[1]
amik <- col.list[2]
amox <- col.list[3]
ampi <- col.list[4]
azit <- col.list[5]
aztr <- col.list[6]
cefa <- col.list[7]
cfra <- col.list[8]
cfep <- col.list[9]
cfot <- col.list[10]
cfox <- col.list[11]
cfta <- col.list[12]
cftr <- col.list[13]
cfur <- col.list[14]
chlo <- col.list[15]
cipr <- col.list[16]
clar <- col.list[17]
clin <- col.list[18]
clox <- col.list[19]
coli <- col.list[20]
czol <- col.list[21]
dapt <- col.list[22]
doxy <- col.list[23]
erta <- col.list[24]
eryt <- col.list[25]
fosf <- col.list[26]
fusi <- col.list[27]
gent <- col.list[28]
imip <- col.list[29]
kana <- col.list[30]
levo <- col.list[31]
linc <- col.list[32]
line <- col.list[33]
mero <- col.list[34]
mino <- col.list[35]
moxi <- col.list[36]
nali <- col.list[37]
neom <- col.list[38]
neti <- col.list[39]
nitr <- col.list[40]
novo <- col.list[41]
norf <- col.list[42]
oflo <- col.list[43]
peni <- col.list[44]
pita <- col.list[45]
poly <- col.list[46]
qida <- col.list[47]
rifa <- col.list[48]
roxi <- col.list[49]
siso <- col.list[50]
teic <- col.list[51]
tetr <- col.list[52]
tica <- col.list[53]
tige <- col.list[54]
tobr <- col.list[55]
trim <- col.list[56]
trsu <- col.list[57]
vanc <- col.list[58]
total <- 0
total_rows <- integer(0)
# helper function for editing the table
edit_rsi <- function(to, rows, cols) {
cols <- cols[!is.na(cols)]
if (length(rows) > 0 & length(cols) > 0) {
tbl[rows, cols] <<- to
total <<- total + (length(rows) * length(cols))
total_rows <<- c(total_rows, rows)
}
}
# join to microorganisms table
joinby <- colnames(AMR::microorganisms)[1]
names(joinby) <- col_bactid
tbl <- tbl %>% left_join(y = AMR::microorganisms, by = joinby, suffix = c("_tempmicroorganisms", ""))
# antibiotic classes
aminoglycosides <- c(tobr, gent, kana, neom, neti, siso)
tetracyclines <- c(doxy, mino, tetr) # since EUCAST v3.1 tige(cycline) is set apart
polymyxins <- c(poly, coli)
macrolides <- c(eryt, azit, roxi, clar) # since EUCAST v3.1 clinda is set apart
glycopeptides <- c(vanc, teic)
streptogramins <- qida # should officially also be pristinamycin and quinupristin/dalfopristin
cephalosporins <- c(cfep, cfot, cfox, cfra, cfta, cftr, cfur, czol)
carbapenems <- c(erta, imip, mero)
aminopenicillins <- c(ampi, amox)
ureidopenicillins <- pita # should officially also be azlo and mezlo
fluoroquinolones <- c(oflo, cipr, norf, levo, moxi)
if (info == TRUE) {
cat(
paste0(
'\nApplying rules to ',
tbl[!is.na(tbl$genus),] %>% nrow() %>% format(big.mark = ","),
' rows according to "EUCAST Expert Rules Version ', EUCAST_VERSION, '"\n')
)
}
# Table 1: Intrinsic resistance in Enterobacteriaceae ----
if (info == TRUE) {
cat('...Table 1: Intrinsic resistance in Enterobacteriaceae\n')
}
# Intrisiek R for this group
edit_rsi(to = 'R',
rows = which(tbl$family == 'Enterobacteriaceae'),
cols = c(peni, glycopeptides, fusi, macrolides, linc, streptogramins, rifa, dapt, line))
# Citrobacter
edit_rsi(to = 'R',
rows = which(tbl$fullname %like% '^Citrobacter (koseri|amalonaticus|sedlakii|farmeri|rodentium)'),
cols = c(aminopenicillins, tica))
edit_rsi(to = 'R',
rows = which(tbl$fullname %like% '^Citrobacter (freundii|braakii|murliniae|werkmanii|youngae)'),
cols = c(aminopenicillins, amcl, czol, cfox))
# Enterobacter
edit_rsi(to = 'R',
rows = which(tbl$fullname %like% '^Enterobacter cloacae'),
cols = c(aminopenicillins, amcl, czol, cfox))
edit_rsi(to = 'R',
rows = which(tbl$fullname %like% '^Enterobacter aerogenes'),
cols = c(aminopenicillins, amcl, czol, cfox))
# Escherichia
edit_rsi(to = 'R',
rows = which(tbl$fullname %like% '^Escherichia hermanni'),
cols = c(aminopenicillins, tica))
# Hafnia
edit_rsi(to = 'R',
rows = which(tbl$fullname %like% '^Hafnia alvei'),
cols = c(aminopenicillins, amcl, czol, cfox))
# Klebsiella
edit_rsi(to = 'R',
rows = which(tbl$fullname %like% '^Klebsiella'),
cols = c(aminopenicillins, tica))
# Morganella / Proteus
edit_rsi(to = 'R',
rows = which(tbl$fullname %like% '^Morganella morganii'),
cols = c(aminopenicillins, amcl, czol, tetracyclines, polymyxins, nitr))
edit_rsi(to = 'R',
rows = which(tbl$fullname %like% '^Proteus mirabilis'),
cols = c(tetracyclines, tige, polymyxins, nitr))
edit_rsi(to = 'R',
rows = which(tbl$fullname %like% '^Proteus penneri'),
cols = c(aminopenicillins, czol, cfur, tetracyclines, tige, polymyxins, nitr))
edit_rsi(to = 'R',
rows = which(tbl$fullname %like% '^Proteus vulgaris'),
cols = c(aminopenicillins, czol, cfur, tetracyclines, tige, polymyxins, nitr))
# Providencia
edit_rsi(to = 'R',
rows = which(tbl$fullname %like% '^Providencia rettgeri'),
cols = c(aminopenicillins, amcl, czol, cfur, tetracyclines, tige, polymyxins, nitr))
edit_rsi(to = 'R',
rows = which(tbl$fullname %like% '^Providencia stuartii'),
cols = c(aminopenicillins, amcl, czol, cfur, tetracyclines, tige, polymyxins, nitr))
# Raoultella
edit_rsi(to = 'R',
rows = which(tbl$fullname %like% '^Raoultella'),
cols = c(aminopenicillins, tica))
# Serratia
edit_rsi(to = 'R',
rows = which(tbl$fullname %like% '^Serratia marcescens'),
cols = c(aminopenicillins, amcl, czol, cfox, cfur, tetracyclines[tetracyclines != 'mino'], polymyxins, nitr))
# Yersinia
edit_rsi(to = 'R',
rows = which(tbl$fullname %like% '^Yersinia enterocolitica'),
cols = c(aminopenicillins, amcl, tica, czol, cfox))
edit_rsi(to = 'R',
rows = which(tbl$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')
}
# Intrisiek R for this group
edit_rsi(to = 'R',
rows = which(tbl$genus %in% c('Achromobacter',
'Acinetobacter',
'Alcaligenes',
'Bordatella',
'Burkholderia',
'Elizabethkingia',
'Flavobacterium',
'Ochrobactrum',
'Pseudomonas',
'Stenotrophomonas')),
cols = c(peni, cfox, cfur, glycopeptides, fusi, macrolides, linc, streptogramins, rifa, dapt, line))
# Acinetobacter
edit_rsi(to = 'R',
rows = which(tbl$fullname %like% '^Acinetobacter (baumannii|pittii|nosocomialis|calcoaceticus)'),
cols = c(aminopenicillins, amcl, czol, cfot, cftr, aztr, erta, trim, fosf, tetracyclines[tetracyclines != 'mino']))
# Achromobacter
edit_rsi(to = 'R',
rows = which(tbl$fullname %like% '^Achromobacter (xylosoxydans|xylosoxidans)'),
cols = c(aminopenicillins, czol, cfot, cftr, erta))
# Burkholderia
edit_rsi(to = 'R',
# onder 'Burkholderia cepacia complex' vallen deze species allemaal: PMID 16217180.
rows = which(tbl$fullname %like% '^Burkholderia (cepacia|multivorans|cenocepacia|stabilis|vietnamiensis|dolosa|ambifaria|anthina|pyrrocinia|ubonensis)'),
cols = c(aminopenicillins, amcl, tica, pita, czol, cfot, cftr, aztr, erta, cipr, chlo, aminoglycosides, trim, fosf, polymyxins))
# Elizabethkingia
edit_rsi(to = 'R',
rows = which(tbl$fullname %like% '^Elizabethkingia meningoseptic(a|um)'),
cols = c(aminopenicillins, amcl, tica, czol, cfot, cftr, cfta, cfep, aztr, erta, imip, mero, polymyxins))
# Ochrobactrum
edit_rsi(to = 'R',
rows = which(tbl$fullname %like% '^Ochrobactrum anthropi'),
cols = c(aminopenicillins, amcl, tica, pita, czol, cfot, cftr, cfta, cfep, aztr, erta))
# Pseudomonas
edit_rsi(to = 'R',
rows = which(tbl$fullname %like% '^Pseudomonas aeruginosa'),
cols = c(aminopenicillins, amcl, czol, cfot, cftr, erta, chlo, kana, neom, trim, trsu, tetracyclines, tige))
# Stenotrophomonas
edit_rsi(to = 'R',
rows = which(tbl$fullname %like% '^Stenotrophomonas maltophilia'),
cols = c(aminopenicillins, amcl, tica, pita, czol, cfot, cftr, cfta, aztr, erta, imip, mero, aminoglycosides, trim, fosf, tetr))
# Table 3: Intrinsic resistance in other Gram-negative bacteria ----
if (info == TRUE) {
cat('...Table 3: Intrinsic resistance in other Gram-negative bacteria\n')
}
# Intrisiek R for this group
edit_rsi(to = 'R',
rows = which(tbl$genus %in% c('Haemophilus',
'Moraxella',
'Neisseria',
'Campylobacter')),
cols = c(glycopeptides, linc, dapt, line))
# Haemophilus
edit_rsi(to = 'R',
rows = which(tbl$fullname %like% '^Haemophilus influenzae'),
cols = c(fusi, streptogramins))
# 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$fullname %like% '^Campylobacter fetus'),
cols = c(fusi, streptogramins, trim, nali))
edit_rsi(to = 'R',
rows = which(tbl$fullname %like% '^Campylobacter (jejuni|coli)'),
cols = c(fusi, streptogramins, trim))
# Table 4: Intrinsic resistance in Gram-positive bacteria ----
if (info == TRUE) {
cat('...Table 4: Intrinsic resistance in Gram-positive bacteria\n')
}
# Intrisiek R for this group
edit_rsi(to = 'R',
rows = which(tbl$gramstain %like% 'Positi(e|)(v|f)'),
cols = c(aztr, polymyxins, nali))
# Staphylococcus
edit_rsi(to = 'R',
rows = which(tbl$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, aminoglycosides))
# Enterococcus
edit_rsi(to = 'R',
rows = which(tbl$fullname %like% '^Enterococcus faecalis'),
cols = c(fusi, cfta, cephalosporins[cephalosporins != cfta], aminoglycosides, macrolides, clin, qida, trim, trsu))
edit_rsi(to = 'R',
rows = which(tbl$fullname %like% '^Enterococcus (gallinarum|casseliflavus)'),
cols = c(fusi, cfta, cephalosporins[cephalosporins != cfta], aminoglycosides, macrolides, clin, qida, vanc, trim, trsu))
edit_rsi(to = 'R',
rows = which(tbl$fullname %like% '^Enterococcus faecium'),
cols = c(fusi, cfta, cephalosporins[cephalosporins != cfta], aminoglycosides, macrolides, trim, trsu))
# Corynebacterium
edit_rsi(to = 'R',
rows = which(tbl$genus == 'Corynebacterium'),
cols = fosf)
# Listeria
edit_rsi(to = 'R',
rows = which(tbl$fullname %like% '^Listeria monocytogenes'),
cols = c(cfta, cephalosporins[cephalosporins != cfta]))
# overig
edit_rsi(to = 'R',
rows = which(tbl$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')
}
# rule 8.3
if (!is.na(peni)) {
edit_rsi(to = 'S',
rows = which(tbl$fullname %like% '^Streptococcus (pyogenes|agalactiae|dysgalactiae|groep A|groep B|groep C|groep G)'
& tbl[, peni] == 'S'),
cols = c(aminopenicillins, cephalosporins, carbapenems))
}
# rule 8.6
if (!is.na(ampi)) {
edit_rsi(to = 'R',
rows = which(tbl$genus == 'Enterococcus'
& tbl[, ampi] == 'R'),
cols = c(ureidopenicillins, carbapenems))
}
if (!is.na(amox)) {
edit_rsi(to = 'R',
rows = which(tbl$genus == 'Enterococcus'
& tbl[, amox] == 'R'),
cols = c(ureidopenicillins, carbapenems))
}
# Table 9: Interpretive rules for B-lactam agents and Gram-negative rods ----
if (info == TRUE) {
cat('...Table 9: Interpretive rules for B-lactam agents and Gram-negative rods\n')
}
# rule 9.3
if (!is.na(tica) & !is.na(pita)) {
edit_rsi(to = 'R',
rows = which(tbl$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')
}
# rule 10.2
if (!is.na(ampi)) {
# you should know first if the are B-lactamase positive, so do not run for now
# edit_rsi(to = 'R',
# rows = which(tbl$fullname %like% '^Haemophilus influenza'
# & tbl[, ampi] == 'R'),
# cols = c(ampi, amox, amcl, pita, cfur))
}
# Table 11: Interpretive rules for macrolides, lincosamides, and streptogramins ----
if (info == TRUE) {
cat('...Table 11: Interpretive rules for macrolides, lincosamides, and streptogramins\n')
}
# rule 11.1
if (!is.na(eryt)) {
if (!is.na(azit)) {
tbl[, azit] <- tbl[, eryt]
}
if (!is.na(clar)) {
tbl[, clar] <- tbl[, eryt]
}
}
# Table 12: Interpretive rules for aminoglycosides ----
if (info == TRUE) {
cat('...Table 12: Interpretive rules for aminoglycosides\n')
}
# rule 12.2
if (!is.na(tobr)) {
edit_rsi(to = 'R',
rows = which(tbl$genus == 'Staphylococcus'
& tbl[, tobr] == 'R'),
cols = c(kana, amik))
}
# rule 12.3
if (!is.na(gent)) {
edit_rsi(to = 'R',
rows = which(tbl$genus == 'Staphylococcus'
& tbl[, gent] == 'R'),
cols = aminoglycosides)
}
# rule 12.8
if (!is.na(gent) & !is.na(tobr)) {
edit_rsi(to = 'R',
rows = which(tbl$family == 'Enterobacteriaceae'
& tbl[, gent] == 'I'
& tbl[, tobr] == 'S'),
cols = gent)
}
# rule 12.9
if (!is.na(gent) & !is.na(tobr)) {
edit_rsi(to = 'R',
rows = which(tbl$family == 'Enterobacteriaceae'
& tbl[, tobr] == 'I'
& tbl[, gent] == 'R'),
cols = tobr)
}
# Table 13: Interpretive rules for quinolones ----
if (info == TRUE) {
cat('...Table 13: Interpretive rules for quinolones\n')
}
# rule 13.2
if (!is.na(moxi)) {
edit_rsi(to = 'R',
rows = which(tbl$genus == 'Staphylococcus'
& tbl[, moxi] == 'R'),
cols = fluoroquinolones)
}
# rule 13.4
if (!is.na(moxi)) {
edit_rsi(to = 'R',
rows = which(tbl$fullname %like% '^Streptococcus pneumoniae'
& tbl[, moxi] == 'R'),
cols = fluoroquinolones)
}
# rule 13.5
if (!is.na(cipr)) {
edit_rsi(to = 'R',
rows = which(tbl$family == 'Enterobacteriaceae'
& tbl[, cipr] == 'R'),
cols = fluoroquinolones)
}
# rule 13.8
if (!is.na(cipr)) {
edit_rsi(to = 'R',
rows = which(tbl$fullname %like% '^Neisseria gonorrhoeae'
& tbl[, cipr] == 'R'),
cols = fluoroquinolones)
}
# Other ----
if (info == TRUE) {
cat('...Non-EUCAST: trim = R where trsu = R and ampi = R where amcl = R\n')
}
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)
}
# Remove added columns again
microorganisms.ncol <- ncol(AMR::microorganisms) - 2
tbl.ncol <- ncol(tbl)
tbl <- tbl %>% select(-c((tbl.ncol - microorganisms.ncol):tbl.ncol))
# and remove added suffices
colnames(tbl) <- gsub("_tempmicroorganisms", "", colnames(tbl))
if (info == TRUE) {
cat('Done.\n\nEUCAST Expert rules applied to',
total_rows %>% unique() %>% length() %>% format(big.mark = ","),
'different rows (isolates); edited a total of',
total %>% format(big.mark = ","), 'test results.\n\n')
}
tbl
}
#' @rdname EUCAST
#' @export
interpretive_reading <- function(...) {
EUCAST_rules(...)
}
#' Poperties of a microorganism
#'
#' @param bactid 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{microorganisms}}
mo_property <- function(bactid, property = 'fullname') {
mocode <- as.character(bactid)
for (i in 1:length(mocode)) {
bug <- mocode[i]
if (!is.na(bug)) {
result = tryCatch({
mocode[i] <-
AMR::microorganisms %>%
filter(bactid == bug) %>%
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
}
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