AMR/man/EUCAST.Rd

% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/eucast.R
\name{EUCAST_rules}
\alias{EUCAST_rules}
\alias{interpretive_reading}
\title{EUCAST expert rules}
\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}
}
\usage{
EUCAST_rules(tbl, col_mo = "mo", info = TRUE, amcl = "amcl",
  amik = "amik", amox = "amox", ampi = "ampi", azit = "azit",
  azlo = "azlo", aztr = "aztr", cefa = "cefa", cfep = "cfep",
  cfot = "cfot", cfox = "cfox", cfra = "cfra", 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", mezl = "mezl", mino = "mino",
  moxi = "moxi", nali = "nali", neom = "neom", neti = "neti",
  nitr = "nitr", norf = "norf", novo = "novo", oflo = "oflo",
  peni = "peni", pita = "pita", poly = "poly", pris = "pris",
  qida = "qida", rifa = "rifa", roxi = "roxi", siso = "siso",
  teic = "teic", tetr = "tetr", tica = "tica", tige = "tige",
  tobr = "tobr", trim = "trim", trsu = "trsu", vanc = "vanc",
  col_bactid = "bactid")

interpretive_reading(...)
}
\arguments{
\item{tbl}{table with antibiotic columns, like e.g. \code{amox} and \code{amcl}}

\item{col_mo}{column name of the bacteria ID in \code{tbl} - values of this column should be present in \code{microorganisms$mo}, see \code{\link{microorganisms}}}

\item{info}{print progress}

\item{amcl, amik, amox, ampi, azit, azlo, aztr, cefa, cfep, cfot, cfox, cfra, cfta, cftr, cfur, chlo, cipr, clar, clin, clox, coli, czol, dapt, doxy, erta, eryt, fosf, fusi, gent, imip, kana, levo, linc, line, mero, mezl, mino, moxi, nali, neom, neti, nitr, norf, novo, oflo, peni, pita, poly, pris, qida, rifa, roxi, siso, teic, tetr, tica, tige, tobr, trim, trsu, vanc}{column name of an antibiotic. Use \code{NA} to skip a column, like \code{tica = NA}. Non-existing columns will anyway be skipped. See the Antibiotics section for an explanation of the abbreviations.}

\item{col_bactid}{Deprecated. Use \code{col_mo} instead.}

\item{...}{parameters that are passed on to \code{EUCAST_rules}}
}
\value{
table with edited variables of antibiotics.
}
\description{
Apply expert rules (like intrinsic resistance), as defined by the European Committee on Antimicrobial Susceptibility Testing (EUCAST, \url{http://eucast.org}), see \emph{Source}.
}
\section{Antibiotics}{

Abbrevations of the column containing antibiotics:

 \strong{amcl}: amoxicillin and beta-lactamase inhibitor (\emph{J01CR02}),
 \strong{amik}: amikacin (\emph{J01GB06}),
 \strong{amox}: amoxicillin (\emph{J01CA04}),
 \strong{ampi}: ampicillin (\emph{J01CA01}),
 \strong{azit}: azithromycin (\emph{J01FA10}),
 \strong{azlo}: azlocillin (\emph{J01CA09}),
 \strong{aztr}: aztreonam (\emph{J01DF01}),
 \strong{cefa}: cefaloridine (\emph{J01DB02}),
 \strong{cfep}: cefepime (\emph{J01DE01}),
 \strong{cfot}: cefotaxime (\emph{J01DD01}),
 \strong{cfox}: cefoxitin (\emph{J01DC01}),
 \strong{cfra}: cefradine (\emph{J01DB09}),
 \strong{cfta}: ceftazidime (\emph{J01DD02}),
 \strong{cftr}: ceftriaxone (\emph{J01DD04}),
 \strong{cfur}: cefuroxime (\emph{J01DC02}),
 \strong{chlo}: chloramphenicol (\emph{J01BA01}),
 \strong{cipr}: ciprofloxacin (\emph{J01MA02}),
 \strong{clar}: clarithromycin (\emph{J01FA09}),
 \strong{clin}: clindamycin (\emph{J01FF01}),
 \strong{clox}: flucloxacillin (\emph{J01CF05}),
 \strong{coli}: colistin (\emph{J01XB01}),
 \strong{czol}: cefazolin (\emph{J01DB04}),
 \strong{dapt}: daptomycin (\emph{J01XX09}),
 \strong{doxy}: doxycycline (\emph{J01AA02}),
 \strong{erta}: ertapenem (\emph{J01DH03}),
 \strong{eryt}: erythromycin (\emph{J01FA01}),
 \strong{fosf}: fosfomycin (\emph{J01XX01}),
 \strong{fusi}: fusidic acid (\emph{J01XC01}),
 \strong{gent}: gentamicin (\emph{J01GB03}),
 \strong{imip}: imipenem and cilastatin (\emph{J01DH51}),
 \strong{kana}: kanamycin (\emph{J01GB04}),
 \strong{levo}: levofloxacin (\emph{J01MA12}),
 \strong{linc}: lincomycin (\emph{J01FF02}),
 \strong{line}: linezolid (\emph{J01XX08}),
 \strong{mero}: meropenem (\emph{J01DH02}),
 \strong{mezl}: mezlocillin (\emph{J01CA10}),
 \strong{mino}: minocycline (\emph{J01AA08}),
 \strong{moxi}: moxifloxacin (\emph{J01MA14}),
 \strong{nali}: nalidixic acid (\emph{J01MB02}),
 \strong{neom}: neomycin (\emph{J01GB05}),
 \strong{neti}: netilmicin (\emph{J01GB07}),
 \strong{nitr}: nitrofurantoin (\emph{J01XE01}),
 \strong{norf}: norfloxacin (\emph{J01MA06}),
 \strong{novo}: novobiocin (an ATCvet code: \emph{QJ01XX95}),
 \strong{oflo}: ofloxacin (\emph{J01MA01}),
 \strong{peni}: penicillins, combinations with other antibacterials (\emph{J01RA01}),
 \strong{pita}: piperacillin and beta-lactamase inhibitor (\emph{J01CR05}),
 \strong{poly}: polymyxin B (\emph{J01XB02}),
 \strong{pris}: pristinamycin (\emph{J01FG01}),
 \strong{qida}: quinupristin/dalfopristin (\emph{J01FG02}),
 \strong{rifa}: rifampicin (\emph{J04AB02}),
 \strong{roxi}: roxithromycin (\emph{J01FA06}),
 \strong{siso}: sisomicin (\emph{J01GB08}),
 \strong{teic}: teicoplanin (\emph{J01XA02}),
 \strong{tetr}: tetracycline (\emph{J01AA07}),
 \strong{tica}: ticarcillin (\emph{J01CA13}),
 \strong{tige}: tigecycline (\emph{J01AA12}),
 \strong{tobr}: tobramycin (\emph{J01GB01}),
 \strong{trim}: trimethoprim (\emph{J01EA01}),
 \strong{trsu}: sulfamethoxazole and trimethoprim (\emph{J01EE01}),
 \strong{vanc}: vancomycin (\emph{J01XA01}).
}

\examples{
a <- EUCAST_rules(septic_patients)
a <- data.frame(mo = 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
}
\keyword{eucast}
\keyword{interpretive}
\keyword{reading}
\keyword{resistance}