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: \cr
  \url{http://www.eucast.org/expert_rules_and_intrinsic_resistance}
}
\usage{
EUCAST_rules(tbl, col_bactcode, 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")

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

\item{col_bactcode}{column name of the bacteria ID in \code{tbl} - should also be present in \code{bactlist$bactid}, see \code{\link{bactlist}}.}

\item{info}{print progress}

\item{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.}

\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}.
}
\examples{
a <- data.frame(bactid = c("STAAUR", "ESCCOL", "KLEPNE", "PSEAER"), 
                vanc = "-",
                amox = "-",
                coli = "-",
                cfta = "-",
                cfur = "-",
                stringsAsFactors = FALSE)
a

b <- EUCAST_rules(a, "bactid")
b
}