mirror of https://github.com/msberends/AMR.git
55 lines
2.6 KiB
R
55 lines
2.6 KiB
R
% Generated by roxygen2: do not edit by hand
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% Please edit documentation in R/EUCAST.R
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\name{EUCAST}
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\alias{EUCAST}
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\alias{EUCAST_rules}
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\alias{interpretive_reading}
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\title{EUCAST expert rules}
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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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}
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\usage{
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EUCAST_rules(tbl, col_bactcode = "bacteriecode", info = TRUE,
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amcl = "amcl", amik = "amik", amox = "amox", ampi = "ampi",
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azit = "azit", aztr = "aztr", cefa = "cefa", cfra = "cfra",
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cfep = "cfep", cfot = "cfot", cfox = "cfox", cfta = "cfta",
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cftr = "cftr", cfur = "cfur", chlo = "chlo", cipr = "cipr",
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clar = "clar", clin = "clin", clox = "clox", coli = "coli",
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czol = "czol", dapt = "dapt", doxy = "doxy", erta = "erta",
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eryt = "eryt", fosf = "fosf", fusi = "fusi", gent = "gent",
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imip = "imip", kana = "kana", levo = "levo", linc = "linc",
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line = "line", mero = "mero", mino = "mino", moxi = "moxi",
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nali = "nali", neom = "neom", neti = "neti", nitr = "nitr",
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novo = "novo", norf = "norf", oflo = "oflo", peni = "peni",
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pita = "pita", poly = "poly", qida = "qida", rifa = "rifa",
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roxi = "roxi", siso = "siso", teic = "teic", tetr = "tetr",
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tica = "tica", tige = "tige", tobr = "tobr", trim = "trim",
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trsu = "trsu", vanc = "vanc")
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interpretive_reading(...)
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}
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\arguments{
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\item{tbl}{table with antibiotic columns, like e.g. \code{amox} and \code{amcl}}
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\item{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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\item{info}{print progress}
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\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.}
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\item{...}{parameters that are passed on to \code{EUCAST_rules}}
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}
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\description{
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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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}
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\examples{
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\dontrun{
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tbl <- interpretive_reading(tbl)
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}
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}
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