mirror of https://github.com/msberends/AMR.git
69 lines
3.3 KiB
R
69 lines
3.3 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_rules}
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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 (Intrinsic Resistance and Exceptional Phenotypes Tables): \cr
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\url{http://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Expert_Rules/Expert_rules_intrinsic_exceptional_V3.1.pdf}
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}
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\usage{
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EUCAST_rules(tbl, col_bactid = "bactid", info = TRUE, amcl = "amcl",
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amik = "amik", amox = "amox", ampi = "ampi", azit = "azit",
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aztr = "aztr", cefa = "cefa", cfra = "cfra", cfep = "cfep",
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cfot = "cfot", cfox = "cfox", cfta = "cfta", cftr = "cftr",
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cfur = "cfur", chlo = "chlo", cipr = "cipr", clar = "clar",
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clin = "clin", clox = "clox", coli = "coli", czol = "czol",
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dapt = "dapt", doxy = "doxy", erta = "erta", eryt = "eryt",
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fosf = "fosf", fusi = "fusi", gent = "gent", imip = "imip",
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kana = "kana", levo = "levo", linc = "linc", line = "line",
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mero = "mero", mino = "mino", moxi = "moxi", nali = "nali",
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neom = "neom", neti = "neti", nitr = "nitr", novo = "novo",
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norf = "norf", oflo = "oflo", peni = "peni", pita = "pita",
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poly = "poly", qida = "qida", rifa = "rifa", roxi = "roxi",
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siso = "siso", teic = "teic", tetr = "tetr", tica = "tica",
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tige = "tige", tobr = "tobr", trim = "trim", trsu = "trsu",
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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_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}}}
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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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\value{
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table with edited variables of antibiotics.
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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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a <- data.frame(bactid = c("STAAUR", # Staphylococcus aureus
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"ENCFAE", # Enterococcus faecalis
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"ESCCOL", # Escherichia coli
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"KLEPNE", # Klebsiella pneumoniae
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"PSEAER"), # Pseudomonas aeruginosa
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vanc = "-", # Vancomycin
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amox = "-", # Amoxicillin
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coli = "-", # Colistin
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cfta = "-", # Ceftazidime
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cfur = "-", # Cefuroxime
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stringsAsFactors = FALSE)
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a
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b <- EUCAST_rules(a)
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b
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}
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