mirror of https://github.com/msberends/AMR.git
179 lines
8.3 KiB
R
179 lines
8.3 KiB
R
% Generated by roxygen2: do not edit by hand
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% Please edit documentation in R/eucast_rules.R
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\name{eucast_rules}
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\alias{eucast_rules}
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\alias{EUCAST_rules}
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\alias{interpretive_reading}
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\title{EUCAST rules}
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\source{
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\itemize{
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\item{
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EUCAST Expert Rules. Version 2.0, 2012. \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}
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}
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\item{
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EUCAST Expert Rules, Intrinsic Resistance and Exceptional Phenotypes Tables. Version 3.1, 2016. \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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\item{
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EUCAST Breakpoint tables for interpretation of MICs and zone diameters. Version 8.1, 2018. \cr
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\url{http://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Breakpoint_tables/v_8.1_Breakpoint_Tables.xlsx}
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}
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}
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}
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\usage{
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eucast_rules(tbl, col_mo = NULL, info = TRUE,
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rules = c("breakpoints", "expert", "other", "all"), verbose = FALSE,
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amcl = "amcl", amik = "amik", amox = "amox", ampi = "ampi",
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azit = "azit", azlo = "azlo", aztr = "aztr", cefa = "cefa",
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cfep = "cfep", cfot = "cfot", cfox = "cfox", cfra = "cfra",
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cfta = "cfta", cftr = "cftr", cfur = "cfur", chlo = "chlo",
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cipr = "cipr", clar = "clar", clin = "clin", clox = "clox",
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coli = "coli", czol = "czol", dapt = "dapt", doxy = "doxy",
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erta = "erta", eryt = "eryt", fosf = "fosf", fusi = "fusi",
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gent = "gent", imip = "imip", kana = "kana", levo = "levo",
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linc = "linc", line = "line", mero = "mero", mezl = "mezl",
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mino = "mino", moxi = "moxi", nali = "nali", neom = "neom",
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neti = "neti", nitr = "nitr", norf = "norf", novo = "novo",
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oflo = "oflo", oxac = "oxac", peni = "peni", pipe = "pipe",
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pita = "pita", poly = "poly", pris = "pris", qida = "qida",
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rifa = "rifa", roxi = "roxi", siso = "siso", teic = "teic",
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tetr = "tetr", tica = "tica", tige = "tige", tobr = "tobr",
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trim = "trim", trsu = "trsu", vanc = "vanc")
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EUCAST_rules(...)
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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_mo}{column name of the unique IDs of the microorganisms (see \code{\link{mo}}), defaults to the first column of class \code{mo}. Values will be coerced using \code{\link{as.mo}}.}
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\item{info}{print progress}
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\item{rules}{a character vector that specifies which rules should be applied - one or more of \code{c("breakpoints", "expert", "other", "all")}}
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\item{verbose}{a logical to indicate whether extensive info should be returned as a \code{data.frame} with info about which rows and columns are effected}
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\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, oxac, peni, pipe, pita, poly, pris, qida, rifa, roxi, siso, teic, tetr, tica, tige, tobr, trim, trsu, vanc}{column name of an antibiotic, see Antibiotics}
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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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The input of \code{tbl}, possibly with edited values of antibiotics. Or, if \code{verbose = TRUE}, a \code{data.frame} with verbose info.
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}
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\description{
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Apply susceptibility rules as defined by the European Committee on Antimicrobial Susceptibility Testing (EUCAST, \url{http://eucast.org}), see \emph{Source}. This includes (1) expert rules, (2) intrinsic resistance and (3) inferred resistance as defined in their breakpoint tables.
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}
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\section{Antibiotics}{
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To define antibiotics column names, input a text (case-insensitive) or use \code{NULL} to skip a column (e.g. \code{tica = NULL}). Non-existing columns will anyway be skipped with a warning.
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Abbrevations of the column containing antibiotics in the form: \strong{abbreviation}: generic name (\emph{ATC code})
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\strong{amcl}: amoxicillin+clavulanic acid (\emph{J01CR02}),
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\strong{amik}: amikacin (\emph{J01GB06}),
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\strong{amox}: amoxicillin (\emph{J01CA04}),
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\strong{ampi}: ampicillin (\emph{J01CA01}),
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\strong{azit}: azithromycin (\emph{J01FA10}),
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\strong{azlo}: azlocillin (\emph{J01CA09}),
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\strong{aztr}: aztreonam (\emph{J01DF01}),
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\strong{cefa}: cefaloridine (\emph{J01DB02}),
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\strong{cfep}: cefepime (\emph{J01DE01}),
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\strong{cfot}: cefotaxime (\emph{J01DD01}),
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\strong{cfox}: cefoxitin (\emph{J01DC01}),
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\strong{cfra}: cefradine (\emph{J01DB09}),
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\strong{cfta}: ceftazidime (\emph{J01DD02}),
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\strong{cftr}: ceftriaxone (\emph{J01DD04}),
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\strong{cfur}: cefuroxime (\emph{J01DC02}),
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\strong{chlo}: chloramphenicol (\emph{J01BA01}),
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\strong{cipr}: ciprofloxacin (\emph{J01MA02}),
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\strong{clar}: clarithromycin (\emph{J01FA09}),
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\strong{clin}: clindamycin (\emph{J01FF01}),
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\strong{clox}: flucloxacillin (\emph{J01CF05}),
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\strong{coli}: colistin (\emph{J01XB01}),
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\strong{czol}: cefazolin (\emph{J01DB04}),
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\strong{dapt}: daptomycin (\emph{J01XX09}),
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\strong{doxy}: doxycycline (\emph{J01AA02}),
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\strong{erta}: ertapenem (\emph{J01DH03}),
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\strong{eryt}: erythromycin (\emph{J01FA01}),
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\strong{fosf}: fosfomycin (\emph{J01XX01}),
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\strong{fusi}: fusidic acid (\emph{J01XC01}),
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\strong{gent}: gentamicin (\emph{J01GB03}),
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\strong{imip}: imipenem (\emph{J01DH51}),
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\strong{kana}: kanamycin (\emph{J01GB04}),
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\strong{levo}: levofloxacin (\emph{J01MA12}),
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\strong{linc}: lincomycin (\emph{J01FF02}),
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\strong{line}: linezolid (\emph{J01XX08}),
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\strong{mero}: meropenem (\emph{J01DH02}),
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\strong{mezl}: mezlocillin (\emph{J01CA10}),
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\strong{mino}: minocycline (\emph{J01AA08}),
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\strong{moxi}: moxifloxacin (\emph{J01MA14}),
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\strong{nali}: nalidixic acid (\emph{J01MB02}),
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\strong{neom}: neomycin (\emph{J01GB05}),
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\strong{neti}: netilmicin (\emph{J01GB07}),
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\strong{nitr}: nitrofurantoin (\emph{J01XE01}),
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\strong{norf}: norfloxacin (\emph{J01MA06}),
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\strong{novo}: novobiocin (an ATCvet code: \emph{QJ01XX95}),
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\strong{oflo}: ofloxacin (\emph{J01MA01}),
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\strong{peni}: penicillin (\emph{J01RA01}),
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\strong{pipe}: piperacillin (\emph{J01CA12}),
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\strong{pita}: piperacillin+tazobactam (\emph{J01CR05}),
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\strong{poly}: polymyxin B (\emph{J01XB02}),
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\strong{pris}: pristinamycin (\emph{J01FG01}),
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\strong{qida}: quinupristin/dalfopristin (\emph{J01FG02}),
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\strong{rifa}: rifampicin (\emph{J04AB02}),
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\strong{roxi}: roxithromycin (\emph{J01FA06}),
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\strong{siso}: sisomicin (\emph{J01GB08}),
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\strong{teic}: teicoplanin (\emph{J01XA02}),
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\strong{tetr}: tetracycline (\emph{J01AA07}),
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\strong{tica}: ticarcillin (\emph{J01CA13}),
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\strong{tige}: tigecycline (\emph{J01AA12}),
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\strong{tobr}: tobramycin (\emph{J01GB01}),
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\strong{trim}: trimethoprim (\emph{J01EA01}),
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\strong{trsu}: sulfamethoxazole and trimethoprim (\emph{J01EE01}),
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\strong{vanc}: vancomycin (\emph{J01XA01}).
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}
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\examples{
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a <- eucast_rules(septic_patients)
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a <- data.frame(mo = c("Staphylococcus aureus",
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"Enterococcus faecalis",
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"Escherichia coli",
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"Klebsiella pneumoniae",
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"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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peni = "S", # Benzylpenicillin
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cfox = "S", # Cefoxitin
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stringsAsFactors = FALSE)
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a
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# mo vanc amox coli cfta cfur peni cfox
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# 1 Staphylococcus aureus - - - - - S S
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# 2 Enterococcus faecalis - - - - - S S
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# 3 Escherichia coli - - - - - S S
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# 4 Klebsiella pneumoniae - - - - - S S
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# 5 Pseudomonas aeruginosa - - - - - S S
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b <- eucast_rules(a, "mo") # 18 results are forced as R or S
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b
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# mo vanc amox coli cfta cfur peni cfox
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# 1 Staphylococcus aureus - S R R S S S
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# 2 Enterococcus faecalis - - R R R S R
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# 3 Escherichia coli R - - - - R S
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# 4 Klebsiella pneumoniae R R - - - R S
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# 5 Pseudomonas aeruginosa R R - - R R R
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}
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\keyword{eucast}
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\keyword{interpretive}
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\keyword{reading}
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\keyword{resistance}
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