% Generated by roxygen2: do not edit by hand % Please edit documentation in R/eucast_rules.R \name{eucast_rules} \alias{eucast_rules} \alias{EUCAST_rules} \alias{interpretive_reading} \title{EUCAST rules} \source{ \itemize{ \item{ EUCAST Expert Rules. Version 2.0, 2012. \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} } \item{ EUCAST Expert Rules, Intrinsic Resistance and Exceptional Phenotypes Tables. Version 3.1, 2016. \cr \url{http://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Expert_Rules/Expert_rules_intrinsic_exceptional_V3.1.pdf} } \item{ EUCAST Breakpoint tables for interpretation of MICs and zone diameters. Version 8.1, 2018. \cr \url{http://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Breakpoint_tables/v_8.1_Breakpoint_Tables.xlsx} } } } \usage{ eucast_rules(tbl, col_mo = NULL, info = TRUE, rules = c("breakpoints", "expert", "other", "all"), verbose = FALSE, amcl = guess_ab(), amik = guess_ab(), amox = guess_ab(), ampi = guess_ab(), azit = guess_ab(), azlo = guess_ab(), aztr = guess_ab(), cefa = guess_ab(), cfep = guess_ab(), cfot = guess_ab(), cfox = guess_ab(), cfra = guess_ab(), cfta = guess_ab(), cftr = guess_ab(), cfur = guess_ab(), chlo = guess_ab(), cipr = guess_ab(), clar = guess_ab(), clin = guess_ab(), clox = guess_ab(), coli = guess_ab(), czol = guess_ab(), dapt = guess_ab(), doxy = guess_ab(), erta = guess_ab(), eryt = guess_ab(), fosf = guess_ab(), fusi = guess_ab(), gent = guess_ab(), imip = guess_ab(), kana = guess_ab(), levo = guess_ab(), linc = guess_ab(), line = guess_ab(), mero = guess_ab(), mezl = guess_ab(), mino = guess_ab(), moxi = guess_ab(), nali = guess_ab(), neom = guess_ab(), neti = guess_ab(), nitr = guess_ab(), norf = guess_ab(), novo = guess_ab(), oflo = guess_ab(), oxac = guess_ab(), peni = guess_ab(), pipe = guess_ab(), pita = guess_ab(), poly = guess_ab(), pris = guess_ab(), qida = guess_ab(), rifa = guess_ab(), roxi = guess_ab(), siso = guess_ab(), teic = guess_ab(), tetr = guess_ab(), tica = guess_ab(), tige = guess_ab(), tobr = guess_ab(), trim = guess_ab(), trsu = guess_ab(), vanc = guess_ab()) EUCAST_rules(...) interpretive_reading(...) } \arguments{ \item{tbl}{table with antibiotic columns, like e.g. \code{amox} and \code{amcl}} \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}}.} \item{info}{print progress} \item{rules}{a character vector that specifies which rules should be applied - one or more of \code{c("breakpoints", "expert", "other", "all")}} \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} \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} \item{...}{parameters that are passed on to \code{eucast_rules}} } \value{ The input of \code{tbl}, possibly with edited values of antibiotics. Or, if \code{verbose = TRUE}, a \code{data.frame} with verbose info. } \description{ 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. } \section{Antibiotics}{ To define antibiotics column names, leave as it is to determine it automatically with \code{\link{guess_ab}} or 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. Abbrevations of the column containing antibiotics in the form: \strong{abbreviation}: generic name (\emph{ATC code}) \strong{amcl}: amoxicillin+clavulanic acid (\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 (\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}: penicillin (\emph{J01RA01}), \strong{pipe}: piperacillin (\emph{J01CA12}), \strong{pita}: piperacillin+tazobactam (\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}). } \section{Read more on our website!}{ \if{html}{\figure{logo.png}{options: height=40px style=margin-bottom:5px} \cr} On our website \url{https://msberends.gitlab.io/AMR} you can find \href{https://msberends.gitlab.io/AMR/articles/AMR.html}{a omprehensive tutorial} about how to conduct AMR analysis and find \href{https://msberends.gitlab.io/AMR/reference}{the complete documentation of all functions}, which reads a lot easier than in R. } \examples{ a <- eucast_rules(septic_patients) a <- data.frame(mo = c("Staphylococcus aureus", "Enterococcus faecalis", "Escherichia coli", "Klebsiella pneumoniae", "Pseudomonas aeruginosa"), vanc = "-", # Vancomycin amox = "-", # Amoxicillin coli = "-", # Colistin cfta = "-", # Ceftazidime cfur = "-", # Cefuroxime peni = "S", # Benzylpenicillin cfox = "S", # Cefoxitin stringsAsFactors = FALSE) a # mo vanc amox coli cfta cfur peni cfox # 1 Staphylococcus aureus - - - - - S S # 2 Enterococcus faecalis - - - - - S S # 3 Escherichia coli - - - - - S S # 4 Klebsiella pneumoniae - - - - - S S # 5 Pseudomonas aeruginosa - - - - - S S b <- eucast_rules(a, "mo") # 18 results are forced as R or S b # mo vanc amox coli cfta cfur peni cfox # 1 Staphylococcus aureus - S R R S S S # 2 Enterococcus faecalis - - R R R S R # 3 Escherichia coli R - - - - R S # 4 Klebsiella pneumoniae R R - - - R S # 5 Pseudomonas aeruginosa R R - - R R R } \keyword{eucast} \keyword{interpretive} \keyword{reading} \keyword{resistance}