mirror of
https://github.com/msberends/AMR.git
synced 2024-12-26 06:46:11 +01:00
190 lines
9.1 KiB
R
190 lines
9.1 KiB
R
% 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}
|