mirror of
https://github.com/msberends/AMR.git
synced 2024-12-25 21:26:11 +01:00
70 lines
3.3 KiB
R
Executable File
70 lines
3.3 KiB
R
Executable File
% Generated by roxygen2: do not edit by hand
|
|
% Please edit documentation in R/eucast.R
|
|
\name{EUCAST_rules}
|
|
\alias{EUCAST_rules}
|
|
\alias{interpretive_reading}
|
|
\title{EUCAST expert rules}
|
|
\source{
|
|
EUCAST Expert Rules Version 2.0: \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} \cr
|
|
\cr
|
|
EUCAST Expert Rules Version 3.1 (Intrinsic Resistance and Exceptional Phenotypes Tables): \cr
|
|
\url{http://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Expert_Rules/Expert_rules_intrinsic_exceptional_V3.1.pdf}
|
|
}
|
|
\usage{
|
|
EUCAST_rules(tbl, col_bactid = "bactid", info = TRUE, amcl = "amcl",
|
|
amik = "amik", amox = "amox", ampi = "ampi", azit = "azit",
|
|
aztr = "aztr", cefa = "cefa", cfra = "cfra", cfep = "cfep",
|
|
cfot = "cfot", cfox = "cfox", cfta = "cfta", cftr = "cftr",
|
|
cfur = "cfur", chlo = "chlo", cipr = "cipr", clar = "clar",
|
|
clin = "clin", clox = "clox", coli = "coli", czol = "czol",
|
|
dapt = "dapt", doxy = "doxy", erta = "erta", eryt = "eryt",
|
|
fosf = "fosf", fusi = "fusi", gent = "gent", imip = "imip",
|
|
kana = "kana", levo = "levo", linc = "linc", line = "line",
|
|
mero = "mero", mino = "mino", moxi = "moxi", nali = "nali",
|
|
neom = "neom", neti = "neti", nitr = "nitr", novo = "novo",
|
|
norf = "norf", oflo = "oflo", peni = "peni", pita = "pita",
|
|
poly = "poly", qida = "qida", rifa = "rifa", roxi = "roxi",
|
|
siso = "siso", teic = "teic", tetr = "tetr", tica = "tica",
|
|
tige = "tige", tobr = "tobr", trim = "trim", trsu = "trsu",
|
|
vanc = "vanc")
|
|
|
|
interpretive_reading(...)
|
|
}
|
|
\arguments{
|
|
\item{tbl}{table with antibiotic columns, like e.g. \code{amox} and \code{amcl}}
|
|
|
|
\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}}}
|
|
|
|
\item{info}{print progress}
|
|
|
|
\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.}
|
|
|
|
\item{...}{parameters that are passed on to \code{EUCAST_rules}}
|
|
}
|
|
\value{
|
|
table with edited variables of antibiotics.
|
|
}
|
|
\description{
|
|
Apply expert rules (like intrinsic resistance), as defined by the European Committee on Antimicrobial Susceptibility Testing (EUCAST, \url{http://eucast.org}), see \emph{Source}.
|
|
}
|
|
\examples{
|
|
a <- EUCAST_rules(septic_patients)
|
|
a <- data.frame(bactid = c("STAAUR", # Staphylococcus aureus
|
|
"ENCFAE", # Enterococcus faecalis
|
|
"ESCCOL", # Escherichia coli
|
|
"KLEPNE", # Klebsiella pneumoniae
|
|
"PSEAER"), # Pseudomonas aeruginosa
|
|
vanc = "-", # Vancomycin
|
|
amox = "-", # Amoxicillin
|
|
coli = "-", # Colistin
|
|
cfta = "-", # Ceftazidime
|
|
cfur = "-", # Cefuroxime
|
|
stringsAsFactors = FALSE)
|
|
a
|
|
|
|
b <- EUCAST_rules(a)
|
|
b
|
|
}
|