mirror of
https://github.com/msberends/AMR.git
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261 lines
10 KiB
R
261 lines
10 KiB
R
% Generated by roxygen2: do not edit by hand
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% Please edit documentation in R/mdro.R
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\name{mdro}
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\alias{mdro}
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\alias{brmo}
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\alias{mrgn}
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\alias{eucast_exceptional_phenotypes}
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\title{Determine multidrug-resistant organisms (MDRO)}
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\usage{
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mdro(tbl, country = NULL, col_mo = NULL, info = TRUE,
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amcl = guess_ab(), amik = guess_ab(), amox = guess_ab(),
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ampi = guess_ab(), azit = guess_ab(), aztr = guess_ab(),
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cefa = guess_ab(), cfra = guess_ab(), cfep = guess_ab(),
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cfot = guess_ab(), cfox = guess_ab(), cfta = guess_ab(),
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cftr = guess_ab(), cfur = guess_ab(), chlo = guess_ab(),
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cipr = guess_ab(), clar = guess_ab(), clin = guess_ab(),
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clox = guess_ab(), coli = guess_ab(), czol = guess_ab(),
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dapt = guess_ab(), doxy = guess_ab(), erta = guess_ab(),
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eryt = guess_ab(), fosf = guess_ab(), fusi = guess_ab(),
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gent = guess_ab(), imip = guess_ab(), kana = guess_ab(),
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levo = guess_ab(), linc = guess_ab(), line = guess_ab(),
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mero = guess_ab(), metr = guess_ab(), mino = guess_ab(),
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moxi = guess_ab(), nali = guess_ab(), neom = guess_ab(),
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neti = guess_ab(), nitr = guess_ab(), novo = guess_ab(),
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norf = guess_ab(), oflo = guess_ab(), peni = guess_ab(),
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pipe = guess_ab(), pita = guess_ab(), poly = guess_ab(),
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qida = guess_ab(), rifa = guess_ab(), roxi = guess_ab(),
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siso = guess_ab(), teic = guess_ab(), tetr = guess_ab(),
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tica = guess_ab(), tige = guess_ab(), tobr = guess_ab(),
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trim = guess_ab(), trsu = guess_ab(), vanc = guess_ab())
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brmo(..., country = "nl")
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mrgn(tbl, country = "de", ...)
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eucast_exceptional_phenotypes(tbl, country = "EUCAST", ...)
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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{country}{country code to determine guidelines. EUCAST rules will be used when left empty, see Details. Should be or a code from the \href{https://en.wikipedia.org/wiki/ISO_3166-1_alpha-2#Officially_assigned_code_elements}{list of ISO 3166-1 alpha-2 country codes}. Case-insensitive. Currently supported are \code{de} (Germany) and \code{nl} (the Netherlands).}
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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{amcl}{column name of an antibiotic, see Antibiotics}
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\item{amik}{column name of an antibiotic, see Antibiotics}
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\item{amox}{column name of an antibiotic, see Antibiotics}
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\item{ampi}{column name of an antibiotic, see Antibiotics}
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\item{azit}{column name of an antibiotic, see Antibiotics}
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\item{aztr}{column name of an antibiotic, see Antibiotics}
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\item{cefa}{column name of an antibiotic, see Antibiotics}
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\item{cfra}{column name of an antibiotic, see Antibiotics}
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\item{cfep}{column name of an antibiotic, see Antibiotics}
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\item{cfot}{column name of an antibiotic, see Antibiotics}
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\item{cfox}{column name of an antibiotic, see Antibiotics}
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\item{cfta}{column name of an antibiotic, see Antibiotics}
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\item{cftr}{column name of an antibiotic, see Antibiotics}
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\item{cfur}{column name of an antibiotic, see Antibiotics}
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\item{chlo}{column name of an antibiotic, see Antibiotics}
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\item{cipr}{column name of an antibiotic, see Antibiotics}
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\item{clar}{column name of an antibiotic, see Antibiotics}
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\item{clin}{column name of an antibiotic, see Antibiotics}
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\item{clox}{column name of an antibiotic, see Antibiotics}
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\item{coli}{column name of an antibiotic, see Antibiotics}
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\item{czol}{column name of an antibiotic, see Antibiotics}
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\item{dapt}{column name of an antibiotic, see Antibiotics}
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\item{doxy}{column name of an antibiotic, see Antibiotics}
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\item{erta}{column name of an antibiotic, see Antibiotics}
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\item{eryt}{column name of an antibiotic, see Antibiotics}
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\item{fosf}{column name of an antibiotic, see Antibiotics}
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\item{fusi}{column name of an antibiotic, see Antibiotics}
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\item{gent}{column name of an antibiotic, see Antibiotics}
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\item{imip}{column name of an antibiotic, see Antibiotics}
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\item{kana}{column name of an antibiotic, see Antibiotics}
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\item{levo}{column name of an antibiotic, see Antibiotics}
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\item{linc}{column name of an antibiotic, see Antibiotics}
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\item{line}{column name of an antibiotic, see Antibiotics}
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\item{mero}{column name of an antibiotic, see Antibiotics}
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\item{metr}{column name of an antibiotic, see Antibiotics}
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\item{mino}{column name of an antibiotic, see Antibiotics}
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\item{moxi}{column name of an antibiotic, see Antibiotics}
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\item{nali}{column name of an antibiotic, see Antibiotics}
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\item{neom}{column name of an antibiotic, see Antibiotics}
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\item{neti}{column name of an antibiotic, see Antibiotics}
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\item{nitr}{column name of an antibiotic, see Antibiotics}
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\item{novo}{column name of an antibiotic, see Antibiotics}
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\item{norf}{column name of an antibiotic, see Antibiotics}
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\item{oflo}{column name of an antibiotic, see Antibiotics}
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\item{peni}{column name of an antibiotic, see Antibiotics}
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\item{pipe}{column name of an antibiotic, see Antibiotics}
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\item{pita}{column name of an antibiotic, see Antibiotics}
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\item{poly}{column name of an antibiotic, see Antibiotics}
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\item{qida}{column name of an antibiotic, see Antibiotics}
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\item{rifa}{column name of an antibiotic, see Antibiotics}
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\item{roxi}{column name of an antibiotic, see Antibiotics}
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\item{siso}{column name of an antibiotic, see Antibiotics}
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\item{teic}{column name of an antibiotic, see Antibiotics}
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\item{tetr}{column name of an antibiotic, see Antibiotics}
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\item{tica}{column name of an antibiotic, see Antibiotics}
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\item{tige}{column name of an antibiotic, see Antibiotics}
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\item{tobr}{column name of an antibiotic, see Antibiotics}
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\item{trim}{column name of an antibiotic, see Antibiotics}
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\item{trsu}{column name of an antibiotic, see Antibiotics}
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\item{vanc}{column name of an antibiotic, see Antibiotics}
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\item{...}{parameters that are passed on to methods}
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}
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\value{
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Ordered factor with levels \code{Negative < Positive, unconfirmed < Positive}.
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}
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\description{
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Determine which isolates are multidrug-resistant organisms (MDRO) according to country-specific guidelines.
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}
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\details{
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When \code{country} will be left blank, guidelines will be taken from EUCAST Expert Rules Version 3.1 "Intrinsic Resistance and Exceptional Phenotypes Tables" (\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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\section{Antibiotics}{
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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.
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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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\section{Read more on our website!}{
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\if{html}{\figure{logo.png}{options: height=40px style=margin-bottom:5px} \cr}
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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.
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}
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\examples{
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library(dplyr)
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septic_patients \%>\%
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mutate(EUCAST = mdro(.),
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BRMO = brmo(.))
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}
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