AMR/man/mdro.Rd

% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/mdro.R
\name{mdro}
\alias{mdro}
\alias{brmo}
\alias{mrgn}
\alias{eucast_exceptional_phenotypes}
\title{Determine multidrug-resistant organisms (MDRO)}
\usage{
mdro(tbl, country = NULL, col_mo = NULL, info = TRUE,
  amcl = guess_ab_col(), amik = guess_ab_col(),
  amox = guess_ab_col(), ampi = guess_ab_col(),
  azit = guess_ab_col(), aztr = guess_ab_col(),
  cefa = guess_ab_col(), cfra = guess_ab_col(),
  cfep = guess_ab_col(), cfot = guess_ab_col(),
  cfox = guess_ab_col(), cfta = guess_ab_col(),
  cftr = guess_ab_col(), cfur = guess_ab_col(),
  chlo = guess_ab_col(), cipr = guess_ab_col(),
  clar = guess_ab_col(), clin = guess_ab_col(),
  clox = guess_ab_col(), coli = guess_ab_col(),
  czol = guess_ab_col(), dapt = guess_ab_col(),
  doxy = guess_ab_col(), erta = guess_ab_col(),
  eryt = guess_ab_col(), fosf = guess_ab_col(),
  fusi = guess_ab_col(), gent = guess_ab_col(),
  imip = guess_ab_col(), kana = guess_ab_col(),
  levo = guess_ab_col(), linc = guess_ab_col(),
  line = guess_ab_col(), mero = guess_ab_col(),
  metr = guess_ab_col(), mino = guess_ab_col(),
  moxi = guess_ab_col(), nali = guess_ab_col(),
  neom = guess_ab_col(), neti = guess_ab_col(),
  nitr = guess_ab_col(), novo = guess_ab_col(),
  norf = guess_ab_col(), oflo = guess_ab_col(),
  peni = guess_ab_col(), pipe = guess_ab_col(),
  pita = guess_ab_col(), poly = guess_ab_col(),
  qida = guess_ab_col(), rifa = guess_ab_col(),
  roxi = guess_ab_col(), siso = guess_ab_col(),
  teic = guess_ab_col(), tetr = guess_ab_col(),
  tica = guess_ab_col(), tige = guess_ab_col(),
  tobr = guess_ab_col(), trim = guess_ab_col(),
  trsu = guess_ab_col(), vanc = guess_ab_col())

brmo(..., country = "nl")

mrgn(tbl, country = "de", ...)

eucast_exceptional_phenotypes(tbl, country = "EUCAST", ...)
}
\arguments{
\item{tbl}{table with antibiotic columns, like e.g. \code{amox} and \code{amcl}}

\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).}

\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{amcl}{column name of an antibiotic, see Antibiotics}

\item{amik}{column name of an antibiotic, see Antibiotics}

\item{amox}{column name of an antibiotic, see Antibiotics}

\item{ampi}{column name of an antibiotic, see Antibiotics}

\item{azit}{column name of an antibiotic, see Antibiotics}

\item{aztr}{column name of an antibiotic, see Antibiotics}

\item{cefa}{column name of an antibiotic, see Antibiotics}

\item{cfra}{column name of an antibiotic, see Antibiotics}

\item{cfep}{column name of an antibiotic, see Antibiotics}

\item{cfot}{column name of an antibiotic, see Antibiotics}

\item{cfox}{column name of an antibiotic, see Antibiotics}

\item{cfta}{column name of an antibiotic, see Antibiotics}

\item{cftr}{column name of an antibiotic, see Antibiotics}

\item{cfur}{column name of an antibiotic, see Antibiotics}

\item{chlo}{column name of an antibiotic, see Antibiotics}

\item{cipr}{column name of an antibiotic, see Antibiotics}

\item{clar}{column name of an antibiotic, see Antibiotics}

\item{clin}{column name of an antibiotic, see Antibiotics}

\item{clox}{column name of an antibiotic, see Antibiotics}

\item{coli}{column name of an antibiotic, see Antibiotics}

\item{czol}{column name of an antibiotic, see Antibiotics}

\item{dapt}{column name of an antibiotic, see Antibiotics}

\item{doxy}{column name of an antibiotic, see Antibiotics}

\item{erta}{column name of an antibiotic, see Antibiotics}

\item{eryt}{column name of an antibiotic, see Antibiotics}

\item{fosf}{column name of an antibiotic, see Antibiotics}

\item{fusi}{column name of an antibiotic, see Antibiotics}

\item{gent}{column name of an antibiotic, see Antibiotics}

\item{imip}{column name of an antibiotic, see Antibiotics}

\item{kana}{column name of an antibiotic, see Antibiotics}

\item{levo}{column name of an antibiotic, see Antibiotics}

\item{linc}{column name of an antibiotic, see Antibiotics}

\item{line}{column name of an antibiotic, see Antibiotics}

\item{mero}{column name of an antibiotic, see Antibiotics}

\item{metr}{column name of an antibiotic, see Antibiotics}

\item{mino}{column name of an antibiotic, see Antibiotics}

\item{moxi}{column name of an antibiotic, see Antibiotics}

\item{nali}{column name of an antibiotic, see Antibiotics}

\item{neom}{column name of an antibiotic, see Antibiotics}

\item{neti}{column name of an antibiotic, see Antibiotics}

\item{nitr}{column name of an antibiotic, see Antibiotics}

\item{novo}{column name of an antibiotic, see Antibiotics}

\item{norf}{column name of an antibiotic, see Antibiotics}

\item{oflo}{column name of an antibiotic, see Antibiotics}

\item{peni}{column name of an antibiotic, see Antibiotics}

\item{pipe}{column name of an antibiotic, see Antibiotics}

\item{pita}{column name of an antibiotic, see Antibiotics}

\item{poly}{column name of an antibiotic, see Antibiotics}

\item{qida}{column name of an antibiotic, see Antibiotics}

\item{rifa}{column name of an antibiotic, see Antibiotics}

\item{roxi}{column name of an antibiotic, see Antibiotics}

\item{siso}{column name of an antibiotic, see Antibiotics}

\item{teic}{column name of an antibiotic, see Antibiotics}

\item{tetr}{column name of an antibiotic, see Antibiotics}

\item{tica}{column name of an antibiotic, see Antibiotics}

\item{tige}{column name of an antibiotic, see Antibiotics}

\item{tobr}{column name of an antibiotic, see Antibiotics}

\item{trim}{column name of an antibiotic, see Antibiotics}

\item{trsu}{column name of an antibiotic, see Antibiotics}

\item{vanc}{column name of an antibiotic, see Antibiotics}

\item{...}{parameters that are passed on to methods}
}
\value{
Ordered factor with levels \code{Negative < Positive, unconfirmed < Positive}.
}
\description{
Determine which isolates are multidrug-resistant organisms (MDRO) according to country-specific guidelines.
}
\details{
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}).
}
\section{Antibiotics}{

To define antibiotics column names, leave as it is to determine it automatically with \code{\link{guess_ab_col}} 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 (\href{https://www.whocc.no/atc_ddd_index/?code=J01CR02}{J01CR02}),
 \strong{amik}: amikacin (\href{https://www.whocc.no/atc_ddd_index/?code=J01GB06}{J01GB06}),
 \strong{amox}: amoxicillin (\href{https://www.whocc.no/atc_ddd_index/?code=J01CA04}{J01CA04}),
 \strong{ampi}: ampicillin (\href{https://www.whocc.no/atc_ddd_index/?code=J01CA01}{J01CA01}),
 \strong{azit}: azithromycin (\href{https://www.whocc.no/atc_ddd_index/?code=J01FA10}{J01FA10}),
 \strong{azlo}: azlocillin (\href{https://www.whocc.no/atc_ddd_index/?code=J01CA09}{J01CA09}),
 \strong{aztr}: aztreonam (\href{https://www.whocc.no/atc_ddd_index/?code=J01DF01}{J01DF01}),
 \strong{cefa}: cefaloridine (\href{https://www.whocc.no/atc_ddd_index/?code=J01DB02}{J01DB02}),
 \strong{cfep}: cefepime (\href{https://www.whocc.no/atc_ddd_index/?code=J01DE01}{J01DE01}),
 \strong{cfot}: cefotaxime (\href{https://www.whocc.no/atc_ddd_index/?code=J01DD01}{J01DD01}),
 \strong{cfox}: cefoxitin (\href{https://www.whocc.no/atc_ddd_index/?code=J01DC01}{J01DC01}),
 \strong{cfra}: cefradine (\href{https://www.whocc.no/atc_ddd_index/?code=J01DB09}{J01DB09}),
 \strong{cfta}: ceftazidime (\href{https://www.whocc.no/atc_ddd_index/?code=J01DD02}{J01DD02}),
 \strong{cftr}: ceftriaxone (\href{https://www.whocc.no/atc_ddd_index/?code=J01DD04}{J01DD04}),
 \strong{cfur}: cefuroxime (\href{https://www.whocc.no/atc_ddd_index/?code=J01DC02}{J01DC02}),
 \strong{chlo}: chloramphenicol (\href{https://www.whocc.no/atc_ddd_index/?code=J01BA01}{J01BA01}),
 \strong{cipr}: ciprofloxacin (\href{https://www.whocc.no/atc_ddd_index/?code=J01MA02}{J01MA02}),
 \strong{clar}: clarithromycin (\href{https://www.whocc.no/atc_ddd_index/?code=J01FA09}{J01FA09}),
 \strong{clin}: clindamycin (\href{https://www.whocc.no/atc_ddd_index/?code=J01FF01}{J01FF01}),
 \strong{clox}: flucloxacillin (\href{https://www.whocc.no/atc_ddd_index/?code=J01CF05}{J01CF05}),
 \strong{coli}: colistin (\href{https://www.whocc.no/atc_ddd_index/?code=J01XB01}{J01XB01}),
 \strong{czol}: cefazolin (\href{https://www.whocc.no/atc_ddd_index/?code=J01DB04}{J01DB04}),
 \strong{dapt}: daptomycin (\href{https://www.whocc.no/atc_ddd_index/?code=J01XX09}{J01XX09}),
 \strong{doxy}: doxycycline (\href{https://www.whocc.no/atc_ddd_index/?code=J01AA02}{J01AA02}),
 \strong{erta}: ertapenem (\href{https://www.whocc.no/atc_ddd_index/?code=J01DH03}{J01DH03}),
 \strong{eryt}: erythromycin (\href{https://www.whocc.no/atc_ddd_index/?code=J01FA01}{J01FA01}),
 \strong{fosf}: fosfomycin (\href{https://www.whocc.no/atc_ddd_index/?code=J01XX01}{J01XX01}),
 \strong{fusi}: fusidic acid (\href{https://www.whocc.no/atc_ddd_index/?code=J01XC01}{J01XC01}),
 \strong{gent}: gentamicin (\href{https://www.whocc.no/atc_ddd_index/?code=J01GB03}{J01GB03}),
 \strong{imip}: imipenem (\href{https://www.whocc.no/atc_ddd_index/?code=J01DH51}{J01DH51}),
 \strong{kana}: kanamycin (\href{https://www.whocc.no/atc_ddd_index/?code=J01GB04}{J01GB04}),
 \strong{levo}: levofloxacin (\href{https://www.whocc.no/atc_ddd_index/?code=J01MA12}{J01MA12}),
 \strong{linc}: lincomycin (\href{https://www.whocc.no/atc_ddd_index/?code=J01FF02}{J01FF02}),
 \strong{line}: linezolid (\href{https://www.whocc.no/atc_ddd_index/?code=J01XX08}{J01XX08}),
 \strong{mero}: meropenem (\href{https://www.whocc.no/atc_ddd_index/?code=J01DH02}{J01DH02}),
 \strong{mezl}: mezlocillin (\href{https://www.whocc.no/atc_ddd_index/?code=J01CA10}{J01CA10}),
 \strong{mino}: minocycline (\href{https://www.whocc.no/atc_ddd_index/?code=J01AA08}{J01AA08}),
 \strong{moxi}: moxifloxacin (\href{https://www.whocc.no/atc_ddd_index/?code=J01MA14}{J01MA14}),
 \strong{nali}: nalidixic acid (\href{https://www.whocc.no/atc_ddd_index/?code=J01MB02}{J01MB02}),
 \strong{neom}: neomycin (\href{https://www.whocc.no/atc_ddd_index/?code=J01GB05}{J01GB05}),
 \strong{neti}: netilmicin (\href{https://www.whocc.no/atc_ddd_index/?code=J01GB07}{J01GB07}),
 \strong{nitr}: nitrofurantoin (\href{https://www.whocc.no/atc_ddd_index/?code=J01XE01}{J01XE01}),
 \strong{norf}: norfloxacin (\href{https://www.whocc.no/atc_ddd_index/?code=J01MA06}{J01MA06}),
 \strong{novo}: novobiocin (an ATCvet code: \href{https://www.whocc.no/atc_ddd_index/?code=QJ01XX95}{QJ01XX95}),
 \strong{oflo}: ofloxacin (\href{https://www.whocc.no/atc_ddd_index/?code=J01MA01}{J01MA01}),
 \strong{peni}: (benzyl)penicillin (\href{https://www.whocc.no/atc_ddd_index/?code=J01CE01}{J01CE01}),
 \strong{pipe}: piperacillin (\href{https://www.whocc.no/atc_ddd_index/?code=J01CA12}{J01CA12}),
 \strong{pita}: piperacillin+tazobactam (\href{https://www.whocc.no/atc_ddd_index/?code=J01CR05}{J01CR05}),
 \strong{poly}: polymyxin B (\href{https://www.whocc.no/atc_ddd_index/?code=J01XB02}{J01XB02}),
 \strong{pris}: pristinamycin (\href{https://www.whocc.no/atc_ddd_index/?code=J01FG01}{J01FG01}),
 \strong{qida}: quinupristin/dalfopristin (\href{https://www.whocc.no/atc_ddd_index/?code=J01FG02}{J01FG02}),
 \strong{rifa}: rifampicin (\href{https://www.whocc.no/atc_ddd_index/?code=J04AB02}{J04AB02}),
 \strong{roxi}: roxithromycin (\href{https://www.whocc.no/atc_ddd_index/?code=J01FA06}{J01FA06}),
 \strong{siso}: sisomicin (\href{https://www.whocc.no/atc_ddd_index/?code=J01GB08}{J01GB08}),
 \strong{teic}: teicoplanin (\href{https://www.whocc.no/atc_ddd_index/?code=J01XA02}{J01XA02}),
 \strong{tetr}: tetracycline (\href{https://www.whocc.no/atc_ddd_index/?code=J01AA07}{J01AA07}),
 \strong{tica}: ticarcillin (\href{https://www.whocc.no/atc_ddd_index/?code=J01CA13}{J01CA13}),
 \strong{tige}: tigecycline (\href{https://www.whocc.no/atc_ddd_index/?code=J01AA12}{J01AA12}),
 \strong{tobr}: tobramycin (\href{https://www.whocc.no/atc_ddd_index/?code=J01GB01}{J01GB01}),
 \strong{trim}: trimethoprim (\href{https://www.whocc.no/atc_ddd_index/?code=J01EA01}{J01EA01}),
 \strong{trsu}: sulfamethoxazole and trimethoprim (\href{https://www.whocc.no/atc_ddd_index/?code=J01EE01}{J01EE01}),
 \strong{vanc}: vancomycin (\href{https://www.whocc.no/atc_ddd_index/?code=J01XA01}{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{
library(dplyr)

septic_patients \%>\%
  mutate(EUCAST = mdro(.),
         BRMO = brmo(.))
}