% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/data.R
\docType{data}
\name{intrinsic_resistant}
\alias{intrinsic_resistant}
\title{Data set with bacterial intrinsic resistance}
\format{
A \code{\link{data.frame}} with 49,462 observations and 2 variables:
\itemize{
\item \code{microorganism}\cr Name of the microorganism
\item \code{antibiotic}\cr Name of the antibiotic drug
}
}
\usage{
intrinsic_resistant
}
\description{
Data set containing defined intrinsic resistance by EUCAST of all bug-drug combinations.
}
\details{
The repository of this \code{AMR} package contains a file comprising this exact data set: \url{https://github.com/msberends/AMR/blob/master/data-raw/intrinsic_resistant.txt}. This file \strong{allows for machine reading EUCAST guidelines about intrinsic resistance}, which is almost impossible with the Excel and PDF files distributed by EUCAST. The file is updated automatically.

This data set is based on 'EUCAST Expert Rules, Intrinsic Resistance and Exceptional Phenotypes', version 3.1, 2016.
}
\section{Read more on our website!}{

On our website \url{https://msberends.github.io/AMR} you can find \href{https://msberends.github.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR analysis, the \href{https://msberends.github.io/AMR/reference}{complete documentation of all functions} (which reads a lot easier than here in R) and \href{https://msberends.github.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}. As we would like to better understand the backgrounds and needs of our users, please \href{https://msberends.github.io/AMR/survey.html}{participate in our survey}!
}

\examples{
if (require("dplyr")) {
  intrinsic_resistant \%>\%
    filter(antibiotic == "Vancomycin", microorganism \%like\% "Enterococcus") \%>\% 
    pull(microorganism)
  # [1] "Enterococcus casseliflavus" "Enterococcus gallinarum"
}
}
\keyword{datasets}