(v1.3.0.9002) intrinsic_resistant data set

man/intrinsic_resistant.Rd

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+% 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"
+}
+}
+\seealso{
+\link{intrinsic_resistant}
+}
+\keyword{datasets}