mirror of https://github.com/msberends/AMR.git
39 lines
1.9 KiB
R
39 lines
1.9 KiB
R
% Generated by roxygen2: do not edit by hand
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% Please edit documentation in R/data.R
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\docType{data}
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\name{intrinsic_resistant}
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\alias{intrinsic_resistant}
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\title{Data set with bacterial intrinsic resistance}
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\format{
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A \code{\link{data.frame}} with 49,462 observations and 2 variables:
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\itemize{
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\item \code{microorganism}\cr Name of the microorganism
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\item \code{antibiotic}\cr Name of the antibiotic drug
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}
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}
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\usage{
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intrinsic_resistant
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}
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\description{
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Data set containing defined intrinsic resistance by EUCAST of all bug-drug combinations.
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}
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\details{
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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.
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This data set is based on 'EUCAST Expert Rules, Intrinsic Resistance and Exceptional Phenotypes', version 3.1, 2016.
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}
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\section{Read more on our website!}{
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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}!
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}
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\examples{
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if (require("dplyr")) {
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intrinsic_resistant \%>\%
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filter(antibiotic == "Vancomycin", microorganism \%like\% "Enterococcus") \%>\%
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pull(microorganism)
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# [1] "Enterococcus casseliflavus" "Enterococcus gallinarum"
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}
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}
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\keyword{datasets}
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