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\docType{data}
\name{intrinsic_resistant}
\alias{intrinsic_resistant}
\title{Data Set with Bacterial Intrinsic Resistance}
\title{Data Set Denoting Bacterial Intrinsic Resistance}
\format{
A \link[tibble:tibble]{tibble} with 196 665 observations and 2 variables:
A \link[tibble:tibble]{tibble} with 271 905 observations and 2 variables:
\itemize{
\item \code{mo}\cr Microorganism ID
\item \code{ab}\cr Antimicrobial ID
\item \code{mo}\cr Microorganism ID which occurs in \code{\link[=microorganisms]{microorganisms$mo}}. Names can be retrieved using \code{\link[=mo_name]{mo_name()}}.
\item \code{ab}\cr Antimicrobial ID which occurs in \code{\link[=antimicrobials]{antimicrobials$ab}}. Names can be retrieved using \code{\link[=ab_name]{ab_name()}}.
}
}
\usage{
intrinsic_resistant
}
\description{
Data set containing defined intrinsic resistance by EUCAST of all bug-drug combinations.
Data set containing 'EUCAST Expected Resistant Phenotypes' of \emph{all} bug-drug combinations between the \link{microorganisms} and \link{antimicrobials} data sets.
}
\details{
This data set is based on \href{https://www.eucast.org/expert_rules_and_expected_phenotypes}{'EUCAST Expected Resistant Phenotypes' v1.2} (2023).
This data set is currently based on \href{https://www.eucast.org/expert_rules_and_expected_phenotypes}{'EUCAST Expected Resistant Phenotypes' v1.2} (2023).
This data set is internally used by \code{\link[=not_intrinsic_resistant]{not_intrinsic_resistant()}} (an \link[=antimicrobial_selectors]{antimicrobial selector}) and \code{\link[=mo_is_intrinsic_resistant]{mo_is_intrinsic_resistant()}}
\subsection{Direct download}{
Like all data sets in this package, this data set is publicly available for download in the following formats: R, MS Excel, Apache Feather, Apache Parquet, SPSS, and Stata. Please visit \href{https://msberends.github.io/AMR/articles/datasets.html}{our website for the download links}. The actual files are of course available on \href{https://github.com/msberends/AMR/tree/main/data-raw}{our GitHub repository}.
They \strong{allow for machine reading EUCAST and CLSI guidelines}, which is almost impossible with the MS Excel and PDF files distributed by EUCAST and CLSI.
This data set is internally used by:
\itemize{
\item \code{\link[=not_intrinsic_resistant]{not_intrinsic_resistant()}} (an \link[=antimicrobial_selectors]{antimicrobial selector})
\item \code{\link[=mo_is_intrinsic_resistant]{mo_is_intrinsic_resistant()}}
}
}
\section{Download Our Reference Data}{
All reference data sets in the AMR package - including information on microorganisms, antimicrobials, and clinical breakpoints - are freely available for download in multiple formats: R, MS Excel, Apache Feather, Apache Parquet, SPSS, and Stata.
For maximum compatibility, we also provide machine-readable, tab-separated plain text files suitable for use in any software, including laboratory information systems.
Visit \href{https://msberends.github.io/AMR/articles/datasets.html}{our website for direct download links}, or explore the actual files in \href{https://github.com/msberends/AMR/tree/main/data-raw}{our GitHub repository}.
}
\examples{
intrinsic_resistant
}