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(v2.1.1.9226) update intrinsic_resistant, unit test fixes

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dr. M.S. (Matthijs) Berends
2025-03-27 15:20:22 +01:00
parent e6f88241b2
commit 969a42cc8c
29 changed files with 139318 additions and 244254 deletions
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man/intrinsic_resistant.Rd
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@ -5,10 +5,10 @@
\alias{intrinsic_resistant}
\title{Data Set with Bacterial Intrinsic Resistance}
\format{
A \link[tibble:tibble]{tibble} with 301 583 observations and 2 variables:
A \link[tibble:tibble]{tibble} with 196 665 observations and 2 variables:
\itemize{
\item \code{mo}\cr Microorganism ID
\item \code{ab}\cr Antimcrobial ID
\item \code{ab}\cr Antimicrobial ID
}
}
\usage{
@ -18,7 +18,9 @@ intrinsic_resistant
Data set containing defined intrinsic resistance by EUCAST of all bug-drug combinations.
}
\details{
This data set is based on \href{https://www.eucast.org/expert_rules_and_expected_phenotypes}{'EUCAST Expert Rules' and 'EUCAST Intrinsic Resistance and Unusual Phenotypes' v3.3} (2021).
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 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}.