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(v1.7.1.9064) eucast 3.3 for mdro(), major change to repeated calling

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dr. M.S. (Matthijs) Berends
2021-12-11 13:41:31 +01:00
parent e18c49ed93
commit 77ba4318ea
64 changed files with 51141 additions and 9840 deletions
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16
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{data.frame} with 93,892 observations and 2 variables:
A \link{data.frame} with 134,956 observations and 2 variables:
\itemize{
\item \code{microorganism}\cr Name of the microorganism
\item \code{antibiotic}\cr Name of the antibiotic drug
\item \code{microorganism}\cr Official taxonomic name of the microorganism, according to the LPSN
\item \code{antibiotic}\cr Official name of the antibiotic drug, according to the WHOCC
}
}
\usage{
@@ -20,7 +20,7 @@ Data set containing defined intrinsic resistance by EUCAST of all bug-drug combi
\details{
The repository of this \code{AMR} package contains a file comprising this exact data set: \url{https://github.com/msberends/AMR/blob/main/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 \href{https://www.eucast.org/expert_rules_and_intrinsic_resistance/}{'EUCAST Expert Rules' and 'EUCAST Intrinsic Resistance and Unusual Phenotypes' v3.2} (2020).
This data set is based on \href{https://www.eucast.org/expert_rules_and_intrinsic_resistance/}{'EUCAST Expert Rules' and 'EUCAST Intrinsic Resistance and Unusual Phenotypes' v3.3} (2021).
}
\section{Reference Data Publicly Available}{
@@ -33,12 +33,16 @@ On our website \url{https://msberends.github.io/AMR/} you can find \href{https:/
}
\examples{
subset(intrinsic_resistant,
antibiotic == "Vancomycin" & microorganism \%like\% "Enterococcus")$microorganism
#> [1] "Enterococcus casseliflavus" "Enterococcus gallinarum"
\donttest{
if (require("dplyr")) {
intrinsic_resistant \%>\%
filter(antibiotic == "Vancomycin", microorganism \%like\% "Enterococcus") \%>\%
filter(antibiotic == "Vancomycin" & microorganism \%like\% "Enterococcus") \%>\%
pull(microorganism)
# [1] "Enterococcus casseliflavus" "Enterococcus gallinarum"
#> [1] "Enterococcus casseliflavus" "Enterococcus gallinarum"
}
}
}