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new tibble export

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dr. M.S. (Matthijs) Berends
2022-08-27 20:49:37 +02:00
parent 164886f50b
commit 303d61b473
115 changed files with 836 additions and 996 deletions
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15
man/intrinsic_resistant.Rd
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@@ -5,7 +5,7 @@
\alias{intrinsic_resistant}
\title{Data Set with Bacterial Intrinsic Resistance}
\format{
A \link{data.frame} with 134,956 observations and 2 variables:
A [tibble\link[tibble:tibble]{tibble::tibble} with 134,956 observations and 2 variables:
\itemize{
\item \code{mo}\cr Microorganism ID
\item \code{ab}\cr Antibiotic ID
@@ -18,16 +18,15 @@ intrinsic_resistant
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 data set with full taxonomic and antibiotic names: \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_expected_phenotypes/}{'EUCAST Expert Rules' and 'EUCAST Intrinsic Resistance and Unusual Phenotypes' v3.3} (2021).
}
\section{Reference Data Publicly Available}{
\subsection{Direct download}{
All reference data sets (about microorganisms, antibiotics, R/SI interpretation, EUCAST rules, etc.) in this \code{AMR} package are publicly and freely available. We continually export our data sets to formats for use in R, SPSS, SAS, Stata and Excel. We also supply flat files that are machine-readable and suitable for input in any software program, such as laboratory information systems. Please find \href{https://msberends.github.io/AMR/articles/datasets.html}{all download links on our website}, which is automatically updated with every code change.
}
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, SAS, 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.
}
}
\examples{
head(intrinsic_resistant)
intrinsic_resistant
}
\keyword{datasets}