mirror of https://github.com/msberends/AMR.git
41 lines
2.1 KiB
R
41 lines
2.1 KiB
R
% Generated by roxygen2: do not edit by hand
|
|
% Please edit documentation in R/data.R
|
|
\docType{data}
|
|
\name{rsi_translation}
|
|
\alias{rsi_translation}
|
|
\title{Data Set for R/SI Interpretation}
|
|
\format{
|
|
A \link[tibble:tibble]{tibble} with 20,369 observations and 11 variables:
|
|
\itemize{
|
|
\item \code{guideline}\cr Name of the guideline
|
|
\item \code{method}\cr Either "DISK" or "MIC"
|
|
\item \code{site}\cr Body site, e.g. "Oral" or "Respiratory"
|
|
\item \code{mo}\cr Microbial ID, see \code{\link[=as.mo]{as.mo()}}
|
|
\item \code{rank_index}\cr Taxonomic rank index of \code{mo} from 1 (subspecies/infraspecies) to 5 (unknown microorganism)
|
|
\item \code{ab}\cr Antibiotic ID, see \code{\link[=as.ab]{as.ab()}}
|
|
\item \code{ref_tbl}\cr Info about where the guideline rule can be found
|
|
\item \code{disk_dose}\cr Dose of the used disk diffusion method
|
|
\item \code{breakpoint_S}\cr Lowest MIC value or highest number of millimetres that leads to "S"
|
|
\item \code{breakpoint_R}\cr Highest MIC value or lowest number of millimetres that leads to "R"
|
|
\item \code{uti}\cr A \link{logical} value (\code{TRUE}/\code{FALSE}) to indicate whether the rule applies to a urinary tract infection (UTI)
|
|
}
|
|
}
|
|
\usage{
|
|
rsi_translation
|
|
}
|
|
\description{
|
|
Data set containing reference data to interpret MIC and disk diffusion to R/SI values, according to international guidelines. Currently implemented guidelines are EUCAST (2011-2022) and CLSI (2011-2022). Use \code{\link[=as.rsi]{as.rsi()}} to transform MICs or disks measurements to R/SI values.
|
|
}
|
|
\details{
|
|
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{
|
|
rsi_translation
|
|
}
|
|
\seealso{
|
|
\link{intrinsic_resistant}
|
|
}
|
|
\keyword{datasets}
|