AMR/man/rsi_translation.Rd

% 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{data.frame} 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{
Overview of the data set:

\if{html}{\out{<div class="sourceCode r">}}\preformatted{head(rsi_translation)
#>     guideline method site           mo rank_index  ab     ref_tbl disk_dose
#> 1 EUCAST 2022    MIC <NA> F_ASPRG_MGTS          2 AMB Aspergillus      <NA>
#> 2 EUCAST 2022    MIC <NA> F_ASPRG_NIGR          2 AMB Aspergillus      <NA>
#> 3 EUCAST 2022    MIC <NA>      F_CANDD          3 AMB     Candida      <NA>
#> 4 EUCAST 2022    MIC <NA> F_CANDD_ALBC          2 AMB     Candida      <NA>
#> 5 EUCAST 2022    MIC <NA> F_CANDD_DBLN          2 AMB     Candida      <NA>
#> 6 EUCAST 2022    MIC <NA> F_CANDD_KRUS          2 AMB     Candida      <NA>
#>   breakpoint_S breakpoint_R   uti
#> 1            1            1 FALSE
#> 2            1            1 FALSE
#> 3            1            1 FALSE
#> 4            1            1 FALSE
#> 5            1            1 FALSE
#> 6            1            1 FALSE
}\if{html}{\out{</div>}}

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/rsi_translation.txt}. This file \strong{allows for machine reading EUCAST and CLSI guidelines}, which is almost impossible with the Excel and PDF files distributed by EUCAST and CLSI. The file is updated automatically and the \code{mo} and \code{ab} columns have been transformed to contain the full official names instead of codes.
}
\section{Reference Data Publicly Available}{

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.
}

\section{Read more on Our Website!}{

On our website \url{https://msberends.github.io/AMR/} you can find \href{https://msberends.github.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR data analysis, the \href{https://msberends.github.io/AMR/reference/}{complete documentation of all functions} and \href{https://msberends.github.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}.
}

\seealso{
\link{intrinsic_resistant}
}
\keyword{datasets}