mirror of https://github.com/msberends/AMR.git
44 lines
2.7 KiB
R
44 lines
2.7 KiB
R
% Generated by roxygen2: do not edit by hand
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% Please edit documentation in R/data.R
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\docType{data}
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\name{clinical_breakpoints}
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\alias{clinical_breakpoints}
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\title{Data Set with Clinical Breakpoints for SIR Interpretation}
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\format{
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A \link[tibble:tibble]{tibble} with 42 599 observations and 12 variables:
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\itemize{
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\item \code{guideline}\cr Name of the guideline
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\item \code{method}\cr Either "DISK" or "MIC"
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\item \code{site}\cr Body site, e.g. "Oral" or "Respiratory"
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\item \code{mo}\cr Microbial ID, see \code{\link[=as.mo]{as.mo()}}
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\item \code{rank_index}\cr Taxonomic rank index of \code{mo} from 1 (subspecies/infraspecies) to 5 (unknown microorganism)
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\item \code{ab}\cr Antibiotic ID, see \code{\link[=as.ab]{as.ab()}}
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\item \code{ref_tbl}\cr Info about where the guideline rule can be found
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\item \code{disk_dose}\cr Dose of the used disk diffusion method
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\item \code{breakpoint_S}\cr Lowest MIC value or highest number of millimetres that leads to "S"
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\item \code{breakpoint_R}\cr Highest MIC value or lowest number of millimetres that leads to "R"
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\item \code{ecoff}\cr Epidemiological cut-off (ECOFF) value, used in antimicrobial susceptibility testing to differentiate between wild-type and non-wild-type strains of bacteria or fungi (use \code{\link[=as.sir]{as.sir(..., ecoff = TRUE)}} to interpret raw data using ECOFF values)
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\item \code{uti}\cr A \link{logical} value (\code{TRUE}/\code{FALSE}) to indicate whether the rule applies to a urinary tract infection (UTI)
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}
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}
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\usage{
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clinical_breakpoints
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}
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\description{
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Data set containing clinical breakpoints to interpret MIC and disk diffusion to SIR values, according to international guidelines. Currently implemented guidelines are EUCAST (2011-2023) and CLSI (2011-2023). Use \code{\link[=as.sir]{as.sir()}} to transform MICs or disks measurements to SIR values.
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}
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\details{
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Clinical breakpoints are validated through \href{https://whonet.org}{WHONET}, a free desktop Windows application developed and supported by the WHO Collaborating Centre for Surveillance of Antimicrobial Resistance. More can be read on \href{https://whonet.org}{their website}.
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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}.
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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.
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}
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\examples{
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clinical_breakpoints
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}
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\seealso{
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\link{intrinsic_resistant}
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}
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\keyword{datasets}
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