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Update clinical breakpoints and fix some as.mo() bugs (#117)

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* Updates clinical breakpoints EUCAST/CLSI 2023, fixes #102, fixes #112, fixes #113, fixes #114, fixes #115
* docs
* implement ecoffs
* unit tests
This commit is contained in:
Dr. Matthijs Berends
2023-06-22 15:10:59 +02:00
committed by GitHub
parent 9591688811
commit f065945d7b
55 changed files with 43056 additions and 18400 deletions
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man/clinical_breakpoints.Rd
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@ -5,7 +5,7 @@
\alias{clinical_breakpoints}
\title{Data Set with Clinical Breakpoints for SIR Interpretation}
\format{
A \link[tibble:tibble]{tibble} with 18 271 observations and 11 variables:
A \link[tibble:tibble]{tibble} with 42 599 observations and 12 variables:
\itemize{
\item \code{guideline}\cr Name of the guideline
\item \code{method}\cr Either "DISK" or "MIC"
@ -17,6 +17,7 @@ A \link[tibble:tibble]{tibble} with 18 271 observations and 11 variables:
\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{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)
\item \code{uti}\cr A \link{logical} value (\code{TRUE}/\code{FALSE}) to indicate whether the rule applies to a urinary tract infection (UTI)
}
}
@ -24,9 +25,11 @@ A \link[tibble:tibble]{tibble} with 18 271 observations and 11 variables:
clinical_breakpoints
}
\description{
Data set containing clinical breakpoints to interpret MIC and disk diffusion to SIR values, according to international guidelines. Currently implemented guidelines are EUCAST (2013-2022) and CLSI (2013-2022). Use \code{\link[=as.sir]{as.sir()}} to transform MICs or disks measurements to SIR values.
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.
}
\details{
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}.
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.