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support veterinary MIC/disk translation

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dr. M.S. (Matthijs) Berends
2024-02-24 15:16:52 +01:00
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man/clinical_breakpoints.Rd
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@ -5,10 +5,11 @@
\alias{clinical_breakpoints}
\title{Data Set with Clinical Breakpoints for SIR Interpretation}
\format{
A \link[tibble:tibble]{tibble} with 29 747 observations and 12 variables:
A \link[tibble:tibble]{tibble} with 29 883 observations and 13 variables:
\itemize{
\item \code{guideline}\cr Name of the guideline
\item \code{type}\cr Breakpoint type, either "ECOFF", "animal", or "human"
\item \code{host}\cr Host of infectious agent. This is mostly useful for veterinary breakpoints and is either "ECOFF", "aquatic", "cats", "cattle", "dogs", "horse", "human", "poultry", or "swine"
\item \code{method}\cr Testing method, either "DISK" or "MIC"
\item \code{site}\cr Body site for which the breakpoint must be applied, e.g. "Oral" or "Respiratory"
\item \code{mo}\cr Microbial ID, see \code{\link[=as.mo]{as.mo()}}
@ -25,7 +26,13 @@ A \link[tibble:tibble]{tibble} with 29 747 observations and 12 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 (2011-2023) and CLSI (2011-2023). 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. This dataset contain breakpoints for humans, 7 different animal groups, and ECOFFs.
Currently available breakpoint guidelines for \strong{clinical microbiology} are EUCAST 2011-2023 and CLSI 2011-2023.
Currently available breakpoint guidelines for \strong{veterinary microbiology} are EUCAST 2021-2023 and CLSI 2019-2023.
Use \code{\link[=as.sir]{as.sir()}} to transform MICs or disks measurements to SIR values.
}
\details{
\subsection{Different types of breakpoints}{