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(v3.0.1.9041) add breakpoints 2026

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dr. M.S. (Matthijs) Berends
2026-03-30 10:01:49 +02:00
parent 9c95aa455c
commit 3a736bc484
37 changed files with 5975 additions and 345 deletions
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10
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 40 217 observations and 14 variables:
A \link[tibble:tibble]{tibble} with 45 797 observations and 14 variables:
\itemize{
\item \code{guideline}\cr Name of the guideline
\item \code{type}\cr Breakpoint type, either "ECOFF", "animal", or "human"
@@ -20,7 +20,7 @@ A \link[tibble:tibble]{tibble} with 40 217 observations and 14 variables:
\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", can be \code{NA}
\item \code{uti}\cr A \link{logical} value (\code{TRUE}/\code{FALSE}) to indicate whether the rule applies to a urinary tract infection (UTI)
\item \code{is_SDD}\cr A \link{logical} value (\code{TRUE}/\code{FALSE}) to indicate whether the intermediate range between "S" and "R" should be interpreted as "SDD", instead of "I". This currently applies to 48 breakpoints.
\item \code{is_SDD}\cr A \link{logical} value (\code{TRUE}/\code{FALSE}) to indicate whether the intermediate range between "S" and "R" should be interpreted as "SDD", instead of "I". This currently applies to 72 breakpoints.
}
}
\usage{
@@ -31,9 +31,9 @@ Data set containing clinical breakpoints to interpret MIC and disk diffusion to
These breakpoints are currently implemented:
\itemize{
\item For \strong{clinical microbiology}: EUCAST 2011-2025 and CLSI 2011-2025;
\item For \strong{veterinary microbiology}: EUCAST 2021-2025 and CLSI 2019-2025;
\item For \strong{ECOFFs} (Epidemiological Cut-off Values): EUCAST 2020-2025 and CLSI 2022-2025.
\item For \strong{clinical microbiology}: EUCAST 2011-2026 and CLSI 2011-2026;
\item For \strong{veterinary microbiology}: EUCAST 2021-2026 and CLSI 2019-2026;
\item For \strong{ECOFFs} (Epidemiological Cut-off Values): EUCAST 2020-2026 and CLSI 2022-2026.
}
Use \code{\link[=as.sir]{as.sir()}} to transform MICs or disks measurements to SIR values.