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(v3.0.1.9070) Fix #293, update EUCAST rules for PEF

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dr. M.S. (Matthijs) Berends
2026-06-26 08:56:59 +02:00
parent 4fac683fac
commit 637ada920b
8 changed files with 31 additions and 1553 deletions
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6
man/as.sir.Rd
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@@ -14,7 +14,7 @@
\alias{sir_interpretation_history}
\title{Interpret MIC and Disk Diffusion as SIR, or Clean Existing SIR Data}
\usage{
as.sir(x, ...)
as.sir(x, ..., enforce_method = "auto")
NA_sir_
@@ -108,7 +108,9 @@ sir_interpretation_history(clean = FALSE)
\arguments{
\item{x}{Vector of values (for class \code{\link{mic}}: MIC values in mg/L, for class \code{\link{disk}}: a disk diffusion radius in millimetres).}
\item{...}{For using on a \link{data.frame}: selection of columns to apply \code{as.sir()} to. Supports \link[tidyselect:starts_with]{tidyselect language} such as \code{where(is.mic)}, \code{starts_with(...)}, or \code{column1:column4}, and can thus also be \link[=amr_selector]{antimicrobial selectors}, e.g. \code{as.sir(df, penicillins())}.
\item{...}{For using on a \link{data.frame}: selection of columns to apply \code{as.sir()} to. Supports \link[tidyselect:starts_with]{tidyselect language} such as \code{where(is.mic)}, \code{starts_with(...)}, or \code{column1:column4}, and can thus also be \link[=amr_selector]{antimicrobial selectors}, e.g. \code{as.sir(df, penicillins())}.}
\item{enforce_method}{A \link{character} string to force interpretation as a specific method, useful when the S3 class of \code{x} is lost (e.g., when called from Python via rpy2). Must be one of \code{"auto"} (default), \code{"mic"}, or \code{"disk"}.
Otherwise: arguments passed on to methods.}