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(v2.1.1.9241) fix sir

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dr. M.S. (Matthijs) Berends
2025-04-18 13:25:59 +02:00
parent cf91e677c6
commit 579025f678
9 changed files with 143 additions and 89 deletions
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5
man/antibiogram.Rd
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@ -46,10 +46,9 @@ retrieve_wisca_parameters(wisca_model, ...)
\arguments{
\item{x}{A \link{data.frame} containing at least a column with microorganisms and columns with antimicrobial results (class 'sir', see \code{\link[=as.sir]{as.sir()}}).}
\item{antimicrobials}{A vector specifying the antimicrobials to include in the antibiogram (see \emph{Examples}). Will be evaluated using \code{\link[=guess_ab_col]{guess_ab_col()}}. This can be:
\item{antimicrobials}{A vector specifying the antimicrobials containing SIR values to include in the antibiogram (see \emph{Examples}). Will be evaluated using \code{\link[=guess_ab_col]{guess_ab_col()}}. This can be:
\itemize{
\item Any antimicrobial name or code that matches to a column name in \code{x}
\item A column name in \code{x} that contains SIR values
\item Any antimicrobial name or code that could match (see \code{\link[=guess_ab_col]{guess_ab_col()}}) to any column in \code{x}
\item Any \link[=antimicrobial_selectors]{antimicrobial selector}, such as \code{\link[=aminoglycosides]{aminoglycosides()}} or \code{\link[=carbapenems]{carbapenems()}}
\item A combination of the above, using \code{c()}, e.g.:
\itemize{