P281424/AMR
1
0
Fork 0
mirror of https://github.com/msberends/AMR.git synced 2025-07-10 00:23:03 +02:00
Code Releases Activity

documentation, unit tests

Browse Source
This commit is contained in:
dr. M.S. (Matthijs) Berends
2023-01-24 10:20:27 +01:00
parent eef00069fd
commit 830c67f1bf
60 changed files with 45 additions and 7 deletions
Download Patch File Download Diff File Expand all files Collapse all files

2
man/as.sir.Rd
View File

@ -82,7 +82,7 @@ sir_interpretation_history(clean = FALSE)
\item{ab}{any (vector of) text that can be coerced to a valid antimicrobial drug code with \code{\link[=as.ab]{as.ab()}}}
\item{guideline}{defaults to EUCAST 2022 (the latest implemented EUCAST guideline in the \link{clinical_breakpoints} data set), but can be set with the \link[=options]{option} \code{AMR_guideline}. Supports EUCAST (2013-2022) and CLSI (2013-2022), see \emph{Details}.}
\item{guideline}{defaults to EUCAST 2022 (the latest implemented EUCAST guideline in the \link{clinical_breakpoints} data set), but can be set with the option \code{\link[=AMR-options]{AMR_guideline}}. Currently supports EUCAST (2013-2022) and CLSI (2013-2022), see \emph{Details}.}
\item{uti}{(Urinary Tract Infection) A vector with \link{logical}s (\code{TRUE} or \code{FALSE}) to specify whether a UTI specific interpretation from the guideline should be chosen. For using \code{\link[=as.sir]{as.sir()}} on a \link{data.frame}, this can also be a column containing \link{logical}s or when left blank, the data set will be searched for a column 'specimen', and rows within this column containing 'urin' (such as 'urine', 'urina') will be regarded isolates from a UTI. See \emph{Examples}.}