P281424/AMR
1
0
Fork 0
mirror of https://github.com/msberends/AMR.git synced 2026-09-11 16:58:56 +02:00
Code Releases Activity

(v3.0.1.9091) unit test

Browse Source
This commit is contained in:
dr. M.S. (Matthijs) Berends
2026-09-08 15:02:07 +02:00
parent 3f50d6b6c3
commit aebad2ae47
5 changed files with 6 additions and 6 deletions
Download Patch File Download Diff File Expand all files Collapse all files

2
man/interpretive_rules.Rd
View File

@@ -94,7 +94,7 @@ To improve the interpretation of the antibiogram before CLSI/EUCAST interpretive
\strong{Note:} This function does not translate MIC or disk values to SIR values. Use \code{\link[=as.sir]{as.sir()}} for that. \cr
\strong{Note:} When ampicillin (AMP, J01CA01) is not available but amoxicillin (AMX, J01CA04) is, the latter will be used for all rules where there is a dependency on ampicillin. These drugs are interchangeable when it comes to expression of antimicrobial resistance. \cr
The file containing all interpretive rules is located here: \url{https://github.com/msberends/AMR/blob/main/data-raw/interpretive_rules.tsv}. \strong{Note:} Old taxonomic names are replaced with the current taxonomy where applicable. For example, \emph{Ochrobactrum anthropi} was renamed to \emph{Brucella anthropi} in 2020; the original EUCAST rules v3.1 and v3.2 did not yet contain this new taxonomic name. The \code{AMR} package contains the full microbial taxonomy updated until 7th of May, 2026, see \link{microorganisms}.
The file containing all interpretive rules is located here: \url{https://github.com/msberends/AMR/blob/main/data-raw/interpretive_rules.tsv}. \strong{Note:} Old taxonomic names are replaced with the current taxonomy where applicable. For example, \emph{Ochrobactrum anthropi} was renamed to \emph{Brucella anthropi} in 2020; older interpretive rules may not yet contain this new taxonomic name. The \code{AMR} package contains the full microbial taxonomy updated until 7th of May, 2026, see \link{microorganisms}.
\subsection{Custom Rules}{
Custom rules can be created using \code{\link[=custom_interpretive_rules]{custom_interpretive_rules()}}, e.g.: