P281424/AMR
1
0
Fork 0
mirror of https://github.com/msberends/AMR.git synced 2025-07-12 23:01:51 +02:00
Code Releases Activity

updated taxonomy

Browse Source
This commit is contained in:
dr. M.S. (Matthijs) Berends
2022-12-12 00:14:56 +01:00
parent eed1c14b96
commit 8da2467209
46 changed files with 132944 additions and 57370 deletions
Download Patch File Download Diff File Expand all files Collapse all files

2
man/eucast_rules.Rd
View File

@ -74,7 +74,7 @@ To improve the interpretation of the antibiogram before EUCAST rules are applied
\strong{Note:} This function does not translate MIC values to RSI values. Use \code{\link[=as.rsi]{as.rsi()}} 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 EUCAST rules is located here: \url{https://github.com/msberends/AMR/blob/main/data-raw/eucast_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 12 September, 2022, see \link{microorganisms}.
The file containing all EUCAST rules is located here: \url{https://github.com/msberends/AMR/blob/main/data-raw/eucast_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 11 December, 2022, see \link{microorganisms}.
\subsection{Custom Rules}{
Custom rules can be created using \code{\link[=custom_eucast_rules]{custom_eucast_rules()}}, e.g.: