P281424/AMR
1
0
Fork 0
mirror of https://github.com/msberends/AMR.git synced 2026-09-11 16:18:54 +02:00
Code Releases Activity

(v3.0.1.9089) Remove old expert rules that conflict with expected resistant phenotypes

Browse Source
This commit is contained in:
dr. M.S. (Matthijs) Berends
2026-09-03 15:53:29 +02:00
parent bbdd3a92e2
commit 177e83aaf8
6 changed files with 4 additions and 207 deletions
Download Patch File Download Diff File Expand all files Collapse all files

4
man/interpretive_rules.Rd
View File

@@ -64,9 +64,9 @@ eucast_dosage(ab, administration = "iv", version_breakpoints = 15)
\item{version_expected_phenotypes}{The version number to use for the EUCAST Expected Phenotypes. Can be \code{"1.2"}.}
\item{version_expertrules}{The version number to use for the EUCAST Expert Rules and Intrinsic Resistance guideline. Can be \code{"3.3"}, \code{"3.2"}, or \code{"3.1"}.}
\item{version_expertrules}{The version number to use for the EUCAST Expert Rules and Intrinsic Resistance guideline. Can be \code{"3.3"}.}
\item{ampc_cephalosporin_resistance}{(only applies when \code{rules} contains \code{"expert"} or \code{"all"}) a \link{character} value that should be applied to cefotaxime, ceftriaxone and ceftazidime for AmpC de-repressed cephalosporin-resistant mutants - the default is \code{NA}. Currently only works when \code{version_expertrules} is \code{3.2} and higher; these versions of '\emph{EUCAST Expert Rules on Enterobacterales}' state that results of cefotaxime, ceftriaxone and ceftazidime should be reported with a note, or results should be suppressed (emptied) for these three drugs. A value of \code{NA} (the default) for this argument will remove results for these three drugs, while e.g. a value of \code{"R"} will make the results for these drugs resistant. Use \code{NULL} or \code{FALSE} to not alter results for these three drugs of AmpC de-repressed cephalosporin-resistant mutants. Using \code{TRUE} is equal to using \code{"R"}. \cr For \emph{EUCAST Expert Rules} v3.2, this rule applies to: \emph{Citrobacter braakii}, \emph{Citrobacter freundii}, \emph{Citrobacter gillenii}, \emph{Citrobacter murliniae}, \emph{Citrobacter rodenticum}, \emph{Citrobacter sedlakii}, \emph{Citrobacter werkmanii}, \emph{Citrobacter youngae}, \emph{Enterobacter}, \emph{Hafnia alvei}, \emph{Klebsiella aerogenes}, \emph{Morganella morganii}, \emph{Providencia}, and \emph{Serratia}.}
\item{ampc_cephalosporin_resistance}{(only applies when \code{rules} contains \code{"expert"} or \code{"all"}) a \link{character} value that should be applied to cefotaxime, ceftriaxone and ceftazidime for AmpC de-repressed cephalosporin-resistant mutants - the default is \code{NA}. Currently only works when \code{version_expertrules} is \code{3.2} and higher; these versions of '\emph{EUCAST Expert Rules on Enterobacterales}' state that results of cefotaxime, ceftriaxone and ceftazidime should be reported with a note, or results should be suppressed (emptied) for these three drugs. A value of \code{NA} (the default) for this argument will remove results for these three drugs, while e.g. a value of \code{"R"} will make the results for these drugs resistant. Use \code{NULL} or \code{FALSE} to not alter results for these three drugs of AmpC de-repressed cephalosporin-resistant mutants. Using \code{TRUE} is equal to using \code{"R"}. \cr For \emph{EUCAST Expert Rules} v3.2, this rule applies to: \emph{Citrobacter braakii}, \emph{Citrobacter freundii}, \emph{Citrobacter gillenii}, \emph{Citrobacter murliniae}, \emph{Citrobacter rodenticum}, \emph{Citrobacter sedlakii}, \emph{Citrobacter werkmanii}, \emph{Citrobacter youngae}, \emph{Enterobacter}, \emph{Hafnia alvei}, and \emph{Klebsiella aerogenes}.}
\item{only_sir_columns}{A \link{logical} to indicate whether only antimicrobial columns must be included that were transformed to class \link[=as.sir]{sir} on beforehand. Defaults to \code{FALSE} if no columns of \code{x} have a class \link[=as.sir]{sir}.}