P281424/AMR
1
0
Fork 0
mirror of https://github.com/msberends/AMR.git synced 2025-07-12 17:41:50 +02:00
Code Releases Activity

(v1.5.0.9016) only_rsi_columns update, documentation

Browse Source
This commit is contained in:
dr. M.S. (Matthijs) Berends
2021-02-08 14:18:42 +01:00
parent 8fda473e49
commit 4a84894f79
88 changed files with 654 additions and 375 deletions
Download Patch File Download Diff File Expand all files Collapse all files

4
man/eucast_rules.Rd
View File

@ -26,7 +26,7 @@ eucast_rules(
version_breakpoints = 11,
version_expertrules = 3.2,
ampc_cephalosporin_resistance = NA,
only_rsi_columns = any(is.rsi(x)),
only_rsi_columns = FALSE,
...
)
@ -49,7 +49,7 @@ eucast_dosage(ab, administration = "iv", version_breakpoints = 11)
\item{ampc_cephalosporin_resistance}{a character value that should be applied for AmpC de-repressed cephalosporin-resistant mutants, defaults to \code{NA}. Currently only works when \code{version_expertrules} is \code{3.2}; '\emph{EUCAST Expert Rules v3.2 on Enterobacterales}' states that results of cefotaxime, ceftriaxone and ceftazidime should be reported with a note, or results should be suppressed (emptied) for these agents. A value of \code{NA} for this argument will remove results for these agents, while e.g. a value of \code{"R"} will make the results for these agents resistant. Use \code{NULL} to not alter the results for AmpC de-repressed cephalosporin-resistant mutants. \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{only_rsi_columns}{a logical to indicate whether only antibiotic columns must be detected that were \href{[rsi]}{transformed to class \verb{<rsi>}} on beforehand. Defaults to \code{TRUE} if any column of \code{x} is of class \verb{<rsi>}.}
\item{only_rsi_columns}{a logical to indicate whether only antibiotic columns must be detected that were \href{[rsi]}{transformed to class \verb{<rsi>}} on beforehand (defaults to \code{FALSE})}
\item{...}{column name of an antibiotic, see section \emph{Antibiotics} below}