P281424/AMR
1
0
Fork 0
mirror of https://github.com/msberends/AMR.git synced 2025-07-09 02:03:04 +02:00
Code Releases Activity

(v1.4.0.9052) replaced all sapply's with type-safe vapply's

Browse Source
This commit is contained in:
dr. M.S. (Matthijs) Berends
2020-12-28 22:24:33 +01:00
parent ccf13dd6c0
commit 526f8afb08
37 changed files with 155 additions and 117 deletions
Download Patch File Download Diff File Expand all files Collapse all files

2
man/eucast_rules.Rd
View File

@ -42,7 +42,7 @@ eucast_rules(
\item{version_expertrules}{the version number to use for the EUCAST Expert Rules and Intrinsic Resistance guideline. Currently supported: 3.1, 3.2.}
\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 susceptible (S) 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{Enterobacter}, \emph{Klebsiella aerogenes}, \emph{Citrobacter freundii}, \emph{Hafnia alvei}, \emph{Serratia}, \emph{Morganella morganii}, \emph{Providencia}.}
\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 susceptible (S) 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{Enterobacter, Klebsiella aerogenes, Citrobacter freundii, Hafnia alvei, Serratia, Morganella morganii, Providencia}.}
\item{...}{column name of an antibiotic, please see section \emph{Antibiotics} below}
}