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(v1.4.0.9048) AmpC de-repressed cephalo-resistant mutants

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dr. M.S. (Matthijs) Berends
2020-12-27 14:23:11 +01:00
parent 8b52f9b1be
commit ed198916bf
24 changed files with 93 additions and 41 deletions
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3
man/eucast_rules.Rd
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@ -23,6 +23,7 @@ eucast_rules(
verbose = FALSE,
version_breakpoints = 10,
version_expertrules = 3.2,
ampc_cephalosporin_resistance = NA,
...
)
}
@ -41,6 +42,8 @@ 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{...}{column name of an antibiotic, please see section \emph{Antibiotics} below}
}
\value{

2
man/get_episode.Rd
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@ -52,7 +52,7 @@ On our website \url{https://msberends.github.io/AMR/} you can find \href{https:/
get_episode(example_isolates$date, episode_days = 60)
is_new_episode(example_isolates$date, episode_days = 60)
# filter on results from the third 60-day episode using base R
# filter on results from the third 60-day episode only, using base R
example_isolates[which(get_episode(example_isolates$date, 60) == 3), ]
\donttest{