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fix add_missing

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dr. M.S. (Matthijs) Berends
2026-04-21 20:48:43 +02:00
parent cd23422a5f
commit c2b9af94ff
38 changed files with 1165 additions and 972 deletions
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6
man/interpretive_rules.Rd
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@@ -54,9 +54,9 @@ eucast_dosage(ab, administration = "iv", version_breakpoints = 15)
\item{version_breakpoints}{The version number to use for the EUCAST Clinical Breakpoints guideline. Can be \code{"16.0"}, \code{"15.0"}, \code{"14.0"}, \code{"13.1"}, \code{"12.0"}, \code{"11.0"}, or \code{"10.0"}.}
\item{version_expected_phenotypes}{The version number to use for the EUCAST Expected Phenotypes. Can be {.val 1.2}.}
\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 {.val 3.3}, {.val 3.2}, or {.val 3.1}.}
\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{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}.}
@@ -72,7 +72,7 @@ eucast_dosage(ab, administration = "iv", version_breakpoints = 15)
\item{ab}{Any (vector of) text that can be coerced to a valid antimicrobial drug code with \code{\link[=as.ab]{as.ab()}}.}
\item{administration}{Route of administration, either {.val }, {.val im}, {.val iv}, {.val oral}, or NA.}
\item{administration}{Route of administration, either \code{""}, \code{"im"}, \code{"iv"}, \code{"oral"}, or NA.}
}
\value{
The input of \code{x}, possibly with edited values of antimicrobials. Or, if \code{verbose = TRUE}, a \link{data.frame} with all original and new values of the affected bug-drug combinations.