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(v3.0.1.9034) Add amr_course()

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dr. M.S. (Matthijs) Berends
2026-03-11 16:07:31 +01:00
parent 353eaa3f38
commit 4dc3ec0008
8 changed files with 110 additions and 17 deletions
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man/interpretive_rules.Rd
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@@ -76,10 +76,6 @@ eucast_dosage(ab, administration = "iv", version_breakpoints = 15)
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.
}
\description{
\strong{WORK IN PROGRESS}
\strong{The \code{interpretive_rules()} function is new, to allow CLSI 'rules' too. The old \code{eucast_rules()} function will stay as a wrapper, but we need to generalise more parts of the underlying code to allow more than just EUCAST.}
Apply rules from clinical breakpoints notes and expected resistant phenotypes as defined by e.g. the European Committee on Antimicrobial Susceptibility Testing (EUCAST, \url{https://www.eucast.org}), see \emph{Source}. Use \code{\link[=eucast_dosage]{eucast_dosage()}} to get a \link{data.frame} with advised dosages of a certain bug-drug combination, which is based on the \link{dosage} data set.
To improve the interpretation of the antibiogram before CLSI/EUCAST interpretive rules are applied, some AMR-specific rules can be applied at default, see \emph{Details}.