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new verbose

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dr. M.S. (Matthijs) Berends
2018-10-19 00:17:03 +02:00
parent 5727800b9a
commit b464dd524a
5 changed files with 42 additions and 19 deletions
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man/EUCAST.Rd
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@ -56,12 +56,12 @@ interpretive_reading(...)
\item{col_bactid}{Deprecated. Use \code{col_mo} instead.}
\item{verbose}{a logical to indicate whether extensive info should be printed to the console about which rows and columns are effected with their old and new values}
\item{verbose}{a logical to indicate whether extensive info should be returned as a \code{data.frame} with info about which rows and columns are effected}
\item{...}{parameters that are passed on to \code{EUCAST_rules}}
}
\value{
Value of parameter \code{tbl}, possibly with edited values of antibiotics.
The input of \code{tbl}, possibly with edited values of antibiotics. Or, if \code{verbose = TRUE}, a \code{data.frame} with verbose info.
}
\description{
Apply susceptibility rules as defined by the European Committee on Antimicrobial Susceptibility Testing (EUCAST, \url{http://eucast.org}), see \emph{Source}. This includes (1) expert rules, (2) intrinsic resistance and (3) inferred resistance as defined in their breakpoint tables.