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dr. M.S. (Matthijs) Berends
2022-11-13 13:44:25 +01:00
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18
man/key_antimicrobials.Rd
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@ -37,13 +37,13 @@ antimicrobials_equal(
\item{col_mo}{column name of the IDs of the microorganisms (see \code{\link[=as.mo]{as.mo()}}), defaults to the first column of class \code{\link{mo}}. Values will be coerced using \code{\link[=as.mo]{as.mo()}}.}
\item{universal}{names of \strong{broad-spectrum} antimicrobial agents, case-insensitive. Set to \code{NULL} to ignore. See \emph{Details} for the default agents.}
\item{universal}{names of \strong{broad-spectrum} antimicrobial drugs, case-insensitive. Set to \code{NULL} to ignore. See \emph{Details} for the default antimicrobial drugs}
\item{gram_negative}{names of antibiotic agents for \strong{Gram-positives}, case-insensitive. Set to \code{NULL} to ignore. See \emph{Details} for the default agents.}
\item{gram_negative}{names of antibiotic drugs for \strong{Gram-positives}, case-insensitive. Set to \code{NULL} to ignore. See \emph{Details} for the default antibiotic drugs}
\item{gram_positive}{names of antibiotic agents for \strong{Gram-negatives}, case-insensitive. Set to \code{NULL} to ignore. See \emph{Details} for the default agents.}
\item{gram_positive}{names of antibiotic drugs for \strong{Gram-negatives}, case-insensitive. Set to \code{NULL} to ignore. See \emph{Details} for the default antibiotic drugs}
\item{antifungal}{names of antifungal agents for \strong{fungi}, case-insensitive. Set to \code{NULL} to ignore. See \emph{Details} for the default agents.}
\item{antifungal}{names of antifungal drugs for \strong{fungi}, case-insensitive. Set to \code{NULL} to ignore. See \emph{Details} for the default antifungal drugs}
\item{only_rsi_columns}{a \link{logical} to indicate whether only columns must be included that were transformed to class \code{rsi} (see \code{\link[=as.rsi]{as.rsi()}}) on beforehand (defaults to \code{FALSE})}
@ -63,11 +63,11 @@ These functions can be used to determine first weighted isolates by considering
\details{
The \code{\link[=key_antimicrobials]{key_antimicrobials()}} and \code{\link[=all_antimicrobials]{all_antimicrobials()}} functions are context-aware. This means that the \code{x} argument can be left blank if used inside a \link{data.frame} call, see \emph{Examples}.
The function \code{\link[=key_antimicrobials]{key_antimicrobials()}} returns a \link{character} vector with 12 antimicrobial results for every isolate. The function \code{\link[=all_antimicrobials]{all_antimicrobials()}} returns a \link{character} vector with all antimicrobial results for every isolate. These vectors can then be compared using \code{\link[=antimicrobials_equal]{antimicrobials_equal()}}, to check if two isolates have generally the same antibiogram. Missing and invalid values are replaced with a dot (\code{"."}) by \code{\link[=key_antimicrobials]{key_antimicrobials()}} and ignored by \code{\link[=antimicrobials_equal]{antimicrobials_equal()}}.
The function \code{\link[=key_antimicrobials]{key_antimicrobials()}} returns a \link{character} vector with 12 antimicrobial results for every isolate. The function \code{\link[=all_antimicrobials]{all_antimicrobials()}} returns a \link{character} vector with all antimicrobial drug results for every isolate. These vectors can then be compared using \code{\link[=antimicrobials_equal]{antimicrobials_equal()}}, to check if two isolates have generally the same antibiogram. Missing and invalid values are replaced with a dot (\code{"."}) by \code{\link[=key_antimicrobials]{key_antimicrobials()}} and ignored by \code{\link[=antimicrobials_equal]{antimicrobials_equal()}}.
Please see the \code{\link[=first_isolate]{first_isolate()}} function how these important functions enable the 'phenotype-based' method for determination of first isolates.
The default antimicrobial agents used for \strong{all rows} (set in \code{universal}) are:
The default antimicrobial drugs used for \strong{all rows} (set in \code{universal}) are:
\itemize{
\item Ampicillin
\item Amoxicillin/clavulanic acid
@ -77,7 +77,7 @@ The default antimicrobial agents used for \strong{all rows} (set in \code{univer
\item Trimethoprim/sulfamethoxazole
}
The default antimicrobial agents used for \strong{Gram-negative bacteria} (set in \code{gram_negative}) are:
The default antimicrobial drugs used for \strong{Gram-negative bacteria} (set in \code{gram_negative}) are:
\itemize{
\item Cefotaxime
\item Ceftazidime
@ -87,7 +87,7 @@ The default antimicrobial agents used for \strong{Gram-negative bacteria} (set i
\item Tobramycin
}
The default antimicrobial agents used for \strong{Gram-positive bacteria} (set in \code{gram_positive}) are:
The default antimicrobial drugs used for \strong{Gram-positive bacteria} (set in \code{gram_positive}) are:
\itemize{
\item Erythromycin
\item Oxacillin
@ -97,7 +97,7 @@ The default antimicrobial agents used for \strong{Gram-positive bacteria} (set i
\item Vancomycin
}
The default antimicrobial agents used for \strong{fungi} (set in \code{antifungal}) are:
The default antimicrobial drugs used for \strong{fungi} (set in \code{antifungal}) are:
\itemize{
\item Anidulafungin
\item Caspofungin