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(v2.1.1.9232) is.mic() iteration, documentation cleanup

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dr. M.S. (Matthijs) Berends
2025-03-31 10:51:31 +02:00
parent 5f5b77bfaf
commit 63099cd81e
93 changed files with 1001 additions and 990 deletions
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16
man/antimicrobial_selectors.Rd
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@@ -131,21 +131,21 @@ not_intrinsic_resistant(only_sir_columns = FALSE, col_mo = NULL,
version_expected_phenotypes = 1.2, ...)
}
\arguments{
\item{only_sir_columns}{a \link{logical} to indicate whether only columns of class \code{sir} must be selected (default is \code{FALSE}), see \code{\link[=as.sir]{as.sir()}}}
\item{only_sir_columns}{A \link{logical} to indicate whether only columns of class \code{sir} must be selected (default is \code{FALSE}), see \code{\link[=as.sir]{as.sir()}}}
\item{only_treatable}{a \link{logical} to indicate whether antimicrobial drugs should be excluded that are only for laboratory tests (default is \code{TRUE}), such as gentamicin-high (\code{GEH}) and imipenem/EDTA (\code{IPE})}
\item{only_treatable}{A \link{logical} to indicate whether antimicrobial drugs should be excluded that are only for laboratory tests (default is \code{TRUE}), such as gentamicin-high (\code{GEH}) and imipenem/EDTA (\code{IPE})}
\item{return_all}{a \link{logical} to indicate whether all matched columns must be returned (default is \code{TRUE}). With \code{FALSE}, only the first of each unique antimicrobial will be returned, e.g. if both columns \code{"genta"} and \code{"gentamicin"} exist in the data, only the first hit for gentamicin will be returned.}
\item{return_all}{A \link{logical} to indicate whether all matched columns must be returned (default is \code{TRUE}). With \code{FALSE}, only the first of each unique antimicrobial will be returned, e.g. if both columns \code{"genta"} and \code{"gentamicin"} exist in the data, only the first hit for gentamicin will be returned.}
\item{...}{ignored, only in place to allow future extensions}
\item{...}{Ignored, only in place to allow future extensions}
\item{amr_class}{an antimicrobial class or a part of it, such as \code{"carba"} and \code{"carbapenems"}. The columns \code{group}, \code{atc_group1} and \code{atc_group2} of the \link{antimicrobials} data set will be searched (case-insensitive) for this value.}
\item{amr_class}{An antimicrobial class or a part of it, such as \code{"carba"} and \code{"carbapenems"}. The columns \code{group}, \code{atc_group1} and \code{atc_group2} of the \link{antimicrobials} data set will be searched (case-insensitive) for this value.}
\item{filter}{an \link{expression} to be evaluated in the \link{antimicrobials} data set, such as \code{name \%like\% "trim"}}
\item{filter}{An \link{expression} to be evaluated in the \link{antimicrobials} data set, such as \code{name \%like\% "trim"}}
\item{col_mo}{column name of the names or codes of the microorganisms (see \code{\link[=as.mo]{as.mo()}}) - the default is the first column of class \code{\link{mo}}. Values will be coerced using \code{\link[=as.mo]{as.mo()}}.}
\item{col_mo}{Column name of the names or codes of the microorganisms (see \code{\link[=as.mo]{as.mo()}}) - the default is the first column of class \code{\link{mo}}. Values will be coerced using \code{\link[=as.mo]{as.mo()}}.}
\item{version_expected_phenotypes}{the version number to use for the EUCAST Expected Phenotypes. Can be "1.2".}
\item{version_expected_phenotypes}{The version number to use for the EUCAST Expected Phenotypes. Can be "1.2".}
}
\value{
When used inside selecting or filtering, this returns a \link{character} vector of column names, with additional class \code{"amr_selector"}. When used individually, this returns an \link[=as.ab]{'ab' vector} with all possible antimicrobials that the function would be able to select or filter.