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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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20
man/bug_drug_combinations.Rd
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@@ -15,25 +15,25 @@ bug_drug_combinations(x, col_mo = NULL, FUN = mo_shortname,
",", ".", ","), ...)
}
\arguments{
\item{x}{a data set with antimicrobials columns, such as \code{amox}, \code{AMX} and \code{AMC}}
\item{x}{A data set with antimicrobials columns, such as \code{amox}, \code{AMX} and \code{AMC}}
\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{FUN}{the function to call on the \code{mo} column to transform the microorganism codes - the default is \code{\link[=mo_shortname]{mo_shortname()}}}
\item{FUN}{The function to call on the \code{mo} column to transform the microorganism codes - the default is \code{\link[=mo_shortname]{mo_shortname()}}}
\item{include_n_rows}{a \link{logical} to indicate if the total number of rows must be included in the output}
\item{include_n_rows}{A \link{logical} to indicate if the total number of rows must be included in the output}
\item{...}{arguments passed on to \code{FUN}}
\item{...}{Arguments passed on to \code{FUN}}
\item{translate_ab}{a \link{character} of length 1 containing column names of the \link{antimicrobials} data set}
\item{translate_ab}{A \link{character} of length 1 containing column names of the \link{antimicrobials} data set}
\item{language}{language of the returned text - the default is the current system language (see \code{\link[=get_AMR_locale]{get_AMR_locale()}}) and can also be set with the package option \code{\link[=AMR-options]{AMR_locale}}. Use \code{language = NULL} or \code{language = ""} to prevent translation.}
\item{language}{Language of the returned text - the default is the current system language (see \code{\link[=get_AMR_locale]{get_AMR_locale()}}) and can also be set with the package option \code{\link[=AMR-options]{AMR_locale}}. Use \code{language = NULL} or \code{language = ""} to prevent translation.}
\item{minimum}{the minimum allowed number of available (tested) isolates. Any isolate count lower than \code{minimum} will return \code{NA} with a warning. The default number of \code{30} isolates is advised by the Clinical and Laboratory Standards Institute (CLSI) as best practice, see \emph{Source}.}
\item{minimum}{The minimum allowed number of available (tested) isolates. Any isolate count lower than \code{minimum} will return \code{NA} with a warning. The default number of \code{30} isolates is advised by the Clinical and Laboratory Standards Institute (CLSI) as best practice, see \emph{Source}.}
\item{combine_SI}{a \link{logical} to indicate whether values S, SDD, and I should be summed, so resistance will be based on only R - the default is \code{TRUE}}
\item{combine_SI}{A \link{logical} to indicate whether values S, SDD, and I should be summed, so resistance will be based on only R - the default is \code{TRUE}}
\item{add_ab_group}{a \link{logical} to indicate where the group of the antimicrobials must be included as a first column}
\item{add_ab_group}{A \link{logical} to indicate where the group of the antimicrobials must be included as a first column}
\item{remove_intrinsic_resistant}{\link{logical} to indicate that rows and columns with 100\% resistance for all tested antimicrobials must be removed from the table}