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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
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man/proportion.Rd
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@ -52,29 +52,29 @@ sir_df(data, translate_ab = "name", language = get_AMR_locale(),
confidence_level = 0.95)
}
\arguments{
\item{...}{one or more vectors (or columns) with antibiotic interpretations. They will be transformed internally with \code{\link[=as.sir]{as.sir()}} if needed. Use multiple columns to calculate (the lack of) co-resistance: the probability where one of two drugs have a resistant or susceptible result. See \emph{Examples}.}
\item{...}{One or more vectors (or columns) with antibiotic interpretations. They will be transformed internally with \code{\link[=as.sir]{as.sir()}} if needed. Use multiple columns to calculate (the lack of) co-resistance: the probability where one of two drugs have a resistant or susceptible result. See \emph{Examples}.}
\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{as_percent}{a \link{logical} to indicate whether the output must be returned as a hundred fold with \% sign (a character). A value of \code{0.123456} will then be returned as \code{"12.3\%"}.}
\item{as_percent}{A \link{logical} to indicate whether the output must be returned as a hundred fold with \% sign (a character). A value of \code{0.123456} will then be returned as \code{"12.3\%"}.}
\item{only_all_tested}{(for combination therapies, i.e. using more than one variable for \code{...}): a \link{logical} to indicate that isolates must be tested for all antimicrobials, see section \emph{Combination Therapy} below}
\item{ab_result}{antibiotic results to test against, must be one or more values of "S", "SDD", "I", or "R"}
\item{ab_result}{Antibiotic results to test against, must be one or more values of "S", "SDD", "I", or "R"}
\item{confidence_level}{the confidence level for the returned confidence interval. For the calculation, the number of S or SI isolates, and R isolates are compared with the total number of available isolates with R, S, or I by using \code{\link[=binom.test]{binom.test()}}, i.e., the Clopper-Pearson method.}
\item{confidence_level}{The confidence level for the returned confidence interval. For the calculation, the number of S or SI isolates, and R isolates are compared with the total number of available isolates with R, S, or I by using \code{\link[=binom.test]{binom.test()}}, i.e., the Clopper-Pearson method.}
\item{side}{the side of the confidence interval to return. The default is \code{"both"} for a length 2 vector, but can also be (abbreviated as) \code{"min"}/\code{"left"}/\code{"lower"}/\code{"less"} or \code{"max"}/\code{"right"}/\code{"higher"}/\code{"greater"}.}
\item{side}{The side of the confidence interval to return. The default is \code{"both"} for a length 2 vector, but can also be (abbreviated as) \code{"min"}/\code{"left"}/\code{"lower"}/\code{"less"} or \code{"max"}/\code{"right"}/\code{"higher"}/\code{"greater"}.}
\item{collapse}{a \link{logical} to indicate whether the output values should be 'collapsed', i.e. be merged together into one value, or a character value to use for collapsing}
\item{collapse}{A \link{logical} to indicate whether the output values should be 'collapsed', i.e. be merged together into one value, or a character value to use for collapsing}
\item{data}{a \link{data.frame} containing columns with class \code{\link{sir}} (see \code{\link[=as.sir]{as.sir()}})}
\item{data}{A \link{data.frame} containing columns with class \code{\link{sir}} (see \code{\link[=as.sir]{as.sir()}})}
\item{translate_ab}{a column name of the \link{antimicrobials} data set to translate the antibiotic abbreviations to, using \code{\link[=ab_property]{ab_property()}}}
\item{translate_ab}{A column name of the \link{antimicrobials} data set to translate the antibiotic abbreviations to, using \code{\link[=ab_property]{ab_property()}}}
\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{combine_SI}{a \link{logical} to indicate whether all values of S, SDD, and I must be merged into one, so the output only consists of S+SDD+I vs. R (susceptible vs. resistant) - the default is \code{TRUE}}
\item{combine_SI}{A \link{logical} to indicate whether all values of S, SDD, and I must be merged into one, so the output only consists of S+SDD+I vs. R (susceptible vs. resistant) - the default is \code{TRUE}}
}
\value{
A \link{double} or, when \code{as_percent = TRUE}, a \link{character}.