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(v1.3.0.9022) mo_matching_score(), poorman update, as.rsi() fix

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dr. M.S. (Matthijs) Berends
2020-09-18 16:05:53 +02:00
parent 89401ede9f
commit 4e40e42011
138 changed files with 2923 additions and 1472 deletions
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4
man/count.Rd
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@ -45,7 +45,7 @@ count_df(
\item{only_all_tested}{(for combination therapies, i.e. using more than one variable for \code{...}): a logical to indicate that isolates must be tested for all antibiotics, see section \emph{Combination therapy} below}
\item{data}{a \code{\link{data.frame}} containing columns with class \code{\link{rsi}} (see \code{\link[=as.rsi]{as.rsi()}})}
\item{data}{a \link{data.frame} containing columns with class \code{\link{rsi}} (see \code{\link[=as.rsi]{as.rsi()}})}
\item{translate_ab}{a column name of the \link{antibiotics} data set to translate the antibiotic abbreviations to, using \code{\link[=ab_property]{ab_property()}}. Use a value}
@ -56,7 +56,7 @@ count_df(
\item{combine_IR}{a logical to indicate whether all values of I and R must be merged into one, so the output only consists of S vs. I+R (susceptible vs. non-susceptible). This is outdated, see parameter \code{combine_SI}.}
}
\value{
An \code{\link{integer}}
An \link{integer}
}
\description{
These functions can be used to count resistant/susceptible microbial isolates. All functions support quasiquotation with pipes, can be used in \code{summarise()} from the \code{dplyr} package and also support grouped variables, please see \emph{Examples}.