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parameter combine_IR

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dr. M.S. (Matthijs) Berends
2018-10-16 09:59:31 +02:00
parent 5b5b95a47b
commit d5a41de711
10 changed files with 110 additions and 48 deletions
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4
man/count.Rd
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@@ -30,7 +30,7 @@ count_all(...)
n_rsi(...)
count_df(data, translate_ab = getOption("get_antibiotic_names",
"official"))
"official"), combine_IR = FALSE)
}
\arguments{
\item{...}{one or more vectors (or columns) with antibiotic interpretations. They will be transformed internally with \code{\link{as.rsi}} if needed.}
@@ -38,6 +38,8 @@ count_df(data, translate_ab = getOption("get_antibiotic_names",
\item{data}{a \code{data.frame} containing columns with class \code{rsi} (see \code{\link{as.rsi}})}
\item{translate_ab}{a column name of the \code{\link{antibiotics}} data set to translate the antibiotic abbreviations to, using \code{\link{abname}}. This can be set with \code{\link{getOption}("get_antibiotic_names")}.}
\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. IR (susceptible vs. non-susceptible)}
}
\value{
Integer