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quasiquotation, alpha for geom_rsi

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dr. M.S. (Matthijs) Berends
2018-08-23 00:40:36 +02:00
parent 43ba16f8ed
commit da5379c881
18 changed files with 304 additions and 235 deletions
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16
man/count.Rd
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@@ -13,23 +13,21 @@
Wickham H. \strong{Tidy Data.} The Journal of Statistical Software, vol. 59, 2014. \url{http://vita.had.co.nz/papers/tidy-data.html}
}
\usage{
count_R(ab1, ab2 = NULL)
count_R(...)
count_IR(ab1, ab2 = NULL)
count_IR(...)
count_I(ab1)
count_I(...)
count_SI(ab1, ab2 = NULL)
count_SI(...)
count_S(ab1, ab2 = NULL)
count_S(...)
count_df(data, translate_ab = getOption("get_antibiotic_names",
"official"))
}
\arguments{
\item{ab1}{vector of antibiotic interpretations, they will be transformed internally with \code{\link{as.rsi}} if needed}
\item{ab2}{like \code{ab}, a vector of antibiotic interpretations. Use this to calculate (the lack of) co-resistance: the probability where one of two drugs have a resistant or susceptible result. See Examples.}
\item{...}{one or more vectors (or columns) with antibiotic interpretations. They will be transformed internally with \code{\link{as.rsi}} 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 Examples.}
\item{data}{a \code{data.frame} containing columns with class \code{rsi} (see \code{\link{as.rsi}})}
@@ -39,7 +37,7 @@ count_df(data, translate_ab = getOption("get_antibiotic_names",
Integer
}
\description{
These functions can be used to count resistant/susceptible microbial isolates. All functions can be used in \code{dplyr}s \code{\link[dplyr]{summarise}} and support grouped variables, see \emph{Examples}.
These functions can be used to count resistant/susceptible microbial isolates. All functions support quasiquotation with pipes, can be used in \code{dplyr}s \code{\link[dplyr]{summarise}} and support grouped variables, see \emph{Examples}.
\code{count_R} and \code{count_IR} can be used to count resistant isolates, \code{count_S} and \code{count_SI} can be used to count susceptible isolates.\cr
}