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fix for as.mo, added also_single_tested

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dr. M.S. (Matthijs) Berends
2018-10-19 13:53:31 +02:00
parent 032c0d51ef
commit 86b03577a7
14 changed files with 128 additions and 66 deletions
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12
man/count.Rd
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@ -15,15 +15,15 @@
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(...)
count_R(..., also_single_tested = FALSE)
count_IR(...)
count_IR(..., also_single_tested = FALSE)
count_I(...)
count_I(..., also_single_tested = FALSE)
count_SI(...)
count_SI(..., also_single_tested = FALSE)
count_S(...)
count_S(..., also_single_tested = FALSE)
count_all(...)
@ -35,6 +35,8 @@ count_df(data, translate_ab = getOption("get_antibiotic_names",
\arguments{
\item{...}{one or more vectors (or columns) with antibiotic interpretations. They will be transformed internally with \code{\link{as.rsi}} if needed.}
\item{also_single_tested}{a logical to indicate whether (in combination therapies) also observations should be included where not all antibiotics were tested, but at least one of the tested antibiotics contains a target interpretation (e.g. S in case of \code{portion_S} and R in case of \code{portion_R}). \strong{This would lead to selection bias in almost all cases.}}
\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")}.}

2
man/microorganisms.certe.Rd
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@ -4,7 +4,7 @@
\name{microorganisms.certe}
\alias{microorganisms.certe}
\title{Translation table for Certe}
\format{A \code{\link{tibble}} with 2,664 observations and 2 variables:
\format{A \code{\link{tibble}} with 2,665 observations and 2 variables:
\describe{
\item{\code{certe}}{Code of microorganism according to Certe MMB}
\item{\code{mo}}{Code of microorganism in \code{\link{microorganisms}}}

17
man/portion.Rd
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@ -15,15 +15,20 @@
Wickham H. \strong{Tidy Data.} The Journal of Statistical Software, vol. 59, 2014. \url{http://vita.had.co.nz/papers/tidy-data.html}
}
\usage{
portion_R(..., minimum = 30, as_percent = FALSE)
portion_R(..., minimum = 30, as_percent = FALSE,
also_single_tested = FALSE)
portion_IR(..., minimum = 30, as_percent = FALSE)
portion_IR(..., minimum = 30, as_percent = FALSE,
also_single_tested = FALSE)
portion_I(..., minimum = 30, as_percent = FALSE)
portion_I(..., minimum = 30, as_percent = FALSE,
also_single_tested = FALSE)
portion_SI(..., minimum = 30, as_percent = FALSE)
portion_SI(..., minimum = 30, as_percent = FALSE,
also_single_tested = FALSE)
portion_S(..., minimum = 30, as_percent = FALSE)
portion_S(..., minimum = 30, as_percent = FALSE,
also_single_tested = FALSE)
portion_df(data, translate_ab = getOption("get_antibiotic_names",
"official"), minimum = 30, as_percent = FALSE, combine_IR = FALSE)
@ -35,6 +40,8 @@ portion_df(data, translate_ab = getOption("get_antibiotic_names",
\item{as_percent}{a 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{also_single_tested}{a logical to indicate whether (in combination therapies) also observations should be included where not all antibiotics were tested, but at least one of the tested antibiotics contains a target interpretation (e.g. S in case of \code{portion_S} and R in case of \code{portion_R}). \strong{This would lead to selection bias in almost all cases.}}
\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")}.}