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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

8
man/portion.Rd
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@ -26,18 +26,20 @@ portion_SI(..., minimum = 30, as_percent = FALSE)
portion_S(..., minimum = 30, as_percent = FALSE)
portion_df(data, translate_ab = getOption("get_antibiotic_names",
"official"), minimum = 30, as_percent = FALSE)
"official"), minimum = 30, as_percent = FALSE, 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. 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{minimum}{minimal amount of available isolates. Any number 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 Source.}
\item{minimum}{the minimal amount of available isolates. Any number 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 Source.}
\item{as_percent}{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 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{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{
Double or, when \code{as_percent = TRUE}, a character.

4
man/rsi.Rd
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@ -12,9 +12,9 @@ rsi(ab1, ab2 = NULL, interpretation = "IR", minimum = 30,
\item{interpretation}{antimicrobial interpretation to check for}
\item{minimum}{minimal amount of available isolates. Any number 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 Source.}
\item{minimum}{the minimal amount of available isolates. Any number 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 Source.}
\item{as_percent}{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 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{...}{deprecated parameters to support usage on older versions}
}