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55 lines
2.0 KiB
R
55 lines
2.0 KiB
R
% Generated by roxygen2: do not edit by hand
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% Please edit documentation in R/rsi_analysis.R
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\name{rsi_df}
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\alias{rsi_df}
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\title{Resistance of isolates in data.frame}
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\usage{
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rsi_df(tbl, antibiotics, interpretation = "IR", minimum = 30,
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percent = FALSE, info = TRUE, warning = TRUE)
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}
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\arguments{
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\item{tbl}{\code{data.frame} containing columns with antibiotic interpretations.}
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\item{antibiotics}{character vector with 1, 2 or 3 antibiotics that occur as column names in \code{tbl}, like \code{antibiotics = c("amox", "amcl")}}
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\item{interpretation}{antimicrobial interpretation of which the portion must be calculated. Valid values are \code{"S"}, \code{"SI"}, \code{"I"}, \code{"IR"} or \code{"R"}.}
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\item{minimum}{minimal amount of available isolates. Any number lower than \code{minimum} will return \code{NA} with a warning (when \code{warning = TRUE}).}
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\item{percent}{return output as percent (text), will else (at default) be a double}
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\item{info}{calculate the amount of available isolates and print it, like \code{n = 423}}
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\item{warning}{show a warning when the available amount of isolates is below \code{minimum}}
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}
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\value{
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Double or, when \code{percent = TRUE}, a character.
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}
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\description{
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\strong{NOTE: use \code{\link{rsi}} in dplyr functions like \code{\link[dplyr]{summarise}}.} \cr Calculate the percentage of S, SI, I, IR or R of a \code{data.frame} containing isolates.
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}
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\details{
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Remember that you should filter your table to let it contain \strong{only first isolates}!
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}
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\examples{
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\dontrun{
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rsi_df(tbl_with_bloodcultures, 'amcl')
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rsi_df(tbl_with_bloodcultures, c('amcl', 'gent'), interpretation = 'IR')
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library(dplyr)
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# calculate current empiric therapy of Helicobacter gastritis:
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my_table \%>\%
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filter(first_isolate == TRUE,
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genus == "Helicobacter") \%>\%
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rsi_df(antibiotics = c("amox", "metr"))
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}
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}
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\seealso{
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\code{\link{rsi}} for the function that can be used with \code{\link[dplyr]{summarise}} directly.
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}
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\keyword{antibiotics}
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\keyword{isolate}
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\keyword{isolates}
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\keyword{rsi}
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