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make rsi work in more cases, documentation update

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dr. M.S. (Matthijs) Berends
2023-02-22 14:38:57 +01:00
parent 380cbec0e8
commit dad25302f2
87 changed files with 401 additions and 327 deletions
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R/proportion.R
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@ -39,10 +39,10 @@
#' @param data a [data.frame] containing columns with class [`sir`] (see [as.sir()])
#' @param translate_ab a column name of the [antibiotics] data set to translate the antibiotic abbreviations to, using [ab_property()]
#' @inheritParams ab_property
#' @param combine_SI a [logical] to indicate whether all values of S and I must be merged into one, so the output only consists of S+I vs. R (susceptible vs. resistant), defaults to `TRUE`
#' @param combine_SI a [logical] to indicate whether all values of S and I must be merged into one, so the output only consists of S+I vs. R (susceptible vs. resistant) - the default is `TRUE`
#' @param ab_result antibiotic results to test against, must be one or more values of "S", "I", or "R"
#' @param confidence_level the confidence level for the returned confidence interval. For the calculation, the number of S or SI isolates, and R isolates are compared with the total number of available isolates with R, S, or I by using [binom.test()], i.e., the Clopper-Pearson method.
#' @param side the side of the confidence interval to return. Defaults to `"both"` for a length 2 vector, but can also be (abbreviated as) `"min"`/`"left"`/`"lower"`/`"less"` or `"max"`/`"right"`/`"higher"`/`"greater"`.
#' @param side the side of the confidence interval to return. The default is `"both"` for a length 2 vector, but can also be (abbreviated as) `"min"`/`"left"`/`"lower"`/`"less"` or `"max"`/`"right"`/`"higher"`/`"greater"`.
#' @inheritSection as.sir Interpretation of SIR
#' @details
#' The function [resistance()] is equal to the function [proportion_R()]. The function [susceptibility()] is equal to the function [proportion_SI()].