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(v1.5.0.9006) major documentation update

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dr. M.S. (Matthijs) Berends
2021-01-18 16:57:56 +01:00
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R/count.R
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@ -23,12 +23,12 @@
# how to conduct AMR analysis: https://msberends.github.io/AMR/ #
# ==================================================================== #
#' Count available isolates
#' Count Available Isolates
#'
#' @description These functions can be used to count resistant/susceptible microbial isolates. All functions support quasiquotation with pipes, can be used in `summarise()` from the `dplyr` package and also support grouped variables, please see *Examples*.
#' @description These functions can be used to count resistant/susceptible microbial isolates. All functions support quasiquotation with pipes, can be used in `summarise()` from the `dplyr` package and also support grouped variables, see *Examples*.
#'
#' [count_resistant()] should be used to count resistant isolates, [count_susceptible()] should be used to count susceptible isolates.
#' @inheritSection lifecycle Stable lifecycle
#' @inheritSection lifecycle Stable Lifecycle
#' @param ... one or more vectors (or columns) with antibiotic interpretations. They will be transformed internally with [as.rsi()] if needed.
#' @inheritParams proportion
#' @inheritSection as.rsi Interpretation of R and S/I
@ -39,13 +39,13 @@
#' The function [n_rsi()] is an alias of [count_all()]. They can be used to count all available isolates, i.e. where all input antibiotics have an available result (S, I or R). Their use is equal to `n_distinct()`. Their function is equal to `count_susceptible(...) + count_resistant(...)`.
#'
#' The function [count_df()] takes any variable from `data` that has an [`rsi`] class (created with [as.rsi()]) and counts the number of S's, I's and R's. It also supports grouped variables. The function [rsi_df()] works exactly like [count_df()], but adds the percentage of S, I and R.
#' @inheritSection proportion Combination therapy
#' @inheritSection proportion Combination Therapy
#' @seealso [`proportion_*`][proportion] to calculate microbial resistance and susceptibility.
#' @return An [integer]
#' @rdname count
#' @name count
#' @export
#' @inheritSection AMR Read more on our website!
#' @inheritSection AMR Read more on Our Website!
#' @examples
#' # example_isolates is a data set available in the AMR package.
#' ?example_isolates