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(v0.8.0.9036) complete documentation rewrite

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dr. M.S. (Matthijs) Berends
2019-11-28 22:32:17 +01:00
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R/count.R
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# Visit our website for more info: https://msberends.gitlab.io/AMR. #
# ==================================================================== #
#' Count 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 \code{dplyr}s \code{\link[dplyr]{summarise}} and support grouped variables, see \emph{Examples}.
#' @description These functions can be used to count resistant/susceptible microbial isolates. All functions support quasiquotation with pipes, can be used in [summarise()] and support grouped variables, see *Examples*.
#'
#' \code{count_resistant()} should be used to count resistant isolates, \code{count_susceptible()} should be used to count susceptible isolates.\cr
#' @param ... one or more vectors (or columns) with antibiotic interpretations. They will be transformed internally with \code{\link{as.rsi}} if needed.
#' [count_resistant()] should be used to count resistant isolates, [count_susceptible()] should be used to count susceptible isolates.
#' @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 S, I and R
#' @details These functions are meant to count isolates. Use the \code{\link{resistance}}/\code{\link{susceptibility}} functions to calculate microbial resistance/susceptibility.
#' @details These functions are meant to count isolates. Use the [resistance()]/[susceptibility()] functions to calculate microbial resistance/susceptibility.
#'
#' The function \code{count_resistant()} is equal to the function \code{count_R()}. The function \code{count_susceptible()} is equal to the function \code{count_SI()}.
#' The function [count_resistant()] is equal to the function [count_R()]. The function [count_susceptible()] is equal to the function [count_SI()].
#'
#' The function \code{n_rsi()} is an alias of \code{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 \code{\link{n_distinct}()}. Their function is equal to \code{count_susceptible(...) + count_resistant(...)}.
#' 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 \code{count_df()} takes any variable from \code{data} that has an \code{"rsi"} class (created with \code{\link{as.rsi}()}) and counts the number of S's, I's and R's. The function \code{rsi_df()} works exactly like \code{count_df()}, but adds the percentage of S, I and R.
#' 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. The function [rsi_df()] works exactly like [count_df()], but adds the percentage of S, I and R.
#' @inheritSection proportion Combination therapy
#' @seealso \code{\link{proportion}_*} to calculate microbial resistance and susceptibility.
#' @return Integer
#' @seealso [`proportion_*`][proportion] to calculate microbial resistance and susceptibility.
#' @return An [`integer`]
#' @rdname count
#' @name count
#' @export