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dr. M.S. (Matthijs) Berends
2022-08-21 16:37:20 +02:00
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R/count.R
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@ -28,7 +28,6 @@
#' @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
#' @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
@ -45,11 +44,11 @@
#' @rdname count
#' @name count
#' @export
#' @inheritSection AMR Read more on Our Website!
#' @examples
#' # example_isolates is a data set available in the AMR package.
#' ?example_isolates
#' # run ?example_isolates for more info.
#'
#' # base R ------------------------------------------------------------
#' count_resistant(example_isolates$AMX) # counts "R"
#' count_susceptible(example_isolates$AMX) # counts "S" and "I"
#' count_all(example_isolates$AMX) # counts "S", "I" and "R"
@ -72,6 +71,7 @@
#' count_susceptible(example_isolates$AMX)
#' susceptibility(example_isolates$AMX) * n_rsi(example_isolates$AMX)
#'
#' # dplyr -------------------------------------------------------------
#' \donttest{
#' if (require("dplyr")) {
#' example_isolates %>%