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AMR/R/n_rsi.R

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2.2 KiB
R

# ==================================================================== #
# TITLE #
# Antimicrobial Resistance (AMR) Analysis #
# #
# AUTHORS #
# Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
# #
# LICENCE #
# This program is free software; you can redistribute it and/or modify #
# it under the terms of the GNU General Public License version 2.0, #
# as published by the Free Software Foundation. #
# #
# This program is distributed in the hope that it will be useful, #
# but WITHOUT ANY WARRANTY; without even the implied warranty of #
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the #
# GNU General Public License for more details. #
# ==================================================================== #
#' Count cases with antimicrobial results
#'
#' This counts all cases where antimicrobial interpretations are available. The way it can be used is equal to \code{\link{n_distinct}}. Its function is equal to \code{count_S(...) + count_IR(...)}.
#' @inheritParams portion
#' @export
#' @seealso \code{\link[AMR]{count}_*} to count resistant and susceptibile isolates per interpretation type.\cr
#' \code{\link{portion}_*} to calculate microbial resistance and susceptibility.
#' @examples
#' library(dplyr)
#'
#' septic_patients %>%
#' group_by(hospital_id) %>%
#' summarise(cipro_p = portion_S(cipr, as_percent = TRUE),
#' cipro_n = n_rsi(cipr),
#' genta_p = portion_S(gent, as_percent = TRUE),
#' genta_n = n_rsi(gent),
#' combination_p = portion_S(cipr, gent, as_percent = TRUE),
#' combination_n = n_rsi(cipr, gent))
n_rsi <- function(...) {
# only print warnings once, if needed
count_S(...) + suppressWarnings(count_IR(...))
}