AMR/R/rsi.R

54 lines
2.5 KiB
R
Raw Normal View History

2018-08-10 15:01:05 +02:00
# ==================================================================== #
# 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. #
# ==================================================================== #
#' Calculate resistance of isolates
#'
#' This function is deprecated. Use the \code{\link{portion}} functions instead.
#' @inheritParams portion
#' @param interpretation antimicrobial interpretation to check for
#' @param ... deprecated parameters to support usage on older versions
#' @importFrom dplyr case_when
#' @export
rsi <- function(ab1,
ab2 = NULL,
interpretation = "IR",
minimum = 30,
as_percent = FALSE,
...) {
result <- case_when(
interpretation == "S" ~ portion_S(ab1 = ab1, ab2 = ab2, minimum = minimum, as_percent = FALSE),
interpretation %in% c("SI", "IS") ~ portion_SI(ab1 = ab1, ab2 = ab2, minimum = minimum, as_percent = FALSE),
interpretation == "I" ~ portion_I(ab1 = ab1, minimum = minimum, as_percent = FALSE),
interpretation %in% c("RI", "IR") ~ portion_IR(ab1 = ab1, ab2 = ab2, minimum = minimum, as_percent = FALSE),
interpretation == "R" ~ portion_R(ab1 = ab1, ab2 = ab2, minimum = minimum, as_percent = FALSE),
TRUE ~ -1
)
if (result == -1) {
stop("invalid interpretation")
}
.Deprecated(new = paste0("portion_", interpretation))
if (as_percent == TRUE) {
percent(result, force_zero = TRUE)
} else {
result
}
}