mirror of
https://github.com/msberends/AMR.git
synced 2024-12-27 11:26:11 +01:00
54 lines
2.5 KiB
R
54 lines
2.5 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. #
|
||
|
|
# ==================================================================== #
|
||
|
|
|
||
|
|
#' 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
|
||
|
|
}
|
||
|
|
}
|