mirror of https://github.com/msberends/AMR.git
62 lines
2.7 KiB
R
62 lines
2.7 KiB
R
# ==================================================================== #
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# TITLE #
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# Antimicrobial Resistance (AMR) Analysis #
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# #
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# AUTHORS #
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# Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
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# #
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# LICENCE #
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# This program is free software; you can redistribute it and/or modify #
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# it under the terms of the GNU General Public License version 2.0, #
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# as published by the Free Software Foundation. #
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# #
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# This program is distributed in the hope that it will be useful, #
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# but WITHOUT ANY WARRANTY; without even the implied warranty of #
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# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the #
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# GNU General Public License for more details. #
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# ==================================================================== #
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#' Calculate resistance of isolates
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#'
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#' This function is deprecated. Use the \code{\link{portion}} functions instead.
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#' @inheritParams portion
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#' @param ab1,ab2 vector (or column) with antibiotic interpretations. It will be transformed internally with \code{\link{as.rsi}} if needed.
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#' @param interpretation antimicrobial interpretation to check for
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#' @param ... deprecated parameters to support usage on older versions
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#' @importFrom dplyr tibble case_when
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#' @export
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rsi <- function(ab1,
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ab2 = NULL,
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interpretation = "IR",
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minimum = 30,
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as_percent = FALSE,
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...) {
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if (all(is.null(ab2))) {
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df <- tibble(ab1 = ab1)
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} else {
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df <- tibble(ab1 = ab1,
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ab2 = ab2)
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}
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result <- case_when(
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interpretation == "S" ~ portion_S(df, minimum = minimum, as_percent = FALSE),
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interpretation %in% c("SI", "IS") ~ portion_SI(df, minimum = minimum, as_percent = FALSE),
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interpretation == "I" ~ portion_I(df, minimum = minimum, as_percent = FALSE),
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interpretation %in% c("RI", "IR") ~ portion_IR(df, minimum = minimum, as_percent = FALSE),
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interpretation == "R" ~ portion_R(df, minimum = minimum, as_percent = FALSE),
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TRUE ~ -1
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)
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if (result == -1) {
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stop("invalid interpretation")
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}
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.Deprecated(new = paste0("portion_", interpretation))
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if (as_percent == TRUE) {
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percent(result, force_zero = TRUE)
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} else {
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result
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}
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}
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