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(v3.0.1.9021) add guideline to resistance() and susceptibility()

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dr. M.S. (Matthijs) Berends
2026-02-12 20:34:06 +01:00
parent 499c830ee7
commit 12cf144b19
14 changed files with 145 additions and 36 deletions
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33
R/proportion.R
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@@ -38,6 +38,11 @@
#' @param only_all_tested (for combination therapies, i.e. using more than one variable for `...`): a [logical] to indicate that isolates must be tested for all antimicrobials, see section *Combination Therapy* below.
#' @param data A [data.frame] containing columns with class [`sir`] (see [as.sir()]).
#' @param translate_ab A column name of the [antimicrobials] data set to translate the antibiotic abbreviations to, using [ab_property()].
#' @param guideline Either `"EUCAST"` (default) or `"CLSI"`. With EUCAST, the 'I' category will be considered as susceptible (see [EUCAST website](https://www.eucast.org/bacteria/clinical-breakpoints-and-interpretation/definition-of-s-i-and-r/)), but with with CLSI, it will be considered resistant. Therefore:
#' * EUCAST: [susceptibility()] \eqn{= \%S + \%I}, [resistance()] \eqn{= \%R}
#' * CLSI: [susceptibility()] \eqn{= \%S + \%SDD}, [resistance()] \eqn{= \%I + \%R}
#'
#' You can also use e.g. [proportion_R()] or [proportion_S()] instead, to be explicit.
#' @inheritParams ab_property
#' @param combine_SI A [logical] to indicate whether all values of S, SDD, and I must be merged into one, so the output only consists of S+SDD+I vs. R (susceptible vs. resistant) - the default is `TRUE`.
#' @param ab_result Antibiotic results to test against, must be one or more values of "S", "SDD", "I", or "R".
@@ -228,10 +233,20 @@
resistance <- function(...,
minimum = 30,
as_percent = FALSE,
only_all_tested = FALSE) {
only_all_tested = FALSE,
guideline = getOption("AMR_guideline", "EUCAST")) {
# other arguments for meet_criteria are handled by sir_calc()
meet_criteria(guideline, allow_class = "character", is_in = c("EUCAST", "CLSI"), has_length = 1)
if (is.null(getOption("AMR_guideline")) && missing(guideline) && message_not_thrown_before("resistance", "eucast_default", entire_session = TRUE)) {
message_("`resistance()` assumes the EUCAST guideline and thus considers the 'I' category susceptible. Set the `guideline` argument or the `AMR_guideline` option to either \"CLSI\" or \"EUCAST\", see `?AMR-options`.")
message_("This message will be shown once per session.")
}
tryCatch(
sir_calc(...,
ab_result = c("R", "NWT", "NS"),
ab_result = c(
"R", "NWT", "NS",
if (identical(guideline, "CLSI")) "I"
),
minimum = minimum,
as_percent = as_percent,
only_all_tested = only_all_tested,
@@ -246,10 +261,20 @@ resistance <- function(...,
susceptibility <- function(...,
minimum = 30,
as_percent = FALSE,
only_all_tested = FALSE) {
only_all_tested = FALSE,
guideline = getOption("AMR_guideline", "EUCAST")) {
# other arguments for meet_criteria are handled by sir_calc()
meet_criteria(guideline, allow_class = "character", is_in = c("EUCAST", "CLSI"), has_length = 1)
if (is.null(getOption("AMR_guideline")) && missing(guideline) && message_not_thrown_before("susceptibility", "eucast_default", entire_session = TRUE)) {
message_("`susceptibility()` assumes the EUCAST guideline and thus considers the 'I' category susceptible. Set the `guideline` argument or the `AMR_guideline` option to either \"CLSI\" or \"EUCAST\", see `?AMR-options`.")
message_("This message will be shown once per session.")
}
tryCatch(
sir_calc(...,
ab_result = c("S", "SDD", "I", "WT"),
ab_result = c(
"S", "SDD", "WT",
if (identical(guideline, "EUCAST")) "I"
),
minimum = minimum,
as_percent = as_percent,
only_all_tested = only_all_tested,