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(v3.0.1.9076) fix: normalise year-qualified AMR_guideline option in all affected functions

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Matthijs Berends
2026-06-27 13:53:25 +02:00
committed by GitHub
parent f7d353361c
commit 12cabca29d
7 changed files with 33 additions and 13 deletions
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10
R/count.R
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@@ -126,6 +126,11 @@ count_resistant <- function(...,
only_all_tested = FALSE,
guideline = getOption("AMR_guideline", "EUCAST")) {
# other arguments for meet_criteria are handled by sir_calc()
if (guideline %like% "EUCAST") {
guideline <- "EUCAST"
} else if (guideline %like% "CLSI") {
guideline <- "CLSI"
}
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("count_resistant", "eucast_default", entire_session = TRUE)) {
message_("{.help [{.fun count_resistant}](AMR::count_resistant)} assumes the EUCAST guideline and thus considers the 'I' category susceptible. Set the {.arg guideline} argument or the {.code AMR_guideline} option to either \"CLSI\" or \"EUCAST\", see {.topic [AMR-options](AMR::AMR-options)}.")
@@ -150,6 +155,11 @@ count_susceptible <- function(...,
only_all_tested = FALSE,
guideline = getOption("AMR_guideline", "EUCAST")) {
# other arguments for meet_criteria are handled by sir_calc()
if (guideline %like% "EUCAST") {
guideline <- "EUCAST"
} else if (guideline %like% "CLSI") {
guideline <- "CLSI"
}
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("count_susceptible", "eucast_default", entire_session = TRUE)) {
message_("{.help [{.fun count_susceptible}](AMR::count_susceptible)} assumes the EUCAST guideline and thus considers the 'I' category susceptible. Set the {.arg guideline} argument or the {.code AMR_guideline} option to either \"CLSI\" or \"EUCAST\", see {.topic [AMR-options](AMR::AMR-options)}.")