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(v2.1.1.9187) WISCA fix

This commit is contained in:
2025-03-07 22:27:21 +01:00
parent f7938289eb
commit b67613ce08
15 changed files with 11 additions and 18 deletions

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@ -606,9 +606,6 @@ antibiogram.default <- function(x,
warning_("All combinations had less than `minimum = ", minimum, "` results, returning an empty antibiogram")
return(as_original_data_class(data.frame(), class(x), extra_class = "antibiogram"))
} else if (any(out$n_tested < minimum, na.rm = TRUE)) {
out <- out %pm>%
# also for WISCA, refrain from anything below 15 isolates:
subset(n_tested > 15)
mins <- sum(out$n_tested < minimum, na.rm = TRUE)
if (wisca == FALSE) {
out <- out %pm>%
@ -620,7 +617,6 @@ antibiogram.default <- function(x,
warning_("Number of tested isolates per regimen should exceed ", minimum, " for each species. Coverage estimates might be inaccurate.", call = FALSE)
}
}
if (NROW(out) == 0) {
return(as_original_data_class(data.frame(), class(x), extra_class = "antibiogram"))
}
@ -671,6 +667,7 @@ antibiogram.default <- function(x,
out_wisca <- out %pm>%
pm_group_by(ab)
}
out_wisca <- out_wisca %pm>%
pm_summarise(
coverage = NA_real_,
@ -680,6 +677,7 @@ antibiogram.default <- function(x,
n_tested = sum(n_tested, na.rm = TRUE),
n_susceptible = sum(n_susceptible, na.rm = TRUE)
)
out_wisca$p_susceptible <- out_wisca$n_susceptible / out_wisca$n_tested
if (isTRUE(has_syndromic_group)) {

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@ -74,7 +74,6 @@
#' * European Commission Public Health PHARMACEUTICALS - COMMUNITY REGISTER: <https://ec.europa.eu/health/documents/community-register/html/reg_hum_atc.htm>
#' @inheritSection WHOCC WHOCC
#' @seealso [microorganisms], [intrinsic_resistant]
#' @aliases antibiotics
#' @examples
#' antimicrobials
#' antivirals

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@ -1 +0,0 @@
test_that("key_antimicrobials works", {

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@ -36,6 +36,7 @@
NULL
#' @rdname AMR-deprecated
#' @usage NULL
#' @export
"antibiotics"

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@ -210,7 +210,9 @@ AMR_env$cross_icon <- if (isTRUE(base::l10n_info()$`UTF-8`)) "\u00d7" else "x"
# deprecated antibiotics data set
makeActiveBinding("antibiotics", function() {
deprecation_warning(old = "antibiotics", new = "antimicrobials", is_function = FALSE, is_dataset = TRUE)
if (interactive()) {
deprecation_warning(old = "antibiotics", new = "antimicrobials", is_function = FALSE, is_dataset = TRUE)
}
AMR::antimicrobials
}, env = asNamespace(pkgname))