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(v2.1.1.9187) WISCA fix

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dr. M.S. (Matthijs) Berends
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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6
R/antibiogram.R
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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)) {