(v2.1.1.9187) WISCA fix

R/antibiogram.R

@@ -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)) {

R/data.R

@@ -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

R/temp_file

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

R/zz_deprecated.R

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

R/zzz.R

@@ -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))