(v3.0.1.9059) Update taxonomy of microorganisms

data-raw/_reproduction_scripts/reproduction_of_clinical_breakpoints.R

@@ -293,7 +293,7 @@ breakpoints_new <- breakpoints |>
     host = ifelse(BREAKPOINT_TYPE == "ECOFF", "ECOFF", tolower(HOST)),
     method = TEST_METHOD,
     site = SITE_OF_INFECTION,
-    mo,
+    mo = as.mo(mo),
     rank_index = case_when(
       is.na(mo_rank(mo, keep_synonyms = TRUE)) ~ 6, # for UNKNOWN, B_GRAMN, B_ANAER, B_ANAER-NEG, etc.
       mo_rank(mo, keep_synonyms = TRUE) %like% "(infra|sub)" ~ 1,
@@ -453,6 +453,9 @@ breakpoints_new$breakpoint_R[breakpoints_new$guideline %like% "EUCAST" & breakpo
 breakpoints_new <- breakpoints_new |>
   filter(!(guideline %like% "EUCAST (2024|2025|2026)" & ref_tbl == "PK/PD"))
 
+# WHONET still contains generic anaerobic rules for EUCAST >= 2021, but this was ended from v12 (2022) on
+breakpoints_new <- breakpoints_new |>
+  filter(!(guideline %like% "EUCAST (2022|2023|2024|2025|2026)" & ref_tbl %like% "anaerob"))
 
 # WHONET adds one log2 level to the R breakpoint for their software, e.g. in AMC in Enterobacterales:
 # EUCAST 2023 guideline: S <= 8 and R > 8

data-raw/_reproduction_scripts/reproduction_of_intrinsic_resistant.R

@@ -35,13 +35,13 @@ for (i in seq_len(nrow(antimicrobials))) {
   colnames(int_resis)[ncol(int_resis)] <- antimicrobials$ab[i]
 }
 
-int_resis <- eucast_rules(int_resis,
-  eucast_rules_df = subset(
-    AMR:::EUCAST_RULES_DF,
-    is.na(have_these_values) & reference.rule_group == "Expected phenotypes" & reference.version == 1.2
-  ),
-  overwrite = TRUE,
-  info = FALSE
+int_resis <- interpretive_rules(int_resis,
+                                interpretive_rules_df = subset(
+                                  AMR:::INTERPRETIVE_RULES_DF,
+                                  is.na(have_these_values) & reference.rule_group == "Expected phenotypes" & reference.version == 1.2
+                                ),
+                                overwrite = TRUE,
+                                info = FALSE
 )
 
 int_resis2 <- int_resis[, sapply(int_resis, function(x) any(!is.sir(x) | x == "R")), drop = FALSE] %>%