(v3.0.1.9088) add version number to intrinsic_resistant

data-raw/_reproduction_scripts/reproduction_of_intrinsic_resistant.R

@@ -61,6 +61,9 @@ all(int_resis3$ab %in% antimicrobials$ab)
 
 intrinsic_resistant <- int_resis3
 
+intrinsic_resistant$version <- paste(EUCAST_VERSION_EXPECTED_PHENOTYPES$`1.2`$title,
+                                     EUCAST_VERSION_EXPECTED_PHENOTYPES$`1.2`$version_txt)
+
 usethis::use_data(intrinsic_resistant, internal = FALSE, overwrite = TRUE, version = 2, compress = "xz")
 rm(intrinsic_resistant)
 

data-raw/_reproduction_scripts/reproduction_of_microorganisms.R

@@ -2361,6 +2361,7 @@ mo_family <- mo_family %>%
 # construct code part for genus - keep old code where available and generate new ones where needed
 mo_genus <- taxonomy %>%
   filter(rank == "genus") %>%
+  arrange(status, fullname) %>% # sort on accepted < synonym < unknown, added 2026-09-03
   distinct(domain, genus) %>%
   # get available old MO codes
   left_join(
@@ -2427,6 +2428,7 @@ mo_genus <- mo_genus %>%
 # same for species - keep old where available and create new per domain-genus where needed:
 mo_species <- taxonomy %>%
   filter(rank == "species") %>%
+  arrange(status, fullname) %>% # sort on accepted < synonym < unknown, added 2026-09-03
   distinct(domain, genus, species) %>%
   left_join(
     existing_mo_tbl %>%
@@ -2488,6 +2490,7 @@ mo_species <- mo_species %>%
 # same for subspecies - keep old where available and create new per domain-genus-species where needed:
 mo_subspecies <- taxonomy %>%
   filter(rank == "subspecies") %>%
+  arrange(status, fullname) %>% # sort on accepted < synonym < unknown, added 2026-09-03
   distinct(domain, genus, species, subspecies) %>%
   left_join(
     existing_mo_tbl %>%