(v1.7.1.9064) eucast 3.3 for mdro(), major change to repeated calling

data-raw/_internals.R

@@ -115,6 +115,7 @@ create_species_cons_cops <- function(type = c("CoNS", "CoPS")) {
 }
 MO_CONS <- create_species_cons_cops("CoNS")
 MO_COPS <- create_species_cons_cops("CoPS")
+MO_STREP_ABCG <- as.mo(MO_lookup[which(MO_lookup$genus == "Streptococcus"), "mo", drop = TRUE], Lancefield = TRUE) %in% c("B_STRPT_GRPA", "B_STRPT_GRPB", "B_STRPT_GRPC", "B_STRPT_GRPG")
 
 # antibiotic groups
 # (these will also be used for eucast_rules() and understanding data-raw/eucast_rules.tsv)
@@ -158,6 +159,7 @@ usethis::use_data(EUCAST_RULES_DF,
                   # EXAMPLE_ISOLATES,
                   MO_CONS,
                   MO_COPS,
+                  MO_STREP_ABCG,
                   AB_AMINOGLYCOSIDES,
                   AB_AMINOPENICILLINS,
                   AB_ANTIFUNGALS,

data-raw/intrinsic_resistant.md5

@@ -1 +1 @@
-43d5b2e1df4e0d12d6ad0c7a4591199c
+d4e080899f438bc1eacb8ec9cfa117b8

data-raw/reproduction_of_intrinsic_resistant.R

@@ -33,7 +33,7 @@ for (i in seq_len(nrow(antibiotics))) {
 
 int_resis <- eucast_rules(int_resis, 
                           eucast_rules_df = subset(AMR:::EUCAST_RULES_DF,
-                                                   is.na(have_these_values) & reference.version == 3.2),
+                                                   is.na(have_these_values) & reference.version == 3.3),
                           info = FALSE)
 
 int_resis2 <- int_resis[, sapply(int_resis, function(x) any(!is.rsi(x) | x == "R"))] %>% 
@@ -41,6 +41,12 @@ int_resis2 <- int_resis[, sapply(int_resis, function(x) any(!is.rsi(x) | x == "R
   filter(value == "R") %>% 
   select(microorganism, antibiotic = name)
 
+# remove lab drugs
+untreatable <- antibiotics[which(antibiotics$name %like% "-high|EDTA|polysorbate|macromethod|screening"), "name", drop = TRUE]
+int_resis2 <- int_resis2 %>% 
+  filter(!antibiotic %in% untreatable) %>% 
+  arrange(microorganism, antibiotic)
+  
 int_resis2$microorganism <- mo_name(int_resis2$microorganism, language = NULL)
 
 intrinsic_resistant <- as.data.frame(int_resis2, stringsAsFactors = FALSE)