Reproduce clinical breakpoints from latest WHONET/AMRIE data

- Ran reproduction_of_microorganisms.groups.R and reproduction_of_clinical_breakpoints.R
  against the latest WHONET/AMRIE source (includes EUCAST 2026, CLSI 2025)
- Updated data/clinical_breakpoints.rda, microorganisms.codes.rda, microorganisms.groups.rda,
  and data-raw/organisms.rds
- Fixed reproduction_of_microorganisms.groups.R: replaced base ifelse() with dplyr::if_else()
  to preserve the <mo> S3 class; base ifelse() strips class attributes, causing
  bind_rows() to fail with strict vctrs type checking in dplyr >= 1.1.0
- Added data-raw/_run_reproduction.R: non-interactive wrapper that overrides View(),
  sets UTF-8 locale, and sources both scripts in the correct order

https://claude.ai/code/session_01S5vMqfsiJb59RN2Gyz1tDY

data-raw/_reproduction_scripts/reproduction_of_microorganisms.groups.R

@@ -85,9 +85,9 @@ microorganisms.groups <- whonet_organisms %>%
                           "Mycobacterium canetti")) %>% 
   filter(!is.na(SPECIES_GROUP), SPECIES_GROUP != ORGANISM_CODE) %>%
   transmute(mo_group = as.mo(SPECIES_GROUP),
-            mo = ifelse(is.na(mo),
-                        as.character(as.mo(ORGANISM, keep_synonyms = TRUE, minimum_matching_score = 0)),
-                        mo)) %>% 
+            mo = if_else(is.na(mo),
+                         as.mo(ORGANISM, keep_synonyms = TRUE, minimum_matching_score = 0),
+                         mo)) %>%
   # add our own CoNS and CoPS, WHONET does not strictly follow Becker et al. (2014, 2019, 2020)
   filter(mo_group != as.mo("CoNS")) %>% 
   bind_rows(tibble(mo_group = as.mo("CoNS"), mo = MO_CONS)) %>% 

data-raw/_run_reproduction.R

@@ -0,0 +1,27 @@
+# Wrapper to run clinical breakpoints reproduction non-interactively
+# Set UTF-8 locale so gsub() can handle Unicode patterns
+Sys.setlocale("LC_CTYPE", "C.utf8")
+Sys.setlocale("LC_ALL", "C.utf8")
+
+# Overrides View() to just print a summary instead
+View <- function(x, title = NULL) {
+  if (is.data.frame(x) || is.matrix(x)) {
+    cat("=== View() called:", if (!is.null(title)) title else deparse(substitute(x)), "===\n")
+    cat("Dimensions:", nrow(x), "rows x", ncol(x), "cols\n")
+    print(head(x, 10))
+    cat("...\n\n")
+  } else {
+    print(x)
+  }
+  invisible(x)
+}
+
+setwd("/home/user/AMR")
+
+cat("=== Step 1: Running reproduction_of_microorganisms.groups.R ===\n")
+source("data-raw/_reproduction_scripts/reproduction_of_microorganisms.groups.R")
+
+cat("\n=== Step 2: Running reproduction_of_clinical_breakpoints.R ===\n")
+source("data-raw/_reproduction_scripts/reproduction_of_clinical_breakpoints.R")
+
+cat("\n=== Done! ===\n")