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

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: AMR
-Version: 3.0.1.9040
+Version: 3.0.1.9041
-Date: 2026-03-24
+Date: 2026-03-26
 Title: Antimicrobial Resistance Data Analysis
 Description: Functions to simplify and standardise antimicrobial resistance (AMR)
   data analysis and to work with microbial and antimicrobial properties by

NEWS.md

@@ -1,4 +1,4 @@
-# AMR 3.0.1.9040
+# AMR 3.0.1.9041
 
 ### New
 * Integration with the **tidymodels** framework to allow seamless use of SIR, MIC and disk data in modelling pipelines via `recipes`
@@ -31,6 +31,7 @@
 * Fixed SIR and MIC coercion of combined values, e.g. `as.sir("<= 0.002; S") ` or `as.mic("S; 0.002")` (#252)
 
 ### Updates
+* Reproduced `clinical_breakpoints`, `microorganisms.codes`, and `microorganisms.groups` from the latest WHONET/AMRIE source data (EUCAST 2026 and CLSI 2025 included); fixed `reproduction_of_microorganisms.groups.R` to use `dplyr::if_else()` instead of base `ifelse()` to preserve the `<mo>` class in `bind_rows()`
 * Extensive `cli` integration for better message handling and clickable links in messages and warnings (#191, #265)
 * `mdro()` now infers resistance for a _missing_ base drug column from an _available_ corresponding drug+inhibitor combination showing resistance (e.g., piperacillin is absent but required, while piperacillin/tazobactam available and resistant). Can be set with the new argument `infer_from_combinations`, which defaults to `TRUE` (#209). Note that this can yield a higher MDRO detection (which is a good thing as it has become more reliable).
 * `susceptibility()` and `resistance()` gained the argument `guideline`, which defaults to EUCAST, for interpreting the 'I' category correctly.

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),
+            mo = if_else(is.na(mo),
-                        as.character(as.mo(ORGANISM, keep_synonyms = TRUE, minimum_matching_score = 0)),
+                         as.mo(ORGANISM, keep_synonyms = TRUE, minimum_matching_score = 0),
-                        mo)) %>% 
+                         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")