Claude/fix issue 245 (#262)

* fix: restore valid AB codes mangled by generalise_antibiotic_name() (#245)

When as.ab() received a vector containing both valid AB codes (like ETH,
PHN, PHE, STH, THA, MTH, THI1) and an untranslatable value, the fast
path at line 100 was skipped. The slow path then applied
generalise_antibiotic_name(), which rewrites "TH"->"T" and "PH"->"F",
mangling these short AB codes (e.g. ETH->"ET", PHN->"FN") so they could
no longer be found in the lookup table.

Fix: save the pre-generalised values before applying
generalise_antibiotic_name(), then restore any elements that were already
valid AB codes in their original form.

https://claude.ai/code/session_01Sujw89qa48NoUmMPDBJLz9

* fix: use toupper() in AB code restoration to handle lowercase input (#245)

Ensures that lowercase user input (e.g. 'eth', 'phn') is matched
case-insensitively against the uppercase AB codes in $ab, and that
the restored value is stored in uppercase to match the lookup table.

https://claude.ai/code/session_01Sujw89qa48NoUmMPDBJLz9

* revert: remove unnecessary toupper() since x is already uppercased

https://claude.ai/code/session_01Sujw89qa48NoUmMPDBJLz9

* Revise versioning and date bump requirements for PRs

Updated versioning instructions for pull requests to include date bump.

---------

Co-authored-by: Claude <noreply@anthropic.com>

CLAUDE.md

@@ -146,7 +146,7 @@ Version format: `major.minor.patch.dev` (e.g., `3.0.1.9021`)
 - Stable CRAN releases drop the dev suffix (e.g., `3.0.1`)
 - `NEWS.md` uses sections **New**, **Fixes**, **Updates** with GitHub issue references (`#NNN`)
 
-### Version bump required for every PR
+### Version and date bump required for every PR
 
 Before opening a pull request, always increment the four-digit dev counter by 1 in **both** of these files:
 
@@ -162,6 +162,12 @@ Before opening a pull request, always increment the four-digit dev counter by 1
 
 Read the current version from `DESCRIPTION`, add 1 to the last numeric component, and write the new version to both files in the same commit as the rest of the PR changes.
 
+Also bump the date to the current date in **`DESCRIPTION`**, where it's in the `Date:` field in ISO format:
+
+```
+Date: 2025-12-31
+```
+
 ## Internal State
 
 The package uses a private `AMR_env` environment (created in `aa_globals.R`) for caching expensive lookups (e.g., microorganism matching scores, breakpoint tables). This avoids re-computation within a session.

DESCRIPTION

@@ -1,5 +1,5 @@
 Package: AMR
-Version: 3.0.1.9022
+Version: 3.0.1.9023
 Date: 2026-03-03
 Title: Antimicrobial Resistance Data Analysis
 Description: Functions to simplify and standardise antimicrobial resistance (AMR)

NEWS.md

@@ -1,4 +1,4 @@
-# AMR 3.0.1.9022
+# AMR 3.0.1.9023
 
 ### New
 * Integration with the **tidymodels** framework to allow seamless use of SIR, MIC and disk data in modelling pipelines via `recipes`
@@ -18,6 +18,7 @@
   - `eucast_rules()` has become a wrapper around that function.
 
 ### Fixes
+* Fixed a bug in `as.ab()` where certain AB codes containing "PH" or "TH" (such as `ETH`, `MTH`, `PHE`, `PHN`, `STH`, `THA`, `THI1`) would incorrectly return `NA` when combined in a vector with any untranslatable value (#245)
 * Fixed a bug in `antibiogram()` for when no antimicrobials are set
 * Fixed a bug in `as.sir()` where for numeric input the arguments `S`,  `I`,  and `R` would not be considered (#244)
 * Fixed some foreign translations of antimicrobial drugs

R/ab.R

@@ -119,7 +119,14 @@ as.ab <- function(x, flag_multiple_results = TRUE, language = get_AMR_locale(),
   x[x %like_case% "^PENICILLIN" & x %unlike_case% "[ /+-]"] <- "benzylpenicillin"
   x_bak_clean <- x
   if (already_regex == FALSE) {
+    x_bak_clean_before_gen <- x_bak_clean
     x_bak_clean <- generalise_antibiotic_name(x_bak_clean)
+    # generalise_antibiotic_name() rewrites "PH"->"F" and "TH"->"T", which
+    # mangles short valid AB codes (e.g. "ETH"->"ET", "PHN"->"FN", "STH"->"ST")
+    # making them unrecognisable in the lookup. Restore any values that were
+    # already valid AB codes before generalisation (#245).
+    is_valid_ab_code <- x_bak_clean_before_gen %in% AMR_env$AB_lookup$ab
+    x_bak_clean[is_valid_ab_code] <- x_bak_clean_before_gen[is_valid_ab_code]
   }
 
   x <- unique(x_bak_clean) # this means that every x is in fact generalise_antibiotic_name(x)