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Author SHA1 Message Date
Matthijs BerendsandClaude 4e3ea95fbd 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>
 2026-03-04 08:59:44 +01:00
dr. M.S. (Matthijs) Berends b6211931f8 (v3.0.1.9022) add ceftibuten/avibactam (CTA), kasugamycin (KAS), ostreogrycin (OST), thiostrepton (THS), xeruborbactam (XER), zorbamycin (ZOR) 2026-03-03 15:41:08 +01:00
dr. M.S. (Matthijs) Berends 12cf144b19 (v3.0.1.9021) add guideline to resistance() and susceptibility() 2026-02-12 20:34:06 +01:00
dr. M.S. (Matthijs) Berends 499c830ee7 (v3.0.1.9020) unit test fixes 2026-02-09 13:16:36 +01:00
dr. M.S. (Matthijs) Berends ba4c159154 (v3.0.1.9019) Wildtype/Non-wildtype support, and start with interpretive_rules() 
Fixes #246
Fixes #254
Fixes #255
Fixes #256
 2026-02-08 23:15:40 +01:00
dr. M.S. (Matthijs) Berends 2df2911cf4 (v3.0.1.9018) fixes #249 
updates AB groups
 2026-01-16 10:57:03 +01:00
dr. M.S. (Matthijs) Berends fd50c51543 (v3.0.1.9017) fix documentation 2026-01-08 14:03:02 +01:00
dr. M.S. (Matthijs) Berends cfd1922dd9 (v3.0.1.9016) fix unit test 2026-01-08 12:29:08 +01:00
dr. M.S. (Matthijs) Berends 7df28bce28 (v3.0.1.9015) fix translations 2026-01-08 10:21:48 +01:00
dr. M.S. (Matthijs) Berends 7b9c151241 (v3.0.1.9014) try-again fix 2026-01-07 15:10:21 +01:00
dr. M.S. (Matthijs) Berends 85e8e814e8 (v3.0.1.9013) fix translations 2026-01-07 13:30:54 +01:00
dr. M.S. (Matthijs) Berends fa827f27f4 (v3.0.1.9012) fix translations 2026-01-07 11:00:58 +01:00
dr. M.S. (Matthijs) Berends 9d1b4565f6 (v3.0.1.9008) fix #246 
Merge branch 'main' of https://github.com/msberends/AMR

# Conflicts:
#	DESCRIPTION
#	NEWS.md
#	R/sysdata.rda
#	data/antibiotics.rda
 2026-01-06 23:11:34 +01:00
dr. M.S. (Matthijs) Berends cfbbfb4fa5 (v3.0.1.9007) fix #246 2026-01-06 23:08:50 +01:00
dr. M.S. (Matthijs) Berends 35debe25ee (v3.0.1.9009) tidymodels vignette 2025-12-23 11:02:26 +01:00
RUG e9cf3d5572 (v3.0.1.9008) tidymodels vignette 2025-12-22 19:04:39 +01:00
RUG a5c6aa9fa8 (v3.0.1.9007) fix vignette 2025-12-22 09:34:58 +01:00
dr. M.S. (Matthijs) Berends f6e28ac95c (v3.0.1.9006) Fix website 2025-12-21 12:29:46 +01:00
dr. M.S. (Matthijs) Berends 151af21f38 (v3.0.1.9005) re-add tidymodels implementation 2025-12-21 12:19:43 +01:00
dr. M.S. (Matthijs) Berends 225c73f7e7 (v3.0.1.9004) Revamp as.sir() interpretation for capped MICs 
Fixes #243
Fixes #244
 2025-12-15 13:18:13 +01:00
dr. M.S. (Matthijs) Berends ba30b08f76 (v3.0.1.9003) Add taniborbactam and cefepime/taniborbactam 2025-11-24 11:24:02 +01:00
dr. M.S. (Matthijs) Berends d366949f1b (v3.0.1.9002) replace WHONET directives with their GitHub repo 2025-10-13 22:12:48 +02:00
dr. M.S. (Matthijs) Berends 0b24967b23 (v3.0.1.9001) fix antibiogram 2025-09-30 10:54:07 +02:00
dr. M.S. (Matthijs) Berends adee419f1c v3.0.1 2025-09-20 17:14:07 +01:00
dr. M.S. (Matthijs) Berends 33fb1849eb (v3.0.0.9036) Prepare for v3.0.1 2025-09-19 12:23:59 +01:00
dr. M.S. (Matthijs) Berends 13f2a864da (v3.0.0.9035) fix mo_pathogenicity unit test following MycoBank bugfix 2025-09-18 14:22:52 +01:00
dr. M.S. (Matthijs) Berends 10ba36821e (v3.0.0.9034) fix MycoBank synonyms 2025-09-18 13:58:34 +01:00
dr. M.S. (Matthijs) Berends 5796e8f3a4 (v3.0.0.9033) rename workflow 2025-09-15 09:10:54 +02:00
dr. M.S. (Matthijs) Berends b11866af57 (v3.0.0.9032) add GitHub Action for dev version of packages 2025-09-13 14:02:59 +02:00
dr. M.S. (Matthijs) Berends e8c99f2775 (v3.0.0.9031) fix for ggplot2 2025-09-12 16:52:59 +02:00
dr. M.S. (Matthijs) Berends 5b99888151 (v3.0.0.9030) fix NEWS 2025-09-11 14:41:28 +02:00
dr. M.S. (Matthijs) Berends c7b2acbeb6 (v3.0.0.9029) fix for vignette and envir data 2025-09-10 16:19:30 +02:00
dr. M.S. (Matthijs) Berends 1922fb5ff2 (v3.0.0.9028) fix as.ab() warning 2025-09-10 15:06:51 +02:00
dr. M.S. (Matthijs) Berends 4d7c4ca52c (v3.0.0.9027) skimr update and as.ab warning - fixes #234, fixes #232 2025-09-10 13:32:52 +02:00
dr. M.S. (Matthijs) Berends d5a568318b (v3.0.0.9026) fix tidymodels doc 2025-09-04 15:03:28 +02:00
dr. M.S. (Matthijs) Berends c1c49fa463 (v3.0.0.9025) fix todo tracker 2025-09-04 14:40:24 +02:00
dr. M.S. (Matthijs) Berends d2ced1db61 (v3.0.0.9024) fix todo tracker 2025-09-04 14:28:01 +02:00
dr. M.S. (Matthijs) Berends 3d40b20c10 (v3.0.0.9023) update todo tracker 2025-09-04 14:04:22 +02:00
dr. M.S. (Matthijs) Berends 3ba1b8a10a (v3.0.0.9022) postpone new features - we like a clearly focussed bugfix release first 2025-09-03 15:39:44 +02:00
dr. M.S. (Matthijs) Berends 0744c6feee (v3.0.0.9021) checkouts 2025-09-03 12:12:05 +02:00
dr. M.S. (Matthijs) Berends 60bd631e1a (v3.0.0.9019) Fixes #229, #230, #227, #225 2025-09-01 16:56:55 +02:00
dr. M.S. (Matthijs) Berends 9b07a8573a (v3.0.0.9018) keep all reasons in mdro(), fixed #227 2025-08-07 16:23:47 +02:00
dr. M.S. (Matthijs) Berends fc72cf9324 (v3.0.0.9017) semantic versioning only on branch main 2025-07-28 12:24:52 +02:00
dr. M.S. (Matthijs) Berends 2f866985c9 (v3.0.0.9016) fix for plotting 2025-07-23 22:05:20 +02:00
RUG 6cb724a208 (v3.0.0.9015) plotting fix 2025-07-19 14:06:36 +02:00
dr. M.S. (Matthijs) Berends 49274f010b (v3.0.0.9014) fix plot colours 2025-07-18 15:57:48 +02:00
Nick Thomson 68442f3042 (v3.0.0.9012) Python wrapper fix 2025-07-17 19:43:07 +02:00
dr. M.S. (Matthijs) Berends 39ea5f6597 (v3.0.0.9011) allow names for age_groups() 2025-07-17 19:32:46 +02:00
dr. M.S. (Matthijs) Berends 65ec098acf (v3.0.0.9010) in as.sir(), add note when higher taxonomic levels are used 2025-07-17 19:06:12 +02:00
Nick Thomson e9e3de4469 (v3.0.0.9009) fix as.sir when uti = FALSE 2025-07-17 17:15:52 +02:00