Matthijs Berends
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
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
12cf144b19
(v3.0.1.9021) add guideline to resistance() and susceptibility()
2026-02-12 20:34:06 +01:00
499c830ee7
(v3.0.1.9020) unit test fixes
2026-02-09 13:16:36 +01:00
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
2df2911cf4
(v3.0.1.9018) fixes #249
...
updates AB groups
2026-01-16 10:57:03 +01:00
fd50c51543
(v3.0.1.9017) fix documentation
2026-01-08 14:03:02 +01:00
cfd1922dd9
(v3.0.1.9016) fix unit test
2026-01-08 12:29:08 +01:00
7df28bce28
(v3.0.1.9015) fix translations
2026-01-08 10:21:48 +01:00
7b9c151241
(v3.0.1.9014) try-again fix
2026-01-07 15:10:21 +01:00
85e8e814e8
(v3.0.1.9013) fix translations
2026-01-07 13:30:54 +01:00
fa827f27f4
(v3.0.1.9012) fix translations
2026-01-07 11:00:58 +01:00
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
cfbbfb4fa5
(v3.0.1.9007) fix #246
2026-01-06 23:08:50 +01:00
35debe25ee
(v3.0.1.9009) tidymodels vignette
2025-12-23 11:02:26 +01:00
e9cf3d5572
(v3.0.1.9008) tidymodels vignette
2025-12-22 19:04:39 +01:00
a5c6aa9fa8
(v3.0.1.9007) fix vignette
2025-12-22 09:34:58 +01:00
f6e28ac95c
(v3.0.1.9006) Fix website
2025-12-21 12:29:46 +01:00
151af21f38
(v3.0.1.9005) re-add tidymodels implementation
2025-12-21 12:19:43 +01:00
225c73f7e7
(v3.0.1.9004) Revamp as.sir() interpretation for capped MICs
...
Fixes #243
Fixes #244
2025-12-15 13:18:13 +01:00
ba30b08f76
(v3.0.1.9003) Add taniborbactam and cefepime/taniborbactam
2025-11-24 11:24:02 +01:00
d366949f1b
(v3.0.1.9002) replace WHONET directives with their GitHub repo
2025-10-13 22:12:48 +02:00
0b24967b23
(v3.0.1.9001) fix antibiogram
2025-09-30 10:54:07 +02:00
adee419f1c
v3.0.1
2025-09-20 17:14:07 +01:00
33fb1849eb
(v3.0.0.9036) Prepare for v3.0.1
2025-09-19 12:23:59 +01:00
13f2a864da
(v3.0.0.9035) fix mo_pathogenicity unit test following MycoBank bugfix
2025-09-18 14:22:52 +01:00
10ba36821e
(v3.0.0.9034) fix MycoBank synonyms
2025-09-18 13:58:34 +01:00
5796e8f3a4
(v3.0.0.9033) rename workflow
2025-09-15 09:10:54 +02:00
b11866af57
(v3.0.0.9032) add GitHub Action for dev version of packages
2025-09-13 14:02:59 +02:00
e8c99f2775
(v3.0.0.9031) fix for ggplot2
2025-09-12 16:52:59 +02:00
5b99888151
(v3.0.0.9030) fix NEWS
2025-09-11 14:41:28 +02:00
c7b2acbeb6
(v3.0.0.9029) fix for vignette and envir data
2025-09-10 16:19:30 +02:00
1922fb5ff2
(v3.0.0.9028) fix as.ab() warning
2025-09-10 15:06:51 +02:00
4d7c4ca52c
(v3.0.0.9027) skimr update and as.ab warning - fixes #234 , fixes #232
2025-09-10 13:32:52 +02:00
d5a568318b
(v3.0.0.9026) fix tidymodels doc
2025-09-04 15:03:28 +02:00
c1c49fa463
(v3.0.0.9025) fix todo tracker
2025-09-04 14:40:24 +02:00
d2ced1db61
(v3.0.0.9024) fix todo tracker
2025-09-04 14:28:01 +02:00
3d40b20c10
(v3.0.0.9023) update todo tracker
2025-09-04 14:04:22 +02:00
3ba1b8a10a
(v3.0.0.9022) postpone new features - we like a clearly focussed bugfix release first
2025-09-03 15:39:44 +02:00
0744c6feee
(v3.0.0.9021) checkouts
2025-09-03 12:12:05 +02:00
60bd631e1a
(v3.0.0.9019) Fixes #229 , #230 , #227 , #225
2025-09-01 16:56:55 +02:00
9b07a8573a
(v3.0.0.9018) keep all reasons in mdro(), fixed #227
2025-08-07 16:23:47 +02:00
fc72cf9324
(v3.0.0.9017) semantic versioning only on branch main
2025-07-28 12:24:52 +02:00
2f866985c9
(v3.0.0.9016) fix for plotting
2025-07-23 22:05:20 +02:00
6cb724a208
(v3.0.0.9015) plotting fix
2025-07-19 14:06:36 +02:00
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
39ea5f6597
(v3.0.0.9011) allow names for age_groups()
2025-07-17 19:32:46 +02:00
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
