dr. M.S. (Matthijs) Berends
60e8f2bae6
(v3.0.1.9026) fix ab_group(NA)
2026-03-06 12:41:27 +01:00
Matthijs Berends and Claude
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
