Claude
6912c9deee
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
2026-03-26 06:01:17 +00:00
353eaa3f38
(v3.0.1.9033) add ionophores(), clorobiocin, aminocoumarins group
2026-03-09 11:57:36 +01:00
daab605ca4
(v3.0.1.9028) fix unique CIDs
2026-03-06 18:53:42 +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
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
cfbbfb4fa5
(v3.0.1.9007) fix #246
2026-01-06 23:08:50 +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
10ba36821e
(v3.0.0.9034) fix MycoBank synonyms
2025-09-18 13:58:34 +01:00
60bd631e1a
(v3.0.0.9019) Fixes #229 , #230 , #227 , #225
2025-09-01 16:56:55 +02:00
Nick Thomson
68442f3042
(v3.0.0.9012) Python wrapper fix
2025-07-17 19:43:07 +02:00
d94bdd2c6a
(v3.0.0.9008) fix ggplot_sir(), support lighter green for SDD
2025-07-17 17:05:41 +02:00
8dab0a3730
(v3.0.0.9007) allow any tidyselect language in as.sir()
2025-07-17 14:29:35 +02:00
72db2b2562
(v3.0.0.9003) eucast_rules fix, new tidymodels integration
2025-06-13 14:03:21 +02:00
5667ce3eae
(v2.1.1.9287) fix antibiotics
2025-06-01 12:17:47 +02:00
e70f3de02e
(v2.1.1.9286) deprecate antibiotics better, add ATC for ceftaroline
2025-06-01 11:54:40 +02:00
fcd8b95e51
(v2.1.1.9272) mo codes sensititre
2025-05-04 18:50:25 +02:00
a778eb9bcf
(v2.1.1.9272) (v2.1.1.9271) add sensititre AB and animal codes
2025-05-04 16:40:08 +02:00
dc5559a2c4
(v2.1.1.9270) Add support for Korean, fix ATCs
2025-05-04 14:24:43 +02:00
b8f0f64287
(v2.1.1.9269) Support 7 new languages
2025-05-02 19:25:19 +02:00
5e6bbdf3d1
(v2.1.1.9267) update ATCs
2025-05-01 11:48:49 +02:00
30caa5e654
(v2.1.1.9262) fix knit printing
2025-04-29 16:31:38 +02:00
faa9ae0d85
(v2.1.1.9260) fix antibiogram
2025-04-29 16:15:18 +02:00
92316d5ddc
(v2.1.1.9254) fix antimicrobial synonyms
2025-04-26 16:23:14 +02:00
4e7fca3b38
(v2.1.1.9253) parallel computing
2025-04-26 15:47:00 +02:00
abee2a954e
(v2.1.1.9252) fix MIC for >= and <=
2025-04-25 10:19:40 +02:00
6135805455
(v2.1.1.9251) fix colour on GitHub docs
2025-04-21 16:04:01 +02:00
4a336d040c
(v2.1.1.9250) Automated README and index.md
2025-04-21 15:37:26 +02:00
9e64d7708e
(v2.1.1.9248) unit test fix
2025-04-20 15:27:36 +02:00
ea443f7483
(v2.1.1.9247) CLSI/EUCAST 2025!
2025-04-20 12:55:31 +02:00
0bab49ff86
(v2.1.1.9246) website fix
2025-04-19 16:23:17 +02:00
492fe6872f
(v2.1.1.9244) automated GPT training data
2025-04-19 15:57:12 +02:00
ca00ed468e
(v2.1.1.9243) fix sir documentation
2025-04-18 16:32:45 +02:00
29b0ef1089
(v2.1.1.9242) sir log
2025-04-18 16:03:50 +02:00
579025f678
(v2.1.1.9241) fix sir
2025-04-18 13:25:59 +02:00
cf91e677c6
(v2.1.1.9240) fix sir interpretation
2025-04-16 15:22:12 +02:00
ec937e8179
(v2.1.1.9239) documentation
2025-04-14 09:40:35 +02:00
7c3320b967
update reproduction scripts links
2025-04-13 10:02:47 +02:00
d31371613e
(v2.1.1.9237) clean-up
2025-04-13 09:59:40 +02:00
40d7a971c3
(v2.1.1.9236) documentation
2025-04-12 11:46:42 +02:00
36fd99e1f4
(v2.1.1.9235) New website!
2025-04-08 15:54:30 +01:00
a905303296
(v2.1.1.9234) fix CLSI
2025-04-07 17:36:01 +01:00
1fdab84103
(v2.1.1.9233) chore: make all argument texts full sentences
2025-03-31 14:53:24 +02:00
63099cd81e
(v2.1.1.9232) is.mic() iteration, documentation cleanup
2025-03-31 10:51:31 +02:00
5f5b77bfaf
(v2.1.1.9231) Update EUCAST vignette
2025-03-29 18:03:31 +01:00
b972bbb96f
(v2.1.1.9230) deprecated resistance_predict(), data set folder name without space
2025-03-28 16:48:56 +01:00
bd873ac1bc
(v2.1.1.9229) unit tests
2025-03-28 11:40:09 +01:00
49da312506
(v2.1.1.9228) repo cleaning
2025-03-28 11:17:49 +01:00
d77ad6bd6e
(v2.1.1.9227) unit test fixes
2025-03-27 15:36:27 +01:00
