Claude
befbccc304
Generalise interpretive rules for multi-guideline support ( #268 )
...
- Rename data-raw/eucast_rules.tsv → interpretive_rules.tsv; add rule.provider
column (value: "EUCAST") to distinguish future CLSI rows
- Rename EUCAST_RULES_DF → INTERPRETIVE_RULES_DF in _pre_commit_checks.R;
filter by rule.provider == guideline when applying rules in interpretive_rules()
- Rename custom_eucast_rules() → custom_interpretive_rules() with new S3 class
"custom_interpretive_rules"; old function becomes a deprecated wrapper in
zz_deprecated.R; backward-compat S3 dispatch shims added for old class
- Remove stop_if(guideline == "CLSI", ...) so clsi_rules() no longer errors
- Add .onLoad shim in zzz.R to create INTERPRETIVE_RULES_DF from EUCAST_RULES_DF
for transitional compatibility until sysdata.rda is regenerated
https://claude.ai/code/session_01D46BTsfJSPo3HnLWp3PRkP
2026-04-30 21:29:26 +00:00
Matthijs Berends
8ff5d4472a
Add add_if_missing parameter to control NA handling in interpretive rules ( #264 )
2026-04-21 21:53:43 +02:00
353eaa3f38
(v3.0.1.9033) add ionophores(), clorobiocin, aminocoumarins group
2026-03-09 11:57:36 +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
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
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
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
30caa5e654
(v2.1.1.9262) fix knit printing
2025-04-29 16:31:38 +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
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
49da312506
(v2.1.1.9228) repo cleaning
2025-03-28 11:17:49 +01:00
969a42cc8c
(v2.1.1.9226) update intrinsic_resistant, unit test fixes
2025-03-27 15:20:22 +01:00
e6f88241b2
(v2.1.1.9225) fix geom_hline()/_vline() in MIC plotting, add EUCAT 1.2 in full, add London contribs, fix mo codes, add Kleb pneu complex
2025-03-26 17:19:17 +01:00
755e6f43b7
(v2.1.1.9219) unit tests
2025-03-19 16:06:23 +01:00
7631e82ae6
(v2.1.1.9206) update precommit hook
2025-03-15 16:17:27 +01:00
ede1cdfd99
(v2.1.1.9205) Fix python wrapper
2025-03-15 16:14:29 +01:00
e134e01418
(v2.1.1.9198) support eucast expert rules 14 and 13.1
2025-03-14 10:10:35 +01:00
067a8aca66
(v2.1.1.9192) fix fluoroquinolones and add bleomycin
2025-03-10 17:04:35 +01:00
a2c2be23c1
(v2.1.1.9190) antibiotics deprecation in antibiogram()
2025-03-09 10:41:11 +01:00
f7938289eb
(v2.1.1.9186) replace antibiotics with antimicrobials!
2025-03-07 20:43:26 +01:00
07efc292bc
(v2.1.1.9163) cleanup
2025-02-27 14:04:29 +01:00
8ba2e4ed94
(v2.1.1.9141) new AMR selectors, eucast overwrite arg
2025-02-07 18:01:22 +01:00
08ddbaa930
(v2.1.1.9123) add EFF code to antibiotics data set
2025-01-15 16:14:09 +01:00
0488d00f20
(v2.1.1.9111) add betalactams_with_inhibitor(), fixes #175
2024-12-06 15:44:20 +01:00
9fb891eee2
(v2.1.1.9087) update unit tests
2024-10-04 15:28:44 +02:00
50a9f8f0e0
(v2.1.1.9086) website update
2024-10-02 10:20:05 +02:00
681fe011fe
(v2.1.1.9082) algorithm updates
2024-09-30 18:46:55 +02:00
ac1c40d8bb
(v2.1.1.9081) HUGE microorganisms update for fungi!
2024-09-29 22:17:56 +02:00
7f344836ea
(v2.1.1.9064) unit tests
2024-07-16 15:55:58 +02:00
640888f408
(v2.1.1.9064) update all microbial taxonomy, add mycobank, big documentation update
2024-07-16 14:53:17 +02:00
af74e1d4f2
(v2.1.1.9041) antibiotics update
2024-06-08 17:35:25 +02:00
0d8a91db49
rename pre-commit hook to pre-commit checks (no-check)
2024-04-23 10:55:48 +02:00
