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Author SHA1 Message Date
Matthijs BerendsandClaude 24f24ecaf8 Generalise interpretive rules for multi-guideline support (#268) (#283) 
* 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

* Fix namespace load failure: remove assignInNamespace from .onLoad (#268)

assignInNamespace cannot add NEW bindings to a locked package namespace
(R locks namespace bindings before .onLoad runs). Replace the .onLoad
shim with a runtime fallback inside interpretive_rules(): if
INTERPRETIVE_RULES_DF is absent (pre-regeneration sysdata.rda), derive
it from EUCAST_RULES_DF by adding the rule.provider column. This also
fixes the screening_abx line to reuse the already-resolved
interpretive_rules_df_total instead of a bare INTERPRETIVE_RULES_DF
reference.

https://claude.ai/code/session_01D46BTsfJSPo3HnLWp3PRkP

* fixes

* fixes

---------

Co-authored-by: Claude <noreply@anthropic.com>
 2026-05-01 18:38:51 +01:00
dr. M.S. (Matthijs) Berends 4dc3ec0008 (v3.0.1.9034) Add amr_course() 2026-03-11 16:07:31 +01:00
dr. M.S. (Matthijs) Berends 353eaa3f38 (v3.0.1.9033) add ionophores(), clorobiocin, aminocoumarins group 2026-03-09 11:57:36 +01:00
dr. M.S. (Matthijs) Berends 60e8f2bae6 (v3.0.1.9026) fix ab_group(NA) 2026-03-06 12:41:27 +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 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 cfbbfb4fa5 (v3.0.1.9007) fix #246 2026-01-06 23:08:50 +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 adee419f1c v3.0.1 2025-09-20 17:14:07 +01:00
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 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 72db2b2562 (v3.0.0.9003) eucast_rules fix, new tidymodels integration 2025-06-13 14:03:21 +02:00
dr. M.S. (Matthijs) Berends 5667ce3eae (v2.1.1.9287) fix antibiotics 2025-06-01 12:17:47 +02:00
dr. M.S. (Matthijs) Berends e70f3de02e (v2.1.1.9286) deprecate antibiotics better, add ATC for ceftaroline 2025-06-01 11:54:40 +02:00
dr. M.S. (Matthijs) Berends 38cebc1541 (v2.1.1.9279) fix documentation, add foreign S3 exports to functions 2025-05-16 16:55:29 +02:00
dr. M.S. (Matthijs) Berends 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
dr. M.S. (Matthijs) Berends bb110646db (v2.1.1.9223) allow + ab 2025-03-20 22:56:32 +01:00
dr. M.S. (Matthijs) Berends 4dc4398ad1 (v2.1.1.9217) allow + in amr selectors 2025-03-18 16:35:22 +01:00
dr. M.S. (Matthijs) Berends f7938289eb (v2.1.1.9186) replace antibiotics with antimicrobials! 2025-03-07 20:43:26 +01:00
dr. M.S. (Matthijs) Berends 195dfb4b91 (v2.1.1.9157) improved as.ab(), fixed knit_print of antibiogram 2025-02-26 13:27:20 +01:00
dr. M.S. (Matthijs) Berends aa8f6af185 (v2.1.1.9155) new mic_p50() and mic_p90() - updated AMR intro 2025-02-23 11:18:08 +01:00
dr. M.S. (Matthijs) Berends d94efb0f5e (v2.1.1.9147) scale fixes and WISCA update, fix conserved capped values 2025-02-14 14:16:46 +01:00
dr. M.S. (Matthijs) Berends bd2887bcd4 (v2.1.1.9146) new scale_*_sir() functions 2025-02-13 19:47:57 +01:00
dr. M.S. (Matthijs) Berends 07757c933c (v2.1.1.9144) new MIC scales and fix for rescale_mic() 2025-02-11 08:48:37 +01:00
dr. M.S. (Matthijs) Berends 8ba2e4ed94 (v2.1.1.9141) new AMR selectors, eucast overwrite arg 2025-02-07 18:01:22 +01:00
dr. M.S. (Matthijs) Berends baea4323c7 (v2.1.1.9140) WISCA fix 2025-02-05 20:48:35 +01:00
dr. M.S. (Matthijs) Berends 7accf6ff13 (v2.1.1.9127) unit tests 2025-01-27 10:46:43 +01:00
dr. M.S. (Matthijs) Berends 66833b4f5a (v2.1.1.9126) implemented WISCA! Also added top_n_microorganisms() and fixed Python wrapper 2025-01-26 23:01:17 +01:00
dr. M.S. (Matthijs) Berends 92c4fc0f94 (v2.1.1.9125) replace 'antibiotic selectors' with 'antimicrobial selectors' 2025-01-17 12:09:39 +01:00
dr. M.S. (Matthijs) Berends 08ddbaa930 (v2.1.1.9123) add EFF code to antibiotics data set 2025-01-15 16:14:09 +01:00
dr. M.S. (Matthijs) Berends 0488d00f20 (v2.1.1.9111) add betalactams_with_inhibitor(), fixes #175 2024-12-06 15:44:20 +01:00
dr. M.S. (Matthijs) Berends 640888f408 (v2.1.1.9064) update all microbial taxonomy, add mycobank, big documentation update 2024-07-16 14:53:17 +02:00
dr. M.S. (Matthijs) Berends 68f7795481 (v2.1.1.9052) unit test fix 2024-06-16 20:53:50 +02:00
dr. M.S. (Matthijs) Berends bdbf5198a2 (v2.1.1.9050) vctrs fix for sir, small documentation fixes 2024-06-15 15:33:49 +02:00
dr. M.S. (Matthijs) Berends 31207952d3 (v2.1.1.9043) fix sir translation with as.double 2024-06-10 10:34:45 +02:00
dr. M.S. (Matthijs) Berends af74e1d4f2 (v2.1.1.9041) antibiotics update 2024-06-08 17:35:25 +02:00
dr. M.S. (Matthijs) Berends c3ce1b551d rename limit_mic_range() to rescale_mic() 2024-05-24 15:07:41 +02:00
dr. M.S. (Matthijs) Berends 2899b3c840 new mo_group_members() 2024-04-19 10:18:21 +02:00
dr. M.S. (Matthijs) Berends 94e9a4d99b update MIC implementation 2024-04-07 20:22:59 +02:00
dr. M.S. (Matthijs) Berends 7be4dabbc0 support veterinary MIC/disk translation 2024-02-24 15:16:52 +01:00
dr. M.S. (Matthijs) Berends c7461766ce Remove RSI from package, add extra MIC scale functions 2023-12-03 11:34:48 +01:00
dr. M.S. (Matthijs) Berends 6f417d0ef2 add scale_x_mic() 2023-12-03 01:06:00 +01:00
dr. M.S. (Matthijs) Berends 7cda9e575b prepare for CRAN 2023-10-20 14:51:48 +02:00
dr. M.S. (Matthijs) Berends 91fa73dedf add oxygen tolerance 2023-05-11 21:56:27 +02:00
dr. M.S. (Matthijs) Berends e70f2cd32c knitr format 2023-02-23 16:27:40 +01:00
dr. M.S. (Matthijs) Berends bc434db835 bring back antibiogram(), without deps 2023-02-10 16:18:00 +01:00
dr. M.S. (Matthijs) Berends 1a0dc4bf46 revert back to pre-antibiogram 2023-02-09 13:07:39 +01:00
dr. M.S. (Matthijs) Berends 9e99e66f01 use dplyr where available, new antibiogram() for WISCA, fixed Salmonella Typhi/Paratyphi 2023-02-06 11:57:22 +01:00
Dr. Matthijs Berends 98e62c9af2 Replace RSI with SIR 2023-01-21 23:47:20 +01:00
dr. M.S. (Matthijs) Berends 86e28bafce add mo_pathogenicity 2023-01-06 13:35:37 +01:00