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202 Commits
Author SHA1 Message Date
dr. M.S. (Matthijs) Berends eb9a9c2fa5 (v3.0.1.9149) Fix WHONET codes in microorganisms.codes that referred to unrelated microorganisms, let codes refer to the name they were named after and add a source column, and replace the fuzzy matching of WHONET names by exact matching with a guard against unreviewed remaps 
WHONET names are now matched exactly (also outdated names, after removing qualifiers), then on GBIF identifier, and fuzzy results are only kept if consistent with that; otherwise the genus or UNKNOWN is used. A code refers to the record of the name it was named after (e.g. EAE is Enterobacter aerogenes) if that name refers to the same taxon. Every remap of an existing code to another taxon must be listed in data-raw/whonet_remaps_reviewed.csv; the 198 remaps of this rebuild were reviewed.
 2026-10-15 21:08:04 +02:00
dr. M.S. (Matthijs) Berends 179eec584f (v3.0.1.9148) Store zone diameters without S category as blocking rows for EUCAST and as R-only rows for CLSI instead of capping them at 50 mm, let as.mo() return the complex for names such as 'Acinetobacter calcoaceticus-baumannii complex', make the breakpoint reproduction scripts stop on unchecked data defects and year-independent, and document that as.disk() returns NA above 50 mm 
The full rebuild of clinical_breakpoints also assigns Salmonella serovars and the Bacteroides fragilis complex correctly and adds ECOFFs for Neocosmospora solani. The rebuilt microorganisms.codes is not included, since it remaps WHONET codes that need review first.
 2026-10-15 17:05:41 +02:00
dr. M.S. (Matthijs) Berends 38ae865a07 Document all values of rank_index in the clinical_breakpoints data set, including species groups, and the stored value of EUCAST's off-scale S breakpoint 2026-10-15 10:37:40 +02:00
Matthijs BerendsandClaude Opus 5.5 dab4c47e86 EUCAST import: blocking rows, note restrictions, PK-PD and parser fixes (#310) 
Make the EUCAST Clinical Breakpoint Tables import (2019-2026) fail-safe:

- Add blocking rows (NA breakpoints, reason in `note`) where EUCAST gives
  no breakpoint for an organism (IE, "-", Note, brackets, "except"
  clauses, table scope), so as.sir() no longer falls back to broader taxa
- Apply restrictions from EUCAST notes via a curated rule table with a
  completeness guard (e.g. zone diameters for E. coli only)
- Import PK-PD (non-species related) breakpoints 2019-2023, H.
  parainfluenzae MIC breakpoints, and explicit screening thresholds from
  notes (high-level aminoglycosides, cefoxitin MIC, unidentified CoNS)
- Parser fixes: lost Staphylococcus sheets 2019/2020, note keys and
  bodies, struck-through cells, hidden sheets, missing disk contents,
  organism groups, site vocabulary, MIC dilution levels, off-scale
  breakpoints stored as 0.0001
- Keep EUCAST antifungal breakpoints 2019-2025 from WHONET; code WHONET
  streptomycin as STR1 instead of STR (streptoduocin)

Co-authored-by: Claude Opus 5.5 <noreply@anthropic.com>
 2026-10-02 06:01:58 +02:00
Matthijs Berends 5d9974e2b9 implement EUCAST >= 2019 directly from their source files 2026-10-01 14:53:00 +01:00
dr. M.S. (Matthijs) Berends bbdd3a92e2 (v3.0.1.9088) add version number to intrinsic_resistant 2026-09-03 12:14:25 +02:00
Matthijs Berends 2c33297cf6 new eucast breakpoints parsing 2026-08-20 13:29:16 +01:00
dr. M.S. (Matthijs) Berends a88150ca4a (v3.0.1.9066) fix documentation 2026-06-24 19:34:47 +02:00
dr. M.S. (Matthijs) Berends bd63794136 (v3.0.1.9064) Documentation updates 2026-06-24 18:32:08 +02:00
Matthijs Berends 3f9f931777 (v3.0.1.9059) Update taxonomy of microorganisms 2026-06-23 01:38:13 +02:00
Matthijs Berends 8ff5d4472a Add add_if_missing parameter to control NA handling in interpretive rules (#264) 2026-04-21 21:53:43 +02:00
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 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 d384b492cf (v2.1.1.9289) unit test fix 2025-06-01 16:00:12 +02:00
dr. M.S. (Matthijs) Berends dc5559a2c4 (v2.1.1.9270) Add support for Korean, fix ATCs 2025-05-04 14:24:43 +02:00
dr. M.S. (Matthijs) Berends 5e6bbdf3d1 (v2.1.1.9267) update ATCs 2025-05-01 11:48:49 +02:00
dr. M.S. (Matthijs) Berends 40d7a971c3 (v2.1.1.9236) documentation 2025-04-12 11:46:42 +02:00
dr. M.S. (Matthijs) Berends 36fd99e1f4 (v2.1.1.9235) New website! 2025-04-08 15:54:30 +01:00
dr. M.S. (Matthijs) Berends b972bbb96f (v2.1.1.9230) deprecated resistance_predict(), data set folder name without space 2025-03-28 16:48:56 +01:00
dr. M.S. (Matthijs) Berends 49da312506 (v2.1.1.9228) repo cleaning 2025-03-28 11:17:49 +01:00
dr. M.S. (Matthijs) Berends 969a42cc8c (v2.1.1.9226) update intrinsic_resistant, unit test fixes 2025-03-27 15:20:22 +01:00
dr. M.S. (Matthijs) Berends e134e01418 (v2.1.1.9198) support eucast expert rules 14 and 13.1 2025-03-14 10:10:35 +01:00
dr. M.S. (Matthijs) Berends a7ef22a21e (v2.1.1.9194) new argument for missing R breakpoints - updated from WHONET 2025-03-12 16:24:38 +01:00
dr. M.S. (Matthijs) Berends b67613ce08 (v2.1.1.9187) WISCA fix 2025-03-07 22:27:21 +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 07efc292bc (v2.1.1.9163) cleanup 2025-02-27 14:04:29 +01:00
dr. M.S. (Matthijs) Berends ac1c40d8bb (v2.1.1.9081) HUGE microorganisms update for fungi! 2024-09-29 22:17:56 +02:00
dr. M.S. (Matthijs) Berends 1ca40e8d67 (v2.1.1.9079) fix for uti in as.sir() 2024-09-24 15:34:12 +02:00
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 c67d003e9e (v2.1.1.9060) SDD results now in as.sir() 2024-06-19 15:08:23 +02:00
dr. M.S. (Matthijs) Berends a4dc37a4e4 (v2.1.1.9057) fix for missing breakpoints 2024-06-17 16:52:12 +02:00
dr. M.S. (Matthijs) Berends 08a27922a8 new SDD and N for as.sir() 2024-05-20 15:27:04 +02:00
dr. M.S. (Matthijs) Berends bc4f8515e2 new Norwegian link 2024-03-03 23:24:57 +01:00
dr. M.S. (Matthijs) Berends 7be4dabbc0 support veterinary MIC/disk translation 2024-02-24 15:16:52 +01:00
dr. M.S. (Matthijs) Berends 7cda9e575b prepare for CRAN 2023-10-20 14:51:48 +02:00
dr. M.S. (Matthijs) Berends eff164ecb1 indicate unique identifiers 2023-07-12 21:26:32 +02:00
dr. M.S. (Matthijs) Berends 70c601ca11 breakpoints UTI interpretation fix 2023-07-10 13:41:52 +02:00
dr. M.S. (Matthijs) Berends acb534102b new species groups, updated clinical breakpoints 2023-07-08 17:30:05 +02:00
Dr. Matthijs Berends f065945d7b Update clinical breakpoints and fix some as.mo() bugs (#117) 
* Updates clinical breakpoints EUCAST/CLSI 2023, fixes #102, fixes #112, fixes #113, fixes #114, fixes #115
* docs
* implement ecoffs
* unit tests
 2023-06-22 15:10:59 +02:00
dr. M.S. (Matthijs) Berends 9591688811 documentation update 2023-05-27 10:39:22 +02:00
dr. M.S. (Matthijs) Berends c6135d2082 updated microorganism codes 2023-05-26 16:10:01 +02:00
dr. M.S. (Matthijs) Berends 91fa73dedf add oxygen tolerance 2023-05-11 21:56:27 +02:00
dr. M.S. (Matthijs) Berends ed70f95380 Fix clinical breakpoints 2023-04-14 23:14:34 +02:00
dr. M.S. (Matthijs) Berends 147f9112e9 Fix some WHONET codes 2023-04-14 11:12:26 +02:00
dr. M.S. (Matthijs) Berends c2cfc5ef84 fix for antibiogram(), transform WHONET data set to sir 2023-02-22 15:40:05 +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