⚠️ SERVICE NOTICE: This instance will be decommissioned 1 december of this year (2026).
Please migrate your projects to our new repository:
https://gitrepo.service.rug.nl
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>
Matthijs BerendsandClaude Opus 5.5
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