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Author	SHA1	Message	Date
Claude	3d3f06be24	Fix candidates_formatted not found in print.mo_uncertainties() ... When there is only one match (candidates field is empty), the "Also matched:" block must be skipped. Wrapping it in if (candidates != "") prevents the error that arose after #288 narrowed filtr to one entry. https://claude.ai/code/session_01VH4Ju4Xq9aW1AHuoVbjGEo	2026-05-06 18:43:00 +00:00
Claude	d23004641f	Revert mo_matching_score.R; fix #288 in mo.R pre-filter instead ... Issue #288: when the abbreviated-genus pre-filter (≤3 char genus) yields exactly one candidate whose species (and subspecies) word(s) exactly match the input, narrow filtr to that single candidate and set minimum_matching_score = 0. This bypasses the automatic 0.55 cutoff that only runs in the is.null() branch, so "S. apiospermum" resolves to Scedosporium apiospermum without touching the validated scoring formula. https://claude.ai/code/session_01VH4Ju4Xq9aW1AHuoVbjGEo	2026-05-06 18:07:37 +00:00
Claude	b3b8d301ff	Fix #287 (complex fallback) and #288 (species epithet scoring bias) ... #287: as.mo() now strips " complex" from input when that exact complex is not in the taxonomy and retries with the bare name, so inputs like "Proteus vulgaris complex" no longer return NA. #288: mo_matching_score() applies a ×2 bonus when the input has an abbreviated genus (≤3 chars) and the candidate's species epithet exactly matches the input species epithet. This ensures "S. apiospermum" resolves to Scedosporium apiospermum rather than Staphylococcus aureus, overcoming the kingdom/prevalence denominator bias in favour of common bacteria. https://claude.ai/code/session_01VH4Ju4Xq9aW1AHuoVbjGEo	2026-05-06 15:11:31 +00:00
Claude	9707450b89	Fix emend. author bug in get_author_year() and update ref documentation ... Strip emend. and everything after it so the ref column retains the combination authority, not the emendation author. Update data.R and mo_property.R docs to describe the correct semantics of the ref field. https://claude.ai/code/session_01VH4Ju4Xq9aW1AHuoVbjGEo	2026-05-02 14:34:45 +00:00