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Fix #287 (complex fallback) and #288 (species epithet scoring bias)

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#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
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Claude
2026-05-06 15:11:31 +00:00
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Package: AMR
Version: 3.0.1.9058
Date: 2026-05-02
Version: 3.0.1.9059
Date: 2026-05-06
Title: Antimicrobial Resistance Data Analysis
Description: Functions to simplify and standardise antimicrobial resistance (AMR)
data analysis and to work with microbial and antimicrobial properties by