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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
parent 155c2707ce
commit b3b8d301ff
5 changed files with 46 additions and 5 deletions
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NEWS.md
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@@ -1,4 +1,4 @@
# AMR 3.0.1.9058
# AMR 3.0.1.9059
Planned as v3.1.0, May 2026.
@@ -18,6 +18,8 @@ Planned as v3.1.0, May 2026.
* `as.mic()`: values in scientific notation (e.g. `1e-3`) now handled correctly
* `as.ab()`: codes containing "PH" or "TH" (e.g. `ETH`, `PHE`) no longer return `NA` when mixed with unrecognised input (#245)
* Combined MIC/SIR input values (e.g. `"<= 0.002; S"` or `"S; 0.002"`) now parsed correctly (#252)
* `as.mo()`: input of the form `"X complex"` now falls back to `"X"` when the complex is not a distinct taxon in the database, preventing `NA` results for valid clinical descriptions such as `"Proteus vulgaris complex"` (#287)
* `mo_matching_score()`: abbreviated-genus input (e.g. `"S. apiospermum"`) now correctly ranks candidates whose species epithet exactly matches the input above more-prevalent organisms whose species does not match; fixes `"S. apiospermum"` resolving to *Staphylococcus* instead of *Scedosporium apiospermum* (#288)
* `get_author_year()` in the microorganism reproduction script now strips `emend.` and everything after it, so `ref` reflects the combination authority rather than the emendation author (e.g. *Rhodococcus equi* now returns "Goodfellow et al., 1977" instead of "Nouioui et al., 2018")
* BRMO classification now includes bacterial complexes (#275)
* Translation fixes for Italian CoNS/CoPS names (#256), Dutch antimicrobials, and `sir_df()` foreign-language output (#272)