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(v3.0.1.9080) fix(as.mo): resolve abbreviated genus when species has subspecies (#288 follow-up) (#301)

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When a genus+species abbreviation like "P. ovale" was used, the previous
bypass (Issue #288) checked sum(sp_exact) == 1, which failed if the species
also had subspecies sharing the epithet (ovale curtisi, ovale wallikeri).
The fix extends the bypass to fire whenever all exact species matches belong
to one genus, collapsing to the species-rank record (subspecies == "") for
genus+species queries and preserving the chosen row for explicit subspecies
queries.

Also extends the data-invariant test to cover all taxonomic rank columns
from domain to subspecies, not just the terminal three.


Claude-Session: https://claude.ai/code/session_01M4fqQYQYJ3drdudkDYNqAY

Co-authored-by: Claude <noreply@anthropic.com>
This commit is contained in:
Matthijs Berends
2026-06-27 15:20:38 +02:00
committed by GitHub
parent 03be4b87fc
commit 518425311e
5 changed files with 60 additions and 8 deletions
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@@ -1,4 +1,4 @@
# AMR 3.0.1.9079
# AMR 3.0.1.9080
Planned as v3.1.0, end of June 2026.
@@ -32,6 +32,7 @@ Planned as v3.1.0, end of June 2026.
* `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)
* 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)
* Abbreviated-genus input for species that have subspecies (e.g. `"P. ovale"`) now collapses to the species-rank record instead of incorrectly matching a more-prevalent organism; explicit subspecies queries (e.g. `"P. ovale curtisi"`) are preserved (#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)