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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
This commit is contained in:
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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10
tests/testthat/test-mo.R
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@@ -84,6 +84,16 @@ test_that("test-mo.R", {
# expect_warning(as.mo("Acinetobacter calcoaceticus/baumannii complex"))
# Issue #287: "X complex" fallback to "X" when complex is not a distinct taxon
expect_identical(as.character(suppressWarnings(as.mo("Proteus vulgaris complex"))), as.character(suppressWarnings(as.mo("Proteus vulgaris"))))
expect_identical(as.character(suppressWarnings(as.mo("Enterobacter cloacae complex"))), as.character(as.mo("Enterobacter cloacae complex")))
# Issue #288: abbreviated genus with exact species epithet match should win
expect_identical(
as.character(suppressWarnings(as.mo("S. apiospermum"))),
as.character(suppressWarnings(as.mo("Scedosporium apiospermum")))
)
# prevalent MO
expect_identical(
suppressWarnings(as.character(