Priority: P3 · Former status: OPEN · Blocks: —
AltHom Phase 1: AlternativeHomology S3 class & core recoding (MVP). Create R/AlternativeHomology.R (constructor, validation, print), R/recode_alt_homology.R (correspondence enumeration, morphotype states, cost matrix, tip assignment). Wire into TreeLength() for scoring on a fixed tree. Reproduce paper's Definition 1 cost matrix + Table 1 as tests.
Notes. WORKTREE (TS-AltHom). Invertible, no external constraints, two part-types only.
Migrated 2026-08-04 from the retired to-do.md; former task id T-280. Full original row: git show findings-md-final:to-do.md. Task state now lives in this tracker — see dev/red-team/migration-map.tsv for red-team ids.
Priority: P3 · Former status: OPEN · Blocks: —
AltHom Phase 1:
AlternativeHomologyS3 class & core recoding (MVP). CreateR/AlternativeHomology.R(constructor, validation, print),R/recode_alt_homology.R(correspondence enumeration, morphotype states, cost matrix, tip assignment). Wire intoTreeLength()for scoring on a fixed tree. Reproduce paper's Definition 1 cost matrix + Table 1 as tests.Notes. WORKTREE (TS-AltHom). Invertible, no external constraints, two part-types only.
Migrated 2026-08-04 from the retired
to-do.md; former task id T-280. Full original row:git show findings-md-final:to-do.md. Task state now lives in this tracker — seedev/red-team/migration-map.tsvfor red-team ids.