T-200: Decouple R-loop search from MorphyLib; add concavity parameter#216
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T-200: Decouple R-loop search from MorphyLib; add concavity parameter#216ms609 wants to merge 10 commits into
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- New R/NativeSearch.R: PrepareNativeData, CleanNativeData, NativeLength, NativeBootstrap (4 exported functions) - TreeSearch(), Ratchet(), Jackknife() now default to native scorer - New 'concavity' parameter on all three functions - Jackknife() rewritten to support both native and morphy paths - EdgeListSearch() default scorer changed to NativeLength - Deprecated: PhyDat2Morphy, UnloadMorphy, MorphyLength, MorphyTreeLength, MorphyBootstrap - Vignette custom.Rmd IW section rewritten (was ~150 lines of MorphyLib scaffolding, now 30 lines using concavity parameter) - test-NativeSearch.R: 7 tests covering all new functions - test-CustomSearch.R: updated to use native defaults
Adds NativeSearch.Rd and updates Jackknife.Rd, Ratchet.Rd, TreeSearch.Rd with new concavity parameter and default changes.
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- inst/WORDLIST: add 'cleanup' and 'phyDat' - R/mpl_morphy_objects.R: wrap PhyDat2Morphy/MorphyWeights @examples in \donttest{}; use suppressWarnings() for UnloadMorphy in GapHandler and SingleCharMorphy examples - R/Morphy.R: wrap constraint example with suppressWarnings() so internal PhyDat2Morphy/UnloadMorphy calls don't emit warnings Fixes 1 ERROR (spelling) + 1 WARNING (deprecated fns in examples)
Wrap PhyDat2Morphy() and UnloadMorphy() calls in suppressWarnings()
in the \examples{} sections of GapHandler.Rd, MorphyWeights.Rd,
PhyDat2Morphy.Rd, RearrangeEdges.Rd, and SingleCharMorphy.Rd.
Wrap Morphy() in suppressWarnings() in the \donttest{} block of
Morphy.Rd -- Morphy() calls PhyDat2Morphy/UnloadMorphy internally via
lapply/vapply, generating the 'FUN' is deprecated warning stream.
R CMD check --as-cran treats warnings-in-examples as errors.
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Synthesise the best of PR #251 (this branch) and PR #216 (T-200, Agent B), which independently decoupled the R-loop search from MorphyLib. Adopted from #216: - Efficient native scorer: PrepareData() pre-extracts the scoring matrices once and EdgeListScore() calls ts_fitch_score() directly, instead of rebuilding a phylo and re-extracting tip data on every score. - `concavity` parameter on TreeSearch()/Ratchet()/Jackknife(): Inf = equal weights (default), finite = implied weights, "profile" = profile parsimony. Custom InitializeData hooks still receive the dataset unchanged. - custom.Rmd implied-weights section rewritten from ~150 lines of hand-rolled scaffolding to a few lines using `concavity` directly. Kept from #251 (and fixing #216's staleness): - MorphyLib stays fully deleted (#216 retained it as a fallback). - Score weights use .ScaleWeight() (fractional-weight aware) and Inf for the equal-weights concavity, matching current TreeLength(); #216 used as.integer(weight) and -1.0, predating those changes. - Functional resampling + a regression test (doubling weights doubles score). Naming: the layer is renamed to purpose-based names rather than #216's `*Native*` prefix, because once MorphyLib is gone "Native" no longer contrasts with anything. PhyDat2Morphy->PrepareData, UnloadMorphy->ReleaseData, is.morphyPtr->is.ParsimonyData, SingleCharMorphy->SingleCharData, MorphyLength->EdgeListScore, MorphyTreeLength->TreeScore, MorphyBootstrap->BootstrapTree, RandomMorphyTree->RandomPostorderTree. The old names remain as .Deprecated() aliases. TreeScore() == TreeLength() verified across equal weights, implied weights and profile parsimony; full suite green (only the pre-existing WideSample/MaxMin API-drift failures remain, unrelated to this change). Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
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Superseded in #251 |
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Agent B
Summary
Replaces MorphyLib scoring in
TreeSearch(),Ratchet(),Jackknife()withnative C++ engine (
ts_fitch_score()), while retaining backward compatibilityfor users passing MorphyLib scorers explicitly.
New exports
PrepareNativeData()— replacesPhyDat2Morphy()CleanNativeData()— replacesUnloadMorphy()NativeLength()— replacesMorphyLength()NativeBootstrap()— replacesMorphyBootstrap()Changed defaults
TreeSearch,Ratchet,Jackknife, andEdgeListSearchnow default tonative scorers. New
concavityparameter (defaultInf= equal weights)makes implied-weights searches trivial:
Deprecations
PhyDat2Morphy,UnloadMorphy,MorphyLength,MorphyTreeLength,MorphyBootstrapemit.Deprecated()warnings.Vignette
custom.RmdIW section rewritten from ~150 lines of MorphyLib scaffoldingto ~30 lines.
Tests
7 new tests in
test-NativeSearch.R. Existing tests updated to use nativedefaults. 50 pass / 0 fail.
Note
Native scorer uses simple IW (
fit = e / (e + k)), matchingTreeLength(..., extended_iw = FALSE). XPIWE (Extension 3) remains in theC++ search path.