T-200: Decouple R-loop search from MorphyLib; add concavity parameter#216
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ms609 wants to merge 10 commits intocpp-searchfrom
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T-200: Decouple R-loop search from MorphyLib; add concavity parameter#216ms609 wants to merge 10 commits intocpp-searchfrom
ms609 wants to merge 10 commits intocpp-searchfrom
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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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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.