Add KRegCCD regularisation family, UniformEscapeCCD, and PIT/held-out experiments#11
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Add KRegCCD regularisation family, UniformEscapeCCD, and PIT/held-out experiments#11alexeid wants to merge 1 commit into
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Brings the full-support CCD regularisers from the BEAST 2.7 line (CCD-Sophie) onto beast3: - ccd.model: KRegCCD, MRegCCD, GRegCCD/GRegZApprox, NNIRegCCD, and the UniformEscapeCCD trivial full-coverage baseline; the CCD0CP/CCD0SJ/ CCD1CP/CCD1SJ variants with CPSupport/SJSupport; sampled-ancestor support (WrappedBeastTreeWithSampledAncestor). - ccd.algorithms.regularisation: KReg/MReg/NNIReg parameter optimisers and NNI clade expansion. - Supporting enhancements to the shared base classes (AbstractCCD, Clade, CladePartition, RegCCD, ...) that the regularisers build on. Also fixes a bug surfaced by the existing CCDCoreTest: CCD2(trees, burnin) reimplemented the burn-in handling instead of delegating to AbstractCCD and failed to set numBaseTrees when burnin == 0. The three commons-math3 optimiser users are migrated to the org.apache.commons.math4.legacy package already required by beast3. pom.xml, module-info, and version.xml are unchanged.
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Brings the full-support CCD regularisers (developed on the BEAST 2.7 line in CCD-Sophie) onto the
beast3branch. Independent beast3 port, reconciled onto this branch's scaffolding (no changes topom.xml,module-info, orversion.xml).What's added
KRegCCD,MRegCCD,GRegCCD/GRegZApprox,NNIRegCCD; theUniformEscapeCCDtrivial full-coverage baseline; theCCD0CP/CCD0SJ/CCD1CP/CCD1SJvariants withCPSupport/SJSupport; sampled-ancestor support (WrappedBeastTreeWithSampledAncestor).doc/plot_pit.pyrenders the full-coverage PIT histograms.AbstractCCD,Clade,CladePartition,RegCCD, …) that the regularisers build on.Bug fix
CCD2(trees, burnin)reimplemented the burn-in handling instead of delegating toAbstractCCDand failed to setnumBaseTreeswhenburnin == 0(CCD0/CCD1set it viasuper()). Surfaced by the existingCCDCoreTest.Notes
org.apache.commons.math4.legacypackage already required by beast3 — no new dependency.CCDCoreTest.