Add VectorElement: scalar view of a RealVector element#61
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rbouckaert merged 2 commits intomasterfrom Apr 8, 2026
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Add optional shape input to KeyVectorParam that allows flat vector storage to be interpreted as a multi-dimensional array. When shape is set (e.g. shape="3 4" for a 3x4 matrix), rank() and shape() reflect the tensor dimensions, and get(int... idx) supports multi-dimensional indexing via row-major strides. Wired up in both RealVectorParam and IntVectorParam. Backward compatible: vectors without shape behave exactly as before. Replaces the deprecated minordimension on Parameter.Base.
Provides a RealScalar view of a single element in a RealVector, enabling vector parameters to be used wherever a scalar is required (e.g. per-partition mutation rates from a single vector state node).
alexeid
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Replace the Concatenate+Slice pattern with single RealVectorParam + VectorElement for element access. This is a cleaner design: create the whole vector, then slice to get parts (instead of building parts and joining them). Changes: - Add VectorSlice for multi-element range slicing (array[0:5]) - Add WeightedDirichletValueToBEAST (RealVectorParam + delta exchange) - Move SliceDoubleArrayToBEAST from feast to core - Replace all Slice usage with VectorElement in BEASTContext - Replace ScalarSlice with VectorElement in ExpMarkovChainToBEAST - Use spec DeltaExchangeOperator instead of deprecated Bactrian version - Simplify FeastValueHandler (remove Concatenate methods) - Delete: ScalarSlice, SliceFactory, feast DoubleArrayValueToBEAST - Delete lphybeast/lib/ (25 unused system-scope JARs) - Update BEAST3-MIGRATION.md Phase 2/3 status Depends on beast3 VectorElement (CompEvol/beast3#61).
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Summary
VectorElement<D extends Real>tobeast.base.spec.inference.parameter— aCalculationNodethat implementsRealScalar<D>by delegating to a single element of aRealVector<D>VectorElementinmodule-info.javafor BEAST's class loaderinitByNameconstructionMotivation
This enables the "vector + slice" pattern: create a single
RealVectorParamstate node and useVectorElementto provide scalar views whereverRealScalaris required (e.g., per-partitionSiteModel.mutationRate).This replaces the inverse pattern of creating individual scalar parameters and joining them with
Concatenate, and serves as the beast3 successor tobeastlabs.core.util.Slicewith proper spec type support.Fixes #60
Test plan
VectorElementTest— 5 tests covering get, domain, mutation tracking, bounds, initByName🤖 Generated with Claude Code