Uses of Interface
pal.eval.LHCalculator.Factory
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Packages that use LHCalculator.Factory Package Description pal.eval Classes for evaluating evolutionary hypothesis (chi-square and likelihood criteria) and estimating model parameters.pal.treesearch -
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Uses of LHCalculator.Factory in pal.eval
Methods in pal.eval that return LHCalculator.Factory Modifier and Type Method Description static LHCalculator.FactoryFastFourStateLHCalculator. getFactory()static LHCalculator.FactoryFastFourStateLHCalculator. getFactory(LHCalculator.Factory fallbackFactory)static LHCalculator.FactorySimpleLHCalculator. getFactory()static LHCalculator.FactorySimpleModelFastFourStateLHCalculator. getFactory()static LHCalculator.FactorySimpleModelFastFourStateLHCalculator. getFactory(LHCalculator.Factory fallbackFactory)Methods in pal.eval with parameters of type LHCalculator.Factory Modifier and Type Method Description static MolecularClockLikelihoodModel.InstanceSimpleMolecularClockLikelihoodModel. createInstance(LHCalculator.Factory baseFactory, SubstitutionModel model)static UnconstrainedLikelihoodModel.InstanceSimpleUnconstrainedLikelihoodModel. createInstance(LHCalculator.Factory base, SubstitutionModel model)Create a SimpleUnconstrainedLikelihoodModel instancestatic MolecularClockLikelihoodModel.InstanceSingleSplitMolecularClockLikelihoodModel. createInstance(RateMatrixGroup beforeSplitMatrices, RateMatrixGroup afterSplitMatrics, NeoParameterized acrossSplitParameters, SingleSplitDistribution probabilityModel, LHCalculator.Factory baseFactory, double splitTime)static LHCalculator.FactoryFastFourStateLHCalculator. getFactory(LHCalculator.Factory fallbackFactory)static LHCalculator.FactorySimpleModelFastFourStateLHCalculator. getFactory(LHCalculator.Factory fallbackFactory) -
Uses of LHCalculator.Factory in pal.treesearch
Constructors in pal.treesearch with parameters of type LHCalculator.Factory Constructor Description UnrootedMLSearcher(Alignment alignment, SubstitutionModel model, LHCalculator.Factory calcFactory)UnrootedMLSearcher(Node root, Alignment alignment, SubstitutionModel model, LHCalculator.Factory calcFactory)
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