Uses of Interface
pal.eval.MolecularClockLikelihoodModel.Instance
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Packages that use MolecularClockLikelihoodModel.Instance Package Description pal.eval Classes for evaluating evolutionary hypothesis (chi-square and likelihood criteria) and estimating model parameters.pal.mep Classes for the analysis of "measurably evolving populations" (mep).pal.treesearch -
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Uses of MolecularClockLikelihoodModel.Instance in pal.eval
Methods in pal.eval that return MolecularClockLikelihoodModel.Instance Modifier and Type Method Description static MolecularClockLikelihoodModel.InstanceSimpleMolecularClockLikelihoodModel. createInstance(LHCalculator.Factory baseFactory, SubstitutionModel model)static MolecularClockLikelihoodModel.InstanceSimpleMolecularClockLikelihoodModel. createInstance(SubstitutionModel model)static MolecularClockLikelihoodModel.InstanceSingleSplitMolecularClockLikelihoodModel. createInstance(RateMatrixGroup beforeSplitMatrices, RateMatrixGroup afterSplitMatrics, NeoParameterized acrossSplitParameters, double splitTime)static MolecularClockLikelihoodModel.InstanceSingleSplitMolecularClockLikelihoodModel. createInstance(RateMatrixGroup beforeSplitMatrices, RateMatrixGroup afterSplitMatrics, NeoParameterized acrossSplitParameters, double[] classProbabilities, double splitTime)static MolecularClockLikelihoodModel.InstanceSingleSplitMolecularClockLikelihoodModel. createInstance(RateMatrixGroup beforeSplitMatrices, RateMatrixGroup afterSplitMatrics, NeoParameterized acrossSplitParameters, SingleSplitDistribution probabilityModel, double splitTime)static MolecularClockLikelihoodModel.InstanceSingleSplitMolecularClockLikelihoodModel. createInstance(RateMatrixGroup beforeSplitMatrices, RateMatrixGroup afterSplitMatrics, NeoParameterized acrossSplitParameters, SingleSplitDistribution probabilityModel, LHCalculator.Factory baseFactory, double splitTime) -
Uses of MolecularClockLikelihoodModel.Instance in pal.mep
Methods in pal.mep with parameters of type MolecularClockLikelihoodModel.Instance Modifier and Type Method Description ConstraintModelDeltaModel. buildConstraintModel(SampleInformation si, MolecularClockLikelihoodModel.Instance likelihoodModel)ConstraintModelMutationRateModel.Factory. buildConstraintModel(SampleInformation si, MolecularClockLikelihoodModel.Instance likelihoodModel) -
Uses of MolecularClockLikelihoodModel.Instance in pal.treesearch
Constructors in pal.treesearch with parameters of type MolecularClockLikelihoodModel.Instance Constructor Description FixedBSRDTGlobalClockModel(SampleInformation sampleInformation, MolecularClockLikelihoodModel.Instance likelihoodModel, double rate)FixedSRDTGlobalClockModel(SampleInformation sampleInformation, MolecularClockLikelihoodModel.Instance likelihoodModel, double rate)GlobalClockModel(MolecularClockLikelihoodModel.Instance likelihoodModel)MRDTGlobalClockModel(SampleInformation sampleInformation, MolecularClockLikelihoodModel.Instance likelihoodModel)MRDTGlobalClockModel(SampleInformation sampleInformation, MolecularClockLikelihoodModel.Instance likelihoodModel, double[] rateChangeTimes)SRDTGlobalClockModel(SampleInformation sampleInformation, MolecularClockLikelihoodModel.Instance likelihoodModel)SRDTGlobalClockModel(SampleInformation sampleInformation, MolecularClockLikelihoodModel.Instance likelihoodModel, boolean allowMetaRate)
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