Uses of Interface
pal.eval.MolecularClockLikelihoodModel.Instance
Packages that use MolecularClockLikelihoodModel.Instance
Package
Description
Classes for evaluating evolutionary hypothesis (chi-square and likelihood
criteria) and estimating model parameters.
Classes for the analysis of "measurably evolving populations" (mep).
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Uses of MolecularClockLikelihoodModel.Instance in pal.eval
Methods in pal.eval that return MolecularClockLikelihoodModel.InstanceModifier and TypeMethodDescriptionstatic final MolecularClockLikelihoodModel.Instance
SimpleMolecularClockLikelihoodModel.createInstance
(LHCalculator.Factory baseFactory, SubstitutionModel model) static final MolecularClockLikelihoodModel.Instance
SimpleMolecularClockLikelihoodModel.createInstance
(SubstitutionModel model) static final MolecularClockLikelihoodModel.Instance
SingleSplitMolecularClockLikelihoodModel.createInstance
(RateMatrixGroup beforeSplitMatrices, RateMatrixGroup afterSplitMatrics, NeoParameterized acrossSplitParameters, double splitTime) static final MolecularClockLikelihoodModel.Instance
SingleSplitMolecularClockLikelihoodModel.createInstance
(RateMatrixGroup beforeSplitMatrices, RateMatrixGroup afterSplitMatrics, NeoParameterized acrossSplitParameters, double[] classProbabilities, double splitTime) static final MolecularClockLikelihoodModel.Instance
SingleSplitMolecularClockLikelihoodModel.createInstance
(RateMatrixGroup beforeSplitMatrices, RateMatrixGroup afterSplitMatrics, NeoParameterized acrossSplitParameters, SingleSplitDistribution probabilityModel, double splitTime) static final MolecularClockLikelihoodModel.Instance
SingleSplitMolecularClockLikelihoodModel.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.InstanceModifier and TypeMethodDescriptionDeltaModel.buildConstraintModel
(SampleInformation si, MolecularClockLikelihoodModel.Instance likelihoodModel) MutationRateModel.Factory.buildConstraintModel
(SampleInformation si, MolecularClockLikelihoodModel.Instance likelihoodModel) -
Uses of MolecularClockLikelihoodModel.Instance in pal.treesearch
Constructors in pal.treesearch with parameters of type MolecularClockLikelihoodModel.InstanceModifierConstructorDescriptionFixedBSRDTGlobalClockModel
(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)