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.Instance
SimpleMolecularClockLikelihoodModel. createInstance(LHCalculator.Factory baseFactory, SubstitutionModel model)
static MolecularClockLikelihoodModel.Instance
SimpleMolecularClockLikelihoodModel. createInstance(SubstitutionModel model)
static MolecularClockLikelihoodModel.Instance
SingleSplitMolecularClockLikelihoodModel. createInstance(RateMatrixGroup beforeSplitMatrices, RateMatrixGroup afterSplitMatrics, NeoParameterized acrossSplitParameters, double splitTime)
static MolecularClockLikelihoodModel.Instance
SingleSplitMolecularClockLikelihoodModel. createInstance(RateMatrixGroup beforeSplitMatrices, RateMatrixGroup afterSplitMatrics, NeoParameterized acrossSplitParameters, double[] classProbabilities, double splitTime)
static MolecularClockLikelihoodModel.Instance
SingleSplitMolecularClockLikelihoodModel. createInstance(RateMatrixGroup beforeSplitMatrices, RateMatrixGroup afterSplitMatrics, NeoParameterized acrossSplitParameters, SingleSplitDistribution probabilityModel, double splitTime)
static MolecularClockLikelihoodModel.Instance
SingleSplitMolecularClockLikelihoodModel. createInstance(RateMatrixGroup beforeSplitMatrices, RateMatrixGroup afterSplitMatrics, NeoParameterized acrossSplitParameters, SingleSplitDistribution probabilityModel, LHCalculator.Factory baseFactory, double splitTime)
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Uses of MolecularClockLikelihoodModel.Instance in pal.mep
Methods in pal.mep with parameters of type MolecularClockLikelihoodModel.Instance Modifier and Type Method Description ConstraintModel
DeltaModel. buildConstraintModel(SampleInformation si, MolecularClockLikelihoodModel.Instance likelihoodModel)
ConstraintModel
MutationRateModel.Factory. buildConstraintModel(SampleInformation si, MolecularClockLikelihoodModel.Instance likelihoodModel)
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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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