Uses of Interface
pal.eval.MolecularClockLikelihoodModel.Instance

Packages that use MolecularClockLikelihoodModel.Instance
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   
 

Uses of MolecularClockLikelihoodModel.Instance in pal.eval
 

Methods in pal.eval that return MolecularClockLikelihoodModel.Instance
static MolecularClockLikelihoodModel.Instance SimpleMolecularClockLikelihoodModel.createInstance(LHCalculator.Factory baseFactory, 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)
           
static MolecularClockLikelihoodModel.Instance SimpleMolecularClockLikelihoodModel.createInstance(SubstitutionModel model)
           
 

Uses of MolecularClockLikelihoodModel.Instance in pal.mep
 

Methods in pal.mep with parameters of type MolecularClockLikelihoodModel.Instance
 ConstraintModel DeltaModel.buildConstraintModel(SampleInformation si, MolecularClockLikelihoodModel.Instance likelihoodModel)
           
 ConstraintModel MutationRateModel.Factory.buildConstraintModel(SampleInformation si, MolecularClockLikelihoodModel.Instance likelihoodModel)
           
 

Uses of MolecularClockLikelihoodModel.Instance in pal.treesearch
 

Constructors in pal.treesearch with parameters of type MolecularClockLikelihoodModel.Instance
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)