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Packages that use MolecularClockLikelihoodModel.Instance | |
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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 |
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Methods in pal.eval that return MolecularClockLikelihoodModel.Instance | |
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static MolecularClockLikelihoodModel.Instance |
SimpleMolecularClockLikelihoodModel.createInstance(LHCalculator.Factory baseFactory,
SubstitutionModel model)
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static MolecularClockLikelihoodModel.Instance |
SingleSplitMolecularClockLikelihoodModel.createInstance(RateMatrixGroup beforeSplitMatrices,
RateMatrixGroup afterSplitMatrics,
NeoParameterized acrossSplitParameters,
double splitTime)
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static MolecularClockLikelihoodModel.Instance |
SingleSplitMolecularClockLikelihoodModel.createInstance(RateMatrixGroup beforeSplitMatrices,
RateMatrixGroup afterSplitMatrics,
NeoParameterized acrossSplitParameters,
double[] classProbabilities,
double splitTime)
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static MolecularClockLikelihoodModel.Instance |
SingleSplitMolecularClockLikelihoodModel.createInstance(RateMatrixGroup beforeSplitMatrices,
RateMatrixGroup afterSplitMatrics,
NeoParameterized acrossSplitParameters,
SingleSplitDistribution probabilityModel,
double splitTime)
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static MolecularClockLikelihoodModel.Instance |
SingleSplitMolecularClockLikelihoodModel.createInstance(RateMatrixGroup beforeSplitMatrices,
RateMatrixGroup afterSplitMatrics,
NeoParameterized acrossSplitParameters,
SingleSplitDistribution probabilityModel,
LHCalculator.Factory baseFactory,
double splitTime)
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static MolecularClockLikelihoodModel.Instance |
SimpleMolecularClockLikelihoodModel.createInstance(SubstitutionModel model)
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Uses of MolecularClockLikelihoodModel.Instance in pal.mep |
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Methods in pal.mep with parameters of type MolecularClockLikelihoodModel.Instance | |
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ConstraintModel |
DeltaModel.buildConstraintModel(SampleInformation si,
MolecularClockLikelihoodModel.Instance likelihoodModel)
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ConstraintModel |
MutationRateModel.Factory.buildConstraintModel(SampleInformation si,
MolecularClockLikelihoodModel.Instance likelihoodModel)
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Uses of MolecularClockLikelihoodModel.Instance in pal.treesearch |
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Constructors in pal.treesearch with parameters of type MolecularClockLikelihoodModel.Instance | |
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FixedBSRDTGlobalClockModel(SampleInformation sampleInformation,
MolecularClockLikelihoodModel.Instance likelihoodModel,
double rate)
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FixedSRDTGlobalClockModel(SampleInformation sampleInformation,
MolecularClockLikelihoodModel.Instance likelihoodModel,
double rate)
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GlobalClockModel(MolecularClockLikelihoodModel.Instance likelihoodModel)
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MRDTGlobalClockModel(SampleInformation sampleInformation,
MolecularClockLikelihoodModel.Instance likelihoodModel)
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MRDTGlobalClockModel(SampleInformation sampleInformation,
MolecularClockLikelihoodModel.Instance likelihoodModel,
double[] rateChangeTimes)
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SRDTGlobalClockModel(SampleInformation sampleInformation,
MolecularClockLikelihoodModel.Instance likelihoodModel)
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SRDTGlobalClockModel(SampleInformation sampleInformation,
MolecularClockLikelihoodModel.Instance likelihoodModel,
boolean allowMetaRate)
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