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 |
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) |
Modifier and Type | Method | Description |
---|---|---|
ConstraintModel |
DeltaModel.buildConstraintModel(SampleInformation si,
MolecularClockLikelihoodModel.Instance likelihoodModel) |
|
ConstraintModel |
MutationRateModel.Factory.buildConstraintModel(SampleInformation si,
MolecularClockLikelihoodModel.Instance likelihoodModel) |
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) |