Uses of Interface
pal.misc.NeoParameterized
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Packages that use NeoParameterized Package Description pal.eval Classes for evaluating evolutionary hypothesis (chi-square and likelihood criteria) and estimating model parameters.pal.misc Classes that don't fit elsewhere ;^)pal.substmodel Classes describing substitution models, i.e.pal.treesearch -
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Uses of NeoParameterized in pal.eval
Methods in pal.eval that return NeoParameterized Modifier and Type Method Description NeoParameterized
MolecularClockLikelihoodModel.Instance. getParameterAccess()
NeoParameterized
UnconstrainedLikelihoodModel.Instance. getParameterAccess()
Methods in pal.eval with parameters of type NeoParameterized Modifier and Type Method Description 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 NeoParameterized in pal.misc
Classes in pal.misc that implement NeoParameterized Modifier and Type Class Description class
ParameterizedDoubleBundle
Title: ParameterizedDoubleBundleclass
ParameterizedNeoWrapper
Title: ParameterizedNeoWrapper -
Uses of NeoParameterized in pal.substmodel
Subinterfaces of NeoParameterized in pal.substmodel Modifier and Type Interface Description interface
SingleSplitDistribution
Classes in pal.substmodel that implement NeoParameterized Modifier and Type Class Description class
ConstantIndependentSingleSplitDistribution
Title: ConstantIndependentSingleSplitDistributionclass
MultiRateMatrixHandler
class
SaturatedSingleSplitDistribution
Title: SaturatedSingleSplitDistributionclass
VariableIndependentSingleSplitDistribution
Title: VariableIndependentSingleSplitDistribution -
Uses of NeoParameterized in pal.treesearch
Classes in pal.treesearch that implement NeoParameterized Modifier and Type Class Description class
FixedBSRDTGlobalClockModel
class
GlobalClockModel
class
MRDTGlobalClockModel
class
SRDTGlobalClockModel
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