Uses of Interface
pal.misc.NeoParameterized
Packages that use NeoParameterized
Package
Description
Classes for evaluating evolutionary hypothesis (chi-square and likelihood
criteria) and estimating model parameters.
Classes that don't fit elsewhere ;^)
Classes describing substitution models, i.e.
-
Uses of NeoParameterized in pal.eval
Methods in pal.eval that return NeoParameterizedModifier and TypeMethodDescriptionMolecularClockLikelihoodModel.Instance.getParameterAccess()
UnconstrainedLikelihoodModel.Instance.getParameterAccess()
Methods in pal.eval with parameters of type NeoParameterizedModifier and TypeMethodDescriptionstatic final MolecularClockLikelihoodModel.Instance
SingleSplitMolecularClockLikelihoodModel.createInstance
(RateMatrixGroup beforeSplitMatrices, RateMatrixGroup afterSplitMatrics, NeoParameterized acrossSplitParameters, double splitTime) static final MolecularClockLikelihoodModel.Instance
SingleSplitMolecularClockLikelihoodModel.createInstance
(RateMatrixGroup beforeSplitMatrices, RateMatrixGroup afterSplitMatrics, NeoParameterized acrossSplitParameters, double[] classProbabilities, double splitTime) static final MolecularClockLikelihoodModel.Instance
SingleSplitMolecularClockLikelihoodModel.createInstance
(RateMatrixGroup beforeSplitMatrices, RateMatrixGroup afterSplitMatrics, NeoParameterized acrossSplitParameters, SingleSplitDistribution probabilityModel, double splitTime) static final MolecularClockLikelihoodModel.Instance
SingleSplitMolecularClockLikelihoodModel.createInstance
(RateMatrixGroup beforeSplitMatrices, RateMatrixGroup afterSplitMatrics, NeoParameterized acrossSplitParameters, SingleSplitDistribution probabilityModel, LHCalculator.Factory baseFactory, double splitTime) -
Uses of NeoParameterized in pal.misc
Classes in pal.misc that implement NeoParameterizedModifier and TypeClassDescriptionclass
Title: ParameterizedDoubleBundleclass
Title: ParameterizedNeoWrapper -
Uses of NeoParameterized in pal.substmodel
Subinterfaces of NeoParameterized in pal.substmodelClasses in pal.substmodel that implement NeoParameterizedModifier and TypeClassDescriptionclass
Title: ConstantIndependentSingleSplitDistributionclass
class
Title: SaturatedSingleSplitDistributionclass
Title: VariableIndependentSingleSplitDistribution -
Uses of NeoParameterized in pal.treesearch
Classes in pal.treesearch that implement NeoParameterizedModifier and TypeClassDescriptionclass
class
class
class
Methods in pal.treesearch that return NeoParameterizedModifier and TypeMethodDescriptionConstraintModel.GroupManager.getAllGroupRelatedParameterAccess()
FixedBSRDTGlobalClockModel.getAllGroupRelatedParameterAccess()
FixedSRDTGlobalClockModel.getAllGroupRelatedParameterAccess()
GlobalClockModel.getAllGroupRelatedParameterAccess()
MRDTGlobalClockModel.getAllGroupRelatedParameterAccess()
SRDTGlobalClockModel.getAllGroupRelatedParameterAccess()
ConstraintModel.getGlobalParameterAccess()
FixedBSRDTGlobalClockModel.getGlobalParameterAccess()
FixedSRDTGlobalClockModel.getGlobalParameterAccess()
GlobalClockModel.getGlobalParameterAccess()
MRDTGlobalClockModel.getGlobalParameterAccess()
SRDTGlobalClockModel.getGlobalParameterAccess()
UnconstrainedModel.getGlobalParameterAccess()
ConstraintModel.GroupManager.getPrimaryGroupRelatedParameterAccess()
FixedBSRDTGlobalClockModel.getPrimaryGroupRelatedParameterAccess()
FixedSRDTGlobalClockModel.getPrimaryGroupRelatedParameterAccess()
GlobalClockModel.getPrimaryGroupRelatedParameterAccess()
MRDTGlobalClockModel.getPrimaryGroupRelatedParameterAccess()
SRDTGlobalClockModel.getPrimaryGroupRelatedParameterAccess()
ConstraintModel.GroupManager.getSecondaryGroupRelatedParameterAccess()
FixedBSRDTGlobalClockModel.getSecondaryGroupRelatedParameterAccess()
FixedSRDTGlobalClockModel.getSecondaryGroupRelatedParameterAccess()
GlobalClockModel.getSecondaryGroupRelatedParameterAccess()
MRDTGlobalClockModel.getSecondaryGroupRelatedParameterAccess()
SRDTGlobalClockModel.getSecondaryGroupRelatedParameterAccess()