Uses of Interface pal.misc.NeoParameterized

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

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)`

Uses of NeoParameterized in pal.misc

Classes in pal.misc that implement NeoParameterized
Modifier and Type	Class	Description
`class`	`ParameterizedDoubleBundle`	Title: ParameterizedDoubleBundle
`class`	`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: ConstantIndependentSingleSplitDistribution
`class`	`MultiRateMatrixHandler`
`class`	`SaturatedSingleSplitDistribution`	Title: SaturatedSingleSplitDistribution
`class`	`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`

Methods in pal.treesearch that return NeoParameterized
Modifier and Type	Method	Description
`NeoParameterized`	ConstraintModel.GroupManager.`getAllGroupRelatedParameterAccess()`
`NeoParameterized`	FixedBSRDTGlobalClockModel.`getAllGroupRelatedParameterAccess()`
`NeoParameterized`	FixedSRDTGlobalClockModel.`getAllGroupRelatedParameterAccess()`
`NeoParameterized`	GlobalClockModel.`getAllGroupRelatedParameterAccess()`
`NeoParameterized`	MRDTGlobalClockModel.`getAllGroupRelatedParameterAccess()`
`NeoParameterized`	SRDTGlobalClockModel.`getAllGroupRelatedParameterAccess()`
`NeoParameterized`	ConstraintModel.`getGlobalParameterAccess()`
`NeoParameterized`	FixedBSRDTGlobalClockModel.`getGlobalParameterAccess()`
`NeoParameterized`	FixedSRDTGlobalClockModel.`getGlobalParameterAccess()`
`NeoParameterized`	GlobalClockModel.`getGlobalParameterAccess()`
`NeoParameterized`	MRDTGlobalClockModel.`getGlobalParameterAccess()`
`NeoParameterized`	SRDTGlobalClockModel.`getGlobalParameterAccess()`
`NeoParameterized`	UnconstrainedModel.`getGlobalParameterAccess()`
`NeoParameterized`	ConstraintModel.GroupManager.`getPrimaryGroupRelatedParameterAccess()`
`NeoParameterized`	FixedBSRDTGlobalClockModel.`getPrimaryGroupRelatedParameterAccess()`
`NeoParameterized`	FixedSRDTGlobalClockModel.`getPrimaryGroupRelatedParameterAccess()`
`NeoParameterized`	GlobalClockModel.`getPrimaryGroupRelatedParameterAccess()`
`NeoParameterized`	MRDTGlobalClockModel.`getPrimaryGroupRelatedParameterAccess()`
`NeoParameterized`	SRDTGlobalClockModel.`getPrimaryGroupRelatedParameterAccess()`
`NeoParameterized`	ConstraintModel.GroupManager.`getSecondaryGroupRelatedParameterAccess()`
`NeoParameterized`	FixedBSRDTGlobalClockModel.`getSecondaryGroupRelatedParameterAccess()`
`NeoParameterized`	FixedSRDTGlobalClockModel.`getSecondaryGroupRelatedParameterAccess()`
`NeoParameterized`	GlobalClockModel.`getSecondaryGroupRelatedParameterAccess()`
`NeoParameterized`	MRDTGlobalClockModel.`getSecondaryGroupRelatedParameterAccess()`
`NeoParameterized`	SRDTGlobalClockModel.`getSecondaryGroupRelatedParameterAccess()`

Uses of Interfacepal.misc.NeoParameterized

Uses of NeoParameterized in pal.eval

Uses of NeoParameterized in pal.misc

Uses of NeoParameterized in pal.substmodel

Uses of NeoParameterized in pal.treesearch

Uses of Interface
pal.misc.NeoParameterized