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.
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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.InstanceSingleSplitMolecularClockLikelihoodModel.createInstance(RateMatrixGroup beforeSplitMatrices, RateMatrixGroup afterSplitMatrics, NeoParameterized acrossSplitParameters, double splitTime) static final MolecularClockLikelihoodModel.InstanceSingleSplitMolecularClockLikelihoodModel.createInstance(RateMatrixGroup beforeSplitMatrices, RateMatrixGroup afterSplitMatrics, NeoParameterized acrossSplitParameters, double[] classProbabilities, double splitTime) static final MolecularClockLikelihoodModel.InstanceSingleSplitMolecularClockLikelihoodModel.createInstance(RateMatrixGroup beforeSplitMatrices, RateMatrixGroup afterSplitMatrics, NeoParameterized acrossSplitParameters, SingleSplitDistribution probabilityModel, double splitTime) static final MolecularClockLikelihoodModel.InstanceSingleSplitMolecularClockLikelihoodModel.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 TypeClassDescriptionclassTitle: ParameterizedDoubleBundleclassTitle: ParameterizedNeoWrapper -
Uses of NeoParameterized in pal.substmodel
Subinterfaces of NeoParameterized in pal.substmodelClasses in pal.substmodel that implement NeoParameterizedModifier and TypeClassDescriptionclassTitle: ConstantIndependentSingleSplitDistributionclassclassTitle: SaturatedSingleSplitDistributionclassTitle: VariableIndependentSingleSplitDistribution -
Uses of NeoParameterized in pal.treesearch
Classes in pal.treesearch that implement NeoParameterizedModifier and TypeClassDescriptionclassclassclassclassMethods 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()