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Packages that use NeoParameterized | |
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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 |
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Methods in pal.eval that return NeoParameterized | |
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NeoParameterized |
MolecularClockLikelihoodModel.Instance.getParameterAccess()
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NeoParameterized |
UnconstrainedLikelihoodModel.Instance.getParameterAccess()
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Methods in pal.eval with parameters of type NeoParameterized | |
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static MolecularClockLikelihoodModel.Instance |
SingleSplitMolecularClockLikelihoodModel.createInstance(RateMatrixGroup beforeSplitMatrices,
RateMatrixGroup afterSplitMatrics,
NeoParameterized acrossSplitParameters,
double splitTime)
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static MolecularClockLikelihoodModel.Instance |
SingleSplitMolecularClockLikelihoodModel.createInstance(RateMatrixGroup beforeSplitMatrices,
RateMatrixGroup afterSplitMatrics,
NeoParameterized acrossSplitParameters,
double[] classProbabilities,
double splitTime)
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static MolecularClockLikelihoodModel.Instance |
SingleSplitMolecularClockLikelihoodModel.createInstance(RateMatrixGroup beforeSplitMatrices,
RateMatrixGroup afterSplitMatrics,
NeoParameterized acrossSplitParameters,
SingleSplitDistribution probabilityModel,
double splitTime)
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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 |
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Classes in pal.misc that implement NeoParameterized | |
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class |
ParameterizedDoubleBundle
Title: ParameterizedDoubleBundle |
class |
ParameterizedNeoWrapper
Title: ParameterizedNeoWrapper |
Uses of NeoParameterized in pal.substmodel |
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Subinterfaces of NeoParameterized in pal.substmodel | |
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interface |
SingleSplitDistribution
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Classes in pal.substmodel that implement NeoParameterized | |
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class |
ConstantIndependentSingleSplitDistribution
Title: ConstantIndependentSingleSplitDistribution |
class |
MultiRateMatrixHandler
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class |
SaturatedSingleSplitDistribution
Title: SaturatedSingleSplitDistribution |
class |
VariableIndependentSingleSplitDistribution
Title: VariableIndependentSingleSplitDistribution |
Uses of NeoParameterized in pal.treesearch |
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Classes in pal.treesearch that implement NeoParameterized | |
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class |
FixedBSRDTGlobalClockModel
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class |
GlobalClockModel
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class |
MRDTGlobalClockModel
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class |
SRDTGlobalClockModel
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