Uses of Interface
pal.eval.LHCalculator.Factory
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Packages that use LHCalculator.Factory Package Description pal.eval Classes for evaluating evolutionary hypothesis (chi-square and likelihood criteria) and estimating model parameters.pal.treesearch -
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Uses of LHCalculator.Factory in pal.eval
Methods in pal.eval that return LHCalculator.Factory Modifier and Type Method Description static LHCalculator.Factory
FastFourStateLHCalculator. getFactory()
static LHCalculator.Factory
FastFourStateLHCalculator. getFactory(LHCalculator.Factory fallbackFactory)
static LHCalculator.Factory
SimpleLHCalculator. getFactory()
static LHCalculator.Factory
SimpleModelFastFourStateLHCalculator. getFactory()
static LHCalculator.Factory
SimpleModelFastFourStateLHCalculator. getFactory(LHCalculator.Factory fallbackFactory)
Methods in pal.eval with parameters of type LHCalculator.Factory Modifier and Type Method Description static MolecularClockLikelihoodModel.Instance
SimpleMolecularClockLikelihoodModel. createInstance(LHCalculator.Factory baseFactory, SubstitutionModel model)
static UnconstrainedLikelihoodModel.Instance
SimpleUnconstrainedLikelihoodModel. createInstance(LHCalculator.Factory base, SubstitutionModel model)
Create a SimpleUnconstrainedLikelihoodModel instancestatic MolecularClockLikelihoodModel.Instance
SingleSplitMolecularClockLikelihoodModel. createInstance(RateMatrixGroup beforeSplitMatrices, RateMatrixGroup afterSplitMatrics, NeoParameterized acrossSplitParameters, SingleSplitDistribution probabilityModel, LHCalculator.Factory baseFactory, double splitTime)
static LHCalculator.Factory
FastFourStateLHCalculator. getFactory(LHCalculator.Factory fallbackFactory)
static LHCalculator.Factory
SimpleModelFastFourStateLHCalculator. getFactory(LHCalculator.Factory fallbackFactory)
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Uses of LHCalculator.Factory in pal.treesearch
Constructors in pal.treesearch with parameters of type LHCalculator.Factory Constructor Description UnrootedMLSearcher(Alignment alignment, SubstitutionModel model, LHCalculator.Factory calcFactory)
UnrootedMLSearcher(Node root, Alignment alignment, SubstitutionModel model, LHCalculator.Factory calcFactory)
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