Uses of Package
pal.eval
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Packages that use pal.eval Package Description pal.eval Classes for evaluating evolutionary hypothesis (chi-square and likelihood criteria) and estimating model parameters.pal.mep Classes for the analysis of "measurably evolving populations" (mep).pal.statistics Classes with useful for statistics (normal distribution, Gamma distribution, chi-square distribution, exponential distribution, likelihood-ratio test, chi-square test, descriptive statistics, bootstrap estimators etc.)pal.treesearch -
Classes in pal.eval used by pal.eval Class Description ConditionalProbabilityStore Title: ConditionalProbabilityStore (was ConditionalLikelihoodStore)ConditionalProbabilityStore.ExtraProcessor LHCalculator LHCalculator.External The External calculator does not maintain any state and is approapriate for calculation where a store is providedLHCalculator.Factory LHCalculator.Generator LHCalculator.Internal The Internal calculator may maintain state and is approapriate permanent attachment to internal nodes of the tree structureLHCalculator.Leaf A LHCalculator.Leaf object is attached to each leaf node and can be used to calculated conditional probabilities across the related branch.LikelihoodCalculator classes that calculate likelihoods should implement this interface.LikelihoodSummary LikelihoodValue Computes the likelihood for a tree given a model of sequence evolution and a sequence alignment; also optimises tree parameters such as branch lengths by maximising the likelihood (for optimal performance special optimisation procedures are employed for UnconstrainedTree, ClockTree and DatedTipsClockTree; a general optimisation precedure is used for another ParameterizedTree).MolecularClockLikelihoodModel MolecularClockLikelihoodModel.External The External calculator does not maintain any state and is approapriate for calculation where a store is providedMolecularClockLikelihoodModel.HeightConverter MolecularClockLikelihoodModel.Instance MolecularClockLikelihoodModel.Internal The Internal calculator may maintain state and is approapriate permanent attachment to internal nodes of the tree structureMolecularClockLikelihoodModel.Leaf A ConstrainedLHCalculator.Leaf object is attached to each leaf node and can be used to calculated conditional probabilities across the related branch.PatternInfo Title: PatternInfoSiteDetails UnconstrainedLikelihoodModel UnconstrainedLikelihoodModel.External The External calculator does not maintain any state and is approapriate for calculation where a store is providedUnconstrainedLikelihoodModel.Instance UnconstrainedLikelihoodModel.Internal The Internal calculator may maintain state and is approapriate permanent attachment to internal nodes of the tree structureUnconstrainedLikelihoodModel.Leaf A LHCalculator.Leaf object is attached to each leaf node and can be used to calculated conditional probabilities across the related branch. -
Classes in pal.eval used by pal.mep Class Description MolecularClockLikelihoodModel.Instance -
Classes in pal.eval used by pal.statistics Class Description SiteDetails -
Classes in pal.eval used by pal.treesearch Class Description ConditionalProbabilityStore Title: ConditionalProbabilityStore (was ConditionalLikelihoodStore)LHCalculator.Factory MolecularClockLikelihoodModel.External The External calculator does not maintain any state and is approapriate for calculation where a store is providedMolecularClockLikelihoodModel.HeightConverter MolecularClockLikelihoodModel.Instance MolecularClockLikelihoodModel.Internal The Internal calculator may maintain state and is approapriate permanent attachment to internal nodes of the tree structureMolecularClockLikelihoodModel.Leaf A ConstrainedLHCalculator.Leaf object is attached to each leaf node and can be used to calculated conditional probabilities across the related branch.PatternInfo Title: PatternInfoSiteDetails UnconstrainedLikelihoodModel.External The External calculator does not maintain any state and is approapriate for calculation where a store is providedUnconstrainedLikelihoodModel.Instance UnconstrainedLikelihoodModel.Internal The Internal calculator may maintain state and is approapriate permanent attachment to internal nodes of the tree structureUnconstrainedLikelihoodModel.Leaf A LHCalculator.Leaf object is attached to each leaf node and can be used to calculated conditional probabilities across the related branch.