Package pal.eval
Classes for evaluating evolutionary hypothesis (chi-square and likelihood
criteria) and estimating model parameters.
-
Interface Summary Interface Description 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.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.MolecularClockLikelihoodModel.Simulator SiteDetails 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. -
Class Summary Class Description ChiSquareValue computes chi-square value of a (parameterized) tree for its set of parameters (e.g., branch lengths) and a given distance matrixConditionalProbabilityStore Title: ConditionalProbabilityStore (was ConditionalLikelihoodStore)DemographicLikelihoodValue Estimates the likelihood for a tree using a specified model of sequence evolution and a sequence alignment and a specific demographic model as a prior on coalescent intervals.DemographicValue estimates demographic parameters by maximising the coalescent prior for a tree with given branch lengths.FastFourStateLHCalculator FastLikelihoodCalculator Title: Fast Likelihood Calculator
Description: A fast likelihood calculator
Original code by Matthew Goode.GeneralLikelihoodCalculator Title: General Likelihood Calculator
Description: A General likelihood calculator
This calculates the likelihood of an topologically invariant tree (on an unchanging alignment) quickly by remembering partial likelihoods of invariant subtrees, and by essentially generating site patterns for each sub tree.LHCalculator.AbstractExternal LikelihoodOptimiser LikelihoodSummary LikelihoodTool 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).ModelParameters estimates substitution model parameters from the dataPatternInfo Title: PatternInfoSimpleLeafCalculator SimpleLHCalculator SimpleLikelihoodCalculator SimpleModelFastFourStateLHCalculator SimpleMolecularClockLikelihoodModel SimpleUnconstrainedLikelihoodModel SimpleUnconstrainedLikelihoodModel.InternalImpl SimpleUnconstrainedLikelihoodModel.LeafImpl SingleSplitMolecularClockLikelihoodModel SiteDetails.Utils