Uses of Package
pal.eval
Packages that use pal.eval
Package
Description
Classes for evaluating evolutionary hypothesis (chi-square and likelihood
criteria) and estimating model parameters.
Classes for the analysis of "measurably evolving populations" (mep).
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.)
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ClassDescriptionTitle: ConditionalProbabilityStore (was ConditionalLikelihoodStore)The External calculator does not maintain any state and is approapriate for calculation where a store is providedThe Internal calculator may maintain state and is approapriate permanent attachment to internal nodes of the tree structureA LHCalculator.Leaf object is attached to each leaf node and can be used to calculated conditional probabilities across the related branch.classes that calculate likelihoods should implement this interface.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).The External calculator does not maintain any state and is approapriate for calculation where a store is providedThe Internal calculator may maintain state and is approapriate permanent attachment to internal nodes of the tree structureA ConstrainedLHCalculator.Leaf object is attached to each leaf node and can be used to calculated conditional probabilities across the related branch.Title: PatternInfoThe External calculator does not maintain any state and is approapriate for calculation where a store is providedThe Internal calculator may maintain state and is approapriate permanent attachment to internal nodes of the tree structureA LHCalculator.Leaf object is attached to each leaf node and can be used to calculated conditional probabilities across the related branch.
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Classes in pal.eval used by pal.statistics
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Classes in pal.eval used by pal.treesearchClassDescriptionTitle: ConditionalProbabilityStore (was ConditionalLikelihoodStore)The External calculator does not maintain any state and is approapriate for calculation where a store is providedThe Internal calculator may maintain state and is approapriate permanent attachment to internal nodes of the tree structureA ConstrainedLHCalculator.Leaf object is attached to each leaf node and can be used to calculated conditional probabilities across the related branch.Title: PatternInfoThe External calculator does not maintain any state and is approapriate for calculation where a store is providedThe Internal calculator may maintain state and is approapriate permanent attachment to internal nodes of the tree structureA LHCalculator.Leaf object is attached to each leaf node and can be used to calculated conditional probabilities across the related branch.