Uses of Package
pal.eval

Packages that use pal.eval
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
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 provided
LHCalculator.Factory
           
LHCalculator.Generator
           
LHCalculator.Internal
          The Internal calculator may maintain state and is approapriate permanent attachment to internal nodes of the tree structure
LHCalculator.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 provided
MolecularClockLikelihoodModel.HeightConverter
           
MolecularClockLikelihoodModel.Instance
           
MolecularClockLikelihoodModel.Internal
          The Internal calculator may maintain state and is approapriate permanent attachment to internal nodes of the tree structure
MolecularClockLikelihoodModel.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: PatternInfo
SiteDetails
           
UnconstrainedLikelihoodModel
           
UnconstrainedLikelihoodModel.External
          The External calculator does not maintain any state and is approapriate for calculation where a store is provided
UnconstrainedLikelihoodModel.Instance
           
UnconstrainedLikelihoodModel.Internal
          The Internal calculator may maintain state and is approapriate permanent attachment to internal nodes of the tree structure
UnconstrainedLikelihoodModel.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
MolecularClockLikelihoodModel.Instance
           
 

Classes in pal.eval used by pal.statistics
SiteDetails
           
 

Classes in pal.eval used by pal.treesearch
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 provided
MolecularClockLikelihoodModel.HeightConverter
           
MolecularClockLikelihoodModel.Instance
           
MolecularClockLikelihoodModel.Internal
          The Internal calculator may maintain state and is approapriate permanent attachment to internal nodes of the tree structure
MolecularClockLikelihoodModel.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: PatternInfo
SiteDetails
           
UnconstrainedLikelihoodModel.External
          The External calculator does not maintain any state and is approapriate for calculation where a store is provided
UnconstrainedLikelihoodModel.Instance
           
UnconstrainedLikelihoodModel.Internal
          The Internal calculator may maintain state and is approapriate permanent attachment to internal nodes of the tree structure
UnconstrainedLikelihoodModel.Leaf
          A LHCalculator.Leaf object is attached to each leaf node and can be used to calculated conditional probabilities across the related branch.