Package pal.eval

Class LikelihoodValue

java.lang.Object
pal.eval.LikelihoodValue
Direct Known Subclasses:
DemographicLikelihoodValue

public class LikelihoodValue extends Object
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).
Version:
$Id: LikelihoodValue.java,v 1.40 2003/09/04 03:22:34 matt Exp $
Author:
Korbinian Strimmer, Alexei Drummond
  • Field Details

    • logL

      public double logL
      Log-Likelihood
    • siteLogL

      public double[] siteLogL
      log-likelihood for each site pattern
    • rateAtSite

      public int[] rateAtSite
      map estimation of rate at site pattern
  • Constructor Details

    • LikelihoodValue

      public LikelihoodValue(SitePattern sp)
      initialization
      Parameters:
      sp - site pattern
  • Method Details

    • getSitePattern

      public SitePattern getSitePattern()
      Returns the site pattern of this likelihood value
    • renewSitePattern

      public void renewSitePattern(SitePattern sp)
      Set new site pattern (while keeping tree and model)
    • setModel

      public void setModel(SubstitutionModel m)
      define model (a site pattern must have been set before calling this method)
      Parameters:
      m - model of substitution (rate matrix + rate distribution)
    • getModel

      public SubstitutionModel getModel()
      Returns the model of this likelihood value.
    • setTree

      public void setTree(Tree t)
      define (parameterized) tree ,(must only be called only after a site pattern has been defined).
      Parameters:
      t - tree
    • getTree

      public Tree getTree()
      Returns the (potentially parameterized) tree of this likelihood value.
    • compute

      public double compute()
      compute log-likelihood for current tree (fixed branch lengths and model) return log-likelihood
    • optimiseParameters

      public double optimiseParameters()
      optimise parameters of tree by maximising its likelihood (this assumes that tree is a ParameterizedTree)
      Returns:
      minimimum log-likelihood value
    • optimiseParameters

      public double optimiseParameters(MultivariateMinimum mm)
      optimise parameters of tree by maximising its likelihood (this assumes that tree is a ParameterizedTree)
      Parameters:
      mm - optimiser for generic ParameterisedTree
      Returns:
      minimimum log-likelihood value