Package pal.eval

Class LikelihoodValue

  • Direct Known Subclasses:
    DemographicLikelihoodValue
    public class LikelihoodValue
extends java.lang.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 Summary

      Fields 
      Modifier and Type Field Description
      double logL
      Log-Likelihood
      int[] rateAtSite
      map estimation of rate at site pattern
      double[] siteLogL
      log-likelihood for each site pattern

    • Method Summary

      All Methods Instance Methods Concrete Methods 
      Modifier and Type Method Description
      double compute()
      compute log-likelihood for current tree (fixed branch lengths and model) return log-likelihood
      SubstitutionModel getModel()
      Returns the model of this likelihood value.
      SitePattern getSitePattern()
      Returns the site pattern of this likelihood value
      Tree getTree()
      Returns the (potentially parameterized) tree of this likelihood value.
      double optimiseParameters()
      optimise parameters of tree by maximising its likelihood (this assumes that tree is a ParameterizedTree)
      double optimiseParameters​(MultivariateMinimum mm)
      optimise parameters of tree by maximising its likelihood (this assumes that tree is a ParameterizedTree)
      void renewSitePattern​(SitePattern sp)
      Set new site pattern (while keeping tree and model)
      void setModel​(SubstitutionModel m)
      define model (a site pattern must have been set before calling this method)
      void setTree​(Tree t)
      define (parameterized) tree ,(must only be called only after a site pattern has been defined).

      • Methods inherited from class java.lang.Object

        clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

    • Field Detail

      • 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 Detail

      • LikelihoodValue

        public LikelihoodValue​(SitePattern sp)
        initialization
        Parameters:
        sp - site pattern

    • Method Detail

      • 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