Package pal.eval

Class DemographicValue

  • All Implemented Interfaces:
    MultivariateFunction

    public class DemographicValue
    extends java.lang.Object
    implements MultivariateFunction
    estimates demographic parameters by maximising the coalescent prior for a tree with given branch lengths.
    Version:
    $Id: DemographicValue.java,v 1.6 2002/04/16 05:37:05 matt Exp $
    Author:
    Alexei Drummond
    • Constructor Detail

      • DemographicValue

        public DemographicValue()
    • Method Detail

      • setDemographicModel

        public void setDemographicModel​(DemographicModel m)
        define model
        Parameters:
        m - model of demographic
      • getDemographicModel

        public DemographicModel getDemographicModel()
        Returns the demographic model of this likelihood value
      • getCoalescentIntervals

        public CoalescentIntervals getCoalescentIntervals()
        Returns the coalescent tree of this likelihood value.
      • setCoalescentIntervals

        public void setCoalescentIntervals​(CoalescentIntervals ci)
        define coalescent tree.
        Parameters:
        t - tree
      • compute

        public double compute()
        compute log-likelihood for current model return negative log-likelihood
      • optimize

        public double optimize()
        optimize log-likelihood using default optimizer return minimum negative log-likelihood
      • optimize

        public double optimize​(MultivariateMinimum givenMvm)
        optimize log-likelihood value and compute corresponding SEs given an optimizer
        Returns:
        minimimum negative log-likelihood value
      • evaluate

        public double evaluate​(double[] params)
        Description copied from interface: MultivariateFunction
        compute function value
        Specified by:
        evaluate in interface MultivariateFunction
        Parameters:
        params - function argument (vector)
        Returns:
        function value
      • computeLogLikelihood

        protected void computeLogLikelihood()