Class Coalescent

  • All Implemented Interfaces:
    MultivariateFunction

    public class Coalescent
    extends java.lang.Object
    implements MultivariateFunction
    A likelihood function for the coalescent. Takes a tree and a demographic model. Parts of this class were derived from C++ code provided by Oliver Pybus.
    Version:
    $Id: Coalescent.java 390 2006-07-20 14:33:51Z rambaut $
    Author:
    Andrew Rambaut, Alexei Drummond
    • Method Detail

      • calculateLogLikelihood

        public double calculateLogLikelihood()
        Calculates the log likelihood of this set of coalescent intervals, given a demographic model.
      • calculateLogLikelihood

        public static final double calculateLogLikelihood​(IntervalList intervals,
                                                          DemographicFunction demographicFunction)
        Calculates the log likelihood of this set of coalescent intervals, given a demographic model.
      • calculateAnalyticalLogLikelihood

        public static final double calculateAnalyticalLogLikelihood​(IntervalList intervals)
        Calculates the log likelihood of this set of coalescent intervals, using an analytical integration over theta.
      • evaluate

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