Package jebl.evolution.coalescent

Class Coalescent

java.lang.Object
jebl.evolution.coalescent.Coalescent
All Implemented Interfaces:
MultivariateFunction
public class Coalescent extends 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

  • Constructor Details

  • Method Details

    • 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

    • getNumArguments

      public int getNumArguments()
      Description copied from interface: MultivariateFunction
      get number of arguments
      Specified by:
      getNumArguments in interface MultivariateFunction
      Returns:
      number of arguments

    • getLowerBound

      public double getLowerBound(int n)
      Description copied from interface: MultivariateFunction
      get lower bound of argument n
      Specified by:
      getLowerBound in interface MultivariateFunction
      Parameters:
      n - argument number
      Returns:
      lower bound

    • getUpperBound

      public double getUpperBound(int n)
      Description copied from interface: MultivariateFunction
      get upper bound of argument n
      Specified by:
      getUpperBound in interface MultivariateFunction
      Parameters:
      n - argument number
      Returns:
      upper bound

    • getOrthogonalHints

      public OrthogonalHints getOrthogonalHints()
      Specified by:
      getOrthogonalHints in interface MultivariateFunction
      Returns:
      an Orthogonal Hints object that can be used by Orthogonal based optimisers to get information about the function