Class CoalescentIntervalGenerator

  • All Implemented Interfaces:
    IntervalGenerator

    public class CoalescentIntervalGenerator
    extends java.lang.Object
    implements IntervalGenerator
    This is a class that draws coalescent intervals under the given demographic function. If the demographic function class has an analytical function for the integral of 1/N(t) then this is used otherwise a numerical integrator is used. To generate a tree using this class, see the TreeSimulator class in jebl.evolution.trees. Much of this class was derived from C++ code provided by Oliver Pybus.
    Version:
    $Id: CoalescentIntervalGenerator.java 1053 2010-05-10 13:00:31Z rambaut $
    Author:
    Andrew Rambaut, Oliver Pybus
    • Method Summary

      All Methods Instance Methods Concrete Methods 
      Modifier and Type Method Description
      double getInterval​(double criticalValue, int lineageCount, double currentHeight)
      Calculates the waiting time to the next coalescent for a given critical value (an intensity).
      • Methods inherited from class java.lang.Object

        equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    • Constructor Detail

      • CoalescentIntervalGenerator

        public CoalescentIntervalGenerator​(DemographicFunction demographicFunction)
    • Method Detail

      • getInterval

        public double getInterval​(double criticalValue,
                                  int lineageCount,
                                  double currentHeight)
        Calculates the waiting time to the next coalescent for a given critical value (an intensity).
        Specified by:
        getInterval in interface IntervalGenerator
        Parameters:
        lineageCount - the number of lineages present
        currentHeight - the starting height
        Returns:
        the interval time