jebl.evolution.coalescent
Class CoalescentIntervalGenerator

java.lang.Object
  jebl.evolution.coalescent.CoalescentIntervalGenerator

All Implemented Interfaces:

IntervalGenerator

public class CoalescentIntervalGenerator
extends 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.

Author:

Andrew Rambaut, Oliver Pybus

Field Summary

protected DemographicFunction

demographicFunction

Constructor Summary

CoalescentIntervalGenerator(DemographicFunction demographicFunction)

Method Summary

double

getInterval(double criticalValue, int lineageCount, double currentHeight)

Methods inherited from class java.lang.Object

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

Field Detail

demographicFunction

protected DemographicFunction demographicFunction

Constructor Detail

CoalescentIntervalGenerator

public CoalescentIntervalGenerator(DemographicFunction demographicFunction)

Method Detail

getInterval

public double getInterval(double criticalValue,
                          int lineageCount,
                          double currentHeight)

Specified by:

getInterval in interface IntervalGenerator