jebl.evolution.treesimulation
Class CoalescentIntervalGenerator

java.lang.Object
  extended by jebl.evolution.treesimulation.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

Constructor Summary
CoalescentIntervalGenerator(DemographicFunction demographicFunction)
           
 
Method Summary
 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


http://code.google.com/p/jebl2/