jebl.evolution.treesimulation

Class CoalescentIntervalGenerator

java.lang.Object

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

Constructors

Constructor and Description
CoalescentIntervalGenerator(DemographicFunction demographicFunction)

Method Summary

Methods

Modifier and Type	Method and 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