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
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 |
CoalescentIntervalGenerator
public CoalescentIntervalGenerator(DemographicFunction demographicFunction)
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 presentcurrentHeight
- the starting height
- Returns:
- the interval time
http://code.google.com/p/jebl2/