Class CoalescentIntervalGenerator

java.lang.Object
jebl.evolution.treesimulation.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.
Version:
$Id: CoalescentIntervalGenerator.java 1053 2010-05-10 13:00:31Z rambaut $
Author:
Andrew Rambaut, Oliver Pybus
  • Constructor Details

    • CoalescentIntervalGenerator

      public CoalescentIntervalGenerator(DemographicFunction demographicFunction)
  • Method Details

    • 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