Class Expansion

All Implemented Interfaces:
DemographicFunction

public class Expansion extends ExponentialGrowth
This class models exponential growth from an initial ancestral population size. (Parameters: N0=present-day population size; N1=ancestral population size; r=growth rate). This model is nested with the exponential-growth population size model (N1=0).
Version:
$Id: Expansion.java 390 2006-07-20 14:33:51Z rambaut $
Author:
Alexei Drummond, Andrew Rambaut
  • Nested Class Summary

    Nested classes/interfaces inherited from interface jebl.evolution.coalescent.DemographicFunction

    DemographicFunction.Utils
  • Constructor Summary

    Constructors
    Constructor
    Description
    Construct demographic model with default settings
    Expansion(double N0, double r, double N1)
    Construct demographic model with given settings
  • Method Summary

    Modifier and Type
    Method
    Description
    double
    getArgument(int n)
    Returns the value of the nth argument of this function.
    int
    Returns the number of arguments for this function.
    Returns the name of the nth argument of this function.
    double
    getDemographic(double t)
    Gets the value of the demographic function N(t) at time t.
    double
    getIntegral(double start, double finish)
    Calculates the integral 1/N(x) dx between start and finish.
    double
    getIntensity(double t)
    Returns value of demographic intensity function at time t (= integral 1/N(x) dx from 0 to t).
    double
    Returns value of inverse demographic intensity function (returns time, needed for simulation of coalescent intervals).
    double
    Returns the lower bound of the nth argument of this function.
    double
     
    double
    Returns the upper bound of the nth argument of this function.
    boolean
    returns whether an analytical expression for the integral is implemented
    void
    setArgument(int n, double value)
    Sets the value of the nth argument of this function.
    void
    setN1(double N1)
     
    void
    setProportion(double p)
     

    Methods inherited from class jebl.evolution.coalescent.ExponentialGrowth

    getGrowthRate, setDoublingTime, setGrowthRate

    Methods inherited from class jebl.evolution.coalescent.ConstantPopulation

    getN0, setN0

    Methods inherited from class java.lang.Object

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