jebl.evolution.coalescent
Class Expansion

java.lang.Object
  jebl.evolution.coalescent.ConstantPopulation
      jebl.evolution.coalescent.ExponentialGrowth
          jebl.evolution.coalescent.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).

Author:

Alexei Drummond, Andrew Rambaut

Nested Class Summary

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

DemographicFunction.Utils

Constructor Summary

Expansion()
Construct demographic model with default settings

Expansion(double N0, double r, double N1)
Construct demographic model with given settings

Method Summary

double	getArgument(int n) Returns the value of the nth argument of this function.
int	getArgumentCount() Returns the number of arguments for this function.
String	getArgumentName(int n) 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	getInverseIntensity(double x) Returns value of inverse demographic intensity function (returns time, needed for simulation of coalescent intervals).
double	getLowerBound(int n) Returns the lower bound of the nth argument of this function.
double	getN1()
double	getUpperBound(int n) Returns the upper bound of the nth argument of this function.
boolean	hasIntegral() 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

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

Constructor Detail

Expansion

public Expansion()

Construct demographic model with default settings

Expansion

public Expansion(double N0,
                 double r,
                 double N1)

Construct demographic model with given settings

Method Detail

getN1

public double getN1()

setN1

public void setN1(double N1)

setProportion

public void setProportion(double p)

getDemographic

public double getDemographic(double t)

Description copied from interface: DemographicFunction

Gets the value of the demographic function N(t) at time t.

Specified by:

getDemographic in interface DemographicFunction

Overrides:

getDemographic in class ExponentialGrowth

getIntensity

public double getIntensity(double t)

Description copied from interface: DemographicFunction

Returns value of demographic intensity function at time t (= integral 1/N(x) dx from 0 to t).

Specified by:

getIntensity in interface DemographicFunction

Overrides:

getIntensity in class ExponentialGrowth

getInverseIntensity

public double getInverseIntensity(double x)

Description copied from interface: DemographicFunction

Returns value of inverse demographic intensity function (returns time, needed for simulation of coalescent intervals).

Specified by:

getInverseIntensity in interface DemographicFunction

Overrides:

getInverseIntensity in class ExponentialGrowth

hasIntegral

public boolean hasIntegral()

Description copied from interface: DemographicFunction

returns whether an analytical expression for the integral is implemented

Specified by:

hasIntegral in interface DemographicFunction

Overrides:

hasIntegral in class ConstantPopulation

Returns:

a boolean

getIntegral

public double getIntegral(double start,
                          double finish)

Description copied from class: ConstantPopulation

Calculates the integral 1/N(x) dx between start and finish. The inherited function in DemographicFunction.Abstract calls a numerical integrater which is unecessary.

Specified by:

getIntegral in interface DemographicFunction

Overrides:

getIntegral in class ConstantPopulation

getArgumentCount

public int getArgumentCount()

Description copied from interface: DemographicFunction

Returns the number of arguments for this function.

Specified by:

getArgumentCount in interface DemographicFunction

Overrides:

getArgumentCount in class ExponentialGrowth

getArgumentName

public String getArgumentName(int n)

Description copied from interface: DemographicFunction

Returns the name of the nth argument of this function.

Specified by:

getArgumentName in interface DemographicFunction

Overrides:

getArgumentName in class ExponentialGrowth

getArgument

public double getArgument(int n)

Description copied from interface: DemographicFunction

Returns the value of the nth argument of this function.

Specified by:

getArgument in interface DemographicFunction

Overrides:

getArgument in class ExponentialGrowth

setArgument

public void setArgument(int n,
                        double value)

Description copied from interface: DemographicFunction

Sets the value of the nth argument of this function.

Specified by:

setArgument in interface DemographicFunction

Overrides:

setArgument in class ExponentialGrowth

getLowerBound

public double getLowerBound(int n)

Description copied from interface: DemographicFunction

Returns the lower bound of the nth argument of this function.

Specified by:

getLowerBound in interface DemographicFunction

Overrides:

getLowerBound in class ExponentialGrowth

getUpperBound

public double getUpperBound(int n)

Description copied from interface: DemographicFunction

Returns the upper bound of the nth argument of this function.

Specified by:

getUpperBound in interface DemographicFunction

Overrides:

getUpperBound in class ExponentialGrowth