jebl.evolution.coalescent

Class ExponentialGrowth

java.lang.Object

jebl.evolution.coalescent.ConstantPopulation

jebl.evolution.coalescent.ExponentialGrowth

All Implemented Interfaces:

DemographicFunction

Direct Known Subclasses:

CataclysmicDemographic, ConstExponential, Expansion, LogisticGrowth

public class ExponentialGrowth
extends ConstantPopulation

This class models an exponentially growing (or shrinking) population (Parameters: N0=present-day population size; r=growth rate). This model is nested with the constant-population size model (r=0).

Version:

$Id: ExponentialGrowth.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 and Description
ExponentialGrowth() Construct demographic model with default settings
ExponentialGrowth(double N0, double r) Construct demographic model with given settings

Method Summary

Methods

Modifier and Type	Method and Description
double	getArgument(int n) Returns the value of the nth argument of this function.
int	getArgumentCount() Returns the number of arguments for this function.
java.lang.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	getGrowthRate() returns growth rate.
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	getUpperBound(int n) Returns the upper bound of the nth argument of this function.
void	setArgument(int n, double value) Sets the value of the nth argument of this function.
void	setDoublingTime(double doublingTime) An alternative parameterization of this model.
void	setGrowthRate(double r) sets growth rate.

Methods inherited from class jebl.evolution.coalescent.ConstantPopulation

getIntegral, getN0, hasIntegral, setN0

Methods inherited from class java.lang.Object

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

Constructor Detail

ExponentialGrowth

public ExponentialGrowth()

Construct demographic model with default settings

ExponentialGrowth

public ExponentialGrowth(double N0,
                 double r)

Construct demographic model with given settings

Method Detail

getGrowthRate

public final double getGrowthRate()

returns growth rate.

setGrowthRate

public void setGrowthRate(double r)

sets growth rate.

setDoublingTime

public void setDoublingTime(double doublingTime)

An alternative parameterization of this model. This function sets growth rate for a given doubling time.

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 ConstantPopulation

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 ConstantPopulation

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 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 ConstantPopulation

getArgumentName

public java.lang.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 ConstantPopulation

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 ConstantPopulation

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 ConstantPopulation

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 ConstantPopulation

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 ConstantPopulation