jebl.evolution.coalescent
Class ConstantPopulation

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

All Implemented Interfaces:

DemographicFunction

Direct Known Subclasses:

ExponentialGrowth

public class ConstantPopulation
extends Object
implements DemographicFunction

This class models coalescent intervals for a constant population (parameter: N0=present-day population size).
If time units are set to Units.EXPECTED_SUBSTITUTIONS then the N0 parameter will be interpreted as N0 * mu.
Also note that if you are dealing with a diploid population N0 will be out by a factor of 2.

Author:

Andrew Rambaut, Alexei Drummond

Nested Class Summary

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

DemographicFunction.Utils

Constructor Summary

ConstantPopulation()
Construct demographic model with default settings

ConstantPopulation(double N0)
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	getN0() returns initial population size.
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	setN0(double N0) sets initial population size.

Methods inherited from class java.lang.Object

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

Constructor Detail

ConstantPopulation

public ConstantPopulation()

Construct demographic model with default settings

ConstantPopulation

public ConstantPopulation(double N0)

Construct demographic model with given settings

Method Detail

getN0

public double getN0()

returns initial population size.

setN0

public void setN0(double N0)

sets initial population size.

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

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

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

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

Returns:

a boolean

getIntegral

public double getIntegral(double start,
                          double finish)

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

getArgumentCount

public int getArgumentCount()

Description copied from interface: DemographicFunction

Returns the number of arguments for this function.

Specified by:

getArgumentCount in interface DemographicFunction

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

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

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

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

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