jebl.evolution.coalescent

Class EmpiricalDemographicFunction

java.lang.Object

jebl.evolution.coalescent.EmpiricalDemographicFunction

All Implemented Interfaces:

DemographicFunction

public class EmpiricalDemographicFunction
extends java.lang.Object
implements DemographicFunction

Version:

$Id$

Author:

Oliver Pybus, Andrew Rambaut

Nested Class Summary

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

DemographicFunction.Utils

Constructor Summary

Constructors

Constructor and Description
EmpiricalDemographicFunction(double[] populationSizes, double[] times, boolean stepwise)

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	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	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.

Methods inherited from class java.lang.Object

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

Constructor Detail

EmpiricalDemographicFunction

public EmpiricalDemographicFunction(double[] populationSizes,
                            double[] times,
                            boolean stepwise)

Method Detail

getDemographic

public double getDemographic(double t)

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

Specified by:

getDemographic in interface DemographicFunction

getIntensity

public double getIntensity(double t)

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)

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)

Description copied from interface: DemographicFunction

Calculates the integral 1/N(x) dx between start and finish

Specified by:

getIntegral in interface DemographicFunction

getArgumentCount

public int getArgumentCount()

Returns the number of arguments for this function.

Specified by:

getArgumentCount in interface DemographicFunction

getArgumentName

public java.lang.String getArgumentName(int n)

Returns the name of the nth argument of this function.

Specified by:

getArgumentName in interface DemographicFunction

getArgument

public double getArgument(int n)

Returns the value of the nth argument of this function.

Specified by:

getArgument in interface DemographicFunction

setArgument

public void setArgument(int n,
               double value)

Sets the value of the nth argument of this function.

Specified by:

setArgument in interface DemographicFunction

getLowerBound

public double getLowerBound(int n)

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

Specified by:

getLowerBound in interface DemographicFunction

getUpperBound

public double getUpperBound(int n)

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

Specified by:

getUpperBound in interface DemographicFunction