jebl.evolution.coalescent
Class LogisticGrowth

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

All Implemented Interfaces:

DemographicFunction

Direct Known Subclasses:

ConstLogistic

public class LogisticGrowth
extends ExponentialGrowth

This class models logistic growth.

Author:

Alexei Drummond, Andrew Rambaut

Nested Class Summary

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

DemographicFunction.Utils

Constructor Summary

LogisticGrowth()
Construct demographic model with default settings

LogisticGrowth(double N0, double r, double c)
Construct demographic model with given settings

Method Summary

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 demographic intensity function at time t (= integral 1/N(x) dx from 0 to t).
double	getShape()
boolean	hasIntegral() returns whether an analytical expression for the integral is implemented
void	setShape(double value)
void	setTime50(double time50) An alternative parameterization of this model.

Methods inherited from class jebl.evolution.coalescent.ExponentialGrowth

getArgument, getArgumentCount, getArgumentName, getGrowthRate, getLowerBound, getUpperBound, setArgument, 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

LogisticGrowth

public LogisticGrowth()

Construct demographic model with default settings

LogisticGrowth

public LogisticGrowth(double N0,
                      double r,
                      double c)

Construct demographic model with given settings

Method Detail

setShape

public void setShape(double value)

getShape

public double getShape()

setTime50

public void setTime50(double time50)

An alternative parameterization of this model. This function sets the time at which there is a 0.5 proportion of N0.

getDemographic

public double getDemographic(double t)

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

Specified by:

getDemographic in interface DemographicFunction

Overrides:

getDemographic in class ExponentialGrowth

Parameters:

t - the time

Returns:

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

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

Overrides:

getIntensity in class ExponentialGrowth

getInverseIntensity

public double getInverseIntensity(double x)

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

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