jebl.evolution.coalescent
Class CataclysmicDemographic

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

All Implemented Interfaces:

DemographicFunction

public class CataclysmicDemographic
extends ExponentialGrowth

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).

Author:

Alexei Drummond, Andrew Rambaut

Nested Class Summary

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

DemographicFunction.Utils

Constructor Summary

CataclysmicDemographic()
Construct demographic model with default settings

CataclysmicDemographic(double N0, double r, double d, double t)
Construct demographic model with given settings

Method Summary

double	getCataclysmTime()
double	getDeclineRate() returns the positive-valued decline rate
double	getDemographic(double t) Gets the value of the demographic function N(t) at time t.
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).
boolean	hasIntegral() returns whether an analytical expression for the integral is implemented
void	setCataclysmTime(double t)
void	setDeclineRate(double d) sets the decline rate.
void	setSpikeFactor(double f) 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

getIntegral, getN0, setN0

Methods inherited from class java.lang.Object

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

Constructor Detail

CataclysmicDemographic

public CataclysmicDemographic()

Construct demographic model with default settings

CataclysmicDemographic

public CataclysmicDemographic(double N0,
                              double r,
                              double d,
                              double t)

Construct demographic model with given settings

Method Detail

getDeclineRate

public final double getDeclineRate()

returns the positive-valued decline rate

setDeclineRate

public void setDeclineRate(double d)

sets the decline rate.

getCataclysmTime

public final double getCataclysmTime()

setCataclysmTime

public final void setCataclysmTime(double t)

setSpikeFactor

public final void setSpikeFactor(double f)

An alternative parameterization of this model. This function sets the decline rate using N0 & t which must already have been set.

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