jebl.evolution.coalescent

Class ExponentialLogistic

java.lang.Object

jebl.evolution.coalescent.ConstantPopulation

jebl.evolution.coalescent.ExponentialGrowth

jebl.evolution.coalescent.LogisticGrowth

jebl.evolution.coalescent.ExponentialLogistic

All Implemented Interfaces:

DemographicFunction

public class ExponentialLogistic
extends LogisticGrowth

This class models logistic growth from an initial exponential phase.

Version:

$Id: ExponentialLogistic.java 937 2008-08-08 00:11:32Z rambaut $

Author:

Andrew Rambaut, Alexei Drummond

Nested Class Summary

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

DemographicFunction.Utils

Constructor Summary

Constructors

Constructor and Description
ExponentialLogistic() Construct demographic model with default settings
ExponentialLogistic(double N0, double r, double c, double time, double r2) 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	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	getLowerBound(int n) Returns the lower bound of the nth argument of this function.
double	getR2()
double	getTime()
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	setR2(double r2)
void	setTime(double time)

Methods inherited from class jebl.evolution.coalescent.LogisticGrowth

getShape, setShape, setTime50

Methods inherited from class jebl.evolution.coalescent.ExponentialGrowth

getGrowthRate, setDoublingTime, setGrowthRate

Methods inherited from class jebl.evolution.coalescent.ConstantPopulation

getN0, setN0

Methods inherited from class java.lang.Object

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

Constructor Detail

ExponentialLogistic

public ExponentialLogistic()

Construct demographic model with default settings

ExponentialLogistic

public ExponentialLogistic(double N0,
                   double r,
                   double c,
                   double time,
                   double r2)

Construct demographic model with given settings

Parameters:

N0 - Current population size

r - Logistic-phase growth rate

c - Logistic shape

time - Exponential-logistic phase transition time

r2 - Exponential-phase growth rate

Method Detail

getR2

public double getR2()

setR2

public void setR2(double r2)

getTime

public double getTime()

setTime

public void setTime(double time)

getDemographic

public double getDemographic(double t)

Description copied from class: LogisticGrowth

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

Specified by:

getDemographic in interface DemographicFunction

Overrides:

getDemographic in class LogisticGrowth

Parameters:

t - the time

Returns:

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

getIntensity

public double getIntensity(double t)

Description copied from class: LogisticGrowth

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 LogisticGrowth

getInverseIntensity

public double getInverseIntensity(double x)

Description copied from class: LogisticGrowth

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 LogisticGrowth

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 LogisticGrowth

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 LogisticGrowth

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 ExponentialGrowth

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 ExponentialGrowth

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 ExponentialGrowth

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 ExponentialGrowth

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 ExponentialGrowth

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 ExponentialGrowth