pal.coalescent

Class ExponentialGrowth

java.lang.Object

pal.coalescent.DemographicModel

pal.coalescent.ConstantPopulation

pal.coalescent.ExponentialGrowth

All Implemented Interfaces:

java.io.Serializable, java.lang.Cloneable, Parameterized, Report, Summarizable, Units

Direct Known Subclasses:

ConstExpGrowth, ExpandingPopulation

public class ExponentialGrowth
extends ConstantPopulation
implements Report, Parameterized, java.io.Serializable, Summarizable

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). Parts of this class were inspired by C++ code generously provided by Oliver Pybus.

Version:

$Id: ExponentialGrowth.java,v 1.10 2001/07/12 12:17:43 korbinian Exp $

Author:

Alexei Drummond, Korbinian Strimmer

See Also:

Serialized Form

Nested Class Summary

Nested classes/interfaces inherited from interface pal.misc.Parameterized

Parameterized.Null, Parameterized.ParameterizedBase, Parameterized.ParameterizedUser, Parameterized.Utils

Field Summary

Fields

Modifier and Type	Field and Description
double	r growth rate r
double	rSE standard error of growth rate r

Fields inherited from class pal.coalescent.ConstantPopulation

N0, N0SE

Fields inherited from class pal.coalescent.DemographicModel

fo

Fields inherited from interface pal.misc.Units

DAYS, EXPECTED_SUBSTITUTIONS, GENERATIONS, MONTHS, SAMPLE, SHORT_UNIT_NAMES, UNIT_NAMES, UNKNOWN, YEARS

Constructor Summary

Constructors

Constructor and Description
ExponentialGrowth(double size, double growth, int units) Construct demographic model of an exponentially growing population
ExponentialGrowth(int units) Construct demographic model with default settings

Method Summary

Methods

Modifier and Type	Method and Description
java.lang.Object	clone()
double	getDefaultValue(int k) get default value of parameter
double	getDemographic(double t) Gets the value of the demographic function N(t) at time t.
double	getGrowthRate() returns growth rate.
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	getLowerLimit(int k) get lower parameter limit
int	getNumParameters() get number of parameters
double	getParameter(int k) get model parameter
java.lang.String[]	getSummaryTypes()
double	getSummaryValue(int summaryType)
double	getUpperLimit(int k) get upper parameter limit
void	report(java.io.PrintWriter out) print human readable report (e.g., on parameters and associated model)
void	setParameter(double value, int k) set model parameter
void	setParameterSE(double value, int k) set standard errors for model parameter
java.lang.String	toString()

Methods inherited from class pal.coalescent.ConstantPopulation

getN0

Methods inherited from class pal.coalescent.DemographicModel

computeLogLikelihood, computeLogLikelihood, getIntegral, getLogL, getSimulatedInterval, getUnits, setLogL, setUnits, testConsistency

Methods inherited from class java.lang.Object

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

Field Detail

r

public double r

growth rate r

rSE

public double rSE

standard error of growth rate r

Constructor Detail

ExponentialGrowth

public ExponentialGrowth(int units)

Construct demographic model with default settings

ExponentialGrowth

public ExponentialGrowth(double size,
                 double growth,
                 int units)

Construct demographic model of an exponentially growing population

Method Detail

getSummaryTypes

public java.lang.String[] getSummaryTypes()

Specified by:

getSummaryTypes in interface Summarizable

Overrides:

getSummaryTypes in class ConstantPopulation

getSummaryValue

public double getSummaryValue(int summaryType)

Specified by:

getSummaryValue in interface Summarizable

Overrides:

getSummaryValue in class ConstantPopulation

clone

public java.lang.Object clone()

Overrides:

clone in class ConstantPopulation

getGrowthRate

public double getGrowthRate()

returns growth rate.

getDemographic

public double getDemographic(double t)

Description copied from class: DemographicModel

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

Overrides:

getDemographic in class ConstantPopulation

getIntensity

public double getIntensity(double t)

Description copied from class: DemographicModel

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

Overrides:

getIntensity in class ConstantPopulation

getInverseIntensity

public double getInverseIntensity(double x)

Description copied from class: DemographicModel

Returns value of inverse demographic intensity function (returns time, needed for simulation of coalescent intervals).

Overrides:

getInverseIntensity in class ConstantPopulation

getNumParameters

public int getNumParameters()

Description copied from interface: Parameterized

get number of parameters

Specified by:

getNumParameters in interface Parameterized

Overrides:

getNumParameters in class ConstantPopulation

Returns:

number of parameters

getParameter

public double getParameter(int k)

Description copied from interface: Parameterized

get model parameter

Specified by:

getParameter in interface Parameterized

Overrides:

getParameter in class ConstantPopulation

Parameters:

k - parameter number

Returns:

parameter value

getUpperLimit

public double getUpperLimit(int k)

Description copied from interface: Parameterized

get upper parameter limit

Specified by:

getUpperLimit in interface Parameterized

Overrides:

getUpperLimit in class ConstantPopulation

Parameters:

k - parameter number

Returns:

upper bound

getLowerLimit

public double getLowerLimit(int k)

Description copied from interface: Parameterized

get lower parameter limit

Specified by:

getLowerLimit in interface Parameterized

Overrides:

getLowerLimit in class ConstantPopulation

Parameters:

k - parameter number

Returns:

lower bound

getDefaultValue

public double getDefaultValue(int k)

Description copied from interface: Parameterized

get default value of parameter

Specified by:

getDefaultValue in interface Parameterized

Overrides:

getDefaultValue in class ConstantPopulation

Parameters:

k - parameter number

Returns:

default value

setParameter

public void setParameter(double value,
                int k)

Description copied from interface: Parameterized

set model parameter

Specified by:

setParameter in interface Parameterized

Overrides:

setParameter in class ConstantPopulation

Parameters:

value - parameter value

k - parameter number

setParameterSE

public void setParameterSE(double value,
                  int k)

Description copied from interface: Parameterized

set standard errors for model parameter

Specified by:

setParameterSE in interface Parameterized

Overrides:

setParameterSE in class ConstantPopulation

Parameters:

value - standard error of parameter value

k - parameter number

toString

public java.lang.String toString()

Overrides:

toString in class ConstantPopulation

report

public void report(java.io.PrintWriter out)

Description copied from interface: Report

print human readable report (e.g., on parameters and associated model)

Specified by:

report in interface Report

Overrides:

report in class ConstantPopulation

Parameters:

out - output stream