pal.coalescent
Class ExpandingPopulation

java.lang.Object
  pal.coalescent.DemographicModel
      pal.coalescent.ConstantPopulation
          pal.coalescent.ExponentialGrowth
              pal.coalescent.ExpandingPopulation

All Implemented Interfaces:

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

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

This class models a population that grows exponentially from an inital population size alpha N0 to a present-day size N0. (Parameters: N0=present-day population size; r=growth rate; alpha: ratio of population sizes). This model is nested with the exponential-growth model (alpha -> 0).

Version:

$Id: ExpandingPopulation.java,v 1.6 2001/07/12 12:17:43 korbinian Exp $

Author:

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

double	alpha ratio of pop.
double	alphaSE standard error of time alpha

Fields inherited from class pal.coalescent.ExponentialGrowth

r, rSE

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

ExpandingPopulation(double size, double growth, double ratio, int units)
Construct demographic model of an expanding population

ExpandingPopulation(int units)
Construct demographic model with default settings

Method Summary

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	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
double	getRatio() returns ratio of population sizes
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.ExponentialGrowth

getGrowthRate, getSummaryTypes, getSummaryValue

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

alpha

public double alpha

ratio of pop. sizes

alphaSE

public double alphaSE

standard error of time alpha

Constructor Detail

ExpandingPopulation

public ExpandingPopulation(int units)

Construct demographic model with default settings

ExpandingPopulation

public ExpandingPopulation(double size,
                           double growth,
                           double ratio,
                           int units)

Construct demographic model of an expanding population

Method Detail

clone

public java.lang.Object clone()

Overrides:

clone in class ExponentialGrowth

getRatio

public double getRatio()

returns ratio of population sizes

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 ExponentialGrowth

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 ExponentialGrowth

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 ExponentialGrowth

getNumParameters

public int getNumParameters()

Description copied from interface: Parameterized

get number of parameters

Specified by:

getNumParameters in interface Parameterized

Overrides:

getNumParameters in class ExponentialGrowth

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 ExponentialGrowth

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 ExponentialGrowth

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 ExponentialGrowth

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 ExponentialGrowth

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 ExponentialGrowth

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 ExponentialGrowth

Parameters:

value - standard error of parameter value

k - parameter number

toString

public java.lang.String toString()

Overrides:

toString in class ExponentialGrowth

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 ExponentialGrowth

Parameters:

out - output stream