pal.coalescent.ExponentialGrowth

All Implemented Interfaces:: Serializable, Cloneable, Parameterized, Report, Summarizable, Units

Direct Known Subclasses:: ConstExpGrowth, ExpandingPopulation

public class ExponentialGrowth extends ConstantPopulation implements Report, Parameterized, 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

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

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

Modifier and Type

Method

Description

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

String[]

getSummaryTypes()

double

getSummaryValue(int summaryType)

double

getUpperLimit(int k)

get upper parameter limit

void

report(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

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 Details
- r
  
  public double r
  
  growth rate r
- rSE
  
  public double rSE
  
  standard error of growth rate r
Constructor Details
- 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 Details
- getSummaryTypes
  
  public 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 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 String toString()
  
  Overrides:
  
  toString in class ConstantPopulation
- report
  
  public void report(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

Class ExponentialGrowth

Nested Class Summary

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

Field Summary

Fields inherited from class pal.coalescent.ConstantPopulation

Fields inherited from class pal.coalescent.DemographicModel

Fields inherited from interface pal.misc.Units

Constructor Summary

Method Summary

Methods inherited from class pal.coalescent.ConstantPopulation

Methods inherited from class pal.coalescent.DemographicModel

Methods inherited from class java.lang.Object

Field Details

r

rSE

Constructor Details

ExponentialGrowth

ExponentialGrowth

Method Details

getSummaryTypes

getSummaryValue

clone

getGrowthRate

getDemographic

getIntensity

getInverseIntensity

getNumParameters

getParameter

getUpperLimit

getLowerLimit

getDefaultValue

setParameter

setParameterSE

toString

report