ExponentialGrowth

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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
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
`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
`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
`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