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 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

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	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

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

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 Detail

r

rSE

Constructor Detail

ExponentialGrowth

ExponentialGrowth

Method Detail

getSummaryTypes

getSummaryValue

clone

getGrowthRate

getDemographic

getIntensity

getInverseIntensity

getNumParameters

getParameter

getUpperLimit

getLowerLimit

getDefaultValue

setParameter

setParameterSE

toString

report