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

Fields
Modifier and Type Field and Description

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

Fields
Modifier and Type	Field and Description
`double`	`alpha` ratio of pop.
`double`	`alphaSE` standard error of time alpha

Constructor Summary

Constructors
Constructor and Description
`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

All Methods Instance Methods Concrete 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`	`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

Class ExpandingPopulation

Nested Class Summary

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

Field Summary

Fields inherited from class pal.coalescent.ExponentialGrowth

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.ExponentialGrowth

Methods inherited from class pal.coalescent.ConstantPopulation

Methods inherited from class pal.coalescent.DemographicModel

Methods inherited from class java.lang.Object

Field Detail

alpha

alphaSE

Constructor Detail

ExpandingPopulation

ExpandingPopulation

Method Detail

clone

getRatio

getDemographic

getIntensity

getInverseIntensity

getNumParameters

getParameter

getUpperLimit

getLowerLimit

getDefaultValue

setParameter

setParameterSE

toString

report