ConstantPopulation

java.lang.Object
- pal.coalescent.DemographicModel
- - pal.coalescent.ConstantPopulation

All Implemented Interfaces:

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

Direct Known Subclasses:

ExponentialGrowth
```
public class ConstantPopulation
extends DemographicModel
implements Report, Summarizable, Parameterized, java.io.Serializable
```
This class models coalescent intervals for a constant population (parameter: N0=present-day population size).
If time units are set to Units.EXPECTED_SUBSTITUTIONS then the N0 parameter will be interpreted as N0 * mu.
Also note that if you are dealing with a diploid population N0 will be out by a factor of 2.

Version:

$Id: ConstantPopulation.java,v 1.14 2003/09/14 05:14:15 matt Exp $

Author:

Alexei Drummond + @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 N0
population size

double N0SE
standard error of population size
- 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`	`N0` population size
`double`	`N0SE` standard error of population size

Constructor Summary

Constructors
Constructor and Description
`ConstantPopulation(double size, int units)` Construct demographic model of a constant population size.
`ConstantPopulation(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
`double`	`getN0()` returns initial population size.
`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.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
  - N0
```
public double N0
```
    population size
  - N0SE
```
public double N0SE
```
    standard error of population size
- Constructor Detail
  - ConstantPopulation
```
public ConstantPopulation(int units)
```
    Construct demographic model with default settings
  - ConstantPopulation
```
public ConstantPopulation(double size,
                          int units)
```
    Construct demographic model of a constant population size.
- Method Detail
  - clone
```
public java.lang.Object clone()
```
    Specified by:
    
    clone in class DemographicModel
  - getSummaryTypes
```
public java.lang.String[] getSummaryTypes()
```
    Specified by:
    
    getSummaryTypes in interface Summarizable
  - getSummaryValue
```
public double getSummaryValue(int summaryType)
```
    Specified by:
    
    getSummaryValue in interface Summarizable
  - getN0
```
public double getN0()
```
    returns initial population size.
  - getDemographic
```
public double getDemographic(double t)
```
    Description copied from class: DemographicModel
    
    Gets the value of the demographic function N(t) at time t.
    
    Specified by:
    
    getDemographic in class DemographicModel
  - 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).
    
    Specified by:
    
    getIntensity in class DemographicModel
  - 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).
    
    Specified by:
    
    getInverseIntensity in class DemographicModel
  - getNumParameters
```
public int getNumParameters()
```
    Description copied from interface: Parameterized
    
    get number of parameters
    
    Specified by:
    
    getNumParameters in interface Parameterized
    
    Returns:
    
    number of parameters
  - getParameter
```
public double getParameter(int k)
```
    Description copied from interface: Parameterized
    
    get model parameter
    
    Specified by:
    
    getParameter in interface Parameterized
    
    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
    
    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
    
    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
    
    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
    
    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
    
    Parameters:
    
    value - standard error of parameter value
    
    k - parameter number
  - toString
```
public java.lang.String toString()
```
    Overrides:
    
    toString in class java.lang.Object
  - 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
    
    Parameters:
    
    out - output stream

Class ConstantPopulation

Nested Class Summary

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

Field Summary

Fields inherited from class pal.coalescent.DemographicModel

Fields inherited from interface pal.misc.Units

Constructor Summary

Method Summary

Methods inherited from class pal.coalescent.DemographicModel

Methods inherited from class java.lang.Object

Field Detail

N0

N0SE

Constructor Detail

ConstantPopulation

ConstantPopulation

Method Detail

clone

getSummaryTypes

getSummaryValue

getN0

getDemographic

getIntensity

getInverseIntensity

getNumParameters

getParameter

getUpperLimit

getLowerLimit

getDefaultValue

setParameter

setParameterSE

toString

report