DemographicValue

java.lang.Object
- pal.eval.DemographicValue

All Implemented Interfaces:

MultivariateFunction
```
public class DemographicValue
extends java.lang.Object
implements MultivariateFunction
```
estimates demographic parameters by maximising the coalescent prior for a tree with given branch lengths.

Version:

$Id: DemographicValue.java,v 1.6 2002/04/16 05:37:05 matt Exp $

Author:

Alexei Drummond

Field Summary

Fields
Modifier and Type Field Description

protected CoalescentIntervals intervals

double logL
Log-Likelihood

protected DemographicModel model

Fields
Modifier and Type	Field	Description
`protected CoalescentIntervals`	`intervals`
`double`	`logL`	Log-Likelihood
`protected DemographicModel`	`model`

Constructor Summary

Constructors
Constructor Description

DemographicValue()

Constructors
Constructor	Description
`DemographicValue()`

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`double`	`compute()`	compute log-likelihood for current model return negative log-likelihood
`protected void`	`computeLogLikelihood()`
`double`	`evaluate(double[] params)`	compute function value
`CoalescentIntervals`	`getCoalescentIntervals()`	Returns the coalescent tree of this likelihood value.
`DemographicModel`	`getDemographicModel()`	Returns the demographic model of this likelihood value
`double`	`getLowerBound(int n)`	get lower bound of argument n
`int`	`getNumArguments()`	get number of arguments
`OrthogonalHints`	`getOrthogonalHints()`
`double`	`getUpperBound(int n)`	get upper bound of argument n
`double`	`optimize()`	optimize log-likelihood using default optimizer return minimum negative log-likelihood
`double`	`optimize(MultivariateMinimum givenMvm)`	optimize log-likelihood value and compute corresponding SEs given an optimizer
`void`	`setCoalescentIntervals(CoalescentIntervals ci)`	define coalescent tree.
`void`	`setDemographicModel(DemographicModel m)`	define model

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

- Field Detail
  - logL
```
public double logL
```
    Log-Likelihood
  - intervals
```
protected CoalescentIntervals intervals
```
  - model
```
protected DemographicModel model
```
- Constructor Detail
  - DemographicValue
```
public DemographicValue()
```
- Method Detail
  - setDemographicModel
```
public void setDemographicModel(DemographicModel m)
```
    define model
    
    Parameters:
    
    m - model of demographic
  - getDemographicModel
```
public DemographicModel getDemographicModel()
```
    Returns the demographic model of this likelihood value
  - getCoalescentIntervals
```
public CoalescentIntervals getCoalescentIntervals()
```
    Returns the coalescent tree of this likelihood value.
  - setCoalescentIntervals
```
public void setCoalescentIntervals(CoalescentIntervals ci)
```
    define coalescent tree.
    
    Parameters:
    
    t - tree
  - compute
```
public double compute()
```
    compute log-likelihood for current model return negative log-likelihood
  - optimize
```
public double optimize()
```
    optimize log-likelihood using default optimizer return minimum negative log-likelihood
  - optimize
```
public double optimize(MultivariateMinimum givenMvm)
```
    optimize log-likelihood value and compute corresponding SEs given an optimizer
    
    Returns:
    
    minimimum negative log-likelihood value
  - evaluate
```
public double evaluate(double[] params)
```
    Description copied from interface: MultivariateFunction
    
    compute function value
    
    Specified by:
    
    evaluate in interface MultivariateFunction
    
    Parameters:
    
    params - function argument (vector)
    
    Returns:
    
    function value
  - getNumArguments
```
public int getNumArguments()
```
    Description copied from interface: MultivariateFunction
    
    get number of arguments
    
    Specified by:
    
    getNumArguments in interface MultivariateFunction
    
    Returns:
    
    number of arguments
  - getLowerBound
```
public double getLowerBound(int n)
```
    Description copied from interface: MultivariateFunction
    
    get lower bound of argument n
    
    Specified by:
    
    getLowerBound in interface MultivariateFunction
    
    Parameters:
    
    n - argument number
    
    Returns:
    
    lower bound
  - getUpperBound
```
public double getUpperBound(int n)
```
    Description copied from interface: MultivariateFunction
    
    get upper bound of argument n
    
    Specified by:
    
    getUpperBound in interface MultivariateFunction
    
    Parameters:
    
    n - argument number
    
    Returns:
    
    upper bound
  - computeLogLikelihood
```
protected void computeLogLikelihood()
```
  - getOrthogonalHints
```
public OrthogonalHints getOrthogonalHints()
```
    Specified by:
    
    getOrthogonalHints in interface MultivariateFunction
    
    Returns:
    
    null

Class DemographicValue

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

logL

intervals

model

Constructor Detail

DemographicValue

Method Detail

setDemographicModel

getDemographicModel

getCoalescentIntervals

setCoalescentIntervals

compute

optimize

optimize

evaluate

getNumArguments

getLowerBound

getUpperBound

computeLogLikelihood

getOrthogonalHints