Coalescent (JEBL2 lib API)

java.lang.Object
- jebl.evolution.coalescent.Coalescent

All Implemented Interfaces:

MultivariateFunction
```
public class Coalescent
extends java.lang.Object
implements MultivariateFunction
```
A likelihood function for the coalescent. Takes a tree and a demographic model. Parts of this class were derived from C++ code provided by Oliver Pybus.

Version:

$Id: Coalescent.java 390 2006-07-20 14:33:51Z rambaut $

Author:

Andrew Rambaut, Alexei Drummond

Constructor Summary

Constructors
Constructor	Description
`Coalescent(IntervalList intervals, DemographicFunction demographicFunction)`
`Coalescent(RootedTree tree, DemographicFunction demographicFunction)`

Method Summary

All Methods Static Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`static double`	`calculateAnalyticalLogLikelihood(IntervalList intervals)`	Calculates the log likelihood of this set of coalescent intervals, using an analytical integration over theta.
`double`	`calculateLogLikelihood()`	Calculates the log likelihood of this set of coalescent intervals, given a demographic model.
`static double`	`calculateLogLikelihood(IntervalList intervals, DemographicFunction demographicFunction)`	Calculates the log likelihood of this set of coalescent intervals, given a demographic model.
`double`	`evaluate(double[] argument)`	compute function 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

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

- Constructor Detail
  - Coalescent
```
public Coalescent(RootedTree tree,
                  DemographicFunction demographicFunction)
```
  - Coalescent
```
public Coalescent(IntervalList intervals,
                  DemographicFunction demographicFunction)
```
- Method Detail
  - calculateLogLikelihood
```
public double calculateLogLikelihood()
```
    Calculates the log likelihood of this set of coalescent intervals, given a demographic model.
  - calculateLogLikelihood
```
public static final double calculateLogLikelihood(IntervalList intervals,
                                                  DemographicFunction demographicFunction)
```
    Calculates the log likelihood of this set of coalescent intervals, given a demographic model.
  - calculateAnalyticalLogLikelihood
```
public static final double calculateAnalyticalLogLikelihood(IntervalList intervals)
```
    Calculates the log likelihood of this set of coalescent intervals, using an analytical integration over theta.
  - evaluate
```
public double evaluate(double[] argument)
```
    Description copied from interface: MultivariateFunction
    
    compute function value
    
    Specified by:
    
    evaluate in interface MultivariateFunction
    
    Parameters:
    
    argument - 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
  - getOrthogonalHints
```
public OrthogonalHints getOrthogonalHints()
```
    Specified by:
    
    getOrthogonalHints in interface MultivariateFunction
    
    Returns:
    
    an Orthogonal Hints object that can be used by Orthogonal based optimisers to get information about the function

Class Coalescent

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Constructor Detail

Coalescent

Coalescent

Method Detail

calculateLogLikelihood

calculateLogLikelihood

calculateAnalyticalLogLikelihood

evaluate

getNumArguments

getLowerBound

getUpperBound

getOrthogonalHints