jebl.evolution.coalescent

Class Coalescent

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 and Description
Coalescent(IntervalList intervals, DemographicFunction demographicFunction)
Coalescent(RootedTree tree, DemographicFunction demographicFunction)

Method Summary

Methods

Modifier and Type	Method and 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