pal.eval

Class ChiSquareValue

java.lang.Object

pal.eval.ChiSquareValue

All Implemented Interfaces:

MultivariateFunction

public class ChiSquareValue
extends java.lang.Object
implements MultivariateFunction

computes chi-square value of a (parameterized) tree for its set of parameters (e.g., branch lengths) and a given distance matrix

Version:

$Id: ChiSquareValue.java,v 1.14 2002/12/05 04:27:28 matt Exp $

Author:

Korbinian Strimmer

Constructor Summary

Constructors

Constructor and Description
ChiSquareValue(DistanceMatrix m, boolean w) initialization

Method Summary

Methods

Modifier and Type	Method and Description
double	compute() compute (weighted) least-square value for current tree (fixed branch lengths) return chi-square value
double	evaluate(double[] params) compute (weighted) least-squares value
double	getLowerBound(int n) get lower bound of argument n
int	getNumArguments() get number of parameters in tree
OrthogonalHints	getOrthogonalHints()
Tree	getTree() Returns the (parameterized) tree of this likelihood value.
double	getUpperBound(int n) get upper bound of argument n
double	optimiseParameters() optimise parameters of a tree by minimising its chi-square value (tree must be a ParameterizedTree)
double	optimiseParameters(MultivariateMinimum mm) optimise parameters of a tree by minimising its chi-square value (tree must be a ParameterizedTree)
void	setTree(Tree t) define (parameterized) tree

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

ChiSquareValue

public ChiSquareValue(DistanceMatrix m,
              boolean w)

initialization

Parameters:

m - distance matrix

w - determines whether weighted or unweighted chi-squares are computed

Method Detail

setTree

public void setTree(Tree t)

define (parameterized) tree

Parameters:

t - tree

getTree

public Tree getTree()

Returns the (parameterized) tree of this likelihood value.

compute

public double compute()

compute (weighted) least-square value for current tree (fixed branch lengths) return chi-square value

optimiseParameters

public double optimiseParameters()

optimise parameters of a tree by minimising its chi-square value (tree must be a ParameterizedTree)

Returns:

minimimum chi-square value

optimiseParameters

public double optimiseParameters(MultivariateMinimum mm)

optimise parameters of a tree by minimising its chi-square value (tree must be a ParameterizedTree)

Parameters:

mm - optimiser for ParameterizedTree

Returns:

minimum chi-square value

evaluate

public double evaluate(double[] params)

compute (weighted) least-squares value

Specified by:

evaluate in interface MultivariateFunction

Parameters:

params - parameters (branch lengths) of the tree

Returns:

function value

getNumArguments

public int getNumArguments()

get number of parameters in tree

Specified by:

getNumArguments in interface MultivariateFunction

Returns:

number of parameters

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:

null