pal.eval
Class ChiSquareValue

java.lang.Object
  extended by 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
ChiSquareValue(DistanceMatrix m, boolean w)
          initialization
 
Method Summary
 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