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 Description

ChiSquareValue(DistanceMatrix m, boolean w)
initialization

Constructors
Constructor	Description
`ChiSquareValue(DistanceMatrix m, boolean w)`	initialization

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	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

Class ChiSquareValue

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Constructor Detail

ChiSquareValue

Method Detail

setTree

getTree

compute

optimiseParameters

optimiseParameters

evaluate

getNumArguments

getLowerBound

getUpperBound

getOrthogonalHints