ModelParameters

java.lang.Object
- pal.eval.ModelParameters

All Implemented Interfaces:

MultivariateFunction
```
public class ModelParameters
extends java.lang.Object
implements MultivariateFunction
```
estimates substitution model parameters from the data

Version:

$Id: ModelParameters.java,v 1.9 2002/12/05 04:27:28 matt Exp $

Author:

Korbinian Strimmer

Field Summary

Fields
Modifier and Type Field Description

static int FRACDIGITS
fractional digits desired for parameters

Fields
Modifier and Type	Field	Description
`static int`	`FRACDIGITS`	fractional digits desired for parameters

Constructor Summary

Constructors
Constructor Description

ModelParameters(SitePattern sp, SubstitutionModel m)
Constructor

Constructors
Constructor	Description
`ModelParameters(SitePattern sp, SubstitutionModel m)`	Constructor

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`double[]`	`estimate()`	estimate (approximate) values for the model parameters from the data using a neighbor-joining tree
`double[]`	`estimateFromTree(ParameterizedTree t)`	estimate (approximate) values for the model parameters from the data using a given (parameterized) tree
`double`	`evaluate(double[] params)`	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
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

- Field Detail
  - FRACDIGITS
```
public static final int FRACDIGITS
```
    fractional digits desired for parameters
    
    See Also:
    
    Constant Field Values
- Constructor Detail
  - ModelParameters
```
public ModelParameters(SitePattern sp,
                       SubstitutionModel m)
```
    Constructor
    
    Parameters:
    
    sp - site pattern
    
    m - substitution model
- Method Detail
  - estimate
```
public double[] estimate()
```
    estimate (approximate) values for the model parameters from the data using a neighbor-joining tree
    
    Returns:
    
    parameter estimates
  - estimateFromTree
```
public double[] estimateFromTree(ParameterizedTree t)
```
    estimate (approximate) values for the model parameters from the data using a given (parameterized) tree
    
    Returns:
    
    parameter estimates
  - evaluate
```
public double evaluate(double[] params)
```
    Description copied from interface: MultivariateFunction
    
    compute function value
    
    Specified by:
    
    evaluate in interface MultivariateFunction
    
    Parameters:
    
    params - 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:
    
    null

Class ModelParameters

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

FRACDIGITS

Constructor Detail

ModelParameters

Method Detail

estimate

estimateFromTree

evaluate

getNumArguments

getLowerBound

getUpperBound

getOrthogonalHints