pal.eval

Class 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 and Description
static int	FRACDIGITS fractional digits desired for parameters

Constructor Summary

Constructors

Constructor and Description
ModelParameters(SitePattern sp, SubstitutionModel m) Constructor

Method Summary

Methods

Modifier and Type	Method and 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