pal.eval
Class ModelParameters

java.lang.Object
  extended by 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
static int FRACDIGITS
          fractional digits desired for parameters
 
Constructor Summary
ModelParameters(SitePattern sp, SubstitutionModel m)
          Constructor
 
Method Summary
 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