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


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
 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
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
Following copied from interface: pal.math.MultivariateFunction
Parameters:
argument - 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
Following copied from interface: pal.math.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
Following copied from interface: pal.math.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
Following copied from interface: pal.math.MultivariateFunction
Parameters:
n - argument number
Returns:
upper bound