Package pal.eval

Class ModelParameters

java.lang.Object
pal.eval.ModelParameters
All Implemented Interfaces:
MultivariateFunction
public class ModelParameters extends 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 Details

    • FRACDIGITS

      public static final int FRACDIGITS
      fractional digits desired for parameters
      See Also:

  • Constructor Details

    • ModelParameters

      public ModelParameters(SitePattern sp, SubstitutionModel m)
      Constructor
      Parameters:
      sp - site pattern
      m - substitution model

  • Method Details

    • 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