Package pal.eval

Class 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 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