Package pal.substmodel

Class GammaRates

  • All Implemented Interfaces:
    java.io.Serializable, java.lang.Cloneable, Parameterized, Report
    public class GammaRates
extends RateDistribution
    discrete Gamma distribution (Z. Yang. 1994. JME 39:306-314)
    Version:
    $Id: GammaRates.java,v 1.10 2003/06/11 05:26:46 matt Exp $
    Author:
    Korbinian Strimmer
    See Also:
    Serialized Form

    • Constructor Detail

      • GammaRates

        public GammaRates​(int n,
                  double a)
        construct discrete Gamma distribution (mean = 1.0)
        Parameters:
        n - number of categories
        a - shape parameter (alpha)

    • Method Detail

      • report

        public void report​(java.io.PrintWriter out)
        Description copied from interface: Report
        print human readable report (e.g., on parameters and associated model)
        Parameters:
        out - output stream

      • getNumParameters

        public int getNumParameters()
        Description copied from interface: Parameterized
        get number of parameters
        Returns:
        number of parameters

      • setParameter

        public void setParameter​(double param,
                         int n)
        Description copied from interface: Parameterized
        set model parameter
        Parameters:
        param - parameter value
        n - parameter number

      • getParameter

        public double getParameter​(int n)
        Description copied from interface: Parameterized
        get model parameter
        Parameters:
        n - parameter number
        Returns:
        parameter value

      • setParameterSE

        public void setParameterSE​(double paramSE,
                           int n)
        Description copied from interface: Parameterized
        set standard errors for model parameter
        Parameters:
        paramSE - standard error of parameter value
        n - parameter number

      • getLowerLimit

        public double getLowerLimit​(int n)
        Description copied from interface: Parameterized
        get lower parameter limit
        Parameters:
        n - parameter number
        Returns:
        lower bound

      • getUpperLimit

        public double getUpperLimit​(int n)
        Description copied from interface: Parameterized
        get upper parameter limit
        Parameters:
        n - parameter number
        Returns:
        upper bound

      • getDefaultValue

        public double getDefaultValue​(int n)
        Description copied from interface: Parameterized
        get default value of parameter
        Parameters:
        n - parameter number
        Returns:
        default value