Package pal.substmodel

Class GammaRates

java.lang.Object
pal.misc.PalObjectListener.EventGenerator
pal.substmodel.RateDistribution
pal.substmodel.GammaRates
All Implemented Interfaces:
Serializable, 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:

  • Constructor Details

    • GammaRates

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

  • Method Details

    • report

      public void report(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