GammaRates

java.lang.Object
- pal.misc.PalObjectListener.EventGenerator
- - pal.substmodel.RateDistribution
  - - pal.substmodel.GammaRates

All Implemented Interfaces:

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

Nested Class Summary
- Nested classes/interfaces inherited from interface pal.misc.Parameterized
  Parameterized.Null, Parameterized.ParameterizedBase, Parameterized.ParameterizedUser, Parameterized.Utils

Field Summary
- Fields inherited from class pal.substmodel.RateDistribution
  format, numRates, probability, rate

Constructor Summary

Constructors
Constructor Description

GammaRates(int n, double a)
construct discrete Gamma distribution (mean = 1.0)

Constructors
Constructor	Description
`GammaRates(int n, double a)`	construct discrete Gamma distribution (mean = 1.0)

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`double`	`getDefaultValue(int n)`	get default value of parameter
`double`	`getLowerLimit(int n)`	get lower parameter limit
`int`	`getNumParameters()`	get number of parameters
`double`	`getParameter(int n)`	get model parameter
`double`	`getUpperLimit(int n)`	get upper parameter limit
`void`	`report(java.io.PrintWriter out)`	print human readable report (e.g., on parameters and associated model)
`void`	`setParameter(double param, int n)`	set model parameter
`void`	`setParameterSE(double paramSE, int n)`	set standard errors for model parameter

Methods inherited from class java.lang.Object
equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Methods inherited from class pal.misc.PalObjectListener.EventGenerator
addPalObjectListener, fireParametersChangedEvent, fireParametersChangedEvent, fireStructureChangedEvent, fireStructureChangedEvent, removePalObjectListener

Methods inherited from class pal.substmodel.RateDistribution
clone, getCategoryProbabilities, getCategoryProbability, getNumberOfRates, getRate, getRates, printRates

- 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

Class GammaRates

Nested Class Summary

Nested classes/interfaces inherited from interface pal.misc.Parameterized

Field Summary

Fields inherited from class pal.substmodel.RateDistribution

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Methods inherited from class pal.misc.PalObjectListener.EventGenerator

Methods inherited from class pal.substmodel.RateDistribution

Constructor Detail

GammaRates

Method Detail

report

getNumParameters

setParameter

getParameter

setParameterSE

getLowerLimit

getUpperLimit

getDefaultValue