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
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:
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Nested Class Summary
Nested classes/interfaces inherited from interface pal.misc.Parameterized
Parameterized.Null, Parameterized.ParameterizedBase, Parameterized.ParameterizedUser, Parameterized.Utils
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Field Summary
Fields inherited from class pal.substmodel.RateDistribution
format, numRates, probability, rate
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Constructor Summary
ConstructorsConstructorDescriptionGammaRates
(int n, double a) construct discrete Gamma distribution (mean = 1.0) -
Method Summary
Modifier and TypeMethodDescriptiondouble
getDefaultValue
(int n) get default value of parameterdouble
getLowerLimit
(int n) get lower parameter limitint
get number of parametersdouble
getParameter
(int n) get model parameterdouble
getUpperLimit
(int n) get upper parameter limitvoid
report
(PrintWriter out) print human readable report (e.g., on parameters and associated model)void
setParameter
(double param, int n) set model parametervoid
setParameterSE
(double paramSE, int n) set standard errors for model parameterMethods inherited from class pal.substmodel.RateDistribution
clone, getCategoryProbabilities, getCategoryProbability, getNumberOfRates, getRate, getRates, printRates
Methods inherited from class pal.misc.PalObjectListener.EventGenerator
addPalObjectListener, fireParametersChangedEvent, fireParametersChangedEvent, fireStructureChangedEvent, fireStructureChangedEvent, removePalObjectListener
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Constructor Details
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GammaRates
public GammaRates(int n, double a) construct discrete Gamma distribution (mean = 1.0)- Parameters:
n
- number of categoriesa
- shape parameter (alpha)
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Method Details
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report
Description copied from interface:Report
print human readable report (e.g., on parameters and associated model)- Parameters:
out
- output stream
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getNumParameters
public int getNumParameters()Description copied from interface:Parameterized
get number of parameters- Returns:
- number of parameters
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setParameter
public void setParameter(double param, int n) Description copied from interface:Parameterized
set model parameter- Parameters:
param
- parameter valuen
- parameter number
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getParameter
public double getParameter(int n) Description copied from interface:Parameterized
get model parameter- Parameters:
n
- parameter number- Returns:
- parameter value
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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 valuen
- parameter number
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getLowerLimit
public double getLowerLimit(int n) Description copied from interface:Parameterized
get lower parameter limit- Parameters:
n
- parameter number- Returns:
- lower bound
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getUpperLimit
public double getUpperLimit(int n) Description copied from interface:Parameterized
get upper parameter limit- Parameters:
n
- parameter number- Returns:
- upper bound
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getDefaultValue
public double getDefaultValue(int n) Description copied from interface:Parameterized
get default value of parameter- Parameters:
n
- parameter number- Returns:
- default value
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