Uses of Class
de.jstacs.models.mixture.gibbssampling.BurnInTest

Packages that use BurnInTest
de.jstacs.models.mixture This package is the super package for any mixture model. 
de.jstacs.models.mixture.gibbssampling This package contains many classes that can be used while a Gibbs sampling. 
de.jstacs.models.mixture.motif   
 

Uses of BurnInTest in de.jstacs.models.mixture
 

Fields in de.jstacs.models.mixture declared as BurnInTest
protected  BurnInTest AbstractMixtureModel.burnInTest
          The BurnInTest that is used to stop the sampling.
 

Constructors in de.jstacs.models.mixture with parameters of type BurnInTest
AbstractMixtureModel(int length, Model[] models, boolean[] optimizeModel, int dimension, int starts, boolean estimateComponentProbs, double[] componentHyperParams, double[] weights, AbstractMixtureModel.Algorithm algorithm, double alpha, double eps, AbstractMixtureModel.Parameterization parametrization, int initialIteration, int stationaryIteration, BurnInTest burnInTest)
          Creates a new AbstractMixtureModel.
MixtureModel(int length, Model[] models, double[] weights, int starts, int initialIteration, int stationaryIteration, BurnInTest burnInTest)
          Creates an instance using Gibbs Sampling and fixed component probabilities.
MixtureModel(int length, Model[] models, int starts, boolean estimateComponentProbs, double[] componentHyperParams, double[] weights, AbstractMixtureModel.Algorithm algorithm, double alpha, double eps, AbstractMixtureModel.Parameterization parametrization, int initialIteration, int stationaryIteration, BurnInTest burnInTest)
          Creates a new MixtureModel.
MixtureModel(int length, Model[] models, int starts, double[] componentHyperParams, int initialIteration, int stationaryIteration, BurnInTest burnInTest)
          Creates an instance using Gibbs Sampling and sampling the component probabilities.
StrandModel(Model model, int starts, boolean estimateComponentProbs, double[] componentHyperParams, double forwardStrandProb, AbstractMixtureModel.Algorithm algorithm, double alpha, double eps, AbstractMixtureModel.Parameterization parametrization, int initialIteration, int stationaryIteration, BurnInTest burnInTest)
          Creates a new StrandModel.
StrandModel(Model model, int starts, double[] componentHyperParams, int initialIteration, int stationaryIteration, BurnInTest burnInTest)
          Creates an instance using Gibbs Sampling and sampling the component probabilities.
StrandModel(Model model, int starts, double forwardStrandProb, int initialIteration, int stationaryIteration, BurnInTest burnInTest)
          Creates an instance using Gibbs Sampling and fixed component probabilities.
 

Uses of BurnInTest in de.jstacs.models.mixture.gibbssampling
 

Subclasses of BurnInTest in de.jstacs.models.mixture.gibbssampling
 class AbstractBurnInTest
          This abstract class implements some of the methods of BurnInTest to alleviate the implementation of efficient and new burn-in tests.
 class SimpleBurnInTest
          This is a very simple test for the length of the burn-in phase.
 class VarianceRatioBurnInTest
          In this class the Variance-Ratio method of Gelman and Rubin is implemented to test the length of the burn-in phase of a multi-chain Gibbs Sampling (number of chains >2).
 

Methods in de.jstacs.models.mixture.gibbssampling that return BurnInTest
 BurnInTest BurnInTest.clone()
           
 

Uses of BurnInTest in de.jstacs.models.mixture.motif
 

Constructors in de.jstacs.models.mixture.motif with parameters of type BurnInTest
HiddenMotifMixture(Model[] models, boolean[] optimzeArray, int components, int starts, boolean estimateComponentProbs, double[] componentHyperParams, double[] weights, PositionPrior posPrior, AbstractMixtureModel.Algorithm algorithm, double alpha, double eps, AbstractMixtureModel.Parameterization parametrization, int initialIteration, int stationaryIteration, BurnInTest burnInTest)
          Creates a new HiddenMotifMixture.
SingleHiddenMotifMixture(Model motif, Model bg, boolean trainOnlyMotifModel, int starts, double[] componentHyperParams, double[] weights, PositionPrior posPrior, AbstractMixtureModel.Algorithm algorithm, double alpha, double eps, AbstractMixtureModel.Parameterization parametrization, int initialIteration, int stationaryIteration, BurnInTest burnInTest)
          Creates a new SingleHiddenMotifMixture.