Uses of Interface
edu.cmu.tetrad.bayes.BayesIm

Packages that use BayesIm

Package	Description
edu.cmu.tetrad.algcomparison.simulation
edu.cmu.tetrad.bayes
edu.cmu.tetrad.classify
edu.cmu.tetrad.search.utils	Contains some utility classes for search algorithms.

Uses of BayesIm in edu.cmu.tetrad.algcomparison.simulation

Methods in edu.cmu.tetrad.algcomparison.simulation that return types with arguments of type BayesIm

Modifier and Type	Method	Description
List<BayesIm>	BayesNetSimulation.getBayesIms()	Returns the list of Bayes IMs.

Constructors in edu.cmu.tetrad.algcomparison.simulation with parameters of type BayesIm

Modifier	Constructor	Description
	BayesNetSimulation(BayesIm im)	Constructs a new BayesNetSimulation.

Uses of BayesIm in edu.cmu.tetrad.bayes

Classes in edu.cmu.tetrad.bayes that implement BayesIm

Modifier and Type	Class	Description
final class	DirichletBayesIm	Stores Dirichlet pseudocounts for the distributions of each variable conditional on particular combinations of its parent values and, together with Bayes Pm and Dag, provides methods to manipulate these tables.
final class	MlBayesIm	Stores a table of probabilities for a Bayes net and, together with BayesPm and Dag, provides methods to manipulate this table.
final class	MlBayesImObs	Stores a table of probabilities for a Bayes net and, together with BayesPm and Dag, provides methods to manipulate this table.
final class	UpdatedBayesIm	Represents a Bayes IM in which all of the conditional probability tables have been updated to take into account evidence.

Methods in edu.cmu.tetrad.bayes that return BayesIm

Modifier and Type	Method	Description
BayesIm	EmBayesProperties.Estimator.estimate(BayesPm bayesPm, DataSet dataSet)	estimate.
BayesIm	MlBayesEstimator.estimate(BayesPm bayesPm, DataSet dataSet)	Estimates parameters of the given Bayes net from the given data using maximum likelihood method.
BayesIm	MlBayesEstimatorOld.estimate(BayesPm bayesPm, DataSet dataSet)	33 Estimates a Bayes IM using the variables, graph, and parameters in the given Bayes PM and the data columns in the given data set.
BayesIm	ApproximateUpdater.getBayesIm()	Getter for the field bayesIm.
BayesIm	BayesUpdater.getBayesIm()	Returns the evidence for the updater.
BayesIm	BayesXmlParser.getBayesIm(nu.xom.Element element)	Returns the BayesIm object represented by the given element.
BayesIm	CptInvariantUpdater.getBayesIm()	Getter for the field bayesIm.
BayesIm	Identifiability.getBayesIm()	The BayesIm that this updater bases its update on.
BayesIm	JunctionTreeUpdater.getBayesIm()	Returns the evidence for the updater.
BayesIm	RowSummingExactUpdater.getBayesIm()	The BayesIm that this updater bases its update on.
BayesIm	MlBayesImObs.getBayesImObs()	Getter for the field bayesImObs.
BayesIm	EmBayesEstimator.getEstimatedIm()	Getter for the field estimatedIm.
BayesIm	ApproximateUpdater.getManipulatedBayesIm()	Getter for the field manipulatedBayesIm.
BayesIm	CptInvariantUpdater.getManipulatedBayesIm()	Getter for the field manipulatedBayesIm.
BayesIm	Identifiability.getManipulatedBayesIm()	Getter for the field manipulatedBayesIm.
BayesIm	JunctionTreeUpdater.getManipulatedBayesIm()	Returns the manipulated Bayes IM.
BayesIm	ManipulatingBayesUpdater.getManipulatedBayesIm()	Returns the manipulated Bayes IM.
BayesIm	RowSummingExactUpdater.getManipulatedBayesIm()	Getter for the field manipulatedBayesIm.
BayesIm	ApproximateUpdater.getUpdatedBayesIm()	getUpdatedBayesIm.
BayesIm	CptInvariantUpdater.getUpdatedBayesIm()	Getter for the field updatedBayesIm.
BayesIm	Identifiability.getUpdatedBayesIm()	The updated BayesIm.
BayesIm	JunctionTreeUpdater.getUpdatedBayesIm()	Returns the updated Bayes IM.
BayesIm	ManipulatingBayesUpdater.getUpdatedBayesIm()	Returns the updated Bayes IM.
BayesIm	RowSummingExactUpdater.getUpdatedBayesIm()	The updated BayesIm.
BayesIm	FactoredBayesStructuralEM.iterate()	This iterate2 method also uses BdeMetricCache but it uses the factorScoreMD method which can handle missing data and latent variables.
static BayesIm	BayesBifParser.makeBayesIm(String text)	Parses a string in BayesBif format and converts it into a BayesIm object.
BayesIm	EmBayesEstimator.maximization(double threshhold)	This method iteratively estimates the parameters of the Bayes net using the dataset until the parameters don't change.
BayesIm	FactoredBayesStructuralEM.maximization(double tolerance)	This method allows specification of the tolerance parameter used in Bayes EM estimation.

Methods in edu.cmu.tetrad.bayes with parameters of type BayesIm

Modifier and Type	Method	Description
static StoredCellProbs	StoredCellProbs.createCellTable(BayesIm bayesIm)	createCellTable.
int	BayesIm.getCorrespondingNodeIndex(int nodeIndex, BayesIm otherBayesIm)	Returns the index of the given node in the given BayesIm.
int	DirichletBayesIm.getCorrespondingNodeIndex(int nodeIndex, BayesIm otherBayesIm)	Returns the index of the given node in the given BayesIm.
int	MlBayesIm.getCorrespondingNodeIndex(int nodeIndex, BayesIm otherBayesIm)	Returns the corresponding node index in the given BayesIm based on the node index in this BayesIm.
int	MlBayesImObs.getCorrespondingNodeIndex(int nodeIndex, BayesIm otherBayesIm)	Returns the index of the given node in the given BayesIm.
int	UpdatedBayesIm.getCorrespondingNodeIndex(int nodeIndex, BayesIm otherBayesIm)	Returns the index of the given node in the given BayesIm.
static nu.xom.Element	BayesXmlRenderer.getElement(BayesIm bayesIm)	Private constructor to prevent instantiation.
double[][]	BdeMetricCache.getObservedCounts(Node node, BayesPm bayesPm, BayesIm bayesIm)	This method is used in testing and debugging and not in the BDe metric calculations.
static String	BayesBifRenderer.render(BayesIm bayesIm)	Renders the given BayesIm object as a Bayesian network in the BIF (Bayesian Interchange Format) format.
double	BdeMetricCache.scoreLnGam(Node node, Set<Node> parents, BayesPm bayesPmMod, BayesIm bayesIm)	Computes the BDe score, using the logarithm of the gamma function, relative to the data, of the factor determined by a node and its parents.

Constructors in edu.cmu.tetrad.bayes with parameters of type BayesIm

Modifier	Constructor	Description
	ApproximateUpdater(BayesIm bayesIm)	Constructs a new updater for the given Bayes net.
	ApproximateUpdater(BayesIm bayesIm, Evidence evidence)	Constructs a new updater for the given Bayes net.
	BayesImProbs(BayesIm bayesIm)	Constructs a BayesImProbs object from the given BayesIm.
	CptInvariantMarginalCalculator(BayesIm bayesIm, Evidence evidence)	Constructs a new marginal calculator for the given updated Bayes IM.
	CptInvariantUpdater(BayesIm bayesIm)	Constructor for CptInvariantUpdater.
	CptInvariantUpdater(BayesIm bayesIm, Evidence evidence)	Constructs a new updater for the given Bayes net.
	EmBayesEstimator(BayesIm inputBayesIm, DataSet dataSet)	Constructor for EmBayesEstimator.
	Identifiability(BayesIm bayesIm)	Constructs a new updater for the given Bayes net.
	Identifiability(BayesIm bayesIm, Evidence evidence)	Constructor for Identifiability.
	JunctionTreeAlgorithm(BayesIm bayesIm)	Constructor for JunctionTreeAlgorithm.
	JunctionTreeUpdater(BayesIm bayesIm)	Constructor for JunctionTreeUpdater.
	JunctionTreeUpdater(BayesIm bayesIm, Evidence evidence)	Constructor for JunctionTreeUpdater.
	MlBayesIm(BayesIm bayesIm)	Copy constructor.
	MlBayesIm(BayesPm bayesPm, BayesIm oldBayesIm, MlBayesIm.InitializationMethod initializationMethod)	Constructs a new BayesIm from the given BayesPm, initializing values either as MANUAL or RANDOM, but using values from the old BayesIm provided where posssible.
	MlBayesImObs(BayesIm bayesIm)	Constructor for MlBayesImObs.
	MlBayesImObs(BayesPm bayesPm, BayesIm oldBayesIm, int initializationMethod)	Constructs a new BayesIm from the given BayesPm, initializing values either as MANUAL or RANDOM, but using values from the old BayesIm provided where posssible.
	RowSummingExactUpdater(BayesIm bayesIm)	Constructs a new updater for the given Bayes net.
	RowSummingExactUpdater(BayesIm bayesIm, Evidence evidence)	Constructs a new updater for the given Bayes net.
	UpdatedBayesIm(BayesIm bayesIm)	Constructs Bayes net in which CPT's updated for the given evidence are calculated on the fly.
	UpdatedBayesIm(BayesIm bayesIm, Evidence evidence)	Constructs Bayes net in which CPT's updated for the given evidence are calculated on the fly.

Uses of BayesIm in edu.cmu.tetrad.classify

Methods in edu.cmu.tetrad.classify that return BayesIm

Modifier and Type	Method	Description
BayesIm	ClassifierBayesUpdaterDiscrete.getBayesIm()	Returns the Bayes IM being used.

Constructors in edu.cmu.tetrad.classify with parameters of type BayesIm

Modifier	Constructor	Description
	ClassifierBayesUpdaterDiscrete(BayesIm bayesIm, DataSet testData)	The constructor sets the values of the private member variables.

Uses of BayesIm in edu.cmu.tetrad.search.utils

Methods in edu.cmu.tetrad.search.utils that return BayesIm

Modifier and Type	Method	Description
BayesIm	BayesImParser.getBayesIm(nu.xom.Element element)	Takes an xml representation of a Bayes IM and reinstantiates the IM.