Uses of Class
edu.cmu.tetrad.data.Knowledge

Packages that use Knowledge

Package	Description
edu.cmu.tetrad.algcomparison
edu.cmu.tetrad.algcomparison.algorithm.cluster
edu.cmu.tetrad.algcomparison.algorithm.continuous.dag
edu.cmu.tetrad.algcomparison.algorithm.multi
edu.cmu.tetrad.algcomparison.algorithm.oracle.cpdag
edu.cmu.tetrad.algcomparison.algorithm.oracle.pag
edu.cmu.tetrad.algcomparison.simulation
edu.cmu.tetrad.algcomparison.statistic
edu.cmu.tetrad.algcomparison.utils
edu.cmu.tetrad.data
edu.cmu.tetrad.graph
edu.cmu.tetrad.search	Contains classes for searching for (mostly structural) causal models given data.
edu.cmu.tetrad.search.utils	Contains some utility classes for search algorithms.
edu.cmu.tetrad.search.work_in_progress	Contains some classes that aren't ready for prime time.
edu.cmu.tetrad.sem
edu.cmu.tetrad.study.performance
edu.cmu.tetrad.util
edu.pitt.dbmi.algo.bayesian.constraint.search

Uses of Knowledge in edu.cmu.tetrad.algcomparison

Methods in edu.cmu.tetrad.algcomparison that return Knowledge

Modifier and Type	Method	Description
Knowledge	Comparison.getKnowledge()	Retrieves the knowledge.

Methods in edu.cmu.tetrad.algcomparison with parameters of type Knowledge

Modifier and Type	Method	Description
void	Comparison.setKnowledge(Knowledge knowledge)	Sets the knowledge for the current instance.

Uses of Knowledge in edu.cmu.tetrad.algcomparison.algorithm.cluster

Methods in edu.cmu.tetrad.algcomparison.algorithm.cluster that return Knowledge

Modifier and Type	Method	Description
Knowledge	Fofc.getKnowledge()	Returns the knowledge associated with this object.
Knowledge	Ftfc.getKnowledge()	Returns the knowledge associated with this algorithm.

Methods in edu.cmu.tetrad.algcomparison.algorithm.cluster with parameters of type Knowledge

Modifier and Type	Method	Description
void	Fofc.setKnowledge(Knowledge knowledge)	Sets the knowledge associated with this object.
void	Ftfc.setKnowledge(Knowledge knowledge)	Sets the knowledge associated with this algorithm.

Uses of Knowledge in edu.cmu.tetrad.algcomparison.algorithm.continuous.dag

Methods in edu.cmu.tetrad.algcomparison.algorithm.continuous.dag that return Knowledge

Modifier and Type	Method	Description
Knowledge	Fask.getKnowledge()	Retrieves the knowledge associated with this object.
Knowledge	FaskOrig.getKnowledge()	Retrieves the knowledge associated with this object.

Methods in edu.cmu.tetrad.algcomparison.algorithm.continuous.dag with parameters of type Knowledge

Modifier and Type	Method	Description
void	Fask.setKnowledge(Knowledge knowledge)	Sets the knowledge associated with this object.
void	FaskOrig.setKnowledge(Knowledge knowledge)	Sets the knowledge associated with this object.

Uses of Knowledge in edu.cmu.tetrad.algcomparison.algorithm.multi

Methods in edu.cmu.tetrad.algcomparison.algorithm.multi that return Knowledge

Modifier and Type	Method	Description
Knowledge	FaskConcatenated.getKnowledge()	Returns a knowledge object.
Knowledge	FaskLofsConcatenated.getKnowledge()	Returns a knowledge object.
Knowledge	FaskVote.getKnowledge()	Returns a knowledge object.
Knowledge	FasLofs.getKnowledge()	Returns a knowledge object.
Knowledge	FciIod.getKnowledge()	Returns a knowledge object.
Knowledge	FgesConcatenated.getKnowledge()	Returns a knowledge object.
Knowledge	Images.getKnowledge()	Retrieves the knowledge of the current instance.
Knowledge	ImagesBoss.getKnowledge()	Returns a knowledge object.

Methods in edu.cmu.tetrad.algcomparison.algorithm.multi with parameters of type Knowledge

Modifier and Type	Method	Description
void	FaskConcatenated.setKnowledge(Knowledge knowledge)	Sets a knowledge object.
void	FaskLofsConcatenated.setKnowledge(Knowledge knowledge)	Sets a knowledge object.
void	FaskVote.setKnowledge(Knowledge knowledge)	Sets a knowledge object.
void	FasLofs.setKnowledge(Knowledge knowledge)	Sets a knowledge object.
void	FciIod.setKnowledge(Knowledge knowledge)	Sets a knowledge object.
void	FgesConcatenated.setKnowledge(Knowledge knowledge)	Sets a knowledge object.
void	Images.setKnowledge(Knowledge knowledge)	Sets the knowledge object for this instance.
void	ImagesBoss.setKnowledge(Knowledge knowledge)	Sets a knowledge object.

Uses of Knowledge in edu.cmu.tetrad.algcomparison.algorithm.oracle.cpdag

Methods in edu.cmu.tetrad.algcomparison.algorithm.oracle.cpdag that return Knowledge

Modifier and Type	Method	Description
Knowledge	Boss.getKnowledge()	Returns a knowledge object.
Knowledge	BossLingam.getKnowledge()	Returns a knowledge object.
Knowledge	Cpc.getKnowledge()	Retrieves the knowledge associated with this object.
Knowledge	Fas.getKnowledge()	Returns a knowledge object.
Knowledge	Fges.getKnowledge()	Returns a knowledge object.
Knowledge	FgesMb.getKnowledge()	Returns a knowledge object.
Knowledge	FgesMeasurement.getKnowledge()	Returns a knowledge object.
Knowledge	Grasp.getKnowledge()	Returns a knowledge object.
Knowledge	Pc.getKnowledge()	Returns a knowledge object.
Knowledge	Pcd.getKnowledge()	Returns a knowledge object.
Knowledge	PcMb.getKnowledge()	Returns a knowledge object.
Knowledge	SingleGraphAlg.getKnowledge()	Returns a knowledge object.
Knowledge	Sp.getKnowledge()	Returns a knowledge object.

Methods in edu.cmu.tetrad.algcomparison.algorithm.oracle.cpdag with parameters of type Knowledge

Modifier and Type	Method	Description
void	Boss.setKnowledge(Knowledge knowledge)	Sets a knowledge object.
void	BossLingam.setKnowledge(Knowledge knowledge)	Sets a knowledge object.
void	Cpc.setKnowledge(Knowledge knowledge)	Sets the knowledge associated with this object.
void	Fas.setKnowledge(Knowledge knowledge)	Sets a knowledge object.
void	Fges.setKnowledge(Knowledge knowledge)	Sets a knowledge object.
void	FgesMb.setKnowledge(Knowledge knowledge)	Sets a knowledge object.
void	FgesMeasurement.setKnowledge(Knowledge knowledge)	Sets a knowledge object.
void	Grasp.setKnowledge(Knowledge knowledge)	Sets a knowledge object.
void	Pc.setKnowledge(Knowledge knowledge)	Sets a knowledge object.
void	Pcd.setKnowledge(Knowledge knowledge)	Sets a knowledge object.
void	PcMb.setKnowledge(Knowledge knowledge)	Sets a knowledge object.
void	SingleGraphAlg.setKnowledge(Knowledge knowledge)	Sets a knowledge object.
void	Sp.setKnowledge(Knowledge knowledge)	Sets a knowledge object.

Uses of Knowledge in edu.cmu.tetrad.algcomparison.algorithm.oracle.pag

Methods in edu.cmu.tetrad.algcomparison.algorithm.oracle.pag that return Knowledge

Modifier and Type	Method	Description
Knowledge	Bfci.getKnowledge()	Retrieves the knowledge associated with the algorithm.
Knowledge	BossDumb.getKnowledge()	Retrieves the knowledge object associated with this method.
Knowledge	BossPag.getKnowledge()	Retrieves the knowledge object associated with this method.
Knowledge	Cfci.getKnowledge()	Returns the knowledge.
Knowledge	Fci.getKnowledge()	Retrieves the knowledge object.
Knowledge	FciMax.getKnowledge()	Retrieves the knowledge associated with the algorithm.
Knowledge	Gfci.getKnowledge()	Retrieves the Knowledge object associated with this instance.
Knowledge	GraspFci.getKnowledge()	Retrieves the knowledge object associated with this method.
Knowledge	LvLite.getKnowledge()	Retrieves the knowledge object associated with this method.
Knowledge	PagSampleRfci.getKnowledge()	Retrieves the knowledge associated with this method.
Knowledge	Rfci.getKnowledge()	Returns a knowledge object.
Knowledge	RfciBsc.getKnowledge()	Retrieves the knowledge associated with this object.
Knowledge	SpFci.getKnowledge()	Retrieves the knowledge object associated with this algorithm.
Knowledge	SvarFci.getKnowledge()	Retrieves the knowledge object associated with this algorithm.
Knowledge	SvarGfci.getKnowledge()	Returns the knowledge associated with this object.

Methods in edu.cmu.tetrad.algcomparison.algorithm.oracle.pag with parameters of type Knowledge

Modifier and Type	Method	Description
void	Bfci.setKnowledge(Knowledge knowledge)	Sets the knowledge associated with the algorithm.
void	BossDumb.setKnowledge(Knowledge knowledge)	Sets the knowledge object associated with this method.
void	BossPag.setKnowledge(Knowledge knowledge)	Sets the knowledge object associated with this method.
void	Cfci.setKnowledge(Knowledge knowledge)	Sets the knowledge object for the algorithm.
void	Fci.setKnowledge(Knowledge knowledge)	Sets the knowledge object for this method.
void	FciMax.setKnowledge(Knowledge knowledge)	Sets the knowledge associated with the algorithm.
void	Gfci.setKnowledge(Knowledge knowledge)	Sets the Knowledge object associated with this instance.
void	GraspFci.setKnowledge(Knowledge knowledge)	Sets the knowledge object associated with this method.
void	LvLite.setKnowledge(Knowledge knowledge)	Sets the knowledge object associated with this method.
void	PagSampleRfci.setKnowledge(Knowledge knowledge)	Sets the knowledge associated with this method.
void	Rfci.setKnowledge(Knowledge knowledge)	Sets a knowledge object.
void	RfciBsc.setKnowledge(Knowledge knowledge)	Sets the knowledge object.
void	SpFci.setKnowledge(Knowledge knowledge)	Sets the knowledge object associated with this algorithm.
void	SvarFci.setKnowledge(Knowledge knowledge)	Sets the knowledge object associated with this algorithm.
void	SvarGfci.setKnowledge(Knowledge knowledge)	Sets the knowledge associated with this object.

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

Methods in edu.cmu.tetrad.algcomparison.simulation that return Knowledge

Modifier and Type	Method	Description
Knowledge	TimeSeriesSemSimulation.getKnowledge()	Returns a knowledge object.

Methods in edu.cmu.tetrad.algcomparison.simulation with parameters of type Knowledge

Modifier and Type	Method	Description
void	TimeSeriesSemSimulation.setKnowledge(Knowledge knowledge)	Sets a knowledge object.

Uses of Knowledge in edu.cmu.tetrad.algcomparison.statistic

Methods in edu.cmu.tetrad.algcomparison.statistic that return Knowledge

Modifier and Type	Method	Description
Knowledge	KnowledgeSatisfied.getKnowledge()

Methods in edu.cmu.tetrad.algcomparison.statistic with parameters of type Knowledge

Modifier and Type	Method	Description
void	KnowledgeSatisfied.setKnowledge(Knowledge knowledge)

Uses of Knowledge in edu.cmu.tetrad.algcomparison.utils

Methods in edu.cmu.tetrad.algcomparison.utils that return Knowledge

Modifier and Type	Method	Description
Knowledge	HasKnowledge.getKnowledge()	Returns a knowledge object.

Methods in edu.cmu.tetrad.algcomparison.utils with parameters of type Knowledge

Modifier and Type	Method	Description
void	HasKnowledge.setKnowledge(Knowledge knowledge)	Sets a knowledge object.

Uses of Knowledge in edu.cmu.tetrad.data

Methods in edu.cmu.tetrad.data that return Knowledge

Modifier and Type	Method	Description
Knowledge	Knowledge.copy()	Makes a shallow copy.
Knowledge	BoxDataSet.getKnowledge()	Getter for the field knowledge.
final Knowledge	CorrelationMatrixOnTheFly.getKnowledge()	getKnowledge.
final Knowledge	CovarianceMatrix.getKnowledge()	Getter for the field knowledge.
final Knowledge	CovarianceMatrixOnTheFly.getKnowledge()	Getter for the field knowledge.
Knowledge	DataModelList.getKnowledge()	Getter for the field knowledge.
Knowledge	ICovarianceMatrix.getKnowledge()	Retrieves the knowledge associated with the ICovarianceMatrix.
Knowledge	IndependenceFacts.getKnowledge()	Getter for the field knowledge.
Knowledge	KnowledgeTransferable.getKnowledge()	getKnowledge.
Knowledge	NumberObjectDataSet.getKnowledge()	Getter for the field knowledge.
Knowledge	TimeSeriesData.getKnowledge()	Getter for the field knowledge.
static Knowledge	SimpleDataLoader.loadKnowledge(File file, DelimiterType delimiter, String commentMarker)	Loads knowledge from a file.
static Knowledge	Knowledge.serializableInstance()	Generates a simple exemplar of this class to test serialization.

Methods in edu.cmu.tetrad.data with parameters of type Knowledge

Modifier and Type	Method	Description
static void	DataWriter.saveKnowledge(Knowledge knowledge, Writer out)	saveKnowledge.
void	BoxDataSet.setKnowledge(Knowledge knowledge)	Sets knowledge to a copy of the given object.
final void	CorrelationMatrixOnTheFly.setKnowledge(Knowledge knowledge)	Sets the knowledge associated with the ICovarianceMatrix.
final void	CovarianceMatrix.setKnowledge(Knowledge knowledge)	Sets the knowledge associated with the ICovarianceMatrix.
final void	CovarianceMatrixOnTheFly.setKnowledge(Knowledge knowledge)	Sets the knowledge associated with the ICovarianceMatrix.
void	DataModelList.setKnowledge(Knowledge knowledge)	Sets knowledge to a copy of the given object.
void	ICovarianceMatrix.setKnowledge(Knowledge knowledge)	Sets the knowledge associated with the ICovarianceMatrix.
void	IndependenceFacts.setKnowledge(Knowledge knowledge)	Sets knowledge to a copy of the given object.
void	KnowledgeTransferable.setKnowledge(Knowledge knowledge)	Sets knowledge to a copy of the given object.
void	NumberObjectDataSet.setKnowledge(Knowledge knowledge)	Sets knowledge to a copy of the given object.
void	TimeSeriesData.setKnowledge(Knowledge knowledge)	Sets knowledge to a copy of the given object.

Constructors in edu.cmu.tetrad.data with parameters of type Knowledge

Modifier	Constructor	Description
	Knowledge(Knowledge knowledge)	Constructor for Knowledge.

Uses of Knowledge in edu.cmu.tetrad.graph

Methods in edu.cmu.tetrad.graph with parameters of type Knowledge

Modifier and Type	Method	Description
static void	GraphUtils.addForbiddenReverseEdgesForDirectedEdges(Graph graph, Knowledge knowledge)	Adds forbidden reverse edges for directed edges in the given graph based on the knowledge.
static boolean	GraphUtils.colliderAllowed(Graph pag, Node x, Node b, Node y, Knowledge knowledge)	Determines if the collider is allowed.
static Graph	GraphTransforms.dagFromCpdag(Graph graph, Knowledge knowledge)	dagFromCpdag.
static Graph	GraphTransforms.dagFromCpdag(Graph cpdag, Knowledge knowledge, boolean meekPreventCycles, boolean verbose)	Returns a random DAG from the given CPDAG.
static void	GraphUtils.doRequiredOrientations(FciOrient fciOrient, Graph pag, List<Node> best, Knowledge knowledge, boolean verbose)	Orient required edges in PAG.
static void	GraphUtils.fciOrientbk(Knowledge knowledge, Graph graph, List<Node> variables)	Attempts to orient the edges in the graph based on the given knowledge.
static List<Graph>	GraphTransforms.getDagsInCpdagMeek(Graph cpdag, Knowledge knowledge)	Retrieves a list of directed acyclic graphs (DAGs) within the given completed partially directed acyclic graph (CPDAG) using the Meek rules.
static void	GraphUtils.gfciR0(Graph pag, Graph cpdag, SepsetProducer sepsets, Knowledge knowledge, boolean verbose, Set<Triple> unshieldedTriples)	Applies the GFCI-R0 algorithm to orient edges in a pag based on a reference CPDAG, sepsets, and knowledge.
static Graph	GraphUtils.guaranteePag(Graph pag, FciOrient fciOrient, Knowledge knowledge, Set<Triple> unshieldedColliders, Set<Triple> extraUnshieldedColliders, boolean verbose, Set<Node> selection)	Guarantees a legal PAG by repairing deviations of a graph from a legal PAG (partial ancestral graph).
static void	GraphUtils.recallUnshieldedTriples(Graph pag, Set<Triple> unshieldedColliders, Knowledge knowledge)	Recall unshielded triples in a given graph.
static boolean	GraphUtils.removeAlmostCycles(Graph pag, Set<Triple> unshieldedColliders, Set<Triple> extraUnshieldedColliders, FciOrient fciOrient, Knowledge knowledge, boolean verbose)	Removes almost cycles from a graph.
static boolean	GraphUtils.removeCycles(Set<Triple> unshieldedColliders, FciOrient fciOrient, Graph pag, Knowledge knowledge, boolean verbose)	Removes cycles from the given graph using the Fast Causal Inference (FCI) algorithm.
static void	GraphUtils.removeNonSkeletonEdges(Graph graph, Knowledge knowledge)	Removes non-skeleton edges from the given graph based on the provided knowledge.
static void	GraphTransforms.transformCpdagIntoRandomDag(Graph graph, Knowledge knowledge, boolean meekPreventCycles, boolean verbose)	Transforms a completed partially directed acyclic graph (CPDAG) into a random directed acyclic graph (DAG) by randomly orienting the undirected edges in the CPDAG in shuffled order.

Uses of Knowledge in edu.cmu.tetrad.search

Methods in edu.cmu.tetrad.search that return Knowledge

Modifier and Type	Method	Description
Knowledge	Cpc.getKnowledge()	Returns the knowledge specification used in the search.
Knowledge	FaskOrig.getKnowledge()	Getter for the field knowledge.
Knowledge	Fci.getKnowledge()	Returns the background knowledge that was set.
Knowledge	FciMax.getKnowledge()	Retrieves the background knowledge that was set.
Knowledge	Fges.getKnowledge()	Returns the background knowledge.
Knowledge	FgesMb.getKnowledge()	Returns the background knowledge.
Knowledge	GFci.getKnowledge()	Returns the knowledge used in search.
Knowledge	MarkovCheck.getKnowledge()	Returns the knowledge object for the Markov checker.
Knowledge	Pc.getKnowledge()	Returns the knowledge specification used in the search.
Knowledge	Pcd.getKnowledge()	Retrieves the Knowledge object used by this method.
Knowledge	PcMb.getKnowledge()	Returns The knowledge used in search.
Knowledge	Rfci.getKnowledge()	Returns the knowledge used in search.
Knowledge	SpFci.getKnowledge()	Returns the knowledge.
Knowledge	SvarFci.getKnowledge()	Returns the knowledge for the search.
Knowledge	SvarFges.getKnowledge()	Getter for the field knowledge.

Methods in edu.cmu.tetrad.search with parameters of type Knowledge

Modifier and Type	Method	Description
static List<Edge>	CheckKnowledge.forbiddenViolations(Graph graph, Knowledge knowledge)	Returns a sorted list of edges that violate the given knowledge.
static Graph	PermutationSearch.getGraph(List<Node> nodes, Map<Node,Set<Node>> parents, Knowledge knowledge, boolean cpDag)	Constructs a graph given a specification of the parents for each node.
static List<Edge>	CheckKnowledge.requiredViolations(Graph graph, Knowledge knowledge)	Returns a sorted list of edges that are required by knowledge but which do not appear in the graph.
void	BFci.setKnowledge(Knowledge knowledge)	Sets the knowledge to be used for the search.
void	Boss.setKnowledge(Knowledge knowledge)	Sets the knowledge to be used for the search.
void	Cfci.setKnowledge(Knowledge knowledge)	Set the knowledge used in the search.
void	Cpc.setKnowledge(Knowledge knowledge)	Sets the knowledge specification used in the search.
void	Fas.setKnowledge(Knowledge knowledge)	Sets the knowledge for this object.
void	Fasd.setKnowledge(Knowledge knowledge)	Sets the knowledge for this object.
void	Fask.setKnowledge(Knowledge knowledge)	Sets the knowledge object for the current instance.
void	FaskOrig.setKnowledge(Knowledge knowledge)	Setter for the field knowledge.
void	Fci.setKnowledge(Knowledge knowledge)	Sets background knowledge for the search.
void	FciMax.setKnowledge(Knowledge knowledge)	Sets background knowledge for the search.
void	Fges.setKnowledge(Knowledge knowledge)	Sets the background knowledge.
void	FgesMb.setKnowledge(Knowledge knowledge)	Sets the background knowledge.
void	GFci.setKnowledge(Knowledge knowledge)	Sets the knowledge to use in search.
void	Grasp.setKnowledge(Knowledge knowledge)	Sets the knowledge used in the search.
void	GraspFci.setKnowledge(Knowledge knowledge)	Sets the knowledge used in search.
void	IFas.setKnowledge(Knowledge knowledge)	Sets the knowledge for the search.
void	Lofs.setKnowledge(Knowledge knowledge)	Sets the knowledge for the object.
void	LvDumb.setKnowledge(Knowledge knowledge)	Sets the knowledge used in search.
void	LvLite.setKnowledge(Knowledge knowledge)	Sets the knowledge used in search.
void	MarkovCheck.setKnowledge(Knowledge knowledge)	Sets the knowledge object for the Markov checker.
void	Mimbuild.setKnowledge(Knowledge knowledge)	Sets the knowledge to be used in the search.
void	MimbuildTrek.setKnowledge(Knowledge knowledge)	The knowledge to use in the search.
void	Pc.setKnowledge(Knowledge knowledge)	Sets the knowledge specification to be used in the search.
void	Pcd.setKnowledge(Knowledge knowledge)	Sets the knowledge object used by this method.
void	PcMb.setKnowledge(Knowledge knowledge)	Sets knowledge, to which the algorithm is in fact sensitive.
void	PermutationSearch.setKnowledge(Knowledge knowledge)	Sets the knowledge to be used for the search.
void	Rfci.setKnowledge(Knowledge knowledge)	Sets the knowledge used in search.
void	Sp.setKnowledge(Knowledge knowledge)	Sets the knowledge associated with this object.
void	SpFci.setKnowledge(Knowledge knowledge)	Sets the knoweldge used in the search.
void	SuborderSearch.setKnowledge(Knowledge knowledge)	The knowledge being used.
void	SvarFas.setKnowledge(Knowledge knowledge)	Sets the knowledge for the search.
void	SvarFci.setKnowledge(Knowledge knowledge)	Sets the knowledge for the search.
void	SvarFges.setKnowledge(Knowledge knowledge)	Sets the background knowledge.
void	SvarGfci.setKnowledge(Knowledge knowledge)	Sets the knowledge for the search.

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

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

Modifier and Type	Method	Description
Knowledge	R0R4Strategy.getknowledge()	Returns the knowledge object used by the strategy.
Knowledge	R0R4StrategyScoreBased.getknowledge()
Knowledge	R0R4StrategyTestBased.getknowledge()	Retrieves the Knowledge object used by the FciOrientDataExaminationStrategy.
Knowledge	BesPermutation.getKnowledge()	Returns the knowledge that BES will use.
Knowledge	DagToPag.getKnowledge()	Getter for the field knowledge.
Knowledge	FgesOrienter.getKnowledge()	Getter for the field knowledge.
Knowledge	PcCommon.getKnowledge()	Getter for the field knowledge.
Knowledge	PossibleMsepFci.getKnowledge()	Getter for the field knowledge.
Knowledge	R0R4StrategyScoreBased.getKnowledge()	Retrieves the knowledge associated with this instance.
Knowledge	ShiftSearch.getKnowledge()	Getter for the field knowledge.
Knowledge	TsDagToPag.getKnowledge()	Getter for the field knowledge.
static Knowledge	TsUtils.getKnowledge(Graph graph)	getKnowledge.

Methods in edu.cmu.tetrad.search.utils with parameters of type Knowledge

Modifier and Type	Method	Description
static void	GraphSearchUtils.arrangeByKnowledgeTiers(Graph graph, Knowledge knowledge)	arrangeByKnowledgeTiers.
static boolean	PcCommon.colliderAllowed(Graph graph, Node x, Node y, Node z, Knowledge knowledge)	Checks if colliders are allowed based on the given knowledge.
static R0R4Strategy	R0R4StrategyScoreBased.defaultConfiguration(TeyssierScorer scorer, Knowledge knowledge, boolean verbose)	Returns a default configuration of the FciOrientDataExaminationStrategy.
static R0R4Strategy	R0R4StrategyTestBased.defaultConfiguration(Graph dag, Knowledge knowledge)	Returns a default configuration of the FciOrientDataExaminationStrategy object.
static R0R4Strategy	R0R4StrategyTestBased.defaultConfiguration(IndependenceTest test, Knowledge knowledge)	Returns a default configuration of the FciOrientDataExaminationStrategy object.
static boolean	TsDagToPag.existsInducingPathInto(Node x, Node y, Graph graph, Knowledge knowledge)	existsInducingPathInto.
static boolean	TsDagToPag.existsInducingPathVisitts(Graph graph, Node a, Node b, Node x, Node y, LinkedList<Node> path, Knowledge knowledge)	existsInducingPathVisitts.
void	FciOrient.fciOrientbk(Knowledge bk, Graph graph, List<Node> variables)	Orient the edges of a graph based on the given knowledge.
static R0R4StrategyTestBased	DagToPag.getFinalStrategyUsingDsep(Graph mag, Knowledge knowledge, boolean verbose)	Returns the final strategy for finding a PAG using D-SEP.
static boolean	FciOrient.isArrowheadAllowed(Node x, Node y, Graph graph, Knowledge knowledge)	Determines whether an arrowhead is allowed between two nodes in a graph, based on specific conditions.
static boolean	GraphSearchUtils.isArrowheadAllowed(Object from, Object to, Knowledge knowledge)	Checks if an arrowhead is allowed by background knowledge.
static void	GraphSearchUtils.orientCollidersUsingSepsets(SepsetMap set, Knowledge knowledge, Graph graph, boolean verbose, boolean enforceCpdag)	Step C of PC; orients colliders using specified sepset.
static void	GraphSearchUtils.pcdOrientC(IndependenceTest test, Knowledge knowledge, Graph graph)	Performs step C of the algorithm, as indicated on page xxx of CPS, with the modification that X--W--Y is oriented as X-->W<--Y if W is *determined by* the sepset of (X, Y), rather than W just being *in* the sepset of (X, Y).
static void	GraphSearchUtils.pcOrientbk(Knowledge bk, Graph graph, List<Node> nodes, boolean verbose)	Orients according to background knowledge.
void	Bes.setKnowledge(Knowledge knowledge)	Sets the knowledge for the search.
void	BesPermutation.setKnowledge(Knowledge knowledge)	Sets the knowledge that BES will use.
void	DagToPag.setKnowledge(Knowledge knowledge)	Setter for the field knowledge.
void	FciOrient.setKnowledge(Knowledge knowledge)	Sets the knowledge to use for the final orientation.
void	FgesOrienter.setKnowledge(Knowledge knowledge)	Sets the background knowledge.
void	MaxP.setKnowledge(Knowledge knowledge)	Sets the knowledge to use for orientation.
void	MeekRules.setKnowledge(Knowledge knowledge)	Sets the knowledge to be used in the orientation.
void	PcCommon.setKnowledge(Knowledge knowledge)	Sets the knowledge specification used in the search.
void	PossibleMsepFci.setKnowledge(Knowledge knowledge)	Setter for the field knowledge.
void	R0R4Strategy.setKnowledge(Knowledge knowledge)	Sets the knowledge object to be used by the strategy.
void	R0R4StrategyScoreBased.setKnowledge(Knowledge knowledge)	Sets the Knowledge object for this instance.
void	R0R4StrategyTestBased.setKnowledge(Knowledge knowledge)	Sets the knowledge object used by the FciOrientDataExaminationStrategy.
void	ShiftSearch.setKnowledge(Knowledge knowledge)	Setter for the field knowledge.
void	TeyssierScorer.setKnowledge(Knowledge knowledge)	Setter for the field knowledge.
void	TsDagToPag.setKnowledge(Knowledge knowledge)	Setter for the field knowledge.
static R0R4Strategy	R0R4StrategyScoreBased.specialConfiguration(TeyssierScorer scorer, Knowledge knowledge, boolean verbose, int depth)	Returns a special configuration of FciOrientDataExaminationStrategy.
static R0R4Strategy	R0R4StrategyTestBased.specialConfiguration(IndependenceTest test, Knowledge knowledge, boolean verbose)	Provides a special configuration for creating an instance of FciOrientDataExaminationStrategy.

Constructors in edu.cmu.tetrad.search.utils with parameters of type Knowledge

Modifier	Constructor	Description
	DagInCpcagIterator(Graph CPDAG, Knowledge knowledge)	The given CPDAG must be a CPDAG.
	DagInCpcagIterator(Graph CPDAG, Knowledge knowledge, boolean allowArbitraryOrientations, boolean allowNewColliders)	The given CPDAG must be a CPDAG.
	SepsetsPossibleMsep(Graph graph, IndependenceTest test, Knowledge knowledge, int depth, int maxDiscriminatingPathLength)	Constructor for SepsetsPossibleMsep.
	SvarSetEndpointStrategy(IndependenceTest independenceTest, Knowledge knowledge)	Creates a new instance of SvarSetEndpointStrategy with the given IndependenceTest and Knowledge.

Uses of Knowledge in edu.cmu.tetrad.search.work_in_progress

Methods in edu.cmu.tetrad.search.work_in_progress that return Knowledge

Modifier and Type	Method	Description
Knowledge	FasDci.getKnowledge()	Getter for the field knowledge.
Knowledge	FasLofs.getKnowledge()	Getter for the field knowledge.
Knowledge	HbsmsBeam.getKnowledge()	Getter for the field knowledge.
Knowledge	HbsmsGes.getKnowledge()	Getter for the field knowledge.
Knowledge	IGFci.getKnowledge()	Returns the knowledge used in the IGFci algorithm.
Knowledge	ISFges.getKnowledge()	Retrieves the Knowledge instance associated with this object.
Knowledge	Kpc.getKnowledge()	Getter for the field knowledge.
Knowledge	Mmhc.getKnowledge()	Getter for the field knowledge.
Knowledge	SampleVcpc.getKnowledge()	Getter for the field knowledge.
Knowledge	SampleVcpcFast.getKnowledge()	Getter for the field knowledge.
Knowledge	VcFas.getKnowledge()	Getter for the field knowledge.
Knowledge	VcPc.getKnowledge()	Getter for the field knowledge.
Knowledge	VcPcAlt.getKnowledge()	Getter for the field knowledge.
Knowledge	VcPcFast.getKnowledge()	Getter for the field knowledge.

Methods in edu.cmu.tetrad.search.work_in_progress with parameters of type Knowledge

Modifier and Type	Method	Description
static boolean	SampleVcpcFast.isArrowheadAllowed1(Node from, Node to, Knowledge knowledge)	isArrowheadAllowed1.
static boolean	VcPc.isArrowheadAllowed1(Node from, Node to, Knowledge knowledge)	isArrowheadAllowed1.
void	FasDci.setKnowledge(Knowledge knowledge)	Setter for the field knowledge.
void	FasFdr.setKnowledge(Knowledge knowledge)	Sets the knowledge for the search.
void	FaskVote.setKnowledge(Knowledge knowledge)	Setter for the field knowledge.
void	FasLofs.setKnowledge(Knowledge knowledge)	Setter for the field knowledge.
void	GraspTol.setKnowledge(Knowledge knowledge)	Setter for the field knowledge.
void	Hbsms.setKnowledge(Knowledge knowledge)	setKnowledge.
void	HbsmsBeam.setKnowledge(Knowledge knowledge)	setKnowledge.
void	HbsmsGes.setKnowledge(Knowledge knowledge)	setKnowledge.
void	IGFci.setKnowledge(Knowledge knowledge)	Sets the knowledge for the IGFci algorithm.
void	Ion.setKnowledge(Knowledge knowledge)	Sets the knowledge to be used for this search.
void	ISFges.setKnowledge(Knowledge knowledge)	Sets the background knowledge.
void	Kpc.setKnowledge(Knowledge knowledge)	Sets the knowledge specification to be used in the search.
void	Mmhc.setKnowledge(Knowledge knowledge)	Setter for the field knowledge.
void	SampleVcpc.setKnowledge(Knowledge knowledge)	Sets the knowledge specification used in the search.
void	SampleVcpcFast.setKnowledge(Knowledge knowledge)	Sets the knowledge specification used in the search.
void	VcFas.setKnowledge(Knowledge knowledge)	Setter for the field knowledge.
void	VcPc.setKnowledge(Knowledge knowledge)	Sets the knowledge specification used in the search.
void	VcPcAlt.setKnowledge(Knowledge knowledge)	Sets the knowledge specification used in the search.
void	VcPcFast.setKnowledge(Knowledge knowledge)	Sets the knowledge specification used in the search.

Constructors in edu.cmu.tetrad.search.work_in_progress with parameters of type Knowledge

Modifier	Constructor	Description
	HbsmsBeam(Graph graph, CovarianceMatrix cov, Knowledge knowledge)	Constructor for HbsmsBeam.
	HbsmsBeam(Graph graph, DataSet data, Knowledge knowledge)	Constructor for HbsmsBeam.

Uses of Knowledge in edu.cmu.tetrad.sem

Methods in edu.cmu.tetrad.sem that return Knowledge

Modifier and Type	Method	Description
Knowledge	LargeScaleSimulation.getKnowledge(Graph graph)	getKnowledge.

Uses of Knowledge in edu.cmu.tetrad.study.performance

Methods in edu.cmu.tetrad.study.performance that return Knowledge

Modifier and Type	Method	Description
static Knowledge	Comparison2.getKnowledge(Graph graph)	getKnowledge.

Uses of Knowledge in edu.cmu.tetrad.util

Methods in edu.cmu.tetrad.util with parameters of type Knowledge

Modifier and Type	Method	Description
Graph	PagCache.getPag(Graph graph, Knowledge knowledge, boolean verbose)	Returns the PAG (Partial Ancestral Graph) corresponding to the given DAG (Directed Acyclic Graph).

Uses of Knowledge in edu.pitt.dbmi.algo.bayesian.constraint.search

Methods in edu.pitt.dbmi.algo.bayesian.constraint.search with parameters of type Knowledge

Modifier and Type	Method	Description
void	PagSamplingRfci.setKnowledge(Knowledge knowledge)	Set the knowledge.