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

Packages that use Knowledge

Package	Description
edu.cmu.tetrad.algcomparison.algorithm.cluster
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.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.pitt.dbmi.algo.bayesian.constraint.search
edu.pitt.dbmi.algo.resampling
edu.pitt.dbmi.algo.resampling.task

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()
Knowledge	Ftfc.getKnowledge()

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

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

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	Fask.getKnowledge()
Knowledge	FaskConcatenated.getKnowledge()
Knowledge	FaskLofsConcatenated.getKnowledge()
Knowledge	FaskVote.getKnowledge()
Knowledge	FasLofs.getKnowledge()
Knowledge	FciIod.getKnowledge()
Knowledge	FgesConcatenated.getKnowledge()
Knowledge	Images.getKnowledge()

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

Modifier and Type	Method	Description
void	Fask.setKnowledge(Knowledge knowledge)
void	FaskConcatenated.setKnowledge(Knowledge knowledge)
void	FaskLofsConcatenated.setKnowledge(Knowledge knowledge)
void	FaskVote.setKnowledge(Knowledge knowledge)
void	FasLofs.setKnowledge(Knowledge knowledge)
void	FciIod.setKnowledge(Knowledge knowledge)
void	FgesConcatenated.setKnowledge(Knowledge knowledge)
void	Images.setKnowledge(Knowledge knowledge)

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()
Knowledge	Cpc.getKnowledge()
Knowledge	Fas.getKnowledge()
Knowledge	Fges.getKnowledge()
Knowledge	FgesMb.getKnowledge()
Knowledge	FgesMeasurement.getKnowledge()
Knowledge	Grasp.getKnowledge()
Knowledge	Pc.getKnowledge()
Knowledge	Pcd.getKnowledge()
Knowledge	PcLingam.getKnowledge()
Knowledge	PcMb.getKnowledge()
Knowledge	SingleGraphAlg.getKnowledge()
Knowledge	Sp.getKnowledge()

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

Modifier and Type	Method	Description
void	Boss.setKnowledge(Knowledge knowledge)
void	Cpc.setKnowledge(Knowledge knowledge)
void	Fas.setKnowledge(Knowledge knowledge)
void	Fges.setKnowledge(Knowledge knowledge)
void	FgesMb.setKnowledge(Knowledge knowledge)
void	FgesMeasurement.setKnowledge(Knowledge knowledge)
void	Grasp.setKnowledge(Knowledge knowledge)
void	Pc.setKnowledge(Knowledge knowledge)
void	Pcd.setKnowledge(Knowledge knowledge)
void	PcLingam.setKnowledge(Knowledge knowledge)
void	PcMb.setKnowledge(Knowledge knowledge)
void	SingleGraphAlg.setKnowledge(Knowledge knowledge)
void	Sp.setKnowledge(Knowledge knowledge)

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()
Knowledge	Cfci.getKnowledge()
Knowledge	Fci.getKnowledge()
Knowledge	FciMax.getKnowledge()
Knowledge	Gfci.getKnowledge()
Knowledge	GraspFci.getKnowledge()
Knowledge	PagSampleRfci.getKnowledge()
Knowledge	Rfci.getKnowledge()
Knowledge	RfciBsc.getKnowledge()
Knowledge	SpFci.getKnowledge()
Knowledge	SvarFci.getKnowledge()
Knowledge	SvarGfci.getKnowledge()

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

Modifier and Type	Method	Description
void	Bfci.setKnowledge(Knowledge knowledge)
void	Cfci.setKnowledge(Knowledge knowledge)
void	Fci.setKnowledge(Knowledge knowledge)
void	FciMax.setKnowledge(Knowledge knowledge)
void	Gfci.setKnowledge(Knowledge knowledge)
void	GraspFci.setKnowledge(Knowledge knowledge)
void	PagSampleRfci.setKnowledge(Knowledge knowledge)
void	Rfci.setKnowledge(Knowledge knowledge)
void	RfciBsc.setKnowledge(Knowledge knowledge)
void	SpFci.setKnowledge(Knowledge knowledge)
void	SvarFci.setKnowledge(Knowledge knowledge)
void	SvarGfci.setKnowledge(Knowledge knowledge)

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()

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

Modifier and Type	Method	Description
void	TimeSeriesSemSimulation.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()
final Knowledge	CorrelationMatrixOnTheFly.getKnowledge()
final Knowledge	CovarianceMatrix.getKnowledge()
final Knowledge	CovarianceMatrixOnTheFly.getKnowledge()
Knowledge	DataModelList.getKnowledge()
Knowledge	ICovarianceMatrix.getKnowledge()
Knowledge	IndependenceFacts.getKnowledge()
Knowledge	KnowledgeTransferable.getKnowledge()
Knowledge	NumberObjectDataSet.getKnowledge()
Knowledge	TimeSeriesData.getKnowledge()
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)
void	BoxDataSet.setKnowledge(Knowledge knowledge)	Sets knowledge to be associated with this data set.
final void	CorrelationMatrixOnTheFly.setKnowledge(Knowledge knowledge)	Associates knowledge with this data.
final void	CovarianceMatrix.setKnowledge(Knowledge knowledge)	Associates knowledge with this data.
final void	CovarianceMatrixOnTheFly.setKnowledge(Knowledge knowledge)	Associates knowledge with this data.
void	DataModelList.setKnowledge(Knowledge knowledge)
void	ICovarianceMatrix.setKnowledge(Knowledge knowledge)
void	IndependenceFacts.setKnowledge(Knowledge knowledge)
void	KnowledgeTransferable.setKnowledge(Knowledge knowledge)	Sets knowledge to a copy of the given object.
void	NumberObjectDataSet.setKnowledge(Knowledge knowledge)	Sets knowledge to be associated with this data set.
void	TimeSeriesData.setKnowledge(Knowledge knowledge)

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

Modifier	Constructor	Description
	Knowledge(Knowledge 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)
static Graph	GraphTransforms.dagFromCPDAG(Graph graph, Knowledge knowledge)
static void	GraphUtils.fciOrientbk(Knowledge knowledge, Graph graph, List<Node> variables)	Orients according to background knowledge
static List<Graph>	GraphTransforms.getDagsInCpdagMeek(Graph cpdag, Knowledge knowledge)
static void	GraphUtils.gfciR0(Graph graph, Graph referenceCpdag, SepsetProducer sepsets, Knowledge knowledge)
static void	GraphUtils.removeNonSkeletonEdges(Graph graph, Knowledge knowledge)

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	Fask.getKnowledge()
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	Pc.getKnowledge()	Returns the knowledge specification used in the search.
Knowledge	Pcd.getKnowledge()
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()

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

Modifier and Type	Method	Description
static Graph	PermutationSearch.getGraph(List<Node> nodes, Map<Node,Set<Node>> parents, Knowledge knowledge, boolean cpDag)	Construct a graph given a specification of the parents for each node.
void	BFci.setKnowledge(Knowledge knowledge)	Sets the knowledge to be used for the search.
void	Boss.setKnowledge(Knowledge knowledge)
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 to be used in the search.
void	Fasd.setKnowledge(Knowledge knowledge)	Sets the knowledge to be used in the search.
void	Fask.setKnowledge(Knowledge 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)
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 specification to be used in the search.
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 in the search.
void	Rfci.setKnowledge(Knowledge knowledge)	Sets the knowledge used in search.
void	Sp.setKnowledge(Knowledge knowledge)
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 used in 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	BesPermutation.getKnowledge()
Knowledge	DagToPag.getKnowledge()
Knowledge	FgesOrienter.getKnowledge()
Knowledge	PcCommon.getKnowledge()
Knowledge	PossibleMsepFci.getKnowledge()
Knowledge	ShiftSearch.getKnowledge()
Knowledge	SvarFciOrient.getKnowledge()	The background knowledge.
Knowledge	TsDagToPag.getKnowledge()
static Knowledge	TsUtils.getKnowledge(Graph graph)

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)
static boolean	TsDagToPag.existsInducingPathInto(Node x, Node y, Graph graph, Knowledge knowledge)
static boolean	TsDagToPag.existsInducingPathVisitts(Graph graph, Node a, Node b, Node x, Node y, LinkedList<Node> path, Knowledge knowledge)
void	FciOrient.fciOrientbk(Knowledge bk, Graph graph, List<Node> variables)	Orients according to background knowledge
static boolean	FciOrient.isArrowheadAllowed(Node x, Node y, Graph graph, Knowledge knowledge)
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)	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)
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)
void	ShiftSearch.setKnowledge(Knowledge knowledge)
void	SvarFciOrient.setKnowledge(Knowledge knowledge)
void	TeyssierScorer.setKnowledge(Knowledge knowledge)
void	TsDagToPag.setKnowledge(Knowledge knowledge)

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.
	SepsetsGreedy(Graph graph, IndependenceTest independenceTest, SepsetMap extraSepsets, int depth, Knowledge knowledge)
	SepsetsPossibleMsep(Graph graph, IndependenceTest test, Knowledge knowledge, int depth, int maxPathLength)

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	Fas2.getKnowledge()
Knowledge	FasDci.getKnowledge()
Knowledge	FasLofs.getKnowledge()
Knowledge	HbsmsBeam.getKnowledge()
Knowledge	HbsmsGes.getKnowledge()
Knowledge	Kpc.getKnowledge()
Knowledge	Mmhc.getKnowledge()
Knowledge	SampleVcpc.getKnowledge()
Knowledge	SampleVcpcFast.getKnowledge()
Knowledge	VcFas.getKnowledge()
Knowledge	VcPc.getKnowledge()
Knowledge	VcPcAlt.getKnowledge()
Knowledge	VcPcFast.getKnowledge()

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)
static boolean	VcPc.isArrowheadAllowed1(Node from, Node to, Knowledge knowledge)
void	Fas2.setKnowledge(Knowledge knowledge)
void	Fas3.setKnowledge(Knowledge knowledge)	Sets the knowledge to be used int the search.
void	FasDci.setKnowledge(Knowledge knowledge)
void	FasFdr.setKnowledge(Knowledge knowledge)	Sets the knowledge to be used in the search.
void	FaskVote.setKnowledge(Knowledge knowledge)
void	FasLofs.setKnowledge(Knowledge knowledge)
void	GraspTol.setKnowledge(Knowledge knowledge)
void	Hbsms.setKnowledge(Knowledge knowledge)
void	HbsmsBeam.setKnowledge(Knowledge knowledge)
void	HbsmsGes.setKnowledge(Knowledge knowledge)
void	Ion.setKnowledge(Knowledge knowledge)	Sets the knowledge to be used for this search.
void	Kpc.setKnowledge(Knowledge knowledge)	Sets the knowledge specification to be used in the search.
void	Mmhc.setKnowledge(Knowledge knowledge)
void	OtherPermAlgs.setKnowledge(Knowledge 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)
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)
	HbsmsBeam(Graph graph, DataSet data, Knowledge knowledge)

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)

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)

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)

Uses of Knowledge in edu.pitt.dbmi.algo.resampling

Methods in edu.pitt.dbmi.algo.resampling with parameters of type Knowledge

Modifier and Type	Method	Description
void	GeneralResamplingSearch.setKnowledge(Knowledge knowledge)	Sets the background knowledge.
void	GeneralResamplingTest.setKnowledge(Knowledge knowledge)	Sets the background knowledge.

Uses of Knowledge in edu.pitt.dbmi.algo.resampling.task

Methods in edu.pitt.dbmi.algo.resampling.task that return Knowledge

Modifier and Type	Method	Description
Knowledge	GeneralResamplingSearchRunnable.getKnowledge()

Methods in edu.pitt.dbmi.algo.resampling.task with parameters of type Knowledge

Modifier and Type	Method	Description
void	GeneralResamplingSearchRunnable.setKnowledge(Knowledge knowledge)	Sets the background knowledge.