Uses of Interface
edu.cmu.tetrad.algcomparison.algorithm.Algorithm

Packages that use Algorithm

Package	Description
edu.cmu.tetrad.algcomparison.algorithm
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.algorithm.other
edu.cmu.tetrad.algcomparison.algorithm.pairwise
edu.cmu.tetrad.algcomparison.utils
edu.cmu.tetrad.search.utils	This package contains utility classes for causal graph search algorithms.
edu.cmu.tetrad.util

Uses of Algorithm in edu.cmu.tetrad.algcomparison.algorithm

Subinterfaces of Algorithm in edu.cmu.tetrad.algcomparison.algorithm

Modifier and Type	Interface	Description
interface	MultiDataSetAlgorithm	Implements an algorithm that takes multiple data sets as input.

Classes in edu.cmu.tetrad.algcomparison.algorithm that implement Algorithm

Modifier and Type	Class	Description
class	AbstractBootstrapAlgorithm	This is a base class for bootstrap algorithms.
class	ExternalAlgorithm	Tags an an algorithm that loads up external graphs for inclusion in reports.
class	FirstInflection	First inflection point.
class	StabilitySelection	Stability selection.
class	StARS	StARS

Methods in edu.cmu.tetrad.algcomparison.algorithm that return Algorithm

Modifier and Type	Method	Description
static Algorithm	AlgorithmFactory.create(Class<? extends Algorithm> algoClass, IndependenceWrapper test, ScoreWrapper score)	Creates an algorithm.
static Algorithm	AlgorithmFactory.create(Class<? extends Algorithm> algoClass, IndependenceWrapper test, ScoreWrapper score, Graph externalGraph)	Creates an algorithm.
static Algorithm	AlgorithmFactory.create(Class<? extends Algorithm> algoClass, Class<? extends IndependenceWrapper> indTestClass, Class<? extends ScoreWrapper> scoreClass)	Creates an algorithm.
static Algorithm	AlgorithmFactory.create(Class<? extends Algorithm> algoClass, Class<? extends IndependenceWrapper> indTestClass, Class<? extends ScoreWrapper> scoreClass, Graph externalGraph)	Creates an algorithm.

Methods in edu.cmu.tetrad.algcomparison.algorithm that return types with arguments of type Algorithm

Modifier and Type	Method	Description
List<Algorithm>	Algorithms.getAlgorithms()	Returns the list of algorithm.

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

Modifier and Type	Method	Description
void	Algorithms.add(Algorithm algorithm)	Adds an algorithm.

Method parameters in edu.cmu.tetrad.algcomparison.algorithm with type arguments of type Algorithm

Modifier and Type	Method	Description
static Algorithm	AlgorithmFactory.create(Class<? extends Algorithm> algoClass, IndependenceWrapper test, ScoreWrapper score)	Creates an algorithm.
static Algorithm	AlgorithmFactory.create(Class<? extends Algorithm> algoClass, IndependenceWrapper test, ScoreWrapper score, Graph externalGraph)	Creates an algorithm.
static Algorithm	AlgorithmFactory.create(Class<? extends Algorithm> algoClass, Class<? extends IndependenceWrapper> indTestClass, Class<? extends ScoreWrapper> scoreClass)	Creates an algorithm.
static Algorithm	AlgorithmFactory.create(Class<? extends Algorithm> algoClass, Class<? extends IndependenceWrapper> indTestClass, Class<? extends ScoreWrapper> scoreClass, Graph externalGraph)	Creates an algorithm.

Constructors in edu.cmu.tetrad.algcomparison.algorithm with parameters of type Algorithm

Modifier	Constructor	Description
	FirstInflection(Algorithm algorithm, String parameter, double low, double high, double increment)	Constructor for FirstInflection.
	StabilitySelection(Algorithm algorithm)	Constructor for StabilitySelection.
	StARS(Algorithm algorithm, String parameter, double low, double high)	Constructor for StARS.

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

Classes in edu.cmu.tetrad.algcomparison.algorithm.continuous.dag that implement Algorithm

Modifier and Type	Class	Description
class	Dagma	Implements the DAGMA algorithm.
class	DirectLingam	Direct LiNGAM.
class	Fask	FASK algorithm.
class	FaskOrig	The FaskOrig class is an implementation of the FASK-Orig algorithm for causal discovery.
class	IcaLingam	IcaLingam class implements the Algorithm and ReturnsBootstrapGraphs interface.
class	IcaLingD	IcaLingD is an implementation of the Algorithm interface that performs the ICA-LiNG-D algorithm for discovering causal models for the linear non-Gaussian case where the underlying model might be cyclic.

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

Modifier and Type	Method	Description
void	Fask.setExternalGraph(Algorithm algorithm)	Sets the external graph to be used by the algorithm.
void	FaskOrig.setExternalGraph(Algorithm algorithm)	Sets the external graph to be used by the algorithm.

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

Classes in edu.cmu.tetrad.algcomparison.algorithm.multi that implement Algorithm

Modifier and Type	Class	Description
class	FaskConcatenated	Wraps the IMaGES algorithm for continuous variables.
class	FaskLofsConcatenated	Wraps the IMaGES algorithm for continuous variables.
class	FaskVote	Wraps the MultiFask algorithm for continuous variables.
class	FasLofs	Wraps the IMaGES algorithm for continuous variables.
class	FciIod	Runs FCI on multiple datasets using the IOD pooled dataset independence test.
class	FgesConcatenated	Requires that the parameter 'randomSelectionSize' be set to indicate how many datasets should be taken at a time (randomly).
class	Images	Wraps the IMaGES algorithm for continuous variables.
class	ImagesBoss	Wraps the IMaGES algorithm for continuous variables.

Constructors in edu.cmu.tetrad.algcomparison.algorithm.multi with parameters of type Algorithm

Modifier	Constructor	Description
	FgesConcatenated(ScoreWrapper score, Algorithm externalGraph)	Constructor for FgesConcatenated.

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

Classes in edu.cmu.tetrad.algcomparison.algorithm.oracle.cpdag that implement Algorithm

Modifier and Type	Class	Description
class	Boss	BOSS (Best Order Score Search)
class	Cam	Represents the CAM algorithm, which is a causal additive model search algorithm.
class	Cdnod	CD-NOD wrapper for algcomparison.
class	Cpc	Deprecated.
class	Cstar	Cstar class.
class	Fas	Fast Adjacency Search (FAS)--i.e., the PC adjacency step, which is used in many algorithms.
class	Fges	FGES (the heuristic version).
class	FgesMb	FGES-MB (the heuristic version).
class	Gin	GIN (Generalized Independent Noise Search)
class	Grasp	GRaSP (Greedy Relaxations of Sparsest Permutation)
class	IsFges	IS-FGES (Instance-Specific FGES) wrapper for the algcomparison interface.
class	Pc	Peter/Clark algorithm (PC).
class	Pcd	PC.
class	PcMax	Deprecated.
class	PcMb	PC.
class	Pcmci	PCMCI wrapper for algcomparison.
class	RestrictedBoss	BOSS-DC (Best Order Score Search Divide and Conquer)
class	SingleGraphAlg	PC.
class	Sp	SP (Sparsest Permutation)
class	TwoStep	Deprecated.

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

Classes in edu.cmu.tetrad.algcomparison.algorithm.oracle.pag that implement Algorithm

Modifier and Type	Class	Description
class	BossFci	Adjusts FGES-FCI to use a permutation algorithm (such as BOSS-Tuck) to do the initial steps of finding adjacencies and unshielded colliders.
class	BossPod	This class represents the FCIT algorithm, which is an implementation of the FGES-FCI algorithm for learning causal structures from observational data using the BOSS algorithm as an initial CPDAG and using all score-based steps afterward.
class	Ccd	CCD (Cyclic Causal Discovery)
class	Cfci	Deprecated.
class	DmFcit	This class represents the Detect-Mimic-FCIT (DM-FCIT) algorithm, a specialized variant of the DM-PC and FCIT algorithms designed to identify intermediate latent variables.
class	DmFciT2	This class represents the Detect-Mimic-FCIT (DM-FCIT) algorithm, a specialized variant of the DM-PC and FCIT algorithms designed to identify intermediate latent variables.
class	DmPc	Detect-Mimic-PC (DM-PC) algorithm.
class	Fci	The Fast Causal Inference (FCI) algorithm.
class	FciCyclicPw	FCI-CPW: Run FCI with internally constructed PW-forbidden knowledge, then orient edges using a pairwise left-right rule on standardized data in cases that are safe under no-selection-bias cyclic semantics: Tail–tail (—) edges Orient per pairwise rule. Tail–circle (—o) edges If pairwise prefers x→y, set x→y (symmetrically, if prefers y→x, set y→x). Circle–circle (o–o) edges If pairwise prefers x→y, set x o→y (symmetrically for y→x).
class	FciMax	Deprecated.
class	Fcit	This class represents the FCI Targeted Testing (FCIT) algorithm, which is variant of the *-FCI algorithm for learning causal structures from observational data using the BOSS algorithm as an initial CPDAG and using all score-based steps afterward.
class	FgesFci	The Fges-FCI class represents the Greedy Fast Causal Inference algorithm, adjusted as in *-FCI.
class	Gfci	The GFCI class represents the Greedy Fast Causal Inference algorithm, adjusted as in *-FCI.
class	GraspFci	GRaSP-FCI, an implentatation of *-FCI using GRaSP.
class	IsGfci	IS-GFCI (Instance-Specific GFCI) wrapper for the algcomparison interface.
class	PagSampleRfci	Jan 29, 2023 3:45:09 PM
class	Rfci	RFCI.
class	RfciBsc	Runs RFCI-BSC, which is RFCI with bootstrap sampling of PAGs.
class	SpFci	Adjusts GFCI to use a permutation algorithm (in this case SP) to do the initial steps of finding adjacencies and unshielded colliders.

Uses of Algorithm in edu.cmu.tetrad.algcomparison.algorithm.other

Classes in edu.cmu.tetrad.algcomparison.algorithm.other that implement Algorithm

Modifier and Type	Class	Description
class	FactorAnalysis	Factor analysis.
class	Glasso	GLASSO.
class	MimbuildBollen	Mimbuild Bollen.
class	MimbuildPca	Mimbuild PCA.

Uses of Algorithm in edu.cmu.tetrad.algcomparison.algorithm.pairwise

Classes in edu.cmu.tetrad.algcomparison.algorithm.pairwise that implement Algorithm

Modifier and Type	Class	Description
class	Eb	EB.
class	FaskPw	FASK-PW (pairwise).
class	R1	R1.
class	R2	R2.
class	R3	R3.
class	Rskew	RSkew.
class	RskewE	RSkewE.
class	Skew	Skew.
class	SkewE	SkewE.
class	Tanh	Tanh.

Methods in edu.cmu.tetrad.algcomparison.algorithm.pairwise with parameters of type Algorithm

Modifier and Type	Method	Description
void	Eb.setExternalGraph(Algorithm algorithm)	Sets the external graph to be used by the algorithm.
void	FaskPw.setExternalGraph(Algorithm algorithm)	Sets the external graph to be used by the algorithm.
void	R1.setExternalGraph(Algorithm algorithm)	Sets the external graph for the algorithm.
void	R2.setExternalGraph(Algorithm algorithm)	Sets the external graph for the algorithm.
void	R3.setExternalGraph(Algorithm algorithm)	Sets the external graph to be used by the algorithm.
void	Rskew.setExternalGraph(Algorithm algorithm)	Sets the external graph for this algorithm.
void	RskewE.setExternalGraph(Algorithm algorithm)	Sets the external graph for the algorithm.
void	Skew.setExternalGraph(Algorithm algorithm)	Sets the external graph to be used by the algorithm.
void	SkewE.setExternalGraph(Algorithm algorithm)	Sets the external graph to be used by the algorithm.
void	Tanh.setExternalGraph(Algorithm algorithm)	Sets the external graph for the algorithm.

Constructors in edu.cmu.tetrad.algcomparison.algorithm.pairwise with parameters of type Algorithm

Modifier	Constructor	Description
	Eb(Algorithm algorithm)	Constructor for Eb.
	FaskPw(Algorithm algorithm)	Constructor for FaskPw.
	R1(Algorithm algorithm)	Constructor for R1.
	R2(Algorithm algorithm)	Constructor for R2.
	R3(Algorithm algorithm)	Constructor for R3.
	Rskew(Algorithm algorithm)	Constructor for Rskew.
	RskewE(Algorithm algorithm)	Constructor for RskewE.
	Skew(Algorithm algorithm)	Constructor for Skew.
	SkewE(Algorithm algorithm)	Constructor for SkewE.
	Tanh(Algorithm algorithm)	Constructor for Tanh.

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

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

Modifier and Type	Method	Description
void	TakesExternalGraph.setExternalGraph(Algorithm algorithm)	setExternalGraph.

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

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

Modifier and Type	Method	Description
static boolean	GraphSearchUtils.isLatentVariableAlgorithmByAnnotation(Algorithm algorithm)	Checks if the provided algorithm is a latent variable algorithm by inspecting the associated annotation.

Uses of Algorithm in edu.cmu.tetrad.util

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

Modifier and Type	Method	Description
static Set<String>	Params.getAlgorithmParameters(Algorithm algorithm)	getAlgorithmParameters.
static Set<String>	Params.getBootstrappingParameters(Algorithm algorithm)	getBootstrappingParameters.
static Set<String>	Params.getScoreParameters(Algorithm algorithm)	getScoreParameters.
static Set<String>	Params.getTestParameters(Algorithm algorithm)	getTestParameters.