Package edu.cmu.tetrad.algcomparison.algorithm.oracle.pag

Class Bfci

java.lang.Object

edu.cmu.tetrad.algcomparison.algorithm.AbstractBootstrapAlgorithm

edu.cmu.tetrad.algcomparison.algorithm.oracle.pag.Bfci

All Implemented Interfaces:

Algorithm, ReturnsBootstrapGraphs, TakesCovarianceMatrix, HasKnowledge, HasParameters, TakesIndependenceWrapper, UsesScoreWrapper, TetradSerializable, Serializable

@Algorithm(name="BFCI",
           command="bfci",
           algoType=allow_latent_common_causes)
@Bootstrapping
public class Bfci
extends AbstractBootstrapAlgorithm
implements Algorithm, UsesScoreWrapper, TakesIndependenceWrapper, HasKnowledge, ReturnsBootstrapGraphs, TakesCovarianceMatrix

Adjusts GFCI to use a permutation algorithm (such as BOSS-Tuck) to do the initial steps of finding adjacencies and unshielded colliders.

GFCI reference is this:

J.M. Ogarrio and P. Spirtes and J. Ramsey, "A Hybrid Causal Search Algorithm for Latent Variable Models," JMLR 2016.

Version:

$Id: $Id

Author:

josephramsey

See Also:

• Serialized Form

Constructor Summary

Constructors

Constructor	Description
Bfci()	No-arg constructor.
Bfci(IndependenceWrapper test, ScoreWrapper score)	Constructs a new BFCI algorithm using the given test and score.

Method Summary

Modifier and Type	Method	Description
Graph	getComparisonGraph(Graph graph)	Retrieves the comparison graph generated by applying the DAG-to-PAG transformation to the given true directed graph.
DataType	getDataType()	Retrieves the data type that the search requires, whether continuous, discrete, or mixed.
String	getDescription()	Returns a description of the BFCI (Best-order FCI) algorithm using the description of its independence test and score.
IndependenceWrapper	getIndependenceWrapper()	Returns the IndependenceWrapper associated with this Bfci algorithm.
Knowledge	getKnowledge()	Retrieves the knowledge associated with the algorithm.
List<String>	getParameters()	Retrieves the list of parameters used for the BFCI (Best-order FCI) algorithm.
ScoreWrapper	getScoreWrapper()	Retrieves the ScoreWrapper associated with this algorithm.
Graph	runSearch(DataModel dataModel, Parameters parameters)	Runs the search algorithm using the given dataset and parameters and returns the resulting graph.
void	setIndependenceWrapper(IndependenceWrapper test)	Sets the IndependenceWrapper object for this algorithm.
void	setKnowledge(Knowledge knowledge)	Sets the knowledge associated with the algorithm.
void	setScoreWrapper(ScoreWrapper score)	Sets the score wrapper for this algorithm.

Methods inherited from class edu.cmu.tetrad.algcomparison.algorithm.AbstractBootstrapAlgorithm

getBootstrapGraphs, search

Methods inherited from class java.lang.Object

equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Methods inherited from interface edu.cmu.tetrad.algcomparison.algorithm.Algorithm

search

Methods inherited from interface edu.cmu.tetrad.algcomparison.algorithm.ReturnsBootstrapGraphs

getBootstrapGraphs

Constructor Details

Bfci

public Bfci()

No-arg constructor. Used for reflection; do not delete.

Bfci

public Bfci(IndependenceWrapper test,
 ScoreWrapper score)

Constructs a new BFCI algorithm using the given test and score.

Parameters:

test - the independence test to use

score - the score to use

Method Details

runSearch

public Graph runSearch(DataModel dataModel,
 Parameters parameters)
                throws InterruptedException

Runs the search algorithm using the given dataset and parameters and returns the resulting graph.

Parameters:

dataModel - the data model to run the search on

parameters - the parameters used for the search algorithm

Returns:

the graph resulting from the search algorithm

Throws:

InterruptedException

getComparisonGraph

public Graph getComparisonGraph(Graph graph)

Retrieves the comparison graph generated by applying the DAG-to-PAG transformation to the given true directed graph.

Specified by:

getComparisonGraph in interface Algorithm

Parameters:

graph - The true directed graph, if there is one.

Returns:

The comparison graph generated by applying the DAG-to-PAG transformation.

getDescription

public String getDescription()

Returns a description of the BFCI (Best-order FCI) algorithm using the description of its independence test and score.

Specified by:

getDescription in interface Algorithm

Returns:

The description of the algorithm.

getDataType

public DataType getDataType()

Retrieves the data type that the search requires, whether continuous, discrete, or mixed.

Specified by:

getDataType in interface Algorithm

Returns:

the data type required by the search algorithm

getParameters

public List<String> getParameters()

Retrieves the list of parameters used for the BFCI (Best-order FCI) algorithm.

Specified by:

getParameters in interface HasParameters

Returns:

the list of parameters used for the BFCI algorithm

getKnowledge

public Knowledge getKnowledge()

Retrieves the knowledge associated with the algorithm.

Specified by:

getKnowledge in interface HasKnowledge

Returns:

the knowledge associated with the algorithm

setKnowledge

public void setKnowledge(Knowledge knowledge)

Sets the knowledge associated with the algorithm.

Specified by:

setKnowledge in interface HasKnowledge

Parameters:

knowledge - a knowledge object

getIndependenceWrapper

public IndependenceWrapper getIndependenceWrapper()

Returns the IndependenceWrapper associated with this Bfci algorithm.

Specified by:

getIndependenceWrapper in interface TakesIndependenceWrapper

Returns:

the IndependenceWrapper object

setIndependenceWrapper

public void setIndependenceWrapper(IndependenceWrapper test)

Sets the IndependenceWrapper object for this algorithm.

Specified by:

setIndependenceWrapper in interface TakesIndependenceWrapper

Parameters:

test - the IndependenceWrapper object to set

getScoreWrapper

public ScoreWrapper getScoreWrapper()

Retrieves the ScoreWrapper associated with this algorithm.

Specified by:

getScoreWrapper in interface UsesScoreWrapper

Returns:

The ScoreWrapper object.

setScoreWrapper

public void setScoreWrapper(ScoreWrapper score)

Sets the score wrapper for this algorithm.

Specified by:

setScoreWrapper in interface UsesScoreWrapper

Parameters:

score - the score wrapper to set