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

Class Bfci

java.lang.Object

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

All Implemented Interfaces:

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

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

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
List<Graph>	getBootstrapGraphs()	Returns the bootstrap graphs.
Graph	getComparisonGraph(Graph graph)	Returns that graph that the result should be compared to.
DataType	getDataType()	Returns the data type that the search requires, whether continuous, discrete, or mixed.
String	getDescription()	Returns a short, one-line description of this algorithm.
IndependenceWrapper	getIndependenceWrapper()	Returns the independence wrapper.
Knowledge	getKnowledge()	Returns a knowledge object.
List<String>	getParameters()	Returns the parameters that this search uses.
ScoreWrapper	getScoreWrapper()	Returns the score wrapper.
Graph	search(DataModel dataModel, Parameters parameters)	Runs the search.
void	setIndependenceWrapper(IndependenceWrapper test)	Sets the independence wrapper.
void	setKnowledge(Knowledge knowledge)	Sets a knowledge object.
void	setScoreWrapper(ScoreWrapper score)	Sets the score wrapper.

Methods inherited from class java.lang.Object

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

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

search

public Graph search(DataModel dataModel,
 Parameters parameters)

Runs the search.

Specified by:

search in interface Algorithm

Parameters:

dataModel - The data set to run to the search on.

parameters - The paramters of the search.

Returns:

The result graph.

getComparisonGraph

public Graph getComparisonGraph(Graph graph)

Returns that graph that the result should be compared to.

Specified by:

getComparisonGraph in interface Algorithm

Parameters:

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

Returns:

The comparison graph.

getDescription

public String getDescription()

Returns a short, one-line description of this algorithm. This will be printed in the report.

Specified by:

getDescription in interface Algorithm

Returns:

This description.

getDataType

public DataType getDataType()

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

Specified by:

getDataType in interface Algorithm

Returns:

This type.

getParameters

public List<String> getParameters()

Returns the parameters that this search uses.

Specified by:

getParameters in interface Algorithm

Specified by:

getParameters in interface HasParameters

Returns:

A list of String names of parameters.

getKnowledge

public Knowledge getKnowledge()

Returns a knowledge object.

Specified by:

getKnowledge in interface HasKnowledge

Returns:

a knowledge object.

setKnowledge

public void setKnowledge(Knowledge knowledge)

Sets a knowledge object.

Specified by:

setKnowledge in interface HasKnowledge

Parameters:

knowledge - a knowledge object.

getIndependenceWrapper

public IndependenceWrapper getIndependenceWrapper()

Returns the independence wrapper.

Specified by:

getIndependenceWrapper in interface TakesIndependenceWrapper

Returns:

the independence wrapper.

setIndependenceWrapper

public void setIndependenceWrapper(IndependenceWrapper test)

Sets the independence wrapper.

Specified by:

setIndependenceWrapper in interface TakesIndependenceWrapper

Parameters:

test - the independence wrapper.

getScoreWrapper

public ScoreWrapper getScoreWrapper()

Returns the score wrapper.

Specified by:

getScoreWrapper in interface UsesScoreWrapper

Returns:

the score wrapper.

setScoreWrapper

public void setScoreWrapper(ScoreWrapper score)

Sets the score wrapper.

Specified by:

setScoreWrapper in interface UsesScoreWrapper

Parameters:

score - the score wrapper.

getBootstrapGraphs

public List<Graph> getBootstrapGraphs()

Returns the bootstrap graphs.

Specified by:

getBootstrapGraphs in interface ReturnsBootstrapGraphs

Returns:

the bootstrap graphs.