Package edu.cmu.tetrad.search

Class Fci

java.lang.Object

edu.cmu.tetrad.search.Fci

All Implemented Interfaces:

IGraphSearch

public final class Fci
extends Object
implements IGraphSearch

Implements the Fast Causal Inference (FCI) algorithm due to Peter Spirtes, which addressed the case where latent common causes cannot be assumed not to exist with respect to the data set being analyzed. That is, it is assumed that there may be variables that are not included in the data that nonetheless may be causes of two or more variables that are included in data.

Two alternatives are provided for doing the final orientation step, one due to Peter Spirtes, which is arrow complete, and another due to Jiji Zhang, which is arrow and tail complete.

This algorithm, with the Spirtes final orientation rules, was given in an earlier version of this book:

Spirtes, P., Glymour, C. N., Scheines, R., & Heckerman, D. (2000). Causation, prediction, and search. MIT press.

The algorithm with the Zhang final orientation rules was given in this reference:

Zhang, J. (2008). On the completeness of orientation rules for causal discovery in the presence of latent confounders and selection bias. Artificial Intelligence, 172(16-17), 1873-1896.

This class is configured to respect knowledge of forbidden and required edges, including knowledge of temporal tiers.

Version:

$Id: $Id

Author:

peterspirtes, clarkglymour, jijizhang, josephramsey

See Also:

• FciOrient
• Pc
• Fas
• Knowledge

Constructor Summary

Constructors

Constructor	Description
Fci(IndependenceTest independenceTest)	Constructor.
Fci(IndependenceTest independenceTest, List<Node> searchVars)	Constructor.

Method Summary

Modifier and Type	Method	Description
long	getElapsedTime()	Returns the elapsed time of search.
IndependenceTest	getIndependenceTest()	Returns the independence test used in search.
Knowledge	getKnowledge()	Returns the background knowledge that was set.
SepsetMap	getSepsets()	Returns the sepset map from FAS.
Graph	search()	Performs a search using the FCI algorithm.
void	setCompleteRuleSetUsed(boolean completeRuleSetUsed)	Sets whether the Zhang complete rule set should be used; false if only R1-R4 (the rule set of the original FCI) should be used.
void	setDepth(int depth)	Sets the depth of search, which is the maximum number of variables conditioned on in any test.
void	setGuaranteePag(boolean guaranteePag)	Sets whether to guarantee the output is a PAG by repairing a faulty PAG.
void	setKnowledge(Knowledge knowledge)	Sets background knowledge for the search.
void	setMaxDiscriminatingPathLength(int maxDiscriminatingPathLength)	Sets the maximum length of any discriminating path.
void	setPcHeuristicType(PcCommon.PcHeuristicType heuristic)	Sets which PC heuristic type should be used in the initial adjacency search.
void	setPossibleDsepSearchDone(boolean possibleMsepSearchDone)	Sets whether the (time-consuming) possible msep step should be done.
void	setStable(boolean stable)	Sets whether the stable options should be used in the initial adjacency search.
void	setVerbose(boolean verbose)	Sets whether verbose output should be printed.

Methods inherited from class java.lang.Object

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

Constructor Details

Fci

public Fci(IndependenceTest independenceTest)

Constructor.

Parameters:

independenceTest - The test to use for oracle conditional independence information.

Fci

public Fci(IndependenceTest independenceTest,
 List<Node> searchVars)

Constructor.

Parameters:

independenceTest - The test to use for oracle conditional independence information.

searchVars - A specific list of variables to search over.

Method Details

search

public Graph search()
             throws InterruptedException

Performs a search using the FCI algorithm.

Specified by:

search in interface IGraphSearch

Returns:

The resulting graph.

Throws:

InterruptedException - if any.

setDepth

public void setDepth(int depth)

Sets the depth of search, which is the maximum number of variables conditioned on in any test.

Parameters:

depth - This maximum.

getElapsedTime

public long getElapsedTime()

Returns the elapsed time of search.

Returns:

This time.

getSepsets

public SepsetMap getSepsets()

Returns the sepset map from FAS.

Returns:

This map.

See Also:

• SepsetMap

getKnowledge

public Knowledge getKnowledge()

Returns the background knowledge that was set.

Returns:

This knowledge.

setKnowledge

public void setKnowledge(Knowledge knowledge)

Sets background knowledge for the search.

Parameters:

knowledge - This knowledge.

setCompleteRuleSetUsed

public void setCompleteRuleSetUsed(boolean completeRuleSetUsed)

Sets whether the Zhang complete rule set should be used; false if only R1-R4 (the rule set of the original FCI) should be used. False by default.

Parameters:

completeRuleSetUsed - True for the complete Zhang rule set.

setPossibleDsepSearchDone

public void setPossibleDsepSearchDone(boolean possibleMsepSearchDone)

Sets whether the (time-consuming) possible msep step should be done.

Parameters:

possibleMsepSearchDone - True, if so.

setMaxDiscriminatingPathLength

public void setMaxDiscriminatingPathLength(int maxDiscriminatingPathLength)

Sets the maximum length of any discriminating path.

Parameters:

maxDiscriminatingPathLength - the maximum length of any discriminating path, or -1 if unlimited.

setVerbose

public void setVerbose(boolean verbose)

Sets whether verbose output should be printed.

Parameters:

verbose - True, if so.

getIndependenceTest

public IndependenceTest getIndependenceTest()

Returns the independence test used in search.

Returns:

This test.

setPcHeuristicType

public void setPcHeuristicType(PcCommon.PcHeuristicType heuristic)

Sets which PC heuristic type should be used in the initial adjacency search.

Parameters:

heuristic - The heuristic type.

See Also:

• PcCommon.PcHeuristicType

setStable

public void setStable(boolean stable)

Sets whether the stable options should be used in the initial adjacency search.

Parameters:

stable - True, if so.

See Also:

• Pc

setGuaranteePag

public void setGuaranteePag(boolean guaranteePag)

Sets whether to guarantee the output is a PAG by repairing a faulty PAG.

Parameters:

guaranteePag - True, if so.