Package edu.cmu.tetrad.search

Class Rfci

java.lang.Object

edu.cmu.tetrad.search.Rfci

All Implemented Interfaces:

IGraphSearch

public final class Rfci
extends Object
implements IGraphSearch

Implements the Really Fast Causal Inference (RFCI) algorithm, which aims to do a correct inference of inferrable causal structure under the assumption that unmeasured common causes of variables in the data may exist. The graph returned is slightly different from the partial ancestral graph (PAG) returned by the FCI algorithm. The goal of of the algorithm is to avoid certain expensive steps in the FCI procedure in a correct way. This was introduced here:

Colombo, D., Maathuis, M. H., Kalisch, M., & Richardson, T. S. (2012). Learning high-dimensional directed acyclic graphs with latent and selection variables. The Annals of Statistics, 294-321.

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

Version:

$Id: $Id

Author:

Erin Korber, June 2004, Alex Smith, December 2008, josephramsey, Choh-Man Teng

See Also:

• Fci
• Knowledge

Constructor Summary

Constructors

Constructor	Description
Rfci(IndependenceTest independenceTest)	Constructs a new RFCI search for the given independence test and background knowledge.
Rfci(IndependenceTest independenceTest, List<Node> searchVars)	Constructs a new RFCI search for the given independence test and background knowledge and a list of variables to search over.

Method Summary

Modifier and Type	Method	Description
long	getElapsedTime()	Returns the elapsed time of the search.
IndependenceTest	getIndependenceTest()	Returns the independence test.
Knowledge	getKnowledge()	Returns the knowledge used in search.
int	getMaxDiscriminatingPathLength()	Returns the maximum length of any discriminating path, or -1 of unlimited.
SepsetMap	getSepsets()	Returns the map from node pairs to sepsets found in search.
boolean	isVerbose()	Returns whether verbose output should be printed.
Graph	search()	Runs the search and returns the RFCI PAG.
Graph	search(IFas fas, List<Node> nodes)	Runs the search and returns the RFCI PAG.
Graph	search(List<Node> nodes)	Searches of a specific sublist of nodes.
void	setDepth(int depth)	Sets the maximum number of variables conditioned on in any test.
void	setKnowledge(Knowledge knowledge)	Sets the knowledge used in search.
void	setMaxDiscriminatingPathLength(int maxDiscriminatingPathLength)	Sets the maximum length of any discriminating path.
void	setVerbose(boolean verbose)	Sets whether verbose output is printed.

Methods inherited from class java.lang.Object

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

Constructor Details

Rfci

public Rfci(IndependenceTest independenceTest)

Constructs a new RFCI search for the given independence test and background knowledge.

Parameters:

independenceTest - a IndependenceTest object

Rfci

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

Constructs a new RFCI search for the given independence test and background knowledge and a list of variables to search over.

Parameters:

independenceTest - a IndependenceTest object

searchVars - a List object

Method Details

search

public Graph search()
             throws InterruptedException

Runs the search and returns the RFCI PAG.

Specified by:

search in interface IGraphSearch

Returns:

This PAG.

Throws:

InterruptedException - if any.

search

public Graph search(List<Node> nodes)
             throws InterruptedException

Searches of a specific sublist of nodes.

Parameters:

nodes - The sublist.

Returns:

The RFCI PAG

Throws:

InterruptedException

search

public Graph search(IFas fas,
 List<Node> nodes)
             throws InterruptedException

Runs the search and returns the RFCI PAG.

Parameters:

fas - The type of FAS to use for the initial step.

nodes - The nodes to search over.

Returns:

The RFCI PAG.

Throws:

InterruptedException

setDepth

public void setDepth(int depth)

Sets the maximum number of variables conditioned on in any test.

Parameters:

depth - This maximum.

getElapsedTime

public long getElapsedTime()

Returns the elapsed time of the search.

Returns:

This time.

getSepsets

public SepsetMap getSepsets()

Returns the map from node pairs to sepsets found in search.

Returns:

This map.

getKnowledge

public Knowledge getKnowledge()

Returns the knowledge used in search.

Returns:

This knowledge.

setKnowledge

public void setKnowledge(Knowledge knowledge)

Sets the knowledge used in search.

Parameters:

knowledge - This knoweldge.

getMaxDiscriminatingPathLength

public int getMaxDiscriminatingPathLength()

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

Returns:

This number.

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.

isVerbose

public boolean isVerbose()

Returns whether verbose output should be printed.

Returns:

True, if so.

setVerbose

public void setVerbose(boolean verbose)

Sets whether verbose output is printed.

Parameters:

verbose - True, if so.

getIndependenceTest

public IndependenceTest getIndependenceTest()

Returns the independence test.

Returns:

This test.