Package edu.cmu.tetrad.search.work_in_progress

Class SampleVcpcFast

java.lang.Object

edu.cmu.tetrad.search.work_in_progress.SampleVcpcFast

All Implemented Interfaces:

IGraphSearch

public final class SampleVcpcFast
extends Object
implements IGraphSearch

Implements a conservative version of PC, in which the Markov condition is assumed but faithfulness is tested locally.

Version:

$Id: $Id

Author:

josephramsey (this version).

Constructor Summary

Constructors

Constructor	Description
SampleVcpcFast(IndependenceTest independenceTest)	Constructs a CPC algorithm that uses the given independence test as oracle.

Method Summary

Modifier and Type	Method	Description
static void	futureNodeVisit(Graph graph, Node b, LinkedList<Node> path, Set<Node> futureNodes)	futureNodeVisit.
Set<Edge>	getAdjacencies()	getAdjacencies.
Set<Triple>	getAmbiguousTriples()	Getter for the field ambiguousTriples.
Set<Edge>	getApparentNonadjacencies()	getApparentNonadjacencies.
Set<Triple>	getColliderTriples()	Getter for the field colliderTriples.
ICovarianceMatrix	getCov()	getCov.
Set<Edge>	getDefiniteNonadjacencies()	getDefiniteNonadjacencies.
int	getDepth()	Getter for the field depth.
long	getElapsedTime()	Getter for the field elapsedTime.
Graph	getGraph()	The graph that's constructed during the search.
IndependenceTest	getIndependenceTest()	Getter for the field independenceTest.
Knowledge	getKnowledge()	Getter for the field knowledge.
Set<Triple>	getNoncolliderTriples()	Getter for the field noncolliderTriples.
SemIm	getSemIm()	Getter for the field semIm.
SemPm	getSemPm()	Getter for the field semPm.
static boolean	isArrowheadAllowed1(Node from, Node to, Knowledge knowledge)	isArrowheadAllowed1.
boolean	isDoOrientation()	isDoOrientation.
boolean	isGuaranteeCpdag()	isMeekPreventCycles.
Graph	search()	search.
void	setDepth(int depth)	Sets the maximum number of variables conditioned on in any conditional independence test.
void	setGraph(Graph graph)	Setter for the field graph.
void	setKnowledge(Knowledge knowledge)	Sets the knowledge specification used in the search.
void	setMeekPreventCycles(boolean setGuaranteeCpdag)	Sets to true just in case the output is guaranteed to be compatible with a CPDAG--i.e., no bidirected edges and no actual or implied cycles due to the Meek rules.
void	setSemIm(SemIm semIm)	Setter for the field semIm.
void	setSemPm(SemPm semPm)	Setter for the field semPm.
void	setVerbose(boolean verbose)	Setter for the field verbose.

Methods inherited from class java.lang.Object

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

Constructor Details

SampleVcpcFast

public SampleVcpcFast(IndependenceTest independenceTest)

Constructs a CPC algorithm that uses the given independence test as oracle. This does not make a copy of the independence test, for fear of duplicating the data set!

Parameters:

independenceTest - a IndependenceTest object

Method Details

futureNodeVisit

public static void futureNodeVisit(Graph graph,
 Node b,
 LinkedList<Node> path,
 Set<Node> futureNodes)

futureNodeVisit.

Parameters:

graph - a Graph object

b - a Node object

path - a LinkedList object

futureNodes - a Set object

isArrowheadAllowed1

public static boolean isArrowheadAllowed1(Node from,
 Node to,
 Knowledge knowledge)

isArrowheadAllowed1.

Parameters:

from - a Node object

to - a Node object

knowledge - a Knowledge object

Returns:

a boolean

getSemIm

public SemIm getSemIm()

Getter for the field semIm.

Returns:

a SemIm object

setSemIm

public void setSemIm(SemIm semIm)

Setter for the field semIm.

Parameters:

semIm - a SemIm object

isGuaranteeCpdag

public boolean isGuaranteeCpdag()

isMeekPreventCycles.

Returns:

true just in case edges will not be added if they would create cycles.

setMeekPreventCycles

public void setMeekPreventCycles(boolean setGuaranteeCpdag)

Sets to true just in case the output is guaranteed to be compatible with a CPDAG--i.e., no bidirected edges and no actual or implied cycles due to the Meek rules.

Parameters:

setGuaranteeCpdag - a boolean

getElapsedTime

public long getElapsedTime()

Getter for the field elapsedTime.

Returns:

the elapsed time of search in milliseconds, after search() has been run.

getKnowledge

public Knowledge getKnowledge()

Getter for the field knowledge.

Returns:

the knowledge specification used in the search. Non-null.

setKnowledge

public void setKnowledge(Knowledge knowledge)

Sets the knowledge specification used in the search. Non-null.

Parameters:

knowledge - a Knowledge object

getIndependenceTest

public IndependenceTest getIndependenceTest()

Getter for the field independenceTest.

Returns:

the independence test used in the search, set in the constructor. This is not returning a copy, for fear of duplicating the data set!

getDepth

public int getDepth()

Getter for the field depth.

Returns:

the depth of the search--that is, the maximum number of variables conditioned on in any conditional independence test.

setDepth

public void setDepth(int depth)

Sets the maximum number of variables conditioned on in any conditional independence test. If set to -1, the value of 1000 will be used. May not be set to Integer.MAX_VALUE, due to a Java bug on multi-core systems.

Parameters:

depth - a int

getAmbiguousTriples

public Set<Triple> getAmbiguousTriples()

Getter for the field ambiguousTriples.

Returns:

the set of ambiguous triples found during the most recent run of the algorithm. Non-null after a call to search().

getColliderTriples

public Set<Triple> getColliderTriples()

Getter for the field colliderTriples.

Returns:

the set of collider triples found during the most recent run of the algorithm. Non-null after a call to search().

getNoncolliderTriples

public Set<Triple> getNoncolliderTriples()

Getter for the field noncolliderTriples.

Returns:

the set of noncollider triples found during the most recent run of the algorithm. Non-null after a call to search().

getAdjacencies

public Set<Edge> getAdjacencies()

getAdjacencies.

Returns:

a Set object

getApparentNonadjacencies

public Set<Edge> getApparentNonadjacencies()

getApparentNonadjacencies.

Returns:

a Set object

getDefiniteNonadjacencies

public Set<Edge> getDefiniteNonadjacencies()

getDefiniteNonadjacencies.

Returns:

a Set object

search

public Graph search()
             throws InterruptedException

search.

Specified by:

search in interface IGraphSearch

Returns:

a Graph object

Throws:

InterruptedException - if any.

getCov

public ICovarianceMatrix getCov()

getCov.

Returns:

a ICovarianceMatrix object

isDoOrientation

public boolean isDoOrientation()

isDoOrientation.

Returns:

a boolean

getGraph

public Graph getGraph()

The graph that's constructed during the search.

Returns:

a Graph object

setGraph

public void setGraph(Graph graph)

Setter for the field graph.

Parameters:

graph - a Graph object

setVerbose

public void setVerbose(boolean verbose)

Setter for the field verbose.

Parameters:

verbose - a boolean

getSemPm

public SemPm getSemPm()

Getter for the field semPm.

Returns:

a SemPm object

setSemPm

public void setSemPm(SemPm semPm)

Setter for the field semPm.

Parameters:

semPm - a SemPm object