Package edu.cmu.tetrad.search.utils

Class PcCommon

java.lang.Object

edu.cmu.tetrad.search.utils.PcCommon

All Implemented Interfaces:

IGraphSearch

public final class PcCommon
extends Object
implements IGraphSearch

Provides some common implementation pieces of various PC-like algorithms, with options for collider discovery type, FAS type, and conflict rule.

Version:

$Id: $Id

Author:

josephramsey

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
static enum	PcCommon.ColliderDiscovery	Gives the options for the collider discovery algorithm to use--FAS with sepsets reasoning, FAS with conservative reasoning, or FAS with Max P reasoning.
static enum	PcCommon.ConflictRule	Gives the type of conflict to be used, priority (when there is a conflict, keep the orientation that has already been made), bidirected (when there is a conflict, orient a bidirected edge), or overwrite (when there is a conflict, use the new orientation).
static enum	PcCommon.FasType	Gives the type of FAS used, regular or stable.
static enum	PcCommon.PcHeuristicType	The PC heuristic type, where this is taken from Causation, Prediction, and Search.

Constructor Summary

Constructors

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

Method Summary

Modifier and Type	Method	Description
static boolean	colliderAllowed(Graph graph, Node x, Node y, Node z, Knowledge knowledge)	Checks if colliders are allowed based on the given knowledge.
Set<Edge>	getAdjacencies()	Returns The edges in the search graph.
Set<Triple>	getAmbiguousTriples()	Getter for the field ambiguousTriples.
Set<Triple>	getColliderTriples()	Getter for the field colliderTriples.
int	getDepth()	Getter for the field depth.
long	getElapsedTime()	Getter for the field elapsedTime.
IndependenceTest	getIndependenceTest()	Getter for the field independenceTest.
Knowledge	getKnowledge()	Getter for the field knowledge.
Set<Triple>	getNoncolliderTriples()	Getter for the field noncolliderTriples.
boolean	isGuaranteeCpdag()	Checks if the current object guarantees a complete directed acyclic graph (CPDAG).
static void	orientCollider(Node x, Node y, Node z, PcCommon.ConflictRule conflictRule, Graph graph, boolean verbose)	Orient a single unshielded triple, x*-*y*-*z, in a graph.
Graph	search()	Runs the search and returns the search graph.
Graph	search(List<Node> nodes)	Runs the search over the given list of nodes only, returning the search graph.
void	setColliderDiscovery(PcCommon.ColliderDiscovery colliderDiscovery)	Sets the type of collider discovery to do.
void	setConflictRule(PcCommon.ConflictRule conflictRule)	Sets the conflict rule to use.
void	setDepth(int depth)	Sets the maximum number of variables conditioned on in any conditional independence test.
void	setFasType(PcCommon.FasType fasType)	Setter for the field fasType.
void	setGuaranteeCpdag(boolean guaranteeCpdag)	Sets to true just in case edges will not be added if they create cycles.
void	setKnowledge(Knowledge knowledge)	Sets the knowledge specification used in the search.
void	setMaxDiscriminatingPathLength(int maxDiscriminatingPathLength)	Setter for the field maxPathLength.
void	setPcHeuristicType(PcCommon.PcHeuristicType pcHeuristic)	Setter for the field pcHeuristicType.
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

PcCommon

public PcCommon(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 - The independence test to use.

Method Details

orientCollider

public static void orientCollider(Node x,
 Node y,
 Node z,
 PcCommon.ConflictRule conflictRule,
 Graph graph,
 boolean verbose)

Orient a single unshielded triple, x*-*y*-*z, in a graph.

Parameters:

x - a Node object

y - a Node object

z - a Node object

conflictRule - The conflict rule to use.

graph - The graph to orient.

verbose - If verbose output should be printed.

See Also:

• PcCommon.ConflictRule

colliderAllowed

public static boolean colliderAllowed(Graph graph,
 Node x,
 Node y,
 Node z,
 Knowledge knowledge)

Checks if colliders are allowed based on the given knowledge.

Parameters:

graph - The graph containing the nodes.

x - The first node.

y - The second node.

z - The third node.

knowledge - The knowledge object containing the required and forbidden relationships.

Returns:

True if colliders are allowed based on the given knowledge, false otherwise.

setMaxDiscriminatingPathLength

public void setMaxDiscriminatingPathLength(int maxDiscriminatingPathLength)

Setter for the field maxPathLength.

Parameters:

maxDiscriminatingPathLength - The max path length for the max p collider orientation heuristic.

setFasType

public void setFasType(PcCommon.FasType fasType)

Setter for the field fasType.

Parameters:

fasType - The type of FAS to be used.

setPcHeuristicType

public void setPcHeuristicType(PcCommon.PcHeuristicType pcHeuristic)

Setter for the field pcHeuristicType.

Parameters:

pcHeuristic - Which PC heuristic to use (see Causation, Prediction and Search). Default is PcHeuristicType.NONE.

See Also:

• PcCommon.PcHeuristicType

isGuaranteeCpdag

public boolean isGuaranteeCpdag()

Checks if the current object guarantees a complete directed acyclic graph (CPDAG).

Returns:

true if the current object guarantees a CPDAG, false otherwise.

setGuaranteeCpdag

public void setGuaranteeCpdag(boolean guaranteeCpdag)

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

Parameters:

guaranteeCpdag - True, just in the output will guarantee a CPDAG.

search

public Graph search()
             throws InterruptedException

Runs the search and returns the search graph.

Specified by:

search in interface IGraphSearch

Returns:

This result graph.

Throws:

InterruptedException - if any.

search

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

Runs the search over the given list of nodes only, returning the search graph.

Parameters:

nodes - The nodes to search over.

Returns:

The result graph.

Throws:

InterruptedException

setColliderDiscovery

public void setColliderDiscovery(PcCommon.ColliderDiscovery colliderDiscovery)

Sets the type of collider discovery to do.

Parameters:

colliderDiscovery - This type.

setConflictRule

public void setConflictRule(PcCommon.ConflictRule conflictRule)

Sets the conflict rule to use.

Parameters:

conflictRule - This rule.

See Also:

• PcCommon.ConflictRule

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 multicore systems.

Parameters:

depth - The depth.

setVerbose

public void setVerbose(boolean verbose)

Sets whether verbose output should be printed.

Parameters:

verbose - True iff the case.

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()

Returns The edges in the search graph.

Returns:

These edges.