Package edu.cmu.tetrad.search

Class Pcd

java.lang.Object

edu.cmu.tetrad.search.Pcd

All Implemented Interfaces:

IGraphSearch

public class Pcd
extends Object
implements IGraphSearch

Modifies the PC algorithm to handle the deterministic case. Edges removals or orientations based on conditional independence test involving deterministic relationships are not done.

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

Version:

$Id: $Id

Author:

peterspirtes, josephramsey.

See Also:

• Fasd
• Pc
• Knowledge

Constructor Summary

Constructors

Constructor	Description
Pcd(IndependenceTest independenceTest)	Constructs a new PC search using the given independence test as oracle.

Method Summary

Modifier and Type	Method	Description
Set<Edge>	getAdjacencies()	Returns the set of adjacent edges in the graph.
int	getDepth()	Getter for the field depth.
long	getElapsedTime()	Returns the elapsed time in milliseconds since the start of the method.
IndependenceTest	getIndependenceTest()	Retrieves the IndependenceTest used by this method.
Knowledge	getKnowledge()	Retrieves the Knowledge object used by this method.
List<Node>	getNodes()	Retrieves the list of nodes in the graph.
int	getNumIndependenceTests()	Retrieves the number of independence tests performed by the graph search.
SepsetMap	getSepsets()	Getter for the field sepsets.
Set<Triple>	getUnshieldedColliders()	Retrieves the set of unshielded colliders in the graph returned by the method search().
Set<Triple>	getUnshieldedNoncolliders()	Retrieves the set of unshielded noncolliders in the graph returned by the method search().
boolean	isFdr()	True iff the algorithm should be run with False Discovery Rate tests.
boolean	isGuaranteeCpdag()	Returns whether the algorithm should prevent cycles during the search.
boolean	isVerbose()	True iff the algorithm should be run with verbose output.
Graph	search()	Runs PC starting with a complete graph over all nodes of the given conditional independence test, using the given independence test and knowledge and returns the resultant graph.
Graph	search(IFas fas, List<Node> nodes)	Searches for a graph using the given IFas instance and list of nodes.
Graph	search(List<Node> nodes)	Runs PC starting with a complete graph over the given list of nodes, using the given independence test and knowledge and returns the resultant graph.
void	setDepth(int depth)	Sets the depth of the search--that is, the maximum number of conditioning nodes for any conditional independence checked.
void	setFdr(boolean fdr)	Sets whether this test will run with False Discovery Rate tests.
void	setGuaranteeCpdag(boolean guaranteeCpdag)	Sets whether the algorithm should prevent cycles during the search.
void	setKnowledge(Knowledge knowledge)	Sets the knowledge object used by this method.
void	setVerbose(boolean verbose)	Sets whether this test will print verbose output.

Methods inherited from class java.lang.Object

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

Constructor Details

Pcd

public Pcd(IndependenceTest independenceTest)

Constructs a new PC search using the given independence test as oracle.

Parameters:

independenceTest - The oracle for conditional independence facts. This does not make a copy of the independence test, for fear of duplicating the data set!

Method Details

isGuaranteeCpdag

public boolean isGuaranteeCpdag()

Returns whether the algorithm should prevent cycles during the search.

Returns:

true if cycles should be prevented, false otherwise.

setGuaranteeCpdag

public void setGuaranteeCpdag(boolean guaranteeCpdag)

Sets whether the algorithm should prevent cycles during the search.

Parameters:

guaranteeCpdag - true if cycles should be prevented, false otherwise

getIndependenceTest

public IndependenceTest getIndependenceTest()

Retrieves the IndependenceTest used by this method.

Returns:

The IndependenceTest used by this method.

getKnowledge

public Knowledge getKnowledge()

Retrieves the Knowledge object used by this method.

Returns:

The Knowledge object used by this method.

setKnowledge

public void setKnowledge(Knowledge knowledge)

Sets the knowledge object used by this method.

Parameters:

knowledge - The knowledge object used by this method.

Throws:

NullPointerException - if knowledge is null.

getSepsets

public SepsetMap getSepsets()

Getter for the field sepsets.

Returns:

the sepset map from the most recent search. Non-null after the first call to search().

getDepth

public int getDepth()

Getter for the field depth.

Returns:

the current depth of search--that is, the maximum number of conditioning nodes for any conditional independence checked.

setDepth

public void setDepth(int depth)

Sets the depth of the search--that is, the maximum number of conditioning nodes for any conditional independence checked.

Parameters:

depth - The depth of the search. The default is 1000. A value of -1 may be used to indicate that the depth should be high (1000). A value of Integer.MAX_VALUE may not be used due to a bug on multicore machines.

search

public Graph search()
             throws InterruptedException

Runs PC starting with a complete graph over all nodes of the given conditional independence test, using the given independence test and knowledge and returns the resultant graph. The returned graph will be a CPDAG if the independence information is consistent with the hypothesis that there are no latent common causes. It may, however, contain cycles or bidirected edges if this assumption is not born out, either due to the actual presence of latent common causes, or due to statistical errors in conditional independence judgments.

Specified by:

search in interface IGraphSearch

Returns:

a Graph object

Throws:

InterruptedException - if any.

search

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

Runs PC starting with a complete graph over the given list of nodes, using the given independence test and knowledge and returns the resultant graph. The returned graph will be a CPDAG if the independence information is consistent with the hypothesis that there are no latent common causes. It may, however, contain cycles or bidirected edges if this assumption is not born out, either due to the actual presence of latent common causes, or due to statistical errors in conditional independence judgments.

All the given nodes must be in the domain of the given conditional independence test.

Parameters:

nodes - a List object

Returns:

a Graph object

Throws:

InterruptedException

search

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

Searches for a graph using the given IFas instance and list of nodes.

Parameters:

fas - The IFas instance to use for the search.

nodes - The list of nodes to search for.

Returns:

The resultant graph. The returned graph will be a CPDAG if the independence information is consistent with the hypothesis that there are no latent common causes. It may, however, contain cycles or bidirected edges if this assumption is not born out, either due to the actual presence of latent common causes, or due to statistical errors in conditional independence judgments.

Throws:

NullPointerException - If fas is null or if the independence test is null.

IllegalArgumentException - If any of the given nodes is not in the domain of the independence test provided.

InterruptedException

getElapsedTime

public long getElapsedTime()

Returns the elapsed time in milliseconds since the start of the method.

Returns:

the elapsed time in milliseconds

getUnshieldedColliders

public Set<Triple> getUnshieldedColliders()

Retrieves the set of unshielded colliders in the graph returned by the method search().

Returns:

The set of unshielded colliders. Non-null after search() is called.

getUnshieldedNoncolliders

public Set<Triple> getUnshieldedNoncolliders()

Retrieves the set of unshielded noncolliders in the graph returned by the method search().

Returns:

The set of unshielded noncolliders. Non-null after search() is called.

getAdjacencies

public Set<Edge> getAdjacencies()

Returns the set of adjacent edges in the graph.

Returns:

The set of adjacent edges.

getNumIndependenceTests

public int getNumIndependenceTests()

Retrieves the number of independence tests performed by the graph search.

Returns:

The number of independence tests performed.

getNodes

public List<Node> getNodes()

Retrieves the list of nodes in the graph.

Returns:

The list of nodes in the graph.

isVerbose

public boolean isVerbose()

True iff the algorithm should be run with verbose output.

Returns:

True, if so.

setVerbose

public void setVerbose(boolean verbose)

Sets whether this test will print verbose output.

Parameters:

verbose - True, if so.

isFdr

public boolean isFdr()

True iff the algorithm should be run with False Discovery Rate tests.

Returns:

True, if so.

setFdr

public void setFdr(boolean fdr)

Sets whether this test will run with False Discovery Rate tests.

Parameters:

fdr - True, if so.