Package edu.cmu.tetrad.search.utils

Class FgesOrienter

java.lang.Object

edu.cmu.tetrad.search.utils.FgesOrienter

All Implemented Interfaces:

IGraphSearch, DagScorer

public final class FgesOrienter
extends Object
implements IGraphSearch, DagScorer

This Orients a given undirected graph such that the edges in the graph are a superset of the edges in the oriented graph, using FGES method.

Version:

$Id: $Id

Author:

AJ Sedgewick, 5/2015

See Also:

• Fges

Constructor Summary

Constructors

Constructor	Description
FgesOrienter(DataSet dataSet)	The data set must either be all continuous or all discrete.

Method Summary

Modifier and Type	Method	Description
Graph	getAdjacencies()	Getter for the field adjacencies.
int	getDepth()	Getter for the field depth.
DiscreteScore	getDiscreteScore()	getDiscreteScore.
long	getElapsedTime()	Getter for the field elapsedTime.
Graph	getExternalGraph()	Getter for the field externalGraph.
Knowledge	getKnowledge()	Getter for the field knowledge.
PrintStream	getOut()	Getter for the field out.
double	getPenaltyDiscount()	For BIC score, a multiplier on the penalty term.
double	getScore(Graph dag)	getScore.
boolean	isFaithfulnessAssumed()	isFaithfulnessAssumed.
boolean	isLog()	True iff log output should be produced.
void	orient(Graph graph)	orient.
double	scoreDag(Graph dag)	scoreDag.
Graph	search()	Greedy equivalence search: Start from the empty graph, add edges till model is significant.
void	setAdjacencies(Graph adjacencies)	Sets the set of preset adjacenies for the algorithm; edges not in this adjacencies graph will not be added.
void	setDepth(int depth)	-1 for unlimited depth, otherwise a number >= 0.
void	setDiscreteScore(DiscreteScore DiscreteScore)	Sets the discrete scoring function to use.
void	setExternalGraph(Graph externalGraph)	Sets the initial graph.
void	setFaithfulnessAssumed(boolean faithfulness)	Set to true if it is assumed that all path pairs with one length 1 path do not cancelAll.
void	setKnowledge(Knowledge knowledge)	Sets the background knowledge.
void	setLog(boolean log)	Sets whether log output should be produced.
void	setOut(PrintStream out)	Sets the output stream that output (except for log output) should be sent to.
void	setPenaltyDiscount(double penaltyDiscount)	For BIC score, a multiplier on the penalty term.
void	setSamplePrior(double samplePrior)	For BDeu score for discrete search; see Chickering (2002).
void	setStructurePrior(double structurePrior)	For BDeu score for discrete search; see Chickering (2002).
void	setTrueGraph(Graph trueGraph)	If the true graph is set, askterisks will be printed in log output for the true edges.
void	setVerbose(boolean verbose)	Sets whether verbose output should be produced.

Methods inherited from class java.lang.Object

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

Constructor Details

FgesOrienter

public FgesOrienter(DataSet dataSet)

The data set must either be all continuous or all discrete.

Parameters:

dataSet - a DataSet object

Method Details

orient

public void orient(Graph graph)

orient.

Parameters:

graph - a Graph object

isFaithfulnessAssumed

public boolean isFaithfulnessAssumed()

isFaithfulnessAssumed.

Returns:

true if it is assumed that all path pairs with one length 1 path do not cancelAll.

setFaithfulnessAssumed

public void setFaithfulnessAssumed(boolean faithfulness)

Set to true if it is assumed that all path pairs with one length 1 path do not cancelAll.

Parameters:

faithfulness - a boolean

search

public Graph search()

Greedy equivalence search: Start from the empty graph, add edges till model is significant. Then start deleting edges till a minimum is achieved.

Specified by:

search in interface IGraphSearch

Returns:

the resulting CPDAG.

getKnowledge

public Knowledge getKnowledge()

Getter for the field knowledge.

Returns:

the background knowledge.

setKnowledge

public void setKnowledge(Knowledge knowledge)

Sets the background knowledge.

Parameters:

knowledge - the knowledge object, specifying forbidden and required edges.

setStructurePrior

public void setStructurePrior(double structurePrior)

For BDeu score for discrete search; see Chickering (2002).

Parameters:

structurePrior - a double

setSamplePrior

public void setSamplePrior(double samplePrior)

For BDeu score for discrete search; see Chickering (2002).

Parameters:

samplePrior - a double

getElapsedTime

public long getElapsedTime()

Getter for the field elapsedTime.

Returns:

a long

getPenaltyDiscount

public double getPenaltyDiscount()

For BIC score, a multiplier on the penalty term. For continuous searches.

Returns:

a double

setPenaltyDiscount

public void setPenaltyDiscount(double penaltyDiscount)

For BIC score, a multiplier on the penalty term. For continuous searches.

Parameters:

penaltyDiscount - a double

setTrueGraph

public void setTrueGraph(Graph trueGraph)

If the true graph is set, askterisks will be printed in log output for the true edges.

Parameters:

trueGraph - a Graph object

getScore

public double getScore(Graph dag)

getScore.

Parameters:

dag - a Graph object

Returns:

the score of the given DAG, up to a constant.

getDiscreteScore

public DiscreteScore getDiscreteScore()

getDiscreteScore.

Returns:

the discrete scoring function being used. By default, BDeu.

setDiscreteScore

public void setDiscreteScore(DiscreteScore DiscreteScore)

Sets the discrete scoring function to use.

Parameters:

DiscreteScore - a DiscreteScore object

isLog

public boolean isLog()

True iff log output should be produced.

Returns:

a boolean

setLog

public void setLog(boolean log)

Sets whether log output should be produced. Set to false a faster search.

Parameters:

log - a boolean

getExternalGraph

public Graph getExternalGraph()

Getter for the field externalGraph.

Returns:

the initial graph for the search. The search is initialized to this graph and proceeds from there.

setExternalGraph

public void setExternalGraph(Graph externalGraph)

Sets the initial graph.

Parameters:

externalGraph - a Graph object

setVerbose

public void setVerbose(boolean verbose)

Sets whether verbose output should be produced.

Parameters:

verbose - a boolean

getOut

public PrintStream getOut()

Getter for the field out.

Returns:

the output stream that output (except for log output) should be sent to.

setOut

public void setOut(PrintStream out)

Sets the output stream that output (except for log output) should be sent to. By detault System.out.

Parameters:

out - a PrintStream object

getAdjacencies

public Graph getAdjacencies()

Getter for the field adjacencies.

Returns:

the set of preset adjacenies for the algorithm; edges not in this adjacencies graph will not be added.

setAdjacencies

public void setAdjacencies(Graph adjacencies)

Sets the set of preset adjacenies for the algorithm; edges not in this adjacencies graph will not be added.

Parameters:

adjacencies - a Graph object

getDepth

public int getDepth()

Getter for the field depth.

Returns:

the depth for the forward reevaluation step.

setDepth

public void setDepth(int depth)

-1 for unlimited depth, otherwise a number >= 0. In the forward reevaluation step, subsets of neighbors up to depth in size are considered. Limiting depth can speed up the algorithm.

Parameters:

depth - a int

scoreDag

public double scoreDag(Graph dag)

scoreDag.

Scores the given DAG, up to a constant.

Specified by:

scoreDag in interface DagScorer

Parameters:

dag - a Graph object

Returns:

a double