Package edu.cmu.tetrad.algcomparison.algorithm.oracle.pag

Class GraspFci

java.lang.Object

edu.cmu.tetrad.algcomparison.algorithm.AbstractBootstrapAlgorithm

edu.cmu.tetrad.algcomparison.algorithm.oracle.pag.GraspFci

All Implemented Interfaces:

Algorithm, ReturnsBootstrapGraphs, TakesCovarianceMatrix, HasKnowledge, HasParameters, TakesIndependenceWrapper, UsesScoreWrapper, TetradSerializable, Serializable

@Algorithm(name="GRASP-FCI",
           command="grasp-fci",
           algoType=allow_latent_common_causes)
@Bootstrapping
public class GraspFci
extends AbstractBootstrapAlgorithm
implements Algorithm, UsesScoreWrapper, TakesIndependenceWrapper, HasKnowledge, ReturnsBootstrapGraphs, TakesCovarianceMatrix

Adjusts GFCI to use a permutation algorithm (such as BOSS-Tuck) to do the initial steps of finding adjacencies and unshielded colliders.

GFCI reference is this:

J.M. Ogarrio and P. Spirtes and J. Ramsey, "A Hybrid Causal Search Algorithm for Latent Variable Models," JMLR 2016.

Version:

$Id: $Id

Author:

josephramsey

See Also:

• Serialized Form

Constructor Summary

Constructors

Constructor	Description
GraspFci()	Constructor for GraspFci.
GraspFci(IndependenceWrapper test, ScoreWrapper score)	Constructor for GraspFci.

Method Summary

Modifier and Type	Method	Description
Graph	getComparisonGraph(Graph graph)	Retrieves a comparison graph by transforming a true directed graph into a partially directed graph (PAG).
DataType	getDataType()	Retrieves the data type required by the search algorithm.
String	getDescription()	Returns a short, one-line description of this algorithm.
IndependenceWrapper	getIndependenceWrapper()	Retrieves the IndependenceWrapper object associated with this method.
Knowledge	getKnowledge()	Retrieves the knowledge object associated with this method.
List<String>	getParameters()	Retrieves the list of parameters used by the algorithm.
ScoreWrapper	getScoreWrapper()	Retrieves the ScoreWrapper object associated with this method.
Graph	runSearch(DataModel dataModel, Parameters parameters)	Runs a search algorithm to find a graph structure based on a given data set and parameters.
void	setIndependenceWrapper(IndependenceWrapper test)	Sets the independence wrapper.
void	setKnowledge(Knowledge knowledge)	Sets the knowledge object associated with this method.
void	setScoreWrapper(ScoreWrapper score)	Sets the score wrapper for the algorithm.

Methods inherited from class edu.cmu.tetrad.algcomparison.algorithm.AbstractBootstrapAlgorithm

getBootstrapGraphs, search

Methods inherited from class java.lang.Object

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

Methods inherited from interface edu.cmu.tetrad.algcomparison.algorithm.Algorithm

search

Methods inherited from interface edu.cmu.tetrad.algcomparison.algorithm.ReturnsBootstrapGraphs

getBootstrapGraphs

Constructor Details

GraspFci

public GraspFci()

Constructor for GraspFci.

GraspFci

public GraspFci(IndependenceWrapper test,
 ScoreWrapper score)

Constructor for GraspFci.

Parameters:

test - a IndependenceWrapper object

score - a ScoreWrapper object

Method Details

runSearch

public Graph runSearch(DataModel dataModel,
 Parameters parameters)
                throws InterruptedException

Runs a search algorithm to find a graph structure based on a given data set and parameters.

Parameters:

dataModel - the data set to be used for the search algorithm

parameters - the parameters for the search algorithm

Returns:

the graph structure found by the search algorithm

Throws:

InterruptedException

getComparisonGraph

public Graph getComparisonGraph(Graph graph)

Retrieves a comparison graph by transforming a true directed graph into a partially directed graph (PAG).

Specified by:

getComparisonGraph in interface Algorithm

Parameters:

graph - The true directed graph, if there is one.

Returns:

The comparison graph.

getDescription

public String getDescription()

Returns a short, one-line description of this algorithm. The description is generated by concatenating the descriptions of the test and score objects associated with this algorithm.

Specified by:

getDescription in interface Algorithm

Returns:

The description of this algorithm.

getDataType

public DataType getDataType()

Retrieves the data type required by the search algorithm.

Specified by:

getDataType in interface Algorithm

Returns:

The data type required by the search algorithm.

getParameters

public List<String> getParameters()

Retrieves the list of parameters used by the algorithm.

Specified by:

getParameters in interface HasParameters

Returns:

The list of parameters used by the algorithm.

getKnowledge

public Knowledge getKnowledge()

Retrieves the knowledge object associated with this method.

Specified by:

getKnowledge in interface HasKnowledge

Returns:

The knowledge object.

setKnowledge

public void setKnowledge(Knowledge knowledge)

Sets the knowledge object associated with this method.

Specified by:

setKnowledge in interface HasKnowledge

Parameters:

knowledge - the knowledge object to be set

getIndependenceWrapper

public IndependenceWrapper getIndependenceWrapper()

Retrieves the IndependenceWrapper object associated with this method. The IndependenceWrapper object contains an IndependenceTest that checks the independence of two variables conditional on a set of variables using a given dataset and parameters .

Specified by:

getIndependenceWrapper in interface TakesIndependenceWrapper

Returns:

The IndependenceWrapper object associated with this method.

setIndependenceWrapper

public void setIndependenceWrapper(IndependenceWrapper test)

Sets the independence wrapper.

Specified by:

setIndependenceWrapper in interface TakesIndependenceWrapper

Parameters:

test - the independence wrapper.

getScoreWrapper

public ScoreWrapper getScoreWrapper()

Retrieves the ScoreWrapper object associated with this method.

Specified by:

getScoreWrapper in interface UsesScoreWrapper

Returns:

The ScoreWrapper object associated with this method.

setScoreWrapper

public void setScoreWrapper(ScoreWrapper score)

Sets the score wrapper for the algorithm.

Specified by:

setScoreWrapper in interface UsesScoreWrapper

Parameters:

score - the score wrapper.