Package edu.cmu.tetrad.search.work_in_progress

Class FasFdr

java.lang.Object

edu.cmu.tetrad.search.work_in_progress.FasFdr

All Implemented Interfaces:

IFas, IGraphSearch

public class FasFdr
extends Object
implements IFas

Implements the "fast adjacency search" used in several causal algorithm in this package. In the fast adjacency search, at a given stage of the search, an edge X*-*Y is removed from the graph if X _||_ Y | S, where S is a subset of size d either of adj(X) or of adj(Y), where d is the depth of the search. The fast adjacency search performs this procedure for each pair of adjacent edges in the graph and for each depth d = 0, 1, 2, ..., d1, where d1 is either the maximum depth or else the first such depth at which no edges can be removed. The interpretation of this adjacency search is different for different algorithm, depending on the assumptions of the algorithm. A mapping from {x, y} to S({x, y}) is returned for edges x *-* y that have been removed.

This variant does each depth twice, gathering up the p values in the first round, using FDR to estimate a cutoff for acceptance, and rerunning using the specified cutoff.

Version:

$Id: $Id

Author:

josephramsey.

Constructor Summary

Constructors

Constructor	Description
FasFdr(IndependenceTest test, int numIndependenceTests)	Constructs a new FastAdjacencySearch.

Method Summary

Modifier and Type	Method	Description
List<Triple>	getAmbiguousTriples(Node node)	Returns the list of ambiguous triples found for a given node.
long	getElapsedTime()	Returns the elapsed time of the search.
List<Node>	getNodes()	Returns the nodes searched over.
int	getNumIndependenceTests()	Returns the nubmer of independence tests done in the course of the search.
SepsetMap	getSepsets()	Returns a map for x _||_ y | z1,...,zn of {x, y} to {z1,...,zn},
Graph	search()	Discovers all adjacencies in data.
void	setDepth(int depth)	Sets the depth of the search--that is, the maximum number of variables conditioned on in the search.
void	setKnowledge(Knowledge knowledge)	Sets the knowledge for the search.
void	setOut(PrintStream out)	sets the print stream to send text to.
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

FasFdr

public FasFdr(IndependenceTest test,
 int numIndependenceTests)

Constructs a new FastAdjacencySearch.

Parameters:

test - The independence test to use.

numIndependenceTests - The number of independence tests total done.

Method Details

search

public Graph search()
             throws InterruptedException

Discovers all adjacencies in data. The procedure is to remove edges in the graph which connect pairs of variables which are independent conditional on some other set of variables in the graph (the "sepset"). These are removed in tiers. First, edges which are independent conditional on zero other variables are removed, then edges which are independent conditional on one other variable are removed, then two, then three, and so on, until no more edges can be removed from the graph. The edges which remain in the graph after this procedure are the adjacencies in the data.

Specified by:

search in interface IGraphSearch

Returns:

a SepSet, which indicates which variables are independent conditional on which other variables

Throws:

InterruptedException - if any.

getNumIndependenceTests

public int getNumIndependenceTests()

Returns the nubmer of independence tests done in the course of the search.

Returns:

This number.

getSepsets

public SepsetMap getSepsets()

Returns a map for x _||_ y | z1,...,zn of {x, y} to {z1,...,zn},

Specified by:

getSepsets in interface IFas

Returns:

This map.

setVerbose

public void setVerbose(boolean verbose)

Sets whether verbose output should be printed.

Sets whether verbose output will be printed.

Specified by:

setVerbose in interface IFas

Parameters:

verbose - True, if so.

getElapsedTime

public long getElapsedTime()

Returns the elapsed time of the search.

Specified by:

getElapsedTime in interface IFas

Returns:

This time.

getNodes

public List<Node> getNodes()

Returns the nodes searched over.

Specified by:

getNodes in interface IFas

Returns:

This list.

getAmbiguousTriples

public List<Triple> getAmbiguousTriples(Node node)

Returns the list of ambiguous triples found for a given node.

Specified by:

getAmbiguousTriples in interface IFas

Parameters:

node - The node

Returns:

The list.

See Also:

• Cpc
• Cfci

setOut

public void setOut(PrintStream out)

sets the print stream to send text to.

Specified by:

setOut in interface IFas

Parameters:

out - This print stream.

setDepth

public void setDepth(int depth)

Sets the depth of the search--that is, the maximum number of variables conditioned on in the search.

Sets the depth of the search--i.e., the maximum number of variables conditioned on for any conditional independence test.

Specified by:

setDepth in interface IFas

Parameters:

depth - This maximum.

setKnowledge

public void setKnowledge(Knowledge knowledge)

Sets the knowledge for the search.

Sets the knowledge to be used in the search.

Specified by:

setKnowledge in interface IFas

Parameters:

knowledge - This knowledge.