Package edu.cmu.tetrad.search.utils

Class ResolveSepsets

java.lang.Object

edu.cmu.tetrad.search.utils.ResolveSepsets

public final class ResolveSepsets
extends Object

Provides some utilities for resolving inconsistencies that arise between sepsets learned for overlapping datasets. This occurs frequently when using the DCI and ION algorithm. A reference is here:

Tillman, R. E., & Eberhardt, F. (2014). Learning causal structure from multiple datasets with similar variable sets. Behaviormetrika, 41(1), 41-64.

Version:

$Id: $Id

Author:

roberttillman

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
static enum	ResolveSepsets.Method	Gives the method to be used to resolve sepsets when they conflict.

Constructor Summary

Constructors

Constructor	Description
ResolveSepsets()	The method to use for resolving sepsets

Method Summary

Modifier and Type	Method	Description
static boolean	isIndependentPooled(ResolveSepsets.Method method, List<IndependenceTest> independenceTests, Node x, Node y, Set<Node> condSet)	Tests for independence using one of the pooled methods
static boolean	isIndependentPooledAverage(List<IndependenceTest> independenceTests, Node x, Node y, Set<Node> condSet)	Checks independence from pooled samples by taking the average p value
static boolean	isIndependentPooledAverageTest(List<IndependenceTest> independenceTests, Node x, Node y, Set<Node> condSet)	Checks independence from pooled samples by taking the average test statistic CURRENTLY ONLY WORKS FOR CHISQUARE TEST
static boolean	isIndependentPooledFisher(List<IndependenceTest> independenceTests, Node x, Node y, Set<Node> condSet)	Checks independence from pooled samples using Fisher's method.
static boolean	isIndependentPooledFisher2(List<IndependenceTest> independenceTests, Node x, Node y, Set<Node> condSet)	Eliminates from considerations independence tests that cannot be evaluated (due to missing variables mainly).
static boolean	isIndependentPooledMudholkerGeorge(List<IndependenceTest> independenceTests, Node x, Node y, Set<Node> condSet)	Checks independence from pooled samples using Mudholker and George's method
static boolean	isIndependentPooledMudholkerGeorge2(List<IndependenceTest> independenceTests, Node x, Node y, Set<Node> condSet)	The same as isIndepenentPooledMudholkerGeoerge, except that only available independence tests are used.
static boolean	isIndependentPooledRandom(List<IndependenceTest> independenceTests, Node x, Node y, Set<Node> condSet)	Checks independence from pooled samples by randomly selecting a p value
static boolean	isIndependentPooledStouffer(List<IndependenceTest> independenceTests, Node x, Node y, Set<Node> condSet)	Checks independence from pooled samples using Stouffer et al.'s method
static boolean	isIndependentPooledTippett(List<IndependenceTest> independenceTests, Node x, Node y, Set<Node> condSet)	Checks independence from pooled samples using Tippett's method
static boolean	isIndependentPooledWilkinson(List<IndependenceTest> independenceTests, Node x, Node y, Set<Node> condSet, int r)	Checks independence from pooled samples using Wilkinson's method
static boolean	isIndependentPooledWorsleyFriston(List<IndependenceTest> independenceTests, Node x, Node y, Set<Node> condSet)	Checks independence from pooled samples using Worsley and Friston's method

Methods inherited from class java.lang.Object

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

Constructor Details

ResolveSepsets

public ResolveSepsets()

The method to use for resolving sepsets

Method Details

isIndependentPooled

public static boolean isIndependentPooled(ResolveSepsets.Method method,
 List<IndependenceTest> independenceTests,
 Node x,
 Node y,
 Set<Node> condSet)
                                   throws InterruptedException

Tests for independence using one of the pooled methods

Parameters:

method - a ResolveSepsets.Method object

independenceTests - a List object

x - a Node object

y - a Node object

condSet - a Set object

Returns:

a boolean

Throws:

InterruptedException

isIndependentPooledFisher

public static boolean isIndependentPooledFisher(List<IndependenceTest> independenceTests,
 Node x,
 Node y,
 Set<Node> condSet)
                                         throws InterruptedException

Checks independence from pooled samples using Fisher's method.

See R. A. Fisher. Statistical Methods for Research Workers. Oliver and Boyd, 11th edition, 1950.

Parameters:

independenceTests - a List object

x - a Node object

y - a Node object

condSet - a Set object

Returns:

a boolean

Throws:

InterruptedException

isIndependentPooledFisher2

public static boolean isIndependentPooledFisher2(List<IndependenceTest> independenceTests,
 Node x,
 Node y,
 Set<Node> condSet)

Eliminates from considerations independence tests that cannot be evaluated (due to missing variables mainly).

Parameters:

independenceTests - a List object

x - a Node object

y - a Node object

condSet - a Set object

Returns:

a boolean

isIndependentPooledTippett

public static boolean isIndependentPooledTippett(List<IndependenceTest> independenceTests,
 Node x,
 Node y,
 Set<Node> condSet)
                                          throws InterruptedException

Checks independence from pooled samples using Tippett's method

See L. H. C. Tippett. The Method of Statistics. Williams and Norgate, 1st edition, 1950.

Parameters:

independenceTests - a List object

x - a Node object

y - a Node object

condSet - a Set object

Returns:

a boolean

Throws:

InterruptedException

isIndependentPooledWilkinson

public static boolean isIndependentPooledWilkinson(List<IndependenceTest> independenceTests,
 Node x,
 Node y,
 Set<Node> condSet,
 int r)
                                            throws InterruptedException

Checks independence from pooled samples using Wilkinson's method

I don't have a reference for this but its basically in between Tippett and Worsley and Friston.

Parameters:

independenceTests - a List object

x - a Node object

y - a Node object

condSet - a Set object

r - a int

Returns:

a boolean

Throws:

InterruptedException

isIndependentPooledWorsleyFriston

public static boolean isIndependentPooledWorsleyFriston(List<IndependenceTest> independenceTests,
 Node x,
 Node y,
 Set<Node> condSet)
                                                 throws InterruptedException

Checks independence from pooled samples using Worsley and Friston's method

See K. J. Worsely and K. J. Friston. A test for conjunction. Statistics and Probability Letters 2000.

Parameters:

independenceTests - a List object

x - a Node object

y - a Node object

condSet - a Set object

Returns:

a boolean

Throws:

InterruptedException

isIndependentPooledStouffer

public static boolean isIndependentPooledStouffer(List<IndependenceTest> independenceTests,
 Node x,
 Node y,
 Set<Node> condSet)
                                           throws InterruptedException

Checks independence from pooled samples using Stouffer et al.'s method

See S. A. Stouffer, E. A. Suchman, L. C. Devinney, S. A. Star, and R. M. Williams. The American Soldier: Vol. 1. Adjustment During Army Life. Princeton University Press, 1949.

Parameters:

independenceTests - a List object

x - a Node object

y - a Node object

condSet - a Set object

Returns:

a boolean

Throws:

InterruptedException

isIndependentPooledMudholkerGeorge

public static boolean isIndependentPooledMudholkerGeorge(List<IndependenceTest> independenceTests,
 Node x,
 Node y,
 Set<Node> condSet)
                                                  throws InterruptedException

Checks independence from pooled samples using Mudholker and George's method

See G. S. Mudholkar and E. O. George. The logit method for combining probabilities. In J. Rustagi, editor, Symposium on Optimizing Method in Statistics, pages 345-366. Academic Press, 1979.

Parameters:

independenceTests - a List object

x - a Node object

y - a Node object

condSet - a Set object

Returns:

a boolean

Throws:

InterruptedException

isIndependentPooledMudholkerGeorge2

public static boolean isIndependentPooledMudholkerGeorge2(List<IndependenceTest> independenceTests,
 Node x,
 Node y,
 Set<Node> condSet)

The same as isIndepenentPooledMudholkerGeoerge, except that only available independence tests are used.

Parameters:

independenceTests - a List object

x - a Node object

y - a Node object

condSet - a Set object

Returns:

a boolean

isIndependentPooledAverage

public static boolean isIndependentPooledAverage(List<IndependenceTest> independenceTests,
 Node x,
 Node y,
 Set<Node> condSet)
                                          throws InterruptedException

Checks independence from pooled samples by taking the average p value

Parameters:

independenceTests - a List object

x - a Node object

y - a Node object

condSet - a Set object

Returns:

a boolean

Throws:

InterruptedException

isIndependentPooledAverageTest

public static boolean isIndependentPooledAverageTest(List<IndependenceTest> independenceTests,
 Node x,
 Node y,
 Set<Node> condSet)
                                              throws InterruptedException

Checks independence from pooled samples by taking the average test statistic CURRENTLY ONLY WORKS FOR CHISQUARE TEST

Parameters:

independenceTests - a List object

x - a Node object

y - a Node object

condSet - a Set object

Returns:

a boolean

Throws:

InterruptedException

isIndependentPooledRandom

public static boolean isIndependentPooledRandom(List<IndependenceTest> independenceTests,
 Node x,
 Node y,
 Set<Node> condSet)
                                         throws InterruptedException

Checks independence from pooled samples by randomly selecting a p value

Parameters:

independenceTests - a List object

x - a Node object

y - a Node object

condSet - a Set object

Returns:

a boolean

Throws:

InterruptedException