Package edu.cmu.tetrad.search.test

Class ChiSquareTest

java.lang.Object

edu.cmu.tetrad.search.test.ChiSquareTest

public class ChiSquareTest
extends Object

Calculates chi-square or g-square for a conditional cross-tabulation table for independence question 0 _||_ 1 | 2, 3, ...max by summing up chi-square and degrees of freedom for each conditional table in turn, where rows or columns that sum to less than a given threshold have been removed. The adjusted conditional tables are required to have more than 0 total counts and at least 2 rows and 2 columns; otherwise, the test is judged to be invalid. Otherwise, a p-value is returned based on the Chi-Square distribution with the total degrees of freedom and total chi-square.

Version:

$Id: $Id

Author:

frankwimberly, josephramsey

See Also:

• ChiSquareTest.TestType

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
static enum	ChiSquareTest.CellTableType	The type of cell table to use.
static class	ChiSquareTest.Result	Simple class to store the parameters of the result returned by the G Square test.
static enum	ChiSquareTest.TestType	The type of test to perform.

Constructor Summary

Constructors

Constructor	Description
ChiSquareTest(DataSet dataSet, double alpha, ChiSquareTest.TestType testType, List<Integer> rows)	Constructs a test using the given data set and significance level.

Method Summary

Modifier and Type	Method	Description
ChiSquareTest.Result	calcChiSquare(int[] testIndices, double sampleSize)	Calculates chi square for a conditional cross-tabulation table for independence question 0 _||_ 1 | 2, 3, ...max by summing up chi square and degrees of freedom for each conditional table in turn.
double	getAlpha()	Returns the model significance level being used for tests.
boolean	isDetermined(int[] testIndices, double p)	Returns a judgment of whether a set of parent variables determines a child variables.
void	setAlpha(double alpha)	Sets the significance level to be used for tests.
void	setCellTableType(ChiSquareTest.CellTableType cellTableType)	Sets the type of cell table to use.
void	setMinCountPerCell(double minCountPerCell)	The minimum number of counts per conditional table for chi-square for that table and its degrees of freedom to be included in the overall chi-square and degrees of freedom.

Methods inherited from class java.lang.Object

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

Constructor Details

ChiSquareTest

public ChiSquareTest(DataSet dataSet,
 double alpha,
 ChiSquareTest.TestType testType,
 List<Integer> rows)

Constructs a test using the given data set and significance level.

Parameters:

dataSet - A data set consisting entirely of discrete variables.

alpha - The significance level, usually 0.05.

testType - The type of test to perform, either CHI_SQUARE or G_SQUARE.

rows - The rows to use in the test; if null, all rows are used.

Method Details

calcChiSquare

public ChiSquareTest.Result calcChiSquare(int[] testIndices,
 double sampleSize)

Calculates chi square for a conditional cross-tabulation table for independence question 0 _||_ 1 | 2, 3, ...max by summing up chi square and degrees of freedom for each conditional table in turn. Rows or columns that with fewer than minSumRowOrCol counts have been removed. The adjusted conditional tables are required to have more than 0 total counts and at least 2 rows and 2 columns; otherwise, the test is judged to be invalid. Otherwise, a p-value is returned based on the Chi-Square distribution with the total degrees of freedom and total chi-square.

Parameters:

testIndices - These indices, in order.

sampleSize - The sample size to use for the test; expected and observed counts will be multiplied by the ratio of this to the sample size of the data.

Returns:

a Chi square test result.

See Also:

• ChiSquareTest.Result

isDetermined

public boolean isDetermined(int[] testIndices,
 double p)

Returns a judgment of whether a set of parent variables determines a child variables.

Parameters:

testIndices - An array of indices for variables in the dataset supplied in the constructor.

p - The probability that some marginal for some table dominates. A good value is 0.99.

Returns:

True if the variable at index 0 is determined by the variables at the other indices.

getAlpha

public double getAlpha()

Returns the model significance level being used for tests.

Returns:

this level.

setAlpha

public void setAlpha(double alpha)

Sets the significance level to be used for tests.

Parameters:

alpha - This significance level.

setMinCountPerCell

public void setMinCountPerCell(double minCountPerCell)

The minimum number of counts per conditional table for chi-square for that table and its degrees of freedom to be included in the overall chi-square and degrees of freedom. Note that this should not be too small, or the chi-square distribution will not be a good approximation to the distribution of the test statistic.

Parameters:

minCountPerCell - The minimum number of counts per conditional table. The default is 1; this must be >= 0.

setCellTableType

public void setCellTableType(ChiSquareTest.CellTableType cellTableType)

Sets the type of cell table to use.

Parameters:

cellTableType - The type of cell table to use.