src/test/org/apache/commons/math/stat/inference/ChiSquareTestTest.java

/*
 * Copyright 2004 The Apache Software Foundation.
 * 
 * Licensed under the Apache License, Version 2.0 (the "License");
 * you may not use this file except in compliance with the License.
 * You may obtain a copy of the License at
 * 
 *      http://www.apache.org/licenses/LICENSE-2.0
 * 
 * Unless required by applicable law or agreed to in writing, software
 * distributed under the License is distributed on an "AS IS" BASIS,
 * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 * See the License for the specific language governing permissions and
 * limitations under the License.
 */
package org.apache.commons.math.stat.inference;

import junit.framework.Test;
import junit.framework.TestCase;
import junit.framework.TestSuite;

/**
 * Test cases for the ChiSquareTestImpl class.
 *
 * @version $Revision$ $Date$
 */

public class ChiSquareTestTest extends TestCase {

    protected ChiSquareTest testStatistic = new ChiSquareTestImpl();

    public ChiSquareTestTest(String name) {
        super(name);
    }

    public void setUp() {
    }

    public static Test suite() {
        TestSuite suite = new TestSuite(ChiSquareTestTest.class);
        suite.setName("TestStatistic Tests");
        return suite;
    }

    public void testChiSquare() throws Exception {
 
        // Target values computed using R version 1.8.1 
        // Some assembly required ;-)  
        //      Use sum((obs - exp)^2/exp) for the chi-square statistic and
        //      1 - pchisq(sum((obs - exp)^2/exp), length(obs) - 1) for the p-value
        
        long[] observed = {10, 9, 11};
        double[] expected = {10, 10, 10};
        assertEquals("chi-square statistic", 0.2,  testStatistic.chiSquare(expected, observed), 10E-12);
        assertEquals("chi-square p-value", 0.904837418036, testStatistic.chiSquareTest(expected, observed), 1E-10);
        
        long[] observed1 = { 500, 623, 72, 70, 31 };
        double[] expected1 = { 485, 541, 82, 61, 37 };
        assertEquals( "chi-square test statistic", 16.4131070362, testStatistic.chiSquare(expected1, observed1), 1E-10);
        assertEquals("chi-square p-value", 0.002512096, testStatistic.chiSquareTest(expected1, observed1), 1E-9);
        assertTrue("chi-square test reject", testStatistic.chiSquareTest(expected1, observed1, 0.003));
        assertTrue("chi-square test accept", !testStatistic.chiSquareTest(expected1, observed1, 0.002));

        try {
            testStatistic.chiSquareTest(expected1, observed1, 95);
            fail("alpha out of range, IllegalArgumentException expected");
        } catch (IllegalArgumentException ex) {
            // expected
        }  
        
        long[] tooShortObs = { 0 };
        double[] tooShortEx = { 1 };
        try {
            testStatistic.chiSquare(tooShortEx, tooShortObs);
            fail("arguments too short, IllegalArgumentException expected");
        } catch (IllegalArgumentException ex) {
            // expected
        }

        // unmatched arrays
        long[] unMatchedObs = { 0, 1, 2, 3 };
        double[] unMatchedEx = { 1, 1, 2 };
        try {
            testStatistic.chiSquare(unMatchedEx, unMatchedObs);
            fail("arrays have different lengths, IllegalArgumentException expected");
        } catch (IllegalArgumentException ex) {
            // expected
        }
        
        // 0 expected count
        expected[0] = 0;
        try {
            testStatistic.chiSquareTest(expected, observed, .01);
            fail("bad expected count, IllegalArgumentException expected");
        } catch (IllegalArgumentException ex) {
            // expected
        } 
        
        // negative observed count
        expected[0] = 1;
        observed[0] = -1;
        try {
            testStatistic.chiSquareTest(expected, observed, .01);
            fail("bad expected count, IllegalArgumentException expected");
        } catch (IllegalArgumentException ex) {
            // expected
        } 
        
    }

    public void testChiSquareIndependence() throws Exception {
        
        // Target values computed using R version 1.8.1 
        
        long[][] counts = { {40, 22, 43}, {91, 21, 28}, {60, 10, 22}};
        assertEquals( "chi-square test statistic", 22.709027688, testStatistic.chiSquare(counts), 1E-9);
        assertEquals("chi-square p-value", 0.000144751460134, testStatistic.chiSquareTest(counts), 1E-9);
        assertTrue("chi-square test reject", testStatistic.chiSquareTest(counts, 0.0002));
        assertTrue("chi-square test accept", !testStatistic.chiSquareTest(counts, 0.0001));    
        
        long[][] counts2 = {{10, 15}, {30, 40}, {60, 90} };
        assertEquals( "chi-square test statistic", 0.168965517241, testStatistic.chiSquare(counts2), 1E-9);
        assertEquals("chi-square p-value",0.918987499852, testStatistic.chiSquareTest(counts2), 1E-9);
        assertTrue("chi-square test accept", !testStatistic.chiSquareTest(counts2, 0.1)); 
        
        // ragged input array
        long[][] counts3 = { {40, 22, 43}, {91, 21, 28}, {60, 10}};
        try {
            testStatistic.chiSquare(counts3);
            fail("Expecting IllegalArgumentException");
        } catch (IllegalArgumentException ex) {
            // expected
        }
        
        // insufficient data
        long[][] counts4 = {{40, 22, 43}};
        try {
            testStatistic.chiSquare(counts4);
            fail("Expecting IllegalArgumentException");
        } catch (IllegalArgumentException ex) {
            // expected
        } 
        long[][] counts5 = {{40}, {40}, {30}, {10}};
        try {
            testStatistic.chiSquare(counts5);
            fail("Expecting IllegalArgumentException");
        } catch (IllegalArgumentException ex) {
            // expected
        } 
        
        // negative counts
        long[][] counts6 = {{10, -2}, {30, 40}, {60, 90} };
        try {
            testStatistic.chiSquare(counts6);
            fail("Expecting IllegalArgumentException");
        } catch (IllegalArgumentException ex) {
            // expected
        } 
        
        // bad alpha
        try {
            testStatistic.chiSquareTest(counts, 0);
            fail("Expecting IllegalArgumentException");
        } catch (IllegalArgumentException ex) {
            // expected
        } 
    }
    
    public void testChiSquareLargeTestStatistic() throws Exception {
        double[] exp = new double[] {
            3389119.5, 649136.6, 285745.4, 25357364.76, 11291189.78, 543628.0, 
            232921.0, 437665.75
        };

        long[] obs = new long[] {
            2372383, 584222, 257170, 17750155, 7903832, 489265, 209628, 393899
        };
        org.apache.commons.math.stat.inference.ChiSquareTestImpl csti =
            new org.apache.commons.math.stat.inference.ChiSquareTestImpl(); 
        double cst = csti.chiSquareTest(exp, obs); 
        assertEquals("chi-square p-value", 0.0, cst, 1E-3);
        assertEquals( "chi-square test statistic", 
                3624883.342907764, testStatistic.chiSquare(exp, obs), 1E-9);
    }
    
    /** Contingency table containing zeros - PR # 32531 */
    public void testChiSquareZeroCount() throws Exception {
        // Target values computed using R version 1.8.1 
        long[][] counts = { {40, 0, 4}, {91, 1, 2}, {60, 2, 0}};
        assertEquals( "chi-square test statistic", 9.67444662263,
                testStatistic.chiSquare(counts), 1E-9);
        assertEquals("chi-square p-value", 0.0462835770603,
                testStatistic.chiSquareTest(counts), 1E-9);       
    }
}