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Java example source code file (ChiSquareTestTest.java)

This example Java source code file (ChiSquareTestTest.java) is included in the alvinalexander.com "Java Source Code Warehouse" project. The intent of this project is to help you "Learn Java by Example" TM.

Learn more about this Java project at its project page.

Java - Java tags/keywords

chisquaretest, chisquaretesttest, dimensionmismatchexception, expecting, notpositiveexception, notstrictlypositiveexception, outofrangeexception, test, zeroexception

The ChiSquareTestTest.java Java example source code

/*
 * Licensed to the Apache Software Foundation (ASF) under one or more
 * contributor license agreements.  See the NOTICE file distributed with
 * this work for additional information regarding copyright ownership.
 * The ASF licenses this file to You 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.math3.stat.inference;

import org.apache.commons.math3.exception.DimensionMismatchException;
import org.apache.commons.math3.exception.NotPositiveException;
import org.apache.commons.math3.exception.NotStrictlyPositiveException;
import org.apache.commons.math3.exception.OutOfRangeException;
import org.apache.commons.math3.exception.ZeroException;
import org.junit.Assert;
import org.junit.Test;


/**
 * Test cases for the ChiSquareTestImpl class.
 *
 */

public class ChiSquareTestTest {

    protected ChiSquareTest testStatistic = new ChiSquareTest();

    @Test
    public void testChiSquare() {

        // 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};
        Assert.assertEquals("chi-square statistic", 0.2,  testStatistic.chiSquare(expected, observed), 10E-12);
        Assert.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 };
        Assert.assertEquals( "chi-square test statistic", 9.023307936427388, testStatistic.chiSquare(expected1, observed1), 1E-10);
        Assert.assertEquals("chi-square p-value", 0.06051952647453607, testStatistic.chiSquareTest(expected1, observed1), 1E-9);
        Assert.assertTrue("chi-square test reject", testStatistic.chiSquareTest(expected1, observed1, 0.08));
        Assert.assertTrue("chi-square test accept", !testStatistic.chiSquareTest(expected1, observed1, 0.05));

        try {
            testStatistic.chiSquareTest(expected1, observed1, 95);
            Assert.fail("alpha out of range, OutOfRangeException expected");
        } catch (OutOfRangeException ex) {
            // expected
        }

        long[] tooShortObs = { 0 };
        double[] tooShortEx = { 1 };
        try {
            testStatistic.chiSquare(tooShortEx, tooShortObs);
            Assert.fail("arguments too short, DimensionMismatchException expected");
        } catch (DimensionMismatchException ex) {
            // expected
        }

        // unmatched arrays
        long[] unMatchedObs = { 0, 1, 2, 3 };
        double[] unMatchedEx = { 1, 1, 2 };
        try {
            testStatistic.chiSquare(unMatchedEx, unMatchedObs);
            Assert.fail("arrays have different lengths, DimensionMismatchException expected");
        } catch (DimensionMismatchException ex) {
            // expected
        }

        // 0 expected count
        expected[0] = 0;
        try {
            testStatistic.chiSquareTest(expected, observed, .01);
            Assert.fail("bad expected count, NotStrictlyPositiveException expected");
        } catch (NotStrictlyPositiveException ex) {
            // expected
        }

        // negative observed count
        expected[0] = 1;
        observed[0] = -1;
        try {
            testStatistic.chiSquareTest(expected, observed, .01);
            Assert.fail("bad expected count, NotPositiveException expected");
        } catch (NotPositiveException ex) {
            // expected
        }

    }

    @Test
    public void testChiSquareIndependence() {

        // Target values computed using R version 1.8.1

        long[][] counts = { {40, 22, 43}, {91, 21, 28}, {60, 10, 22}};
        Assert.assertEquals( "chi-square test statistic", 22.709027688, testStatistic.chiSquare(counts), 1E-9);
        Assert.assertEquals("chi-square p-value", 0.000144751460134, testStatistic.chiSquareTest(counts), 1E-9);
        Assert.assertTrue("chi-square test reject", testStatistic.chiSquareTest(counts, 0.0002));
        Assert.assertTrue("chi-square test accept", !testStatistic.chiSquareTest(counts, 0.0001));

        long[][] counts2 = {{10, 15}, {30, 40}, {60, 90} };
        Assert.assertEquals( "chi-square test statistic", 0.168965517241, testStatistic.chiSquare(counts2), 1E-9);
        Assert.assertEquals("chi-square p-value",0.918987499852, testStatistic.chiSquareTest(counts2), 1E-9);
        Assert.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);
            Assert.fail("Expecting DimensionMismatchException");
        } catch (DimensionMismatchException ex) {
            // expected
        }

        // insufficient data
        long[][] counts4 = {{40, 22, 43}};
        try {
            testStatistic.chiSquare(counts4);
            Assert.fail("Expecting DimensionMismatchException");
        } catch (DimensionMismatchException ex) {
            // expected
        }
        long[][] counts5 = {{40}, {40}, {30}, {10}};
        try {
            testStatistic.chiSquare(counts5);
            Assert.fail("Expecting DimensionMismatchException");
        } catch (DimensionMismatchException ex) {
            // expected
        }

        // negative counts
        long[][] counts6 = {{10, -2}, {30, 40}, {60, 90} };
        try {
            testStatistic.chiSquare(counts6);
            Assert.fail("Expecting NotPositiveException");
        } catch (NotPositiveException ex) {
            // expected
        }

        // bad alpha
        try {
            testStatistic.chiSquareTest(counts, 0);
            Assert.fail("Expecting OutOfRangeException");
        } catch (OutOfRangeException ex) {
            // expected
        }
    }

    @Test
    public void testChiSquareLargeTestStatistic() {
        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.math3.stat.inference.ChiSquareTest csti =
            new org.apache.commons.math3.stat.inference.ChiSquareTest();
        double cst = csti.chiSquareTest(exp, obs);
        Assert.assertEquals("chi-square p-value", 0.0, cst, 1E-3);
        Assert.assertEquals( "chi-square test statistic",
                114875.90421929007, testStatistic.chiSquare(exp, obs), 1E-9);
    }

    /** Contingency table containing zeros - PR # 32531 */
    @Test
    public void testChiSquareZeroCount() {
        // Target values computed using R version 1.8.1
        long[][] counts = { {40, 0, 4}, {91, 1, 2}, {60, 2, 0}};
        Assert.assertEquals( "chi-square test statistic", 9.67444662263,
                testStatistic.chiSquare(counts), 1E-9);
        Assert.assertEquals("chi-square p-value", 0.0462835770603,
                testStatistic.chiSquareTest(counts), 1E-9);
    }

    /** Target values verified using DATAPLOT version 2006.3 */
    @Test
    public void testChiSquareDataSetsComparisonEqualCounts()
        {
        long[] observed1 = {10, 12, 12, 10};
        long[] observed2 = {5, 15, 14, 10};
        Assert.assertEquals("chi-square p value", 0.541096,
                testStatistic.chiSquareTestDataSetsComparison(
                observed1, observed2), 1E-6);
        Assert.assertEquals("chi-square test statistic", 2.153846,
                testStatistic.chiSquareDataSetsComparison(
                observed1, observed2), 1E-6);
        Assert.assertFalse("chi-square test result",
                testStatistic.chiSquareTestDataSetsComparison(
                observed1, observed2, 0.4));
    }

    /** Target values verified using DATAPLOT version 2006.3 */
    @Test
    public void testChiSquareDataSetsComparisonUnEqualCounts()
        {
        long[] observed1 = {10, 12, 12, 10, 15};
        long[] observed2 = {15, 10, 10, 15, 5};
        Assert.assertEquals("chi-square p value", 0.124115,
                testStatistic.chiSquareTestDataSetsComparison(
                observed1, observed2), 1E-6);
        Assert.assertEquals("chi-square test statistic", 7.232189,
                testStatistic.chiSquareDataSetsComparison(
                observed1, observed2), 1E-6);
        Assert.assertTrue("chi-square test result",
                testStatistic.chiSquareTestDataSetsComparison(
                observed1, observed2, 0.13));
        Assert.assertFalse("chi-square test result",
                testStatistic.chiSquareTestDataSetsComparison(
                observed1, observed2, 0.12));
    }

    @Test
    public void testChiSquareDataSetsComparisonBadCounts()
        {
        long[] observed1 = {10, -1, 12, 10, 15};
        long[] observed2 = {15, 10, 10, 15, 5};
        try {
            testStatistic.chiSquareTestDataSetsComparison(
                    observed1, observed2);
            Assert.fail("Expecting NotPositiveException - negative count");
        } catch (NotPositiveException ex) {
            // expected
        }
        long[] observed3 = {10, 0, 12, 10, 15};
        long[] observed4 = {15, 0, 10, 15, 5};
        try {
            testStatistic.chiSquareTestDataSetsComparison(
                    observed3, observed4);
            Assert.fail("Expecting ZeroException - double 0's");
        } catch (ZeroException ex) {
            // expected
        }
        long[] observed5 = {10, 10, 12, 10, 15};
        long[] observed6 = {0, 0, 0, 0, 0};
        try {
            testStatistic.chiSquareTestDataSetsComparison(
                    observed5, observed6);
            Assert.fail("Expecting ZeroException - vanishing counts");
        } catch (ZeroException ex) {
            // expected
        }
    }
}

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