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Java example source code file (GTestTest.java)

This example Java source code file (GTestTest.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

dimensionmismatchexception, exception, expecting, gtest, gtesttest, notpositiveexception, notstrictlypositiveexception, outofrangeexception, test, zeroexception

The GTestTest.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.apache.commons.math3.util.FastMath;
import org.junit.Assert;
import org.junit.Test;

/**
 * Test cases for the GTest class.
 *
 * Data for the tests are from p64-69 in: McDonald, J.H. 2009. Handbook of
 * Biological Statistics (2nd ed.). Sparky House Publishing, Baltimore,
 * Maryland.
 *
 */
public class GTestTest {

    protected GTest testStatistic = new GTest();

    @Test
    public void testGTestGoodnesOfFit1() throws Exception {
        final double[] exp = new double[]{
            3d, 1d
        };

        final long[] obs = new long[]{
            423, 133
        };

        Assert.assertEquals("G test statistic",
                0.348721, testStatistic.g(exp, obs), 1E-6);
        final double p_gtgf = testStatistic.gTest(exp, obs);
        Assert.assertEquals("g-Test p-value", 0.55483, p_gtgf, 1E-5);

        Assert.assertFalse(testStatistic.gTest(exp, obs, 0.05));
    }

    @Test
    public void testGTestGoodnesOfFit2() throws Exception {
        final double[] exp = new double[]{
            0.54d, 0.40d, 0.05d, 0.01d
        };

        final long[] obs = new long[]{
            70, 79, 3, 4
        };
        Assert.assertEquals("G test statistic",
                13.144799, testStatistic.g(exp, obs), 1E-6);
        final double p_gtgf = testStatistic.gTest(exp, obs);
        Assert.assertEquals("g-Test p-value", 0.004333, p_gtgf, 1E-5);

        Assert.assertTrue(testStatistic.gTest(exp, obs, 0.05));
    }

    @Test
    public void testGTestGoodnesOfFit3() throws Exception {
        final double[] exp = new double[]{
            0.167d, 0.483d, 0.350d
        };

        final long[] obs = new long[]{
            14, 21, 25
        };

        Assert.assertEquals("G test statistic",
                4.5554, testStatistic.g(exp, obs), 1E-4);
        // Intrinisic (Hardy-Weinberg proportions) P-Value should be 0.033
        final double p_gtgf = testStatistic.gTestIntrinsic(exp, obs);
        Assert.assertEquals("g-Test p-value", 0.0328, p_gtgf, 1E-4);

        Assert.assertFalse(testStatistic.gTest(exp, obs, 0.05));
    }

    @Test
    public void testGTestIndependance1() throws Exception {
        final long[] obs1 = new long[]{
            268, 199, 42
        };

        final long[] obs2 = new long[]{
            807, 759, 184
        };

        final double g = testStatistic.gDataSetsComparison(obs1, obs2);

        Assert.assertEquals("G test statistic",
                7.3008170, g, 1E-6);
        final double p_gti = testStatistic.gTestDataSetsComparison(obs1, obs2);

        Assert.assertEquals("g-Test p-value", 0.0259805, p_gti, 1E-6);
        Assert.assertTrue(testStatistic.gTestDataSetsComparison(obs1, obs2, 0.05));
    }

    @Test
    public void testGTestIndependance2() throws Exception {
        final long[] obs1 = new long[]{
            127, 99, 264
        };

        final long[] obs2 = new long[]{
            116, 67, 161
        };

        final double g = testStatistic.gDataSetsComparison(obs1, obs2);

        Assert.assertEquals("G test statistic",
                6.227288, g, 1E-6);
        final double p_gti = testStatistic.gTestDataSetsComparison(obs1, obs2);

        Assert.assertEquals("g-Test p-value", 0.04443, p_gti, 1E-5);
        Assert.assertTrue(testStatistic.gTestDataSetsComparison(obs1, obs2, 0.05));
    }

    @Test
    public void testGTestIndependance3() throws Exception {
        final long[] obs1 = new long[]{
            190, 149
        };

        final long[] obs2 = new long[]{
            42, 49
        };

        final double g = testStatistic.gDataSetsComparison(obs1, obs2);
        Assert.assertEquals("G test statistic",
                2.8187, g, 1E-4);
        final double p_gti = testStatistic.gTestDataSetsComparison(obs1, obs2);
        Assert.assertEquals("g-Test p-value", 0.09317325, p_gti, 1E-6);

        Assert.assertFalse(testStatistic.gTestDataSetsComparison(obs1, obs2, 0.05));
    }

    @Test
    public void testGTestSetsComparisonBadCounts() {
        long[] observed1 = {10, -1, 12, 10, 15};
        long[] observed2 = {15, 10, 10, 15, 5};
        try {
            testStatistic.gTestDataSetsComparison(
                    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.gTestDataSetsComparison(
                    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.gTestDataSetsComparison(
                    observed5, observed6);
            Assert.fail("Expecting ZeroException - vanishing counts");
        } catch (ZeroException ex) {
            // expected
        }
    }

    @Test
    public void testUnmatchedArrays() {
        final long[] observed = { 0, 1, 2, 3 };
        final double[] expected = { 1, 1, 2 };
        final long[] observed2 = {3, 4};
        try {
            testStatistic.gTest(expected, observed);
            Assert.fail("arrays have different lengths, DimensionMismatchException expected");
        } catch (DimensionMismatchException ex) {
            // expected
        }
        try {
            testStatistic.gTestDataSetsComparison(observed, observed2);
            Assert.fail("arrays have different lengths, DimensionMismatchException expected");
        } catch (DimensionMismatchException ex) {
            // expected
        }
    }

    @Test
    public void testNegativeObservedCounts() {
        final long[] observed = { 0, 1, 2, -3 };
        final double[] expected = { 1, 1, 2, 3};
        final long[] observed2 = {3, 4, 5, 0};
        try {
            testStatistic.gTest(expected, observed);
            Assert.fail("negative observed count, NotPositiveException expected");
        } catch (NotPositiveException ex) {
            // expected
        }
        try {
            testStatistic.gTestDataSetsComparison(observed, observed2);
            Assert.fail("negative observed count, NotPositiveException expected");
        } catch (NotPositiveException ex) {
            // expected
        }
    }

    @Test
    public void testZeroExpectedCounts() {
        final long[] observed = { 0, 1, 2, -3 };
        final double[] expected = { 1, 0, 2, 3};
        try {
            testStatistic.gTest(expected, observed);
            Assert.fail("zero expected count, NotStrictlyPositiveException expected");
        } catch (NotStrictlyPositiveException ex) {
            // expected
        }
    }

    @Test
    public void testBadAlpha() {
        final long[] observed = { 0, 1, 2, 3 };
        final double[] expected = { 1, 2, 2, 3};
        final long[] observed2 = { 0, 2, 2, 3 };
        try {
            testStatistic.gTest(expected, observed, 0.8);
            Assert.fail("zero expected count, NotStrictlyPositiveException expected");
        } catch (OutOfRangeException ex) {
            // expected
        }
        try {
            testStatistic.gTestDataSetsComparison(observed, observed2, -0.5);
            Assert.fail("zero expected count, NotStrictlyPositiveException expected");
        } catch (OutOfRangeException ex) {
            // expected
        }
    }

    @Test
    public void testScaling() {
      final long[] observed = {9, 11, 10, 8, 12};
      final double[] expected1 = {10, 10, 10, 10, 10};
      final double[] expected2 = {1000, 1000, 1000, 1000, 1000};
      final double[] expected3 = {1, 1, 1, 1, 1};
      final double tol = 1E-15;
      Assert.assertEquals(
              testStatistic.gTest(expected1, observed),
              testStatistic.gTest(expected2, observed),
              tol);
      Assert.assertEquals(
              testStatistic.gTest(expected1, observed),
              testStatistic.gTest(expected3, observed),
              tol);
    }

    @Test
    public void testRootLogLikelihood() {
        // positive where k11 is bigger than expected.
        Assert.assertTrue(testStatistic.rootLogLikelihoodRatio(904, 21060, 1144, 283012) > 0.0);

        // negative because k11 is lower than expected
        Assert.assertTrue(testStatistic.rootLogLikelihoodRatio(36, 21928, 60280, 623876) < 0.0);

        Assert.assertEquals(FastMath.sqrt(2.772589), testStatistic.rootLogLikelihoodRatio(1, 0, 0, 1), 0.000001);
        Assert.assertEquals(-FastMath.sqrt(2.772589), testStatistic.rootLogLikelihoodRatio(0, 1, 1, 0), 0.000001);
        Assert.assertEquals(FastMath.sqrt(27.72589), testStatistic.rootLogLikelihoodRatio(10, 0, 0, 10), 0.00001);

        Assert.assertEquals(FastMath.sqrt(39.33052), testStatistic.rootLogLikelihoodRatio(5, 1995, 0, 100000), 0.00001);
        Assert.assertEquals(-FastMath.sqrt(39.33052), testStatistic.rootLogLikelihoodRatio(0, 100000, 5, 1995), 0.00001);

        Assert.assertEquals(FastMath.sqrt(4730.737), testStatistic.rootLogLikelihoodRatio(1000, 1995, 1000, 100000), 0.001);
        Assert.assertEquals(-FastMath.sqrt(4730.737), testStatistic.rootLogLikelihoodRatio(1000, 100000, 1000, 1995), 0.001);

        Assert.assertEquals(FastMath.sqrt(5734.343), testStatistic.rootLogLikelihoodRatio(1000, 1000, 1000, 100000), 0.001);
        Assert.assertEquals(FastMath.sqrt(5714.932), testStatistic.rootLogLikelihoodRatio(1000, 1000, 1000, 99000), 0.001);
    }
}

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