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Java example source code file (TTestTest.java)

This example Java source code file (TTestTest.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

before, nullargumentexception, numberistoosmallexception, outofrangeexception, summarystatistics, test, ttest, ttesttest

The TTestTest.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.NullArgumentException;
import org.apache.commons.math3.exception.NumberIsTooSmallException;
import org.apache.commons.math3.exception.OutOfRangeException;
import org.apache.commons.math3.stat.descriptive.SummaryStatistics;
import org.junit.Assert;
import org.junit.Before;
import org.junit.Test;

/**
 * Test cases for the TTestImpl class.
 *
 */
public class TTestTest {

    protected TTest testStatistic = new TTest();

    private double[] tooShortObs = { 1.0 };
    private double[] emptyObs = {};
    private SummaryStatistics emptyStats = new SummaryStatistics();
   SummaryStatistics tooShortStats = null;

    @Before
    public void setUp() {
        tooShortStats = new SummaryStatistics();
        tooShortStats.addValue(0d);
    }

    @Test
    public void testOneSampleT() {
        double[] observed =
            {93.0, 103.0, 95.0, 101.0, 91.0, 105.0, 96.0, 94.0, 101.0,  88.0, 98.0, 94.0, 101.0, 92.0, 95.0 };
        double mu = 100.0;
        SummaryStatistics sampleStats = null;
        sampleStats = new SummaryStatistics();
        for (int i = 0; i < observed.length; i++) {
            sampleStats.addValue(observed[i]);
        }

        // Target comparison values computed using R version 1.8.1 (Linux version)
        Assert.assertEquals("t statistic",  -2.81976445346,
                testStatistic.t(mu, observed), 10E-10);
        Assert.assertEquals("t statistic",  -2.81976445346,
                testStatistic.t(mu, sampleStats), 10E-10);
        Assert.assertEquals("p value", 0.0136390585873,
                testStatistic.tTest(mu, observed), 10E-10);
        Assert.assertEquals("p value", 0.0136390585873,
                testStatistic.tTest(mu, sampleStats), 10E-10);

        try {
            testStatistic.t(mu, (double[]) null);
            Assert.fail("arguments too short, NullArgumentException expected");
        } catch (NullArgumentException ex) {
            // expected
        }

        try {
            testStatistic.t(mu, (SummaryStatistics) null);
            Assert.fail("arguments too short, NullArgumentException expected");
        } catch (NullArgumentException ex) {
            // expected
        }

        try {
            testStatistic.t(mu, emptyObs);
            Assert.fail("arguments too short, NumberIsTooSmallException expected");
        } catch (NumberIsTooSmallException ex) {
            // expected
        }

        try {
            testStatistic.t(mu, emptyStats);
            Assert.fail("arguments too short, NumberIsTooSmallException expected");
        } catch (NumberIsTooSmallException ex) {
            // expected
        }

        try {
            testStatistic.t(mu, tooShortObs);
            Assert.fail("insufficient data to compute t statistic, NumberIsTooSmallException expected");
        } catch (NumberIsTooSmallException ex) {
            // expected
        }
        try {
            testStatistic.tTest(mu, tooShortObs);
            Assert.fail("insufficient data to perform t test, NumberIsTooSmallException expected");
        } catch (NumberIsTooSmallException ex) {
           // expected
        }

        try {
            testStatistic.t(mu, tooShortStats);
            Assert.fail("insufficient data to compute t statistic, NumberIsTooSmallException expected");
        } catch (NumberIsTooSmallException ex) {
            // expected
        }
        try {
            testStatistic.tTest(mu, tooShortStats);
            Assert.fail("insufficient data to perform t test, NumberIsTooSmallException expected");
        } catch (NumberIsTooSmallException ex) {
            // expected
        }
    }

    @Test
    public void testOneSampleTTest() {
        double[] oneSidedP =
            {2d, 0d, 6d, 6d, 3d, 3d, 2d, 3d, -6d, 6d, 6d, 6d, 3d, 0d, 1d, 1d, 0d, 2d, 3d, 3d };
        SummaryStatistics oneSidedPStats = new SummaryStatistics();
        for (int i = 0; i < oneSidedP.length; i++) {
            oneSidedPStats.addValue(oneSidedP[i]);
        }
        // Target comparison values computed using R version 1.8.1 (Linux version)
        Assert.assertEquals("one sample t stat", 3.86485535541,
                testStatistic.t(0d, oneSidedP), 10E-10);
        Assert.assertEquals("one sample t stat", 3.86485535541,
                testStatistic.t(0d, oneSidedPStats),1E-10);
        Assert.assertEquals("one sample p value", 0.000521637019637,
                testStatistic.tTest(0d, oneSidedP) / 2d, 10E-10);
        Assert.assertEquals("one sample p value", 0.000521637019637,
                testStatistic.tTest(0d, oneSidedPStats) / 2d, 10E-5);
        Assert.assertTrue("one sample t-test reject", testStatistic.tTest(0d, oneSidedP, 0.01));
        Assert.assertTrue("one sample t-test reject", testStatistic.tTest(0d, oneSidedPStats, 0.01));
        Assert.assertTrue("one sample t-test accept", !testStatistic.tTest(0d, oneSidedP, 0.0001));
        Assert.assertTrue("one sample t-test accept", !testStatistic.tTest(0d, oneSidedPStats, 0.0001));

        try {
            testStatistic.tTest(0d, oneSidedP, 95);
            Assert.fail("alpha out of range, OutOfRangeException expected");
        } catch (OutOfRangeException ex) {
            // expected
        }

        try {
            testStatistic.tTest(0d, oneSidedPStats, 95);
            Assert.fail("alpha out of range, OutOfRangeException expected");
        } catch (OutOfRangeException ex) {
            // expected
        }

    }

    @Test
    public void testTwoSampleTHeterscedastic() {
        double[] sample1 = { 7d, -4d, 18d, 17d, -3d, -5d, 1d, 10d, 11d, -2d };
        double[] sample2 = { -1d, 12d, -1d, -3d, 3d, -5d, 5d, 2d, -11d, -1d, -3d };
        SummaryStatistics sampleStats1 = new SummaryStatistics();
        for (int i = 0; i < sample1.length; i++) {
            sampleStats1.addValue(sample1[i]);
        }
        SummaryStatistics sampleStats2 = new SummaryStatistics();
        for (int i = 0; i < sample2.length; i++) {
            sampleStats2.addValue(sample2[i]);
        }

        // Target comparison values computed using R version 1.8.1 (Linux version)
        Assert.assertEquals("two sample heteroscedastic t stat", 1.60371728768,
                testStatistic.t(sample1, sample2), 1E-10);
        Assert.assertEquals("two sample heteroscedastic t stat", 1.60371728768,
                testStatistic.t(sampleStats1, sampleStats2), 1E-10);
        Assert.assertEquals("two sample heteroscedastic p value", 0.128839369622,
                testStatistic.tTest(sample1, sample2), 1E-10);
        Assert.assertEquals("two sample heteroscedastic p value", 0.128839369622,
                testStatistic.tTest(sampleStats1, sampleStats2), 1E-10);
        Assert.assertTrue("two sample heteroscedastic t-test reject",
                testStatistic.tTest(sample1, sample2, 0.2));
        Assert.assertTrue("two sample heteroscedastic t-test reject",
                testStatistic.tTest(sampleStats1, sampleStats2, 0.2));
        Assert.assertTrue("two sample heteroscedastic t-test accept",
                !testStatistic.tTest(sample1, sample2, 0.1));
        Assert.assertTrue("two sample heteroscedastic t-test accept",
                !testStatistic.tTest(sampleStats1, sampleStats2, 0.1));

        try {
            testStatistic.tTest(sample1, sample2, .95);
            Assert.fail("alpha out of range, OutOfRangeException expected");
        } catch (OutOfRangeException ex) {
            // expected
        }

        try {
            testStatistic.tTest(sampleStats1, sampleStats2, .95);
            Assert.fail("alpha out of range, OutOfRangeException expected");
        } catch (OutOfRangeException ex) {
            // expected
        }

        try {
            testStatistic.tTest(sample1, tooShortObs, .01);
            Assert.fail("insufficient data, NumberIsTooSmallException expected");
        } catch (NumberIsTooSmallException ex) {
            // expected
        }

        try {
            testStatistic.tTest(sampleStats1, tooShortStats, .01);
            Assert.fail("insufficient data, NumberIsTooSmallException expected");
        } catch (NumberIsTooSmallException ex) {
            // expected
        }

        try {
            testStatistic.tTest(sample1, tooShortObs);
            Assert.fail("insufficient data, NumberIsTooSmallException expected");
        } catch (NumberIsTooSmallException ex) {
           // expected
        }

        try {
            testStatistic.tTest(sampleStats1, tooShortStats);
            Assert.fail("insufficient data, NumberIsTooSmallException expected");
        } catch (NumberIsTooSmallException ex) {
            // expected
        }

        try {
            testStatistic.t(sample1, tooShortObs);
            Assert.fail("insufficient data, NumberIsTooSmallException expected");
        } catch (NumberIsTooSmallException ex) {
            // expected
        }

        try {
            testStatistic.t(sampleStats1, tooShortStats);
            Assert.fail("insufficient data, NumberIsTooSmallException expected");
        } catch (NumberIsTooSmallException ex) {
           // expected
        }
    }
    @Test
    public void testTwoSampleTHomoscedastic() {
        double[] sample1 ={2, 4, 6, 8, 10, 97};
        double[] sample2 = {4, 6, 8, 10, 16};
        SummaryStatistics sampleStats1 = new SummaryStatistics();
        for (int i = 0; i < sample1.length; i++) {
            sampleStats1.addValue(sample1[i]);
        }
        SummaryStatistics sampleStats2 = new SummaryStatistics();
        for (int i = 0; i < sample2.length; i++) {
            sampleStats2.addValue(sample2[i]);
        }

        // Target comparison values computed using R version 1.8.1 (Linux version)
        Assert.assertEquals("two sample homoscedastic t stat", 0.73096310086,
              testStatistic.homoscedasticT(sample1, sample2), 10E-11);
        Assert.assertEquals("two sample homoscedastic p value", 0.4833963785,
                testStatistic.homoscedasticTTest(sampleStats1, sampleStats2), 1E-10);
        Assert.assertTrue("two sample homoscedastic t-test reject",
                testStatistic.homoscedasticTTest(sample1, sample2, 0.49));
        Assert.assertTrue("two sample homoscedastic t-test accept",
                !testStatistic.homoscedasticTTest(sample1, sample2, 0.48));
    }

    @Test
    public void testSmallSamples() {
        double[] sample1 = {1d, 3d};
        double[] sample2 = {4d, 5d};

        // Target values computed using R, version 1.8.1 (linux version)
        Assert.assertEquals(-2.2360679775, testStatistic.t(sample1, sample2),
                1E-10);
        Assert.assertEquals(0.198727388935, testStatistic.tTest(sample1, sample2),
                1E-10);
    }

    @Test
    public void testPaired() {
        double[] sample1 = {1d, 3d, 5d, 7d};
        double[] sample2 = {0d, 6d, 11d, 2d};
        double[] sample3 = {5d, 7d, 8d, 10d};

        // Target values computed using R, version 1.8.1 (linux version)
        Assert.assertEquals(-0.3133, testStatistic.pairedT(sample1, sample2), 1E-4);
        Assert.assertEquals(0.774544295819, testStatistic.pairedTTest(sample1, sample2), 1E-10);
        Assert.assertEquals(0.001208, testStatistic.pairedTTest(sample1, sample3), 1E-6);
        Assert.assertFalse(testStatistic.pairedTTest(sample1, sample3, .001));
        Assert.assertTrue(testStatistic.pairedTTest(sample1, sample3, .002));
    }
}

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