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Commons Math example source code file (TTestTest.java)

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

Java - Commons Math tags/keywords

exception, exception, illegalargumentexception, illegalargumentexception, override, summarystatistics, summarystatistics, testcase, ttest, ttestimpl, ttesttest, ttesttest

The Commons Math TTestTest.java 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.math.stat.inference;

import junit.framework.TestCase;

import org.apache.commons.math.stat.descriptive.SummaryStatistics;
/**
 * Test cases for the TTestImpl class.
 *
 * @version $Revision: 902201 $ $Date: 2010-01-22 13:18:16 -0500 (Fri, 22 Jan 2010) $
 */

public class TTestTest extends TestCase {

    protected TTest testStatistic = new TTestImpl();

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

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

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

    public void testOneSampleT() throws Exception {
        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)
        assertEquals("t statistic",  -2.81976445346,
                testStatistic.t(mu, observed), 10E-10);
        assertEquals("t statistic",  -2.81976445346,
                testStatistic.t(mu, sampleStats), 10E-10);
        assertEquals("p value", 0.0136390585873,
                testStatistic.tTest(mu, observed), 10E-10);
        assertEquals("p value", 0.0136390585873,
                testStatistic.tTest(mu, sampleStats), 10E-10);

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

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

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

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

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

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

    public void testOneSampleTTest() throws Exception {
        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)
        assertEquals("one sample t stat", 3.86485535541,
                testStatistic.t(0d, oneSidedP), 10E-10);
        assertEquals("one sample t stat", 3.86485535541,
                testStatistic.t(0d, oneSidedPStats),1E-10);
        assertEquals("one sample p value", 0.000521637019637,
                testStatistic.tTest(0d, oneSidedP) / 2d, 10E-10);
        assertEquals("one sample p value", 0.000521637019637,
                testStatistic.tTest(0d, oneSidedPStats) / 2d, 10E-5);
        assertTrue("one sample t-test reject", testStatistic.tTest(0d, oneSidedP, 0.01));
        assertTrue("one sample t-test reject", testStatistic.tTest(0d, oneSidedPStats, 0.01));
        assertTrue("one sample t-test accept", !testStatistic.tTest(0d, oneSidedP, 0.0001));
        assertTrue("one sample t-test accept", !testStatistic.tTest(0d, oneSidedPStats, 0.0001));

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

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

    }

    public void testTwoSampleTHeterscedastic() throws Exception {
        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)
        assertEquals("two sample heteroscedastic t stat", 1.60371728768,
                testStatistic.t(sample1, sample2), 1E-10);
        assertEquals("two sample heteroscedastic t stat", 1.60371728768,
                testStatistic.t(sampleStats1, sampleStats2), 1E-10);
        assertEquals("two sample heteroscedastic p value", 0.128839369622,
                testStatistic.tTest(sample1, sample2), 1E-10);
        assertEquals("two sample heteroscedastic p value", 0.128839369622,
                testStatistic.tTest(sampleStats1, sampleStats2), 1E-10);
        assertTrue("two sample heteroscedastic t-test reject",
                testStatistic.tTest(sample1, sample2, 0.2));
        assertTrue("two sample heteroscedastic t-test reject",
                testStatistic.tTest(sampleStats1, sampleStats2, 0.2));
        assertTrue("two sample heteroscedastic t-test accept",
                !testStatistic.tTest(sample1, sample2, 0.1));
        assertTrue("two sample heteroscedastic t-test accept",
                !testStatistic.tTest(sampleStats1, sampleStats2, 0.1));

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

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

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

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

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

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

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

        try {
            testStatistic.t(sampleStats1, tooShortStats);
            fail("insufficient data, IllegalArgumentException expected");
        } catch (IllegalArgumentException ex) {
           // expected
        }
    }
    public void testTwoSampleTHomoscedastic() throws Exception {
        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)
        assertEquals("two sample homoscedastic t stat", 0.73096310086,
              testStatistic.homoscedasticT(sample1, sample2), 10E-11);
        assertEquals("two sample homoscedastic p value", 0.4833963785,
                testStatistic.homoscedasticTTest(sampleStats1, sampleStats2), 1E-10);
        assertTrue("two sample homoscedastic t-test reject",
                testStatistic.homoscedasticTTest(sample1, sample2, 0.49));
        assertTrue("two sample homoscedastic t-test accept",
                !testStatistic.homoscedasticTTest(sample1, sample2, 0.48));
    }

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

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

    public void testPaired() throws Exception {
        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)
        assertEquals(-0.3133, testStatistic.pairedT(sample1, sample2), 1E-4);
        assertEquals(0.774544295819, testStatistic.pairedTTest(sample1, sample2), 1E-10);
        assertEquals(0.001208, testStatistic.pairedTTest(sample1, sample3), 1E-6);
        assertFalse(testStatistic.pairedTTest(sample1, sample3, .001));
        assertTrue(testStatistic.pairedTTest(sample1, sample3, .002));
    }
}

Other Commons Math examples (source code examples)

Here is a short list of links related to this Commons Math TTestTest.java source code file:

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