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Java example source code file (StatUtilsTest.java)

This example Java source code file (StatUtilsTest.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.

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Java - Java tags/keywords

descriptivestatistics, expecting, mathillegalargumentexception, mean, nan, one, runtimeexception, sum, test, three, tolerance, two, var, variance

The StatUtilsTest.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;


import org.apache.commons.math3.TestUtils;
import org.apache.commons.math3.stat.descriptive.DescriptiveStatistics;
import org.apache.commons.math3.util.FastMath;
import org.apache.commons.math3.util.Precision;
import org.apache.commons.math3.exception.MathIllegalArgumentException;
import org.junit.Assert;
import org.junit.Test;

/**
 * Test cases for the {@link StatUtils} class.
 */

public final class StatUtilsTest {

    private static final double ONE = 1;
    private static final float  TWO = 2;
    private static final int    THREE = 3;
    private static final double MEAN = 2;
    private static final double SUMSQ = 18;
    private static final double SUM = 8;
    private static final double VAR = 0.666666666666666666667;
    private static final double MIN = 1;
    private static final double MAX = 3;
    private static final double TOLERANCE = 10E-15;
    private static final double NAN = Double.NaN;

    /** test stats */
    @Test
    public void testStats() {
        double[] values = new double[] { ONE, TWO, TWO, THREE };
        Assert.assertEquals("sum", SUM, StatUtils.sum(values), TOLERANCE);
        Assert.assertEquals("sumsq", SUMSQ, StatUtils.sumSq(values), TOLERANCE);
        Assert.assertEquals("var", VAR, StatUtils.variance(values), TOLERANCE);
        Assert.assertEquals("var with mean", VAR, StatUtils.variance(values, MEAN), TOLERANCE);
        Assert.assertEquals("mean", MEAN, StatUtils.mean(values), TOLERANCE);
        Assert.assertEquals("min", MIN, StatUtils.min(values), TOLERANCE);
        Assert.assertEquals("max", MAX, StatUtils.max(values), TOLERANCE);
    }

    @Test
    public void testN0andN1Conditions() {
        double[] values = new double[0];

        Assert.assertTrue(
            "Mean of n = 0 set should be NaN",
            Double.isNaN(StatUtils.mean(values)));
        Assert.assertTrue(
            "Variance of n = 0 set should be NaN",
            Double.isNaN(StatUtils.variance(values)));

        values = new double[] { ONE };

        Assert.assertTrue(
            "Mean of n = 1 set should be value of single item n1",
            StatUtils.mean(values) == ONE);
        Assert.assertTrue(
            "Variance of n = 1 set should be zero",
            StatUtils.variance(values) == 0);
    }

    @Test
    public void testArrayIndexConditions() {
        double[] values = { 1.0, 2.0, 3.0, 4.0 };

        Assert.assertEquals(
            "Sum not expected",
            5.0,
            StatUtils.sum(values, 1, 2),
            Double.MIN_VALUE);
        Assert.assertEquals(
            "Sum not expected",
            3.0,
            StatUtils.sum(values, 0, 2),
            Double.MIN_VALUE);
        Assert.assertEquals(
            "Sum not expected",
            7.0,
            StatUtils.sum(values, 2, 2),
            Double.MIN_VALUE);

        try {
            StatUtils.sum(values, 2, 3);
            Assert.fail("Expected RuntimeException");
        } catch (RuntimeException e) {
            // expected
        }

        try {
            StatUtils.sum(values, -1, 2);
            Assert.fail("Expected RuntimeException");
        } catch (RuntimeException e) {
            // expected
        }

    }

    @Test
    public void testSumSq() {
        double[] x = null;

        // test null
        try {
            StatUtils.sumSq(x);
            Assert.fail("null is not a valid data array.");
        } catch (MathIllegalArgumentException ex) {
            // success
        }

        try {
            StatUtils.sumSq(x, 0, 4);
            Assert.fail("null is not a valid data array.");
        } catch (MathIllegalArgumentException ex) {
            // success
        }

        // test empty
        x = new double[] {};
        TestUtils.assertEquals(0, StatUtils.sumSq(x), TOLERANCE);
        TestUtils.assertEquals(0, StatUtils.sumSq(x, 0, 0), TOLERANCE);

        // test one
        x = new double[] {TWO};
        TestUtils.assertEquals(4, StatUtils.sumSq(x), TOLERANCE);
        TestUtils.assertEquals(4, StatUtils.sumSq(x, 0, 1), TOLERANCE);

        // test many
        x = new double[] {ONE, TWO, TWO, THREE};
        TestUtils.assertEquals(18, StatUtils.sumSq(x), TOLERANCE);
        TestUtils.assertEquals(8, StatUtils.sumSq(x, 1, 2), TOLERANCE);
    }

    @Test
    public void testProduct() {
        double[] x = null;

        // test null
        try {
            StatUtils.product(x);
            Assert.fail("null is not a valid data array.");
        } catch (MathIllegalArgumentException ex) {
            // success
        }

        try {
            StatUtils.product(x, 0, 4);
            Assert.fail("null is not a valid data array.");
        } catch (MathIllegalArgumentException ex) {
            // success
        }

        // test empty
        x = new double[] {};
        TestUtils.assertEquals(1, StatUtils.product(x), TOLERANCE);
        TestUtils.assertEquals(1, StatUtils.product(x, 0, 0), TOLERANCE);

        // test one
        x = new double[] {TWO};
        TestUtils.assertEquals(TWO, StatUtils.product(x), TOLERANCE);
        TestUtils.assertEquals(TWO, StatUtils.product(x, 0, 1), TOLERANCE);

        // test many
        x = new double[] {ONE, TWO, TWO, THREE};
        TestUtils.assertEquals(12, StatUtils.product(x), TOLERANCE);
        TestUtils.assertEquals(4, StatUtils.product(x, 1, 2), TOLERANCE);
    }

    @Test
    public void testSumLog() {
        double[] x = null;

        // test null
        try {
            StatUtils.sumLog(x);
            Assert.fail("null is not a valid data array.");
        } catch (MathIllegalArgumentException ex) {
            // success
        }

        try {
            StatUtils.sumLog(x, 0, 4);
            Assert.fail("null is not a valid data array.");
        } catch (MathIllegalArgumentException ex) {
            // success
        }

        // test empty
        x = new double[] {};
        TestUtils.assertEquals(0, StatUtils.sumLog(x), TOLERANCE);
        TestUtils.assertEquals(0, StatUtils.sumLog(x, 0, 0), TOLERANCE);

        // test one
        x = new double[] {TWO};
        TestUtils.assertEquals(FastMath.log(TWO), StatUtils.sumLog(x), TOLERANCE);
        TestUtils.assertEquals(FastMath.log(TWO), StatUtils.sumLog(x, 0, 1), TOLERANCE);

        // test many
        x = new double[] {ONE, TWO, TWO, THREE};
        TestUtils.assertEquals(FastMath.log(ONE) + 2.0 * FastMath.log(TWO) + FastMath.log(THREE), StatUtils.sumLog(x), TOLERANCE);
        TestUtils.assertEquals(2.0 * FastMath.log(TWO), StatUtils.sumLog(x, 1, 2), TOLERANCE);
    }

    @Test
    public void testMean() {
        double[] x = null;

        try {
            StatUtils.mean(x, 0, 4);
            Assert.fail("null is not a valid data array.");
        } catch (MathIllegalArgumentException ex) {
            // success
        }

        // test empty
        x = new double[] {};
        TestUtils.assertEquals(Double.NaN, StatUtils.mean(x, 0, 0), TOLERANCE);

        // test one
        x = new double[] {TWO};
        TestUtils.assertEquals(TWO, StatUtils.mean(x, 0, 1), TOLERANCE);

        // test many
        x = new double[] {ONE, TWO, TWO, THREE};
        TestUtils.assertEquals(2.5, StatUtils.mean(x, 2, 2), TOLERANCE);
    }

    @Test
    public void testVariance() {
        double[] x = null;

        try {
            StatUtils.variance(x, 0, 4);
            Assert.fail("null is not a valid data array.");
        } catch (MathIllegalArgumentException ex) {
            // success
        }

        // test empty
        x = new double[] {};
        TestUtils.assertEquals(Double.NaN, StatUtils.variance(x, 0, 0), TOLERANCE);

        // test one
        x = new double[] {TWO};
        TestUtils.assertEquals(0.0, StatUtils.variance(x, 0, 1), TOLERANCE);

        // test many
        x = new double[] {ONE, TWO, TWO, THREE};
        TestUtils.assertEquals(0.5, StatUtils.variance(x, 2, 2), TOLERANCE);

        // test precomputed mean
        x = new double[] {ONE, TWO, TWO, THREE};
        TestUtils.assertEquals(0.5, StatUtils.variance(x,2.5, 2, 2), TOLERANCE);
    }

    @Test
    public void testPopulationVariance() {
        double[] x = null;

        try {
            StatUtils.variance(x, 0, 4);
            Assert.fail("null is not a valid data array.");
        } catch (MathIllegalArgumentException ex) {
            // success
        }

        // test empty
        x = new double[] {};
        TestUtils.assertEquals(Double.NaN, StatUtils.populationVariance(x, 0, 0), TOLERANCE);

        // test one
        x = new double[] {TWO};
        TestUtils.assertEquals(0.0, StatUtils.populationVariance(x, 0, 1), TOLERANCE);

        // test many
        x = new double[] {ONE, TWO, TWO, THREE};
        TestUtils.assertEquals(0.25, StatUtils.populationVariance(x, 0, 2), TOLERANCE);

        // test precomputed mean
        x = new double[] {ONE, TWO, TWO, THREE};
        TestUtils.assertEquals(0.25, StatUtils.populationVariance(x, 2.5, 2, 2), TOLERANCE);
    }


    @Test
    public void testMax() {
        double[] x = null;

        try {
            StatUtils.max(x, 0, 4);
            Assert.fail("null is not a valid data array.");
        } catch (MathIllegalArgumentException ex) {
            // success
        }

        // test empty
        x = new double[] {};
        TestUtils.assertEquals(Double.NaN, StatUtils.max(x, 0, 0), TOLERANCE);

        // test one
        x = new double[] {TWO};
        TestUtils.assertEquals(TWO, StatUtils.max(x, 0, 1), TOLERANCE);

        // test many
        x = new double[] {ONE, TWO, TWO, THREE};
        TestUtils.assertEquals(THREE, StatUtils.max(x, 1, 3), TOLERANCE);

        // test first nan is ignored
        x = new double[] {NAN, TWO, THREE};
        TestUtils.assertEquals(THREE, StatUtils.max(x), TOLERANCE);

        // test middle nan is ignored
        x = new double[] {ONE, NAN, THREE};
        TestUtils.assertEquals(THREE, StatUtils.max(x), TOLERANCE);

        // test last nan is ignored
        x = new double[] {ONE, TWO, NAN};
        TestUtils.assertEquals(TWO, StatUtils.max(x), TOLERANCE);

        // test all nan returns nan
        x = new double[] {NAN, NAN, NAN};
        TestUtils.assertEquals(NAN, StatUtils.max(x), TOLERANCE);
    }

    @Test
    public void testMin() {
        double[] x = null;

        try {
            StatUtils.min(x, 0, 4);
            Assert.fail("null is not a valid data array.");
        } catch (MathIllegalArgumentException ex) {
            // success
        }

        // test empty
        x = new double[] {};
        TestUtils.assertEquals(Double.NaN, StatUtils.min(x, 0, 0), TOLERANCE);

        // test one
        x = new double[] {TWO};
        TestUtils.assertEquals(TWO, StatUtils.min(x, 0, 1), TOLERANCE);

        // test many
        x = new double[] {ONE, TWO, TWO, THREE};
        TestUtils.assertEquals(TWO, StatUtils.min(x, 1, 3), TOLERANCE);

        // test first nan is ignored
        x = new double[] {NAN, TWO, THREE};
        TestUtils.assertEquals(TWO, StatUtils.min(x), TOLERANCE);

        // test middle nan is ignored
        x = new double[] {ONE, NAN, THREE};
        TestUtils.assertEquals(ONE, StatUtils.min(x), TOLERANCE);

        // test last nan is ignored
        x = new double[] {ONE, TWO, NAN};
        TestUtils.assertEquals(ONE, StatUtils.min(x), TOLERANCE);

        // test all nan returns nan
        x = new double[] {NAN, NAN, NAN};
        TestUtils.assertEquals(NAN, StatUtils.min(x), TOLERANCE);
    }

    @Test
    public void testPercentile() {
        double[] x = null;

        // test null
        try {
            StatUtils.percentile(x, .25);
            Assert.fail("null is not a valid data array.");
        } catch (MathIllegalArgumentException ex) {
            // success
        }

        try {
            StatUtils.percentile(x, 0, 4, 0.25);
            Assert.fail("null is not a valid data array.");
        } catch (MathIllegalArgumentException ex) {
            // success
        }

        // test empty
        x = new double[] {};
        TestUtils.assertEquals(Double.NaN, StatUtils.percentile(x, 25), TOLERANCE);
        TestUtils.assertEquals(Double.NaN, StatUtils.percentile(x, 0, 0, 25), TOLERANCE);

        // test one
        x = new double[] {TWO};
        TestUtils.assertEquals(TWO, StatUtils.percentile(x, 25), TOLERANCE);
        TestUtils.assertEquals(TWO, StatUtils.percentile(x, 0, 1, 25), TOLERANCE);

        // test many
        x = new double[] {ONE, TWO, TWO, THREE};
        TestUtils.assertEquals(2.5, StatUtils.percentile(x, 70), TOLERANCE);
        TestUtils.assertEquals(2.5, StatUtils.percentile(x, 1, 3, 62.5), TOLERANCE);
    }

    @Test
    public void testDifferenceStats() {
        double sample1[] = {1d, 2d, 3d, 4d};
        double sample2[] = {1d, 3d, 4d, 2d};
        double diff[] = {0d, -1d, -1d, 2d};
        double small[] = {1d, 4d};
        double meanDifference = StatUtils.meanDifference(sample1, sample2);
        Assert.assertEquals(StatUtils.sumDifference(sample1, sample2), StatUtils.sum(diff), TOLERANCE);
        Assert.assertEquals(meanDifference, StatUtils.mean(diff), TOLERANCE);
        Assert.assertEquals(StatUtils.varianceDifference(sample1, sample2, meanDifference),
                StatUtils.variance(diff), TOLERANCE);
        try {
            StatUtils.meanDifference(sample1, small);
            Assert.fail("Expecting MathIllegalArgumentException");
        } catch (MathIllegalArgumentException ex) {
            // expected
        }
        try {
            StatUtils.varianceDifference(sample1, small, meanDifference);
            Assert.fail("Expecting MathIllegalArgumentException");
        } catch (MathIllegalArgumentException ex) {
            // expected
        }
        try {
            double[] single = {1.0};
            StatUtils.varianceDifference(single, single, meanDifference);
            Assert.fail("Expecting MathIllegalArgumentException");
        } catch (MathIllegalArgumentException ex) {
            // expected
        }
    }

    @Test
    public void testGeometricMean() {
        double[] test = null;
        try {
            StatUtils.geometricMean(test);
            Assert.fail("Expecting MathIllegalArgumentException");
        } catch (MathIllegalArgumentException ex) {
            // expected
        }
        test = new double[] {2, 4, 6, 8};
        Assert.assertEquals(FastMath.exp(0.25d * StatUtils.sumLog(test)),
                StatUtils.geometricMean(test), Double.MIN_VALUE);
        Assert.assertEquals(FastMath.exp(0.5 * StatUtils.sumLog(test, 0, 2)),
                StatUtils.geometricMean(test, 0, 2), Double.MIN_VALUE);
    }


    /**
     * Run the test with the values 50 and 100 and assume standardized values
     */

    @Test
    public void testNormalize1() {
        double sample[] = { 50, 100 };
        double expectedSample[] = { -25 / FastMath.sqrt(1250), 25 / FastMath.sqrt(1250) };
        double[] out = StatUtils.normalize(sample);
        for (int i = 0; i < out.length; i++) {
            Assert.assertTrue(Precision.equals(out[i], expectedSample[i], 1));
        }

    }

    /**
     * Run with 77 random values, assuming that the outcome has a mean of 0 and a standard deviation of 1 with a
     * precision of 1E-10.
     */

    @Test
    public void testNormalize2() {
        // create an sample with 77 values
        int length = 77;
        double sample[] = new double[length];
        for (int i = 0; i < length; i++) {
            sample[i] = FastMath.random();
        }
        // normalize this sample
        double standardizedSample[] = StatUtils.normalize(sample);

        DescriptiveStatistics stats = new DescriptiveStatistics();
        // Add the data from the array
        for (int i = 0; i < length; i++) {
            stats.addValue(standardizedSample[i]);
        }
        // the calculations do have a limited precision
        double distance = 1E-10;
        // check the mean an standard deviation
        Assert.assertEquals(0.0, stats.getMean(), distance);
        Assert.assertEquals(1.0, stats.getStandardDeviation(), distance);

    }

    @Test
    public void testMode() {
        final double[] singleMode = {0, 1, 0, 2, 7, 11, 12};
        final double[] modeSingle = StatUtils.mode(singleMode);
        Assert.assertEquals(0, modeSingle[0], Double.MIN_VALUE);
        Assert.assertEquals(1, modeSingle.length);

        final double[] twoMode = {0, 1, 2, 0, 2, 3, 7, 11};
        final double[] modeDouble = StatUtils.mode(twoMode);
        Assert.assertEquals(0, modeDouble[0], Double.MIN_VALUE);
        Assert.assertEquals(2, modeDouble[1], Double.MIN_VALUE);
        Assert.assertEquals(2, modeDouble.length);

        final double[] nanInfested = {0, 0, 0, Double.NaN, Double.NaN, Double.NaN, Double.NaN, 2, 2, 2, 3, 5};
        final double[] modeNan = StatUtils.mode(nanInfested);
        Assert.assertEquals(0, modeNan[0], Double.MIN_VALUE);
        Assert.assertEquals(2, modeNan[1], Double.MIN_VALUE);
        Assert.assertEquals(2, modeNan.length);

        final double[] infInfested = {0, 0, Double.POSITIVE_INFINITY, Double.POSITIVE_INFINITY,
            Double.NEGATIVE_INFINITY, Double.NEGATIVE_INFINITY, 2, 2, 3, 5};
        final double[] modeInf = StatUtils.mode(infInfested);
        Assert.assertEquals(Double.NEGATIVE_INFINITY, modeInf[0], Double.MIN_VALUE);
        Assert.assertEquals(0, modeInf[1], Double.MIN_VALUE);
        Assert.assertEquals(2, modeInf[2], Double.MIN_VALUE);
        Assert.assertEquals(Double.POSITIVE_INFINITY, modeInf[3], Double.MIN_VALUE);
        Assert.assertEquals(4, modeInf.length);

        final double[] noData = {};
        final double[] modeNodata = StatUtils.mode(noData);
        Assert.assertEquals(0, modeNodata.length);

        final double[] nansOnly = {Double.NaN, Double.NaN};
        final double[] modeNansOnly = StatUtils.mode(nansOnly);
        Assert.assertEquals(0, modeNansOnly.length);

        final double[] nullArray = null;
        try {
            StatUtils.mode(nullArray);
            Assert.fail("Expecting MathIllegalArgumentException");
        } catch (MathIllegalArgumentException ex) {
            // Expected
        }
    }

}

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