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* 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.math4.stat.inference;
import org.apache.commons.math4.exception.DimensionMismatchException;
import org.apache.commons.math4.exception.NotPositiveException;
import org.apache.commons.math4.exception.NotStrictlyPositiveException;
import org.apache.commons.math4.exception.OutOfRangeException;
import org.apache.commons.math4.exception.ZeroException;
import org.apache.commons.math4.stat.inference.ChiSquareTest;
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.math4.stat.inference.ChiSquareTest csti =
new org.apache.commons.math4.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
}
}
}