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Commons Math example source code file (ChiSquareTestTest.java)
The Commons Math ChiSquareTestTest.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; /** * Test cases for the ChiSquareTestImpl class. * * @version $Revision: 902201 $ $Date: 2010-01-22 13:18:16 -0500 (Fri, 22 Jan 2010) $ */ public class ChiSquareTestTest extends TestCase { protected UnknownDistributionChiSquareTest testStatistic = new ChiSquareTestImpl(); public ChiSquareTestTest(String name) { super(name); } public void testChiSquare() throws Exception { // 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}; assertEquals("chi-square statistic", 0.2, testStatistic.chiSquare(expected, observed), 10E-12); 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 }; assertEquals( "chi-square test statistic", 9.023307936427388, testStatistic.chiSquare(expected1, observed1), 1E-10); assertEquals("chi-square p-value", 0.06051952647453607, testStatistic.chiSquareTest(expected1, observed1), 1E-9); assertTrue("chi-square test reject", testStatistic.chiSquareTest(expected1, observed1, 0.08)); assertTrue("chi-square test accept", !testStatistic.chiSquareTest(expected1, observed1, 0.05)); try { testStatistic.chiSquareTest(expected1, observed1, 95); fail("alpha out of range, IllegalArgumentException expected"); } catch (IllegalArgumentException ex) { // expected } long[] tooShortObs = { 0 }; double[] tooShortEx = { 1 }; try { testStatistic.chiSquare(tooShortEx, tooShortObs); fail("arguments too short, IllegalArgumentException expected"); } catch (IllegalArgumentException ex) { // expected } // unmatched arrays long[] unMatchedObs = { 0, 1, 2, 3 }; double[] unMatchedEx = { 1, 1, 2 }; try { testStatistic.chiSquare(unMatchedEx, unMatchedObs); fail("arrays have different lengths, IllegalArgumentException expected"); } catch (IllegalArgumentException ex) { // expected } // 0 expected count expected[0] = 0; try { testStatistic.chiSquareTest(expected, observed, .01); fail("bad expected count, IllegalArgumentException expected"); } catch (IllegalArgumentException ex) { // expected } // negative observed count expected[0] = 1; observed[0] = -1; try { testStatistic.chiSquareTest(expected, observed, .01); fail("bad expected count, IllegalArgumentException expected"); } catch (IllegalArgumentException ex) { // expected } } public void testChiSquareIndependence() throws Exception { // Target values computed using R version 1.8.1 long[][] counts = { {40, 22, 43}, {91, 21, 28}, {60, 10, 22}}; assertEquals( "chi-square test statistic", 22.709027688, testStatistic.chiSquare(counts), 1E-9); assertEquals("chi-square p-value", 0.000144751460134, testStatistic.chiSquareTest(counts), 1E-9); assertTrue("chi-square test reject", testStatistic.chiSquareTest(counts, 0.0002)); assertTrue("chi-square test accept", !testStatistic.chiSquareTest(counts, 0.0001)); long[][] counts2 = {{10, 15}, {30, 40}, {60, 90} }; assertEquals( "chi-square test statistic", 0.168965517241, testStatistic.chiSquare(counts2), 1E-9); assertEquals("chi-square p-value",0.918987499852, testStatistic.chiSquareTest(counts2), 1E-9); 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); fail("Expecting IllegalArgumentException"); } catch (IllegalArgumentException ex) { // expected } // insufficient data long[][] counts4 = {{40, 22, 43}}; try { testStatistic.chiSquare(counts4); fail("Expecting IllegalArgumentException"); } catch (IllegalArgumentException ex) { // expected } long[][] counts5 = {{40}, {40}, {30}, {10}}; try { testStatistic.chiSquare(counts5); fail("Expecting IllegalArgumentException"); } catch (IllegalArgumentException ex) { // expected } // negative counts long[][] counts6 = {{10, -2}, {30, 40}, {60, 90} }; try { testStatistic.chiSquare(counts6); fail("Expecting IllegalArgumentException"); } catch (IllegalArgumentException ex) { // expected } // bad alpha try { testStatistic.chiSquareTest(counts, 0); fail("Expecting IllegalArgumentException"); } catch (IllegalArgumentException ex) { // expected } } public void testChiSquareLargeTestStatistic() throws Exception { 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.math.stat.inference.ChiSquareTestImpl csti = new org.apache.commons.math.stat.inference.ChiSquareTestImpl(); double cst = csti.chiSquareTest(exp, obs); assertEquals("chi-square p-value", 0.0, cst, 1E-3); assertEquals( "chi-square test statistic", 114875.90421929007, testStatistic.chiSquare(exp, obs), 1E-9); } /** Contingency table containing zeros - PR # 32531 */ public void testChiSquareZeroCount() throws Exception { // Target values computed using R version 1.8.1 long[][] counts = { {40, 0, 4}, {91, 1, 2}, {60, 2, 0}}; assertEquals( "chi-square test statistic", 9.67444662263, testStatistic.chiSquare(counts), 1E-9); assertEquals("chi-square p-value", 0.0462835770603, testStatistic.chiSquareTest(counts), 1E-9); } /** Target values verified using DATAPLOT version 2006.3 */ public void testChiSquareDataSetsComparisonEqualCounts() throws Exception { long[] observed1 = {10, 12, 12, 10}; long[] observed2 = {5, 15, 14, 10}; assertEquals("chi-square p value", 0.541096, testStatistic.chiSquareTestDataSetsComparison( observed1, observed2), 1E-6); assertEquals("chi-square test statistic", 2.153846, testStatistic.chiSquareDataSetsComparison( observed1, observed2), 1E-6); assertFalse("chi-square test result", testStatistic.chiSquareTestDataSetsComparison( observed1, observed2, 0.4)); } /** Target values verified using DATAPLOT version 2006.3 */ public void testChiSquareDataSetsComparisonUnEqualCounts() throws Exception { long[] observed1 = {10, 12, 12, 10, 15}; long[] observed2 = {15, 10, 10, 15, 5}; assertEquals("chi-square p value", 0.124115, testStatistic.chiSquareTestDataSetsComparison( observed1, observed2), 1E-6); assertEquals("chi-square test statistic", 7.232189, testStatistic.chiSquareDataSetsComparison( observed1, observed2), 1E-6); assertTrue("chi-square test result", testStatistic.chiSquareTestDataSetsComparison( observed1, observed2, 0.13)); assertFalse("chi-square test result", testStatistic.chiSquareTestDataSetsComparison( observed1, observed2, 0.12)); } public void testChiSquareDataSetsComparisonBadCounts() throws Exception { long[] observed1 = {10, -1, 12, 10, 15}; long[] observed2 = {15, 10, 10, 15, 5}; try { testStatistic.chiSquareTestDataSetsComparison( observed1, observed2); fail("Expecting IllegalArgumentException - negative count"); } catch (IllegalArgumentException ex) { // expected } long[] observed3 = {10, 0, 12, 10, 15}; long[] observed4 = {15, 0, 10, 15, 5}; try { testStatistic.chiSquareTestDataSetsComparison( observed3, observed4); fail("Expecting IllegalArgumentException - double 0's"); } catch (IllegalArgumentException ex) { // expected } long[] observed5 = {10, 10, 12, 10, 15}; long[] observed6 = {0, 0, 0, 0, 0}; try { testStatistic.chiSquareTestDataSetsComparison( observed5, observed6); fail("Expecting IllegalArgumentException - vanishing counts"); } catch (IllegalArgumentException ex) { // expected } } } Other Commons Math examples (source code examples)Here is a short list of links related to this Commons Math ChiSquareTestTest.java source code file: |
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