| /* |
| * 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 |
| } |
| } |
| } |