diff --git a/commons-math-legacy/src/test/java/org/apache/commons/math4/legacy/stat/StatUtilsTest.java.orig b/commons-math-legacy/src/test/java/org/apache/commons/math4/legacy/stat/StatUtilsTest.java.orig deleted file mode 100644 index dad6cd582..000000000 --- a/commons-math-legacy/src/test/java/org/apache/commons/math4/legacy/stat/StatUtilsTest.java.orig +++ /dev/null @@ -1,556 +0,0 @@ -/* - * 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; - - -import org.apache.commons.math4.TestUtils; -import org.apache.commons.math4.exception.MathIllegalArgumentException; -import org.apache.commons.math4.exception.NullArgumentException; -import org.apache.commons.math4.stat.descriptive.DescriptiveStatistics; -import org.apache.commons.math4.util.FastMath; -import org.apache.commons.numbers.core.Precision; -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 (NullArgumentException ex) { - // success - } - - try { - StatUtils.sumSq(x, 0, 4); - Assert.fail("null is not a valid data array."); - } catch (NullArgumentException 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 (NullArgumentException ex) { - // success - } - - try { - StatUtils.product(x, 0, 4); - Assert.fail("null is not a valid data array."); - } catch (NullArgumentException 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 (NullArgumentException ex) { - // success - } - - try { - StatUtils.sumLog(x, 0, 4); - Assert.fail("null is not a valid data array."); - } catch (NullArgumentException 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 (NullArgumentException 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 (NullArgumentException 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 (NullArgumentException 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 (NullArgumentException 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 (NullArgumentException 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 (NullArgumentException ex) { - // success - } - - try { - StatUtils.percentile(x, 0, 4, 0.25); - Assert.fail("null is not a valid data array."); - } catch (NullArgumentException 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 NullArgumentException"); - } catch (NullArgumentException 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 NullArgumentException"); - } catch (NullArgumentException ex) { - // Expected - } - } - -}