2010/12/30 Luc Maisonobe <luc.maison...@free.fr>: > Le 30/12/2010 16:44, Mikkel Meyer Andersen a écrit : >> 2010/12/30 Luc Maisonobe <luc.maison...@free.fr>: >>> Le 30/12/2010 16:18, Luc Maisonobe a écrit : >>>> Le 30/12/2010 11:00, Mikkel Meyer Andersen a écrit : >>>>> Hi, >>>> >>>> Hi Mikkel, >>>> >>>>> >>>>> This commit consists of new files, so I put >>>>> @version $Revision: $ $Date: $ >>>>> in the top. I thought SVN would then auto update these, but after >>>>> checking out again to see if it worked, I see that it didn't. What >>>>> should I do to make it work? Fire a svn propXXX, use other variables, >>>>> or? >>>> >>>> You should set some properties. The ones we traditionally use are: >>>> svn:eol-style=native >>>> svn:keywords="Author Date Id Revision" >>> >>> Well, in fact we have a policy not to use Author, but rather to put the >>> author names in the contibutor and developpers sections of the pom.xml file. >>> >>> Luc >>> >>>> >>>> One way to have these properties automatically set is to use a "config" >>>> file in subversion configuration folder. I have put the file I use here: >>>> <http://people.apache.org/~luc/config>. >>>> >>>> I think the file is used only for newly created files, so now that the >>>> files are already in the repository, you should probably set the >>>> properties manually. >>>> >>>> best regards, >>>> Luc >>>> >>>>> >>>>> Cheers, Mikkel. >>>>> >>>>> 2010/12/30 <m...@apache.org>: >>>>>> Author: mikl >>>>>> Date: Thu Dec 30 09:52:00 2010 >>>>>> New Revision: 1053836 >>>>>> >>>>>> URL: http://svn.apache.org/viewvc?rev=1053836&view=rev >>>>>> Log: >>>>>> Starting point for fixing MATH-431. Still some validation tests and >>>>>> documentation are missing. >>>>>> >>>>>> Added: >>>>>> >>>>>> commons/proper/math/trunk/src/main/java/org/apache/commons/math/stat/inference/MannWhitneyUTest.java >>>>>> >>>>>> commons/proper/math/trunk/src/main/java/org/apache/commons/math/stat/inference/MannWhitneyUTestImpl.java >>>>>> >>>>>> commons/proper/math/trunk/src/main/java/org/apache/commons/math/stat/inference/WilcoxonSignedRankTest.java >>>>>> >>>>>> commons/proper/math/trunk/src/main/java/org/apache/commons/math/stat/inference/WilcoxonSignedRankTestImpl.java >>>>>> >>>>>> commons/proper/math/trunk/src/test/java/org/apache/commons/math/stat/inference/MannWhitneyUTestTest.java >>>>>> >>>>>> commons/proper/math/trunk/src/test/java/org/apache/commons/math/stat/inference/WilcoxonSignedRankTestTest.java >>>>>> >>>>>> Added: >>>>>> commons/proper/math/trunk/src/main/java/org/apache/commons/math/stat/inference/MannWhitneyUTest.java >>>>>> URL: >>>>>> http://svn.apache.org/viewvc/commons/proper/math/trunk/src/main/java/org/apache/commons/math/stat/inference/MannWhitneyUTest.java?rev=1053836&view=auto >>>>>> ============================================================================== >>>>>> --- >>>>>> commons/proper/math/trunk/src/main/java/org/apache/commons/math/stat/inference/MannWhitneyUTest.java >>>>>> (added) >>>>>> +++ >>>>>> commons/proper/math/trunk/src/main/java/org/apache/commons/math/stat/inference/MannWhitneyUTest.java >>>>>> Thu Dec 30 09:52:00 2010 >>>>>> @@ -0,0 +1,96 @@ >>>>>> +/* >>>>>> + * 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 org.apache.commons.math.MathException; >>>>>> + >>>>>> +/** >>>>>> + * An interface for Mann-Whitney U test (also called Wilcoxon rank-sum >>>>>> test). >>>>>> + * >>>>>> + * @version $Revision: $ $Date: $ >>>>>> + */ >>>>>> +public interface MannWhitneyUTest { >>>>>> + >>>>>> + /** >>>>>> + * Computes the <a >>>>>> + * href="http://en.wikipedia.org/wiki/Mann%E2%80%93Whitney_U";> >>>>>> Mann-Whitney >>>>>> + * U statistic</a> comparing mean for two independent samples >>>>>> possibly of >>>>>> + * different length. >>>>>> + * <p> >>>>>> + * This statistic can be used to perform a Mann-Whitney U test >>>>>> evaluating >>>>>> + * the null hypothesis that the two independent samples has equal >>>>>> mean. >>>>>> + * </p> >>>>>> + * <p> >>>>>> + * Let X<sub>i</sub> denote the i'th individual of the first sample >>>>>> and >>>>>> + * Y<sub>j</sub> the j'th individual in the second sample. Note >>>>>> that the >>>>>> + * samples would often have different length. >>>>>> + * </p> >>>>>> + * <p> >>>>>> + * <strong>Preconditions</strong>: >>>>>> + * <ul> >>>>>> + * <li>All observations in the two samples are independent.</li> >>>>>> + * <li>The observations are at least ordinal (continuous are also >>>>>> ordinal).</li> >>>>>> + * </ul> >>>>>> + * </p> >>>>>> + * >>>>>> + * @param x >>>>>> + * the first sample >>>>>> + * @param y >>>>>> + * the second sample >>>>>> + * @return mannWhitneyU statistic >>>>>> + * @throws IllegalArgumentException >>>>>> + * if preconditions are not met >>>>>> + */ >>>>>> + double mannWhitneyU(final double[] x, final double[] y) >>>>>> + throws IllegalArgumentException; >>>>>> + >>>>>> + /** >>>>>> + * Returns the asymptotic <i>observed significance level</i>, or <a >>>>>> href= >>>>>> + * "http://www.cas.lancs.ac.uk/glossary_v1.1/hyptest.html#pvalue";> >>>>>> + * p-value</a>, associated with a <a >>>>>> + * href="http://en.wikipedia.org/wiki/Mann%E2%80%93Whitney_U";> >>>>>> Mann-Whitney >>>>>> + * U statistic</a> comparing mean for two independent samples. >>>>>> + * <p> >>>>>> + * Let X<sub>i</sub> denote the i'th individual of the first sample >>>>>> and >>>>>> + * Y<sub>j</sub> the j'th individual in the second sample. Note >>>>>> that the >>>>>> + * samples would often have different length. >>>>>> + * </p> >>>>>> + * <p> >>>>>> + * <strong>Preconditions</strong>: >>>>>> + * <ul> >>>>>> + * <li>All observations in the two samples are independent.</li> >>>>>> + * <li>The observations are at least ordinal (continuous are also >>>>>> ordinal).</li> >>>>>> + * </ul> >>>>>> + * </p> >>>>>> + * >>>>>> + * @param x >>>>>> + * the first sample >>>>>> + * @param y >>>>>> + * the second sample >>>>>> + * @param exactPValue >>>>>> + * if the exact p-value is wanted (only works for >>>>>> x.length <= 30, >>>>>> + * if true and x.length > 30, this is ignored because >>>>>> + * calculations may take too long) >>>>>> + * @return asymptotic p-value >>>>>> + * @throws IllegalArgumentException >>>>>> + * if preconditions are not met >>>>>> + * @throws MathException >>>>>> + * if an error occurs computing the p-value >>>>>> + */ >>>>>> + double mannWhitneyUTest(final double[] x, final double[] y) >>>>>> + throws IllegalArgumentException, MathException; >>>>>> +} >>>>>> >>>>>> Added: >>>>>> commons/proper/math/trunk/src/main/java/org/apache/commons/math/stat/inference/MannWhitneyUTestImpl.java >>>>>> URL: >>>>>> http://svn.apache.org/viewvc/commons/proper/math/trunk/src/main/java/org/apache/commons/math/stat/inference/MannWhitneyUTestImpl.java?rev=1053836&view=auto >>>>>> ============================================================================== >>>>>> --- >>>>>> commons/proper/math/trunk/src/main/java/org/apache/commons/math/stat/inference/MannWhitneyUTestImpl.java >>>>>> (added) >>>>>> +++ >>>>>> commons/proper/math/trunk/src/main/java/org/apache/commons/math/stat/inference/MannWhitneyUTestImpl.java >>>>>> Thu Dec 30 09:52:00 2010 >>>>>> @@ -0,0 +1,199 @@ >>>>>> +/* >>>>>> + * 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 org.apache.commons.math.MathException; >>>>>> +import org.apache.commons.math.distribution.NormalDistributionImpl; >>>>>> +import org.apache.commons.math.stat.ranking.NaNStrategy; >>>>>> +import org.apache.commons.math.stat.ranking.NaturalRanking; >>>>>> +import org.apache.commons.math.stat.ranking.TiesStrategy; >>>>>> +import org.apache.commons.math.util.FastMath; >>>>>> + >>>>>> +/** >>>>>> + * An implementation of the Mann-Whitney U test (also called Wilcoxon >>>>>> rank-sum >>>>>> + * test). >>>>>> + * >>>>>> + * @version $Revision: $ $Date: $ >>>>>> + */ >>>>>> +public class MannWhitneyUTestImpl implements MannWhitneyUTest { >>>>>> + private NaturalRanking naturalRanking; >>>>>> + >>>>>> + /** >>>>>> + * Create a test instance using where NaN's are left in place and >>>>>> ties get >>>>>> + * the average of applicable ranks. Use this unless you are very >>>>>> sure of >>>>>> + * what you are doing. >>>>>> + */ >>>>>> + public MannWhitneyUTestImpl() { >>>>>> + naturalRanking = new NaturalRanking(NaNStrategy.FIXED, >>>>>> + TiesStrategy.AVERAGE); >>>>>> + } >>>>>> + >>>>>> + /** >>>>>> + * Create a test instance using the given strategies for NaN's and >>>>>> ties. >>>>>> + * Only use this if you are sure of what you are doing. >>>>>> + * >>>>>> + * @param nanStrategy >>>>>> + * specifies the strategy that should be used for >>>>>> Double.NaN's >>>>>> + * @param tiesStrategy >>>>>> + * specifies the strategy that should be used for ties >>>>>> + */ >>>>>> + public MannWhitneyUTestImpl(NaNStrategy nanStrategy, >>>>>> + TiesStrategy tiesStrategy) { >>>>>> + naturalRanking = new NaturalRanking(nanStrategy, tiesStrategy); >>>>>> + } >>>>>> + >>>>>> + /** >>>>>> + * Ensures that the provided arrays fulfills the assumptions. >>>>>> + * >>>>>> + * @param x >>>>>> + * @param y >>>>>> + * @throws IllegalArgumentException >>>>>> + * if assumptions are not met >>>>>> + */ >>>>>> + private void ensureDataConformance(final double[] x, final double[] >>>>>> y) >>>>>> + throws IllegalArgumentException { >>>>>> + if (x == null) { >>>>>> + throw new IllegalArgumentException("x must not be null"); >>>>>> + } >>>>>> + >>>>>> + if (y == null) { >>>>>> + throw new IllegalArgumentException("y must not be null"); >>>>>> + } >>>>>> + >>>>>> + if (x.length == 0) { >>>>>> + throw new IllegalArgumentException( >>>>>> + "x must contain at least one element"); >>>>>> + } >>>>>> + >>>>>> + if (y.length == 0) { >>>>>> + throw new IllegalArgumentException( >>>>>> + "y must contain at least one element"); >>>>>> + } >>>>>> + } >>>>>> + >>>>>> + private double[] concatinateSamples(final double[] x, final >>>>>> double[] y) { >>>>>> + final double[] z = new double[x.length + y.length]; >>>>>> + >>>>>> + System.arraycopy(x, 0, z, 0, x.length); >>>>>> + System.arraycopy(y, 0, z, x.length, y.length); >>>>>> + >>>>>> + return z; >>>>>> + } >>>>>> + >>>>>> + /** >>>>>> + * {...@inheritdoc} >>>>>> + * >>>>>> + * @param x >>>>>> + * the first sample >>>>>> + * @param y >>>>>> + * the second sample >>>>>> + * @return mannWhitneyU statistic U (maximum of U<sup>x</sup> and >>>>>> U<sup>y</sup>) >>>>>> + * @throws IllegalArgumentException >>>>>> + * if preconditions are not met >>>>>> + */ >>>>>> + public double mannWhitneyU(final double[] x, final double[] y) >>>>>> + throws IllegalArgumentException { >>>>>> + >>>>>> + ensureDataConformance(x, y); >>>>>> + >>>>>> + final double[] z = concatinateSamples(x, y); >>>>>> + final double[] ranks = naturalRanking.rank(z); >>>>>> + >>>>>> + double sumRankX = 0; >>>>>> + >>>>>> + /* >>>>>> + * The ranks for x is in the first x.length entries in ranks >>>>>> because x >>>>>> + * is in the first x.length entries in z >>>>>> + */ >>>>>> + for (int i = 0; i < x.length; ++i) { >>>>>> + sumRankX += ranks[i]; >>>>>> + } >>>>>> + >>>>>> + /* >>>>>> + * U1 = R1 - (n1 * (n1 + 1)) / 2 where R1 is sum of ranks for >>>>>> sample 1, >>>>>> + * e.g. x, n1 is the number of observations in sample 1. >>>>>> + */ >>>>>> + final double U1 = sumRankX - (x.length * (x.length + 1)) / 2; >>>>>> + >>>>>> + /* >>>>>> + * It can be shown that U1 + U2 = n1 * n2 >>>>>> + */ >>>>>> + final double U2 = x.length * y.length - U1; >>>>>> + >>>>>> + return FastMath.max(U1, U2); >>>>>> + } >>>>>> + >>>>>> + /** >>>>>> + * @param Umin >>>>>> + * smallest Mann-Whitney U value >>>>>> + * @param N >>>>>> + * number of subjects (corresponding to x.length) >>>>>> + * @return two-sided asymptotic p-value >>>>>> + * @throws MathException >>>>>> + * if an error occurs computing the p-value >>>>>> + */ >>>>>> + private double calculateAsymptoticPValue(final double Umin, final >>>>>> int n1, >>>>>> + final int n2) throws MathException { >>>>>> + >>>>>> + final int n1n2prod = n1 * n2; >>>>>> + >>>>>> + // >>>>>> http://en.wikipedia.org/wiki/Mann%E2%80%93Whitney_U#Normal_approximation >>>>>> + final double EU = (double) n1n2prod / 2.0; >>>>>> + final double VarU = (double) (n1n2prod * (n1 + n2 + 1)) / 12.0; >>>>>> + >>>>>> + final double z = (Umin - EU) / FastMath.sqrt(VarU); >>>>>> + >>>>>> + final NormalDistributionImpl standardNormal = new >>>>>> NormalDistributionImpl( >>>>>> + 0, 1); >>>>>> + >>>>>> + return 2 * standardNormal.cumulativeProbability(z); >>>>>> + } >>>>>> + >>>>>> + /** >>>>>> + * Ties give rise to biased variance at the moment. See e.g. <a >>>>>> + * >>>>>> href="http://mlsc.lboro.ac.uk/resources/statistics/Mannwhitney.pdf"; >>>>>> + * >>>>>> >http://mlsc.lboro.ac.uk/resources/statistics/Mannwhitney.pdf</a>. >>>>>> + * >>>>>> + * {...@inheritdoc} >>>>>> + * >>>>>> + * @param x >>>>>> + * the first sample >>>>>> + * @param y >>>>>> + * the second sample >>>>>> + * @param exactPValue >>>>>> + * if the exact p-value is wanted (only for x.length <= >>>>>> 50) >>>>>> + * @return asymptotic p-value (biased for samples with ties) >>>>>> + * @throws IllegalArgumentException >>>>>> + * if preconditions are not met >>>>>> + * @throws MathException >>>>>> + * if an error occurs computing the p-value >>>>>> + */ >>>>>> + public double mannWhitneyUTest(final double[] x, final double[] y) >>>>>> + throws IllegalArgumentException, MathException { >>>>>> + >>>>>> + ensureDataConformance(x, y); >>>>>> + >>>>>> + final double Umax = mannWhitneyU(x, y); >>>>>> + >>>>>> + /* >>>>>> + * It can be shown that U1 + U2 = n1 * n2 >>>>>> + */ >>>>>> + final double Umin = x.length * y.length - Umax; >>>>>> + >>>>>> + return calculateAsymptoticPValue(Umin, x.length, y.length); >>>>>> + } >>>>>> +} >>>>>> >>>>>> Added: >>>>>> commons/proper/math/trunk/src/main/java/org/apache/commons/math/stat/inference/WilcoxonSignedRankTest.java >>>>>> URL: >>>>>> http://svn.apache.org/viewvc/commons/proper/math/trunk/src/main/java/org/apache/commons/math/stat/inference/WilcoxonSignedRankTest.java?rev=1053836&view=auto >>>>>> ============================================================================== >>>>>> --- >>>>>> commons/proper/math/trunk/src/main/java/org/apache/commons/math/stat/inference/WilcoxonSignedRankTest.java >>>>>> (added) >>>>>> +++ >>>>>> commons/proper/math/trunk/src/main/java/org/apache/commons/math/stat/inference/WilcoxonSignedRankTest.java >>>>>> Thu Dec 30 09:52:00 2010 >>>>>> @@ -0,0 +1,107 @@ >>>>>> +/* >>>>>> + * 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 org.apache.commons.math.MathException; >>>>>> + >>>>>> +/** >>>>>> + * An interface for Wilcoxon signed-rank test. >>>>>> + * >>>>>> + * @version $Revision: $ $Date: $ >>>>>> + */ >>>>>> +public interface WilcoxonSignedRankTest { >>>>>> + >>>>>> + /** >>>>>> + * Computes the <a >>>>>> + * href="http://en.wikipedia.org/wiki/Wilcoxon_signed-rank_test";> >>>>>> + * Wilcoxon signed ranked statistic</a> comparing mean for two >>>>>> related >>>>>> + * samples or repeated measurements on a single sample. >>>>>> + * <p> >>>>>> + * This statistic can be used to perform a Wilcoxon signed ranked >>>>>> test >>>>>> + * evaluating the null hypothesis that the two related samples or >>>>>> repeated >>>>>> + * measurements on a single sample has equal mean. >>>>>> + * </p> >>>>>> + * <p> >>>>>> + * Let X<sub>i</sub> denote the i'th individual of the first sample >>>>>> and >>>>>> + * Y<sub>i</sub> the related i'th individual in the second sample. >>>>>> Let >>>>>> + * Z<sub>i</sub> = Y<sub>i</sub> - X<sub>i</sub>. >>>>>> + * </p> >>>>>> + * <p> >>>>>> + * <strong>Preconditions</strong>: >>>>>> + * <ul> >>>>>> + * <li>The differences Z<sub>i</sub> must be independent.</li> >>>>>> + * <li>Each Z<sub>i</sub> comes from a continuous population (they >>>>>> must be >>>>>> + * identical) and is symmetric about a common median.</li> >>>>>> + * <li>The values that X<sub>i</sub> and Y<sub>i</sub> represent are >>>>>> + * ordered, so the comparisons greater than, less than, and equal >>>>>> to are >>>>>> + * meaningful.</li> >>>>>> + * </ul> >>>>>> + * </p> >>>>>> + * >>>>>> + * @param x >>>>>> + * the first sample >>>>>> + * @param y >>>>>> + * the second sample >>>>>> + * @return wilcoxonSignedRank statistic >>>>>> + * @throws IllegalArgumentException >>>>>> + * if preconditions are not met >>>>>> + */ >>>>>> + double wilcoxonSignedRank(final double[] x, final double[] y) >>>>>> + throws IllegalArgumentException; >>>>>> + >>>>>> + /** >>>>>> + * Returns the <i>observed significance level</i>, or <a href= >>>>>> + * "http://www.cas.lancs.ac.uk/glossary_v1.1/hyptest.html#pvalue";> >>>>>> + * p-value</a>, associated with a <a >>>>>> + * href="http://en.wikipedia.org/wiki/Wilcoxon_signed-rank_test";> >>>>>> + * Wilcoxon signed ranked statistic</a> comparing mean for two >>>>>> related >>>>>> + * samples or repeated measurements on a single sample. >>>>>> + * <p> >>>>>> + * Let X<sub>i</sub> denote the i'th individual of the first sample >>>>>> and >>>>>> + * Y<sub>i</sub> the related i'th individual in the second sample. >>>>>> Let >>>>>> + * Z<sub>i</sub> = Y<sub>i</sub> - X<sub>i</sub>. >>>>>> + * </p> >>>>>> + * <p> >>>>>> + * <strong>Preconditions</strong>: >>>>>> + * <ul> >>>>>> + * <li>The differences Z<sub>i</sub> must be independent.</li> >>>>>> + * <li>Each Z<sub>i</sub> comes from a continuous population (they >>>>>> must be >>>>>> + * identical) and is symmetric about a common median.</li> >>>>>> + * <li>The values that X<sub>i</sub> and Y<sub>i</sub> represent are >>>>>> + * ordered, so the comparisons greater than, less than, and equal >>>>>> to are >>>>>> + * meaningful.</li> >>>>>> + * </ul> >>>>>> + * </p> >>>>>> + * >>>>>> + * @param x >>>>>> + * the first sample >>>>>> + * @param y >>>>>> + * the second sample >>>>>> + * @param exactPValue >>>>>> + * if the exact p-value is wanted (only works for >>>>>> x.length <= 30, >>>>>> + * if true and x.length > 30, this is ignored because >>>>>> + * calculations may take too long) >>>>>> + * @return p-value >>>>>> + * @throws IllegalArgumentException >>>>>> + * if preconditions are not met >>>>>> + * @throws MathException >>>>>> + * if an error occurs computing the p-value >>>>>> + */ >>>>>> + double wilcoxonSignedRankTest(final double[] x, final double[] y, >>>>>> + boolean exactPValue) throws IllegalArgumentException, >>>>>> + MathException; >>>>>> +} >>>>>> >>>>>> Added: >>>>>> commons/proper/math/trunk/src/main/java/org/apache/commons/math/stat/inference/WilcoxonSignedRankTestImpl.java >>>>>> URL: >>>>>> http://svn.apache.org/viewvc/commons/proper/math/trunk/src/main/java/org/apache/commons/math/stat/inference/WilcoxonSignedRankTestImpl.java?rev=1053836&view=auto >>>>>> ============================================================================== >>>>>> --- >>>>>> commons/proper/math/trunk/src/main/java/org/apache/commons/math/stat/inference/WilcoxonSignedRankTestImpl.java >>>>>> (added) >>>>>> +++ >>>>>> commons/proper/math/trunk/src/main/java/org/apache/commons/math/stat/inference/WilcoxonSignedRankTestImpl.java >>>>>> Thu Dec 30 09:52:00 2010 >>>>>> @@ -0,0 +1,271 @@ >>>>>> +/* >>>>>> + * 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 org.apache.commons.math.MathException; >>>>>> +import org.apache.commons.math.distribution.NormalDistributionImpl; >>>>>> +import org.apache.commons.math.stat.ranking.NaNStrategy; >>>>>> +import org.apache.commons.math.stat.ranking.NaturalRanking; >>>>>> +import org.apache.commons.math.stat.ranking.TiesStrategy; >>>>>> +import org.apache.commons.math.util.FastMath; >>>>>> + >>>>>> +/** >>>>>> + * An implementation of the Wilcoxon signed-rank test. >>>>>> + * >>>>>> + * @version $Revision: $ $Date: $ >>>>>> + */ >>>>>> +public class WilcoxonSignedRankTestImpl implements >>>>>> WilcoxonSignedRankTest { >>>>>> + private NaturalRanking naturalRanking; >>>>>> + >>>>>> + /** >>>>>> + * Create a test instance where NaN's are left in place and ties get >>>>>> + * the average of applicable ranks. Use this unless you are very >>>>>> sure >>>>>> + * of what you are doing. >>>>>> + */ >>>>>> + public WilcoxonSignedRankTestImpl() { >>>>>> + naturalRanking = new NaturalRanking(NaNStrategy.FIXED, >>>>>> + TiesStrategy.AVERAGE); >>>>>> + } >>>>>> + >>>>>> + /** >>>>>> + * Create a test instance using the given strategies for NaN's and >>>>>> ties. >>>>>> + * Only use this if you are sure of what you are doing. >>>>>> + * >>>>>> + * @param nanStrategy >>>>>> + * specifies the strategy that should be used for >>>>>> Double.NaN's >>>>>> + * @param tiesStrategy >>>>>> + * specifies the strategy that should be used for ties >>>>>> + */ >>>>>> + public WilcoxonSignedRankTestImpl(NaNStrategy nanStrategy, >>>>>> + TiesStrategy tiesStrategy) { >>>>>> + naturalRanking = new NaturalRanking(nanStrategy, tiesStrategy); >>>>>> + } >>>>>> + >>>>>> + /** >>>>>> + * Ensures that the provided arrays fulfills the assumptions. >>>>>> + * >>>>>> + * @param x >>>>>> + * @param y >>>>>> + * @throws IllegalArgumentException >>>>>> + * if assumptions are not met >>>>>> + */ >>>>>> + private void ensureDataConformance(final double[] x, final double[] >>>>>> y) >>>>>> + throws IllegalArgumentException { >>>>>> + if (x == null) { >>>>>> + throw new IllegalArgumentException("x must not be null"); >>>>>> + } >>>>>> + >>>>>> + if (y == null) { >>>>>> + throw new IllegalArgumentException("y must not be null"); >>>>>> + } >>>>>> + >>>>>> + if (x.length != y.length) { >>>>>> + throw new IllegalArgumentException( >>>>>> + "x and y must contain the same number of elements"); >>>>>> + } >>>>>> + >>>>>> + if (x.length == 0) { >>>>>> + throw new IllegalArgumentException( >>>>>> + "x and y must contain at least one element"); >>>>>> + } >>>>>> + } >>>>>> + >>>>>> + /** >>>>>> + * Calculates y[i] - x[i] for all i >>>>>> + * >>>>>> + * @param x >>>>>> + * @param y >>>>>> + * @throws IllegalArgumentException >>>>>> + * if assumptions are not met >>>>>> + */ >>>>>> + private double[] calculateDifferences(final double[] x, final >>>>>> double[] y) >>>>>> + throws IllegalArgumentException { >>>>>> + >>>>>> + final double[] z = new double[x.length]; >>>>>> + >>>>>> + for (int i = 0; i < x.length; ++i) { >>>>>> + z[i] = y[i] - x[i]; >>>>>> + } >>>>>> + >>>>>> + return z; >>>>>> + } >>>>>> + >>>>>> + /** >>>>>> + * Calculates |z[i]| for all i >>>>>> + * >>>>>> + * @param z >>>>>> + * @throws IllegalArgumentException >>>>>> + * if assumptions are not met >>>>>> + */ >>>>>> + private double[] calculateAbsoluteDifferences(final double[] z) >>>>>> + throws IllegalArgumentException { >>>>>> + if (z == null) { >>>>>> + throw new IllegalArgumentException("z must not be null"); >>>>>> + } >>>>>> + >>>>>> + if (z.length == 0) { >>>>>> + throw new IllegalArgumentException( >>>>>> + "z must contain at least one element"); >>>>>> + } >>>>>> + >>>>>> + final double[] zAbs = new double[z.length]; >>>>>> + >>>>>> + for (int i = 0; i < z.length; ++i) { >>>>>> + zAbs[i] = FastMath.abs(z[i]); >>>>>> + } >>>>>> + >>>>>> + return zAbs; >>>>>> + } >>>>>> + >>>>>> + /** >>>>>> + * {...@inheritdoc} >>>>>> + * >>>>>> + * @param x >>>>>> + * the first sample >>>>>> + * @param y >>>>>> + * the second sample >>>>>> + * @return wilcoxonSignedRank statistic (the larger of W+ and W-) >>>>>> + * @throws IllegalArgumentException >>>>>> + * if preconditions are not met >>>>>> + */ >>>>>> + public double wilcoxonSignedRank(final double[] x, final double[] y) >>>>>> + throws IllegalArgumentException { >>>>>> + >>>>>> + ensureDataConformance(x, y); >>>>>> + >>>>>> + // throws IllegalArgumentException if x and y are not correctly >>>>>> + // specified >>>>>> + final double[] z = calculateDifferences(x, y); >>>>>> + final double[] zAbs = calculateAbsoluteDifferences(z); >>>>>> + >>>>>> + final double[] ranks = naturalRanking.rank(zAbs); >>>>>> + >>>>>> + double Wplus = 0; >>>>>> + >>>>>> + for (int i = 0; i < z.length; ++i) { >>>>>> + if (z[i] > 0) { >>>>>> + Wplus += ranks[i]; >>>>>> + } >>>>>> + } >>>>>> + >>>>>> + final int N = x.length; >>>>>> + final double Wminus = (((double) (N * (N + 1))) / 2.0) - Wplus; >>>>>> + >>>>>> + return FastMath.max(Wplus, Wminus); >>>>>> + } >>>>>> + >>>>>> + /** >>>>>> + * Algorithm inspired by >>>>>> + * >>>>>> http://www.fon.hum.uva.nl/Service/Statistics/Signed_Rank_Algorihms.html#C >>>>>> + * by Rob van Son, Institute of Phonetic Sciences & IFOTT, >>>>>> + * University of Amsterdam >>>>>> + * >>>>>> + * @param Wmax largest Wilcoxon signed rank value >>>>>> + * @param N number of subjects (corresponding to x.length) >>>>>> + * @return two-sided exact p-value >>>>>> + */ >>>>>> + private double calculateExactPValue(final double Wmax, final int N) >>>>>> { >>>>>> + >>>>>> + // Total number of outcomes (equal to 2^N but a lot faster) >>>>>> + final int m = 1 << N; >>>>>> + >>>>>> + int largerRankSums = 0; >>>>>> + >>>>>> + for (int i = 0; i < m; ++i) { >>>>>> + int rankSum = 0; >>>>>> + >>>>>> + // Generate all possible rank sums >>>>>> + for (int j = 0; j < N; ++j) { >>>>>> + >>>>>> + // (i >> j) & 1 extract i's j-th bit from the right >>>>>> + if (((i >> j) & 1) == 1) { >>>>>> + rankSum += j + 1; >>>>>> + } >>>>>> + } >>>>>> + >>>>>> + if (rankSum >= Wmax) { >>>>>> + ++largerRankSums; >>>>>> + } >>>>>> + } >>>>>> + >>>>>> + /* >>>>>> + * largerRankSums / m gives the one-sided p-value, so it's >>>>>> multiplied >>>>>> + * with 2 to get the two-sided p-value >>>>>> + */ >>>>>> + return 2 * ((double) largerRankSums) / ((double) m); >>>>>> + } >>>>>> + >>>>>> + /** >>>>>> + * @param Wmin smallest Wilcoxon signed rank value >>>>>> + * @param N number of subjects (corresponding to x.length) >>>>>> + * @return two-sided asymptotic p-value >>>>>> + * @throws MathException if an error occurs computing the p-value >>>>>> + */ >>>>>> + private double calculateAsymptoticPValue(final double Wmin, final >>>>>> int N) throws MathException { >>>>>> + >>>>>> + final double ES = (double) (N * (N + 1)) / 4.0; >>>>>> + >>>>>> + /* Same as (but saves computations): >>>>>> + * final double VarW = ((double) (N * (N + 1) * (2*N + 1))) / >>>>>> 24; >>>>>> + */ >>>>>> + final double VarS = ES * ((double) (2 * N + 1) / 6.0); >>>>>> + >>>>>> + // - 0.5 is a continuity correction >>>>>> + final double z = (Wmin - ES - 0.5) / FastMath.sqrt(VarS); >>>>>> + >>>>>> + final NormalDistributionImpl standardNormal = new >>>>>> NormalDistributionImpl(0, 1); >>>>>> + >>>>>> + return 2*standardNormal.cumulativeProbability(z); >>>>>> + } >>>>>> + >>>>>> + /** >>>>>> + * {...@inheritdoc} >>>>>> + * >>>>>> + * @param x >>>>>> + * the first sample >>>>>> + * @param y >>>>>> + * the second sample >>>>>> + * @param exactPValue >>>>>> + * if the exact p-value is wanted (only for x.length <= >>>>>> 30) >>>>>> + * @return p-value >>>>>> + * @throws IllegalArgumentException >>>>>> + * if preconditions are not met or exact p-value is >>>>>> wanted for >>>>>> + * when x.length > 30 >>>>>> + * @throws MathException >>>>>> + * if an error occurs computing the p-value >>>>>> + */ >>>>>> + public double wilcoxonSignedRankTest(final double[] x, final >>>>>> double[] y, >>>>>> + boolean exactPValue) throws IllegalArgumentException, >>>>>> + MathException { >>>>>> + >>>>>> + ensureDataConformance(x, y); >>>>>> + >>>>>> + final int N = x.length; >>>>>> + final double Wmax = wilcoxonSignedRank(x, y); >>>>>> + >>>>>> + if (exactPValue && N > 30) { >>>>>> + throw new IllegalArgumentException("Exact test can only be >>>>>> made for N <= 30."); >>>>>> + } >>>>>> + >>>>>> + if (exactPValue) { >>>>>> + return calculateExactPValue(Wmax, N); >>>>>> + } else { >>>>>> + final double Wmin = ( (double)(N*(N+1)) / 2.0 ) - Wmax; >>>>>> + return calculateAsymptoticPValue(Wmin, N); >>>>>> + } >>>>>> + } >>>>>> +} >>>>>> >>>>>> Added: >>>>>> commons/proper/math/trunk/src/test/java/org/apache/commons/math/stat/inference/MannWhitneyUTestTest.java >>>>>> URL: >>>>>> http://svn.apache.org/viewvc/commons/proper/math/trunk/src/test/java/org/apache/commons/math/stat/inference/MannWhitneyUTestTest.java?rev=1053836&view=auto >>>>>> ============================================================================== >>>>>> --- >>>>>> commons/proper/math/trunk/src/test/java/org/apache/commons/math/stat/inference/MannWhitneyUTestTest.java >>>>>> (added) >>>>>> +++ >>>>>> commons/proper/math/trunk/src/test/java/org/apache/commons/math/stat/inference/MannWhitneyUTestTest.java >>>>>> Thu Dec 30 09:52:00 2010 >>>>>> @@ -0,0 +1,101 @@ >>>>>> +/* >>>>>> + * 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: $ $Date: $ >>>>>> + */ >>>>>> + >>>>>> +public class MannWhitneyUTestTest extends TestCase { >>>>>> + >>>>>> + protected MannWhitneyUTest testStatistic = new >>>>>> MannWhitneyUTestImpl(); >>>>>> + >>>>>> + public MannWhitneyUTestTest(String name) { >>>>>> + super(name); >>>>>> + } >>>>>> + >>>>>> + public void testMannWhitneyUSimple() throws Exception { >>>>>> + /* Target values computed using R version 2.11.1 >>>>>> + * x <- c(19, 22, 16, 29, 24) >>>>>> + * y <- c(20, 11, 17, 12) >>>>>> + * wilcox.test(x, y, alternative = "two.sided", mu = 0, paired >>>>>> = FALSE, exact = FALSE, correct = FALSE) >>>>>> + * W = 17, p-value = 0.08641 >>>>>> + */ >>>>>> + final double x[] = {19, 22, 16, 29, 24}; >>>>>> + final double y[] = {20, 11, 17, 12}; >>>>>> + >>>>>> + assertEquals(17, testStatistic.mannWhitneyU(x, y), 1e-10); >>>>>> + assertEquals(0.08641, testStatistic.mannWhitneyUTest(x, y), >>>>>> 1e-5); >>>>>> + } >>>>>> + >>>>>> + >>>>>> + public void testMannWhitneyUInputValidation() throws Exception { >>>>>> + /* Samples must be present, i.e. length > 0 >>>>>> + */ >>>>>> + try { >>>>>> + testStatistic.mannWhitneyUTest(new double[] { }, new >>>>>> double[] { 1.0 }); >>>>>> + fail("x does not contain samples (exact), >>>>>> IllegalArgumentException expected"); >>>>>> + } catch (IllegalArgumentException ex) { >>>>>> + // expected >>>>>> + } >>>>>> + >>>>>> + try { >>>>>> + testStatistic.mannWhitneyUTest(new double[] { 1.0 }, new >>>>>> double[] { }); >>>>>> + fail("y does not contain samples (exact), >>>>>> IllegalArgumentException expected"); >>>>>> + } catch (IllegalArgumentException ex) { >>>>>> + // expected >>>>>> + } >>>>>> + >>>>>> + /* >>>>>> + * x and y is null >>>>>> + */ >>>>>> + try { >>>>>> + testStatistic.mannWhitneyUTest(null, null); >>>>>> + fail("x and y is null (exact), IllegalArgumentException >>>>>> expected"); >>>>>> + } catch (IllegalArgumentException ex) { >>>>>> + // expected >>>>>> + } >>>>>> + >>>>>> + try { >>>>>> + testStatistic.mannWhitneyUTest(null, null); >>>>>> + fail("x and y is null (asymptotic), >>>>>> IllegalArgumentException expected"); >>>>>> + } catch (IllegalArgumentException ex) { >>>>>> + // expected >>>>>> + } >>>>>> + >>>>>> + /* >>>>>> + * x or y is null >>>>>> + */ >>>>>> + try { >>>>>> + testStatistic.mannWhitneyUTest(null, new double[] { 1.0 }); >>>>>> + fail("x is null (exact), IllegalArgumentException >>>>>> expected"); >>>>>> + } catch (IllegalArgumentException ex) { >>>>>> + // expected >>>>>> + } >>>>>> + >>>>>> + try { >>>>>> + testStatistic.mannWhitneyUTest(new double[] { 1.0 }, null); >>>>>> + fail("y is null (exact), IllegalArgumentException >>>>>> expected"); >>>>>> + } catch (IllegalArgumentException ex) { >>>>>> + // expected >>>>>> + } >>>>>> + } >>>>>> +} >>>>>> >>>>>> Added: >>>>>> commons/proper/math/trunk/src/test/java/org/apache/commons/math/stat/inference/WilcoxonSignedRankTestTest.java >>>>>> URL: >>>>>> http://svn.apache.org/viewvc/commons/proper/math/trunk/src/test/java/org/apache/commons/math/stat/inference/WilcoxonSignedRankTestTest.java?rev=1053836&view=auto >>>>>> ============================================================================== >>>>>> --- >>>>>> commons/proper/math/trunk/src/test/java/org/apache/commons/math/stat/inference/WilcoxonSignedRankTestTest.java >>>>>> (added) >>>>>> +++ >>>>>> commons/proper/math/trunk/src/test/java/org/apache/commons/math/stat/inference/WilcoxonSignedRankTestTest.java >>>>>> Thu Dec 30 09:52:00 2010 >>>>>> @@ -0,0 +1,180 @@ >>>>>> +/* >>>>>> + * 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: $ $Date: $ >>>>>> + */ >>>>>> + >>>>>> +public class WilcoxonSignedRankTestTest extends TestCase { >>>>>> + >>>>>> + protected WilcoxonSignedRankTest testStatistic = new >>>>>> WilcoxonSignedRankTestImpl(); >>>>>> + >>>>>> + public WilcoxonSignedRankTestTest(String name) { >>>>>> + super(name); >>>>>> + } >>>>>> + >>>>>> + public void testWilcoxonSignedRankSimple() throws Exception { >>>>>> + /* Target values computed using R version 2.11.1 >>>>>> + * x <- c(1.83, 0.50, 1.62, 2.48, 1.68, 1.88, 1.55, 3.06, 1.30) >>>>>> + * y <- c(0.878, 0.647, 0.598, 2.05, 1.06, 1.29, 1.06, 3.14, >>>>>> 1.29) >>>>>> + */ >>>>>> + final double x[] = {1.83, 0.50, 1.62, 2.48, 1.68, 1.88, 1.55, >>>>>> 3.06, 1.30}; >>>>>> + final double y[] = {0.878, 0.647, 0.598, 2.05, 1.06, 1.29, >>>>>> 1.06, 3.14, 1.29}; >>>>>> + >>>>>> + /* EXACT: >>>>>> + * wilcox.test(x, y, alternative = "two.sided", mu = 0, paired >>>>>> = TRUE, exact = TRUE, correct = FALSE) >>>>>> + * V = 40, p-value = 0.03906 >>>>>> + * >>>>>> + * Corresponds to the value obtained in R. >>>>>> + */ >>>>>> + assertEquals(40, testStatistic.wilcoxonSignedRank(x, y), 1e-10); >>>>>> + assertEquals(0.03906, testStatistic.wilcoxonSignedRankTest(x, >>>>>> y, true), 1e-5); >>>>>> + >>>>>> + /* ASYMPTOTIC: >>>>>> + * wilcox.test(x, y, alternative = "two.sided", mu = 0, paired >>>>>> = TRUE, exact = FALSE, correct = FALSE) >>>>>> + * V = 40, p-value = 0.03815 >>>>>> + * >>>>>> + * This is not entirely the same due to different corrects, >>>>>> + * e.g. http://mlsc.lboro.ac.uk/resources/statistics/wsrt.pdf >>>>>> + * and src/library/stats/R/wilcox.test.R in the R source >>>>>> + */ >>>>>> + assertEquals(40, testStatistic.wilcoxonSignedRank(x, y), 1e-10); >>>>>> + assertEquals(0.0329693812, >>>>>> testStatistic.wilcoxonSignedRankTest(x, y, false), 1e-10); >>>>>> + } >>>>>> + >>>>>> + public void testWilcoxonSignedRankInputValidation() throws >>>>>> Exception { >>>>>> + /* >>>>>> + * Exact only for sample size <= 30 >>>>>> + */ >>>>>> + final double[] x1 = new double[30]; >>>>>> + final double[] x2 = new double[31]; >>>>>> + final double[] y1 = new double[30]; >>>>>> + final double[] y2 = new double[31]; >>>>>> + for (int i = 0; i < 30; ++i) { >>>>>> + x1[i] = x2[i] = y1[i] = y2[i] = i; >>>>>> + } >>>>>> + >>>>>> + // Exactly 30 is okay >>>>>> + testStatistic.wilcoxonSignedRankTest(x1, y1, true); >>>>>> + >>>>>> + try { >>>>>> + testStatistic.wilcoxonSignedRankTest(x2, y2, true); >>>>>> + fail("More than 30 samples and exact chosen, >>>>>> IllegalArgumentException expected"); >>>>>> + } catch (IllegalArgumentException ex) { >>>>>> + // expected >>>>>> + } >>>>>> + >>>>>> + /* Samples must be present, i.e. length > 0 >>>>>> + */ >>>>>> + try { >>>>>> + testStatistic.wilcoxonSignedRankTest(new double[] { }, new >>>>>> double[] { 1.0 }, true); >>>>>> + fail("x does not contain samples (exact), >>>>>> IllegalArgumentException expected"); >>>>>> + } catch (IllegalArgumentException ex) { >>>>>> + // expected >>>>>> + } >>>>>> + >>>>>> + try { >>>>>> + testStatistic.wilcoxonSignedRankTest(new double[] { }, new >>>>>> double[] { 1.0 }, false); >>>>>> + fail("x does not contain samples (asymptotic), >>>>>> IllegalArgumentException expected"); >>>>>> + } catch (IllegalArgumentException ex) { >>>>>> + // expected >>>>>> + } >>>>>> + >>>>>> + try { >>>>>> + testStatistic.wilcoxonSignedRankTest(new double[] { 1.0 }, >>>>>> new double[] { }, true); >>>>>> + fail("y does not contain samples (exact), >>>>>> IllegalArgumentException expected"); >>>>>> + } catch (IllegalArgumentException ex) { >>>>>> + // expected >>>>>> + } >>>>>> + >>>>>> + try { >>>>>> + testStatistic.wilcoxonSignedRankTest(new double[] { 1.0 }, >>>>>> new double[] { }, false); >>>>>> + fail("y does not contain samples (asymptotic), >>>>>> IllegalArgumentException expected"); >>>>>> + } catch (IllegalArgumentException ex) { >>>>>> + // expected >>>>>> + } >>>>>> + >>>>>> + /* Samples not same size, i.e. cannot be pairred >>>>>> + */ >>>>>> + try { >>>>>> + testStatistic.wilcoxonSignedRankTest(new double[] { 1.0, >>>>>> 2.0 }, new double[] { 3.0 }, true); >>>>>> + fail("x and y not same size (exact), >>>>>> IllegalArgumentException expected"); >>>>>> + } catch (IllegalArgumentException ex) { >>>>>> + // expected >>>>>> + } >>>>>> + >>>>>> + try { >>>>>> + testStatistic.wilcoxonSignedRankTest(new double[] { 1.0, >>>>>> 2.0 }, new double[] { 3.0 }, false); >>>>>> + fail("x and y not same size (asymptotic), >>>>>> IllegalArgumentException expected"); >>>>>> + } catch (IllegalArgumentException ex) { >>>>>> + // expected >>>>>> + } >>>>>> + >>>>>> + /* >>>>>> + * x and y is null >>>>>> + */ >>>>>> + try { >>>>>> + testStatistic.wilcoxonSignedRankTest(null, null, true); >>>>>> + fail("x and y is null (exact), IllegalArgumentException >>>>>> expected"); >>>>>> + } catch (IllegalArgumentException ex) { >>>>>> + // expected >>>>>> + } >>>>>> + >>>>>> + try { >>>>>> + testStatistic.wilcoxonSignedRankTest(null, null, false); >>>>>> + fail("x and y is null (asymptotic), >>>>>> IllegalArgumentException expected"); >>>>>> + } catch (IllegalArgumentException ex) { >>>>>> + // expected >>>>>> + } >>>>>> + >>>>>> + /* >>>>>> + * x or y is null >>>>>> + */ >>>>>> + try { >>>>>> + testStatistic.wilcoxonSignedRankTest(null, new double[] { >>>>>> 1.0 }, true); >>>>>> + fail("x is null (exact), IllegalArgumentException >>>>>> expected"); >>>>>> + } catch (IllegalArgumentException ex) { >>>>>> + // expected >>>>>> + } >>>>>> + >>>>>> + try { >>>>>> + testStatistic.wilcoxonSignedRankTest(null, new double[] { >>>>>> 1.0 }, false); >>>>>> + fail("x is null (asymptotic), IllegalArgumentException >>>>>> expected"); >>>>>> + } catch (IllegalArgumentException ex) { >>>>>> + // expected >>>>>> + } >>>>>> + >>>>>> + try { >>>>>> + testStatistic.wilcoxonSignedRankTest(new double[] { 1.0 }, >>>>>> null, true); >>>>>> + fail("y is null (exact), IllegalArgumentException >>>>>> expected"); >>>>>> + } catch (IllegalArgumentException ex) { >>>>>> + // expected >>>>>> + } >>>>>> + >>>>>> + try { >>>>>> + testStatistic.wilcoxonSignedRankTest(new double[] { 1.0 }, >>>>>> null, false); >>>>>> + fail("y is null (asymptotic), IllegalArgumentException >>>>>> expected"); >>>>>> + } catch (IllegalArgumentException ex) { >>>>>> + // expected >>>>>> + } >>>>>> + } >>>>>> +} >>>>>> >>>>>> >>>>>> >>>>> >>>>> --------------------------------------------------------------------- >>>>> To unsubscribe, e-mail: dev-unsubscr...@commons.apache.org >>>>> For additional commands, e-mail: dev-h...@commons.apache.org >>>>> >>>>> >>>> >>>> >>>> --------------------------------------------------------------------- >>>> To unsubscribe, e-mail: dev-unsubscr...@commons.apache.org >>>> For additional commands, e-mail: dev-h...@commons.apache.org >>>> >>> >>> >>> --------------------------------------------------------------------- >>> To unsubscribe, e-mail: dev-unsubscr...@commons.apache.org >>> For additional commands, e-mail: dev-h...@commons.apache.org >>> >>> >> >> Hi Luc, >> >> Thanks for the help, including the config-file. I've manually changed >> the properties for the newly created files in revision 1053918 using >> svn propset svn:eol-style native >> src/main/java/org/apache/commons/math/stat/inference/WilcoxonSignedRankTest* >> etc. >> >> And now that I'm using a config-file similar to yours, new files >> should be dealt with automatically. >> >> In regards to the pom.xml, then I should just make an entry for myself >> in the developers-section, right? > > Yes, of course. Thanks for the help with this practical stuff :-).
Cheers, Mikkel. > > Luc > >> >> Cheers, Mikkel. >> >> --------------------------------------------------------------------- >> To unsubscribe, e-mail: dev-unsubscr...@commons.apache.org >> For additional commands, e-mail: dev-h...@commons.apache.org >> > > > --------------------------------------------------------------------- > To unsubscribe, e-mail: dev-unsubscr...@commons.apache.org > For additional commands, e-mail: dev-h...@commons.apache.org > > --------------------------------------------------------------------- To unsubscribe, e-mail: dev-unsubscr...@commons.apache.org For additional commands, e-mail: dev-h...@commons.apache.org
