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Posted to issues@commons.apache.org by GitBox <gi...@apache.org> on 2021/02/19 13:19:24 UTC
[GitHub] [commons-statistics] aherbert commented on a change in pull request #26: Add truncated normal distribution.
aherbert commented on a change in pull request #26:
URL: https://github.com/apache/commons-statistics/pull/26#discussion_r579159518
##########
File path: commons-statistics-distribution/src/test/java/org/apache/commons/statistics/distribution/TruncatedNormalDistributionTest.java
##########
@@ -0,0 +1,283 @@
+/*
+ * 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.statistics.distribution;
+
+import org.junit.jupiter.api.Assertions;
+import org.junit.jupiter.api.BeforeEach;
+import org.junit.jupiter.api.Test;
+
+/**
+ * Test class for {@link TruncatedNormalDistribution}.
+ * All test values were computed using Python with SciPy v1.6.0.
+ */
+class TruncatedNormalDistributionTest extends ContinuousDistributionAbstractTest {
+ /**
+ * Default tolerance.
+ */
+ private static final double TOLERANCE = 1e-7;
+
+ /**
+ * Distribution to test with.
+ */
+ private TruncatedNormalDistribution distribution = new TruncatedNormalDistribution(1.9, 1.3, -1.1, 3.4);
+ /**
+ * Percentiles to test with.
+ */
+ private double[] ppfValues = new double[]{0, 0.0001, 0.001, 0.01, 0.025, 0.05, 0.1, 0.25, 0.5, 0.75, 0.9, 0.95,
+ 0.975, 0.99, 0.999, 0.9999, 1};
+ /**
+ * Expected cumulative values for percentiles.
+ */
+ private double[] cdfValues = new double[]{-1.1, -1.09597275767544, -1.0609616183922, -0.79283350106842,
+ -0.505331829887808, -0.192170173599874, 0.21173317261645,
+ 0.925791281910463, 1.71399518338879, 2.43413009451536, 2.94473113856785,
+ 3.15310057075828, 3.27036798398733, 3.34641874981679, 3.39452729074341,
+ 3.39945153287941, 3.4};
+ /**
+ * Expected density values for percentiles.
+ */
+ private double[] pdfValues = new double[]{0.0247422752302618, 0.0249196707321102, 0.0265057408263321,
+ 0.0415071096500185, 0.0640403254340905, 0.0971457789636,
+ 0.152622492901864, 0.267853863255995, 0.35107475879338, 0.325977522502844,
+ 0.25680502248913, 0.222886115806507, 0.203494915087054, 0.190997946666992,
+ 0.183167918885238, 0.182370706542209, 0.182281965373914};
+ /**
+ * Expected distribution mean.
+ */
+ private double mean = 1.63375792365723;
+ /**
+ * Expected distribution variance.
+ */
+ private double variance = 1.03158703914439;
+
+ /**
+ * Overrides tolerance and sets up distribution.
+ */
+ @BeforeEach
+ void setUp() {
+ setTolerance(TOLERANCE);
+ super.setUp();
+ }
+
+ /**
+ * {@inheritDoc}
+ */
+ @Override
+ public ContinuousDistribution makeDistribution() {
+ return distribution;
+ }
+
+ /**
+ * {@inheritDoc}
+ */
+ @Override
+ public double[] makeCumulativeTestPoints() {
+ return cdfValues;
+ }
+
+ /**
+ * {@inheritDoc}
+ */
+ @Override
+ public double[] makeCumulativeTestValues() {
+ return ppfValues;
+ }
+
+ /**
+ * {@inheritDoc}
+ */
+ @Override
+ public double[] makeDensityTestValues() {
+ return pdfValues;
+ }
+
+ /**
+ * Configures new test values and runs relevant tests in this class and {@link ContinuousDistributionAbstractTest}.
+ * @param testDistribution distribution to test with.
+ * @param expectedPpfValues expected percentiles to test with.
+ * @param expectedCdfValues expected cumulative values for percentiles.
+ * @param expectedPdfValues expected density values for percentiles.
+ * @param expectedMean expected mean.
+ * @param expectedVariance expected variance.
+ */
+ private void testAdditionalDistribution(
+ TruncatedNormalDistribution testDistribution,
+ double[] expectedPpfValues,
+ double[] expectedCdfValues,
+ double[] expectedPdfValues,
+ double expectedMean,
+ double expectedVariance
+ ) {
+ this.distribution = testDistribution;
+ this.ppfValues = expectedPpfValues;
+ this.cdfValues = expectedCdfValues;
+ this.pdfValues = expectedPdfValues;
+ this.mean = expectedMean;
+ this.variance = expectedVariance;
+
+ setUp();
+
+ testMoments();
+
+ testConsistency();
+ testSampler();
+ testOutsideSupport();
+ testDensities();
+ testLogDensities();
+ testOutsideSupport();
+ testInverseCumulativeProbabilities();
+ testDensityIntegrals();
+ testCumulativeProbabilities();
+ testIsSupportConnected();
+ testPrecondition1();
+ testPrecondition2();
+ testPrecondition3();
+ }
+
+ /**
+ * Test a one-sided truncation with a lower tail.
+ */
+ @Test
+ void testOneSidedLowerTail() {
+ testAdditionalDistribution(
+ new TruncatedNormalDistribution(12, 2.4, -Double.POSITIVE_INFINITY, 7.1),
Review comment:
Use `Double.NEGATIVE_INFINITY` in place of `-Double.POSITIVE_INFINITY` here and through the rest of the tests.
##########
File path: commons-statistics-distribution/src/main/java/org/apache/commons/statistics/distribution/TruncatedNormalDistribution.java
##########
@@ -0,0 +1,206 @@
+/*
+ * 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.statistics.distribution;
+
+/**
+ * Implementation of the truncated normal distribution.
+ *
+ * @see <a href="http://en.wikipedia.org/wiki/Truncated_normal_distribution">
+ * Truncated normal distribution (Wikipedia)</a>.
Review comment:
Remove the period after the `</a>`
##########
File path: commons-statistics-distribution/src/main/java/org/apache/commons/statistics/distribution/TruncatedNormalDistribution.java
##########
@@ -0,0 +1,206 @@
+/*
+ * 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.statistics.distribution;
+
+/**
+ * Implementation of the truncated normal distribution.
+ *
+ * @see <a href="http://en.wikipedia.org/wiki/Truncated_normal_distribution">
+ * Truncated normal distribution (Wikipedia)</a>.
+ */
+public class TruncatedNormalDistribution extends AbstractContinuousDistribution {
+ /**
+ * Mean of parent normal distribution.
+ */
+ private final double parentMean;
+ /**
+ * Standard deviation of parent normal distribution.
+ */
+ private final double parentSd;
+ /**
+ * Mean of this distribution.
+ */
+ private final double mean;
+ /**
+ * Variance of this distribution.
+ */
+ private final double variance;
+ /**
+ * Lower bound of this distribution.
+ */
+ private final double lower;
+ /**
+ * Upper bound of this distribution.
+ */
+ private final double upper;
+
+ /**
+ * A standard normal distribution used for calculations.
+ */
+ private final NormalDistribution standardNormal;
+ /**
+ * Stored value of @{code standardNormal.cumulativeProbability((lower - mean) / sd)} for faster computations.
+ */
+ private final double cdfAlpha;
+ /**
+ * Stored value of @{code (upper - mean) / sd) - cdfAlpha} for faster computations.
+ */
+ private final double cdfDelta;
+
+ /**
+ * Creates a truncated normal distribution.
+ * Note that the {@code mean} and {@code sd} is of the parent normal distribution,
+ * and not the true mean and standard deviation of the truncated normal distribution.
+ *
+ * @param mean mean for this distribution.
+ * @param sd standard deviation for this distribution.
+ * @param lower lower bound (inclusive) of the distribution, can be {@link Double#NEGATIVE_INFINITY}.
+ * @param upper upper bound (inclusive) of the distribution, can be {@link Double#POSITIVE_INFINITY}.
+ * @throws IllegalArgumentException if {@code sd <= 0} or if {@code upper <= lower}.
+ */
+ public TruncatedNormalDistribution(double mean, double sd, double lower, double upper) {
+ if (sd <= 0) {
+ throw new DistributionException(DistributionException.NEGATIVE, sd);
+ }
+ if (upper <= lower) {
+ throw new DistributionException(DistributionException.TOO_LARGE, lower, upper);
+ }
+
+ this.lower = lower;
+ this.upper = upper;
+
+ parentMean = mean;
+ parentSd = sd;
+ standardNormal = new NormalDistribution(0, 1);
+
+ double alpha = (lower - mean) / sd;
+ double beta = (upper - mean) / sd;
+
+ cdfAlpha = standardNormal.cumulativeProbability(alpha);
+ double cdfBeta = standardNormal.cumulativeProbability(beta);
+ cdfDelta = cdfBeta - cdfAlpha;
+
+ // Calculation of variance and mean.
+ double pdfAlpha = standardNormal.density(alpha);
+ double pdfBeta = standardNormal.density(beta);
+ double pdfCdfDelta = (pdfAlpha - pdfBeta) / cdfDelta;
+ double alphaBetaDelta = (alpha * pdfAlpha - beta * pdfBeta) / cdfDelta;
+
+ if (lower == Double.NEGATIVE_INFINITY && upper != Double.POSITIVE_INFINITY) {
+ // One-sided lower tail truncation
+ double betaRatio = pdfBeta / cdfBeta;
+ this.mean = mean - sd * betaRatio;
+ variance = sd * sd * (1 - beta * betaRatio - betaRatio * betaRatio);
+ } else if (lower != Double.NEGATIVE_INFINITY && upper == Double.POSITIVE_INFINITY) {
+ // One-sided upper tail truncation
+ double alphaRatio = pdfAlpha / cdfDelta;
+ this.mean = mean + sd * alphaRatio;
+ variance = sd * sd * (1 + alpha * alphaRatio - alphaRatio * alphaRatio);
+ } else if (lower != Double.NEGATIVE_INFINITY && upper != Double.POSITIVE_INFINITY) {
+ // Two-sided truncation
+ this.mean = mean + pdfCdfDelta * parentSd;
+ variance = sd * sd * (1 + alphaBetaDelta - pdfCdfDelta * pdfCdfDelta);
+ } else {
+ // No truncation
+ this.mean = mean;
+ variance = sd * sd;
+ }
+ }
+
+ /**
+ * {@inheritDoc}
+ */
+ @Override
+ public double density(double x) {
+ if (x < lower || x > upper) {
+ return 0;
+ }
+ return standardNormal.density((x - parentMean) / parentSd) / (parentSd * cdfDelta);
+ }
+
+ /**
+ * {@inheritDoc}
+ */
+ @Override
+ public double cumulativeProbability(double x) {
+ if (x <= lower) {
+ return 0;
+ } else if (x >= upper) {
+ return 1;
+ } else {
+ return (standardNormal.cumulativeProbability((x - parentMean) / parentSd) - cdfAlpha) / cdfDelta;
+ }
+ }
+
+ /**
+ * {@inheritDoc}
+ */
+ @Override
+ public double inverseCumulativeProbability(double p) {
+ if (p < 0 || p > 1) {
+ throw new DistributionException(DistributionException.INVALID_PROBABILITY, p);
+ }
+ return standardNormal.inverseCumulativeProbability(cdfAlpha + p * cdfDelta) * parentSd + parentMean;
+ }
+
+ /**
+ * {@inheritDoc}
+ *
+ * Represents the true mean of the truncated normal distribution rather
+ * than the parent normal distribution mean.
+ */
+ @Override
+ public double getMean() {
+ return mean;
+ }
+
+ /**
+ * {@inheritDoc}
+ *
+ * Represents the true variance of the truncated normal distribution rather
+ * than the parent normal distribution variance.
+ */
+ @Override
+ public double getVariance() {
+ return variance;
+ }
+
+ /**
Review comment:
In this case where nothing is added to the javadoc the rest of the codebase uses a single line `/** {@inheritDoc} */`
##########
File path: commons-statistics-distribution/src/main/java/org/apache/commons/statistics/distribution/TruncatedNormalDistribution.java
##########
@@ -0,0 +1,206 @@
+/*
+ * 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.statistics.distribution;
+
+/**
+ * Implementation of the truncated normal distribution.
+ *
+ * @see <a href="http://en.wikipedia.org/wiki/Truncated_normal_distribution">
+ * Truncated normal distribution (Wikipedia)</a>.
+ */
+public class TruncatedNormalDistribution extends AbstractContinuousDistribution {
+ /**
+ * Mean of parent normal distribution.
+ */
+ private final double parentMean;
+ /**
+ * Standard deviation of parent normal distribution.
+ */
+ private final double parentSd;
+ /**
+ * Mean of this distribution.
+ */
+ private final double mean;
+ /**
+ * Variance of this distribution.
+ */
+ private final double variance;
+ /**
+ * Lower bound of this distribution.
+ */
+ private final double lower;
+ /**
+ * Upper bound of this distribution.
+ */
+ private final double upper;
+
+ /**
+ * A standard normal distribution used for calculations.
+ */
+ private final NormalDistribution standardNormal;
+ /**
+ * Stored value of @{code standardNormal.cumulativeProbability((lower - mean) / sd)} for faster computations.
+ */
+ private final double cdfAlpha;
+ /**
+ * Stored value of @{code (upper - mean) / sd) - cdfAlpha} for faster computations.
Review comment:
Missing `standardNormal.cumulativeProbability(` inside the the `@code` tag as there is an unmatched close parenthesis.
##########
File path: commons-statistics-distribution/src/test/java/org/apache/commons/statistics/distribution/TruncatedNormalDistributionTest.java
##########
@@ -0,0 +1,283 @@
+/*
+ * 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.statistics.distribution;
+
+import org.junit.jupiter.api.Assertions;
+import org.junit.jupiter.api.BeforeEach;
+import org.junit.jupiter.api.Test;
+
+/**
+ * Test class for {@link TruncatedNormalDistribution}.
+ * All test values were computed using Python with SciPy v1.6.0.
+ */
+class TruncatedNormalDistributionTest extends ContinuousDistributionAbstractTest {
+ /**
+ * Default tolerance.
+ */
+ private static final double TOLERANCE = 1e-7;
Review comment:
This can be removed and the `1e-7` placed in the call to `setTolerance(...)`
##########
File path: commons-statistics-distribution/src/main/java/org/apache/commons/statistics/distribution/TruncatedNormalDistribution.java
##########
@@ -0,0 +1,206 @@
+/*
+ * 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.statistics.distribution;
+
+/**
+ * Implementation of the truncated normal distribution.
+ *
+ * @see <a href="http://en.wikipedia.org/wiki/Truncated_normal_distribution">
+ * Truncated normal distribution (Wikipedia)</a>.
+ */
+public class TruncatedNormalDistribution extends AbstractContinuousDistribution {
+ /**
+ * Mean of parent normal distribution.
+ */
+ private final double parentMean;
+ /**
+ * Standard deviation of parent normal distribution.
+ */
+ private final double parentSd;
+ /**
+ * Mean of this distribution.
+ */
+ private final double mean;
+ /**
+ * Variance of this distribution.
+ */
+ private final double variance;
+ /**
+ * Lower bound of this distribution.
+ */
+ private final double lower;
+ /**
+ * Upper bound of this distribution.
+ */
+ private final double upper;
+
+ /**
+ * A standard normal distribution used for calculations.
+ */
+ private final NormalDistribution standardNormal;
+ /**
+ * Stored value of @{code standardNormal.cumulativeProbability((lower - mean) / sd)} for faster computations.
+ */
+ private final double cdfAlpha;
+ /**
+ * Stored value of @{code (upper - mean) / sd) - cdfAlpha} for faster computations.
+ */
+ private final double cdfDelta;
+
+ /**
+ * Creates a truncated normal distribution.
+ * Note that the {@code mean} and {@code sd} is of the parent normal distribution,
+ * and not the true mean and standard deviation of the truncated normal distribution.
+ *
+ * @param mean mean for this distribution.
+ * @param sd standard deviation for this distribution.
+ * @param lower lower bound (inclusive) of the distribution, can be {@link Double#NEGATIVE_INFINITY}.
+ * @param upper upper bound (inclusive) of the distribution, can be {@link Double#POSITIVE_INFINITY}.
+ * @throws IllegalArgumentException if {@code sd <= 0} or if {@code upper <= lower}.
+ */
+ public TruncatedNormalDistribution(double mean, double sd, double lower, double upper) {
+ if (sd <= 0) {
+ throw new DistributionException(DistributionException.NEGATIVE, sd);
Review comment:
I am thinking that we should have a `DistributionException.NOT_STRICTLY_POSITIVE` constant here. However the same message is used in NormalDistribution (and others) for zero so if you introduce this new constant then I can propagate it where appropriate through the rest of the code. Or you can leave it and I can do this after this PR is merged.
##########
File path: commons-statistics-distribution/src/test/java/org/apache/commons/statistics/distribution/TruncatedNormalDistributionTest.java
##########
@@ -0,0 +1,283 @@
+/*
+ * 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.statistics.distribution;
+
+import org.junit.jupiter.api.Assertions;
+import org.junit.jupiter.api.BeforeEach;
+import org.junit.jupiter.api.Test;
+
+/**
+ * Test class for {@link TruncatedNormalDistribution}.
+ * All test values were computed using Python with SciPy v1.6.0.
+ */
+class TruncatedNormalDistributionTest extends ContinuousDistributionAbstractTest {
+ /**
+ * Default tolerance.
+ */
+ private static final double TOLERANCE = 1e-7;
+
+ /**
+ * Distribution to test with.
+ */
+ private TruncatedNormalDistribution distribution = new TruncatedNormalDistribution(1.9, 1.3, -1.1, 3.4);
+ /**
+ * Percentiles to test with.
+ */
+ private double[] ppfValues = new double[]{0, 0.0001, 0.001, 0.01, 0.025, 0.05, 0.1, 0.25, 0.5, 0.75, 0.9, 0.95,
+ 0.975, 0.99, 0.999, 0.9999, 1};
+ /**
+ * Expected cumulative values for percentiles.
+ */
+ private double[] cdfValues = new double[]{-1.1, -1.09597275767544, -1.0609616183922, -0.79283350106842,
+ -0.505331829887808, -0.192170173599874, 0.21173317261645,
+ 0.925791281910463, 1.71399518338879, 2.43413009451536, 2.94473113856785,
+ 3.15310057075828, 3.27036798398733, 3.34641874981679, 3.39452729074341,
+ 3.39945153287941, 3.4};
+ /**
+ * Expected density values for percentiles.
+ */
+ private double[] pdfValues = new double[]{0.0247422752302618, 0.0249196707321102, 0.0265057408263321,
+ 0.0415071096500185, 0.0640403254340905, 0.0971457789636,
+ 0.152622492901864, 0.267853863255995, 0.35107475879338, 0.325977522502844,
+ 0.25680502248913, 0.222886115806507, 0.203494915087054, 0.190997946666992,
+ 0.183167918885238, 0.182370706542209, 0.182281965373914};
+ /**
+ * Expected distribution mean.
+ */
+ private double mean = 1.63375792365723;
+ /**
+ * Expected distribution variance.
+ */
+ private double variance = 1.03158703914439;
+
+ /**
+ * Overrides tolerance and sets up distribution.
+ */
+ @BeforeEach
+ void setUp() {
+ setTolerance(TOLERANCE);
+ super.setUp();
+ }
+
+ /**
+ * {@inheritDoc}
+ */
+ @Override
+ public ContinuousDistribution makeDistribution() {
+ return distribution;
+ }
+
+ /**
+ * {@inheritDoc}
+ */
+ @Override
+ public double[] makeCumulativeTestPoints() {
+ return cdfValues;
+ }
+
+ /**
+ * {@inheritDoc}
+ */
+ @Override
+ public double[] makeCumulativeTestValues() {
+ return ppfValues;
+ }
+
+ /**
+ * {@inheritDoc}
+ */
+ @Override
+ public double[] makeDensityTestValues() {
+ return pdfValues;
+ }
+
+ /**
+ * Configures new test values and runs relevant tests in this class and {@link ContinuousDistributionAbstractTest}.
+ * @param testDistribution distribution to test with.
+ * @param expectedPpfValues expected percentiles to test with.
+ * @param expectedCdfValues expected cumulative values for percentiles.
+ * @param expectedPdfValues expected density values for percentiles.
+ * @param expectedMean expected mean.
+ * @param expectedVariance expected variance.
+ */
+ private void testAdditionalDistribution(
+ TruncatedNormalDistribution testDistribution,
+ double[] expectedPpfValues,
+ double[] expectedCdfValues,
+ double[] expectedPdfValues,
+ double expectedMean,
+ double expectedVariance
+ ) {
+ this.distribution = testDistribution;
+ this.ppfValues = expectedPpfValues;
+ this.cdfValues = expectedCdfValues;
+ this.pdfValues = expectedPdfValues;
+ this.mean = expectedMean;
+ this.variance = expectedVariance;
+
+ setUp();
+
+ testMoments();
+
+ testConsistency();
+ testSampler();
+ testOutsideSupport();
+ testDensities();
+ testLogDensities();
+ testOutsideSupport();
+ testInverseCumulativeProbabilities();
+ testDensityIntegrals();
+ testCumulativeProbabilities();
+ testIsSupportConnected();
+ testPrecondition1();
+ testPrecondition2();
+ testPrecondition3();
+ }
+
+ /**
+ * Test a one-sided truncation with a lower tail.
+ */
+ @Test
+ void testOneSidedLowerTail() {
+ testAdditionalDistribution(
+ new TruncatedNormalDistribution(12, 2.4, -Double.POSITIVE_INFINITY, 7.1),
+ new double[]{0, 0.00108276414971883, 0.00433032247708514, 0.0155754809421998, 0.0504271331622245,
+ 0.147106879016387, 0.387159643321778, 0.920668099879139, 1},
+ new double[]{-Double.POSITIVE_INFINITY, 2.20249292901062, 3.00511196424565, 3.80773099948069,
+ 4.61035003471573, 5.41296906995077, 6.21558810518581, 7.01820714042084, 7.1},
+ new double[]{0, 0.00194181137319567, 0.00719165311538403, 0.0238165586714952, 0.0705273999981105,
+ 0.186752027463317, 0.442182309739316, 0.936194292830215, 1.00423817618302},
+ 6.21558810518581,
+ 0.644197315721623
+ );
+ }
+
+ /**
+ * Test a one-sided truncation with an upper tail.
+ */
+ @Test
+ void testOneSidedUpperTail() {
+ testAdditionalDistribution(
+ new TruncatedNormalDistribution(-9.6, 17, -15, Double.POSITIVE_INFINITY),
+ new double[]{0, 0.164539974698729, 0.564800349576255, 0.836443289017693, 0.957226746540945,
+ 0.992394081771774, 0.999093968560336, 0.999928403010774, 1},
+ new double[]{-15, -10.5314720401464, 0.723583450712814, 11.978638941572, 23.2336944324312,
+ 34.4887499232902, 45.7438054141485, 56.9988609050074, Double.POSITIVE_INFINITY},
+ new double[]{0.035721742043989, 0.0375137766818179, 0.0312438063187719, 0.0167870518464031,
+ 0.00581865051705663, 0.00130109036611494, 0.000187685186297558, 1.74658560715427e-05, 0},
+ 0.723583450712812,
+ 126.676274102319
+ );
+ }
+
+ /**
+ * Test no truncation.
+ */
+ @Test
+ void testNoTruncation() {
+ testAdditionalDistribution(
+ new TruncatedNormalDistribution(3, 1.1, -Double.POSITIVE_INFINITY, Double.POSITIVE_INFINITY),
+ new double[]{0, 2.86651571879193e-07, 3.16712418331199e-05, 0.00134989803163009, 0.0227501319481792,
+ 0.158655253931457, 0.5, 0.841344746068543, 0.977249868051821, 0.99865010196837,
+ 0.999968328758167, 0.999999713348428, 1},
+ new double[]{-Double.POSITIVE_INFINITY, -2.5, -1.4, -0.300000000000001, 0.799999999999999, 1.9, 3,
+ 4.1, 5.2, 6.3, 7.4, 8.49999999996719, Double.POSITIVE_INFINITY},
+ new double[]{0, 1.35156319521299e-06, 0.000121663841604441, 0.00402895310176182, 0.0490826968301709,
+ 0.219973385926494, 0.362674800364939, 0.219973385926494, 0.0490826968301709,
+ 0.00402895310176184, 0.000121663841604441, 1.35156319541454e-06, 0},
+ 3,
+ 1.21
+ );
+ }
+
+ /**
+ * Test a truncation range that is completely below the mean.
+ */
+ @Test
+ void testLowerTailOnly() {
+ testAdditionalDistribution(
+ new TruncatedNormalDistribution(0, 1, -Double.POSITIVE_INFINITY, -5),
+ new double[]{0, 0.00196196451357246, 0.00597491488512203, 0.0176247203066899, 0.0503595643590926,
+ 0.139390045971621, 0.373761183487683, 0.970943041215359, 1},
+ new double[]{-Double.POSITIVE_INFINITY, -6.09061174025149, -5.90979018562636, -5.72896863100123,
+ -5.54814707637611, -5.36732552175098, -5.18650396712585, -5.00568241250073, -5},
+ new double[]{0, 0.0122562922051934, 0.0362705138555484, 0.103883943928261, 0.287967362544455,
+ 0.772570689127439, 2.00601097433085, 5.04113700754108, 5.18650396712585},
+ -5.18650396712585,
+ 0.0326964346170475
+ );
+ }
+
+ /**
+ * Test a truncation range that is completely above the mean.
+ */
+ @Test
+ void testUpperTailOnly() {
+ testAdditionalDistribution(
+ new TruncatedNormalDistribution(0, 1, 5, Double.POSITIVE_INFINITY),
+ new double[]{0, 0.0290569590230917, 0.626238816822898, 0.860609954247549, 0.949640435971243,
+ 0.982375279755296, 0.994025085266282, 0.998038035551444, 1},
+ new double[]{5, 5.00568241254803, 5.18650396728068, 5.36732552203467, 5.54814707752324,
+ 5.72896863159791, 5.90979018980065, 6.09061174555624, Double.POSITIVE_INFINITY},
+ new double[]{5.18650396712585, 5.04113700634745, 2.00601097272001, 0.772570687951075,
+ 0.287967360711704, 0.103883943573147, 0.0362705129607846, 0.0122562918092027, 0},
+ 5.18650396712585,
+ 0.0326964346170475
+ );
+ }
+
+ /**
+ * Test a narrow truncation range.
+ */
+ @Test
+ void testNarrowTruncatedRange() {
+ testAdditionalDistribution(
+ new TruncatedNormalDistribution(7.1, 9.9, 7.0999999, 7.1000001),
+ new double[]{0, 0.5, 1},
+ new double[]{7.0999999, 7.1, 7.1000001},
+ new double[]{5000000.00238838, 5000000.00238838, 5000000.00238838},
+ 7.1,
+ 1.13584123966337e-07
+ );
+ }
+
+ /**
+ * Test mean and variance moments.
+ */
+ @Test
+ void testMoments() {
+ Assertions.assertEquals(mean, distribution.getMean(), TOLERANCE);
Review comment:
Can use `getTolerance()` here and avoid a class level constant
##########
File path: commons-statistics-distribution/src/main/java/org/apache/commons/statistics/distribution/TruncatedNormalDistribution.java
##########
@@ -0,0 +1,206 @@
+/*
+ * 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.statistics.distribution;
+
+/**
+ * Implementation of the truncated normal distribution.
+ *
+ * @see <a href="http://en.wikipedia.org/wiki/Truncated_normal_distribution">
+ * Truncated normal distribution (Wikipedia)</a>.
+ */
+public class TruncatedNormalDistribution extends AbstractContinuousDistribution {
+ /**
+ * Mean of parent normal distribution.
+ */
+ private final double parentMean;
+ /**
+ * Standard deviation of parent normal distribution.
+ */
+ private final double parentSd;
+ /**
+ * Mean of this distribution.
+ */
+ private final double mean;
+ /**
+ * Variance of this distribution.
+ */
+ private final double variance;
+ /**
+ * Lower bound of this distribution.
+ */
+ private final double lower;
+ /**
+ * Upper bound of this distribution.
+ */
+ private final double upper;
+
+ /**
+ * A standard normal distribution used for calculations.
+ */
+ private final NormalDistribution standardNormal;
+ /**
+ * Stored value of @{code standardNormal.cumulativeProbability((lower - mean) / sd)} for faster computations.
+ */
+ private final double cdfAlpha;
+ /**
+ * Stored value of @{code (upper - mean) / sd) - cdfAlpha} for faster computations.
+ */
+ private final double cdfDelta;
+
+ /**
+ * Creates a truncated normal distribution.
+ * Note that the {@code mean} and {@code sd} is of the parent normal distribution,
+ * and not the true mean and standard deviation of the truncated normal distribution.
+ *
+ * @param mean mean for this distribution.
+ * @param sd standard deviation for this distribution.
+ * @param lower lower bound (inclusive) of the distribution, can be {@link Double#NEGATIVE_INFINITY}.
+ * @param upper upper bound (inclusive) of the distribution, can be {@link Double#POSITIVE_INFINITY}.
+ * @throws IllegalArgumentException if {@code sd <= 0} or if {@code upper <= lower}.
+ */
+ public TruncatedNormalDistribution(double mean, double sd, double lower, double upper) {
+ if (sd <= 0) {
+ throw new DistributionException(DistributionException.NEGATIVE, sd);
+ }
+ if (upper <= lower) {
+ throw new DistributionException(DistributionException.TOO_LARGE, lower, upper);
+ }
+
+ this.lower = lower;
+ this.upper = upper;
+
+ parentMean = mean;
+ parentSd = sd;
+ standardNormal = new NormalDistribution(0, 1);
+
+ double alpha = (lower - mean) / sd;
+ double beta = (upper - mean) / sd;
+
+ cdfAlpha = standardNormal.cumulativeProbability(alpha);
+ double cdfBeta = standardNormal.cumulativeProbability(beta);
+ cdfDelta = cdfBeta - cdfAlpha;
+
+ // Calculation of variance and mean.
+ double pdfAlpha = standardNormal.density(alpha);
+ double pdfBeta = standardNormal.density(beta);
+ double pdfCdfDelta = (pdfAlpha - pdfBeta) / cdfDelta;
+ double alphaBetaDelta = (alpha * pdfAlpha - beta * pdfBeta) / cdfDelta;
+
+ if (lower == Double.NEGATIVE_INFINITY && upper != Double.POSITIVE_INFINITY) {
+ // One-sided lower tail truncation
+ double betaRatio = pdfBeta / cdfBeta;
+ this.mean = mean - sd * betaRatio;
+ variance = sd * sd * (1 - beta * betaRatio - betaRatio * betaRatio);
+ } else if (lower != Double.NEGATIVE_INFINITY && upper == Double.POSITIVE_INFINITY) {
+ // One-sided upper tail truncation
+ double alphaRatio = pdfAlpha / cdfDelta;
+ this.mean = mean + sd * alphaRatio;
+ variance = sd * sd * (1 + alpha * alphaRatio - alphaRatio * alphaRatio);
+ } else if (lower != Double.NEGATIVE_INFINITY && upper != Double.POSITIVE_INFINITY) {
+ // Two-sided truncation
+ this.mean = mean + pdfCdfDelta * parentSd;
+ variance = sd * sd * (1 + alphaBetaDelta - pdfCdfDelta * pdfCdfDelta);
+ } else {
+ // No truncation
+ this.mean = mean;
+ variance = sd * sd;
+ }
+ }
+
+ /**
+ * {@inheritDoc}
+ */
+ @Override
+ public double density(double x) {
+ if (x < lower || x > upper) {
+ return 0;
+ }
+ return standardNormal.density((x - parentMean) / parentSd) / (parentSd * cdfDelta);
+ }
+
+ /**
+ * {@inheritDoc}
+ */
+ @Override
+ public double cumulativeProbability(double x) {
+ if (x <= lower) {
+ return 0;
+ } else if (x >= upper) {
+ return 1;
+ } else {
Review comment:
Remove the unnecessary `else`
##########
File path: commons-statistics-distribution/src/main/java/org/apache/commons/statistics/distribution/TruncatedNormalDistribution.java
##########
@@ -0,0 +1,206 @@
+/*
+ * 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.statistics.distribution;
+
+/**
+ * Implementation of the truncated normal distribution.
+ *
+ * @see <a href="http://en.wikipedia.org/wiki/Truncated_normal_distribution">
+ * Truncated normal distribution (Wikipedia)</a>.
+ */
+public class TruncatedNormalDistribution extends AbstractContinuousDistribution {
+ /**
+ * Mean of parent normal distribution.
+ */
+ private final double parentMean;
Review comment:
Single line javadoc can be left on one line: `/** Something short. */`
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