MATH-1158 Removed deprecated sampling API.
Project: http://git-wip-us.apache.org/repos/asf/commons-math/repo Commit: http://git-wip-us.apache.org/repos/asf/commons-math/commit/77c24aa9 Tree: http://git-wip-us.apache.org/repos/asf/commons-math/tree/77c24aa9 Diff: http://git-wip-us.apache.org/repos/asf/commons-math/diff/77c24aa9 Branch: refs/heads/feature-MATH-1158 Commit: 77c24aa92600598ee7994a1504b7bafc560b3809 Parents: 9867d9f Author: Gilles <er...@apache.org> Authored: Thu Mar 17 19:55:26 2016 +0100 Committer: Gilles <er...@apache.org> Committed: Thu Mar 17 19:55:26 2016 +0100 ---------------------------------------------------------------------- .../distribution/AbstractRealDistribution.java | 51 ------------ .../math4/distribution/BetaDistribution.java | 4 +- .../distribution/ConstantRealDistribution.java | 15 ---- .../distribution/EnumeratedDistribution.java | 1 + .../EnumeratedRealDistribution.java | 9 -- .../distribution/ExponentialDistribution.java | 52 ------------ .../math4/distribution/GammaDistribution.java | 84 +------------------ .../distribution/LogNormalDistribution.java | 12 +-- .../math4/distribution/NormalDistribution.java | 7 -- .../math4/distribution/ParetoDistribution.java | 8 -- .../math4/distribution/RealDistribution.java | 27 ------ .../distribution/UniformRealDistribution.java | 8 -- .../math4/random/EmpiricalDistribution.java | 88 -------------------- .../stat/inference/KolmogorovSmirnovTest.java | 5 +- .../fitting/PolynomialCurveFitterTest.java | 7 +- .../math4/fitting/SimpleCurveFitterTest.java | 6 +- .../math4/linear/EigenDecompositionTest.java | 6 +- .../math4/linear/HessenbergTransformerTest.java | 6 +- .../math4/linear/SchurTransformerTest.java | 6 +- .../AggregateSummaryStatisticsTest.java | 8 +- .../UnivariateStatisticAbstractTest.java | 5 +- .../descriptive/rank/PSquarePercentileTest.java | 19 +++-- .../commons/math4/util/MathUtilsTest.java | 5 +- 23 files changed, 55 insertions(+), 384 deletions(-) ---------------------------------------------------------------------- http://git-wip-us.apache.org/repos/asf/commons-math/blob/77c24aa9/src/main/java/org/apache/commons/math4/distribution/AbstractRealDistribution.java ---------------------------------------------------------------------- diff --git a/src/main/java/org/apache/commons/math4/distribution/AbstractRealDistribution.java b/src/main/java/org/apache/commons/math4/distribution/AbstractRealDistribution.java index 1f6c006..057dd8a 100644 --- a/src/main/java/org/apache/commons/math4/distribution/AbstractRealDistribution.java +++ b/src/main/java/org/apache/commons/math4/distribution/AbstractRealDistribution.java @@ -20,11 +20,9 @@ import java.io.Serializable; import org.apache.commons.math4.analysis.UnivariateFunction; import org.apache.commons.math4.analysis.solvers.UnivariateSolverUtils; -import org.apache.commons.math4.exception.NotStrictlyPositiveException; import org.apache.commons.math4.exception.NumberIsTooLargeException; import org.apache.commons.math4.exception.OutOfRangeException; import org.apache.commons.math4.exception.util.LocalizedFormats; -import org.apache.commons.math4.random.RandomGenerator; import org.apache.commons.math4.rng.UniformRandomProvider; import org.apache.commons.math4.util.FastMath; @@ -51,14 +49,6 @@ public abstract class AbstractRealDistribution private static final long serialVersionUID = 20160311L; /** - * RNG instance used to generate samples from the distribution. - * @since 3.1 - * XXX: hard-coded value to prevent "NullPointerException". - */ - @Deprecated - protected final RandomGenerator random = new org.apache.commons.math4.random.Well19937c(); - - /** * For a random variable {@code X} whose values are distributed according * to this distribution, this method returns {@code P(x0 < X <= x1)}. * @@ -211,47 +201,6 @@ public abstract class AbstractRealDistribution return SOLVER_DEFAULT_ABSOLUTE_ACCURACY; } - /** {@inheritDoc} */ - @Override - @Deprecated - public void reseedRandomGenerator(long seed) { - random.setSeed(seed); - } - - /** - * {@inheritDoc} - * - * The default implementation uses the - * <a href="http://en.wikipedia.org/wiki/Inverse_transform_sampling";> - * inversion method. - * </a> - */ - @Override - @Deprecated - public double sample() { - return inverseCumulativeProbability(random.nextDouble()); - } - - /** - * {@inheritDoc} - * - * The default implementation generates the sample by calling - * {@link #sample()} in a loop. - */ - @Override - @Deprecated - public double[] sample(int sampleSize) { - if (sampleSize <= 0) { - throw new NotStrictlyPositiveException(LocalizedFormats.NUMBER_OF_SAMPLES, - sampleSize); - } - double[] out = new double[sampleSize]; - for (int i = 0; i < sampleSize; i++) { - out[i] = sample(); - } - return out; - } - /** * {@inheritDoc} * http://git-wip-us.apache.org/repos/asf/commons-math/blob/77c24aa9/src/main/java/org/apache/commons/math4/distribution/BetaDistribution.java ---------------------------------------------------------------------- diff --git a/src/main/java/org/apache/commons/math4/distribution/BetaDistribution.java b/src/main/java/org/apache/commons/math4/distribution/BetaDistribution.java index 0644eb1..987e8eb 100644 --- a/src/main/java/org/apache/commons/math4/distribution/BetaDistribution.java +++ b/src/main/java/org/apache/commons/math4/distribution/BetaDistribution.java @@ -254,7 +254,7 @@ public class BetaDistribution extends AbstractRealDistribution { * @since 3.6 */ private static class ChengBetaSampler implements RealDistribution.Sampler { - /** RNG (uniform distribution. */ + /** RNG (uniform distribution). */ private final UniformRandomProvider rng; /** First shape parameter. */ private final double alphaShape; @@ -264,7 +264,7 @@ public class BetaDistribution extends AbstractRealDistribution { /** * Creates a sampler instance. * - * @param rng Generator. + * @param generator RNG. * @param alpha Distribution first shape parameter. * @param beta Distribution second shape parameter. */ http://git-wip-us.apache.org/repos/asf/commons-math/blob/77c24aa9/src/main/java/org/apache/commons/math4/distribution/ConstantRealDistribution.java ---------------------------------------------------------------------- diff --git a/src/main/java/org/apache/commons/math4/distribution/ConstantRealDistribution.java b/src/main/java/org/apache/commons/math4/distribution/ConstantRealDistribution.java index a9b3383..a34179a 100644 --- a/src/main/java/org/apache/commons/math4/distribution/ConstantRealDistribution.java +++ b/src/main/java/org/apache/commons/math4/distribution/ConstantRealDistribution.java @@ -104,21 +104,6 @@ public class ConstantRealDistribution extends AbstractRealDistribution { return true; } - /** {@inheritDoc} */ - @Override - @Deprecated - public double sample() { - return value; - } - - /** - * Override with no-op (there is no generator). - * @param seed (ignored) - */ - @Override - @Deprecated - public void reseedRandomGenerator(long seed) {} - /** * {@inheritDoc} * http://git-wip-us.apache.org/repos/asf/commons-math/blob/77c24aa9/src/main/java/org/apache/commons/math4/distribution/EnumeratedDistribution.java ---------------------------------------------------------------------- diff --git a/src/main/java/org/apache/commons/math4/distribution/EnumeratedDistribution.java b/src/main/java/org/apache/commons/math4/distribution/EnumeratedDistribution.java index fd339b2..3f9acc8 100644 --- a/src/main/java/org/apache/commons/math4/distribution/EnumeratedDistribution.java +++ b/src/main/java/org/apache/commons/math4/distribution/EnumeratedDistribution.java @@ -310,6 +310,7 @@ public class EnumeratedDistribution<T> implements Serializable { * Creates a {@link Sampler}. * * @param rng Random number generator. + * @return a new sampler instance. */ public Sampler createSampler(final UniformRandomProvider rng) { return new Sampler(rng); http://git-wip-us.apache.org/repos/asf/commons-math/blob/77c24aa9/src/main/java/org/apache/commons/math4/distribution/EnumeratedRealDistribution.java ---------------------------------------------------------------------- diff --git a/src/main/java/org/apache/commons/math4/distribution/EnumeratedRealDistribution.java b/src/main/java/org/apache/commons/math4/distribution/EnumeratedRealDistribution.java index 7cf834b..0e34f5a 100644 --- a/src/main/java/org/apache/commons/math4/distribution/EnumeratedRealDistribution.java +++ b/src/main/java/org/apache/commons/math4/distribution/EnumeratedRealDistribution.java @@ -273,15 +273,6 @@ public class EnumeratedRealDistribution extends AbstractRealDistribution { return true; } - /** - * {@inheritDoc} - */ - @Override - @Deprecated - public double sample() { - return innerDistribution.sample(); - } - /** {@inheritDoc} */ @Override public RealDistribution.Sampler createSampler(final UniformRandomProvider rng) { http://git-wip-us.apache.org/repos/asf/commons-math/blob/77c24aa9/src/main/java/org/apache/commons/math4/distribution/ExponentialDistribution.java ---------------------------------------------------------------------- diff --git a/src/main/java/org/apache/commons/math4/distribution/ExponentialDistribution.java b/src/main/java/org/apache/commons/math4/distribution/ExponentialDistribution.java index 1dbd6b1..9527aa0 100644 --- a/src/main/java/org/apache/commons/math4/distribution/ExponentialDistribution.java +++ b/src/main/java/org/apache/commons/math4/distribution/ExponentialDistribution.java @@ -186,58 +186,6 @@ public class ExponentialDistribution extends AbstractRealDistribution { return ret; } - /** - * {@inheritDoc} - * - * <p><strong>Algorithm Description</strong>: this implementation uses the - * <a href="http://www.jesus.ox.ac.uk/~clifford/a5/chap1/node5.html";> - * Inversion Method</a> to generate exponentially distributed random values - * from uniform deviates.</p> - * - * @return a random value. - * @since 2.2 - */ - @Override - @Deprecated - public double sample() { - // Step 1: - double a = 0; - double u = random.nextDouble(); - - // Step 2 and 3: - while (u < 0.5) { - a += EXPONENTIAL_SA_QI[0]; - u *= 2; - } - - // Step 4 (now u >= 0.5): - u += u - 1; - - // Step 5: - if (u <= EXPONENTIAL_SA_QI[0]) { - return mean * (a + u); - } - - // Step 6: - int i = 0; // Should be 1, be we iterate before it in while using 0 - double u2 = random.nextDouble(); - double umin = u2; - - // Step 7 and 8: - do { - ++i; - u2 = random.nextDouble(); - - if (u2 < umin) { - umin = u2; - } - - // Step 8: - } while (u > EXPONENTIAL_SA_QI[i]); // Ensured to exit since EXPONENTIAL_SA_QI[MAX] = 1 - - return mean * (a + umin * EXPONENTIAL_SA_QI[0]); - } - /** {@inheritDoc} */ @Override protected double getSolverAbsoluteAccuracy() { http://git-wip-us.apache.org/repos/asf/commons-math/blob/77c24aa9/src/main/java/org/apache/commons/math4/distribution/GammaDistribution.java ---------------------------------------------------------------------- diff --git a/src/main/java/org/apache/commons/math4/distribution/GammaDistribution.java b/src/main/java/org/apache/commons/math4/distribution/GammaDistribution.java index c50c974..413493f 100644 --- a/src/main/java/org/apache/commons/math4/distribution/GammaDistribution.java +++ b/src/main/java/org/apache/commons/math4/distribution/GammaDistribution.java @@ -351,88 +351,6 @@ public class GammaDistribution extends AbstractRealDistribution { } /** - * <p>This implementation uses the following algorithms: </p> - * - * <p>For 0 < shape < 1: <br/> - * Ahrens, J. H. and Dieter, U., <i>Computer methods for - * sampling from gamma, beta, Poisson and binomial distributions.</i> - * Computing, 12, 223-246, 1974.</p> - * - * <p>For shape >= 1: <br/> - * Marsaglia and Tsang, <i>A Simple Method for Generating - * Gamma Variables.</i> ACM Transactions on Mathematical Software, - * Volume 26 Issue 3, September, 2000.</p> - * - * @return random value sampled from the Gamma(shape, scale) distribution - */ - @Override - @Deprecated - public double sample() { - if (shape < 1) { - // [1]: p. 228, Algorithm GS - - while (true) { - // Step 1: - final double u = random.nextDouble(); - final double bGS = 1 + shape / FastMath.E; - final double p = bGS * u; - - if (p <= 1) { - // Step 2: - - final double x = FastMath.pow(p, 1 / shape); - final double u2 = random.nextDouble(); - - if (u2 > FastMath.exp(-x)) { - // Reject - continue; - } else { - return scale * x; - } - } else { - // Step 3: - - final double x = -1 * FastMath.log((bGS - p) / shape); - final double u2 = random.nextDouble(); - - if (u2 > FastMath.pow(x, shape - 1)) { - // Reject - continue; - } else { - return scale * x; - } - } - } - } - - // Now shape >= 1 - - final double d = shape - 0.333333333333333333; - final double c = 1 / (3 * FastMath.sqrt(d)); - - while (true) { - final double x = random.nextGaussian(); - final double v = (1 + c * x) * (1 + c * x) * (1 + c * x); - - if (v <= 0) { - continue; - } - - final double x2 = x * x; - final double u = random.nextDouble(); - - // Squeeze - if (u < 1 - 0.0331 * x2 * x2) { - return scale * d * v; - } - - if (FastMath.log(u) < 0.5 * x2 + d * (1 - v + FastMath.log(v))) { - return scale * d * v; - } - } - } - - /** * {@inheritDoc} * * <p> @@ -461,7 +379,7 @@ public class GammaDistribution extends AbstractRealDistribution { public RealDistribution.Sampler createSampler(final UniformRandomProvider rng) { return new RealDistribution.Sampler() { /** Gaussian sampling. */ - final RealDistribution.Sampler gaussian = new NormalDistribution().createSampler(rng); + private final RealDistribution.Sampler gaussian = new NormalDistribution().createSampler(rng); /** {@inheritDoc} */ @Override http://git-wip-us.apache.org/repos/asf/commons-math/blob/77c24aa9/src/main/java/org/apache/commons/math4/distribution/LogNormalDistribution.java ---------------------------------------------------------------------- diff --git a/src/main/java/org/apache/commons/math4/distribution/LogNormalDistribution.java b/src/main/java/org/apache/commons/math4/distribution/LogNormalDistribution.java index eafb90e..6b155d5 100644 --- a/src/main/java/org/apache/commons/math4/distribution/LogNormalDistribution.java +++ b/src/main/java/org/apache/commons/math4/distribution/LogNormalDistribution.java @@ -290,23 +290,15 @@ public class LogNormalDistribution extends AbstractRealDistribution { /** {@inheritDoc} */ @Override - @Deprecated - public double sample() { - final double n = random.nextGaussian(); - return FastMath.exp(scale + shape * n); - } - - /** {@inheritDoc} */ - @Override public RealDistribution.Sampler createSampler(final UniformRandomProvider rng) { return new RealDistribution.Sampler() { /** Gaussian sampling. */ - final RealDistribution.Sampler gaussian = new NormalDistribution().createSampler(rng); + private final RealDistribution.Sampler gaussian = new NormalDistribution().createSampler(rng); /** {@inheritDoc} */ @Override public double sample() { - final double n = random.nextGaussian(); + final double n = gaussian.sample(); return FastMath.exp(scale + shape * n); } }; http://git-wip-us.apache.org/repos/asf/commons-math/blob/77c24aa9/src/main/java/org/apache/commons/math4/distribution/NormalDistribution.java ---------------------------------------------------------------------- diff --git a/src/main/java/org/apache/commons/math4/distribution/NormalDistribution.java b/src/main/java/org/apache/commons/math4/distribution/NormalDistribution.java index a8330d5..b8e919b 100644 --- a/src/main/java/org/apache/commons/math4/distribution/NormalDistribution.java +++ b/src/main/java/org/apache/commons/math4/distribution/NormalDistribution.java @@ -237,13 +237,6 @@ public class NormalDistribution extends AbstractRealDistribution { /** {@inheritDoc} */ @Override - @Deprecated - public double sample() { - return standardDeviation * random.nextGaussian() + mean; - } - - /** {@inheritDoc} */ - @Override public RealDistribution.Sampler createSampler(final UniformRandomProvider rng) { return new RealDistribution.Sampler() { /** Next gaussian. */ http://git-wip-us.apache.org/repos/asf/commons-math/blob/77c24aa9/src/main/java/org/apache/commons/math4/distribution/ParetoDistribution.java ---------------------------------------------------------------------- diff --git a/src/main/java/org/apache/commons/math4/distribution/ParetoDistribution.java b/src/main/java/org/apache/commons/math4/distribution/ParetoDistribution.java index 2174322..04427da 100644 --- a/src/main/java/org/apache/commons/math4/distribution/ParetoDistribution.java +++ b/src/main/java/org/apache/commons/math4/distribution/ParetoDistribution.java @@ -250,14 +250,6 @@ public class ParetoDistribution extends AbstractRealDistribution { /** {@inheritDoc} */ @Override - @Deprecated - public double sample() { - final double n = random.nextDouble(); - return scale / FastMath.pow(n, 1 / shape); - } - - /** {@inheritDoc} */ - @Override public RealDistribution.Sampler createSampler(final UniformRandomProvider rng) { return new RealDistribution.Sampler() { /** {@inheritDoc} */ http://git-wip-us.apache.org/repos/asf/commons-math/blob/77c24aa9/src/main/java/org/apache/commons/math4/distribution/RealDistribution.java ---------------------------------------------------------------------- diff --git a/src/main/java/org/apache/commons/math4/distribution/RealDistribution.java b/src/main/java/org/apache/commons/math4/distribution/RealDistribution.java index f0e453a..7ddc1fd 100644 --- a/src/main/java/org/apache/commons/math4/distribution/RealDistribution.java +++ b/src/main/java/org/apache/commons/math4/distribution/RealDistribution.java @@ -161,33 +161,6 @@ public interface RealDistribution { boolean isSupportConnected(); /** - * Reseed the random generator used to generate samples. - * - * @param seed the new seed - */ - @Deprecated - void reseedRandomGenerator(long seed); - - /** - * Generate a random value sampled from this distribution. - * - * @return a random value. - */ - @Deprecated - double sample(); - - /** - * Generate a random sample from the distribution. - * - * @param sampleSize the number of random values to generate - * @return an array representing the random sample - * @throws org.apache.commons.math4.exception.NotStrictlyPositiveException - * if {@code sampleSize} is not positive - */ - @Deprecated - double[] sample(int sampleSize); - - /** * Creates a sampler. * * @param rng Generator of uniformly distributed numbers. http://git-wip-us.apache.org/repos/asf/commons-math/blob/77c24aa9/src/main/java/org/apache/commons/math4/distribution/UniformRealDistribution.java ---------------------------------------------------------------------- diff --git a/src/main/java/org/apache/commons/math4/distribution/UniformRealDistribution.java b/src/main/java/org/apache/commons/math4/distribution/UniformRealDistribution.java index 404cc02..a7a1c4d 100644 --- a/src/main/java/org/apache/commons/math4/distribution/UniformRealDistribution.java +++ b/src/main/java/org/apache/commons/math4/distribution/UniformRealDistribution.java @@ -160,14 +160,6 @@ public class UniformRealDistribution extends AbstractRealDistribution { /** {@inheritDoc} */ @Override - @Deprecated - public double sample() { - final double u = random.nextDouble(); - return u * upper + (1 - u) * lower; - } - - /** {@inheritDoc} */ - @Override public RealDistribution.Sampler createSampler(final UniformRandomProvider rng) { return new RealDistribution.Sampler() { /** {@inheritDoc} */ http://git-wip-us.apache.org/repos/asf/commons-math/blob/77c24aa9/src/main/java/org/apache/commons/math4/random/EmpiricalDistribution.java ---------------------------------------------------------------------- diff --git a/src/main/java/org/apache/commons/math4/random/EmpiricalDistribution.java b/src/main/java/org/apache/commons/math4/random/EmpiricalDistribution.java index 926ad09..fad5226 100644 --- a/src/main/java/org/apache/commons/math4/random/EmpiricalDistribution.java +++ b/src/main/java/org/apache/commons/math4/random/EmpiricalDistribution.java @@ -42,7 +42,6 @@ import org.apache.commons.math4.exception.util.LocalizedFormats; import org.apache.commons.math4.stat.descriptive.StatisticalSummary; import org.apache.commons.math4.stat.descriptive.SummaryStatistics; import org.apache.commons.math4.rng.UniformRandomProvider; -import org.apache.commons.math4.rng.RandomSource; import org.apache.commons.math4.util.FastMath; import org.apache.commons.math4.util.MathUtils; @@ -113,10 +112,6 @@ public class EmpiricalDistribution extends AbstractRealDistribution { /** Serializable version identifier */ private static final long serialVersionUID = 5729073523949762654L; - /** RandomDataGenerator instance to use in repeated calls to getNext() */ - @Deprecated - protected final RandomDataGenerator randomData; - /** List of SummaryStatistics objects characterizing the bins */ private final List<SummaryStatistics> binStats; @@ -160,55 +155,9 @@ public class EmpiricalDistribution extends AbstractRealDistribution { } this.binCount = binCount; binStats = new ArrayList<SummaryStatistics>(); - randomData = null; // XXX remove } /** - * Creates a new EmpiricalDistribution with the specified bin count using the - * provided {@link RandomGenerator} as the source of random data. - * - * @param binCount number of bins. Must be strictly positive. - * @param generator random data generator (may be null, resulting in default JDK generator) - * @throws NotStrictlyPositiveException if {@code binCount <= 0}. - * @since 3.0 - */ - @Deprecated - public EmpiricalDistribution(int binCount, RandomGenerator generator) { - this(binCount, new RandomDataGenerator(generator)); - } - - /** - * Creates a new EmpiricalDistribution with default bin count using the - * provided {@link RandomGenerator} as the source of random data. - * - * @param generator random data generator (may be null, resulting in default JDK generator) - * @since 3.0 - */ - @Deprecated - public EmpiricalDistribution(RandomGenerator generator) { - this(DEFAULT_BIN_COUNT, generator); - } - - /** - * Private constructor to allow lazy initialisation of the RNG contained - * in the {@link #randomData} instance variable. - * - * @param binCount number of bins. Must be strictly positive. - * @param randomData Random data generator. - * @throws NotStrictlyPositiveException if {@code binCount <= 0}. - */ - @Deprecated - private EmpiricalDistribution(int binCount, - RandomDataGenerator randomData) { - if (binCount <= 0) { - throw new NotStrictlyPositiveException(binCount); - } - this.binCount = binCount; - this.randomData = randomData; - binStats = new ArrayList<SummaryStatistics>(); - } - - /** * Computes the empirical distribution from the provided * array of numbers. * @@ -456,21 +405,6 @@ public class EmpiricalDistribution extends AbstractRealDistribution { } /** - * Generates a random value from this distribution. - * <strong>Preconditions:</strong><ul> - * <li>the distribution must be loaded before invoking this method</li></ul> - * @return the random value. - * @throws MathIllegalStateException if the distribution has not been loaded - */ - @Deprecated - public double getNextValue() throws MathIllegalStateException { - if (!loaded) { - throw new MathIllegalStateException(LocalizedFormats.DISTRIBUTION_NOT_LOADED); - } - return sample(); - } - - /** * Returns a {@link StatisticalSummary} describing this distribution. * <strong>Preconditions:</strong><ul> * <li>the distribution must be loaded before invoking this method</li></ul> @@ -556,18 +490,6 @@ public class EmpiricalDistribution extends AbstractRealDistribution { return loaded; } - /** - * Reseeds the random number generator used by {@link #getNextValue()}. - * - * @param seed random generator seed - * @since 3.0 - * XXX REMOVE - */ - @Deprecated - public void reSeed(long seed) { - randomData.reSeed(seed); - } - // Distribution methods --------------------------- /** @@ -742,16 +664,6 @@ public class EmpiricalDistribution extends AbstractRealDistribution { return true; } - /** - * {@inheritDoc} - * @since 3.1 - */ - @Override - @Deprecated - public void reseedRandomGenerator(long seed) { - randomData.reSeed(seed); - } - /**{@inheritDoc} */ @Override public RealDistribution.Sampler createSampler(final UniformRandomProvider rng) { http://git-wip-us.apache.org/repos/asf/commons-math/blob/77c24aa9/src/main/java/org/apache/commons/math4/stat/inference/KolmogorovSmirnovTest.java ---------------------------------------------------------------------- diff --git a/src/main/java/org/apache/commons/math4/stat/inference/KolmogorovSmirnovTest.java b/src/main/java/org/apache/commons/math4/stat/inference/KolmogorovSmirnovTest.java index b75de0e..79451dd 100644 --- a/src/main/java/org/apache/commons/math4/stat/inference/KolmogorovSmirnovTest.java +++ b/src/main/java/org/apache/commons/math4/stat/inference/KolmogorovSmirnovTest.java @@ -160,7 +160,8 @@ public class KolmogorovSmirnovTest { * The #monteCarloP(double, int, int, boolean, int) that uses the generator supplied to this * constructor is deprecated as of version 3.6. * - * @param rng random data generator used by {@link #monteCarloP(double, int, int, boolean, int)} + * @param source random data generator used by {@link #monteCarloP(double, int, int, boolean, int)} + * @param seed Seed. */ @Deprecated public KolmogorovSmirnovTest(RandomSource source, @@ -1209,10 +1210,8 @@ public class KolmogorovSmirnovTest { private static void jitter(double[] data, RealDistribution.Sampler sampler) { for (int i = 0; i < data.length; i++) { final double d = sampler.sample(); - System.out.println("d=" + d); // XXX data[i] += d; } - System.out.println(); // XXX } /** http://git-wip-us.apache.org/repos/asf/commons-math/blob/77c24aa9/src/test/java/org/apache/commons/math4/fitting/PolynomialCurveFitterTest.java ---------------------------------------------------------------------- diff --git a/src/test/java/org/apache/commons/math4/fitting/PolynomialCurveFitterTest.java b/src/test/java/org/apache/commons/math4/fitting/PolynomialCurveFitterTest.java index 89ebc2b..2b1e2d3 100644 --- a/src/test/java/org/apache/commons/math4/fitting/PolynomialCurveFitterTest.java +++ b/src/test/java/org/apache/commons/math4/fitting/PolynomialCurveFitterTest.java @@ -26,6 +26,7 @@ import org.apache.commons.math4.exception.ConvergenceException; import org.apache.commons.math4.fitting.PolynomialCurveFitter; import org.apache.commons.math4.fitting.WeightedObservedPoints; import org.apache.commons.math4.util.FastMath; +import org.apache.commons.math4.rng.RandomSource; import org.junit.Assert; import org.junit.Test; @@ -35,9 +36,9 @@ import org.junit.Test; public class PolynomialCurveFitterTest { @Test public void testFit() { - final RealDistribution rng = new UniformRealDistribution(-100, 100); - rng.reseedRandomGenerator(64925784252L); - + final RealDistribution.Sampler rng + = new UniformRealDistribution(-100, 100).createSampler(RandomSource.create(RandomSource.WELL_512_A, + 64925784252L)); final double[] coeff = { 12.9, -3.4, 2.1 }; // 12.9 - 3.4 x + 2.1 x^2 final PolynomialFunction f = new PolynomialFunction(coeff); http://git-wip-us.apache.org/repos/asf/commons-math/blob/77c24aa9/src/test/java/org/apache/commons/math4/fitting/SimpleCurveFitterTest.java ---------------------------------------------------------------------- diff --git a/src/test/java/org/apache/commons/math4/fitting/SimpleCurveFitterTest.java b/src/test/java/org/apache/commons/math4/fitting/SimpleCurveFitterTest.java index 01d28b2..4a3867c 100644 --- a/src/test/java/org/apache/commons/math4/fitting/SimpleCurveFitterTest.java +++ b/src/test/java/org/apache/commons/math4/fitting/SimpleCurveFitterTest.java @@ -25,6 +25,7 @@ import org.apache.commons.math4.distribution.RealDistribution; import org.apache.commons.math4.distribution.UniformRealDistribution; import org.apache.commons.math4.fitting.SimpleCurveFitter; import org.apache.commons.math4.fitting.WeightedObservedPoints; +import org.apache.commons.math4.rng.RandomSource; import org.junit.Test; /** @@ -34,8 +35,9 @@ public class SimpleCurveFitterTest { @Test public void testPolynomialFit() { final Random randomizer = new Random(53882150042L); - final RealDistribution rng = new UniformRealDistribution(-100, 100); - rng.reseedRandomGenerator(64925784252L); + final RealDistribution.Sampler rng + = new UniformRealDistribution(-100, 100).createSampler(RandomSource.create(RandomSource.WELL_512_A, + 64925784253L)); final double[] coeff = { 12.9, -3.4, 2.1 }; // 12.9 - 3.4 x + 2.1 x^2 final PolynomialFunction f = new PolynomialFunction(coeff); http://git-wip-us.apache.org/repos/asf/commons-math/blob/77c24aa9/src/test/java/org/apache/commons/math4/linear/EigenDecompositionTest.java ---------------------------------------------------------------------- diff --git a/src/test/java/org/apache/commons/math4/linear/EigenDecompositionTest.java b/src/test/java/org/apache/commons/math4/linear/EigenDecompositionTest.java index fba9e90..683954f 100644 --- a/src/test/java/org/apache/commons/math4/linear/EigenDecompositionTest.java +++ b/src/test/java/org/apache/commons/math4/linear/EigenDecompositionTest.java @@ -20,6 +20,7 @@ package org.apache.commons.math4.linear; import java.util.Arrays; import java.util.Random; +import org.apache.commons.math4.distribution.RealDistribution; import org.apache.commons.math4.distribution.NormalDistribution; import org.apache.commons.math4.exception.MathUnsupportedOperationException; import org.apache.commons.math4.linear.ArrayRealVector; @@ -32,6 +33,7 @@ import org.apache.commons.math4.linear.TriDiagonalTransformer; import org.apache.commons.math4.util.FastMath; import org.apache.commons.math4.util.MathArrays; import org.apache.commons.math4.util.Precision; +import org.apache.commons.math4.rng.RandomSource; import org.junit.After; import org.junit.Assert; import org.junit.Before; @@ -468,7 +470,9 @@ public class EigenDecompositionTest { public void testNormalDistributionUnsymmetricMatrix() { for (int run = 0; run < 100; run++) { Random r = new Random(System.currentTimeMillis()); - NormalDistribution dist = new NormalDistribution(0.0, r.nextDouble() * 5); + RealDistribution.Sampler dist + = new NormalDistribution(0.0, r.nextDouble() * 5).createSampler(RandomSource.create(RandomSource.WELL_512_A, + 64925784252L)); // matrix size int size = r.nextInt(20) + 4; http://git-wip-us.apache.org/repos/asf/commons-math/blob/77c24aa9/src/test/java/org/apache/commons/math4/linear/HessenbergTransformerTest.java ---------------------------------------------------------------------- diff --git a/src/test/java/org/apache/commons/math4/linear/HessenbergTransformerTest.java b/src/test/java/org/apache/commons/math4/linear/HessenbergTransformerTest.java index 310f23d..af6e837 100644 --- a/src/test/java/org/apache/commons/math4/linear/HessenbergTransformerTest.java +++ b/src/test/java/org/apache/commons/math4/linear/HessenbergTransformerTest.java @@ -19,11 +19,13 @@ package org.apache.commons.math4.linear; import java.util.Random; +import org.apache.commons.math4.distribution.RealDistribution; import org.apache.commons.math4.distribution.NormalDistribution; import org.apache.commons.math4.linear.HessenbergTransformer; import org.apache.commons.math4.linear.MatrixUtils; import org.apache.commons.math4.linear.NonSquareMatrixException; import org.apache.commons.math4.linear.RealMatrix; +import org.apache.commons.math4.rng.RandomSource; import org.junit.Test; import org.junit.Assert; @@ -112,7 +114,9 @@ public class HessenbergTransformerTest { public void testRandomDataNormalDistribution() { for (int run = 0; run < 100; run++) { Random r = new Random(System.currentTimeMillis()); - NormalDistribution dist = new NormalDistribution(0.0, r.nextDouble() * 5); + RealDistribution.Sampler dist + = new NormalDistribution(0.0, r.nextDouble() * 5).createSampler(RandomSource.create(RandomSource.WELL_512_A, + 64925784252L)); // matrix size int size = r.nextInt(20) + 4; http://git-wip-us.apache.org/repos/asf/commons-math/blob/77c24aa9/src/test/java/org/apache/commons/math4/linear/SchurTransformerTest.java ---------------------------------------------------------------------- diff --git a/src/test/java/org/apache/commons/math4/linear/SchurTransformerTest.java b/src/test/java/org/apache/commons/math4/linear/SchurTransformerTest.java index e0a5611..f2cf72e 100644 --- a/src/test/java/org/apache/commons/math4/linear/SchurTransformerTest.java +++ b/src/test/java/org/apache/commons/math4/linear/SchurTransformerTest.java @@ -19,11 +19,13 @@ package org.apache.commons.math4.linear; import java.util.Random; +import org.apache.commons.math4.distribution.RealDistribution; import org.apache.commons.math4.distribution.NormalDistribution; import org.apache.commons.math4.linear.MatrixUtils; import org.apache.commons.math4.linear.NonSquareMatrixException; import org.apache.commons.math4.linear.RealMatrix; import org.apache.commons.math4.linear.SchurTransformer; +import org.apache.commons.math4.rng.RandomSource; import org.junit.Test; import org.junit.Assert; @@ -116,7 +118,9 @@ public class SchurTransformerTest { public void testRandomDataNormalDistribution() { for (int run = 0; run < 100; run++) { Random r = new Random(System.currentTimeMillis()); - NormalDistribution dist = new NormalDistribution(0.0, r.nextDouble() * 5); + RealDistribution.Sampler dist + = new NormalDistribution(0.0, r.nextDouble() * 5).createSampler(RandomSource.create(RandomSource.WELL_512_A, + 64925784252L)); // matrix size int size = r.nextInt(20) + 4; http://git-wip-us.apache.org/repos/asf/commons-math/blob/77c24aa9/src/test/java/org/apache/commons/math4/stat/descriptive/AggregateSummaryStatisticsTest.java ---------------------------------------------------------------------- diff --git a/src/test/java/org/apache/commons/math4/stat/descriptive/AggregateSummaryStatisticsTest.java b/src/test/java/org/apache/commons/math4/stat/descriptive/AggregateSummaryStatisticsTest.java index 5324ecf..139a060 100644 --- a/src/test/java/org/apache/commons/math4/stat/descriptive/AggregateSummaryStatisticsTest.java +++ b/src/test/java/org/apache/commons/math4/stat/descriptive/AggregateSummaryStatisticsTest.java @@ -23,9 +23,11 @@ import java.util.Collection; import org.apache.commons.math4.TestUtils; import org.apache.commons.math4.distribution.IntegerDistribution; import org.apache.commons.math4.distribution.RealDistribution; +import org.apache.commons.math4.distribution.AbstractRealDistribution; import org.apache.commons.math4.distribution.UniformIntegerDistribution; import org.apache.commons.math4.distribution.UniformRealDistribution; import org.apache.commons.math4.util.Precision; +import org.apache.commons.math4.rng.RandomSource; import org.junit.Assert; import org.junit.Test; @@ -281,9 +283,11 @@ public class AggregateSummaryStatisticsTest { */ private double[] generateSample() { final IntegerDistribution size = new UniformIntegerDistribution(10, 100); - final RealDistribution randomData = new UniformRealDistribution(-100, 100); + final RealDistribution.Sampler randomData + = new UniformRealDistribution(-100, 100).createSampler(RandomSource.create(RandomSource.WELL_512_A, + 64925784252L));; final int sampleSize = size.sample(); - final double[] out = randomData.sample(sampleSize); + final double[] out = AbstractRealDistribution.sample(sampleSize, randomData); return out; } http://git-wip-us.apache.org/repos/asf/commons-math/blob/77c24aa9/src/test/java/org/apache/commons/math4/stat/descriptive/UnivariateStatisticAbstractTest.java ---------------------------------------------------------------------- diff --git a/src/test/java/org/apache/commons/math4/stat/descriptive/UnivariateStatisticAbstractTest.java b/src/test/java/org/apache/commons/math4/stat/descriptive/UnivariateStatisticAbstractTest.java index 6f12b1e..cd5be56 100644 --- a/src/test/java/org/apache/commons/math4/stat/descriptive/UnivariateStatisticAbstractTest.java +++ b/src/test/java/org/apache/commons/math4/stat/descriptive/UnivariateStatisticAbstractTest.java @@ -27,6 +27,7 @@ import org.apache.commons.math4.distribution.UniformIntegerDistribution; import org.apache.commons.math4.stat.descriptive.UnivariateStatistic; import org.apache.commons.math4.stat.descriptive.WeightedEvaluation; import org.apache.commons.math4.util.FastMath; +import org.apache.commons.math4.rng.RandomSource; import org.junit.Assert; import org.junit.Test; @@ -187,7 +188,9 @@ public abstract class UnivariateStatisticAbstractTest { // Fill values array with random data from N(mu, sigma) // and fill valuesList with values from values array with // values[i] repeated weights[i] times, each i - final RealDistribution valueDist = new NormalDistribution(mu, sigma); + final RealDistribution.Sampler valueDist + = new NormalDistribution(mu, sigma).createSampler(RandomSource.create(RandomSource.WELL_512_A, + 64925784252L)); List<Double> valuesList = new ArrayList<Double>(); for (int i = 0; i < len; i++) { double value = valueDist.sample(); http://git-wip-us.apache.org/repos/asf/commons-math/blob/77c24aa9/src/test/java/org/apache/commons/math4/stat/descriptive/rank/PSquarePercentileTest.java ---------------------------------------------------------------------- diff --git a/src/test/java/org/apache/commons/math4/stat/descriptive/rank/PSquarePercentileTest.java b/src/test/java/org/apache/commons/math4/stat/descriptive/rank/PSquarePercentileTest.java index fdbf689..52cea33 100644 --- a/src/test/java/org/apache/commons/math4/stat/descriptive/rank/PSquarePercentileTest.java +++ b/src/test/java/org/apache/commons/math4/stat/descriptive/rank/PSquarePercentileTest.java @@ -27,6 +27,7 @@ import java.util.Set; import org.apache.commons.math4.distribution.LogNormalDistribution; import org.apache.commons.math4.distribution.NormalDistribution; import org.apache.commons.math4.distribution.RealDistribution; +import org.apache.commons.math4.distribution.AbstractRealDistribution; import org.apache.commons.math4.exception.MathIllegalArgumentException; import org.apache.commons.math4.exception.NullArgumentException; import org.apache.commons.math4.exception.OutOfRangeException; @@ -714,39 +715,39 @@ public class PSquarePercentileTest extends distribution.createSampler(RandomSource.create(RandomSource.WELL_19937_C, 1000)); double data[]; - data = distribution.sample(VERY_LARGE); + data = AbstractRealDistribution.sample(VERY_LARGE, sampler); doCalculatePercentile(50, data, 0.0001); doCalculatePercentile(95, data, 0.0001); - data = distribution.sample(LARGE); + data = AbstractRealDistribution.sample(LARGE, sampler); doCalculatePercentile(50, data, 0.001); doCalculatePercentile(95, data, 0.001); - data = distribution.sample(VERY_BIG); + data = AbstractRealDistribution.sample(VERY_BIG, sampler); doCalculatePercentile(50, data, 0.001); doCalculatePercentile(95, data, 0.001); - data = distribution.sample(BIG); + data = AbstractRealDistribution.sample(BIG, sampler); doCalculatePercentile(50, data, 0.001); doCalculatePercentile(95, data, 0.001); - data = distribution.sample(STANDARD); + data = AbstractRealDistribution.sample(STANDARD, sampler); doCalculatePercentile(50, data, 0.005); doCalculatePercentile(95, data, 0.005); - data = distribution.sample(MEDIUM); + data = AbstractRealDistribution.sample(MEDIUM, sampler); doCalculatePercentile(50, data, 0.005); doCalculatePercentile(95, data, 0.005); - data = distribution.sample(NOMINAL); + data = AbstractRealDistribution.sample(NOMINAL, sampler); doCalculatePercentile(50, data, 0.01); doCalculatePercentile(95, data, 0.01); - data = distribution.sample(SMALL); + data = AbstractRealDistribution.sample(SMALL, sampler); doCalculatePercentile(50, data, 0.01); doCalculatePercentile(95, data, 0.01); - data = distribution.sample(TINY); + data = AbstractRealDistribution.sample(TINY, sampler); doCalculatePercentile(50, data, 0.05); doCalculatePercentile(95, data, 0.05); http://git-wip-us.apache.org/repos/asf/commons-math/blob/77c24aa9/src/test/java/org/apache/commons/math4/util/MathUtilsTest.java ---------------------------------------------------------------------- diff --git a/src/test/java/org/apache/commons/math4/util/MathUtilsTest.java b/src/test/java/org/apache/commons/math4/util/MathUtilsTest.java index b9beee3..8ce9a2d 100644 --- a/src/test/java/org/apache/commons/math4/util/MathUtilsTest.java +++ b/src/test/java/org/apache/commons/math4/util/MathUtilsTest.java @@ -20,6 +20,7 @@ import org.apache.commons.math4.exception.NotFiniteNumberException; import org.apache.commons.math4.exception.NullArgumentException; import org.apache.commons.math4.exception.util.LocalizedFormats; import org.apache.commons.math4.random.RandomDataGenerator; +import org.apache.commons.math4.rng.RandomSource; import org.apache.commons.math4.util.FastMath; import org.apache.commons.math4.util.MathUtils; import org.junit.Assert; @@ -100,7 +101,9 @@ public final class MathUtilsTest { // Generate 10 distinct random values for (int i = 0; i < 10; i++) { - final RealDistribution u = new UniformRealDistribution(i + 0.5, i + 0.75); + final RealDistribution.Sampler u + = new UniformRealDistribution(i + 0.5, i + 0.75).createSampler(RandomSource.create(RandomSource.WELL_512_A, + 64925784252L)); original[i] = u.sample(); }
