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Merge branch 'master' of https://git-wip-us.apache.org/repos/asf/commons-math

This commit is contained in:
Gilles 2015-03-09 00:44:45 +01:00
parent 86eb3a2fa7 4aa4c6d31f
commit c1c61ce70d
35 changed files with 129 additions and 104 deletions
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7
src/changes/changes.xml
View File

@ -54,6 +54,13 @@ If the output is not quite correct, check for invisible trailing spaces!
</release>
<release version="4.0" date="XXXX-XX-XX" description="">
<action dev="psteitz" type="fix" issue="MATH-1203">
EmpiricalDistribution getKernel fails for buckets with only multiple instances of the same value.
</action>
<action dev="tn" type="update" issue="MATH-869">
"SpearmansCorrelation" will now throw an "MathIllegalArgumentException"
if provided with a "NaturalRanking" instance that uses "REMOVED" as "NaNStrategy".
</action>
<action dev="tn" type="update" issue="MATH-869">
"NullArgumentException" extends now "java.lang.NullPointerException"
instead of "MathIllegalArgumentException".

1
src/main/java/org/apache/commons/math4/exception/util/LocalizedFormats.java
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@ -241,6 +241,7 @@ public enum LocalizedFormats implements Localizable {
NOT_STRICTLY_INCREASING_SEQUENCE("points {3} and {2} are not strictly increasing ({1} >= {0})"), /* keep */
NOT_SUBTRACTION_COMPATIBLE_MATRICES("{0}x{1} and {2}x{3} matrices are not subtraction compatible"),
NOT_SUPPORTED_IN_DIMENSION_N("method not supported in dimension {0}"),
NOT_SUPPORTED_NAN_STRATEGY("NaN strategy {0} not supported"),
NOT_SYMMETRIC_MATRIX("not symmetric matrix"),
NON_SYMMETRIC_MATRIX("non symmetric matrix: the difference between entries at ({0},{1}) and ({1},{0}) is larger than {2}"), /* keep */
NO_BIN_SELECTED("no bin selected"),

6
src/main/java/org/apache/commons/math4/filter/DefaultMeasurementModel.java
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@ -33,12 +33,12 @@ public class DefaultMeasurementModel implements MeasurementModel {
* The measurement matrix, used to associate the measurement vector to the
* internal state estimation vector.
*/
private RealMatrix measurementMatrix;
private final RealMatrix measurementMatrix;
/**
* The measurement noise covariance matrix.
*/
private RealMatrix measurementNoise;
private final RealMatrix measurementNoise;
/**
* Create a new {@link MeasurementModel}, taking double arrays as input parameters for the
@ -73,11 +73,13 @@ public class DefaultMeasurementModel implements MeasurementModel {
}
/** {@inheritDoc} */
@Override
public RealMatrix getMeasurementMatrix() {
return measurementMatrix;
}
/** {@inheritDoc} */
@Override
public RealMatrix getMeasurementNoise() {
return measurementNoise;
}

15
src/main/java/org/apache/commons/math4/filter/DefaultProcessModel.java
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@ -33,21 +33,21 @@ public class DefaultProcessModel implements ProcessModel {
/**
* The state transition matrix, used to advance the internal state estimation each time-step.
*/
private RealMatrix stateTransitionMatrix;
private final RealMatrix stateTransitionMatrix;
/**
* The control matrix, used to integrate a control input into the state estimation.
*/
private RealMatrix controlMatrix;
private final RealMatrix controlMatrix;
/** The process noise covariance matrix. */
private RealMatrix processNoiseCovMatrix;
private final RealMatrix processNoiseCovMatrix;
/** The initial state estimation of the observed process. */
private RealVector initialStateEstimateVector;
private final RealVector initialStateEstimateVector;
/** The initial error covariance matrix of the observed process. */
private RealMatrix initialErrorCovMatrix;
private final RealMatrix initialErrorCovMatrix;
/**
* Create a new {@link ProcessModel}, taking double arrays as input parameters.
@ -139,26 +139,31 @@ public class DefaultProcessModel implements ProcessModel {
}
/** {@inheritDoc} */
@Override
public RealMatrix getStateTransitionMatrix() {
return stateTransitionMatrix;
}
/** {@inheritDoc} */
@Override
public RealMatrix getControlMatrix() {
return controlMatrix;
}
/** {@inheritDoc} */
@Override
public RealMatrix getProcessNoise() {
return processNoiseCovMatrix;
}
/** {@inheritDoc} */
@Override
public RealVector getInitialStateEstimate() {
return initialStateEstimateVector;
}
/** {@inheritDoc} */
@Override
public RealMatrix getInitialErrorCovariance() {
return initialErrorCovMatrix;
}

9
src/main/java/org/apache/commons/math4/fraction/BigFraction.java
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@ -509,6 +509,7 @@ public class BigFraction
* @return a {@link BigFraction} instance with the resulting values.
* @throws NullArgumentException if the {@link BigFraction} is {@code null}.
*/
@Override
public BigFraction add(final BigFraction fraction) {
if (fraction == null) {
throw new NullArgumentException(LocalizedFormats.FRACTION);
@ -596,6 +597,7 @@ public class BigFraction
* than {@code object}, 0 if they are equal.
* @see java.lang.Comparable#compareTo(java.lang.Object)
*/
@Override
public int compareTo(final BigFraction object) {
BigInteger nOd = numerator.multiply(object.denominator);
BigInteger dOn = denominator.multiply(object.numerator);
@ -662,6 +664,7 @@ public class BigFraction
* @throws NullArgumentException if the {@code fraction} is {@code null}.
* @throws MathArithmeticException if the fraction to divide by is zero
*/
@Override
public BigFraction divide(final BigFraction fraction) {
if (fraction == null) {
throw new NullArgumentException(LocalizedFormats.FRACTION);
@ -883,6 +886,7 @@ public class BigFraction
* the {@code int} to multiply by.
* @return a {@link BigFraction} instance with the resulting values.
*/
@Override
public BigFraction multiply(final int i) {
return multiply(BigInteger.valueOf(i));
}
@ -911,6 +915,7 @@ public class BigFraction
* @return a {@link BigFraction} instance with the resulting values.
* @throws NullArgumentException if {@code fraction} is {@code null}.
*/
@Override
public BigFraction multiply(final BigFraction fraction) {
if (fraction == null) {
throw new NullArgumentException(LocalizedFormats.FRACTION);
@ -931,6 +936,7 @@ public class BigFraction
*
* @return the negation of this fraction.
*/
@Override
public BigFraction negate() {
return new BigFraction(numerator.negate(), denominator);
}
@ -1026,6 +1032,7 @@ public class BigFraction
*
* @return the reciprocal fraction.
*/
@Override
public BigFraction reciprocal() {
return new BigFraction(denominator, numerator);
}
@ -1096,6 +1103,7 @@ public class BigFraction
* @return a {@link BigFraction} instance with the resulting values
* @throws NullArgumentException if the {@code fraction} is {@code null}.
*/
@Override
public BigFraction subtract(final BigFraction fraction) {
if (fraction == null) {
throw new NullArgumentException(LocalizedFormats.FRACTION);
@ -1140,6 +1148,7 @@ public class BigFraction
}
/** {@inheritDoc} */
@Override
public BigFractionField getField() {
return BigFractionField.getInstance();
}

3
src/main/java/org/apache/commons/math4/fraction/BigFractionField.java
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@ -48,16 +48,19 @@ public class BigFractionField implements Field<BigFraction>, Serializable {
}
/** {@inheritDoc} */
@Override
public BigFraction getOne() {
return BigFraction.ONE;
}
/** {@inheritDoc} */
@Override
public BigFraction getZero() {
return BigFraction.ZERO;
}
/** {@inheritDoc} */
@Override
public Class<? extends FieldElement<BigFraction>> getRuntimeClass() {
return BigFraction.class;
}

9
src/main/java/org/apache/commons/math4/fraction/Fraction.java
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@ -310,6 +310,7 @@ public class Fraction
* @return -1 if this is less than {@code object}, +1 if this is greater
* than {@code object}, 0 if they are equal.
*/
@Override
public int compareTo(Fraction object) {
long nOd = ((long) numerator) * object.denominator;
long dOn = ((long) denominator) * object.numerator;
@ -409,6 +410,7 @@ public class Fraction
* Return the additive inverse of this fraction.
* @return the negation of this fraction.
*/
@Override
public Fraction negate() {
if (numerator==Integer.MIN_VALUE) {
throw new MathArithmeticException(LocalizedFormats.OVERFLOW_IN_FRACTION, numerator, denominator);
@ -420,6 +422,7 @@ public class Fraction
* Return the multiplicative inverse of this fraction.
* @return the reciprocal fraction
*/
@Override
public Fraction reciprocal() {
return new Fraction(denominator, numerator);
}
@ -434,6 +437,7 @@ public class Fraction
* @throws MathArithmeticException if the resulting numerator or denominator exceeds
* {@code Integer.MAX_VALUE}
*/
@Override
public Fraction add(Fraction fraction) {
return addSub(fraction, true /* add */);
}
@ -457,6 +461,7 @@ public class Fraction
* @throws MathArithmeticException if the resulting numerator or denominator
* cannot be represented in an {@code int}.
*/
@Override
public Fraction subtract(Fraction fraction) {
return addSub(fraction, false /* subtract */);
}
@ -537,6 +542,7 @@ public class Fraction
* @throws MathArithmeticException if the resulting numerator or denominator exceeds
* {@code Integer.MAX_VALUE}
*/
@Override
public Fraction multiply(Fraction fraction) {
if (fraction == null) {
throw new NullArgumentException(LocalizedFormats.FRACTION);
@ -558,6 +564,7 @@ public class Fraction
* @param i the {@code integer} to multiply by.
* @return this * i
*/
@Override
public Fraction multiply(final int i) {
return new Fraction(numerator * i, denominator);
}
@ -572,6 +579,7 @@ public class Fraction
* @throws MathArithmeticException if the resulting numerator or denominator exceeds
* {@code Integer.MAX_VALUE}
*/
@Override
public Fraction divide(Fraction fraction) {
if (fraction == null) {
throw new NullArgumentException(LocalizedFormats.FRACTION);
@ -666,6 +674,7 @@ public class Fraction
}
/** {@inheritDoc} */
@Override
public FractionField getField() {
return FractionField.getInstance();
}

3
src/main/java/org/apache/commons/math4/fraction/FractionField.java
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@ -48,16 +48,19 @@ public class FractionField implements Field<Fraction>, Serializable {
}
/** {@inheritDoc} */
@Override
public Fraction getOne() {
return Fraction.ONE;
}
/** {@inheritDoc} */
@Override
public Fraction getZero() {
return Fraction.ZERO;
}
/** {@inheritDoc} */
@Override
public Class<? extends FieldElement<Fraction>> getRuntimeClass() {
return Fraction.class;
}

1
src/main/java/org/apache/commons/math4/genetics/BinaryMutation.java
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@ -36,6 +36,7 @@ public class BinaryMutation implements MutationPolicy {
* @return the mutated chromosome.
* @throws MathIllegalArgumentException if <code>original</code> is not an instance of {@link BinaryChromosome}.
*/
@Override
public Chromosome mutate(Chromosome original) throws MathIllegalArgumentException {
if (!(original instanceof BinaryChromosome)) {
throw new MathIllegalArgumentException(LocalizedFormats.INVALID_BINARY_CHROMOSOME);

1
src/main/java/org/apache/commons/math4/genetics/Chromosome.java
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@ -57,6 +57,7 @@ public abstract class Chromosome implements Comparable<Chromosome>,Fitness {
* <li>0 if the two chromosomes have the same fitness</li>
* </ul>
*/
@Override
public int compareTo(final Chromosome another) {
return Double.compare(getFitness(), another.getFitness());
}

1
src/main/java/org/apache/commons/math4/genetics/CycleCrossover.java
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@ -98,6 +98,7 @@ public class CycleCrossover<T> implements CrossoverPolicy {
* @throws MathIllegalArgumentException if the chromosomes are not an instance of {@link AbstractListChromosome}
* @throws DimensionMismatchException if the length of the two chromosomes is different
*/
@Override
@SuppressWarnings("unchecked")
public ChromosomePair crossover(final Chromosome first, final Chromosome second)
throws DimensionMismatchException, MathIllegalArgumentException {

1
src/main/java/org/apache/commons/math4/genetics/ElitisticListPopulation.java
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@ -77,6 +77,7 @@ public class ElitisticListPopulation extends ListPopulation {
*
* @return the beginnings of the next generation.
*/
@Override
public Population nextGeneration() {
// initialize a new generation with the same parameters
ElitisticListPopulation nextGeneration =

6
src/main/java/org/apache/commons/math4/genetics/FixedElapsedTime.java
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@ -23,8 +23,9 @@ import org.apache.commons.math4.exception.NumberIsTooSmallException;
/**
* Stops after a fixed amount of time has elapsed.
* <p>
* The first time {@link #isSatisfied(Population)} is invoked, the end time of the evolution is determined based on the
* provided <code>maxTime</code> value. Once the elapsed time reaches the configured <code>maxTime</code> value,
* The first time {@link #isSatisfied(Population)} is invoked, the end time of
* the evolution is determined based on the provided <code>maxTime</code> value.
* Once the elapsed time reaches the configured <code>maxTime</code> value,
* {@link #isSatisfied(Population)} returns true.
*
* @since 3.1
@ -67,6 +68,7 @@ public class FixedElapsedTime implements StoppingCondition {
* @param population ignored (no impact on result)
* @return <code>true</code> IFF the maximum allowed time period has elapsed
*/
@Override
public boolean isSatisfied(final Population population) {
if (endTime < 0) {
endTime = System.nanoTime() + maxTimePeriod;

9
src/main/java/org/apache/commons/math4/genetics/FixedGenerationCount.java
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@ -19,9 +19,11 @@ package org.apache.commons.math4.genetics;
import org.apache.commons.math4.exception.NumberIsTooSmallException;
/**
* Stops after a fixed number of generations. Each time {@link #isSatisfied(Population)} is invoked, a generation
* counter is incremented. Once the counter reaches the configured <code>maxGenerations</code> value,
* {@link #isSatisfied(Population)} returns true.
* Stops after a fixed number of generations.
* <p>
* Each time {@link #isSatisfied(Population)} is invoked, a generation counter
* is incremented. Once the counter reaches the configured
* {@code maxGenerations} value, {@link #isSatisfied(Population)} returns true.
*
* @since 2.0
*/
@ -52,6 +54,7 @@ public class FixedGenerationCount implements StoppingCondition {
* @param population ignored (no impact on result)
* @return <code>true</code> IFF the maximum number of generations has been exceeded
*/
@Override
public boolean isSatisfied(final Population population) {
if (this.numGenerations < this.maxGenerations) {
numGenerations++;

7
src/main/java/org/apache/commons/math4/genetics/ListPopulation.java
View File

@ -36,7 +36,7 @@ import org.apache.commons.math4.exception.util.LocalizedFormats;
public abstract class ListPopulation implements Population {
/** List of chromosomes */
private List<Chromosome> chromosomes;
private final List<Chromosome> chromosomes;
/** maximal size of the population */
private int populationLimit;
@ -119,6 +119,7 @@ public abstract class ListPopulation implements Population {
* @throws NumberIsTooLargeException if the population would exceed the {@code populationLimit} after
* adding this chromosome
*/
@Override
public void addChromosome(final Chromosome chromosome) throws NumberIsTooLargeException {
if (chromosomes.size() >= populationLimit) {
throw new NumberIsTooLargeException(LocalizedFormats.LIST_OF_CHROMOSOMES_BIGGER_THAN_POPULATION_SIZE,
@ -131,6 +132,7 @@ public abstract class ListPopulation implements Population {
* Access the fittest chromosome in this population.
* @return the fittest chromosome.
*/
@Override
public Chromosome getFittestChromosome() {
// best so far
Chromosome bestChromosome = this.chromosomes.get(0);
@ -147,6 +149,7 @@ public abstract class ListPopulation implements Population {
* Access the maximum population size.
* @return the maximum population size.
*/
@Override
public int getPopulationLimit() {
return this.populationLimit;
}
@ -172,6 +175,7 @@ public abstract class ListPopulation implements Population {
* Access the current population size.
* @return the current population size.
*/
@Override
public int getPopulationSize() {
return this.chromosomes.size();
}
@ -190,6 +194,7 @@ public abstract class ListPopulation implements Population {
*
* @return chromosome iterator
*/
@Override
public Iterator<Chromosome> iterator() {
return getChromosomes().iterator();
}

1
src/main/java/org/apache/commons/math4/genetics/NPointCrossover.java
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@ -103,6 +103,7 @@ public class NPointCrossover<T> implements CrossoverPolicy {
* not an instance of {@link AbstractListChromosome}
* @throws DimensionMismatchException if the length of the two chromosomes is different
*/
@Override
@SuppressWarnings("unchecked") // OK because of instanceof checks
public ChromosomePair crossover(final Chromosome first, final Chromosome second)
throws DimensionMismatchException, MathIllegalArgumentException {

1
src/main/java/org/apache/commons/math4/genetics/OnePointCrossover.java
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@ -74,6 +74,7 @@ public class OnePointCrossover<T> implements CrossoverPolicy {
* not an instance of {@link AbstractListChromosome}
* @throws DimensionMismatchException if the length of the two chromosomes is different
*/
@Override
@SuppressWarnings("unchecked") // OK because of instanceof checks
public ChromosomePair crossover(final Chromosome first, final Chromosome second)
throws DimensionMismatchException, MathIllegalArgumentException {

1
src/main/java/org/apache/commons/math4/genetics/OrderedCrossover.java
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@ -66,6 +66,7 @@ public class OrderedCrossover<T> implements CrossoverPolicy {
* not an instance of {@link AbstractListChromosome}
* @throws DimensionMismatchException if the length of the two chromosomes is different
*/
@Override
@SuppressWarnings("unchecked")
public ChromosomePair crossover(final Chromosome first, final Chromosome second)
throws DimensionMismatchException, MathIllegalArgumentException {

1
src/main/java/org/apache/commons/math4/genetics/RandomKey.java
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@ -94,6 +94,7 @@ public abstract class RandomKey<T> extends AbstractListChromosome<Double> implem
/**
* {@inheritDoc}
*/
@Override
public List<T> decode(final List<T> sequence) {
return decodeGeneric(sequence, getRepresentation(), sortedRepresentation);
}

1
src/main/java/org/apache/commons/math4/genetics/RandomKeyMutation.java
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@ -35,6 +35,7 @@ public class RandomKeyMutation implements MutationPolicy {
*
* @throws MathIllegalArgumentException if <code>original</code> is not a {@link RandomKey} instance
*/
@Override
public Chromosome mutate(final Chromosome original) throws MathIllegalArgumentException {
if (!(original instanceof RandomKey<?>)) {
throw new MathIllegalArgumentException(LocalizedFormats.RANDOMKEY_MUTATION_WRONG_CLASS,

2
src/main/java/org/apache/commons/math4/genetics/TournamentSelection.java
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@ -54,6 +54,7 @@ public class TournamentSelection implements SelectionPolicy {
* @return the selected chromosomes.
* @throws MathIllegalArgumentException if the tournament arity is bigger than the population size
*/
@Override
public ChromosomePair select(final Population population) throws MathIllegalArgumentException {
return new ChromosomePair(tournament((ListPopulation) population),
tournament((ListPopulation) population));
@ -74,6 +75,7 @@ public class TournamentSelection implements SelectionPolicy {
}
// auxiliary population
ListPopulation tournamentPopulation = new ListPopulation(this.arity) {
@Override
public Population nextGeneration() {
// not useful here
return null;

1
src/main/java/org/apache/commons/math4/genetics/UniformCrossover.java
View File

@ -82,6 +82,7 @@ public class UniformCrossover<T> implements CrossoverPolicy {
* not an instance of {@link AbstractListChromosome}
* @throws DimensionMismatchException if the length of the two chromosomes is different
*/
@Override
@SuppressWarnings("unchecked")
public ChromosomePair crossover(final Chromosome first, final Chromosome second)
throws DimensionMismatchException, MathIllegalArgumentException {

1
src/main/java/org/apache/commons/math4/ml/clustering/DoublePoint.java
View File

@ -58,6 +58,7 @@ public class DoublePoint implements Clusterable, Serializable {
}
/** {@inheritDoc} */
@Override
public double[] getPoint() {
return point;
}

1
src/main/java/org/apache/commons/math4/ml/distance/CanberraDistance.java
View File

@ -29,6 +29,7 @@ public class CanberraDistance implements DistanceMeasure {
private static final long serialVersionUID = -6972277381587032228L;
/** {@inheritDoc} */
@Override
public double compute(double[] a, double[] b) {
double sum = 0;
for (int i = 0; i < a.length; i++) {

1
src/main/java/org/apache/commons/math4/ml/distance/ChebyshevDistance.java
View File

@ -29,6 +29,7 @@ public class ChebyshevDistance implements DistanceMeasure {
private static final long serialVersionUID = -4694868171115238296L;
/** {@inheritDoc} */
@Override
public double compute(double[] a, double[] b) {
return MathArrays.distanceInf(a, b);
}

1
src/main/java/org/apache/commons/math4/ml/distance/EarthMoversDistance.java
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@ -31,6 +31,7 @@ public class EarthMoversDistance implements DistanceMeasure {
private static final long serialVersionUID = -5406732779747414922L;
/** {@inheritDoc} */
@Override
public double compute(double[] a, double[] b) {
double lastDistance = 0;
double totalDistance = 0;

1
src/main/java/org/apache/commons/math4/ml/distance/EuclideanDistance.java
View File

@ -29,6 +29,7 @@ public class EuclideanDistance implements DistanceMeasure {
private static final long serialVersionUID = 1717556319784040040L;
/** {@inheritDoc} */
@Override
public double compute(double[] a, double[] b) {
return MathArrays.distance(a, b);
}

1
src/main/java/org/apache/commons/math4/ml/distance/ManhattanDistance.java
View File

@ -29,6 +29,7 @@ public class ManhattanDistance implements DistanceMeasure {
private static final long serialVersionUID = -9108154600539125566L;
/** {@inheritDoc} */
@Override
public double compute(double[] a, double[] b) {
return MathArrays.distance1(a, b);
}

2
src/main/java/org/apache/commons/math4/random/EmpiricalDistribution.java
View File

@ -799,7 +799,7 @@ public class EmpiricalDistribution extends AbstractRealDistribution {
* @return within-bin kernel parameterized by bStats
*/
protected RealDistribution getKernel(SummaryStatistics bStats) {
if (bStats.getN() == 1) {
if (bStats.getN() == 1 || bStats.getVariance() == 0) {
return new ConstantRealDistribution(bStats.getMean());
} else {
return new NormalDistribution(randomData.getRandomGenerator(),

2
src/main/java/org/apache/commons/math4/special/Beta.java
View File

@ -47,8 +47,6 @@ import org.apache.commons.math4.util.FastMath;
* this library are license free. Since no such notice appears in the code these
* functions can safely be ported to Commons-Math.
* </p>
*
*
*/
public class Beta {
/** Maximum allowed numerical error. */

109
src/main/java/org/apache/commons/math4/stat/correlation/SpearmansCorrelation.java
View File

@ -17,11 +17,6 @@
package org.apache.commons.math4.stat.correlation;
import java.util.ArrayList;
import java.util.HashSet;
import java.util.List;
import java.util.Set;
import org.apache.commons.math4.exception.DimensionMismatchException;
import org.apache.commons.math4.exception.MathIllegalArgumentException;
import org.apache.commons.math4.exception.util.LocalizedFormats;
@ -62,14 +57,21 @@ public class SpearmansCorrelation {
/**
* Create a SpearmansCorrelation with the given ranking algorithm.
* <p>
* From version 4.0 onwards this constructor will throw an exception
* if the provided {@link NaturalRanking} uses a {@link NaNStrategy#REMOVED} strategy.
*
* @param rankingAlgorithm ranking algorithm
* @throws MathIllegalArgumentException if the provided {@link RankingAlgorithm} is of
* type {@link NaturalRanking} and uses a {@link NaNStrategy#REMOVED} strategy
* @since 3.1
*/
public SpearmansCorrelation(final RankingAlgorithm rankingAlgorithm) {
public SpearmansCorrelation(final RankingAlgorithm rankingAlgorithm)
throws MathIllegalArgumentException {
if (rankingAlgorithm instanceof NaturalRanking &&
NaNStrategy.REMOVED == ((NaturalRanking) rankingAlgorithm).getNanStrategy()) {
throw new MathIllegalArgumentException(LocalizedFormats.NOT_SUPPORTED_NAN_STRATEGY,
NaNStrategy.REMOVED);
}
data = null;
this.rankingAlgorithm = rankingAlgorithm;
rankCorrelation = null;
@ -88,15 +90,22 @@ public class SpearmansCorrelation {
/**
* Create a SpearmansCorrelation with the given input data matrix
* and ranking algorithm.
* <p>
* From version 4.0 onwards this constructor will throw an exception
* if the provided {@link NaturalRanking} uses a {@link NaNStrategy#REMOVED} strategy.
*
* @param dataMatrix matrix of data with columns representing
* variables to correlate
* @param rankingAlgorithm ranking algorithm
* @throws MathIllegalArgumentException if the provided {@link RankingAlgorithm} is of
* type {@link NaturalRanking} and uses a {@link NaNStrategy#REMOVED} strategy
*/
public SpearmansCorrelation(final RealMatrix dataMatrix, final RankingAlgorithm rankingAlgorithm) {
public SpearmansCorrelation(final RealMatrix dataMatrix, final RankingAlgorithm rankingAlgorithm)
throws MathIllegalArgumentException {
if (rankingAlgorithm instanceof NaturalRanking &&
NaNStrategy.REMOVED == ((NaturalRanking) rankingAlgorithm).getNanStrategy()) {
throw new MathIllegalArgumentException(LocalizedFormats.NOT_SUPPORTED_NAN_STRATEGY,
NaNStrategy.REMOVED);
}
this.rankingAlgorithm = rankingAlgorithm;
this.data = rankTransform(dataMatrix);
rankCorrelation = new PearsonsCorrelation(data);
@ -167,19 +176,8 @@ public class SpearmansCorrelation {
throw new MathIllegalArgumentException(LocalizedFormats.INSUFFICIENT_DIMENSION,
xArray.length, 2);
} else {
double[] x = xArray;
double[] y = yArray;
if (rankingAlgorithm instanceof NaturalRanking &&
NaNStrategy.REMOVED == ((NaturalRanking) rankingAlgorithm).getNanStrategy()) {
final Set<Integer> nanPositions = new HashSet<Integer>();
nanPositions.addAll(getNaNPositions(xArray));
nanPositions.addAll(getNaNPositions(yArray));
x = removeValues(xArray, nanPositions);
y = removeValues(yArray, nanPositions);
}
return new PearsonsCorrelation().correlation(rankingAlgorithm.rank(x), rankingAlgorithm.rank(y));
return new PearsonsCorrelation().correlation(rankingAlgorithm.rank(xArray),
rankingAlgorithm.rank(yArray));
}
}
@ -191,29 +189,7 @@ public class SpearmansCorrelation {
* @return a rank-transformed matrix
*/
private RealMatrix rankTransform(final RealMatrix matrix) {
RealMatrix transformed = null;
if (rankingAlgorithm instanceof NaturalRanking &&
((NaturalRanking) rankingAlgorithm).getNanStrategy() == NaNStrategy.REMOVED) {
final Set<Integer> nanPositions = new HashSet<Integer>();
for (int i = 0; i < matrix.getColumnDimension(); i++) {
nanPositions.addAll(getNaNPositions(matrix.getColumn(i)));
}
// if we have found NaN values, we have to update the matrix size
if (!nanPositions.isEmpty()) {
transformed = new BlockRealMatrix(matrix.getRowDimension() - nanPositions.size(),
matrix.getColumnDimension());
for (int i = 0; i < transformed.getColumnDimension(); i++) {
transformed.setColumn(i, removeValues(matrix.getColumn(i), nanPositions));
}
}
}
if (transformed == null) {
transformed = matrix.copy();
}
RealMatrix transformed = matrix.copy();
for (int i = 0; i < transformed.getColumnDimension(); i++) {
transformed.setColumn(i, rankingAlgorithm.rank(transformed.getColumn(i)));
}
@ -221,39 +197,4 @@ public class SpearmansCorrelation {
return transformed;
}
/**
* Returns a list containing the indices of NaN values in the input array.
*
* @param input the input array
* @return a list of NaN positions in the input array
*/
private List<Integer> getNaNPositions(final double[] input) {
final List<Integer> positions = new ArrayList<Integer>();
for (int i = 0; i < input.length; i++) {
if (Double.isNaN(input[i])) {
positions.add(i);
}
}
return positions;
}
/**
* Removes all values from the input array at the specified indices.
*
* @param input the input array
* @param indices a set containing the indices to be removed
* @return the input array without the values at the specified indices
*/
private double[] removeValues(final double[] input, final Set<Integer> indices) {
if (indices.isEmpty()) {
return input;
}
final double[] result = new double[input.length - indices.size()];
for (int i = 0, j = 0; i < input.length; i++) {
if (!indices.contains(i)) {
result[j++] = input[i];
}
}
return result;
}
}

1
src/main/resources/assets/org/apache/commons/math4/exception/util/LocalizedFormats_fr.properties
View File

@ -214,6 +214,7 @@ NOT_STRICTLY_INCREASING_NUMBER_OF_POINTS = les points {0} et {1} ne sont pas str
NOT_STRICTLY_INCREASING_SEQUENCE = les points {3} et {2} ne sont pas strictement croissants ({1} >= {0})
NOT_SUBTRACTION_COMPATIBLE_MATRICES = les dimensions {0}x{1} et {2}x{3} sont incompatibles pour la soustraction matricielle
NOT_SUPPORTED_IN_DIMENSION_N = m\u00e9thode non disponible en dimension {0}
NOT_SUPPORTED_NAN_STRATEGY = strat\u00e9gie "NaN" {0} non disponible
NOT_SYMMETRIC_MATRIX = matrice non symm\u00e9trique
NON_SYMMETRIC_MATRIX = matrice non symm\u00e9trique: la diff\u00e9rence entre les \u00e9l\u00e9ments ({0},{1}) et ({1},{0}) est sup\u00e9rieure \u00e0 {2}
NO_BIN_SELECTED = aucun compartiment s\u00e9lectionn\u00e9

2
src/test/java/org/apache/commons/math4/exception/util/LocalizedFormatsTest.java
View File

@ -29,7 +29,7 @@ public class LocalizedFormatsTest {
@Test
public void testMessageNumber() {
Assert.assertEquals(321, LocalizedFormats.values().length);
Assert.assertEquals(322, LocalizedFormats.values().length);
}
@Test

15
src/test/java/org/apache/commons/math4/random/EmpiricalDistributionTest.java
View File

@ -430,6 +430,21 @@ public final class EmpiricalDistributionTest extends RealDistributionAbstractTes
}
}
/**
* MATH-1203
*/
@Test
public void testNoBinVariance() {
final double[] data = {0, 0, 1, 1};
EmpiricalDistribution dist = new EmpiricalDistribution(2);
dist.load(data);
dist.reseedRandomGenerator(1000);
for (int i = 0; i < 1000; i++) {
final double dev = dist.sample();
Assert.assertTrue(dev == 0 || dev == 1);
}
}
/**
* Find the bin that x belongs (relative to {@link #makeDistribution()}).
*/

9
src/test/java/org/apache/commons/math4/stat/correlation/SpearmansRankCorrelationTest.java
View File

@ -17,6 +17,7 @@
package org.apache.commons.math4.stat.correlation;
import org.apache.commons.math4.TestUtils;
import org.apache.commons.math4.exception.MathIllegalArgumentException;
import org.apache.commons.math4.linear.BlockRealMatrix;
import org.apache.commons.math4.linear.MatrixUtils;
import org.apache.commons.math4.linear.RealMatrix;
@ -121,19 +122,21 @@ public class SpearmansRankCorrelationTest extends PearsonsCorrelationTest {
new SpearmansCorrelation().computeCorrelationMatrix(data), Double.MIN_VALUE);
}
@Test
@Test(expected = MathIllegalArgumentException.class)
public void testMath891Array() {
// NaNStrategy.REMOVED is not supported since 4.0
final double[] xArray = new double[] { Double.NaN, 1.9, 2, 100, 3 };
final double[] yArray = new double[] { 10, 2, 10, Double.NaN, 4 };
NaturalRanking ranking = new NaturalRanking(NaNStrategy.REMOVED);
SpearmansCorrelation spearman = new SpearmansCorrelation(ranking);
Assert.assertEquals(0.5, spearman.correlation(xArray, yArray), Double.MIN_VALUE);
}
@Test
@Test(expected = MathIllegalArgumentException.class)
public void testMath891Matrix() {
// NaNStrategy.REMOVED is not supported since 4.0
final double[] xArray = new double[] { Double.NaN, 1.9, 2, 100, 3 };
final double[] yArray = new double[] { 10, 2, 10, Double.NaN, 4 };