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https://issues.apache.org/jira/browse/MATH-348
  https://issues.apache.org/jira/browse/MATH-349



git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@920852 13f79535-47bb-0310-9956-ffa450edef68
This commit is contained in:
Gilles Sadowski 2010-03-09 12:53:44 +00:00
parent 09a4643e10
commit 2e3e082984
29 changed files with 426 additions and 114 deletions
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8
pom.xml
View File

@ -102,6 +102,11 @@
<id>brentworden</id>
<email>brentworden at apache dot org</email>
</developer>
<developer>
<name>Gilles Sadowski</name>
<id>erans</id>
<email>erans at apache dot org</email>
</developer>
</developers>
<contributors>
<contributor>
@ -191,9 +196,6 @@
<contributor>
<name>Matthew Rowles</name>
</contributor>
<contributor>
<name>Gilles Sadowski</name>
</contributor>
<contributor>
<name>Joni Salonen</name>
</contributor>

12
src/main/java/org/apache/commons/math/distribution/BetaDistribution.java
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@ -27,10 +27,12 @@ import org.apache.commons.math.MathException;
*/
public interface BetaDistribution extends ContinuousDistribution, HasDensity<Double> {
/**
* Modify the shape parameter, alpha.
* @param alpha the new shape parameter.
*/
void setAlpha(double alpha);
* Modify the shape parameter, alpha.
* @param alpha the new shape parameter.
* @deprecated as of 2.1
*/
@Deprecated
void setAlpha(double alpha);
/**
* Access the shape parameter, alpha
@ -41,7 +43,9 @@ public interface BetaDistribution extends ContinuousDistribution, HasDensity<Dou
/**
* Modify the shape parameter, beta.
* @param beta the new scale parameter.
* @deprecated as of 2.1
*/
@Deprecated
void setBeta(double beta);
/**

10
src/main/java/org/apache/commons/math/distribution/BetaDistributionImpl.java
View File

@ -60,7 +60,10 @@ public class BetaDistributionImpl
z = Double.NaN;
}
/** {@inheritDoc} */
/** {@inheritDoc}
* @deprecated as of 2.1 (class will become immutable in 3.0)
*/
@Deprecated
public void setAlpha(double alpha) {
this.alpha = alpha;
z = Double.NaN;
@ -71,7 +74,10 @@ public class BetaDistributionImpl
return alpha;
}
/** {@inheritDoc} */
/** {@inheritDoc}
* @deprecated as of 2.1 (class will become immutable in 3.0)
*/
@Deprecated
public void setBeta(double beta) {
this.beta = beta;
z = Double.NaN;

4
src/main/java/org/apache/commons/math/distribution/BinomialDistribution.java
View File

@ -45,12 +45,16 @@ public interface BinomialDistribution extends IntegerDistribution {
/**
* Change the number of trials for this distribution.
* @param trials the new number of trials.
* @deprecated as of v2.1
*/
@Deprecated
void setNumberOfTrials(int trials);
/**
* Change the probability of success for this distribution.
* @param p the new probability of success.
* @deprecated as of v2.1
*/
@Deprecated
void setProbabilityOfSuccess(double p);
}

36
src/main/java/org/apache/commons/math/distribution/BinomialDistributionImpl.java
View File

@ -48,8 +48,8 @@ public class BinomialDistributionImpl extends AbstractIntegerDistribution
*/
public BinomialDistributionImpl(int trials, double p) {
super();
setNumberOfTrials(trials);
setProbabilityOfSuccess(p);
setNumberOfTrialsInternal(trials);
setProbabilityOfSuccessInternal(p);
}
/**
@ -76,8 +76,20 @@ public class BinomialDistributionImpl extends AbstractIntegerDistribution
* @param trials the new number of trials.
* @throws IllegalArgumentException if <code>trials</code> is not a valid
* number of trials.
* @deprecated as of 2.1 (class will become immutable in 3.0)
*/
@Deprecated
public void setNumberOfTrials(int trials) {
setNumberOfTrialsInternal(trials);
}
/**
* Change the number of trials for this distribution.
*
* @param trials the new number of trials.
* @throws IllegalArgumentException if <code>trials</code> is not a valid
* number of trials.
*/
private void setNumberOfTrialsInternal(int trials) {
if (trials < 0) {
throw MathRuntimeException.createIllegalArgumentException(
"number of trials must be non-negative ({0})", trials);
@ -91,8 +103,20 @@ public class BinomialDistributionImpl extends AbstractIntegerDistribution
* @param p the new probability of success.
* @throws IllegalArgumentException if <code>p</code> is not a valid
* probability.
* @deprecated as of 2.1 (class will become immutable in 3.0)
*/
@Deprecated
public void setProbabilityOfSuccess(double p) {
setProbabilityOfSuccessInternal(p);
}
/**
* Change the probability of success for this distribution.
*
* @param p the new probability of success.
* @throws IllegalArgumentException if <code>p</code> is not a valid
* probability.
*/
private void setProbabilityOfSuccessInternal(double p) {
if (p < 0.0 || p > 1.0) {
throw MathRuntimeException.createIllegalArgumentException(
"{0} out of [{1}, {2}] range", p, 0.0, 1.0);
@ -123,7 +147,7 @@ public class BinomialDistributionImpl extends AbstractIntegerDistribution
*/
@Override
protected int getDomainUpperBound(double p) {
return getNumberOfTrials();
return numberOfTrials;
}
/**
@ -139,11 +163,11 @@ public class BinomialDistributionImpl extends AbstractIntegerDistribution
double ret;
if (x < 0) {
ret = 0.0;
} else if (x >= getNumberOfTrials()) {
} else if (x >= numberOfTrials) {
ret = 1.0;
} else {
ret = 1.0 - Beta.regularizedBeta(getProbabilityOfSuccess(),
x + 1.0, getNumberOfTrials() - x);
x + 1.0, numberOfTrials - x);
}
return ret;
}
@ -156,7 +180,7 @@ public class BinomialDistributionImpl extends AbstractIntegerDistribution
*/
public double probability(int x) {
double ret;
if (x < 0 || x > getNumberOfTrials()) {
if (x < 0 || x > numberOfTrials) {
ret = 0.0;
} else {
ret = Math.exp(SaddlePointExpansion.logBinomialProbability(x,

4
src/main/java/org/apache/commons/math/distribution/CauchyDistribution.java
View File

@ -48,12 +48,16 @@ public interface CauchyDistribution extends ContinuousDistribution {
/**
* Modify the median.
* @param median for this distribution
* @deprecated as of v2.1
*/
@Deprecated
void setMedian(double median);
/**
* Modify the scale parameter.
* @param s scale parameter for this distribution
* @deprecated as of v2.1
*/
@Deprecated
void setScale(double s);
}

33
src/main/java/org/apache/commons/math/distribution/CauchyDistributionImpl.java
View File

@ -55,8 +55,8 @@ public class CauchyDistributionImpl extends AbstractContinuousDistribution
*/
public CauchyDistributionImpl(double median, double s){
super();
setMedian(median);
setScale(s);
setMedianInternal(median);
setScaleInternal(s);
}
/**
@ -115,8 +115,17 @@ public class CauchyDistributionImpl extends AbstractContinuousDistribution
/**
* Modify the median.
* @param median for this distribution
* @deprecated as of 2.1 (class will become immutable in 3.0)
*/
@Deprecated
public void setMedian(double median) {
setMedianInternal(median);
}
/**
* Modify the median.
* @param median for this distribution
*/
private void setMedianInternal(double median) {
this.median = median;
}
@ -124,8 +133,18 @@ public class CauchyDistributionImpl extends AbstractContinuousDistribution
* Modify the scale parameter.
* @param s scale parameter for this distribution
* @throws IllegalArgumentException if <code>sd</code> is not positive.
* @deprecated as of 2.1 (class will become immutable in 3.0)
*/
@Deprecated
public void setScale(double s) {
setScaleInternal(s);
}
/**
* Modify the scale parameter.
* @param s scale parameter for this distribution
* @throws IllegalArgumentException if <code>sd</code> is not positive.
*/
private void setScaleInternal(double s) {
if (s <= 0.0) {
throw MathRuntimeException.createIllegalArgumentException(
"scale must be positive ({0})", s);
@ -149,7 +168,7 @@ public class CauchyDistributionImpl extends AbstractContinuousDistribution
if (p < .5) {
ret = -Double.MAX_VALUE;
} else {
ret = getMedian();
ret = median;
}
return ret;
@ -169,7 +188,7 @@ public class CauchyDistributionImpl extends AbstractContinuousDistribution
double ret;
if (p < .5) {
ret = getMedian();
ret = median;
} else {
ret = Double.MAX_VALUE;
}
@ -190,11 +209,11 @@ public class CauchyDistributionImpl extends AbstractContinuousDistribution
double ret;
if (p < .5) {
ret = getMedian() - getScale();
ret = median - scale;
} else if (p > .5) {
ret = getMedian() + getScale();
ret = median + scale;
} else {
ret = getMedian();
ret = median;
}
return ret;

2
src/main/java/org/apache/commons/math/distribution/ChiSquaredDistribution.java
View File

@ -33,7 +33,9 @@ public interface ChiSquaredDistribution extends ContinuousDistribution, HasDensi
/**
* Modify the degrees of freedom.
* @param degreesOfFreedom the new degrees of freedom.
* @deprecated as of v2.1
*/
@Deprecated
void setDegreesOfFreedom(double degreesOfFreedom);
/**

35
src/main/java/org/apache/commons/math/distribution/ChiSquaredDistributionImpl.java
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@ -48,19 +48,31 @@ public class ChiSquaredDistributionImpl
* @param df degrees of freedom.
* @param g the underlying gamma distribution used to compute probabilities.
* @since 1.2
* @deprecated as of 2.1 (to avoid possibly inconsistent state, the
* "GammaDistribution" will be instantiated internally)
*/
@Deprecated
public ChiSquaredDistributionImpl(double df, GammaDistribution g) {
super();
setGamma(g);
setDegreesOfFreedom(df);
setGammaInternal(g);
setDegreesOfFreedomInternal(df);
}
/**
* Modify the degrees of freedom.
* @param degreesOfFreedom the new degrees of freedom.
* @deprecated as of 2.1 (class will become immutable in 3.0)
*/
@Deprecated
public void setDegreesOfFreedom(double degreesOfFreedom) {
getGamma().setAlpha(degreesOfFreedom / 2.0);
setDegreesOfFreedomInternal(degreesOfFreedom);
}
/**
* Modify the degrees of freedom.
* @param degreesOfFreedom the new degrees of freedom.
*/
private void setDegreesOfFreedomInternal(double degreesOfFreedom) {
gamma.setAlpha(degreesOfFreedom / 2.0);
}
/**
@ -68,7 +80,7 @@ public class ChiSquaredDistributionImpl
* @return the degrees of freedom.
*/
public double getDegreesOfFreedom() {
return getGamma().getAlpha() * 2.0;
return gamma.getAlpha() * 2.0;
}
/**
@ -89,7 +101,7 @@ public class ChiSquaredDistributionImpl
* computed due to convergence or other numerical errors.
*/
public double cumulativeProbability(double x) throws MathException {
return getGamma().cumulativeProbability(x);
return gamma.cumulativeProbability(x);
}
/**
@ -128,7 +140,7 @@ public class ChiSquaredDistributionImpl
*/
@Override
protected double getDomainLowerBound(double p) {
return Double.MIN_VALUE * getGamma().getBeta();
return Double.MIN_VALUE * gamma.getBeta();
}
/**
@ -189,8 +201,19 @@ public class ChiSquaredDistributionImpl
* insuring the gamma distribution has the proper parameter settings.
* @param g the new distribution.
* @since 1.2 made public
* @deprecated as of 2.1 (class will become immutable in 3.0)
*/
@Deprecated
public void setGamma(GammaDistribution g) {
setGammaInternal(g);
}
/**
* Modify the underlying gamma distribution. The caller is responsible for
* insuring the gamma distribution has the proper parameter settings.
* @param g the new distribution.
* @since 1.2 made public
*/
private void setGammaInternal(GammaDistribution g) {
this.gamma = g;
}

2
src/main/java/org/apache/commons/math/distribution/ExponentialDistribution.java
View File

@ -33,7 +33,9 @@ public interface ExponentialDistribution extends ContinuousDistribution, HasDens
/**
* Modify the mean.
* @param mean the new mean.
* @deprecated as of v2.1
*/
@Deprecated
void setMean(double mean);
/**

24
src/main/java/org/apache/commons/math/distribution/ExponentialDistributionImpl.java
View File

@ -41,15 +41,25 @@ public class ExponentialDistributionImpl extends AbstractContinuousDistribution
*/
public ExponentialDistributionImpl(double mean) {
super();
setMean(mean);
setMeanInternal(mean);
}
/**
* Modify the mean.
* @param mean the new mean.
* @throws IllegalArgumentException if <code>mean</code> is not positive.
* @deprecated as of 2.1 (class will become immutable in 3.0)
*/
@Deprecated
public void setMean(double mean) {
setMeanInternal(mean);
}
/**
* Modify the mean.
* @param mean the new mean.
* @throws IllegalArgumentException if <code>mean</code> is not positive.
*/
private void setMeanInternal(double mean) {
if (mean <= 0.0) {
throw MathRuntimeException.createIllegalArgumentException(
"mean must be positive ({0})", mean);
@ -75,7 +85,7 @@ public class ExponentialDistributionImpl extends AbstractContinuousDistribution
if (x < 0) {
return 0;
}
return Math.exp(-x / getMean()) / getMean();
return Math.exp(-x / mean) / mean;
}
/**
@ -98,7 +108,7 @@ public class ExponentialDistributionImpl extends AbstractContinuousDistribution
if (x <= 0.0) {
ret = 0.0;
} else {
ret = 1.0 - Math.exp(-x / getMean());
ret = 1.0 - Math.exp(-x / mean);
}
return ret;
}
@ -125,7 +135,7 @@ public class ExponentialDistributionImpl extends AbstractContinuousDistribution
} else if (p == 1.0) {
ret = Double.POSITIVE_INFINITY;
} else {
ret = -getMean() * Math.log(1.0 - p);
ret = -mean * Math.log(1.0 - p);
}
return ret;
@ -159,7 +169,7 @@ public class ExponentialDistributionImpl extends AbstractContinuousDistribution
if (p < .5) {
// use mean
return getMean();
return mean;
} else {
// use max
return Double.MAX_VALUE;
@ -181,10 +191,10 @@ public class ExponentialDistributionImpl extends AbstractContinuousDistribution
// Exponential is skewed to the left, therefore, P(X < &mu;) > .5
if (p < .5) {
// use 1/2 mean
return getMean() * .5;
return mean * .5;
} else {
// use mean
return getMean();
return mean;
}
}
}

4
src/main/java/org/apache/commons/math/distribution/FDistribution.java
View File

@ -33,7 +33,9 @@ public interface FDistribution extends ContinuousDistribution {
/**
* Modify the numerator degrees of freedom.
* @param degreesOfFreedom the new numerator degrees of freedom.
* @deprecated as of v2.1
*/
@Deprecated
void setNumeratorDegreesOfFreedom(double degreesOfFreedom);
/**
@ -45,7 +47,9 @@ public interface FDistribution extends ContinuousDistribution {
/**
* Modify the denominator degrees of freedom.
* @param degreesOfFreedom the new denominator degrees of freedom.
* @deprecated as of v2.1
*/
@Deprecated
void setDenominatorDegreesOfFreedom(double degreesOfFreedom);
/**

36
src/main/java/org/apache/commons/math/distribution/FDistributionImpl.java
View File

@ -51,10 +51,10 @@ public class FDistributionImpl
* @param denominatorDegreesOfFreedom the denominator degrees of freedom.
*/
public FDistributionImpl(double numeratorDegreesOfFreedom,
double denominatorDegreesOfFreedom) {
double denominatorDegreesOfFreedom) {
super();
setNumeratorDegreesOfFreedom(numeratorDegreesOfFreedom);
setDenominatorDegreesOfFreedom(denominatorDegreesOfFreedom);
setNumeratorDegreesOfFreedomInternal(numeratorDegreesOfFreedom);
setDenominatorDegreesOfFreedomInternal(denominatorDegreesOfFreedom);
}
/**
@ -77,8 +77,8 @@ public class FDistributionImpl
if (x <= 0.0) {
ret = 0.0;
} else {
double n = getNumeratorDegreesOfFreedom();
double m = getDenominatorDegreesOfFreedom();
double n = numeratorDegreesOfFreedom;
double m = denominatorDegreesOfFreedom;
ret = Beta.regularizedBeta((n * x) / (m + n * x),
0.5 * n,
@ -151,7 +151,7 @@ public class FDistributionImpl
@Override
protected double getInitialDomain(double p) {
double ret = 1.0;
double d = getDenominatorDegreesOfFreedom();
double d = denominatorDegreesOfFreedom;
if (d > 2.0) {
// use mean
ret = d / (d - 2.0);
@ -164,8 +164,20 @@ public class FDistributionImpl
* @param degreesOfFreedom the new numerator degrees of freedom.
* @throws IllegalArgumentException if <code>degreesOfFreedom</code> is not
* positive.
* @deprecated as of 2.1 (class will become immutable in 3.0)
*/
@Deprecated
public void setNumeratorDegreesOfFreedom(double degreesOfFreedom) {
setNumeratorDegreesOfFreedomInternal(degreesOfFreedom);
}
/**
* Modify the numerator degrees of freedom.
* @param degreesOfFreedom the new numerator degrees of freedom.
* @throws IllegalArgumentException if <code>degreesOfFreedom</code> is not
* positive.
*/
private void setNumeratorDegreesOfFreedomInternal(double degreesOfFreedom) {
if (degreesOfFreedom <= 0.0) {
throw MathRuntimeException.createIllegalArgumentException(
NON_POSITIVE_DEGREES_OF_FREEDOM_MESSAGE, degreesOfFreedom);
@ -186,8 +198,20 @@ public class FDistributionImpl
* @param degreesOfFreedom the new denominator degrees of freedom.
* @throws IllegalArgumentException if <code>degreesOfFreedom</code> is not
* positive.
* @deprecated as of 2.1 (class will become immutable in 3.0)
*/
@Deprecated
public void setDenominatorDegreesOfFreedom(double degreesOfFreedom) {
setDenominatorDegreesOfFreedomInternal(degreesOfFreedom);
}
/**
* Modify the denominator degrees of freedom.
* @param degreesOfFreedom the new denominator degrees of freedom.
* @throws IllegalArgumentException if <code>degreesOfFreedom</code> is not
* positive.
*/
private void setDenominatorDegreesOfFreedomInternal(double degreesOfFreedom) {
if (degreesOfFreedom <= 0.0) {
throw MathRuntimeException.createIllegalArgumentException(
NON_POSITIVE_DEGREES_OF_FREEDOM_MESSAGE, degreesOfFreedom);

4
src/main/java/org/apache/commons/math/distribution/GammaDistribution.java
View File

@ -33,7 +33,9 @@ public interface GammaDistribution extends ContinuousDistribution, HasDensity<Do
/**
* Modify the shape parameter, alpha.
* @param alpha the new shape parameter.
* @deprecated as of v2.1
*/
@Deprecated
void setAlpha(double alpha);
/**
@ -45,7 +47,9 @@ public interface GammaDistribution extends ContinuousDistribution, HasDensity<Do
/**
* Modify the scale parameter, beta.
* @param beta the new scale parameter.
* @deprecated as of v2.1
*/
@Deprecated
void setBeta(double beta);
/**

36
src/main/java/org/apache/commons/math/distribution/GammaDistributionImpl.java
View File

@ -46,8 +46,8 @@ public class GammaDistributionImpl extends AbstractContinuousDistribution
*/
public GammaDistributionImpl(double alpha, double beta) {
super();
setAlpha(alpha);
setBeta(beta);
setAlphaInternal(alpha);
setBetaInternal(beta);
}
/**
@ -73,7 +73,7 @@ public class GammaDistributionImpl extends AbstractContinuousDistribution
if (x <= 0.0) {
ret = 0.0;
} else {
ret = Gamma.regularizedGammaP(getAlpha(), x / getBeta());
ret = Gamma.regularizedGammaP(alpha, x / beta);
}
return ret;
@ -108,8 +108,19 @@ public class GammaDistributionImpl extends AbstractContinuousDistribution
* Modify the shape parameter, alpha.
* @param alpha the new shape parameter.
* @throws IllegalArgumentException if <code>alpha</code> is not positive.
* @deprecated as of 2.1 (class will become immutable in 3.0)
*/
@Deprecated
public void setAlpha(double alpha) {
setAlphaInternal(alpha);
}
/**
* Modify the shape parameter, alpha.
* @param alpha the new shape parameter.
* @throws IllegalArgumentException if <code>alpha</code> is not positive.
*/
private void setAlphaInternal(double alpha) {
if (alpha <= 0.0) {
throw MathRuntimeException.createIllegalArgumentException(
"alpha must be positive ({0})",
@ -130,8 +141,19 @@ public class GammaDistributionImpl extends AbstractContinuousDistribution
* Modify the scale parameter, beta.
* @param beta the new scale parameter.
* @throws IllegalArgumentException if <code>beta</code> is not positive.
* @deprecated as of 2.1 (class will become immutable in 3.0)
*/
@Deprecated
public void setBeta(double beta) {
setBetaInternal(beta);
}
/**
* Modify the scale parameter, beta.
* @param beta the new scale parameter.
* @throws IllegalArgumentException if <code>beta</code> is not positive.
*/
private void setBetaInternal(double beta) {
if (beta <= 0.0) {
throw MathRuntimeException.createIllegalArgumentException(
"beta must be positive ({0})",
@ -156,7 +178,7 @@ public class GammaDistributionImpl extends AbstractContinuousDistribution
*/
public double density(Double x) {
if (x < 0) return 0;
return Math.pow(x / getBeta(), getAlpha() - 1) / getBeta() * Math.exp(-x / getBeta()) / Math.exp(Gamma.logGamma(getAlpha()));
return Math.pow(x / beta, alpha - 1) / beta * Math.exp(-x / beta) / Math.exp(Gamma.logGamma(alpha));
}
/**
@ -193,7 +215,7 @@ public class GammaDistributionImpl extends AbstractContinuousDistribution
if (p < .5) {
// use mean
ret = getAlpha() * getBeta();
ret = alpha * beta;
} else {
// use max value
ret = Double.MAX_VALUE;
@ -219,10 +241,10 @@ public class GammaDistributionImpl extends AbstractContinuousDistribution
if (p < .5) {
// use 1/2 mean
ret = getAlpha() * getBeta() * .5;
ret = alpha * beta * .5;
} else {
// use mean
ret = getAlpha() * getBeta();
ret = alpha * beta;
}
return ret;

7
src/main/java/org/apache/commons/math/distribution/HypergeometricDistribution.java
View File

@ -53,19 +53,24 @@ public interface HypergeometricDistribution extends IntegerDistribution {
/**
* Modify the number of successes.
* @param num the new number of successes.
* @deprecated as of v2.1
*/
@Deprecated
void setNumberOfSuccesses(int num);
/**
* Modify the population size.
* @param size the new population size.
* @deprecated as of v2.1
*/
@Deprecated
void setPopulationSize(int size);
/**
* Modify the sample size.
* @param size the new sample size.
* @deprecated as of v2.1
*/
@Deprecated
void setSampleSize(int size);
}

78
src/main/java/org/apache/commons/math/distribution/HypergeometricDistributionImpl.java
View File

@ -65,9 +65,10 @@ public class HypergeometricDistributionImpl extends AbstractIntegerDistribution
"sample size ({0}) must be less than or equal to population size ({1})",
sampleSize, populationSize);
}
setPopulationSize(populationSize);
setSampleSize(sampleSize);
setNumberOfSuccesses(numberOfSuccesses);
setPopulationSizeInternal(populationSize);
setSampleSizeInternal(sampleSize);
setNumberOfSuccessesInternal(numberOfSuccesses);
}
/**
@ -80,17 +81,14 @@ public class HypergeometricDistributionImpl extends AbstractIntegerDistribution
public double cumulativeProbability(int x) {
double ret;
int n = getPopulationSize();
int m = getNumberOfSuccesses();
int k = getSampleSize();
int[] domain = getDomain(n, m, k);
int[] domain = getDomain(populationSize, numberOfSuccesses, sampleSize);
if (x < domain[0]) {
ret = 0.0;
} else if (x >= domain[1]) {
ret = 1.0;
} else {
ret = innerCumulativeProbability(domain[0], x, 1, n, m, k);
ret = innerCumulativeProbability(domain[0], x, 1, populationSize,
numberOfSuccesses, sampleSize);
}
return ret;
@ -119,8 +117,7 @@ public class HypergeometricDistributionImpl extends AbstractIntegerDistribution
*/
@Override
protected int getDomainLowerBound(double p) {
return getLowerDomain(getPopulationSize(), getNumberOfSuccesses(),
getSampleSize());
return getLowerDomain(populationSize, numberOfSuccesses, sampleSize);
}
/**
@ -133,7 +130,7 @@ public class HypergeometricDistributionImpl extends AbstractIntegerDistribution
*/
@Override
protected int getDomainUpperBound(double p) {
return getUpperDomain(getSampleSize(), getNumberOfSuccesses());
return getUpperDomain(sampleSize, numberOfSuccesses);
}
/**
@ -197,23 +194,19 @@ public class HypergeometricDistributionImpl extends AbstractIntegerDistribution
public double probability(int x) {
double ret;
int m = getPopulationSize();
int s = getNumberOfSuccesses();
int f = m - s;
int k = getSampleSize();
int[] domain = getDomain(m, s, k);
int[] domain = getDomain(populationSize, numberOfSuccesses, sampleSize);
if (x < domain[0] || x > domain[1]) {
ret = 0.0;
} else {
double p = (double) sampleSize / (double) m;
double q = (double) (m - sampleSize) / (double) m;
double p = (double) sampleSize / (double) populationSize;
double q = (double) (populationSize - sampleSize) / (double) populationSize;
double p1 = SaddlePointExpansion.logBinomialProbability(x,
numberOfSuccesses, p, q);
double p2 =
SaddlePointExpansion.logBinomialProbability(sampleSize - x, f, p, q);
SaddlePointExpansion.logBinomialProbability(sampleSize - x,
populationSize - numberOfSuccesses, p, q);
double p3 =
SaddlePointExpansion.logBinomialProbability(sampleSize, m, p, q);
SaddlePointExpansion.logBinomialProbability(sampleSize, populationSize, p, q);
ret = Math.exp(p1 + p2 - p3);
}
@ -241,8 +234,19 @@ public class HypergeometricDistributionImpl extends AbstractIntegerDistribution
*
* @param num the new number of successes.
* @throws IllegalArgumentException if <code>num</code> is negative.
* @deprecated as of 2.1 (class will become immutable in 3.0)
*/
@Deprecated
public void setNumberOfSuccesses(int num) {
setNumberOfSuccessesInternal(num);
}
/**
* Modify the number of successes.
*
* @param num the new number of successes.
* @throws IllegalArgumentException if <code>num</code> is negative.
*/
private void setNumberOfSuccessesInternal(int num) {
if (num < 0) {
throw MathRuntimeException.createIllegalArgumentException(
"number of successes must be non-negative ({0})", num);
@ -255,8 +259,19 @@ public class HypergeometricDistributionImpl extends AbstractIntegerDistribution
*
* @param size the new population size.
* @throws IllegalArgumentException if <code>size</code> is not positive.
* @deprecated as of 2.1 (class will become immutable in 3.0)
*/
@Deprecated
public void setPopulationSize(int size) {
setPopulationSizeInternal(size);
}
/**
* Modify the population size.
*
* @param size the new population size.
* @throws IllegalArgumentException if <code>size</code> is not positive.
*/
private void setPopulationSizeInternal(int size) {
if (size <= 0) {
throw MathRuntimeException.createIllegalArgumentException(
"population size must be positive ({0})", size);
@ -269,8 +284,19 @@ public class HypergeometricDistributionImpl extends AbstractIntegerDistribution
*
* @param size the new sample size.
* @throws IllegalArgumentException if <code>size</code> is negative.
* @deprecated as of 2.1 (class will become immutable in 3.0)
*/
@Deprecated
public void setSampleSize(int size) {
setSampleSizeInternal(size);
}
/**
* Modify the sample size.
*
* @param size the new sample size.
* @throws IllegalArgumentException if <code>size</code> is negative.
*/
private void setSampleSizeInternal(int size) {
if (size < 0) {
throw MathRuntimeException.createIllegalArgumentException(
"sample size must be positive ({0})", size);
@ -288,17 +314,13 @@ public class HypergeometricDistributionImpl extends AbstractIntegerDistribution
public double upperCumulativeProbability(int x) {
double ret;
int n = getPopulationSize();
int m = getNumberOfSuccesses();
int k = getSampleSize();
int[] domain = getDomain(n, m, k);
final int[] domain = getDomain(populationSize, numberOfSuccesses, sampleSize);
if (x < domain[0]) {
ret = 1.0;
} else if (x > domain[1]) {
ret = 0.0;
} else {
ret = innerCumulativeProbability(domain[1], x, -1, n, m, k);
ret = innerCumulativeProbability(domain[1], x, -1, populationSize, numberOfSuccesses, sampleSize);
}
return ret;

4
src/main/java/org/apache/commons/math/distribution/NormalDistribution.java
View File

@ -39,7 +39,9 @@ public interface NormalDistribution extends ContinuousDistribution, HasDensity<D
/**
* Modify the mean.
* @param mean for this distribution
* @deprecated as of v2.1
*/
@Deprecated
void setMean(double mean);
/**
* Access the standard deviation.
@ -49,7 +51,9 @@ public interface NormalDistribution extends ContinuousDistribution, HasDensity<D
/**
* Modify the standard deviation.
* @param sd standard deviation for this distribution
* @deprecated as of v2.1
*/
@Deprecated
void setStandardDeviation(double sd);
/**

37
src/main/java/org/apache/commons/math/distribution/NormalDistributionImpl.java
View File

@ -70,8 +70,8 @@ public class NormalDistributionImpl extends AbstractContinuousDistribution
*/
public NormalDistributionImpl(double mean, double sd, double inverseCumAccuracy) {
super();
this.mean = mean;
this.standardDeviation = sd;
setMeanInternal(mean);
setStandardDeviationInternal(sd);
solverAbsoluteAccuracy = inverseCumAccuracy;
}
@ -94,8 +94,17 @@ public class NormalDistributionImpl extends AbstractContinuousDistribution
/**
* Modify the mean.
* @param mean for this distribution
* @deprecated as of 2.1 (class will become immutable in 3.0)
*/
@Deprecated
public void setMean(double mean) {
setMeanInternal(mean);
}
/**
* Modify the mean.
* @param mean for this distribution
*/
private void setMeanInternal(double mean) {
this.mean = mean;
}
@ -111,8 +120,18 @@ public class NormalDistributionImpl extends AbstractContinuousDistribution
* Modify the standard deviation.
* @param sd standard deviation for this distribution
* @throws IllegalArgumentException if <code>sd</code> is not positive.
* @deprecated as of 2.1 (class will become immutable in 3.0)
*/
@Deprecated
public void setStandardDeviation(double sd) {
setStandardDeviationInternal(sd);
}
/**
* Modify the standard deviation.
* @param sd standard deviation for this distribution
* @throws IllegalArgumentException if <code>sd</code> is not positive.
*/
private void setStandardDeviationInternal(double sd) {
if (sd <= 0.0) {
throw MathRuntimeException.createIllegalArgumentException(
"standard deviation must be positive ({0})",
@ -128,8 +147,8 @@ public class NormalDistributionImpl extends AbstractContinuousDistribution
* @return The pdf at point x.
*/
public double density(Double x) {
double x0 = x - getMean();
return Math.exp(-x0 * x0 / (2 * getStandardDeviation() * getStandardDeviation())) / (getStandardDeviation() * SQRT2PI);
double x0 = x - mean;
return Math.exp(-x0 * x0 / (2 * standardDeviation * standardDeviation)) / (standardDeviation * SQRT2PI);
}
/**
@ -208,7 +227,7 @@ public class NormalDistributionImpl extends AbstractContinuousDistribution
if (p < .5) {
ret = -Double.MAX_VALUE;
} else {
ret = getMean();
ret = mean;
}
return ret;
@ -228,7 +247,7 @@ public class NormalDistributionImpl extends AbstractContinuousDistribution
double ret;
if (p < .5) {
ret = getMean();
ret = mean;
} else {
ret = Double.MAX_VALUE;
}
@ -249,11 +268,11 @@ public class NormalDistributionImpl extends AbstractContinuousDistribution
double ret;
if (p < .5) {
ret = getMean() - getStandardDeviation();
ret = mean - standardDeviation;
} else if (p > .5) {
ret = getMean() + getStandardDeviation();
ret = mean + standardDeviation;
} else {
ret = getMean();
ret = mean;
}
return ret;

4
src/main/java/org/apache/commons/math/distribution/PascalDistribution.java
View File

@ -57,13 +57,17 @@ public interface PascalDistribution extends IntegerDistribution {
* Change the number of successes for this distribution.
*
* @param successes the new number of successes
* @deprecated as of v2.1
*/
@Deprecated
void setNumberOfSuccesses(int successes);
/**
* Change the probability of success for this distribution.
*
* @param p the new probability of success
* @deprecated as of v2.1
*/
@Deprecated
void setProbabilityOfSuccess(double p);
}

36
src/main/java/org/apache/commons/math/distribution/PascalDistributionImpl.java
View File

@ -48,8 +48,8 @@ public class PascalDistributionImpl extends AbstractIntegerDistribution
*/
public PascalDistributionImpl(int r, double p) {
super();
setNumberOfSuccesses(r);
setProbabilityOfSuccess(p);
setNumberOfSuccessesInternal(r);
setProbabilityOfSuccessInternal(p);
}
/**
@ -73,8 +73,19 @@ public class PascalDistributionImpl extends AbstractIntegerDistribution
* @param successes the new number of successes
* @throws IllegalArgumentException if <code>successes</code> is not
* positive.
* @deprecated as of 2.1 (class will become immutable in 3.0)
*/
@Deprecated
public void setNumberOfSuccesses(int successes) {
setNumberOfSuccessesInternal(successes);
}
/**
* Change the number of successes for this distribution.
* @param successes the new number of successes
* @throws IllegalArgumentException if <code>successes</code> is not
* positive.
*/
private void setNumberOfSuccessesInternal(int successes) {
if (successes < 0) {
throw MathRuntimeException.createIllegalArgumentException(
"number of successes must be non-negative ({0})",
@ -88,8 +99,19 @@ public class PascalDistributionImpl extends AbstractIntegerDistribution
* @param p the new probability of success
* @throws IllegalArgumentException if <code>p</code> is not a valid
* probability.
* @deprecated as of 2.1 (class will become immutable in 3.0)
*/
@Deprecated
public void setProbabilityOfSuccess(double p) {
setProbabilityOfSuccessInternal(p);
}
/**
* Change the probability of success for this distribution.
* @param p the new probability of success
* @throws IllegalArgumentException if <code>p</code> is not a valid
* probability.
*/
private void setProbabilityOfSuccessInternal(double p) {
if (p < 0.0 || p > 1.0) {
throw MathRuntimeException.createIllegalArgumentException(
"{0} out of [{1}, {2}] range", p, 0.0, 1.0);
@ -135,8 +157,8 @@ public class PascalDistributionImpl extends AbstractIntegerDistribution
if (x < 0) {
ret = 0.0;
} else {
ret = Beta.regularizedBeta(getProbabilityOfSuccess(),
getNumberOfSuccesses(), x + 1);
ret = Beta.regularizedBeta(probabilityOfSuccess,
numberOfSuccesses, x + 1);
}
return ret;
}
@ -152,9 +174,9 @@ public class PascalDistributionImpl extends AbstractIntegerDistribution
ret = 0.0;
} else {
ret = MathUtils.binomialCoefficientDouble(x +
getNumberOfSuccesses() - 1, getNumberOfSuccesses() - 1) *
Math.pow(getProbabilityOfSuccess(), getNumberOfSuccesses()) *
Math.pow(1.0 - getProbabilityOfSuccess(), x);
numberOfSuccesses - 1, numberOfSuccesses - 1) *
Math.pow(probabilityOfSuccess, numberOfSuccesses) *
Math.pow(1.0 - probabilityOfSuccess, x);
}
return ret;
}

2
src/main/java/org/apache/commons/math/distribution/PoissonDistribution.java
View File

@ -47,7 +47,9 @@ public interface PoissonDistribution extends IntegerDistribution {
*
* @param p the mean
* @throws IllegalArgumentException if p &le; 0
* @deprecated as of v2.1
*/
@Deprecated
void setMean(double p);
/**

30
src/main/java/org/apache/commons/math/distribution/PoissonDistributionImpl.java
View File

@ -121,11 +121,13 @@ public class PoissonDistributionImpl extends AbstractIntegerDistribution
* @param z a normal distribution used to compute normal approximations.
* @throws IllegalArgumentException if p &le; 0
* @since 1.2
* @deprecated as of 2.1 (to avoid possibly inconsistent state, the
* "NormalDistribution" will be instantiated internally)
*/
@Deprecated
public PoissonDistributionImpl(double p, NormalDistribution z) {
super();
setNormal(z);
setMean(p);
setNormalAndMeanInternal(z, p);
}
/**
@ -134,7 +136,7 @@ public class PoissonDistributionImpl extends AbstractIntegerDistribution
* @return the Poisson mean for the distribution.
*/
public double getMean() {
return this.mean;
return mean;
}
/**
@ -143,13 +145,28 @@ public class PoissonDistributionImpl extends AbstractIntegerDistribution
*
* @param p the Poisson mean value
* @throws IllegalArgumentException if p &le; 0
* @deprecated as of 2.1 (class will become immutable in 3.0)
*/
@Deprecated
public void setMean(double p) {
setNormalAndMeanInternal(normal, p);
}
/**
* Set the Poisson mean for the distribution. The mean value must be
* positive; otherwise an <code>IllegalArgument</code> is thrown.
*
* @param z the new distribution
* @param p the Poisson mean value
* @throws IllegalArgumentException if p &le; 0
*/
private void setNormalAndMeanInternal(NormalDistribution z,
double p) {
if (p <= 0) {
throw MathRuntimeException.createIllegalArgumentException(
"the Poisson mean must be positive ({0})", p);
}
this.mean = p;
mean = p;
normal = z;
normal.setMean(p);
normal.setStandardDeviation(Math.sqrt(p));
}
@ -248,9 +265,10 @@ public class PoissonDistributionImpl extends AbstractIntegerDistribution
*
* @param value the new distribution
* @since 1.2
* @deprecated as of 2.1 (class will become immutable in 3.0)
*/
@Deprecated
public void setNormal(NormalDistribution value) {
normal = value;
setNormalAndMeanInternal(value, mean);
}
}

2
src/main/java/org/apache/commons/math/distribution/TDistribution.java
View File

@ -33,7 +33,9 @@ public interface TDistribution extends ContinuousDistribution {
/**
* Modify the degrees of freedom.
* @param degreesOfFreedom the new degrees of freedom.
* @deprecated as of v2.1
*/
@Deprecated
void setDegreesOfFreedom(double degreesOfFreedom);
/**

15
src/main/java/org/apache/commons/math/distribution/TDistributionImpl.java
View File

@ -44,14 +44,23 @@ public class TDistributionImpl
*/
public TDistributionImpl(double degreesOfFreedom) {
super();
setDegreesOfFreedom(degreesOfFreedom);
setDegreesOfFreedomInternal(degreesOfFreedom);
}
/**
* Modify the degrees of freedom.
* @param degreesOfFreedom the new degrees of freedom.
* @deprecated as of 2.1 (class will become immutable in 3.0)
*/
@Deprecated
public void setDegreesOfFreedom(double degreesOfFreedom) {
setDegreesOfFreedomInternal(degreesOfFreedom);
}
/**
* Modify the degrees of freedom.
* @param degreesOfFreedom the new degrees of freedom.
*/
private void setDegreesOfFreedomInternal(double degreesOfFreedom) {
if (degreesOfFreedom <= 0.0) {
throw MathRuntimeException.createIllegalArgumentException(
"degrees of freedom must be positive ({0})",
@ -82,8 +91,8 @@ public class TDistributionImpl
} else {
double t =
Beta.regularizedBeta(
getDegreesOfFreedom() / (getDegreesOfFreedom() + (x * x)),
0.5 * getDegreesOfFreedom(),
degreesOfFreedom / (degreesOfFreedom + (x * x)),
0.5 * degreesOfFreedom,
0.5);
if (x < 0.0) {
ret = 0.5 * t;

4
src/main/java/org/apache/commons/math/distribution/WeibullDistribution.java
View File

@ -51,12 +51,16 @@ public interface WeibullDistribution extends ContinuousDistribution {
/**
* Modify the shape parameter.
* @param alpha The new shape parameter value.
* @deprecated as of v2.1
*/
@Deprecated
void setShape(double alpha);
/**
* Modify the scale parameter.
* @param beta The new scale parameter value.
* @deprecated as of v2.1
*/
@Deprecated
void setScale(double beta);
}

28
src/main/java/org/apache/commons/math/distribution/WeibullDistributionImpl.java
View File

@ -48,8 +48,8 @@ public class WeibullDistributionImpl extends AbstractContinuousDistribution
*/
public WeibullDistributionImpl(double alpha, double beta){
super();
setShape(alpha);
setScale(beta);
setShapeInternal(alpha);
setScaleInternal(beta);
}
/**
@ -62,7 +62,7 @@ public class WeibullDistributionImpl extends AbstractContinuousDistribution
if (x <= 0.0) {
ret = 0.0;
} else {
ret = 1.0 - Math.exp(-Math.pow(x / getScale(), getShape()));
ret = 1.0 - Math.exp(-Math.pow(x / scale, shape));
}
return ret;
}
@ -106,7 +106,7 @@ public class WeibullDistributionImpl extends AbstractContinuousDistribution
} else if (p == 1) {
ret = Double.POSITIVE_INFINITY;
} else {
ret = getScale() * Math.pow(-Math.log(1.0 - p), 1.0 / getShape());
ret = scale * Math.pow(-Math.log(1.0 - p), 1.0 / shape);
}
return ret;
}
@ -114,8 +114,17 @@ public class WeibullDistributionImpl extends AbstractContinuousDistribution
/**
* Modify the shape parameter.
* @param alpha the new shape parameter value.
* @deprecated as of 2.1 (class will become immutable in 3.0)
*/
@Deprecated
public void setShape(double alpha) {
setShapeInternal(alpha);
}
/**
* Modify the shape parameter.
* @param alpha the new shape parameter value.
*/
private void setShapeInternal(double alpha) {
if (alpha <= 0.0) {
throw MathRuntimeException.createIllegalArgumentException(
"shape must be positive ({0})",
@ -127,8 +136,17 @@ public class WeibullDistributionImpl extends AbstractContinuousDistribution
/**
* Modify the scale parameter.
* @param beta the new scale parameter value.
* @deprecated as of 2.1 (class will become immutable in 3.0)
*/
@Deprecated
public void setScale(double beta) {
setScaleInternal(beta);
}
/**
* Modify the scale parameter.
* @param beta the new scale parameter value.
*/
private void setScaleInternal(double beta) {
if (beta <= 0.0) {
throw MathRuntimeException.createIllegalArgumentException(
"scale must be positive ({0})",
@ -176,6 +194,6 @@ public class WeibullDistributionImpl extends AbstractContinuousDistribution
@Override
protected double getInitialDomain(double p) {
// use median
return Math.pow(getScale() * Math.log(2.0), 1.0 / getShape());
return Math.pow(scale * Math.log(2.0), 1.0 / shape);
}
}

5
src/main/java/org/apache/commons/math/distribution/ZipfDistribution.java
View File

@ -45,7 +45,9 @@ public interface ZipfDistribution extends IntegerDistribution {
*
* @param n the number of elements
* @throws IllegalArgumentException if n &le; 0
* @deprecated as of v2.1
*/
@Deprecated
void setNumberOfElements(int n);
/**
@ -62,7 +64,8 @@ public interface ZipfDistribution extends IntegerDistribution {
*
* @param s the exponent
* @throws IllegalArgumentException if s &le; 0.0
* @deprecated as of v2.1
*/
@Deprecated
void setExponent(double s);
}

38
src/main/java/org/apache/commons/math/distribution/ZipfDistributionImpl.java
View File

@ -49,8 +49,8 @@ public class ZipfDistributionImpl extends AbstractIntegerDistribution
*/
public ZipfDistributionImpl(final int numberOfElements, final double exponent)
throws IllegalArgumentException {
setNumberOfElements(numberOfElements);
setExponent(exponent);
setNumberOfElementsInternal(numberOfElements);
setExponentInternal(exponent);
}
/**
@ -69,8 +69,21 @@ public class ZipfDistributionImpl extends AbstractIntegerDistribution
*
* @param n the number of elements
* @exception IllegalArgumentException if n &le; 0
* @deprecated as of 2.1 (class will become immutable in 3.0)
*/
public void setNumberOfElements(final int n)
@Deprecated
public void setNumberOfElements(final int n) {
setNumberOfElementsInternal(n);
}
/**
* Set the number of elements (e.g. corpus size) for the distribution.
* The parameter value must be positive; otherwise an
* <code>IllegalArgumentException</code> is thrown.
*
* @param n the number of elements
* @exception IllegalArgumentException if n &le; 0
*/
private void setNumberOfElementsInternal(final int n)
throws IllegalArgumentException {
if (n <= 0) {
throw MathRuntimeException.createIllegalArgumentException(
@ -96,8 +109,21 @@ public class ZipfDistributionImpl extends AbstractIntegerDistribution
*
* @param s the exponent
* @exception IllegalArgumentException if s &le; 0.0
* @deprecated as of 2.1 (class will become immutable in 3.0)
*/
public void setExponent(final double s)
@Deprecated
public void setExponent(final double s) {
setExponentInternal(s);
}
/**
* Set the exponent characterising the distribution.
* The parameter value must be positive; otherwise an
* <code>IllegalArgumentException</code> is thrown.
*
* @param s the exponent
* @exception IllegalArgumentException if s &le; 0.0
*/
private void setExponentInternal(final double s)
throws IllegalArgumentException {
if (s <= 0.0) {
throw MathRuntimeException.createIllegalArgumentException(
@ -114,7 +140,7 @@ public class ZipfDistributionImpl extends AbstractIntegerDistribution
* @return the value of the probability mass function at x
*/
public double probability(final int x) {
if (x <= 0 || x > getNumberOfElements()) {
if (x <= 0 || x > numberOfElements) {
return 0.0;
}
@ -132,7 +158,7 @@ public class ZipfDistributionImpl extends AbstractIntegerDistribution
public double cumulativeProbability(final int x) {
if (x <= 0) {
return 0.0;
} else if (x >= getNumberOfElements()) {
} else if (x >= numberOfElements) {
return 1.0;
}