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/*
* File: NegativeBinomialDistribution.java
* Authors: Kevin R. Dixon
* Company: Sandia National Laboratories
* Project: Cognitive Foundry
*
* Copyright Mar 23, 2010, Sandia Corporation.
* Under the terms of Contract DE-AC04-94AL85000, there is a non-exclusive
* license for use of this work by or on behalf of the U.S. Government.
* Export of this program may require a license from the United States
* Government. See CopyrightHistory.txt for complete details.
*
*/
package gov.sandia.cognition.statistics.distribution;
import gov.sandia.cognition.annotation.PublicationReference;
import gov.sandia.cognition.annotation.PublicationType;
import gov.sandia.cognition.collection.IntegerSpan;
import gov.sandia.cognition.math.MathUtil;
import gov.sandia.cognition.math.ProbabilityUtil;
import gov.sandia.cognition.math.UnivariateStatisticsUtil;
import gov.sandia.cognition.math.matrix.Vector;
import gov.sandia.cognition.math.matrix.VectorFactory;
import gov.sandia.cognition.statistics.AbstractClosedFormIntegerDistribution;
import gov.sandia.cognition.statistics.ClosedFormCumulativeDistributionFunction;
import gov.sandia.cognition.statistics.ClosedFormDiscreteUnivariateDistribution;
import gov.sandia.cognition.statistics.DistributionEstimator;
import gov.sandia.cognition.statistics.DistributionWeightedEstimator;
import gov.sandia.cognition.statistics.EstimableDistribution;
import gov.sandia.cognition.statistics.ProbabilityMassFunction;
import gov.sandia.cognition.statistics.ProbabilityMassFunctionUtil;
import gov.sandia.cognition.util.AbstractCloneableSerializable;
import gov.sandia.cognition.util.Pair;
import gov.sandia.cognition.util.WeightedValue;
import java.util.ArrayList;
import java.util.Collection;
import java.util.Random;
/**
* Negative binomial distribution, also known as the Polya distribution,
* gives the number of successes of a series of Bernoulli trials before
* recording a given number of failures.
* @author Kevin R. Dixon
* @since 3.0
*/
@PublicationReference(
author="Wikipedia",
title="Negative binomial distribution",
type=PublicationType.WebPage,
year=2010,
url="http://en.wikipedia.org/wiki/Negative_binomial_distribution"
)
public class NegativeBinomialDistribution
extends AbstractClosedFormIntegerDistribution
implements ClosedFormDiscreteUnivariateDistribution,
EstimableDistribution
{
/**
* Default p, {@value}.
*/
public static final double DEFAULT_P = 0.5;
/**
* Default r, {@value}.
*/
public static final double DEFAULT_R = 1.0;
/**
* Number of trials before the experiment is stopped,
* must be greater than zero.
*/
protected double r;
/**
* Probability of a positive outcome (Bernoulli probability), [0,1]
*/
protected double p;
/**
* Creates a new instance of NegativeBinomialDistribution
*/
public NegativeBinomialDistribution()
{
this( DEFAULT_R, DEFAULT_P );
}
/**
* Creates a new instance of NegativeBinomialDistribution
* @param r
* Number of trials before the experiment is stopped,
* must be greater than zero.
* @param p
* Probability of a positive outcome (Bernoulli probability), [0,1]
*/
public NegativeBinomialDistribution(
final double r,
final double p)
{
this.setR(r);
this.setP(p);
}
/**
* Copy constructor
* @param other
* NegativeBinomialDistribution to copy
*/
public NegativeBinomialDistribution(
final NegativeBinomialDistribution other )
{
this( other.getR(), other.getP() );
}
@Override
public NegativeBinomialDistribution clone()
{
return (NegativeBinomialDistribution) super.clone();
}
/**
* Getter for p
* @return
* Probability of a positive outcome (Bernoulli probability), [0,1]
*/
public double getP()
{
return this.p;
}
/**
* Setter for p
* @param p
* Probability of a positive outcome (Bernoulli probability), [0,1]
*/
public void setP(
final double p )
{
ProbabilityUtil.assertIsProbability(p);
this.p = p;
}
/**
* Getter for r.
* @return
* Number of trials before the experiment is stopped,
* must be greater than zero.
*/
public double getR()
{
return this.r;
}
/**
* Setter for r.
* @param r
* Number of trials before the experiment is stopped,
* must be greater than zero.
*/
public void setR(
final double r)
{
if( r <= 0.0 )
{
throw new IllegalArgumentException( "R must be > 0" );
}
this.r = r;
}
@Override
public Double getMean()
{
return this.getMeanAsDouble();
}
@Override
public double getMeanAsDouble()
{
return this.r * this.p / (1.0-this.p);
}
@Override
public void sampleInto(
final Random random,
final int sampleCount,
final Collection output)
{
ProbabilityMassFunctionUtil.sampleInto(
this.getProbabilityFunction(), random, sampleCount, output);
}
@Override
public int sampleAsInt(
final Random random)
{
// TODO: See if there is a way to do this without any boxing.
return ProbabilityMassFunctionUtil.sampleSingle(
this.getProbabilityFunction(), random).intValue();
}
@Override
public void sampleInto(
final Random random,
final int[] output,
final int start,
final int length)
{
// TODO: See if there is a way to do this without any boxing.
final ArrayList samples = this.sample(random, length);
for (int i = 0; i < length; i++)
{
output[start + i] = samples.get(i).intValue();
}
}
@Override
public NegativeBinomialDistribution.CDF getCDF()
{
return new NegativeBinomialDistribution.CDF( this );
}
@Override
public Vector convertToVector()
{
return VectorFactory.getDefault().copyValues( this.r, this.p );
}
@Override
public void convertFromVector(
final Vector parameters)
{
parameters.assertDimensionalityEquals(2);
this.setR( parameters.getElement(0) );
this.setP( parameters.getElement(1) );
}
@Override
public Integer getMinSupport()
{
return 0;
}
@Override
public Integer getMaxSupport()
{
return Integer.MAX_VALUE;
}
@Override
public double getVariance()
{
final double np = 1.0-this.p;
return this.r * this.p / (np*np);
}
@Override
public IntegerSpan getDomain()
{
final int max = (int) Math.ceil( 10 * this.getMean() + 10 );
return new IntegerSpan(0, max);
}
@Override
public int getDomainSize()
{
return this.getDomain().size();
}
@Override
public NegativeBinomialDistribution.PMF getProbabilityFunction()
{
return new NegativeBinomialDistribution.PMF( this );
}
@Override
public NegativeBinomialDistribution.MaximumLikelihoodEstimator getEstimator()
{
return new NegativeBinomialDistribution.MaximumLikelihoodEstimator();
}
@Override
public String toString()
{
return "(r = " + this.getR() + ", p = " + this.getP() + ")";
}
/**
* PMF of the NegativeBinomialDistribution.
*/
public static class PMF
extends NegativeBinomialDistribution
implements ProbabilityMassFunction
{
/**
* Creates a new instance of PMF
*/
public PMF()
{
super();
}
/**
* Creates a new instance of PMF
* @param r
* Number of trials before the experiment is stopped,
* must be greater than zero.
* @param p
* Probability of a positive outcome (Bernoulli probability), [0,1]
*/
public PMF(
final double r,
final double p)
{
super( r, p );
}
/**
* Copy constructor
* @param other
* NegativeBinomialDistribution to copy
*/
public PMF(
final NegativeBinomialDistribution other )
{
super( other );
}
@Override
public NegativeBinomialDistribution.PMF getProbabilityFunction()
{
return this;
}
@Override
public double getEntropy()
{
return ProbabilityMassFunctionUtil.getEntropy(this);
}
@Override
public double logEvaluate(
final Number input)
{
final int k = input.intValue();
if( k < 0 )
{
return Math.log(0.0);
}
else
{
double logSum = 0.0;
logSum += MathUtil.logGammaFunction(k+this.r);
logSum -= MathUtil.logFactorial(k);
logSum -= MathUtil.logGammaFunction(this.r);
logSum += this.r * Math.log(1.0-this.p);
logSum += k * Math.log(this.p);
return logSum;
}
}
@Override
public Double evaluate(
final Number input)
{
return Math.exp( this.logEvaluate(input) );
}
}
/**
* CDF of the NegativeBinomialDistribution
*/
public static class CDF
extends NegativeBinomialDistribution
implements ClosedFormCumulativeDistributionFunction
{
/**
* Creates a new instance of CDF
*/
public CDF()
{
super();
}
/**
* Creates a new instance of CDF
* @param r
* Number of trials before the experiment is stopped,
* must be greater than zero.
* @param p
* Probability of a positive outcome (Bernoulli probability), [0,1]
*/
public CDF(
final double r,
final double p)
{
super( r, p );
}
/**
* Copy constructor
* @param other
* NegativeBinomialDistribution to copy
*/
public CDF(
final NegativeBinomialDistribution other )
{
super( other );
}
@Override
public Double evaluate(
final Number input)
{
final int k = input.intValue();
if( k < 0 )
{
return 0.0;
}
else
{
return MathUtil.regularizedIncompleteBetaFunction(
this.r, k+1, 1.0-p );
}
}
@Override
public NegativeBinomialDistribution.CDF getCDF()
{
return this;
}
}
/**
* Maximum likelihood estimator of the distribution
*/
public static class MaximumLikelihoodEstimator
extends AbstractCloneableSerializable
implements DistributionEstimator
{
/**
* Default constructor
*/
public MaximumLikelihoodEstimator()
{
}
@Override
public NegativeBinomialDistribution.PMF learn(
final Collection data )
{
Pair pair =
UnivariateStatisticsUtil.computeMeanAndVariance(data);
double mean = pair.getFirst();
double variance = pair.getSecond();
double ratio = mean/variance;
double r = Math.abs(mean * ratio / (ratio-1.0));
double p = mean / (mean + r);
return new NegativeBinomialDistribution.PMF(r, p);
}
}
/**
* Weighted maximum likelihood estimator of the distribution
*/
public static class WeightedMaximumLikelihoodEstimator
extends AbstractCloneableSerializable
implements DistributionWeightedEstimator
{
/**
* Default constructor
*/
public WeightedMaximumLikelihoodEstimator()
{
}
@Override
public NegativeBinomialDistribution learn(
final Collection> data)
{
Pair pair =
UnivariateStatisticsUtil.computeWeightedMeanAndVariance(data);
double mean = pair.getFirst();
double variance = pair.getSecond();
double ratio = mean/variance;
double r = Math.abs(mean * ratio / (ratio-1.0));
double p = mean / (mean + r);
return new NegativeBinomialDistribution.PMF(r, p);
}
}
}