/// <summary>
/// Computes the exponential distribution that best fits the given sample.
/// </summary>
/// <param name="sample">The sample to fit.</param>
/// <returns>The best fit parameter.</returns>
/// <remarks>
/// <para>The returned fit parameter is μ (the <see cref="Mean"/>).
/// This is the same parameter that is required by the <see cref="ExponentialDistribution(double)"/> constructor to
/// specify a new exponential distribution.</para>
/// </remarks>
/// <exception cref="ArgumentNullException"><paramref name="sample"/> is null.</exception>
/// <exception cref="InsufficientDataException"><paramref name="sample"/> contains fewer than two values.</exception>
/// <exception cref="InvalidOperationException"><paramref name="sample"/> contains non-positive values.</exception>
public static FitResult FitToSample(Sample sample)
{
if (sample == null)
{
throw new ArgumentNullException("sample");
}
if (sample.Count < 2)
{
throw new InsufficientDataException();
}
// none of the data is allowed to be negative
foreach (double value in sample)
{
if (value < 0.0)
{
throw new InvalidOperationException();
}
}
// the best-fit exponential's mean is the sample mean, with corresponding uncertainly
double lambda = sample.Mean;
double dLambda = lambda / Math.Sqrt(sample.Count);
Distribution distribution = new ExponentialDistribution(lambda);
TestResult test = sample.KolmogorovSmirnovTest(distribution);
return(new FitResult(lambda, dLambda, test));
}
public void KendallNullDistributionTest()
{
// pick independent distributions for x and y, which needn't be normal and needn't be related
Distribution xDistrubtion = new LogisticDistribution();
Distribution yDistribution = new ExponentialDistribution();
Random rng = new Random(314159265);
// generate bivariate samples of various sizes
//int n = 64; {
foreach (int n in TestUtilities.GenerateIntegerValues(4, 64, 8)) {
Sample testStatistics = new Sample();
Distribution testDistribution = null;
for (int i = 0; i < 128; i++) {
BivariateSample sample = new BivariateSample();
for (int j = 0; j < n; j++) {
sample.Add(xDistrubtion.GetRandomValue(rng), yDistribution.GetRandomValue(rng));
}
TestResult result = sample.KendallTauTest();
testStatistics.Add(result.Statistic);
testDistribution = result.Distribution;
}
//TestResult r2 = testStatistics.KolmogorovSmirnovTest(testDistribution);
//Console.WriteLine("n={0} P={1}", n, r2.LeftProbability);
//Assert.IsTrue(r2.RightProbability > 0.05);
Console.WriteLine("{0} {1}", testStatistics.PopulationVariance, testDistribution.Variance);
Assert.IsTrue(testStatistics.PopulationMean.ConfidenceInterval(0.95).ClosedContains(testDistribution.Mean));
Assert.IsTrue(testStatistics.PopulationVariance.ConfidenceInterval(0.95).ClosedContains(testDistribution.Variance));
}
}
/// <summary>
/// Computes the exponential distribution that best fits the given sample.
/// </summary>
/// <param name="sample">The sample to fit.</param>
/// <returns>The best fit parameter.</returns>
/// <remarks>
/// <para>The returned fit parameter is μ (the <see cref="Mean"/>).
/// This is the same parameter that is required by the <see cref="ExponentialDistribution(double)"/> constructor to
/// specify a new exponential distribution.</para>
/// </remarks>
/// <exception cref="ArgumentNullException"><paramref name="sample"/> is null.</exception>
/// <exception cref="InsufficientDataException"><paramref name="sample"/> contains fewer than two values.</exception>
/// <exception cref="InvalidOperationException"><paramref name="sample"/> contains non-positive values.</exception>
public static FitResult FitToSample(Sample sample)
{
if (sample == null)
{
throw new ArgumentNullException(nameof(sample));
}
if (sample.Count < 2)
{
throw new InsufficientDataException();
}
// None of the data is allowed to be negative.
foreach (double value in sample)
{
if (value < 0.0)
{
throw new InvalidOperationException();
}
}
// It's easy to show that the MLE estimator of \mu is the sample mean and that its variance
// is \mu^2 / n, which is just the the variance of the mean, since the variance of the individual
// values is \mu^2.
// We can do better than an asymptotic result, though. Since we know that the sum
// of exponential-distributed values is Gamma-distributed, we know the exact
// distribution of the mean is Gamma(n, \mu / n). This has mean \mu and variance
// \mu^2 / n, so the asymptotic results are actually exact.
double lambda = sample.Mean;
double dLambda = lambda / Math.Sqrt(sample.Count);
ContinuousDistribution distribution = new ExponentialDistribution(lambda);
TestResult test = sample.KolmogorovSmirnovTest(distribution);
return(new FitResult(lambda, dLambda, test));
}
public void GammaFromExponential()
{
// test that x_1 + x_2 + ... + x_n ~ Gamma(n) when z ~ Exponential()
Random rng = new Random(1);
ExponentialDistribution eDistribution = new ExponentialDistribution();
// pick some low values of n so distribution is not simply normal
foreach (int n in new int[] { 2, 3, 4, 5 }) {
Sample gSample = new Sample();
for (int i = 0; i < 100; i++) {
double sum = 0.0;
for (int j = 0; j < n; j++) {
sum += eDistribution.GetRandomValue(rng);
}
gSample.Add(sum);
}
GammaDistribution gDistribution = new GammaDistribution(n);
TestResult result = gSample.KolmogorovSmirnovTest(gDistribution);
Assert.IsTrue(result.LeftProbability < 0.95);
}
}
public void SampleMaximumLikelihoodFit()
{
// normal distriubtion
Console.WriteLine("normal");
double mu = -1.0;
double sigma = 2.0;
Distribution nd = new NormalDistribution(mu, sigma);
Sample ns = CreateSample(nd, 500);
//FitResult nr = ns.MaximumLikelihoodFit(new NormalDistribution(mu + 1.0, sigma + 1.0));
FitResult nr = ns.MaximumLikelihoodFit((IList<double> p) => new NormalDistribution(p[0], p[1]), new double[] { mu + 1.0, sigma + 1.0 });
Console.WriteLine(nr.Parameter(0));
Console.WriteLine(nr.Parameter(1));
Assert.IsTrue(nr.Dimension == 2);
Assert.IsTrue(nr.Parameter(0).ConfidenceInterval(0.95).ClosedContains(mu));
Assert.IsTrue(nr.Parameter(1).ConfidenceInterval(0.95).ClosedContains(sigma));
FitResult nr2 = NormalDistribution.FitToSample(ns);
Console.WriteLine(nr.Covariance(0,1));
// test analytic expression
Assert.IsTrue(TestUtilities.IsNearlyEqual(nr.Parameter(0).Value, ns.Mean, Math.Sqrt(TestUtilities.TargetPrecision)));
// we don't expect to be able to test sigma against analytic expression because ML value has known bias for finite sample size
// exponential distribution
Console.WriteLine("exponential");
double em = 3.0;
Distribution ed = new ExponentialDistribution(em);
Sample es = CreateSample(ed, 100);
//FitResult er = es.MaximumLikelihoodFit(new ExponentialDistribution(em + 1.0));
FitResult er = es.MaximumLikelihoodFit((IList<double> p) => new ExponentialDistribution(p[0]), new double[] { em + 1.0 });
Console.WriteLine(er.Parameter(0));
Assert.IsTrue(er.Dimension == 1);
Assert.IsTrue(er.Parameter(0).ConfidenceInterval(0.95).ClosedContains(em));
// test against analytic expression
Assert.IsTrue(TestUtilities.IsNearlyEqual(er.Parameter(0).Value, es.Mean, Math.Sqrt(TestUtilities.TargetPrecision)));
Assert.IsTrue(TestUtilities.IsNearlyEqual(er.Parameter(0).Uncertainty, es.Mean / Math.Sqrt(es.Count), Math.Sqrt(Math.Sqrt(TestUtilities.TargetPrecision))));
// lognormal distribution
Console.WriteLine("lognormal");
double l1 = -4.0;
double l2 = 5.0;
Distribution ld = new LognormalDistribution(l1, l2);
Sample ls = CreateSample(ld, 100);
//FitResult lr = ls.MaximumLikelihoodFit(new LognormalDistribution(l1 + 1.0, l2 + 1.0));
FitResult lr = ls.MaximumLikelihoodFit((IList<double> p) => new LognormalDistribution(p[0], p[1]), new double[] { l1 + 1.0, l2 + 1.0 });
Console.WriteLine(lr.Parameter(0));
Console.WriteLine(lr.Parameter(1));
Console.WriteLine(lr.Covariance(0, 1));
Assert.IsTrue(lr.Dimension == 2);
Assert.IsTrue(lr.Parameter(0).ConfidenceInterval(0.99).ClosedContains(l1));
Assert.IsTrue(lr.Parameter(1).ConfidenceInterval(0.99).ClosedContains(l2));
// weibull distribution
Console.WriteLine("weibull");
double w_scale = 4.0;
double w_shape = 2.0;
WeibullDistribution w_d = new WeibullDistribution(w_scale, w_shape);
Sample w_s = CreateSample(w_d, 20);
//FitResult w_r = w_s.MaximumLikelihoodFit(new WeibullDistribution(1.0, 0.5));
FitResult w_r = w_s.MaximumLikelihoodFit((IList<double> p) => new WeibullDistribution(p[0], p[1]), new double[] { 2.0, 2.0 });
Console.WriteLine(w_r.Parameter(0));
Console.WriteLine(w_r.Parameter(1));
Console.WriteLine(w_r.Covariance(0, 1));
Assert.IsTrue(w_r.Parameter(0).ConfidenceInterval(0.95).ClosedContains(w_d.ScaleParameter));
Assert.IsTrue(w_r.Parameter(1).ConfidenceInterval(0.95).ClosedContains(w_d.ShapeParameter));
// logistic distribution
Console.WriteLine("logistic");
double logistic_m = -3.0;
double logistic_s = 2.0;
Distribution logistic_distribution = new LogisticDistribution(logistic_m, logistic_s);
Sample logistic_sample = CreateSample(logistic_distribution, 100);
//FitResult logistic_result = logistic_sample.MaximumLikelihoodFit(new LogisticDistribution());
FitResult logistic_result = logistic_sample.MaximumLikelihoodFit((IList<double> p) => new LogisticDistribution(p[0], p[1]), new double[] { 2.0, 3.0 });
Console.WriteLine(logistic_result.Parameter(0));
Console.WriteLine(logistic_result.Parameter(1));
Assert.IsTrue(logistic_result.Dimension == 2);
Assert.IsTrue(logistic_result.Parameter(0).ConfidenceInterval(0.95).ClosedContains(logistic_m));
Assert.IsTrue(logistic_result.Parameter(1).ConfidenceInterval(0.95).ClosedContains(logistic_s));
// beta distribution
// not yet!
/*
double beta_alpha = 0.5;
double beta_beta = 2.0;
Distribution beta_distribution = new BetaDistribution(beta_alpha, beta_beta);
Sample beta_sample = CreateSample(beta_distribution, 100);
FitResult beta_result = beta_sample.MaximumLikelihoodFit(new BetaDistribution(1.0, 1.0));
Console.WriteLine("Beta:");
Console.WriteLine(beta_result.Parameter(0));
Console.WriteLine(beta_result.Parameter(1));
Assert.IsTrue(beta_result.Dimension == 2);
Assert.IsTrue(beta_result.Parameter(0).ConfidenceInterval(0.95).ClosedContains(beta_alpha));
Assert.IsTrue(beta_result.Parameter(1).ConfidenceInterval(0.95).ClosedContains(beta_beta));
*/
}
public void SampleMannWhitneyTest()
{
// define two non-normal distributions
Distribution d1 = new ExponentialDistribution(2.0);
Distribution d2 = new ExponentialDistribution(3.0);
// create three samples from them
Sample s1a = CreateSample(d1, 20, 1);
Sample s1b = CreateSample(d1, 30, 2);
Sample s2 = CreateSample(d2, 40, 3);
// Mann-Whitney test 1a vs. 1b; they should not be distinguished
TestResult rab = Sample.MannWhitneyTest(s1a, s1b);
Console.WriteLine("{0} {1}", rab.Statistic, rab.LeftProbability);
Assert.IsTrue((rab.LeftProbability < 0.95) && (rab.RightProbability < 0.95));
// Mann-Whitney test 1 vs. 2; they should be distinguished
// with 1 consistently less than 2, so U abnormally small
TestResult r12 = Sample.MannWhitneyTest(s1b, s2);
Console.WriteLine("{0} {1}", r12.Statistic, r12.LeftProbability);
Assert.IsTrue(r12.RightProbability > 0.95);
}
public void SampleKuiperTest()
{
// this test has a whiff of meta-statistics about it
// we want to make sure that the Kuiper test statistic V is distributed according to the Kuiper
// distribution; to do this, we create a sample of V statistics and do KS/Kuiper tests
// comparing it to the claimed Kuiper distribution
// start with any 'ol underlying distribution
Distribution distribution = new ExponentialDistribution(2.0);
// generate some samples from it, and for each one get a V statistic from a KS test
Sample VSample = new Sample();
Distribution VDistribution = null;
for (int i = 0; i < 25; i++) {
// the sample size must be large enough that the asymptotic assumptions are satistifed
// at the moment this test fails if we make the sample size much smaller; we should
// be able shrink this number when we expose the finite-sample distributions
Sample sample = CreateSample(distribution, 250, i);
TestResult kuiper = sample.KuiperTest(distribution);
double V = kuiper.Statistic;
Console.WriteLine("V = {0}", V);
VSample.Add(V);
VDistribution = kuiper.Distribution;
}
// check on the mean
Console.WriteLine("m = {0} vs. {1}", VSample.PopulationMean, VDistribution.Mean);
Assert.IsTrue(VSample.PopulationMean.ConfidenceInterval(0.95).ClosedContains(VDistribution.Mean));
// check on the standard deviation
Console.WriteLine("s = {0} vs. {1}", VSample.PopulationStandardDeviation, VDistribution.StandardDeviation);
Assert.IsTrue(VSample.PopulationStandardDeviation.ConfidenceInterval(0.95).ClosedContains(VDistribution.StandardDeviation));
// do a KS test comparing the sample to the expected distribution
TestResult kst = VSample.KolmogorovSmirnovTest(VDistribution);
Console.WriteLine("D = {0}, P = {1}", kst.Statistic, kst.LeftProbability);
Assert.IsTrue(kst.LeftProbability < 0.95);
// do a Kuiper test comparing the sample to the expected distribution
TestResult kut = VSample.KuiperTest(VDistribution);
Console.WriteLine("V = {0}, P = {1}", kut.Statistic, kut.LeftProbability);
Assert.IsTrue(kut.LeftProbability < 0.95);
}
public void ExponentialFitUncertainty()
{
// check that the uncertainty in reported fit parameters is actually meaningful
// it should be the standard deviation of fit parameter values in a sample of many fits
// define a population distribution
Distribution distribution = new ExponentialDistribution(4.0);
// draw a lot of samples from it; fit each sample and
// record the reported parameter value and error of each
Sample values = new Sample();
Sample uncertainties = new Sample();
for (int i = 0; i < 50; i++) {
Sample sample = CreateSample(distribution, 10, i);
FitResult fit = ExponentialDistribution.FitToSample(sample);
UncertainValue lambda = fit.Parameter(0);
values.Add(lambda.Value);
uncertainties.Add(lambda.Uncertainty);
}
Console.WriteLine(uncertainties.Mean);
Console.WriteLine(values.PopulationStandardDeviation);
// the reported errors should agree with the standard deviation of the reported parameters
Assert.IsTrue(values.PopulationStandardDeviation.ConfidenceInterval(0.95).ClosedContains(uncertainties.Mean));
}
public void ExponentialFit()
{
ExponentialDistribution distribution = new ExponentialDistribution(5.0);
Sample sample = CreateSample(distribution, 100);
// fit to normal should be bad
FitResult nfit = NormalDistribution.FitToSample(sample);
Console.WriteLine("P_n = {0}", nfit.GoodnessOfFit.LeftProbability);
Assert.IsTrue(nfit.GoodnessOfFit.LeftProbability > 0.95);
// fit to exponential should be good
FitResult efit = ExponentialDistribution.FitToSample(sample);
Console.WriteLine("P_e = {0}", efit.GoodnessOfFit.LeftProbability);
Assert.IsTrue(efit.GoodnessOfFit.LeftProbability < 0.95);
Assert.IsTrue(efit.Parameter(0).ConfidenceInterval(0.95).ClosedContains(distribution.Mean));
}
public void SignTestDistribution()
{
// start with a non-normally distributed population
Distribution xDistribution = new ExponentialDistribution();
Random rng = new Random(1);
// draw 100 samples from it and compute the t statistic for each
Sample wSample = new Sample();
for (int i = 0; i < 100; i++) {
// each sample has 8 observations
Sample xSample = new Sample();
for (int j = 0; j < 8; j++) { xSample.Add(xDistribution.GetRandomValue(rng)); }
//Sample xSample = CreateSample(xDistribution, 8, i);
TestResult wResult = xSample.SignTest(xDistribution.Median);
double W = wResult.Statistic;
//Console.WriteLine("W = {0}", W);
wSample.Add(W);
}
// sanity check our sample of t's
Assert.IsTrue(wSample.Count == 100);
// check that the t statistics are distributed as expected
DiscreteDistribution wDistribution = new BinomialDistribution(0.5, 8);
// check on the mean
Console.WriteLine("m = {0} vs. {1}", wSample.PopulationMean, wDistribution.Mean);
Assert.IsTrue(wSample.PopulationMean.ConfidenceInterval(0.95).ClosedContains(wDistribution.Mean));
// check on the standard deviation
Console.WriteLine("s = {0} vs. {1}", wSample.PopulationStandardDeviation, wDistribution.StandardDeviation);
Assert.IsTrue(wSample.PopulationStandardDeviation.ConfidenceInterval(0.95).ClosedContains(wDistribution.StandardDeviation));
// check on the skew
Console.WriteLine("t = {0} vs. {1}", wSample.PopulationMomentAboutMean(3), wDistribution.MomentAboutMean(3));
Assert.IsTrue(wSample.PopulationMomentAboutMean(3).ConfidenceInterval(0.95).ClosedContains(wDistribution.MomentAboutMean(3)));
// check on the kuritosis
Console.WriteLine("u = {0} vs. {1}", wSample.PopulationMomentAboutMean(4), wDistribution.MomentAboutMean(4));
Assert.IsTrue(wSample.PopulationMomentAboutMean(4).ConfidenceInterval(0.95).ClosedContains(wDistribution.MomentAboutMean(4)));
// KS tests are only for continuous distributions
}
/// <summary>
/// Computes the exponential distribution that best fits the given sample.
/// </summary>
/// <param name="sample">The sample to fit.</param>
/// <returns>The best fit parameter.</returns>
/// <remarks>
/// <para>The returned fit parameter is μ (the <see cref="Mean"/>).
/// This is the same parameter that is required by the <see cref="ExponentialDistribution(double)"/> constructor to
/// specify a new exponential distribution.</para>
/// </remarks>
/// <exception cref="ArgumentNullException"><paramref name="sample"/> is null.</exception>
/// <exception cref="InsufficientDataException"><paramref name="sample"/> contains fewer than two values.</exception>
/// <exception cref="InvalidOperationException"><paramref name="sample"/> contains non-positive values.</exception>
public static FitResult FitToSample(Sample sample)
{
if (sample == null) throw new ArgumentNullException("sample");
if (sample.Count < 2) throw new InsufficientDataException();
// none of the data is allowed to be negative
foreach (double value in sample) {
if (value < 0.0) throw new InvalidOperationException();
}
// the best-fit exponential's mean is the sample mean, with corresponding uncertainly
double lambda = sample.Mean;
double dLambda = lambda / Math.Sqrt(sample.Count);
Distribution distribution = new ExponentialDistribution(lambda);
TestResult test = sample.KolmogorovSmirnovTest(distribution);
return (new FitResult(lambda, dLambda, test));
}
public void TwoSampleKolmogorovNullDistributionTest()
{
Distribution population = new ExponentialDistribution();
int[] sizes = new int[] { 23, 30, 175 };
foreach (int na in sizes) {
foreach (int nb in sizes) {
Console.WriteLine("{0} {1}", na, nb);
Sample d = new Sample();
Distribution nullDistribution = null;
for (int i = 0; i < 128; i++) {
Sample a = TestUtilities.CreateSample(population, na, 31415 + na + i);
Sample b = TestUtilities.CreateSample(population, nb, 27182 + nb + i);
TestResult r = Sample.KolmogorovSmirnovTest(a, b);
d.Add(r.Statistic);
nullDistribution = r.Distribution;
}
// Only do full KS test if the number of bins is larger than the sample size, otherwise we are going to fail
// because the KS test detects the granularity of the distribution
TestResult mr = d.KolmogorovSmirnovTest(nullDistribution);
Console.WriteLine(mr.LeftProbability);
if (AdvancedIntegerMath.LCM(na, nb) > d.Count) Assert.IsTrue(mr.LeftProbability < 0.99);
// But always test that mean and standard deviation are as expected
Console.WriteLine("{0} {1}", nullDistribution.Mean, d.PopulationMean.ConfidenceInterval(0.99));
Assert.IsTrue(d.PopulationMean.ConfidenceInterval(0.99).ClosedContains(nullDistribution.Mean));
Console.WriteLine("{0} {1}", nullDistribution.StandardDeviation, d.PopulationStandardDeviation.ConfidenceInterval(0.99));
Assert.IsTrue(d.PopulationStandardDeviation.ConfidenceInterval(0.99).ClosedContains(nullDistribution.StandardDeviation));
Console.WriteLine("{0} {1}", nullDistribution.MomentAboutMean(3), d.PopulationMomentAboutMean(3).ConfidenceInterval(0.99));
//Assert.IsTrue(d.PopulationMomentAboutMean(3).ConfidenceInterval(0.99).ClosedContains(nullDistribution.MomentAboutMean(3)));
//Console.WriteLine("m {0} {1}", nullDistribution.Mean, d.PopulationMean);
}
}
}
public void MultivariateMoments()
{
// create a random sample
MultivariateSample M = new MultivariateSample(3);
Distribution d0 = new NormalDistribution();
Distribution d1 = new ExponentialDistribution();
Distribution d2 = new UniformDistribution();
Random rng = new Random(1);
int n = 10;
for (int i = 0; i < n; i++) {
M.Add(d0.GetRandomValue(rng), d1.GetRandomValue(rng), d2.GetRandomValue(rng));
}
// test that moments agree
for (int i = 0; i < 3; i++) {
int[] p = new int[3];
p[i] = 1;
Assert.IsTrue(TestUtilities.IsNearlyEqual(M.Column(i).Mean, M.Moment(p)));
p[i] = 2;
Assert.IsTrue(TestUtilities.IsNearlyEqual(M.Column(i).Variance, M.MomentAboutMean(p)));
for (int j = 0; j < i; j++) {
int[] q = new int[3];
q[i] = 1;
q[j] = 1;
Assert.IsTrue(TestUtilities.IsNearlyEqual(M.TwoColumns(i, j).Covariance, M.MomentAboutMean(q)));
}
}
}
