// // Math.NET Numerics, part of the Math.NET Project // http://numerics.mathdotnet.com // http://github.com/mathnet/mathnet-numerics // // Copyright (c) 2009-2010 Math.NET // // Permission is hereby granted, free of charge, to any person // obtaining a copy of this software and associated documentation // files (the "Software"), to deal in the Software without // restriction, including without limitation the rights to use, // copy, modify, merge, publish, distribute, sublicense, and/or sell // copies of the Software, and to permit persons to whom the // Software is furnished to do so, subject to the following // conditions: // // The above copyright notice and this permission notice shall be // included in all copies or substantial portions of the Software. // // THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, // EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES // OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND // NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT // HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, // WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING // FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR // OTHER DEALINGS IN THE SOFTWARE. // using System; using IStation.Numerics.Distributions; using IStation.Numerics.Random; namespace IStation.Numerics.Statistics.Mcmc { /// /// A hybrid Monte Carlo sampler for univariate distributions. /// public class UnivariateHybridMC : HybridMCGeneric { /// /// Distribution to sample momentum from. /// private readonly Normal _distribution; /// /// Standard deviations used in the sampling of the /// momentum. /// private double _sdv; /// /// Gets or sets the standard deviation used in the sampling of the /// momentum. /// /// When standard deviation is negative. public double MomentumStdDev { get => _sdv; set { if (_sdv != value) { _sdv = SetPositive(value); } } } /// /// Constructs a new Hybrid Monte Carlo sampler for a univariate probability distribution. /// The momentum will be sampled from a normal distribution with standard deviation /// specified by pSdv using the default random /// number generator. A three point estimation will be used for differentiation. /// This constructor will set the burn interval. /// /// The initial sample. /// The log density of the distribution we want to sample from. /// Number frog leap simulation steps. /// Size of the frog leap simulation steps. /// The number of iterations in between returning samples. /// The standard deviation of the normal distribution that is used to sample /// the momentum. /// When the number of burnInterval iteration is negative. public UnivariateHybridMC(double x0, DensityLn pdfLnP, int frogLeapSteps, double stepSize, int burnInterval = 0, double pSdv = 1) : this(x0, pdfLnP, frogLeapSteps, stepSize, burnInterval, pSdv, SystemRandomSource.Default) { } /// /// Constructs a new Hybrid Monte Carlo sampler for a univariate probability distribution. /// The momentum will be sampled from a normal distribution with standard deviation /// specified by pSdv using a random /// number generator provided by the user. A three point estimation will be used for differentiation. /// This constructor will set the burn interval. /// /// The initial sample. /// The log density of the distribution we want to sample from. /// Number frog leap simulation steps. /// Size of the frog leap simulation steps. /// The number of iterations in between returning samples. /// The standard deviation of the normal distribution that is used to sample /// the momentum. /// Random number generator used to sample the momentum. /// When the number of burnInterval iteration is negative. public UnivariateHybridMC(double x0, DensityLn pdfLnP, int frogLeapSteps, double stepSize, int burnInterval, double pSdv, System.Random randomSource) : this(x0, pdfLnP, frogLeapSteps, stepSize, burnInterval, pSdv, randomSource, Grad) { } /// /// Constructs a new Hybrid Monte Carlo sampler for a multivariate probability distribution. /// The momentum will be sampled from a normal distribution with standard deviation /// given by pSdv using a random /// number generator provided by the user. This constructor will set both the burn interval and the method used for /// numerical differentiation. /// /// The initial sample. /// The log density of the distribution we want to sample from. /// Number frog leap simulation steps. /// Size of the frog leap simulation steps. /// The number of iterations in between returning samples. /// The standard deviation of the normal distribution that is used to sample /// the momentum. /// The method used for numerical differentiation. /// Random number generator used for sampling the momentum. /// When the number of burnInterval iteration is negative. public UnivariateHybridMC(double x0, DensityLn pdfLnP, int frogLeapSteps, double stepSize, int burnInterval, double pSdv, System.Random randomSource, DiffMethod diff) : base(x0, pdfLnP, frogLeapSteps, stepSize, burnInterval, randomSource, diff) { MomentumStdDev = pSdv; _distribution = new Normal(0.0, MomentumStdDev, RandomSource); Burn(BurnInterval); } /// /// Use for copying objects in the Burn method. /// /// The source of copying. /// A copy of the source object. protected override double Copy(double source) { return source; } /// /// Use for creating temporary objects in the Burn method. /// /// An object of type T. protected override double Create() { return 0; } /// protected override void DoAdd(ref double first, double factor, double second) { first += factor * second; } /// protected override double DoProduct(double first, double second) { return first * second; } /// protected override void DoSubtract(ref double first, double factor, double second) { first -= factor * second; } /// /// Samples the momentum from a normal distribution. /// /// The momentum to be randomized. protected override void RandomizeMomentum(ref double p) { p = _distribution.Sample(); } /// /// The default method used for computing the derivative. Uses a simple three point estimation. /// /// Function for which the derivative is to be evaluated. /// The location where the derivative is to be evaluated. /// The derivative of the function at the point x. static double Grad(DensityLn function, double x) { double h = Math.Max(10e-4, (10e-7) * x); double increment = x + h; double decrement = x - h; return (function(increment) - function(decrement)) / (2 * h); } } }