JointIBD

Mathematica code for joint inference of identities by descent along multiple chromosomes from population samples.

Last updated November 30, 2016 MCMC statistics genetics History Delete Edit Link

Mathematica Markov Chain Monte Carlo

Mathematica package containing a general-purpose Markov chain Monte Carlo routine. Includes various examples and documentation.

Features:

  • Convenience wrapper for fitting models to arbitrary-dimensional data with Gaussian errors
  • Handles both real-valued and discrete-valued model parameters
  • Uses Metropolis algorithm with decaying exponential proposal distribution
  • Progress monitor; support for auto save/resume

Usage examples are available on Mathematica.StackExchange:

http://mathematica.stackexchange.com/a/137636/1089

Last updated February 12, 2017 MCMC History Delete Edit Link

MathematicaStan

MathematicaStan is an interface for Stan, which is a probabilistic language for Bayesian inference, with MCMC sampling, approximate Bayesian inference, with variational sampling, and penalized maximum likelihood methods with optimizations.

Last updated September 16, 2016 statistics bayesian inference MCMC History Delete Edit Link