tristanz / ScytheMCMC (http://bytebucket.org/tristanz/scythemcmc/wiki/html/index.html)

A Scythe Markov Chain Monte Carlo C++ Framework

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Updated README
Tristan Zajonc / tristanz
14 months ago

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Up to file-list README:

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INTRODUCTION:
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Scythe MCMC is a C++ header library that eases the development of Markov Chain 
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Monte Carlo (MCMC).  It is based on the Scythe Statistical Library. Scythe MCMC 
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provides an execution framework, including command line and option file 
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Monte Carlo (MCMC) samplers.  It is based on the Scythe Statistical Library. Scythe 
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MCMC provides an execution framework, including command line and option file 
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parsing, that reduces the amount of boilerplate code needed to write custom 
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MCMC routines.  It also provides common MCMC step types, including Gibbs, 
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Metropolis-Hastings, and Slice sampling.  Users can experiment with which 
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sampling steps provide the best results and implement their own sampling steps 
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as desired.
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Scythe MCMC was motivated with the need to combine simpler samplers, such as 
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univariate slice sampling, with more specialized samplers for particular 
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problems.  Future versions of Scythe MCMC will include common samplers for 
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nonparametric Bayesian models, including a Collapsed Gibbs sampler for the 
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Dirichlet Process, and Slice samplers for the Dirichlet Process and Indian 
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Buffet Process.
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DOCUMENTATION:
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There are many choices for writing MCMC samplers.  Scythe MCMC is similar to, 
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and heavily inspired by, MCMC++, but is based on the Scythe, which provides 
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convenient matrix types, random number generators,  and probability 
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distributions. Scythe MCMC is different in focus from  MCMCPack, which is also 
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based on Scythe and interfaces with R.  Users wishing to distribute a specific 
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model to R users should consider contributing to MCMCPack directly. Unlike 
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MCMCPack, Scythe MCMC makes no attempt to interface with R and assumes samplers 
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are executed from the command line (although this is not required). It also 
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provides common algorithms (Gibbs, Metropolis-Hastings, Slice Sampling) that 
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ease development of samplers for many models.
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Even though implementing models in ScytheMCMC requires more work than 
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implementing comparable models in Bugs  or JAGS, Scythe MCMC generally leads to 
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faster samplers that can exploit the particular structure of a given problem.  
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It also allows development of models that cannot be sampled effectively using 
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either Bugs or Jags, such nonparametric Bayesian models without truncation 
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approximations.
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Doxygen docs: http://bytebucket.org/tristanz/scythemcmc/wiki/html/index.html
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FEATURES:
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- Eliminates commandline and option parsing boilerplate code using
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  SimpleOpt and SimpleIni.
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- Built in sampling steps:
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    - Deterministic
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    - Gibbs,
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    - Metropolis-Hastings,
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    - Slice Sampling.
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- Planned: nonparameteric samplers including:
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   - Collapsed gibbs samplers for Dirichlet Process,
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   - Slice sampler for Dirichlet Process and Indian Buffet Process.
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- GPL License.
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