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
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DOXYFILE_ENCODING = UTF-8 |
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PROJECT_NAME = "Scythe MCMC" |
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PROJECT_NUMBER = 0.1 |
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OUTPUT_DIRECTORY = /Users/tristanz/Data/OpenIRT/ScytheMCMC/docs |
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OUTPUT_DIRECTORY = /Users/tristanz/Data/OpenIRT/ScytheMCMC/docs/wiki |
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CREATE_SUBDIRS = NO |
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OUTPUT_LANGUAGE = English |
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BRIEF_MEMBER_DESC = YES |
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ALWAYS_DETAILED_SEC = NO |
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INLINE_INHERITED_MEMB = NO |
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FULL_PATH_NAMES = YES |
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STRIP_FROM_PATH = /Users/ |
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STRIP_FROM_PATH = /Users/tristanz/Data/OpenIRT/ScytheMCMC/src |
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STRIP_FROM_INC_PATH = |
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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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- GPL License. |
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