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MCMC

EDISON

Package EDISON (Estimation of Directed Interactions from Sequences Of Nonhomogeneous gene expression) runs an MCMC simulation to reconstruct networks from time series data, using a non-homogeneous, time-varying dynamic Bayesian network. Networks segments and changepoints are inferred concurrently, and information sharing priors provide a reduction of the inference uncertainty.

BMS

Bayesian Model Averaging for linear models with a wide choice of (customizable) priors. Built-in priorss include coefficient priors (fixed, flexible and hyper-g priors), 5 kinds of model priors, moreover model sampling by enumeration or various MCMC approaches. Post-processing functions allow for inferring posterior inclusion and model probabilitites, various moments, coefficient and predictive densities. Plotting functions available for posterior model size, MCMC convergence, predictive and coefficient densities, best models representation, BMA comparison.

MCMCglmm

MCMC Generalised Linear Mixed Models

BRugs

Fully-interactive R interface to the OpenBUGS software for Bayesian analysis using MCMC sampling. Runs natively and stably in 32-bit R under Windows. Versions running on Linux and on 64-bit R under Windows are in "beta" status and less efficient.

rv

Simulation-based random variable objects

lme4

Fit linear and generalized linear mixed-effects models. The models and their components are represented using S4 classes and methods. The core computational algorithms are implemented using the Eigen C++ library for numerical linear algebra and RcppEigen "glue".

coda

Output analysis and diagnostics for Markov Chain Monte Carlo simulations.

R2WinBUGS

Using this package, it is possible to call a BUGS model, summarize inferences and convergence in a table and graph, and save the simulations in arrays for easy access in R / S-PLUS. In S-PLUS, the openbugs functionality and the windows emulation functionality is not yet available.

MasterBayes

The primary aim of MasterBayes is to use MCMC techniques to integrate over uncertainty in pedigree configurations estimated from molecular markers and phenotypic data. Emphasis is put on the marginal distribution of parameters that relate the phenotypic data to the pedigree. All simulation is done in compiled C++ for efficiency.

MCMCpack

This package contains functions to perform Bayesian inference using posterior simulation for a number of statistical models. Most simulation is done in compiled C++ written in the Scythe Statistical Library Version 1.0.3. All models return coda mcmc objects that can then be summarized using the coda package. MCMCpack also contains some useful utility functions, including some additional density functions and pseudo-random number generators for statistical distributions, a general purpose Metropolis sampling algorithm, and tools for visualization.