Martyn Plummer

Martyn Plummer

8 packages on CRAN

coda

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Provides functions for summarizing and plotting the output from Markov Chain Monte Carlo (MCMC) simulations, as well as diagnostic tests of convergence to the equilibrium distribution of the Markov chain.

rjags

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Interface to the JAGS MCMC library.

BART

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Bayesian Additive Regression Trees (BART) provide flexible nonparametric modeling of covariates for continuous, binary, categorical and time-to-event outcomes. For more information on BART, see Chipman, George and McCulloch (2010) <doi:10.1214/09-AOAS285> and Sparapani, Logan, McCulloch and Laud (2016) <doi:10.1002/sim.6893>.

bayesmix

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The fitting of finite mixture models of univariate Gaussian distributions using JAGS within a Bayesian framework is provided.

Epi

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Functions for demographic and epidemiological analysis in the Lexis diagram, i.e. register and cohort follow-up data, in particular representation, manipulation and simulation of multistate data - the Lexis suite of functions, which includes interfaces to 'mstate', 'etm' and 'cmprsk' packages. Also contains functions for Age-Period-Cohort and Lee-Carter modeling and a function for interval censored data and some useful functions for tabulation and plotting, as well as a number of epidemiological data sets.

HWEBayes

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Estimation and testing of HWE using Bayesian methods. Three models are currently considered: HWE, a model parameterized in terms of the allele frequencies and a single inbreeding coefficient f, and the saturated model. Testing is based on Bayes factors.

runjags

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User-friendly interface utilities for MCMC models via Just Another Gibbs Sampler (JAGS), facilitating the use of parallel (or distributed) processors for multiple chains, automated control of convergence and sample length diagnostics, and evaluation of the performance of a model using drop-k validation or against simulated data. Template model specifications can be generated using a standard lme4-style formula interface to assist users less familiar with the BUGS syntax. A JAGS extension module provides additional distributions including the Pareto family of distributions, the DuMouchel prior and the half-Cauchy prior.

sBIC

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Computes the sBIC for various singular model collections including: binomial mixtures, factor analysis models, Gaussian mixtures, latent forests, latent class analyses, and reduced rank regressions.