runjags: Interface Utilities, Model Templates, Parallel Computing Methods and Additional Distributions for MCMC Models in JAGS

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.

AuthorMatthew Denwood [aut, cre], Martyn Plummer [cph] (Copyright holder of the code in /src/distributions/jags, src/distributions/DPar1.*, configure.ac, and original copyright holder of some modified code where indicated)
Date of publication2016-07-25 20:30:21
MaintainerMatthew Denwood <md@sund.ku.dk>
LicenseGPL-2
Version2.0.4-2
http://runjags.sourceforge.net

View on CRAN

Man pages

add.summary: Summary statistics and plot methods for runjags class objects

ask: Obtain Input from User With Error Handling

autorun.jags: Run or extend a user-specified Bayesian MCMC model in JAGS...

combine.mcmc: Combining and dividing runjags and MCMC objects

extract.runjags: Extract peripheral information from runjags objects

findjags: Attempt to Locate a JAGS Install

list.dump.format: Conversion Between a Named List and a Character String in the...

load.runjagsmodule: Load the internal JAGS module provided by runjags

mutate.functions: Mutate functions to be used with runjags summary methods

new_unique: Create a Unique Filename

read.jagsfile: Extract Any Models, Data, Monitored Variables or Initial...

results.jags: Importing of saved JAGS simulations with partial error...

runjags: Interface Utilities, Model Templates, Parallel Computing...

run.jags: Run or extend a user-specified Bayesian MCMC model in JAGS...

runjags-class: The runjags class and available S3 methods

runjags.options: Options for the runjags package

runjags.printmethods: Print methods for runjags helper classes

run.jags.study: Drop-k and simulated dataset studies using JAGS

template.jags: Generate a generalised linear mixed model (GLMM)...

testjags: Analyse the System to Check That JAGS Is Installed

timestring: Calculate the Elapsed Time in Sensible Units

write.jagsfile: Write a complete JAGS model to a text file

xgrid.run: Remote execution of user-specified R functions on Apple Xgrid...

xgrid.run.jags: Run a JAGS Model using an Apple Xgrid distributed computing...

Files in this package

runjags
runjags/COPYING
runjags/inst
runjags/inst/CITATION
runjags/inst/doc
runjags/inst/doc/UserGuide.pdf
runjags/inst/doc/UserGuide.Rtex
runjags/inst/doc/quickjags.R
runjags/inst/doc/quickjags.html
runjags/inst/doc/quickjags.Rmd
runjags/inst/xgrid
runjags/inst/xgrid/mgrid.sh
runjags/inst/xgrid/beep.bat
runjags/configure.ac
runjags/tests
runjags/tests/checkstudy.R
runjags/tests/checkinputs.R
runjags/tests/moduletargets.Rsave
runjags/tests/checkmethods.R
runjags/tests/checkmodule.R
runjags/src
runjags/src/distributions
runjags/src/distributions/jags
runjags/src/distributions/jags/DPQFunction.h
runjags/src/distributions/jags/QFunction.h
runjags/src/distributions/jags/DFunction.cc
runjags/src/distributions/jags/RScalarDist.h
runjags/src/distributions/jags/PFunction.h
runjags/src/distributions/jags/PFunction.cc
runjags/src/distributions/jags/DFunction.h
runjags/src/distributions/jags/RScalarDist.cc
runjags/src/distributions/jags/QFunction.cc
runjags/src/distributions/jags/DPQFunction.cc
runjags/src/distributions/DPar4.h
runjags/src/distributions/DMouchel.cc
runjags/src/distributions/DGenPar.cc
runjags/src/distributions/DPar2.h
runjags/src/distributions/DPar2.cc
runjags/src/distributions/DLomax.h
runjags/src/distributions/DHalfCauchy.cc
runjags/src/distributions/DPar1.h
runjags/src/distributions/DMouchel.h
runjags/src/distributions/DHalfCauchy.h
runjags/src/distributions/DPar1.cc
runjags/src/distributions/DLomax.cc
runjags/src/distributions/DPar4.cc
runjags/src/distributions/DPar3.cc
runjags/src/distributions/DPar3.h
runjags/src/distributions/DGenPar.h
runjags/src/testrunjags.cc
runjags/src/Makevars.in
runjags/src/jagsversions.h
runjags/src/runjags.cc
runjags/src/Makevars.win
runjags/NAMESPACE
runjags/CHANGELOG
runjags/R
runjags/R/extract.runjags.R runjags/R/results.jags.R runjags/R/xgrid.utilities.R runjags/R/read.jagsfile.R runjags/R/runjags.readin.R runjags/R/combine.mcmc.R runjags/R/setup.jags.jagsfile.R runjags/R/print.methods.R runjags/R/template.jags.R runjags/R/xgrid.run.jags.R runjags/R/utilities.R runjags/R/dump.list.format.R runjags/R/autoextend.jags.R runjags/R/load.module.runjags.R runjags/R/xgrid.run.R runjags/R/runjags.start.R runjags/R/runjags.summaries.R runjags/R/utilities.invisible.R runjags/R/mutate.functions.R runjags/R/summary.R runjags/R/extend.jags.R runjags/R/runjagsclass.R runjags/R/zzz.R runjags/R/run.jags.study.R
runjags/vignettes
runjags/vignettes/UserGuide.Rtex
runjags/vignettes/traceplots.pdf
runjags/vignettes/quickjags.Rmd
runjags/MD5
runjags/README
runjags/build
runjags/build/vignette.rds
runjags/DESCRIPTION
runjags/configure
runjags/man
runjags/man/runjags.Rd runjags/man/run.jags.study.Rd runjags/man/runjags-class.Rd runjags/man/findjags.Rd runjags/man/read.jagsfile.Rd runjags/man/ask.Rd runjags/man/mutate.functions.Rd runjags/man/runjags.options.Rd runjags/man/load.runjagsmodule.Rd runjags/man/add.summary.Rd runjags/man/combine.mcmc.Rd runjags/man/xgrid.run.Rd runjags/man/extract.runjags.Rd runjags/man/xgrid.run.jags.Rd runjags/man/list.dump.format.Rd runjags/man/runjags.printmethods.Rd runjags/man/testjags.Rd runjags/man/new_unique.Rd runjags/man/template.jags.Rd runjags/man/results.jags.Rd runjags/man/write.jagsfile.Rd runjags/man/run.jags.Rd runjags/man/autorun.jags.Rd runjags/man/timestring.Rd
runjags/cleanup

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