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

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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.

Author
Matthew 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 publication
2016-07-25 20:30:21
Maintainer
Matthew Denwood <md@sund.ku.dk>
License
GPL-2
Version
2.0.4-2
URLs

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