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.

Install the latest version of this package by entering the following in R:
install.packages("runjags")
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...

Functions

add.summary Man page
as.jags Man page
as.jags.runjags Man page
ask Man page
as.mcmc.list.runjags Man page
as.mcmc.runjags Man page
as.runjags Man page
as.runjags.jags Man page
autoextend.jags Man page
autoextend.JAGS Man page
autorun.jags Man page
autorun.JAGS Man page
cleanup.jags Man page
cleanup.JAGS Man page
combine.jags Man page
combine.JAGS Man page
combine.mcmc Man page
combine.MCMC Man page
contrasts.mcmc Man page
contrasts.MCMC Man page
dic.runjags Man page
divide.jags Man page
divide.JAGS Man page
drop.k Man page
drop.k.jags Man page
drop.k.JAGS Man page
dump.format Man page
extend.jags Man page
extend.JAGS Man page
extract Man page
extract.jags Man page
extract.runjags Man page
failedjags Man page
failed.jags Man page
failed.JAGS Man page
findjags Man page
findJAGS Man page
fitted.runjags Man page
is.runjags Man page
list.format Man page
load.runjagsmodule Man page
load.runJAGSmodule Man page
mutate.functions Man page
new_unique Man page
plot.runjags Man page
plot.runjagsplots Man page
plot.runjagsstudy Man page
prec2sd Man page
predict.runjags Man page
print.crosscorrstats Man page
print.dicstats Man page
print.failedjags Man page
print.gelmanwithtarget Man page
print.gelman.with.target Man page
print.mcsestats Man page
print.rjagsoutput Man page
print.runjags Man page
print.runjagsbginfo Man page
print.runjagsdata Man page
print.runjagsinits Man page
print.runjagsmodel Man page
print.runjagsoutput Man page
print.runjagsplots Man page
print.runjagsstudy Man page
read.jagsfile Man page
read.JAGSfile Man page
read.winbugs Man page
read.WinBUGS Man page
residuals.runjags Man page
results.jags Man page
results.JAGS Man page
run.jags Man page
run.JAGS Man page
runjags} \alias{runjags-package} \alias{runjagspackage Man page
runjagsclass Man page
runjags-class Man page
runjags.getOption Man page
runJAGS.getOption Man page
runjags.options Man page
runJAGS.options Man page
runjags.printmethods Man page
run.jags.study Man page
run.JAGS.study Man page
runjagsstudyclass Man page
runjagsstudy-class Man page
summary.runjags Man page
summary.runjagsstudy Man page
template.jags Man page
template.JAGS Man page
testjags} \alias{testJAGS Man page
timestring Man page
unload.runjagsmodule Man page
unload.runJAGSmodule Man page
write.jagsfile Man page
write.JAGSfile Man page
xapply Man page
xgrid.autoextend.jags Man page
xgrid.autoextend.JAGS Man page
xgrid.autorun.jags Man page
xgrid.autorun.JAGS Man page
xgrid.autorun.jagsfile Man page
xgrid.autorun.JAGSfile Man page
xgrid.delete Man page
xgrid.extend.jags Man page
xgrid.extend.JAGS Man page
xgrid.jobs Man page
xgrid.results Man page
xgrid.results.jags Man page
xgrid.results.JAGS Man page
xgrid.run Man page
xgrid.run.jags Man page
xgrid.run.JAGS Man page
xgrid.run.jagsfile Man page
xgrid.run.JAGSfile Man page
xgrid.submit Man page
xgrid.submit.jags Man page
xgrid.submit.JAGS Man page
xgrid.submit.jagsfile Man page
xgrid.submit.JAGSfile Man page

Files

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

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.