runjags: Interface Utilities, Model Templates, Parallel Computing Methods and Additional Distributions for MCMC Models in JAGS
Version 2.0.4-2

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
URL http://runjags.sourceforge.net
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("runjags")

Popular man pages

add.summary: Summary statistics and plot methods for runjags class objects
autorun.jags: Run or extend a user-specified Bayesian MCMC model in JAGS...
read.jagsfile: Extract Any Models, Data, Monitored Variables or Initial...
results.jags: Importing of saved JAGS simulations with partial error...
run.jags: Run or extend a user-specified Bayesian MCMC model in JAGS...
runjags.options: Options for the runjags package
template.jags: Generate a generalised linear mixed model (GLMM)...
See all...

All man pages Function index File listing

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 Source code
addmutated Source code
alphabeticalvars Source code
as.jags Man page Source code
as.jags.default Source code
as.jags.runjags Man page Source code
as.mcmc.list.runjags Man page Source code
as.mcmc.runjags Man page Source code
as.runjags Man page Source code
as.runjags.default Source code
as.runjags.jags Man page Source code
ask Man page Source code
autoextend.JAGS Man page
autoextend.jags Man page Source code
autorun.JAGS Man page
autorun.jags Man page Source code
checkadaptrequired Source code
checkdataformat Source code
checkmodfact Source code
checkvalidforjags Source code
checkvalidmonitorname Source code
checkvalidrunjagsobject Source code
cleanup.JAGS Man page
cleanup.jags Man page Source code
combine.JAGS Man page
combine.MCMC Man page
combine.jags Man page Source code
combine.mcmc Man page Source code
contrasts.MCMC Man page
contrasts.mcmc Man page Source code
crosscorr.plot.lattice Source code
dic.runjags Man page Source code
divide.JAGS Man page
divide.jags Man page Source code
drop.k Man page Source code
drop.k.JAGS Man page
drop.k.jags Man page
dump.format Man page Source code
dynloadmodule Source code
dynunloadmodule Source code
expandindexnames Source code
extend.JAGS Man page
extend.jags Man page Source code
extract Man page Source code
extract.jags Man page
extract.runjags Man page Source code
failed.JAGS Man page
failed.jags Man page Source code
failedjags Man page
findJAGS Man page
findjags Man page Source code
fitted.runjags Man page Source code
getRvers Source code
getargs Source code
getarraynames Source code
getdefaultmethodoptions Source code
getdefaultsummarypars Source code
getjagsnames Source code
getrunjagsmethod Source code
getstoptexts Source code
getsummaryargs Source code
getvers Source code
is.runjags Man page Source code
list.format Man page Source code
load.runJAGSmodule Man page
load.runjagsmodule Man page Source code
loadandcheckrjags Source code
makerunjagsobject Source code
matchvars Source code
mutate.functions Man page
new_unique Man page Source code
normalise.mcmcfun Source code
old.winbugs.extract.small Source code
oldsortjagsvsbugs Source code
onAttach Source code
onDetach Source code
onLoad Source code
plot.runjags Man page Source code
plot.runjagsplots Man page
plot.runjagsstudy Man page Source code
prec2sd Man page Source code
predict.runjags Man page Source code
prettifytable Source code
print.crosscorrstats Man page Source code
print.dicstats Man page Source code
print.failedjags Man page Source code
print.gelman.with.target Man page
print.gelmanwithtarget Man page Source code
print.mcsestats Man page Source code
print.rjagsoutput Man page Source code
print.runjags Man page Source code
print.runjagsbginfo Man page Source code
print.runjagsdata Man page Source code
print.runjagsinits Man page Source code
print.runjagsmodel Man page Source code
print.runjagsoutput Man page Source code
print.runjagsplots Man page Source code
print.runjagsstudy Man page Source code
read.JAGSfile Man page
read.WinBUGS Man page
read.coda.subset Source code
read.jagsfile Man page Source code
read.openbugs.subset Source code
read.winbugs Man page
residuals.runjags Man page Source code
results.JAGS Man page
results.jags Man page Source code
run.JAGS Man page
run.JAGS.study Man page
run.jags Man page Source code
run.jags.study Man page Source code
runJAGS.getOption Man page
runJAGS.options Man page
runjags-class Man page
runjags.background Source code
runjags.dic Source code
runjags.getOption Man page Source code
runjags.interruptible Source code
runjags.options Man page Source code
runjags.parallel Source code
runjags.printmethods Man page
runjags.readin Source code
runjags.rjags Source code
runjags.rjparallel Source code
runjags.simple Source code
runjags.snow Source code
runjags.start Source code
runjags.summaries Source code
runjags.xgrid Source code
runjagsclass Man page
runjagsplots Source code
runjagsstudy-class Man page
runjagsstudyclass Man page
runjags} \alias{runjags-package} \alias{runjagspackage Man page
safe.autocorr.diag Source code
safe.gelman.diag Source code
setup.jags Source code
setup.jagsfile Source code
setup.xgrid Source code
sortjagsvsbugs Source code
summarise.jags.study Source code
summary.runjags Man page Source code
summary.runjagsstudy Man page Source code
swcat Source code
tailf Source code
template.JAGS Man page
template.jags Man page Source code
testjags Source code
testjags} \alias{testJAGS Man page
timestring Man page Source code
unload.runJAGSmodule Man page
unload.runjagsmodule Man page Source code
userunjagsmodule Source code
versionmatch Source code
waitforxgridjob Source code
weightedaverage Source code
winbugs.extract.big Source code
winbugs.extract.small Source code
write.JAGSfile Man page
write.jagsfile Man page Source code
xapply Man page Source code
xgrid.autoextend.JAGS Man page
xgrid.autoextend.jags Man page Source code
xgrid.autorun.JAGS Man page
xgrid.autorun.JAGSfile Man page
xgrid.autorun.jags Man page Source code
xgrid.autorun.jagsfile Man page
xgrid.delete Man page Source code
xgrid.extend.JAGS Man page
xgrid.extend.jags Man page Source code
xgrid.jobs Man page Source code
xgrid.read Source code
xgrid.results Man page Source code
xgrid.results.JAGS Man page
xgrid.results.jags Man page Source code
xgrid.retrieve Source code
xgrid.run Man page Source code
xgrid.run.JAGS Man page
xgrid.run.JAGSfile Man page
xgrid.run.jags Man page Source code
xgrid.run.jagsfile Man page
xgrid.start Source code
xgrid.submit Man page Source code
xgrid.submit.JAGS Man page
xgrid.submit.JAGSfile Man page
xgrid.submit.jags Man page Source code
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
runjags documentation built on May 20, 2017, 12:58 a.m.

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

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

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