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

## Documentation for package ‘runjags’ version 2.0.4-2

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

A C D E F I L M N P R S T U W X

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

## -- A --

add.summary | Summary statistics and plot methods for runjags class objects
as.jags | The runjags class and available S3 methods
as.jags.runjags | The runjags class and available S3 methods
as.mcmc.list.runjags | The runjags class and available S3 methods
as.mcmc.runjags | The runjags class and available S3 methods
as.runjags | The runjags class and available S3 methods
as.runjags.jags | The runjags class and available S3 methods
ask | Obtain Input from User With Error Handling
autoextend.JAGS | Run or extend a user-specified Bayesian MCMC model in JAGS with automatically calculated run-length and convergence diagnostics
autoextend.jags | Run or extend a user-specified Bayesian MCMC model in JAGS with automatically calculated run-length and convergence diagnostics
autorun.JAGS | Run or extend a user-specified Bayesian MCMC model in JAGS with automatically calculated run-length and convergence diagnostics
autorun.jags | Run or extend a user-specified Bayesian MCMC model in JAGS with automatically calculated run-length and convergence diagnostics

## -- C --

cleanup.JAGS | The runjags class and available S3 methods
cleanup.jags | The runjags class and available S3 methods
combine.JAGS | Combining and dividing runjags and MCMC objects
combine.jags | Combining and dividing runjags and MCMC objects
combine.MCMC | Combining and dividing runjags and MCMC objects
combine.mcmc | Combining and dividing runjags and MCMC objects
contrasts.MCMC | Mutate functions to be used with runjags summary methods
contrasts.mcmc | Mutate functions to be used with runjags summary methods

## -- D --

dic.runjags | Extract peripheral information from runjags objects
divide.JAGS | Combining and dividing runjags and MCMC objects
divide.jags | Combining and dividing runjags and MCMC objects
drop.k | Drop-k and simulated dataset studies using JAGS
drop.k.JAGS | Drop-k and simulated dataset studies using JAGS
drop.k.jags | Drop-k and simulated dataset studies using JAGS
dump.format | Conversion Between a Named List and a Character String in the R Dump Format

## -- E --

extend.JAGS | Run or extend a user-specified Bayesian MCMC model in JAGS from within R
extend.jags | Run or extend a user-specified Bayesian MCMC model in JAGS from within R
extract | Extract peripheral information from runjags objects
extract.jags | Extract peripheral information from runjags objects
extract.runjags | Extract peripheral information from runjags objects

## -- F --

failed.JAGS | The runjags class and available S3 methods
failed.jags | The runjags class and available S3 methods
failedjags | The runjags class and available S3 methods
findJAGS | Attempt to Locate a JAGS Install
findjags | Attempt to Locate a JAGS Install
fitted.runjags | The runjags class and available S3 methods

## -- I --

is.runjags | The runjags class and available S3 methods

## -- L --

list.format | Conversion Between a Named List and a Character String in the R Dump Format
load.runJAGSmodule | Load the internal JAGS module provided by runjags
load.runjagsmodule | Load the internal JAGS module provided by runjags

## -- M --

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

## -- N --

new_unique | Create a Unique Filename

## -- P --

plot.runjags | Summary statistics and plot methods for runjags class objects
plot.runjagsplots | Summary statistics and plot methods for runjags class objects
plot.runjagsstudy | Print methods for runjags helper classes
prec2sd | Mutate functions to be used with runjags summary methods
predict.runjags | The runjags class and available S3 methods
print.crosscorrstats | Print methods for runjags helper classes
print.dicstats | Print methods for runjags helper classes
print.failedjags | Print methods for runjags helper classes
print.gelman.with.target | Print methods for runjags helper classes
print.gelmanwithtarget | Print methods for runjags helper classes
print.mcsestats | Print methods for runjags helper classes
print.rjagsoutput | Print methods for runjags helper classes
print.runjags | Summary statistics and plot methods for runjags class objects
print.runjagsbginfo | Print methods for runjags helper classes
print.runjagsdata | Print methods for runjags helper classes
print.runjagsinits | Print methods for runjags helper classes
print.runjagsmodel | Print methods for runjags helper classes
print.runjagsoutput | Print methods for runjags helper classes
print.runjagsplots | Summary statistics and plot methods for runjags class objects
print.runjagsstudy | Print methods for runjags helper classes

## -- R --

read.JAGSfile | Extract Any Models, Data, Monitored Variables or Initial Values As Character Vectors from a JAGS or WinBUGS Format Textfile
read.jagsfile | Extract Any Models, Data, Monitored Variables or Initial Values As Character Vectors from a JAGS or WinBUGS Format Textfile
read.WinBUGS | Extract Any Models, Data, Monitored Variables or Initial Values As Character Vectors from a JAGS or WinBUGS Format Textfile
read.winbugs | Extract Any Models, Data, Monitored Variables or Initial Values As Character Vectors from a JAGS or WinBUGS Format Textfile
residuals.runjags | The runjags class and available S3 methods
results.JAGS | Importing of saved JAGS simulations with partial error recovery
results.jags | Importing of saved JAGS simulations with partial error recovery
run.JAGS | Run or extend a user-specified Bayesian MCMC model in JAGS from within R
run.jags | Run or extend a user-specified Bayesian MCMC model in JAGS from within R
run.JAGS.study | Drop-k and simulated dataset studies using JAGS
run.jags.study | Drop-k and simulated dataset studies using JAGS
runjags | Interface Utilities, Model Templates, Parallel Computing Methods and Additional Distributions for MCMC Models in JAGS
runjags-class | The runjags class and available S3 methods
runJAGS.getOption | Options for the runjags package
runjags.getOption | Options for the runjags package
runJAGS.options | Options for the runjags package
runjags.options | Options for the runjags package
runjags.printmethods | Print methods for runjags helper classes
runjagsclass | The runjags class and available S3 methods
runjagspackage | Interface Utilities, Model Templates, Parallel Computing Methods and Additional Distributions for MCMC Models in JAGS
runjagsstudy-class | The runjags class and available S3 methods
runjagsstudyclass | The runjags class and available S3 methods

## -- S --

summary.runjags | Summary statistics and plot methods for runjags class objects
summary.runjagsstudy | Print methods for runjags helper classes

## -- T --

template.JAGS | Generate a generalised linear mixed model (GLMM) specification in JAGS
template.jags | Generate a generalised linear mixed model (GLMM) specification in JAGS
testJAGS | Analyse the System to Check That JAGS Is Installed
testjags | Analyse the System to Check That JAGS Is Installed
timestring | Calculate the Elapsed Time in Sensible Units

## -- U --

unload.runJAGSmodule | Load the internal JAGS module provided by runjags
unload.runjagsmodule | Load the internal JAGS module provided by runjags

## -- W --

write.JAGSfile | Write a complete JAGS model to a text file
write.jagsfile | Write a complete JAGS model to a text file

## -- X --

xapply | Remote execution of user-specified R functions on Apple Xgrid distributed computing clusters
xgrid.autoextend.JAGS | Run a JAGS Model using an Apple Xgrid distributed computing cluster from Within R
xgrid.autoextend.jags | Run a JAGS Model using an Apple Xgrid distributed computing cluster from Within R
xgrid.autorun.JAGS | Run a JAGS Model using an Apple Xgrid distributed computing cluster from Within R
xgrid.autorun.jags | Run a JAGS Model using an Apple Xgrid distributed computing cluster from Within R
xgrid.autorun.JAGSfile | Run a JAGS Model using an Apple Xgrid distributed computing cluster from Within R
xgrid.autorun.jagsfile | Run a JAGS Model using an Apple Xgrid distributed computing cluster from Within R
xgrid.delete | Remote execution of user-specified R functions on Apple Xgrid distributed computing clusters
xgrid.extend.JAGS | Run a JAGS Model using an Apple Xgrid distributed computing cluster from Within R
xgrid.extend.jags | Run a JAGS Model using an Apple Xgrid distributed computing cluster from Within R
xgrid.jobs | Remote execution of user-specified R functions on Apple Xgrid distributed computing clusters
xgrid.results | Remote execution of user-specified R functions on Apple Xgrid distributed computing clusters
xgrid.results.JAGS | Run a JAGS Model using an Apple Xgrid distributed computing cluster from Within R
xgrid.results.jags | Run a JAGS Model using an Apple Xgrid distributed computing cluster from Within R
xgrid.run | Remote execution of user-specified R functions on Apple Xgrid distributed computing clusters
xgrid.run.JAGS | Run a JAGS Model using an Apple Xgrid distributed computing cluster from Within R
xgrid.run.jags | Run a JAGS Model using an Apple Xgrid distributed computing cluster from Within R
xgrid.run.JAGSfile | Run a JAGS Model using an Apple Xgrid distributed computing cluster from Within R
xgrid.run.jagsfile | Run a JAGS Model using an Apple Xgrid distributed computing cluster from Within R
xgrid.submit | Remote execution of user-specified R functions on Apple Xgrid distributed computing clusters
xgrid.submit.JAGS | Run a JAGS Model using an Apple Xgrid distributed computing cluster from Within R
xgrid.submit.jags | Run a JAGS Model using an Apple Xgrid distributed computing cluster from Within R
xgrid.submit.JAGSfile | Run a JAGS Model using an Apple Xgrid distributed computing cluster from Within R
xgrid.submit.jagsfile | Run a JAGS Model using an Apple Xgrid distributed computing cluster from Within R