runjags (version 1.2.1-0)

runjags.options: Options for the runjags package

Description

Utility function to change the default options for the runjags package. Options will be used for all runjags function calls until the runjags package is unloaded. For a permanent solution, create a list named named '.runjags.options' containing the desired options in an R profile file - on loading, runjags will check to see if this object exists in the global environment and set the options automatically.

Usage

runjags.options(...)
	runjags.getOption(name)

Arguments

...

named option(s) to change - for a list of available options, see details below.

name

the name of the option to get the current value of - for a list of available options, see details below.

Value

• The current value of all available runjags options (after applying any changes specified) is returned invisibly as a named list.

Details

The following default options can be specified:

jagspath - the path to JAGS to use unless over-ridden in a function call (uses the findjags() function by default)

method - the runjags method to use unless over-ridden in a function call (default is 'rjags' if the rjags package is installed, or 'interruptible' otherwise)

tempdir - default to temporary directory unless over-ridden in a function call (default TRUE)

newwindows - use multiple windows for plots unless over-ridden in a function call (default is platform dependent)

modules - the modules to load unless over-ridden in a function call (default none)

linenumbers - display line numbers when printing runjags model, data and inits class objects unless over-ridden in a function call (default none)

factories - the factories to load unless over-ridden in a function call (default none)

inits.warning - display warning messages about initial values being not specified or re-used (set to FALSE to suppress warnings)

rng.warning - display warning messages relating to pseudo-random number generation for parallel chains (set to FALSE to suppress warnings)

summary.warning - display a warning message if summary statistics are requested for a small number of samples (and a few other similar situations)

blockcombine.warning - display a warning message if multiple data or inits blocks are combined in a WinBUGS style model file

silent.jags - suppress output of JAGS (or rjags) when updating models

silent.runjags - suppress feedback provided by the runjags functions

predraw.plots - automatically pre-calculate convergence diagnostic plots (this will save time when displaying plots at the cost of increased storage requirement for the runjags object)

See Also

run.jags,

findjags,

runjags-class

Examples

# Create a list of options in the global environment (perhaps in an
# R startup profile file) BEFORE load()ing runjags:
.runjags.options <- list(inits.warning=FALSE, rng.warning=FALSE)
# Or if it is run in a different environment:
# .runjags.options <<- list(inits.warning=FALSE, rng.warning=FALSE)

# Then load runjags and verify that the options have been set:
library('runjags')
print(runjags.options())


# Change the default option to remove all feedback provided by
# runjags and JAGS/rjags (only errors will be printed to screen):
runjags.options(silent.jags=TRUE, silent.runjags=TRUE)