Usage
bugs.script(parameters.to.save, n.chains, n.iter, n.burnin, n.thin, saveExec, restart, model.file.bug, model.file, debug=FALSE, is.inits, DIC=FALSE, useWINE=FALSE, newWINE=TRUE, WINEPATH=NULL, bugs.seed=NULL, summary.only=FALSE, save.history=(.Platform$OS.type == "windows" | useWINE==TRUE), bugs.data.file, bugs.inits.files, over.relax = FALSE)
Arguments
parameters.to.save
parameters that should be monitored
n.chains
number of Markov chains
n.iter
number of total iterations (including burn in)
n.burnin
length of burn in
saveExec
If TRUE, a re-startable image of the OpenBUGS execution is
saved with basename(model.file) and extension .bug in the working
directory, which must be specified. The .bug files can be large, so
users should monitor them carefully and remove them when not needed.
restart
If TRUE, execution resumes with the final status from
the previous execution stored in the .bug file in the working directory.
If n.burnin=0,additional iterations are performed and all iterations since
the previous burnin are used (including those from past executions). If
n.burnin>0, a new burnin is performed, and the previous iterations are
discarded, but execution continues from the status at the end of the previous
execution. When restart=TRUE, only n.burnin, n.iter,
and saveExec inputs
should be changed from the call creating the .bug file, otherwise
failed or erratic results may be produced.
model.file.bug
If saveExec or restart is TRUE, then model.file.bug
receives/contains the OpenBUGS program image for restarting the program.
model.file.bug is the name of the file with its full path
model.file
file containing the model written in OpenBUGS code
debug
if FALSE, OpenBUGS is closed automatically,
otherwise OpenBUGS remains open for further investigation. With
debug = TRUE, no modelQuit() command is added to the
end of the script, which can cause an infinite loop with linux
execution.
is.inits
logical; whether initial values are given by the user
(TRUE) or have to be generated by OpenBUGS
DIC
logical; if TRUE, compute deviance, pD, and DIC
automatically in OpenBUGS
bugs.seed
random seed for OpenBUGS (default is no seed specified)
summary.only
If TRUE, only a parameter summary for very quick analyses is given,
temporary created files are not removed in that case.
save.history
If TRUE (the default), trace plots are generated at the end.
bugs.data.file
character name of the data file
bugs.inits.files
character vector of names of the inits files
over.relax
If TRUE, over-relaxed form of MCMC is used if available from OpenBUGS.