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# R package rjags file R/jags.object.R
# Copyright (C) 2007-2011 Martyn Plummer
#
# This program is free software; you can redistribute it and/or
# modify it under the terms of the GNU General Public License version
# 2 as published by the Free Software Foundation.
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
#
# A copy of the GNU General Public License is available at
# http://www.r-project.org/Licenses/
#
update.jags <- function(object, n.iter = 1, by, progress.bar, ...)
{
if (!is.numeric(n.iter) || n.iter < 1) {
stop("Invalid n.iter")
}
adapting <- .Call("is_adapting", object$ptr(), PACKAGE="rjags")
on.exit(object$sync())
if (missing(progress.bar)) {
progress.bar <- getOption("jags.pb")
}
if (!is.null(progress.bar)) {
match.arg(progress.bar, c("text","gui","none"))
if (progress.bar=="none")
progress.bar <- NULL
}
do.pb <- interactive() && !is.null(progress.bar) && n.iter >= 100
if (do.pb) {
start.iter <- object$iter()
end.iter <- start.iter + n.iter
pb <- switch(progress.bar,
"text" = txtProgressBar(start.iter, end.iter,
initial = start.iter, style=3, width=50,
char=ifelse(adapting,"+","*")),
"gui" = updatePB(start.iter, end.iter, adapting))
}
## Set refresh frequency for progress bar
if (missing(by) || by <= 0) {
##In JAGS 3.x.y there is a memory reallocation bug when
##monitoring that slows down updates. Drop refresh
##frequency to avoid triggering memory reallocations.
##by <- min(ceiling(n.iter/50), 100)
by <- ceiling(n.iter/50)
}
else {
by <- ceiling(by)
}
## Do updates
n <- n.iter
while (n > 0) {
.Call("update", object$ptr(), min(n,by), PACKAGE="rjags")
if (do.pb) {
switch(progress.bar,
"text" = setTxtProgressBar(pb, object$iter()),
"gui" = setPB(pb, object$iter()))
}
n <- n - by
}
if (do.pb) {
close(pb)
}
invisible(NULL)
}
adapt <- function(object, n.iter, end.adaptation = FALSE, ...)
{
if(.Call("is_adapting", object$ptr(), PACKAGE="rjags")) {
update(object, n.iter, ...)
ok <- .Call("check_adaptation", object$ptr(), PACKAGE="rjags")
if (end.adaptation) {
.Call("adapt_off", object$ptr(), PACKAGE="rjags")
}
return(ok)
}
else {
return(TRUE)
}
}
coef.jags <- function(object, chain = 1, ...) {
if (!is.numeric(chain) || chain < 1 || chain > object$nchain()) {
stop("Invalid chain")
}
object$state(internal=FALSE)[[chain]]
}
variable.names.jags <- function(object, ...) {
.Call("get_variable_names", object$ptr(), PACKAGE="rjags")
}