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jags.object.R    90 lines (77 with data), 2.7 kB

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update.jags <- function(object, n.iter = 1, by, progress.bar, ...)
{
if (!is.numeric(n.iter) || n.iter < 1) {
stop("Invalid n.iter")
}
if ("update" %in% names(object)) {
## Old-style jags.model object
## The progress bar was created by the object$update() function
if (missing(by))
by <- floor(n.iter/50)
object$update(n.iter, by)
}
else {
## New jags.model object (in version 1.0.3-6)
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$iter()
end.iter <- start.iter + n.iter
pb <- switch(progress.bar,
"text" = txtProgressBar(start.iter, end.iter,
initial = start.iter, style=3, width=50,
char=ifelse(adapting,"+","*")),
"gui" = updatePB(start.iter, end.iter, adapting))
}
## Set refresh frequency for progress bar
if (missing(by) || by <= 0) {
by <- min(ceiling(n.iter/50), 100)
}
else {
by <- ceiling(by)
}
## Do updates
n <- n.iter
while (n > 0) {
.Call("update", object$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, ...)
{
if(.Call("is_adapting", object$ptr(), PACKAGE="rjags")) {
update(object, n.iter, ...)
if (!.Call("adapt_off", object$ptr(), PACKAGE="rjags")) {
warning("Adaptation incomplete. Recreate the model with a longer adaptive phase.")
}
}
invisible(NULL)
}
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")
}