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# R package rjags file R/mcarray.R
# Copyright (C) 2007-2009 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/
#
print.mcarray <- function(x, ...)
{
if (is.null(dim(x))) {
NextMethod()
}
print(summary(x, mean))
}
summary.mcarray <- function(object, FUN, ...)
{
if (is.null(dim(object))) {
NextMethod()
}
# In case it is already pooled over chains and iterations (no dimnames):
if(length(dim(object))==1 || is.null(names(dim(object)))
|| !any(c("iteration","chain") %in% names(dim(object)))){
dims <- dim(object)
attributes(object) <- NULL
dim(object) <- dims
ans <- list("stat"=object,
"drop.dims" = character(0))
class(ans) <- "summary.mcarray"
return(ans)
}
dn <- names(dim(object))
drop.dims <- dn %in% c("iteration","chain")
ans <- list("stat"=apply(object, which(!drop.dims), FUN, ...),
"drop.dims" = dim(object)[drop.dims])
class(ans) <- "summary.mcarray"
return(ans)
}
print.summary.mcarray <- function(x, ...)
{
cat("mcarray:\n")
print(x$stat,...)
if (length(x$drop.dims) > 0) {
cat("\nMarginalizing over:",
paste(paste(names(x$drop.dims), "(", x$drop.dims,")" , sep=""),
collapse=","),"\n")
}
}
make.coda.names <- function(basename, dim)
{
if (all(dim == 1)) {
return(basename)
}
else {
ll <- lapply(as.list(dim), function(n) seq(from=1, to=n))
elements <- expand.grid(ll)
elt.names <- apply(elements, 1, paste, collapse=",")
elt.names <- paste0(basename, "[", elt.names, "]")
return(elt.names)
}
}
as.mcmc.list.mcarray <- function(x, ...)
{
if (is.null(dim(x)) || is.null(names(dim(x)))) {
NextMethod()
}
xdim <- dim(x)
ndim <- length(xdim)
dn <- names(xdim)
which.iter <- which(dn=="iteration")
if (length(which.iter) != 1) {
stop("Bad iteration dimension in mcarray")
}
which.chain <- which(dn=="chain")
if (length(which.chain) > 1) {
stop("Bad chain dimension in mcarray")
}
niter <- xdim[which.iter]
if (length(which.chain) == 0) {
perm <- c((1:ndim)[-which.iter], which.iter)
y <- matrix(aperm(x, perm), nrow=niter, byrow=TRUE)
ans <- mcmc.list(mcmc(y))
}
else {
nchain <- xdim[which.chain]
ans <- vector("list",nchain)
len <- prod(xdim[-which.chain])
perm <- c((1:ndim)[-c(which.iter,which.chain)], which.iter, which.chain)
y <- aperm(x,perm)
for (i in 1:nchain) {
ans[[i]] <- mcmc(matrix(y[1:len + (i-1)*len], nrow=niter,
byrow=TRUE))
}
ans <- mcmc.list(ans)
}
# If elementnames is set this takes precedence over varname (for eventual use with new monitor types in JAGS 5):
elt.names <- NULL
if(!is.null(attr(x, 'elementnames', exact=TRUE))){
elt.names <- attr(x, 'elementnames')
if(length(elt.names) != nvar(ans)){
stop(paste0('The length of the elementnames attr (', length(elt.names), ') does not match the number of variables (', nvar(ans), ')'))
}
}
else if(!is.null(attr(x, "varname", exact=TRUE))){
elt.names <- coda.names(attr(x, "varname", exact=TRUE),
xdim[-c(which.iter, which.chain)])
}
if(!is.null(elt.names)){
### Work around bug in coda::varnames<-
for (i in 1:nchain) {
colnames(ans[[i]]) <-elt.names
}
}
return(ans)
}
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