#' @title Convert runjags posterior to list
#' @description Convert runjags posterior to named list of vectors or arrays.
#'
#' @param post list of class `runjags`. The output from a call to
#' \link[runjags]{run.jags}.
#' @param collapse.chains return array with dimension for each chain?
#'
#' @note If \code{collapse.chains = TRUE}, the last dimension of arrays will always
#' be samples from the posterior. If \code{collapse.chains = FALSE}, the last
#' dimension of arrays will be individual chains, and the one prior to that
#' will be samples from the posterior for each chain.
#'
#' @seealso
#' \link[base]{aperm} to transpose the array if necessary.
#' \link[base]{as.data.frame.table} to convert arrays to data.frames.
#'
#' @export
runjags2list <- function(post, collapse.chains = TRUE) {
if(!methods::is(post, "runjags")) stop("'post' must be of class 'runjags'")
params <- colnames(runjags::combine.mcmc(post$mcmc))
p <- sapply(post$monitor, function(p) {
p1 <- paste0("^", p, "$")
p2 <- paste0("^", p, "\\[")
grep(paste0(p1, "|", p2), params, value = TRUE)
}, simplify = FALSE)
p <- p[sapply(p, length) > 0]
post.comb <- runjags::combine.mcmc(post$mcmc, collapse.chains = F)
if(!is.list(post.comb)) post.comb <- list(post.comb)
sapply(names(p), function(x) {
dim.nums <- gsub(x, "", p[[x]])
dim.nums <- gsub("\\[|\\]", "", dim.nums)
dim.nums <- do.call(rbind, strsplit(dim.nums, ","))
dim.nums <- apply(dim.nums, 2, as.numeric)
mat <- lapply(post.comb, function(chain) {
chain <- chain[, p[[x]]]
if(length(dim.nums) == 0) {
stats::setNames(as.vector(chain), rownames(chain))
} else {
dims <- apply(dim.nums, 2, max)
arr <- array(as.vector(t(chain)), dim = c(dims, nrow(chain)))
dimnames(arr)[length(dims) + 1] <- list(rownames(chain))
arr
}
})
if(length(dim.nums) == 0) {
if(collapse.chains) unlist(mat) else do.call(cbind, mat)
} else {
iter.dim <- ncol(dim.nums) + if(collapse.chains) 1 else 2
do.call(abind::abind, c(mat, list(along = iter.dim)))
}
}, simplify = FALSE)
}
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