bugs.sims <- function(parameters.to.save, n.chains, n.iter, n.burnin,
n.thin, error.ch, program = "winbugs") {
if (length(error.ch) == 0) {
real.chains <- seq_len(n.chains)
} else {
if (length(error.ch) == n.chains) {
stop("No chain ran properly.")
}
real.chains <- seq_len(n.chains)[-error.ch]
n.chains <- n.chains - length(error.ch)
}
if (program == "winbugs") {
coda.names <- c("coda", "codaIndex.txt")
} else {
coda.names <- c("CODAchain", "CODAindex.txt")
}
sims.files <- paste0(coda.names[1], real.chains, ".txt")
index <- data.table::fread(
file = coda.names[2],
header = FALSE,
sep = "\t",
stringsAsFactors = FALSE
)
parameter.names <- index[[1]]
n.keep <- as.numeric(index[1, 3] - index[1, 2] + 1)
n.parameters <- length(parameter.names)
n.sims <- n.keep * n.chains
sims <- matrix(NA, n.sims, n.parameters)
sims.array <- array(NA, c(n.keep, n.chains, n.parameters))
root.long <- character(n.parameters)
indexes.long <- vector(n.parameters, mode = "list")
for (i in seq_len(n.parameters)) {
temp <- decode.parameter.name(parameter.names[i])
root.long[i] <- temp$root
indexes.long[[i]] <- temp$indexes
}
n.roots <- length(parameters.to.save)
left.bracket.short <- as.vector(regexpr("[[]", parameters.to.save))
right.bracket.short <- as.vector(regexpr("[]]", parameters.to.save))
root.short <- ifelse(left.bracket.short == -1, parameters.to.save,
substring(parameters.to.save, 1, left.bracket.short - 1))
dimension.short <- rep(0, n.roots)
indexes.short <- vector(n.roots, mode = "list")
n.indexes.short <- vector(n.roots, mode = "list")
long.short <- vector(n.roots, mode = "list")
length.short <- numeric(n.roots)
for (j in seq_len(n.roots)) {
long.short[[j]] <- (seq_len(n.parameters))[root.long == root.short[j]]
length.short[j] <- length(long.short[[j]])
if (length.short[j] == 0)
stop(paste("parameter", root.short[[j]], "is not in the model"))
else if (length.short[j] > 1) {
dimension.short[j] <- length(indexes.long[[long.short[[j]][1]]])
n.indexes.short[[j]] <- numeric(dimension.short[j])
for (k in seq_len(dimension.short[j]))
n.indexes.short[[j]][k] <- length(
unique(unlist(lapply(indexes.long[long.short[[j]]], .subset, k)))
)
length.short[j] <- prod(n.indexes.short[[j]])
indexes.short[[j]] <- as.list(numeric(length.short[j]))
for (k in seq_len(length.short[j]))
indexes.short[[j]][[k]] <- indexes.long[[long.short[[j]][k]]]
}
}
rank.long <- unlist(long.short)
for (i in seq_len(n.chains)) {
sims.i <- data.table::fread(
file = sims.files[i],
header = FALSE,
sep = "\t",
stringsAsFactors = FALSE
)[[2]][seq_len(n.keep * n.parameters)]
sims[(n.keep * (i - 1) + 1):(n.keep * i), ] <- sims.i
sims.array[, i, ] <- sims.i
}
dimnames(sims) <- list(NULL, parameter.names)
dimnames(sims.array) <- list(NULL, NULL, parameter.names)
summary <- R2WinBUGS::monitor(sims.array, n.chains, keep.all = TRUE)
last.values <- as.list(numeric(n.chains))
for (i in seq_len(n.chains)) {
n.roots.0 <- n.roots
last.values[[i]] <- as.list(numeric(n.roots.0))
names(last.values[[i]]) <- root.short[1:n.roots.0]
for (j in 1:n.roots.0) {
if (dimension.short[j] <= 1) {
last.values[[i]][[j]] <- sims.array[n.keep, i, long.short[[j]]]
names(last.values[[i]][[j]]) <- NULL
}
else last.values[[i]][[j]] <- aperm(
array(sims.array[n.keep, i, long.short[[j]]], rev(n.indexes.short[[j]])),
dimension.short[j]:1
)
}
}
# sims <- sims[sample(n.sims), , drop = FALSE]
sims.list <- summary.mean <- summary.sd <- summary.median <- vector(n.roots, mode = "list")
names(sims.list) <- names(summary.mean) <- names(summary.sd) <- names(summary.median) <- root.short
for (j in seq_len(n.roots)) {
if (length.short[j] == 1) {
sims.list[[j]] <- sims[, long.short[[j]]]
summary.mean[[j]] <- summary[long.short[[j]], "mean"]
summary.sd[[j]] <- summary[long.short[[j]], "sd"]
summary.median[[j]] <- summary[long.short[[j]], "50%"]
} else {
temp2 <- dimension.short[j]:1
sims.list[[j]] <- aperm(
array(sims[, long.short[[j]]], c(n.sims, rev(n.indexes.short[[j]]))),
c(1, (dimension.short[j] + 1):2)
)
summary.mean[[j]] <- aperm(
array(summary[long.short[[j]], "mean"], rev(n.indexes.short[[j]])),
temp2
)
summary.sd[[j]] <- aperm(
array(summary[long.short[[j]], "sd"], rev(n.indexes.short[[j]])),
temp2
)
summary.median[[j]] <- aperm(
array(summary[long.short[[j]], "50%"], rev(n.indexes.short[[j]])),
temp2
)
}
}
summary <- summary[rank.long, ]
all <- list(n.chains = n.chains, n.iter = n.iter, n.burnin = n.burnin,
n.thin = n.thin, n.keep = n.keep, n.sims = n.sims,
sims.array = sims.array[, , rank.long, drop = FALSE], sims.list = sims.list,
sims.matrix = sims[, rank.long], summary = summary, mean = summary.mean,
sd = summary.sd, median = summary.median, root.short = root.short,
long.short = long.short, dimension.short = dimension.short,
indexes.short = indexes.short, last.values = last.values)
all <- c(all, isDIC = FALSE)
return(all)
}
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