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#' Function to combine chains
#'
#' @param x a list of MCMC chains
#' @param merge logical determines whether chains should be merged
#' @return combined chains
#'
#' @note to combine several chains to a single McmcSamplerList, see \code{\link{createMcmcSamplerList}}
#'
#' @keywords internal
combineChains <- function(x, merge = T){
if(merge == T){
temp1 = as.matrix(x[[1]])
names = colnames(temp1)
sel = seq(1, by = length(x), len = nrow(temp1) )
out = matrix(NA, nrow = length(x) * nrow(temp1), ncol = ncol(temp1))
out[sel, ] = temp1
if (length(x) > 1){
for (i in 2:length(x)){
out[sel+i-1, ] = as.matrix(x[[i]])
}
}
colnames(out) = names
} else{
out = as.matrix(x[[1]])
if (length(x) > 1){
for (i in 2:length(x)){
out = rbind(out, as.matrix(x[[i]]))
}
}
}
return(out)
}
#' Helper function to change an object to a coda mcmc class,
#'
#' @param chain mcmc Chain
#' @param start for mcmc samplers start value in the chain. For SMC samplers, start particle
#' @param end for mcmc samplers end value in the chain. For SMC samplers, end particle
#' @param thin thinning parameter
#' @return object of class coda::mcmc
#' @details Very similar to coda::mcmc but with less overhead
#' @keywords internal
makeObjectClassCodaMCMC <- function (chain, start = 1, end = numeric(0), thin = 1){
attr(chain, "mcpar") <- c(start, end, thin)
attr(chain, "class") <- "mcmc"
chain
}
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