'S-PLUS'

"bugs.sims" <-
function (parameters.to.save, n.chains, n.iter, n.burnin, n.thin, DIC=TRUE)
{
  ## Read the simulations from Bugs into R, format them, and monitor convergence
  sims.files <- paste ("coda", 1:n.chains, ".txt", sep="")
  ## read in the names of the parameters and the indices of their samples
  index <- read.table("codaIndex.txt", header = FALSE, sep = "\t")
  ## in Splus, read.table interprets the first row of the file as row names,
  ## while in R it does not
  if(is.R()) {
      parameter.names <- as.vector(index[, 1])
      n.keep <- index[1, 3] - index[1, 2] + 1
  }
  else {
      parameter.names <- row.names(index)
      n.keep <- index[1, 2] - index[1, 1] + 1
  }
  n.parameters <- length(parameter.names)
  n.sims <- n.keep*n.chains
  sims <- matrix( , 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 1: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)
  ##SS, UL##: Let's optimize the following loops ...
  for (j in 1:n.roots) {
    long.short[[j]] <- (1: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 1: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 1:length.short[j])
        indexes.short[[j]][[k]] <- indexes.long[[long.short[[j]][k]]]
    }
  }
#  rank.long <- rank(paste(rep(root.short,length.short),
#    (1:n.parameters)/10^ceiling(log10(n.parameters)),sep="."))
  rank.long <- unlist(long.short)

  for (i in 1:n.chains){
    if(is.R()) {
      sims.i <- scan(sims.files[i], quiet = TRUE)[2 * (1:(n.keep * n.parameters))]
    } else {
      sims.i <- scan(sims.files[i])[2 * (1:(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)
#
#  Perform convergence checks and compute medians and quantiles.
#
  summary <- monitor (sims.array, n.chains, keep.all=TRUE)
#
#  Create outputs
#
  last.values <- as.list (numeric(n.chains))
  for (i in 1:n.chains){
    n.roots.0 <- if(DIC) n.roots-1 else 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]    # scramble (for convenience in analysis)
  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 1: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)
  if(DIC) {
     ## Read DIC from BUGS log
     LOG <- bugs.log("log.txt")$DIC
     if(any(is.na(LOG))) { ## Something went wrong --> Use Gelman's tweak
        deviance <- all$sims.array[, , dim(sims.array)[3], drop = FALSE]
        if(!is.R()) dimnames(deviance) <- NULL
        dim(deviance) <- dim(deviance)[1:2]
        pD <- numeric(n.chains)
        DIC <- numeric(n.chains)
        for (i in 1:n.chains) {
            pD[i] <- var(deviance[, i])/2
            DIC[i] <- mean(deviance[, i]) + pD[i]
        }
        all <- c(all, list(isDIC=TRUE, DICbyR=TRUE,
                           pD=mean(pD), DIC=mean(DIC)))
      } else { ## Use BUGS calculation of DIC
        all <- c(all, list(isDIC=TRUE, DICbyR=FALSE,
                           pD=LOG[nrow(LOG),3], DIC=LOG[nrow(LOG),4]))
      }
  } else {
    all <- c(all, isDIC=FALSE)
  }
  all
}

if(!is.R()) .subset <- function(x, index) x[index]