R/bugs.log.R

In MultiBUGS/R2MultiBUGS: Running MultiBUGS from R

#' Read data from MultiBUGS logfile
#'
#' Read data such as summary statistics and DIC information from the
#' \pkg{MultiBUGS} logfile
#'
#' Returns the MultiBUGS summary statistics and DIC extracted directly from the
#' log file.
#'
#' @param file Location of the \pkg{MultiBUGS} logfile
#' @return A list with components:
#' \describe{
#' \item{stats}{A matrix containing summary statistics for each saved
#'   parameter. Comparable to the information in the element \code{summary}
#'   of a bugs object as returned by \code{\link{bugs}}}.
#' \item{DIC}{A matrix containing the DIC statistics as returned from
#'   \pkg{MultiBUGS}.}
#' }
#' @author Jouni Kerman
#' @seealso The main function that generates the log file is \code{\link{bugs}}.
#' @keywords IO file
#' @export bugs.log
bugs.log <- function(file){
  # Extracts the summary statistics from log.txt written by
  # MultiBUGS.  Jouni Kerman 2007-01-30 does essentially the
  # same thing as bugs.log() but - won't crash if DIC is not
  # there - makes fewer assumptions about the structure of the
  # matrix
  if (!file.exists(file)){
    stop("Log file", file, "does not exist")
  }
  log.txt <- readLines(file, warn = FALSE)

  extract <- function(m, line.match, skip = 0, empty.left.col = TRUE){
    start <- (skip + which(m == line.match)[1])
    if (is.na(start)){
      return(NA)
    }
    if (length(start) < 1){
      return(NA)
    }
    mx <- strsplit(m[-(1:start)], "\t")
    n.cols <- length(mx[[1]])
    if (n.cols < 1){
      return(NA)
    }
    mxlen <- sapply(mx, length)
    end <- which(mxlen != n.cols)[1] - 1
    if (!is.na(end)){
      ### if output block does not end mx
      mx <- mx[1:end]
    }
    cm <- matrix(unlist(mx), ncol = n.cols, byrow = TRUE)  # character format
    if (empty.left.col){
      cm <- cm[, -1]  # empty column
    }
    col.names <- cm[1, -1]  # first column is just 'node'
    row.names <- cm[, 1][-1]  # first row is just ''
    col.names <- gsub("[[:space:]]+", "", col.names)  # get rid of spaces
    cm <- cm[-1, -1]  # delete dimname row/columns
    m <- matrix(as.numeric(cm), nrow = nrow(cm))  # convert to numeric
    dimnames(m) <- list(row.names, col.names)
    return(m)
  }

  stats <- extract(log.txt, "Summary statistics")
  DIC <- extract(log.txt,
                 "Deviance information",
                 skip = 0,
                 empty.left.col = FALSE)
  list(stats = stats, DIC = DIC)
}