R/mcsim.R

In nanhung/RMCSim: R Interface to GNU MCSim

#' Conduct MCSim in simulation
#'
#' The function needs both MCSim model and input files to conduct the simulation.
#'
#' @param model a string giving the name of the MCSim model file.
#' @param input a string giving the name of the MCSim input file.
#' @param dir a character to set the directory of the MCSim model file.
#' @param parallel a logical value to conduct parallel computing.
#'
#' @export
mcsim <- function(model, input, dir = NULL, parallel = F, check = F){
  
  MD <- paste0(dir, "/", model)
  IP <- paste0(dir, "/", input)
  
  if (file.exists(MD) == F) stop("'", model, "' is not exist.")
  if (file.exists(IP) == F) stop("'", input, "' is not exist.")
  
  
  
  exc = paste0("mcsim.", model, ".exe")
  if (file.exists(exc) == F) {
    makemcsim(model, dir = dir)
    if (file.exists(exc) == F) stop("Can not create '", exc, "'.")
  }
  
  tx  <- readLines(paste0(dir, "/", input))
  MCMC_line <- grep("MCMC \\(", x=tx)
  #MonteCarlo_line <- grep("MonteCarlo \\(", x=tx)
  #SetPoints_line <- grep("SetPoints \\(", x=tx)
  
  if (length(MCMC_line) != 0){
    RandomSeed <- sample(1111:9999, 1)
    tx2 <- gsub(pattern = "10101010", replacement = paste(RandomSeed), x = tx)
  }
  
  if (parallel == T){
    
    i <- RandomSeed
    name <- gsub("\\..*", "", input)
    mcmc_input <- paste0(name, "_", i, ".in")
    mcmc_output <- paste0(name, "_", i, ".out")
    tx3 <- gsub(pattern = "MCMC.default.out", replacement = mcmc_output, x = tx2)
    writeLines(tx3, con = mcmc_input)
    
    message(paste0("\nExecute:", " ./mcsim.", model, ".exe ", dir, "/", input))
    system(paste("./mcsim.", model, ".exe -i 1000 '", mcmc_input, "'", sep = ""))
    
    if (check == T){
      checkfile <- paste0(name, "_check_", i,".out")
      
      tx4 <- gsub(pattern = ",0,", replacement = ",1,", x = tx3)
      tx5 <- gsub(pattern = paste0("\"", mcmc_output, "\",\"\""),
                  replacement = paste0("\"", checkfile, "\",\"", mcmc_output, "\""),
                  x = tx4)
      tmp <- paste0("tmp_", mcmc_input)
      writeLines(tx5, con=paste0(dir, "/", tmp))
      system(paste("./mcsim.", model, ".exe '", dir, "/", tmp, "'", sep = ""))
      file.remove(paste0(dir, "/", tmp))
      if(file.exists(checkfile))
        message(paste0("* Create '", checkfile, "' from the last iteration."))  
    }
    
  } else { # single chain
    checkfile <- "MCMC.check.out"
    tmp <- paste0("tmp_", input)
    writeLines(tx, con=paste0(dir, "/", tmp))
    
    message(paste0("\nExecute:", " ./mcsim.", model, ".exe ", dir, "/", input))
    system(paste("./mcsim.", model, ".exe '", dir, "/", tmp, "'", sep = ""))
    
    if (check == T){
      outfile <- "MCMC.default.out"
      tx2 <- gsub(pattern = ",0,", replacement = ",1,", x = tx)
      tx3 <- gsub(pattern = paste0("\"", outfile, "\",\"\""),
                  replacement = paste0("\"", checkfile, "\",\"", outfile, "\""),
                  x = tx2)
      writeLines(tx3, con=paste0(dir, "/", tmp))
      system(paste("./mcsim.", model, ".exe '", dir, "/", tmp, "'", sep = ""))
      file.remove(paste0(dir, "/", tmp))
      if(file.exists(checkfile))
        message(paste0("* Create '", checkfile, "' from the last iteration.")) 
    }
  }
}