R/experiment.env_setup.R

In qBioTurin/epimod: Epidemiological modelling (epimod)

#' @title Sets up the environment (directory and files) required to run a simulartion
#' @description This is an internal function creating the required structure of files and directiry to run a simulation.
#' @param id, a numeric identifier used to format the output's file name (optional, if not provided copy files in dest_dir. Otherwise, create a sub-directory id)
#' @param confg, configuration provided by the function experiment.configurations
#' @author Beccuti Marco, Castagno Paolo, Pernice Simone

#' @export
#' @examples
#'\dontrun{
#' experiment.env_cleanup(id=1, run_dir="/run/directory", out_fname="simulation", out_dir="/out/directory",)
#' }

experiment.env_setup <- function(id = NULL,
																 files,
																 dest_dir,
																 config = NULL)
{
	print("[experiment.env_setup] Setting up environment")
	# Set the directory
	if(!is.null(id))
		dest_dir <- paste0(dest_dir, id)
	# Create the directory
	#if(file.exists(dest_dir))
	#{
	#    unlink(dest_dir, recursive = TRUE)
	#}
	dir.create(dest_dir, recursive = TRUE, showWarnings = FALSE)
	# Copy files in the new directory
	lapply(files,function(x){
		lapply(x,
					 function(x1)
					 	file.copy(from = x1, to = dest_dir,overwrite = T)
		)
	})
	w_dir <- getwd()
	setwd(dest_dir)
	if(!is.null(id) && !is.null(config))
		# Write configurations files to the run_directory
		lapply(c(1:length(config)),function(x){
			if(length(config[[x]]) > 1)
				idx <- id
			else
				idx <- 1
			# Check how to handle the parameter
			# if(config[[x]][[idx]][[2]] > 0)
			if(config[[x]][[idx]][[2]] %in% c("i", "g"))
			{
				print(paste0("[experiment.env_setup] Creating file for parameter ",config[[x]][[idx]][[1]], "(", config[[x]][[idx]][[1]],")"))
				# Write the (set of) parameter(s) to file
				write.table(x = config[[x]][[idx]][[3]],
										file = config[[x]][[idx]][[1]],
										col.names = FALSE,
										row.names = FALSE,
										sep = ",")
			}
			else
			{
				if(config[[x]][[idx]][[2]] == "c")
				{
					print(paste0("[experiment.env_setup] Adding parameter to transitions' file ",config[[x]][[idx]][[1]], "(", config[[x]][[idx]][[1]],")"))
					# Write single parameter to file (cmdln_params) using the format
					# <parameter name> <parameter value>
					write.table(x = paste(config[[x]][[idx]][[1]],
																config[[x]][[idx]][[3]]),
											file="cmdln_exp",
											append = TRUE,
											quote = FALSE,
											row.names = FALSE,
											col.names = FALSE)
				} else {
					# Write single parameter to file (cmdln_params) using the format
					# <parameter name> <parameter value>
					print(paste0("[experiment.env_setup] Adding parameter to places' file ",config[[x]][[idx]][[1]], "(", config[[x]][[idx]][[1]],")"))
					write.table(x = paste(config[[x]][[idx]][[1]],
																config[[x]][[idx]][[3]]),
											file="cmdln_mrk",
											append = TRUE,
											quote = FALSE,
											row.names = FALSE,
											col.names = FALSE)
				}
			}
		})
	setwd(w_dir)
	print("[experiment.env_setup] Done setting up environment")
}