R/copy_ss3models.r

In ss3sim: Fisheries Stock Assessment Simulation Testing with Stock Synthesis

#' Copy the operating and estimation models and create a folder
#' structure
#'
#' @param model_dir A directory containing the operating or estimation
#' model. Each folder should be named according to a scenario ID. (See
#' the vignette \code{vignette("ss3sim-vignette")} or
#' \code{\link{get_caseargs}} for details on the scenario ID format.)
#' @param iterations A numeric vector of the iterations to copy to.
#' The function will create the folders as needed.
#' @param scenarios Which scenarios to copy to. Supply a vector of
#' character elements.
#' @param type Are you copying operating or estimation models? This
#' affects whether the model folder gets named "om" or "em"
#' @author Sean Anderson, Kelli Johnson
#' @export
#' @return An invisible boolean for whether that iteration already
#' existed. A set of nested folders starting with the scenario ID, then the
#' iterations, then "om" or "em", and then the SS model files.
#'
#' @examples
#' # Locate the package data:
#' om_folder <- system.file("extdata", "models", "cod-om", package =
#'   "ss3sim")
#'
#' # Copy the operating model:
#' copy_ss3models(model_dir = om_folder, type = "om", iterations =
#'   1:3, scenarios = "D0-F0-testing")
#' # Now look at your working directory in your file system
#'
#' # Copy the estimation model with two scenario IDs:
#' copy_ss3models(model_dir = om_folder, type = "em", iterations = 1:2,
#'   scenarios = c("D1-F0-testing", "D2-F0-testing"))
#' # (Note that all the scenario argument does here is affect the
#' # folder names.)
#'
#' # Clean up:
#' unlink("D0-F0-testing", recursive = TRUE)
#' unlink("D1-F0-testing", recursive = TRUE)
#' unlink("D2-F0-testing", recursive = TRUE)

copy_ss3models <- function(model_dir, scenarios,
                           iterations = 1:100, type = c("om", "em")) {
    type <- type[1]
    if(!type %in% c("om", "em"))
        stop("The value passed to the argument type must be either om or em.")
    for(sc in scenarios) {
        for(it in iterations) {
            from <- file.path(model_dir)
            to <- file.path(sc, it)
            dir.create(to, showWarnings = FALSE, recursive = TRUE)
            if(file.exists(file.path(to, type))){
                warning(paste0(to, "/", type, " already exists. Have you already run this model? Skipping this iteration"))
                iteration_exists <- TRUE
            } else {
                file.copy(from, to, recursive = TRUE)
                orig_model_folder <- rev(strsplit(from, "/")[[1]])[1]
                file.rename(file.path(to, orig_model_folder), file.path(to, type))
                ## sanity check and rename for consistency:
                verify_input(model_dir = file.path(to, type), type = type)
                iteration_exists <- FALSE
            }
        }
    }
    return(invisible(iteration_exists))
}