R/taf.skeleton.sa.org.R

In icesTAF: Functions to Support the ICES Transparent Assessment Framework

#' TAF Skeleton
#'
#' Create initial directories and R scripts for a new TAF analysis using
#' a stock assessment created on stockassessment.org.
#'
#' @param path where to create initial directories and R scripts. The default is
#'        the current working directory.
#' @param stockname The short-form name of a stock on stockassessment.org.
#' @param force whether to overwrite existing scripts.
#'
#' @return Full path to analysis directory.
#'
#' @seealso
#' \code{\link{package.skeleton}} creates an empty template for a new R package.
#'
#' \code{\link{TAF-package}} gives an overview of the package.
#'
#' @examples
#' \dontrun{
#' taf.skeleton.sa.org(stockname = "WBCod_2021_cand01")
#' }
#'
#' @importFrom TAF draft.data taf.skeleton
#' @export

taf.skeleton.sa.org <- function(path = ".", stockname, force = FALSE) {
  taf.skeleton(path, pkgs = c("icesTAF", "stockassessment"))
  owd <- setwd(path)
  on.exit(setwd(owd))

  cat(paste0('sam_assessment <- "', stockname, '"

sam_dir <-
  paste0(
    "https://stockassessment.org/datadisk/stockassessment/userdirs/user3/",
    sam_assessment,
    "/conf/"
  )

files <- "model.cfg"

for (file in files) {
  download(paste0(sam_dir, file))
}

'),
    file = "boot/sam_config.R"
  )

  cat(paste0('sam_assessment <- "', stockname, '"

sam_dir <-
  paste0(
    "https://stockassessment.org/datadisk/stockassessment/userdirs/user3/",
    sam_assessment,
    "/data/"
  )

# read dat files from html
files <-
  gsub(
    ".*>(.+)</a>.*",
    "\\\\1",
    grep("[.]dat", readLines(sam_dir), value = TRUE)
  )

for (file in files) {
  download(paste0(sam_dir, file))
}

'),
    file = "boot/sam_data.R"
  )

  draft.data(
    data.files = NULL,
    data.scripts = c("sam_data", "sam_config"),
    originator = "stockassessment.org",
    title = c("SAM input data for ...", "SAM configuration file for ..."),
    file = TRUE,
    append = TRUE
  )

  message(
    "To run this template please ensure you have the package:\n",
    "\tstockasessment\n",
    "by running:\n",
    '\tinstall.packages("stockassessment", repos = "https://fishfollower.r-universe.dev")'
  )

  invisible(path)
}