R/utils.R

In atlantistools: Process and Visualise Output from Atlantis Models

# This function is used to debug the NS model.
# Health care warning: Heavy use of the assign function...
# Variables are created in the GlobalEnvironment...
# debug_ns <- function() {
#   d <- "z:/Atlantis_models/Runs/dummy_01_ATLANTIS_NS/"
#   assign("dir", d, envir = .GlobalEnv)
#   assign("fgs", "functionalGroups.csv", envir = .GlobalEnv)
#   assign("nc", "outputNorthSea.nc", envir = .GlobalEnv)
#   assign("nc_gen", "outputNorthSea.nc", envir = .GlobalEnv)
#   assign("nc_prod", "outputNorthSeaPROD.nc", envir = .GlobalEnv)
#   assign("dietcheck", "outputNorthSeaDietCheck.txt", envir = .GlobalEnv)
#   assign("yoy", "outputNorthSeaYOY.txt", envir = .GlobalEnv)
#   assign("ssb", "outputNorthSeaSSB.txt", envir = .GlobalEnv)
#   assign("specmort", "outputNorthSeaSpecificMort.txt", envir = .GlobalEnv)
#   assign("specpredmort", "outputNorthSeaSpecificPredMort.txt", envir = .GlobalEnv)
#   assign("prm_biol", "NorthSea_biol_fishing.prm", envir = .GlobalEnv)
#   assign("prm_run", "NorthSea_run_fishing_F.prm", envir = .GlobalEnv)
#   assign("bps", load_bps(dir = d, fgs = "functionalGroups.csv", init = "init_NorthSea.nc"), envir = .GlobalEnv)
#   assign("fgs", "functionalGroups.csv", envir = .GlobalEnv)
#   assign("select_groups", get_groups(dir = d, fgs = "functionalGroups.csv"), envir = .GlobalEnv)
#   assign("bboxes", get_boundary(load_box(dir = d, bgm = "NorthSea.bgm")), envir = .GlobalEnv)
#   assign("out", "preprocess-north-sea.rda", envir = .GlobalEnv)
#   assign("save_to_disc", FALSE, envir = .GlobalEnv)
#   assign("check_acronyms", TRUE, envir = .GlobalEnv)
#   assign("report", TRUE, envir = .GlobalEnv)
#   assign("warn_zeros", TRUE, envir = .GlobalEnv)
# }

# split dataframe in list of dataframe based on multiple (or a single) column.
multisplit <- function(df, groups) {
  for (i in seq_along(groups)) {
    # first split results in a list of dataframes!
    if (i == 1) result <- split(df, df[, groups[i]])
    # sucessive splits work with a list of dataframes.
    if (i > 1) {
      result <- purrr::map(result, function(x) split(x, x[, groups[i]]))
      # remove one dimension of the list to allow for the next split to work.
      result <- purrr::flatten(result)
    }
  }
  return(result)
}

# This function is not used anymore.
file_ending <- function(filename, ending = "nc") {
  file_ending <- strsplit(filename, "\\.")[[1]][length(strsplit(filename, "\\.")[[1]])]
  if (file_ending != ending) stop(paste("The file", filename, "does not end in", ending))
}


release_questions <- function() {
  c(
    "Have you updated the version number",
    "Have you updated the vignettes and the index from the local package installation?",
    "Have you run devtools::release(args = '--compact-vignettes=both')",
    "Have you checked the vignette size after devtools::build(args = '--compact-vignettes=both')",
    "Have you updated cran-comments.md?",
    "Have you run devtools::build_win(args = '--compact-vignettes=both') to check with win-builder?"
  )
}


# dir <- "C:/Users/alexanderke/Dropbox/Atlantis_SoS_Files_Alex"
# setwd(dir)
# nomeNc <- "output/out_newfleet9"
#
# nc_gen <- paste(nomeNc,".nc",sep="")
# nc_prod <- paste(nomeNc,"PROD.nc",sep="")
# dietcheck <- paste(nomeNc,"DietCheck.txt",sep="")
# yoy <- paste(nomeNc,"YOY.txt",sep="")
# ssb <- paste(nomeNc,"SSB.txt",sep="")
# specmort <- paste(nomeNc,"SpecificMort.txt",sep="")
# predspecmort <-paste(nomeNc,"SpecificPredMort.txt",sep="")
# version_flag <- 1
#
# prm_run <- "Sic_run_fishing_F_gape100_65yr.prm"
# prm_biol <- "Sic_biol_newfleet21.prm"
# fgs <- "newFGHorMigr.csv"
# bgm <- "geometry.bgm"
# init <- "inSic26042017.nc"
#
# bboxes <- get_boundary(boxinfo = load_box(bgm))
# bps <- load_bps(fgs, init)
# bio_conv <- get_conv_mgnbiot(prm_biol)
#
# groups <- get_groups(fgs)
# groups_age <- get_age_groups(fgs)
#
# load_nc(nc = nc_gen, bps = bps, select_groups = groups_age[1:5], select_variable = "ResN", fgs = fgs, prm_run = prm_run, bboxes = bboxes)
#
# nc = nc_gen
# select_groups = groups_age[1:5]
# select_variable = "ResN"
#
# agemat <- prm_to_df(prm_biol,  fgs, group = get_age_acronyms(fgs), "age_mat")