R/set_args.R

In trashbirdecology/dubcorms: Unifying BBS and eBird Data for Integrating Modeling

#' Specify Arguments and Directories
#'
#' Function to specify arugments and create/point to directories based on those arguments.
#' @importFrom stringr str_replace
#' @noRd
set_args <- function(# general args
  dir.orig.data,
  dir.proj,
  species,
  species.abbr,
  states = NULL,
  countries = NULL,
  year.range = 2008:2019,
  crs.target = 4326,
  get.sunlight = FALSE,
  base.julian.date = (paste0(min(year.range), c("-01-01"))),
  #GRID: arguments for creating spatial sampling grid
  grid.size = 1.00,
  hexagonal = TRUE,
  overwrite.grid = FALSE,
  #BBS: arguments for filtering, downloading, and munging BBS data specifcally
  usgs.layer          = "US_BBS_Route-Paths-Snapshot_Taken-Feb-2020",
  cws.layer           = "ALL_ROUTES",
  overwrite.bbs       = FALSE,
  #EBIRD: arguments for filtering and munging the eBird data specifically
  overwrite.ebird     = FALSE,
  max.C.ebird         = 100,
  remove.bbs.obs      = TRUE,
  max.effort.km       = 5,
  max.num.observers   = 10,
  max.effort.mins     = 180,
  complete.checklists.only = TRUE,
  ebird.protocol      = c("Traveling", "Stationary"),
  min.yday            = 91,
  max.yday            = 245,
  mmyyyy              = "nov-2021",
  #JAGS: arguments for customizing the resulting JAGS data list
  overwrite.jdat      = FALSE,
  jagam.args          = list(
    bs = "ds",
    k = 20,
    family = "poisson",
    sp.prior = "log.uniform",
    diagonalize = TRUE
  ),
  scale.vars          = TRUE) {
  ## check args
  temp = c(
    "complete.checklists.only",
    "scale.vars",
    'overwrite.ebird',
    "remove.bbs.obs" ,
    "overwrite.bbs",
    "hexagonal",
    "get.sunlight"
  )

  for (i in seq_along(temp)) {
    stopifnot(is.logical(eval(parse(text = temp[i]))),
              msg = paste("argument ", temp[i], "must be a logical."))
  }


  temp = c(
    "min.yday",
    "max.yday",
    "max.effort.km",
    "max.effort.mins",
    "max.C.ebird",
    "grid.size",
    "crs.target",
    "year.range"
  )

  for (i in seq_along(temp)) {
    stopifnot(
      class(eval(parse(text = temp[i]))) %in% c("integer", "numeric"),
      msg = paste("argument ", temp[i], "must be a logical.")
    )
  }
  rm(temp)

  ## munge the states and countries indexes for use in dir/proj dir reation
  if (!exists("states"))
    states <- NULL
  if (!is.null(states)) {
    regions <- states
  } else{
    regions <- countries
  }

  ## proj.shorthand: this will make all directories within a new dir in dir.proj. this is useful for iterating over species/time/space and saving all resulting information in those directories.
  subdir.proj <-
    proj.shorthand(species.abbr, regions, grid.size, year.range, max.C.ebird)
  if (nchar(subdir.proj) > 100) {
    cat("subdir.proj is very long. specifing a new name for project.")
    subdir.proj = "myproject"
  }
  dirs        <-
    dir_spec(dir.orig.data, dir.proj, subdir.proj) # create and/or specify directories for later use.

  # ensure all directories exist
  suppressWarnings(stopifnot(all(lapply(dirs, dir.exists))))


  # bundle all arguments
  args <-
    c(
      ##directories
      "dirs$dir.proj",
      "dirs$dir.jags",
      "dirs$dir.plots",
      "dirs$dir.models",
      "dirs$dir.bbs.out",
      "dirs$dir.ebird.out",
      "dirs$dir.spatial.out",
      "dirs$dir.ebird.in",
      "dirs$cws.routes.dir",
      "dirs$usgs.routes.dir",
      ##others
      "species",
      "species.abbr",
      "states",
      "countries",
      "year.range",
      "crs.target",
      "get.sunlight",
      "base.julian.date",
      "grid.size",
      "hexagonal",
      "overwrite.grid",
      "usgs.layer",
      "cws.layer",
      "overwrite.bbs",
      "overwrite.ebird",
      "max.C.ebird",
      "remove.bbs.obs",
      "max.effort.km",
      "max.num.observers",
      "max.effort.mins",
      "complete.checklists.only",
      "ebird.protocol",
      "min.yday",
      "max.yday",
      "mmyyyy",
      "overwrite.jdat",
      "jagam.args",
      "scale.vars"
    )

  ## create the list of ebird elements
  list.out <- NULL
  for (z in seq_along(args)) {
    new = eval(parse(text = args[z]))# this is necessary for some reason idk why
    list.out[[args[z]]] <- new
  }
  ## list names
  names = NULL
  for (i in seq_along(args)) {
    names[i] <-
      stringr::str_replace(args[i], pattern = "dirs\\$", replacement = "")
  }

  names(list.out) <- names
  # create an output
  return(list.out)
}