R/future_cmcc_bioclim.R

In itsdm: Isolation Forest-Based Presence-Only Species Distribution Modeling

#' @title Download future Bioclimatic indicators (BIOs) named CMCC-BioClimInd.
#' @description Parse future CMCC-BioClimInd bioclimatic indicators obtained by
#' different Earth System Models (ESMs) optionally with a setting of boundary
#' and a few other options.
#' @param bry (\code{\link{sf}} or \code{sp}) The boundary to mask the
#' downloaded original data. If \code{NULL}, it would get global map.
#' If not \code{NULL}, it can take \code{\link{sf}}, \code{\link{sfc}},
#' \code{SpatialPolygonsDataFrame}, \code{SpatialPolygons}, etc.
#' The default is \code{NULL}.
#' @param path (\code{character}) The path to save the downloaded imagery.
#' If \code{NULL}, it would use the current working directory.
#' The default is \code{NULL}.
#' @param esm (\code{character}) The option for Earth System Models (ESMs).
#' Should be one of "CMCC-CESM", 'GFDL-ESM2M', 'HadGEM2-ES',
#' 'IPSL-CM5A-LR', 'MIROC-ESM-CHEM', 'NorESM1-M'.
#' The default is CMCC-CESM.
#' @param rcp (\code{numeric}) The option of Representative Concentration
#' Pathways (RCPs).
#' Should be 45 or 85. Only 85 is available for CMCC-CESM. The default is 85.
#' @param interval (\code{character}) The option for time interval.
#' Should be one of "2040-2079", "2060-2099". The default is "2040-2079".
#' @param nm_mark (\code{character}) the name mark of clipped images.
#' The default is "clip". It would be ignored if \code{bry} is \code{NULL}.
#' @param return_stack (\code{logical}) if \code{TRUE}, stack the imagery
#' together and return.
#' If the area is large and resolution is high, it is better not to stack them.
#' The default is \code{TRUE}.
#' @return if \code{return_stack} is \code{TRUE}, the images would be
#' returned as a \code{stars}. Otherwise, nothing to return, but the user
#' would receive a message of where the images are.
#' @references
#' Noce, Sergio, Luca
#' Caporaso, and Monia Santini."A new global dataset of bioclimatic indicators.
#' "\emph{Scientific data} 7.1 (2020): 1-12.\doi{10.1038/s41597-020-00726-5}
#'
#' @details
#' \url{https://doi.pangaea.de/10.1594/PANGAEA.904278?format=html#download}
#'
#' @note The function is experimental at the moment, because the download server
#' of this dataset is not as stable as Worldclim yet. If it fails due to slow
#' internet, try to set a larger timeout option,
#' e.g., using `options(timeout = 1e3)`.
#'
#' @import ncdf4
#' @importFrom raster stack
#' @importFrom sf st_as_sf st_make_valid st_crop
#' @importFrom stars read_stars write_stars st_as_stars st_set_dimensions
#' @importFrom utils tail download.file
#' @importFrom methods is
#' @export
#' @examples
#' \dontrun{
#' library(itsdm)
#' future_cmcc_bioclim(path = tempdir(),
#'   esm = 'GFDL-ESM2M', rcp = 45,
#'   interval = "2040-2079", return_stack = FALSE)
#'}
#'
future_cmcc_bioclim <- function(bry = NULL,
                                path = NULL,
                                esm = 'CMCC-CESM',
                                rcp = 85,
                                interval = "2040-2079",
                                nm_mark = "clip",
                                return_stack = TRUE) {
    # Check the inputs
    stopifnot(esm %in% c("CMCC-CESM", 'GFDL-ESM2M', 'HadGEM2-ES',
                         'IPSL-CM5A-LR', 'MIROC-ESM-CHEM', 'NorESM1-M'))
    stopifnot(rcp %in% c(45, 85))
    if(esm == "CMCC-CESM" & rcp == 45){
        stop("There is no such var to download.")}
    stopifnot(interval %in% c("2040-2079", "2060-2099"))
    ## bry
    if (is.null(bry)) {
        nm_mark <- 'global'
        message("No bry set, download global map.")
    } else {
        if (!(is(bry, "sf") | is(bry, 'sfc') |
              is(bry, "SpatialPolygonsDataFrame") |
              is(bry, 'SpatialPolygons'))) {
            stop("Only support sf or sp.")
        }
    }
    ## path
    if (is.null(path)) {
        path <- getwd()
    } else {
        if (!dir.exists(path)) {
            stop("Path does not exist!")
        }
    }

    # Set up
    ## Convert inputs
    esm <- switch(esm,
                  `CMCC-CESM` = "CMCC",
                  `GFDL-ESM2M` = "GFDL",
                  `HadGEM2-ES` = "HADGEM",
                  `IPSL-CM5A-LR` = 'IPSL',
                  `MIROC-ESM-CHEM` = 'MIROC',
                  `NorESM1-M` = 'NORESM')
    interval <- switch(interval,
                       `2040-2079` = '2040_79',
                       `2060-2099` = '2060_99')

    ## Path
    path <- file.path(path, "cmcc_bioclim")
    dir.create(path, showWarnings = FALSE)

    # Download and extract historical variables
    url_base <- "https://hs.pangaea.de/model/NoceS-etal_2019"
    invisible(lapply(paste0('BIO', 1:35), function(var){
        if (!file.exists(
            sprintf("%s/%s_%s_%s_%s.nc",
                    path, var, esm, rcp, interval))){
            zip_name <- sprintf("%s.zip", var)
            url <- file.path(url_base, zip_name)

            # Download to local
            temp <- tempfile()
            dl <- try(download.file(url, temp))
            if (inherits(dl, "try-error")) {
              Sys.sleep(10)
              download.file(url, temp)
            }

            # Extract hist file from downloaded zip
            decompression <- system2(
                "unzip",
                args = c("-j", "-o", temp,
                         sprintf("%s_%s_%s_%s.nc",
                                 var, esm, rcp, interval),
                         sprintf("-d %s", path)),
                stdout = TRUE)
            if (grepl("Warning message", tail(decompression, 1))) {
                print(decompression)
            }
            unlink(temp)
        }
    }))

    ####################################################
    ############## Deal with BIO18 #####################
    imgs_in <- list.files(path, pattern = "*.nc", full.names = T)
    imgs <- file.path(
      path, sprintf("BIO%s_%s_%s_%s.nc", 1:35, esm, rcp, interval))
    if (any(c('BIO18_CMCC_85_2040_79.nc',
              'BIO18_GFDL_45_2040_79.nc',
              'BIO18_GFDL_45_2060_99.nc',
              'BIO18_GFDL_85_2040_79.nc',
              'BIO18_GFDL_85_2060_99.nc',
              'BIO18_HADGEM_85_2060_99.nc') %in%
            basename(imgs))) {
      warning('BIO18 does not have such product, skip it.')

      # Remove it and check
      imgs <- file.path(
        path, sprintf("BIO%s_%s_%s_%s.nc", c(1:17, 19:35),
                      esm, rcp, interval))
      if (length(intersect(imgs, imgs_in)) != 34) {
        stop("Wrong file numbers unzipped.")}

      # Read imgs
      clip_imgs <- stack(imgs) %>% st_as_stars()
      clip_imgs <- st_set_dimensions(
        clip_imgs, 'band', values = paste0('bio', c(1:17, 19:35)))
    } else {
      if (length(intersect(imgs, imgs_in)) != 35) {
        stop("Wrong file numbers unzipped.")}

      # Read files
      clip_imgs <- stack(imgs) %>% st_as_stars()
      clip_imgs <- st_set_dimensions(
        clip_imgs, 'band', values = paste0('bio', 1:35))
    }
    ####################################################

    ####################################################
    ################ Original code #####################
    # ## Check unzipped files
    # imgs_in <- list.files(path, pattern = "*.nc", full.names = T)
    # imgs <- file.path(
    #   path, sprintf("BIO%s_%s_%s_%s.nc", 1:35, esm, rcp, interval))
    #
    # if (length(intersect(imgs, imgs_in)) != 35) {
    #   stop("Wrong file numbers unzipped.")}
    #
    # # Read files
    # clip_imgs <- stack(imgs) %>% st_as_stars()
    # clip_imgs <- st_set_dimensions(
    #   clip_imgs, 'band', values = paste0('bio', 1:35))
    ####################################################

    names(clip_imgs) <- sprintf('bioclim_%s_%s_%s',
                                esm, rcp, interval)
    if (!is.null(bry)) {
        # Read files
        bry <- st_as_sf(bry) %>% st_make_valid()
        clip_imgs <- st_crop(clip_imgs, bry)
    }

    ## Save out
    rst_name <- paste(nm_mark,
                      sprintf('bioclim_%s_%s_%s.tif', esm, rcp, interval),
                      sep = '_')
    rst_path <- file.path(path, rst_name)
    write_stars(clip_imgs, rst_path)

    # Clean temporary files
    unlink(imgs)

    # Return
    if (return_stack == TRUE) {
        clip_imgs
    } else {
      message(sprintf("Files are written to %s.", path))
    }
}

# future_cmcc_bioclim end