Copernicus Digital Elevation Models (an example use case)

In this vignette I’ll explain how to use the CopernicusDEM R package based on a use case of the Movebank animal tracking data. I picked animal tracking data because there is an abundance in the Movebank archive from all over the world. In this specific vignette I’ll use data of Wolves from the northeastern Alberta and Caribou from the British Columbia (see the reference papers at the end of the vignette for more information).

The following wrapped code snippet creates the leaflet and tmap maps of this vignette, and it does the following:

files = c(system.file('vignette_data/Alberta_Wolves.csv', package = "CopernicusDEM"),
          system.file('vignette_data/Mountain_caribou.csv', package = "CopernicusDEM"))


leafgl_data = tmap_data = list()


for (FILE in files) {

  cat(glue::glue("Processing of the '{basename(FILE)}' file ..."), '\n')

  dtbl = data.table::fread(FILE, header = TRUE, stringsAsFactors = FALSE)
  cols = c('location-long', 'location-lat', 'timestamp', 'individual-local-identifier', 
           'individual-taxon-canonical-name')

  dtbl_subs = dtbl[, ..cols]
  colnames(dtbl_subs) = c('longitude', 'latitude', 'timestamp', 'individual_local_identifier',
                          'individual-taxon-canonical-name')

  leafgl_data[[unique(dtbl_subs$`individual-taxon-canonical-name`)]] = dtbl_subs

  dtbl_subs_sf = sf::st_as_sf(dtbl_subs, coords = c("longitude", "latitude"), crs = 4326)

  sf_rst_ext = fitbitViz::extend_AOI_buffer(dat_gps_tcx = dtbl_subs_sf,
                                            buffer_in_meters = 250,
                                            CRS = 4326,
                                            verbose = TRUE)

  #................................................................
  # Download the Copernicus DEM 30m elevation data because it has
  # a better resolution, it takes a bit longer to download because
  # the .tif file size is bigger
  #...............................................................

  dem_dir = tempdir()

  dem30 = CopernicusDEM::aoi_geom_save_tif_matches(sf_or_file = sf_rst_ext$sfc_obj,
                                                   dir_save_tifs = dem_dir,
                                                   resolution = 30,
                                                   crs_value = 4326,
                                                   threads = parallel::detectCores(),
                                                   verbose = TRUE)

  TIF = list.files(dem_dir, pattern = '.tif', full.names = TRUE)

  if (length(TIF) > 1) {

    #....................................................
    # create a .VRT file if I have more than 1 .tif files
    #....................................................

    file_out = file.path(dem_dir, 'VRT_mosaic_FILE.vrt')

    vrt_dem30 = CopernicusDEM::create_VRT_from_dir(dir_tifs = dem_dir,
                                                   output_path_VRT = file_out,
                                                   verbose = TRUE)
  }

  if (length(TIF) == 1) {

    #..................................................
    # if I have a single .tif file keep the first index
    #..................................................

    file_out = TIF[1]
  }

  raysh_rst = fitbitViz::crop_DEM(tif_or_vrt_dem_file = file_out,
                                  sf_buffer_obj = sf_rst_ext$sfc_obj,
                                  CRS = 4326,
                                  digits = 6,
                                  verbose = TRUE)

  # convert to character to receive the correct labels in the 'tmap' object
  dtbl_subs_sf$individual_local_identifier = as.character(dtbl_subs_sf$individual_local_identifier)

  # open with interactive viewer
  tmap::tmap_mode("view")
  
  map_coords = tmap::tm_shape(shp = dtbl_subs_sf) + 
    tmap::tm_dots(col = 'individual_local_identifier')
  
  map_coords = map_coords + tmap::tm_shape(shp = raysh_rst, is.master = FALSE, name = 'Elevation') +
    tmap::tm_raster(alpha = 0.65, legend.reverse = TRUE)

  tmap_data[[unique(dtbl_subs$`individual-taxon-canonical-name`)]] = map_coords
}

Now, based on the saved data.tables we can create first the leaflet map to view the data of both animals in the same map,

#.....................................
# create the 'leafGl' of both datasets
#.....................................

dtbl_all = rbind(leafgl_data$`Canis lupus`, leafgl_data$`Rangifer tarandus`)

# see the number of observations for each animal
table(dtbl_all$`individual-taxon-canonical-name`)

# create an 'sf' object of both data.tables
dat_gps_tcx = sf::st_as_sf(dtbl_all, coords = c("longitude", "latitude"), crs = 4326)

lft = leaflet::leaflet()
lft = leaflet::addProviderTiles(map = lft, provider = leaflet::providers$OpenTopoMap)

lft = leafgl::addGlPoints(map = lft,
                          data = dat_gps_tcx,
                          opacity = 1.0,
                          fillColor = 'individual-taxon-canonical-name',
                          popup = 'individual-taxon-canonical-name')
lft

The tracking data of the Caribou are on a higher elevation compared to the data of the Wolves. This is verified by the next tmap which includes the Elevation legend (layer). The additional legend shows the individual identifier of the animal - for the Tarandus there are 138 unique id’s whereas

tmap_data$`Rangifer tarandus`                            # caribou

tmap_data$`Canis lupus`                                  # wolves

Elevation data using the CopernicusDEM R package can be visualized also in 3-dimensional space. For the corresponding use case have a look to the Vignette of the fitbitViz package which uses internally the Rayshader package.