Altitude data

This vignette illustrates how you can get altitude data for the wrapper function check_eunis. Since the altitude data for Europe is too big for a R package, you have to get it on your own.

Example

First, we illustrate the altitude data for our example dataset.

library(dplyr)
library(ggplot2)
library(here)
library(sf)
library(terra)
library(tidyterra)

Load the example data

Load the altitude data for the area of our example.

altitude <- terra::rast(
  system.file("extdata", "data_example_altitude.tif", package = "RESY")
)
altitude
#> class       : SpatRaster
#> size        : 63, 168, 1  (nrow, ncol, nlyr)
#> resolution  : 0.0005555556, 0.0005555556  (x, y)
#> extent      : 10.69171, 10.78504, 44.12662, 44.16162  (xmin, xmax, ymin, ymax)
#> coord. ref. : lon/lat WGS 84 (EPSG:4326)
#> source      : data_example_altitude.tif
#> name        : eurodem
#> min value   :     771
#> max value   :    1927

We load the example plots.

data_sites <- readr::read_csv(
  system.file("extdata", "data_example_sites.csv", package = "RESY"),
  show_col_types = FALSE
) |>
  dplyr::select(PlotObservationID, Longitude, Latitude) |>
  sf::st_as_sf(coords = c("Longitude", "Latitude"), crs = 4326) |>
  sf::st_transform(terra::crs(altitude))

Map

We show the map with altitude data and the plots

ggplot() +
  tidyterra::geom_spatraster(data = altitude) +
  tidyterra::scale_fill_whitebox_c(
    palette = "high_relief",
    na.value = "lightblue"
    ) +
  geom_sf(data = data_sites, color = "red", size = 1) +
  labs(fill = "Altitude (m)") +
  theme_minimal()

altitude_values <- terra::extract(altitude, terra::vect(data_sites))
data_sites <- data_sites |>
  mutate("Altitude (m)" = altitude_values$eurodem)
data_sites
#> Simple feature collection with 200 features and 2 fields
#> Geometry type: POINT
#> Dimension:     XY
#> Bounding box:  xmin: 9.809499 ymin: 42.32483 xmax: 12.08963 ymax: 44.32464
#> Geodetic CRS:  WGS 84
#> # A tibble: 200 × 3
#>    PlotObservationID            geometry `Altitude (m)`
#>  * <chr>                     <POINT [°]>          <dbl>
#>  1 JZ37               (9.93798 44.32464)             NA
#>  2 FR49              (11.09287 43.91546)             NA
#>  3 PT45              (11.65339 43.09104)             NA
#>  4 ZH63              (10.53301 43.73897)             NA
#>  5 TF93              (10.40239 44.23978)             NA
#>  6 KG68              (10.40203 44.24087)             NA
#>  7 QJ27               (10.40635 44.2413)             NA
#>  8 JN90              (10.40602 44.24296)             NA
#>  9 ZM18              (10.66071 44.12734)             NA
#> 10 BQ20               (10.6589 44.12456)             NA
#> # ℹ 190 more rows

Crop your own altitude data

Download the elevation data from EuroDEM (European Digital Elevation Model) from https://www.mapsforeurope.org/datasets/euro-dem which is from EuroGeographics and the project is cofounded by the European Union.

Load and adapt EuroDEM data

Save it in your data folder of your R project with your coordinates of your vegetation surveys (sites).

# altitude <- terra::rast(
#   here::here("data", "euro-dem-tif", "data", "eurodem.tif")
# )

EuroDEM is in arcseconds and we have to rescale it to degrees.

# e <- terra::ext(altitude)
# terra::ext(altitude) <- terra::ext(
#   e[1] / 3600, e[2] / 3600, e[3] / 3600, e[4] / 3600
# )

The altitude data needs the right coordination system: EPSG:4258 - ETRS89 (European Terrestrial Reference System 1989) in degrees.

# terra::crs(altitude) <- "EPSG:4258"  # geographic ETRS89, degrees

Get an overview of the status of the EuroDEM data.

# altitude

Load example sites

Now, we can load the sites data and transform it to an sf object and align the CRS to the raster altitude data.

# data_sites <- readr::read_csv(
#   here::here("data", "data_example_sites.csv", package = "RESY"),
#   show_col_types = FALSE
# ) |>
#   sf::st_as_sf(coords = c("Longitude", "Latitude"), crs = 4326) |>
#   sf::st_transform(terra::crs(altitude))

Crop and save altitude data

We can crop the altitude data to the region of our plots.

# altitude_cropped <- data_sites |>
#   sf::st_buffer(0.5) |> # degrees now, ~50 km
#   sf::st_bbox() |>
#   terra::crop(x = altitude, y = _) |>
#   terra::project("EPSG:4326")

Save the smaller file for a latter use.

# terra::writeRaster(
#   altitude_cropped,
#   here::here("data", "data_example_altitude.tif"),
#   overwrite = TRUE
# )

Markus Bauer