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Retrieve, crop, resample, and link environmental rasters to sampling sites

Source: R/get_enviro_data.R
get_enviro_data.Rd

get_enviro_data() automates six steps:

  1. AOI build - buffers the convex hull of all input points.

  2. Raster acquisition - downloads or loads a multi-layer stack (WorldClim, SoilGrids, footprint, population, or user-supplied).

  3. Cropping - trims the stack to the buffered AOI.

  4. Optional resampling - resamples the cropped stack to a user-defined grid resolution.

  5. Extraction & gap fill - pulls raster values at each site and linearly interpolates isolated NAs.

  6. Assembly - returns a tidy site x environment table plus the cropped (and resampled) raster and an sf layer of sites.

Usage

get_enviro_data(
  data,
  buffer_km = 10,
  source = "geodata",
  var = "bio",
  res = 2.5,
  grid_r = NULL,
  path = "data/",
  year = NULL,
  depth = NULL,
  stat = "mean",
  model = NULL,
  ssp = NULL,
  time = NULL,
  sp_cols = NULL,
  ext_cols = NULL
)

Arguments

data

Data frame of spatial points; must include lon/lat columns such as "x","y" or "centroid_lon","centroid_lat".

buffer_km

Buffer width (km) for the AOI. Default 10.

source

"geodata" (default) to fetch layers via geodata or "local" to supply a local SpatRaster or file path.

var

Raster product to download (see details) or ignored when source = "local".

res

Resolution (arc-min) for WorldClim/WorldPop layers (geodata).

grid_r

Optional grid resolution (in same CRS units) to which the cropped raster is resampled before extraction. If NULL, no resampling is performed.

path

Cache folder for downloaded rasters (created if absent).

year, model, ssp, time

Optional arguments for time-stamped products (human footprint, population, CMIP6, etc.).

depth, stat

Arguments passed to geodata::soil_world().

sp_cols

Columns to drop from the final table (e.g. a large species matrix). Accepts names or numeric indices relative to data.

ext_cols

Columns to append verbatim (e.g. "obs_sum","spp_rich").

Value

A list with

  • env_rast SpatRaster - cropped (and optionally resampled) environmental stack

  • sites_sf sf POINT layer (WGS-84) of the input sites

  • env_df Tibble with site ID, coordinates, every raster variable, plus any columns requested in ext_cols

Examples

if (FALSE) { # \dontrun{
# Example sites with longitude/latitude columns
sites <- data.frame(
  site_id = 1:3,
  x = c(18.5, 19.0, 19.5),
  y = c(-33.9, -33.5, -34.1)
)

# Download WorldClim bioclimatic variables and link them to the sites
enviro <- get_enviro_data(
  data   = sites,
  source = "geodata",
  var    = "bio",
  res    = 5
)
head(enviro$env_df)
} # }