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Extract Raster Values at Point Locations for BORG

Source: R/borg_extract.R
borg_extract.Rd

Convenience function that extracts environmental raster values at species occurrence (or other point) locations and returns a BORG-ready data frame with coordinates attached.

Usage

borg_extract(
  raster,
  points,
  coords = NULL,
  na.rm = TRUE,
  coord_names = c("x", "y")
)

Arguments

raster

A terra::SpatRaster of environmental layers (predictors).

points

Occurrence locations. One of:

  • A terra::SpatVector of point geometries

  • An sf object with point geometries

  • A data.frame with coordinate columns (requires coords)

  • A two-column matrix of coordinates (x/lon, y/lat)

coords

Character vector of length 2 giving coordinate column names. Required when points is a data.frame. Ignored for sf/SpatVector.

na.rm

Logical. If TRUE (default), rows with any NA in extracted raster values are removed. Set to FALSE to keep all rows.

coord_names

Character vector of length 2. Column names for the coordinates in the output. Default: c("x", "y").

Value

A data frame with columns for coordinates (named by coord_names), one column per raster layer (environmental variables), and any additional columns from the input points data. The returned data frame has a "borg_coords" attribute storing the coordinate column names, so that borg() can auto-detect them.

Details

This bridges the standard SDM workflow (rasters + points) with BORG's data.frame interface. The returned data frame can be passed directly to borg(), borg_cv(), or borg_diagnose().

Requires the terra package. If points is an sf object, the sf package is also required.

The function performs the equivalent of:


env_data <- terra::extract(raster, points, ID = FALSE)
coords <- terra::crds(points)
cbind(coords, env_data)

but handles edge cases (NA removal, coordinate injection, CRS checks) and attaches metadata so downstream BORG functions can auto-detect spatial structure.

Examples

# \donttest{
if (requireNamespace("terra", quietly = TRUE)) {
  # Create example raster and points
  r <- terra::rast(nrows = 50, ncols = 50,
                   xmin = 0, xmax = 100, ymin = 0, ymax = 100)
  terra::values(r) <- runif(terra::ncell(r))
  names(r) <- "bio1"

  pts <- terra::vect(
    cbind(x = runif(100, 0, 100), y = runif(100, 0, 100)),
    crs = terra::crs(r)
  )

  # Extract and run BORG
  d <- borg_extract(r, pts)
  result <- borg(d, coords = c("x", "y"), target = "bio1")
}
# }