Identify Environmental Blocks and Group Nearby Records in Environmental Space

This function creates a multidimensional grid in environmental space by splitting each environmental variable into n_bins equally sized intervals. It then assigns each occurrence record to an environmental block (bin combination) and identifies records that fall into the same block (i.e., records that are close to each other in environmental space).

The results can be visualized using the plot_env_bins() function.

Usage

get_env_bins(
  occ,
  species = "species",
  long = "decimalLongitude",
  lat = "decimalLatitude",
  env_layers,
  n_bins = 5
)

Arguments

occ

(data.frame or data.table) a data frame containing the occurrence records for a single species. Must contain columns for species, longitude, and latitude.

species

(character) the name of the column in occ that contains the species scientific names. Default is "species".

long

(character) the name of the column in occ that contains the longitude values. Default is "decimalLongitude".

lat

(character) the name of the column in occ that contains the latitude values. Default is "decimalLatitude".

env_layers

(SpatRaster) object containing environmental variables.

n_bins

(numeric) number of bins into which each environmental variable will be divided.

Value

A list with:

• data: a data frame including extracted environmental values, bin indices, and a unique block_id for each record.

• breaks: a named list of numeric vectors containing the break points for each variable (used by plot_env_bins()).

Examples

# Load example data
data("occurrences", package = "RuHere")
# Get only occurrences from Araucaria
occ <- occurrences[occurrences$species == "Araucaria angustifolia", ]
# Load example of raster variables
data("worldclim", package = "RuHere")
# Unwrap Packed raster
r <- terra::unwrap(worldclim)
# Get bins
b <- get_env_bins(occ = occ, env_layers = r, n_bins = 5)