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Assign species presence records to H3 hexagons

Source: R/h3sdm_pres.R
h3sdm_pres.Rd

Generates a hexagonal grid over the AOI, downloads species occurrence records, and assigns them to hexagons. Returns only hexagons with at least one presence record. This is the first step of a two-stage workflow where pseudo-absences are generated later using h3sdm_pa() after environmental variables have been extracted with h3sdm_extract_num() and related functions.

Usage

h3sdm_pres(
  species,
  aoi_sf,
  res = 6,
  providers = NULL,
  remove_duplicates = FALSE,
  date = NULL,
  limit = 500,
  expand_factor = 0.1
)

Arguments

species

character Species name (single string) for which records are requested.

aoi_sf

sf AOI (area of interest) polygon.

res

integer H3 resolution for the hexagonal grid.

providers

character Optional vector of data providers. Accepted values: any provider supported by spocc (e.g., "gbif", "inat") plus "biodatacr" for BiodataCR (Costa Rica), queried via the rbiodatacr package. If NULL (default), all spocc providers are used.

remove_duplicates

logical Remove duplicate records at the same coordinates. Default is FALSE.

date

character Optional date filter for records.

limit

integer Maximum number of records to download. Default is 500.

expand_factor

numeric Factor to expand AOI before creating the hexagonal grid. Default is 0.1.

Value

sf object with columns:

  • h3_address: H3 index of the hexagon.

  • presence: integer column with value 1 for all returned hexagons.

  • geometry: MULTIPOLYGON of each hexagon.

Details

Unlike h3sdm_pa(), this function does not sample pseudo-absences. It is intended to be used as the first step of a workflow where environmental variables are extracted for the full hexagonal grid before pseudo-absences are selected in environmental space using h3sdm_pa().

Examples

if (FALSE) { # \dontrun{
data(cr_outline_c, package = "h3sdm")
pres <- h3sdm_pres("Agalychnis callidryas", cr_outline_c, res = 7)
} # }