Taxa occurrences check within a radius using GBIF data

Performs a species occurrence check within a fixed radius around a GPS point using GBIF occurrence data.

Usage

tax_occur_check(
  taxa_name,
  longitude,
  latitude,
  radius_km = 50,
  method = c("download", "search"),
  circle_form = TRUE,
  clean_coord = TRUE,
  info_names = c("decimalLongitude", "decimalLatitude", "country", "year",
    "scientificName", "recordedBy", "gbifRegion"),
  return_all_occ = FALSE,
  verbose = TRUE,
  clean_coord_verbose = FALSE,
  n_occur = 1000,
  ...
)

Arguments

taxa_name: Character. Scientific name of the species to check.
longitude: Numeric. Longitude of the test point in decimal degrees.
latitude: Numeric. Latitude of the test point in decimal degrees.
radius_km: Numeric. Search radius in kilometers (default: 50).
method: (character, default `"download"`). How occurrences are fetched: - `"download"`: a single [rgbif::occ_download()] request constrained to the search bounding box (mints a citable DOI). **Requires GBIF credentials** (see [check_gbif_credentials()]). - `"search"`: the legacy [rgbif::occ_search()] call (fast, capped at `n_occur` records, no credentials).
circle_form: (Logical, default: TRUE). Whether to use a circular search area. If FALSE, a square bounding box is used.
clean_coord: (Logical, default: TRUE). Whether to clean coordinates using CoordinateCleaner
info_names: Character vector. Columns to select from GBIF data (default:c("decimalLongitude", "decimalLatitude", "country", "year", "scientificName", "recordedBy", "gbifRegion")). Note that "scientificName", "decimalLongitude" and "decimalLatitude" are required. With `method = "download"`, `"country"` is mapped to `"countryCode"` and download-only absent columns (e.g. `"gbifRegion"`) are silently dropped.
return_all_occ: (Logical, default: FALSE). If TRUE, return all occurrences found within the radius in a data frame called "occ_data" in the resulting list.
verbose: (Logical, default: TRUE). Whether to print progress messages.
clean_coord_verbose: (Logical, default: FALSE). Whether to print messages from CoordinateCleaner.
n_occur: Numeric (default: 1000). Maximum number of occurrences to retrieve from GBIF. A server-side limit with `method = "search"`; applied as a local sample after import with `method = "download"`.
...: Additional parameters passed to [rgbif::occ_search()] (only used when `method = "search"`).

Value

A list containing: - count_in_radius: Number of occurrences found within the radius - closest_distance_km: Distance to the closest occurrence in kilometers - mean_distance_km: Mean distance to all occurrences in kilometers - total_count_in_world: Total number of occurrences with coordinates worldwide - search_radius: The search radius used (in kilometers) - closest_point_lat: Latitude of the closest occurrence - closest_point_lon: Longitude of the closest occurrence - sample_point_lat: Latitude of the tested point - sample_point_lon: Longitude of the tested point - occ_data (optional, if `return_all_occ` is TRUE): Data frame of all occurrences found within the radius

Author

Adrien Taudiere

Examples

if (FALSE) { # \dontrun{
# Check for Oak species near Paris
long <- 2.3522
lat <- 48.8566

Q_rob_in_Paris <- tax_occur_check("Quercus robur", long, lat, radius_km=10)
Q_rob_in_Paris

tax_occur_check("Trametopsis brasiliensis", long, lat, radius_km=100)


# Visualize occurrences around Paris for Fagus sylvatica
res_occ <- tax_occur_check("Fagus sylvatica", long, lat, radius_km=20,
  return_all_occ = TRUE
)

occ_data_sf <- sf::st_as_sf(res_occ$occ_data,
  coords = c("decimalLongitude", "decimalLatitude"),
  crs = 4326
)

if (requireNamespace("leaflet")) {
  library(leaflet)
}
if (requireNamespace("leafpop")) {
  library(leafpop)
}
leaflet() |>
  addTiles() |>
  setView(lat, long, zoom = 12) |>
  fitBounds(
    lat1 = as.vector(sf::st_bbox(occ_data_sf))[2],
    lng1 = as.vector(sf::st_bbox(occ_data_sf))[1],
    lat2 = as.vector(sf::st_bbox(occ_data_sf))[4],
    lng2 = as.vector(sf::st_bbox(occ_data_sf))[3]
  ) |>
  leaflet::addCircles(data = occ_data_sf, color = "blue", stroke = 1, opacity = 0.8) |>
  leaflet::addCircleMarkers(lat, long, color = "orange", radius = 2, opacity = 1)
} # }

Taxa occurrences check within a radius using GBIF data

Usage

Arguments

Value

See also

Author

Examples