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Retrieve species occurrences within an eLTER site boundary

Source: R/get_site_speciesOccurrences.R
get_site_speciesOccurrences.Rd

[Stable] This function downloads species occurrence records from GBIF, iNaturalist and OBIS via the spocc package (SPecies OCCurrence data from across the web), and intersects them with the boundary of an eLTER site retrieved from the DEIMS-SDR API. Only occurrences falling within the site polygon are returned, enriched with eLTER site metadata.

iNaturalist observations are filtered to research grade only via the quality parameter of rinat::get_inat_obs(), which is the quality level required by ReLTER.inatEnrich enrichment functions. Note that the iNaturalist API has a hard limit of 10,000 observations per query. For sites with more than 10,000 research grade observations in the bounding box, consider using GBIF with the iNaturalist dataset key ("50c9509d-22c7-4a22-a47d-8c48425ef4a7") as an alternative, which indexes all iNaturalist research grade observations and has no such limit (though with a synchronisation lag of a few days).

Usage

get_site_speciesOccurrences(
  deimsid,
  list_DS,
  show_map = TRUE,
  limit = 500,
  exclude_inat_from_gbif = TRUE
)

Arguments

deimsid

A character. The DEIMS ID of the site from DEIMS-SDR website. DEIMS ID information here.

list_DS

A character vector. Data sources to query; any combination of "gbif", "inat", and/or "obis".

show_map

A boolean. If TRUE the leaflet map is both printed and returned in the output list as $map. If FALSE the map is not printed but is still built and returned in $map for later use. Default FALSE.

limit

A numeric. Maximum number of records to download per source. Default 500. Note that when querying for many species the total number of records can be large and slow to download; start with a small value (e.g. 10) to verify results before increasing. For iNaturalist, the maximum allowed by the API is 10000.

exclude_inat_from_gbif

A boolean. If TRUE, and both "gbif" and "inat" are in list_DS, records originating from iNaturalist are removed from the GBIF results to avoid duplicates. Default TRUE.

Value

A list with one sf element per data source (named gbif, inat, obis) containing only occurrences that fall within the site boundary, and a map element with a leaflet object. Each sf element contains the occurrence geometry and the following eLTER site metadata fields (prefixed with eLTER_): title, uri, created, changed, geoCoord, country, geoElev.avg, geoElev.min, geoElev.max, biogeographicalRegion, biome, ecosystemType, eunisHabitat, landforms, geoBonBiome, geology, hydrology, soils, vegetation, size.value. If no occurrences are found within the boundary for a given source, that source is omitted from the list and an informative message is printed. Returns invisible(NULL) if the site has no boundary or if no occurrences are found for any source.

Note

iNaturalist observations are downloaded as research grade only. This is consistent with the quality level required by the ReLTER.inatEnrich enrichment pipeline (add_iucn_to_occ(), add_nativeness_to_occ(), add_eunis_legal_to_occ()).

The iNaturalist API enforces a hard limit of 10,000 observations per query. Spatial filtering is performed on a bounding box (not the exact site polygon); the exact polygon intersection is applied afterwards via sf::st_intersection(), so the number of records returned may be slightly higher than those visible in the corresponding iNaturalist project for the site.

The function output

Map of occurrences acquired from OBIS in the marine site Gulf of Venice

See also

spocc::occ()

spocc::obis_search()

RColorBrewer::brewer.pal()

get_site_info()

Author

Alessandro Oggioni, PhD (2020) oggioni.a@irea.cnr.it

Paolo Tagliolato, PhD (2020) tagliolato.p@irea.cnr.it

Martina Zilioli zilioli.m@irea.cnr.it

Examples

if (FALSE) { # \dontrun{
# Terrestrial site: Saldur River Catchment (GBIF and iNaturalist,
# excluding records sourced from iNaturalist in GBIF)
occ_SRC <- get_site_speciesOccurrences(
  deimsid = "https://deims.org/97ff6180-e5d1-45f2-a559-8a7872eb26b1",
  list_DS = c("gbif", "inat"),
  show_map = TRUE,
  limit = 50,
  exclude_inat_from_gbif = TRUE
)
occ_SRC

# Terrestrial site: Gran Paradiso National Park (only GBIF,
# excluding records sourced from iNaturalist)
occ_GPNP <- get_site_speciesOccurrences(
  deimsid = "https://deims.org/15c3e841-8494-42d2-a44e-c49a0ff25946",
  list_DS = "gbif",
  show_map = TRUE,
  limit = 50,
  exclude_inat_from_gbif = TRUE
)
occ_GPNP

# Terrestrial site: Tenuta di Castelporziano (iNaturalist only,
# research grade, up to 10000 records -- the iNaturalist API hard limit)
occ_CP <- get_site_speciesOccurrences(
  deimsid = "https://deims.org/0d2269d3-5423-4939-a30d-077c8bc38b03",
  list_DS = "inat",
  show_map = TRUE,
  limit = 10000
)
occ_CP$inat

# Marine site: Gulf of Venice (OBIS only)
occ_GoV <- get_site_speciesOccurrences(
  deimsid = "https://deims.org/758087d7-231f-4f07-bd7e-6922e0c283fd",
  list_DS = "obis",
  show_map = FALSE,
  limit = 10
)
occ_GoV

# Marine site: Gulf of Venice (all sources excluding records of GBIF
# sourced from iNaturalist)
occ_GoV_all <- get_site_speciesOccurrences(
  deimsid = "https://deims.org/758087d7-231f-4f07-bd7e-6922e0c283fd",
  list_DS = c("gbif", "inat", "obis"),
  show_map = TRUE,
  limit = 10,
  exclude_inat_from_gbif = TRUE
)
occ_GoV_all$obis
occ_GoV_all$map
} # }