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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 https://www.gbif.org, iNaturalist https://www.inaturalist.org/ and OBIS https://obis.org/ and intersects them with the boundary of an eLTER site retrieved from the DEIMS-SDR API https://deims.org/. Only occurrences falling within the site polygon are returned, enriched with eLTER site metadata.

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.

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. 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.

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)
occ_SRC <- get_site_speciesOccurrences(
  deimsid = "https://deims.org/97ff6180-e5d1-45f2-a559-8a7872eb26b1",
  list_DS = c("gbif", "inat"),
  show_map = TRUE,
  limit = 50
)
occ_SRC

# 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, with map)
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
)
occ_GoV_all$obis
occ_GoV_all$map
} # }