get_site_speciesOccurrences: Trims by eLTER site the species occurrence from different...

In oggioniale/ReLTER: An Interface for the eLTER Community

Trims by eLTER site the species occurrence from different sources

Description

This function acquires data from GBIF https://www.gbif.org (via rgbif), iNaturalist https://www.inaturalist.org/ and OBIS https://obis.org/ and crops to an eLTER site boundary, which is obtained from the DEIMS-SDR sites API.

Usage

get_site_speciesOccurrences(
  deimsid,
  list_DS,
  show_map = FALSE,
  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. Data source to get data from, any combination of gbif, inat and/or obis.
show_map	A boolean. If TRUE a Leaflet map with occurrences is shown. Default FALSE.
limit	A numeric. Number of records to return. This is passed across all sources. Default: 500 for each source. BEWARE: if you have a lot of species to query for (e.g., n = 10), that's 10 * 500 = 5000, which can take a while to collect. So, when you first query, set the limit to something smallish so that you can get a result quickly, then do more as needed.
exclude_inat_from_gbif	A boolean. If TRUE, when list_DS contains both "gbif" and "inat", filter out gbif records originating from iNaturalist (in order to avoid duplicates). Default TRUE.

Value

The output of the function is a list of sf one for each of the repositories specified in the list_DS parameter.

The function output

Author(s)

Alessandro Oggioni, PhD (2020) [e-mail]

Paolo Tagliolato, PhD (2020) [e-mail]

Martina Zilioli [e-mail]

Examples

## Not run: 
# terrestrial site Saldur River Catchment
occ_SRC <- get_site_speciesOccurrences(
  deimsid =
    "https://deims.org/97ff6180-e5d1-45f2-a559-8a7872eb26b1",
  list_DS = c("gbif", "inat"),
  show_map = FALSE,
  limit = 10
)
occ_SRC

# marine site Gulf of Venice only obis
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 repositories are invoked
# gbif, inat and obis
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

## End(Not run)

oggioniale/ReLTER documentation built on Jan. 4, 2024, 3:48 p.m.