Enrich eLTER site iNaturalist occurrences with IUCN conservation status

This function enriches all the eLTER site iNaturalist occurrences acquired by the ReLTER::get_site_speciesOccurrences() function with the IUCN Red List conservation status as recorded in iNaturalist.

Observations are filtered to include only "Research Grade" data that meet the following criteria: have a valid date and exclude captive or cultivated organisms.

Observations are not filtered with respect to geoprivacy. In iNaturalist, each observation can be assigned one of three geoprivacy levels: open, obscured, or private (for more information, see: https://www.inaturalist.org/pages/geoprivacy). Given the need to gather information on species with critical conservation status, even if the geographic information is not precise, it is still important to record the presence of a species within a given area.

The function queries the iNaturalist Taxa API once per unique taxon.id and stores the returned IUCN assessments (if available) in a nested list-column.

If not already present, the function automatically assigns eLTER Standard Observations to each record via .assign_eLTER_SOs, adding two logical columns: SOBIO_014 (Flying insects — Insecta) and SOBIO_018 (Acoustic recording — Aves, Anura, Chiroptera, Orthoptera). Orthoptera contribute to both SOs simultaneously. If the columns are already present (e.g. because a previous enrichment function was already run), the assignment step is skipped.

Usage

add_iucn_to_occ(occ_eLTER)

Arguments

occ_eLTER

A data.frame or sf object representing the occurrences of an eLTER site acquired by the ReLTER::get_site_speciesOccurrences() function (typically occ_eLTER$inat).

Value

A data.frame or sf object with the same structure as the input, enriched with the following additional columns:

status_IUCN

A list-column (list of tibbles) containing the IUCN Red List assessments retrieved from iNaturalist for each taxon.id. Each tibble has the columns status, authority, name, and url. If no IUCN information is available, a tibble with NA values is stored.

has_IUCN

A logical value indicating whether at least one valid (non-NA) IUCN status is available for the given taxon.id.

SOBIO_014

logical. Whether the observation contributes to SOBIO_014 (Flying insects). Assigned only if not already present.

SOBIO_018

logical. Whether the observation contributes to SOBIO_018 (Acoustic recording). Assigned only if not already present.

Details

The IUCN conservation status is retrieved from the iNaturalist Taxa API and reflects the information available within iNaturalist. This information may not be up to date with respect to the official IUCN Red List.

Note

The IUCN conservation status is retrieved from the iNaturalist Taxa API and reflects the information available within iNaturalist. This may not be up to date with respect to the official IUCN Red List.

eLTER Standard Observation assignments are based on taxonomic ancestry (taxon.ancestor_ids) retrieved from the iNaturalist API.

See also

get_conservation_status, add_nativeness_to_occ, add_eunis_legal_to_occ, obs_SO_pie_chart

Author

Alessandro Oggioni, PhD (2023) alessandro.oggioni@cnr.it

Examples

if (FALSE) { # \dontrun{
## Not run:
# Download taxa occurrences from iNaturalist using ReLTER's
# get_site_speciesOccurrences() function
# e.g. Montagna di Torricchio eLTER site
deimsid <- "https://deims.org/6b62feb2-61bf-47e1-b97f-0e909c408db8"

occ_eLTER <- ReLTER::get_site_speciesOccurrences(
  deimsid = deimsid,
  list_DS = "inat",
  show_map = FALSE,
  limit = 5000
)

occ <- add_iucn_to_occ(
  occ_eLTER = occ_eLTER$inat
)
} # }
## End (Not run)