Add nativeness information to iNaturalist occurrence records

Filters a tibble of iNaturalist occurrence records to retain only research-grade, non-captive observations with a valid date, then fetches establishment means information from iNaturalist for each unique taxon via get_nativeness_degree. The results are joined back to the filtered occurrence tibble as a nested establishmentMeans 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_nativeness_to_occ(occ_eLTER, country)

Arguments

occ_eLTER

tibble. A tibble of iNaturalist occurrence records, typically obtained via ReLTER::get_site_speciesOccurrences(). Must contain at least the columns quality_grade, observed_on, captive, taxon.id, and taxon.ancestor_ids.

country

character. The country name to filter establishment means by (e.g., "Italy"). Must match the place name as recorded in iNaturalist. Cannot be NULL.

Value

A tibble of filtered occurrence records (research-grade, non-captive, with valid date) with the following additional columns:

establishmentMeans

list-column. Each element is a one-row tibble containing nativeness and authority, or NA if not recorded in iNaturalist for the specified country.

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.

Note

The establishment means information is sourced from iNaturalist and may refer to the IUCN Red List. It may not always be up to date.

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

Progress messages are printed to the console for each taxon processed, including the iNaturalist taxon ID, nativeness status, and authority. A summary of taxa with and without establishment means is printed at the end.

The establishment means information is sourced from iNaturalist and may refer to the IUCN Red List. It may not always be up to date.

See also

get_nativeness_degree, add_iucn_to_occ, add_eunis_legal_to_occ, obs_SO_pie_chart

Author

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

Examples

if (FALSE) { # \dontrun{
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
)

site_boundary <- ReLTER::get_site_info(deimsid = deimsid)
country <- site_boundary$country

occ <- add_nativeness_to_occ(
  occ_eLTER = occ_eLTER$inat,
  country = country
)
} # }