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Detect native status from WGSRPD distributions

Source: R/native_detect.R
detect_native_status.Rd

Assigns a native status classification to each occurrence record by matching validated coordinates to WCVP distribution data via WGSRPD Level 3 polygons.

Native status is determined in two stages, working one taxon at a time.

Stage 1 — classify WGSRPD areas. The internal Distributions dataset links each WGSRPD Level 3 area code to WCVP flags (introduced, extinct, location_doubtful). These flags are resolved into a single status label with the following priority:

  1. If location_doubtful == 1, the area is classified as "location_doubtful" regardless of other flags.

  2. Otherwise, if introduced == 1, the area is "introduced".

  3. Otherwise, if extinct == 1, the area is "extinct".

  4. If all three flags are 0, the area is "native".

  5. Any remaining case defaults to "unknown".

Stage 2 — spatial intersection. For each taxon, the validated occurrence points are overlaid on the WGSRPD Level 3 polygon map (via terra::extract()) to assign an area code to each record. That area code is then looked up in the classified distribution table. Records falling outside any documented area, or whose taxon has no entry in Distributions, are labelled "unknown".

Usage

detect_native_status(CoordinateCleaned)

Arguments

CoordinateCleaned

A data.table of records that passed coordinate validation, containing at minimum gbifID, VasGBIF_decimalLongitude, VasGBIF_decimalLatitude, and VasGBIF_wcvp_taxon_name.

Value

A data.table with columns:

  • gbifID: the record identifier

  • LEVEL3_COD: the assigned WGSRPD Level 3 area code, or NA if the taxon has no distribution data

  • native_status: one of "native", "introduced", "extinct", "location_doubtful", or "unknown"