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Add WCVP native range status

Source: R/add-wcvp.R
add_wcvp.Rd

Joins WCVP (World Checklist of Vascular Plants, Kew) native range data to a taxify() result, filtered by TDWG botanical region.

Usage

add_wcvp(x, region, cols = NULL, verbose = TRUE)

Arguments

x

A data.frame returned by taxify().

region

Character. TDWG Level 3 region code(s), or "all". See taxify_regions() for the full list of codes.

  • Single code (e.g., "BGM" for Belgium): adds native_status column (no suffix).

  • Multiple codes (e.g., c("BGM", "GER")): adds native_status_BGM, native_status_GER.

  • "all": adds one column per region in the dataset.

List the region codes WCVP covers with enrichment_groups("wcvp").

cols

Which columns to attach. NULL (the default) attaches the curated set; a character vector of column names attaches just those, and "all" attaches every column the source carries (see enrichment_cols()).

verbose

Logical. Default TRUE.

Value

The same data.frame with additional column(s):

native_status

One of "native", "introduced", "extinct", or NA if not recorded for that region.

Details

Source: WCVP (Kew, CC BY). Coverage: ~340k plant species. Plants only.

The range reported is that of the taxon taxify() matched, as its backbone circumscribes it: the matched name's own records plus those of every name the backbone sinks into it. Where these disagree on a region, native wins over introduced, and introduced over extinct, since the taxon is native wherever any part of it is.

A region is left NA rather than filled from a broader taxon, or from one the matched backbone accepts as separate, when that is the only name another backbone offers for it. Those names are listed as refused in the wcvp entry of attr(x, "taxify_meta")$enrichments (the queried and refused name, the reason, the backbones offering it and the number of regions it would have filled), and counted by summary().

Examples

# Runs offline against the bundled example database.
old <- options(taxify.data_dir = taxify_example_data())

taxify("Quercus robur") |>
  add_wcvp(region = "GER")

taxify("Quercus robur") |>
  add_wcvp(region = c("GER", "BGM"))

options(old)