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Add Euro+Med PlantBase distribution status

Source: R/add-euromed-distribution.R
add_euromed_distribution.Rd

Joins the per-area status Euro+Med PlantBase states for a taxon (native, naturalised, introduced, casual, ...) to a taxify() result, for the areas or countries asked for. The names and the ids of the euromed backbone are the same taxa the status is recorded on, so a result matched against any backbone joins through its accepted name.

Usage

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

Arguments

x

A data.frame returned by taxify().

region

Character. ISO 3166-1 alpha-2 country code(s), Euro+Med area code(s), or "all". A code that is an ISO code of a Euro+Med area is read as the country; anything else must be an area code, as listed by euromed_areas().

  • Single region: adds euromed_status (no suffix).

  • Several regions: adds euromed_status_<code> per region.

  • "all": one column per area.

cols

Which columns to attach. NULL (the default) attaches euromed_status; a character vector attaches just those, and "all" attaches every column the source carries (see enrichment_cols()), among them euromed_status_detail, euromed_status_source, area_name, iso2 and the taxon's Euro+Med UUID, taxon_id.

verbose

Logical. Default TRUE.

Value

The same data.frame with euromed_status, one of "native", "naturalised", "introduced", "casual", "cultivated", "doubtful" or "extinct", and NA where Euro+Med states nothing for the region. euromed_status_detail carries the term as Euro+Med words it ("endemic", "introduced: uncertain degree of naturalisation"). euromed_status_source holds the ids of the citing references; resolve them with cite(x$euromed_status_source, source = "euromed_distribution").

Details

Source: Euro+Med PlantBase (CC BY-SA), European and Mediterranean vascular plants, bryophytes and some fungi and algae. A report Euro+Med marks as made in error is not carried; a former presence is "extinct". Where the records of one taxon and area disagree, the stronger claim wins in the order given above (a taxon is native wherever a record says so), and the references are those of the records stating it. The country of an area comes from its own name, so a combined area has none and its countries are read from the level-2 areas.

See also

euromed_areas(), add_wcvp()

Examples

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

taxify("Solidago canadensis") |>
  add_euromed_distribution(region = "DE")

options(old)