Resolve scientific names to common (vernacular) names

The forward direction of comm2sci(): given a scientific name, return the common name(s) it is known by. Reads the bundled common_names enrichment (GBIF, NCBI, and Open Tree vernaculars) offline; the first call may trigger the one-time download. Where add_common_names() attaches vernaculars to a taxify() result as columns, sci2comm() takes bare names and returns the long lookup table – one row per (name, vernacular). A name maps to many common names (across languages and synonyms), so a query can carry several rows.

Usage

sci2comm(x, lang = NULL, resolve = TRUE, backbone = NULL, verbose = TRUE)

Arguments

x

Character vector of scientific names.

lang

Character. Restrict to one language: an ISO 639-1 code ("en", "de", ...) as used by the GBIF source, or NA for the untagged NCBI/Open Tree names. NULL (default) returns every language. List the languages present with enrichment_groups("common_names").

resolve

Logical. When TRUE (default), each input is run through taxify() first so a synonym or misspelling reports its accepted taxon's vernaculars. When FALSE, the input name is looked up verbatim (faster, offline; use when the names are already accepted).

backbone

Passed to taxify() when resolve = TRUE; NULL (default) uses every installed backbone. Ignored when resolve = FALSE.

verbose

Logical. Default TRUE.

Value

A data.frame with one row per (query, vernacular):

input_name

The scientific name as supplied.

accepted_name

The accepted name looked up (equals input_name when resolve = FALSE or the input_name was already accepted).

common_name

A vernacular name.

lang

Language tag (NA for NCBI/Open Tree).

A query with no vernacular contributes no rows.

See also

comm2sci() for the reverse direction (common -> scientific), add_common_names() to attach vernaculars to a taxify() result.

Examples

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

# The bundled example maps Quercus robur -> "example_common_name" (en + de)
sci2comm("Quercus robur", resolve = FALSE)

options(old)