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Parse taxonomic names into their structural parts

Source: R/parse-name.R
parse_name.Rd

Decomposes each name into genus, specific epithet, infraspecific rank and epithet, authorship, hybrid status, and any open-nomenclature qualifier, without matching against a backbone. Where taxify() cleans a name and then resolves it, parse_name() returns the cleaning step itself (the parts of the name) for callers who need the decomposition rather than a match (the role rgbif::name_parse() or gnparser fill). The same cleaning pipeline the matcher uses drives the parse, so a name breaks apart the way it matches.

Usage

parse_name(x, code = c("taxon", "syntaxon"))

Arguments

x

Character vector of taxonomic names.

code

Character. The nomenclature the names follow: "taxon" (default; botanical and zoological names) or "syntaxon" (vegetation units under the International Code of Phytosociological Nomenclature, the names a syntaxon backbone such as "evc" matches; see taxify()).

Value

For code = "taxon", a data.frame with one row per input name and columns:

input_name

The original name as supplied.

genus

The genus (first token), or a single-letter initial for an abbreviated genus ("Q. robur"). NA for an unresolvable hybrid formula.

specific_epithet

The specific epithet, or NA for a bare genus.

infrasp_rank

The infraspecific rank marker ("subsp.", "var.", "f.", ...) when the name has one, else NA.

infrasp_epithet

The infraspecific epithet, else NA.

authorship

The authorship the name carries (trailing form, e.g. "(L.) H.Karst."), or NA.

qualifier

Any open-nomenclature / uncertainty qualifier ("cf.", "aff.", "sp.", "agg.", "s.l.", ...), canonicalized, or NA. Infraspecific rank markers are reported in infrasp_rank, not here.

is_hybrid

Logical. Was a hybrid marker detected?

hybrid_type

"nothogenus", "nothospecies", "formula", or NA.

rank

"genus", "species", "infraspecies", "hybrid_formula", or NA for an empty input.

canonical

The cleaned name used for matching (genus plus epithets and any infraspecific rank marker in its canonical spelling, qualifiers and authorship removed, hybrid sign dropped). NA for a hybrid formula, which is not a single taxon.

For code = "syntaxon", a data.frame with one row per input name and columns:

input_name

The original name as supplied.

code

A national or database code written in front of the name ("TDA - Arrhenatherion elatioris", "41BB03 - Tilio-Carpinetum"), or NA.

name

The syntaxon name without author or annotations, the form the matcher looks up. Where a record names several units, the most specific rank-labelled one ("all. X, ord. Y"), else the first.

authorship

The author citation ("(Oberd. 1957) Passarge 1964"), or NA.

rank

The rank the name's suffix denotes: "class" (-etea), "order" (-etalia), "alliance" (-ion), "suballiance" (-enion), "association" (-etum), "subassociation" (a trailing -etosum), "subclass", "suborder", or NA.

qualifier

"?" for a doubtful assignment, "cf.", "s.l.", "s.str.", or NA.

name_status

Nomenclatural annotations after the citation ("nom. inval. (5a)", "(syntax.syn.)", "(Regionalverband)"), or NA.

See also

taxify() to match a name; parse_name() exposes the same internal cleaning pipeline the matcher runs.

Examples

parse_name(c("Quercus robur L.",
             "Poa annua var. annua",
             "Q. robur",
             "Pinus cf. sylvestris",
             "Salix alba x Salix fragilis"))

parse_name(c("Caricenion gracilis (Neuhausl 1959) Oberd. et al. 1967",
             "TDA - Arrhenatherion elatioris",
             "Conioselinion tatarici Golub et al. 2003 nom. inval. (5a)"),
           code = "syntaxon")