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Classify Scientific Plant Names into Taxonomic Components

Source: R/build_tbl.R
classify_spnames.Rd

[Experimental]

Parse and classify scientific plant names into taxonomic components: genus, specific epithet, infraspecific rank, infraspecific epithet, and author.

Output is aligned to a backbone convention:

  • Orig.Genus in Title Case (first letter uppercase, rest lowercase).

  • Orig.Species and Orig.Infraspecies epithets in lowercase.

  • Infra.Rank in lowercase (subsp., var., subvar., f., subf.).

  • Author is recovered from the input and preserved in its original casing/punctuation (no forced uppercasing).

  • Orig.Name is reconstructed as: genus + species + (rank + infra) + author.

Robustness rules:

  • cf. / aff. are removed from parsing but preserved as flags (has_cf, has_aff).

  • Hybrid markers (x/\u00D7) as standalone tokens are removed with had_hybrid = TRUE.

  • sp. / spp. triggers genus-only classification (Rank = 1, Orig.Species = NA) and sets is_sp/is_spp.

  • If an infraspecific rank is present but the infraspecific epithet is missing, sets rank_missing_infra = TRUE and keeps Infra.Rank while Orig.Infraspecies = NA.

  • If rank appears "late" (after author-like tokens), parsing is best-effort and rank_late = TRUE.

  • If there is no explicit rank and a third token exists, the function can infer an unranked infraspecific epithet when the third token looks epithet-like (all lowercase), and does not look like the start of an author. In that case implied_infra = TRUE, Orig.Infraspecies is filled, Infra.Rank = NA, and Rank = 3.

Usage

classify_spnames(splist)

Arguments

splist

Character vector. Scientific plant names.

Value

A tibble with one row per input name and standardized columns/flags:

sorter

Numeric index of original order.

Input.Name

Original input string as provided by user.

Orig.Name

Reconstructed standardized name aligned to backbone + original-cased author.

Orig.Genus

Genus in Title Case.

Orig.Species

Specific epithet in lowercase, or NA for genus-only (sp./spp.).

Author

Recovered author string (original casing/punctuation) or "".

Orig.Infraspecies

Infraspecific epithet in lowercase (ranked or implied), or NA.

Infra.Rank

Infraspecific rank in lowercase (subsp., var., subvar., f., subf.), or NA.

Rank

Numeric level: 1 genus-only, 2 genus+species, 3 includes infraspecific epithet.

has_cf,has_aff,is_sp,is_spp,had_hybrid,rank_late,rank_missing_infra,had_na_author,implied_infra

Logical flags.

Examples

library(wcvpmatch)
classify_spnames(c("Opuntia sp.", "Rosa canina subsp. coriifolia (Fr.) Leffler"))
#> Warning: Undetermined species indicator detected ('sp.'/'spp.'). Classified at genus
#> level only; Orig.Species set to NA for
#> • Opuntia sp.
#> # A tibble: 2 × 18
#>   sorter Input.Name   Orig.Name Orig.Genus Orig.Species Author Orig.Infraspecies
#>    <dbl> <chr>        <chr>     <chr>      <chr>        <chr>  <chr>            
#> 1      1 Opuntia sp.  Opuntia   Opuntia    NA           ""     NA               
#> 2      2 Rosa canina… Rosa can… Rosa       canina       "(Fr.… coriifolia       
#> # ℹ 11 more variables: Infra.Rank <chr>, Rank <dbl>, has_cf <lgl>,
#> #   has_aff <lgl>, is_sp <lgl>, is_spp <lgl>, had_hybrid <lgl>,
#> #   rank_late <lgl>, rank_missing_infra <lgl>, had_na_author <lgl>,
#> #   implied_infra <lgl>
classify_spnames(c("Cydonia japonica tricolor")) # implied unranked infra epithet
#> # A tibble: 1 × 18
#>   sorter Input.Name   Orig.Name Orig.Genus Orig.Species Author Orig.Infraspecies
#>    <dbl> <chr>        <chr>     <chr>      <chr>        <chr>  <chr>            
#> 1      1 Cydonia jap… Cydonia … Cydonia    japonica     ""     tricolor         
#> # ℹ 11 more variables: Infra.Rank <chr>, Rank <dbl>, has_cf <lgl>,
#> #   has_aff <lgl>, is_sp <lgl>, is_spp <lgl>, had_hybrid <lgl>,
#> #   rank_late <lgl>, rank_missing_infra <lgl>, had_na_author <lgl>,
#> #   implied_infra <lgl>