cast_scientificname: Cast scientific name using taxonomic fields

In taxotools: Taxonomic List Processing

Cast scientific name using taxonomic fields

Description

Combine scientific names using Genus, Species, Subspecies, Author etc.

Usage

cast_scientificname(
  dat = NULL,
  sciname = "scientificname",
  genus = "",
  subgenus = "",
  species = "",
  subspecies = "",
  author = "",
  verbose = FALSE
)

Arguments

dat	data frame containing taxonomic data
sciname	column name for scientific names, Default: 'scientificname'
genus	column name for genus, Default: 'genus'
subgenus	column name for subgenus, Default: ”
species	column name for species, Default: 'species'
subspecies	column name for subspecies, Default: 'subspecies'
author	column name for author, Default: 'author'
verbose	verbose output, Default: FALSE

Details

Helpful function to break down Scientific names into Genus, Subgenus, species, Subspecies, Author so that the names can be constructed into canonical names for matching

Value

data frame with additional columns for taxonomic fields

See Also

Other Name functions: build_gen_syn(), cast_canonical(), check_scientific(), expand_name(), get_accepted_names(), guess_taxo_rank(), list_higher_taxo(), melt_canonical(), melt_scientificname(), resolve_names(), taxo_fuzzy_match()

Examples

mylist <- data.frame("id" = c(11,12,13,14,15,16,17,18,19),
                     "genus" = c("Hypochlorosis","Hypochlorosis","Hypochlorosis",
                                 "Myrina","Hypochlorosis","Hypochlorosis",
                                 "Hypochlorosis","Seuku","Sithon"),
                     "subgenus" = c("","","","","","","(Pseudonotis)","",""),
                     "species" = c("ancharia","ancharia","ancharia",
                                   "lorquinii","ancharia","ancharia",
                                   "metilia","emlongi","lorquinii"),
                     "subspecies" = c("","ancharia","humboldti",
                                      "","tenebrosa"," tenebrosa",
                                      "","",""),
                     "author" = c("(Hewitson, 1869)","(Hewitson, 1869)","Druce, 1894",
                                  "C. & R. Felder, 1865","Rothschild, 1915",
                                  "Rothschild, 1915","Fruhstorfer, 1908",
                                  "(Domning et al., 1986)",""),
                     stringsAsFactors = FALSE)

cast_scientificname(mylist,genus = "genus", subgenus = "subgenus",
                    species = "species", subspecies = "subspecies",
                    author = "author")

taxotools documentation built on May 29, 2024, 3:09 a.m.