taxizedb (version 0.3.2)

name2taxid: Convert species names to taxon IDs

Description

name2taxid() returns a vector and dies if there are any ambiguous names. name2taxid_map() returns a data.frame mapping names to ids

Usage

name2taxid(x, db = "ncbi", verbose = TRUE, out_type = c("uid", "summary"), ...)

Value

A character vector if taxonomy identifiers.

Arguments

x

(character) Vector of taxon keys for the given database

db

(character) The database to search, one of ncbi, itis, gbif, wfo, or tpl

verbose

(logical) Print verbose messages

out_type

(logical) character "uid" for an ID vector, "summary" for a table with columns 'tax_id' and 'tax_name'.

...

Additional arguments passed to database specific classification functions.

NCBI database

The NCBI taxonomy database includes common names, synonyms and misspellings. However, the database is a little inconsistent. For some species, such as Arabidopsis thaliana, the misspelling Arabidopsis_thaliana is included, but the same is NOT done for humans. However, underscores are supported when querying through entrez, as is done in taxize, which implies entrez is replacing underscores with spaces. So I do the same. A corner case appears when an organism uses underscores as part of the name, not just a standin for space ("haloarchaeon 3A1_DGR"). To deal with this case, we replace underscores with spaces ONLY if there are not spaces in the original name.

Examples

if (FALSE) {
name2taxid(c('Arabidopsis thaliana', 'pig'))
name2taxid(c('Arabidopsis thaliana', 'pig'), out_type="summary")
name2taxid(x=c('Arabidopsis thaliana', 'Apis mellifera'), db = "itis")
name2taxid(x=c('Arabidopsis thaliana', 'Apis mellifera'), db = "itis",
 out_type="summary")
name2taxid(x=c('Arabidopsis thaliana', 'Quercus kelloggii'), db = "wfo")
name2taxid(x=c('Arabidopsis thaliana', 'Quercus kelloggii'), db = "wfo",
 out_type="summary")
name2taxid("Austrobaileyaceae", db = "wfo")
name2taxid("Quercus kelloggii", db = "gbif")
name2taxid(c("Quercus", "Fabaceae", "Animalia"), db = "gbif")
name2taxid(c("Abies Mill.", "Pinales Gorozh.", "Tracheophyta"), db = "col")
name2taxid(c("Abies mangifica", "Acanthopale aethiogermanica",
  "Acanthopale albosetulosa"), db = "tpl")
}