tax_name {taxize}

Get taxonomic names for a given rank

Description

Get taxonomic names for a given rank

Usage

tax_name(
  sci,
  get,
  db = "itis",
  pref = "ncbi",
  messages = TRUE,
  query = NULL,
  ...
)

Arguments

sci

(character) Vector of taxonomic names to query. required.

get

(character) The ranks of the taxonomic name to get, see rank_ref. required.

db

(character) The database to search from: 'itis', 'ncbi' or 'both'. If 'both' both NCBI and ITIS will be queried. Result will be the union of both. If using ncbi, we recommend getting an API key; see taxize-authentication

pref

(character) If db = 'both', sets the preference for the union. Either 'ncbi' (default) or 'itis'. Currently not implemented.

messages

(logical) If TRUE the actual taxon queried is printed on the console.

query

Deprecated, see sci

...

Other arguments passed to get_tsn() or get_uid().

Value

A data.frame with one column for every queried rank, in addition to a column for db and queried term.

Authentication

See taxize-authentication for help on authentication

Note

While tax_rank() returns the actual rank of a taxon, tax_name() searches and returns any specified rank higher in taxonomy.

See Also

classification()

Examples

## Not run: 
# A case where itis and ncbi use the same names
tax_name(sci = "Helianthus annuus", get = "family", db = "itis")
tax_name(sci = "Helianthus annuus", get = "family", db = "ncbi")
tax_name(sci = "Helianthus annuus", get = c("genus","family","order"),
  db = "ncbi")

# Case where itis and ncbi use different names
tax_name(sci = "Helianthus annuus", get = "kingdom", db = "itis")
tax_name(sci = "Helianthus annuus", get = "kingdom", db = "ncbi")

# multiple rank arguments
tax_name(sci = c("Helianthus annuus","Baetis rhodani"), get = c("genus",
"kingdom"), db = "ncbi")
tax_name(sci = c("Helianthus annuus","Baetis rhodani"), get = c("genus",
"kingdom"), db = "itis")

# query both sources
tax_name(sci=c("Helianthus annuus", 'Baetis rhodani'), get=c("genus",
"kingdom"), db="both")

## End(Not run)