Get taxonomic names for a given rank
Get taxonomic names for a given rank
tax_name( sci, get, db = "itis", pref = "ncbi", messages = TRUE, query = NULL, ... )
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 |
query |
Deprecated, see |
... |
A data.frame with one column for every queried rank, in addition to a column for db and queried term.
See taxize-authentication for help on authentication
While tax_rank() returns the actual rank of a
taxon, tax_name() searches and returns any specified rank
higher in taxonomy.
## 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)Please choose more modern alternatives, such as Google Chrome or Mozilla Firefox.