View source: R/taxonomy.retrieve.R
taxonomy.retrieve | R Documentation |
After downloading sequences from genbank, this function curates sequences
based on taxonomic information. Note that this function provides two summary
datasets. First, the accession numbers. Second, the taxonomic information
for each species in the database. The taxonomy strictly follows
the gbif taxonomic backbone. The resulting files are saved to
"1.CuratedSequences"
. The resulting files also have the most recent
curated taxonomy following the gbif taxonomic backbone.
taxonomy.retrieve(
species_names = NULL,
database = "gbif",
kingdom = NULL,
ranks = c("kingdom", "phylum", "class", "order", "family", "genus", "species")
)
species_names |
A vector of species names |
database |
A name of a database with taxonomic information. 'gbif' only works for animals and plants. Databases follows taxize::classification |
kingdom |
Optional and only used when database = 'gbif'. Two possible options: "animals" or "plants." |
ranks |
Taxonomic ranks to retrieve from the target species. |
data.frame
of taxonomic information for the target species
(valid in the database)
## Not run:
taxonomy.retrieve(
species_names = c(
"Felis_catus", "PREDICTED:_Vulpes",
"Phoca_largha", "PREDICTED:_Phoca",
"PREDICTED:_Manis", "Felis_silvestris", "Felis_nigripes"
),
database = "gbif", kingdom = "animals"
)
## End(Not run)
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