This function downloads an up-to-date copy of the taxonomy database.
character string specifying which taxonomy database to download. Currently only "NCBI" is supported.
logical indicating whether synonyms should be included. Note that this increases the size of the returned object by around 10%.
This function downloads the specified taxonomy database as a data.frame
object with the following columns:
"taxID", "parent_taxID", "rank", "name".
As of early 2018 the zip archive to download the NCBI taxonomy database
is approximately 40Mb in size, and the output dataframe object is around
200Mb in memory. Once downloaded, the dataframe can be pruned
for increased speed and memory efficiency using the function
a dataframe with the following elements: "taxID", "parent_taxID", "rank", "name".
Federhen S (2012) The NCBI Taxonomy database. Nucleic Acids Research 40, D136-D143. doi:10.1093/nar/gkr1178.
db <- taxonomy()
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