taxonomy: Download taxonomy database.

Description Usage Arguments Details Value Author(s) References Examples

View source: R/taxonomy.R

Description

This function downloads an up-to-date copy of the taxonomy database.

Usage

1
taxonomy(db = "NCBI", synonyms = FALSE)

Arguments

db

character string specifying which taxonomy database to download. Currently only "NCBI" is supported.

synonyms

logical indicating whether synonyms should be included. Note that this increases the size of the returned object by around 10%.

Details

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 prune_taxonomy.

Value

a dataframe with the following elements: "taxID", "parent_taxID", "rank", "name".

Author(s)

Shaun Wilkinson

References

Federhen S (2012) The NCBI Taxonomy database. Nucleic Acids Research 40, D136-D143. doi:10.1093/nar/gkr1178.

https://www.ncbi.nlm.nih.gov/taxonomy/

Examples

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  # db <- taxonomy()

shaunpwilkinson/insect documentation built on Dec. 2, 2018, 7:37 p.m.