ncbiTaxonomy: NCBI Taxonomy Database
In megaptera: MEGAPhylogeny Techniques in R

Description Usage Arguments Value Author(s) References See Also

Retrieve taxonomic classifiactions from the taxonomy database at the NCBI.

1 2	ncbiTaxonomy(taxon, species.list = FALSE, kingdom, trim, parallel = FALSE, type = "SOCK")

`taxon`	a character string giving the name of the clade of interest.
`species.list`	logical: is `tax` alist of species or a set of higher taxon names?
`kingdom`	a character string giving the kingdom to which `term` belongs. This in information is sometimes necessary as the lineages in different kingdoms can have identical names (e.g., Glaucidium in Metazoa and Viridiplantae) and the value of `kingdom` is then used for disambiguation.
`trim`	a character string determining if and how to drop uninformative higher ranks. The default, `trim = "auto"`, drops all ranks higher than the rank of `term`. Alternatively, any existing name of a higher rank (e.g., `"family", "kingdom", ...`) may be given.
`parallel`	logical, indicating if `ncbiTaxonomy` should be executed serial or parallel
`type`	character

a data frame containing the taxonomic classification of all species belonging to term, for which molecular sequence information is found at the NCBI.

Christoph Heibl

Taxonomy Database website: http://www.ncbi.nlm.nih.gov/taxonomy

Federhen, Scott. 2012. The NCBI taxonomy databse. Nucleic Acids Research 40: DI36-DI43.

dbUpdateTaxonomy and dbReadTaxonomy for storing and retrieving taxonomic information in a megaptera project database.

megaptera documentation built on Jan. 15, 2017, 11:19 p.m.