aptg (version 0.1.1)

downto.tree: Hierarchical Tree Generator

Description

Generates a phylogenetic tree from a taxon down to a chosen lower taxon.

Usage

downto.tree(taxon, downto, key = NULL, db = "ncbi")

Arguments

taxon

The higher taxon from which the tree will start. (i.e. Family, Genus)

downto

The lowest level of taxonomy wanted. Must be lower than the one in taxon argument. Only species can be outputed from the Mammals tree.

key

API key. To create one use taxize::use_entrez().

db

Database used. Default is "ncbi". For possible datbases see ?taxize::downstream

Examples

# NOT RUN {
#Choose a certain taxon and the level you want the tree to stop
downto.tree("Cervidae", "species")
# }