pd_taxa: Gather taxonomic hierarchies

In ropensci/phylodiv: Phylogenetic Biodiversity Query Tools

Description

Gather taxonomic hierarchies

Usage

pd_taxa(x, db = "ncbi", drop_no_data = TRUE, ...)

Arguments

x	an object of class 'phylodiv'
db	(character) the database to use to get taxonomic information. only option is "ncbi" for now
drop_no_data	(logical) drop tips w/o taxonomic hierarchy data. default: 'TRUE'
...	ignored

Value

an object of class 'phylodiv', a named list with slots:

- tree - tips - nodes - hierarchies

taxonomic data

Uses taxizedb internally

Examples

## Not run: 
library(ape)
data(chiroptera)
st <- ape::subtrees(chiroptera)[[393]]
(x <- pd_read(st))
(res <- pd_taxa(x))
res$trees
res$trees[[1]]$hierarchies
res$fetch_hierarchies()

## End(Not run)

ropensci/phylodiv documentation built on March 13, 2020, 3:14 p.m.