as.phylo.formula: Conversion from Taxonomy Variables to Phylogenetic Trees

In gjuggler/ape: Analyses of Phylogenetics and Evolution

Description

The function as.phylo.formula (short form as.phylo) builds a phylogenetic tree (an object of class phylo) from a set of nested taxonomic variables.

Usage

## S3 method for class 'formula'
as.phylo(x, data = parent.frame(), ...)

Arguments

x	a right-side formula describing the taxonomic relationship: ~C1/C2/.../Cn.
data	the data.frame where to look for the variables (default to environment).
...	further arguments to be passed from other methods.

Details

Taxonomic variables must be nested and passed in the correct order: the higher clade must be on the left of the formula, for instance ~Order/Family/Genus/Species. In most cases, the resulting tree will be unresolved and contain polytomies.

Value

An object of class phylo.

Author(s)

Julien Dutheil [e-mail]

See Also

as.phylo, read.tree for a description of phylo objects, multi2di

Examples

data(carnivora)
plot(as.phylo(~SuperFamily/Family/Genus/Species, data=carnivora))

gjuggler/ape documentation built on May 17, 2019, 6:03 a.m.