ape (version 5.1)

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

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 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.

Value

An object of class phylo.

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.

See Also

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

Examples

# NOT RUN {
data(carnivora)
plot(as.phylo(~SuperFamily/Family/Genus/Species, data=carnivora))
# }