phylo4-class {phylobase}R Documentation

The phylo4 class

Description

Classes for phylogenetic trees

Objects from the Class

Phylogenetic tree objects can be created by calls to the phylo4 constructor function. Translation functions from other phylogenetic packages are also available. See coerce-methods.

Slots

edge:
Matrix of edges
edge.label:
Character vector of edge (branch) labels
edge.length:
Numeric vector of edge (branch) lengths
label:
Character vector of tip (and optionally internal) node labels
order:
character: tree ordering (allowable values are listed in phylo4_orderings, currently "unknown", "preorder" (="cladewise" in ape), and "postorder", with "cladewise" and "pruningwise" also allowed for compatibility with ape)
annote:
annotation data for tree (currently unstructured/unused by methods)
metadata:
metadata for node/tip data (currently unstructured/unused by methods)

Author(s)

Ben Bolker, Thibaut Jombart

See Also

The phylo4 constructor, the checkPhylo4 function to check the validity of phylo4 objects. See also the phylo4d constructor and the phylo4d class.


[Package phylobase version 0.5 Index]