phylo4d-class {phylobase}R Documentation

phylo4d class

Description

S4 class for phylogenetic tree and data.

Objects from the Class

Objects can be created from various trees and a data.frame using the constructor phylo4d, or using new("phylo4d", ...) for empty objects.

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
data:
data frame for traits of tips and internal nodes
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

coerce-methods for translation functions. The phylo4d constructor and the formatData function to check the validity of trees and data. See also the phylo4 constructor, the phylo4 class, and the checkPhylo4 function to check the validity of phylo4 trees.

Examples

  library(ape)
  example(read.tree)
  obj <- phylo4d(as(tree.owls.bis,"phylo4"), data.frame(wing=1:3))
  obj
  names(obj)
  summary(obj)

[Package phylobase version 0.5 Index]