phylo4com-class: phylo4com class

In ecoPD: Ecologically-informed phylodiversity metrics

Description

S4 class for community phylogenies.

Objects from the Class

Objects can be created from trees and community-specific abundance data using various forms of the phylo4d constructor, or using new("phylo4com", ...) 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

subtrees:

list of subset trees corresponding to individual communities

order:

character: tree ordering

annote:

annotation data for tree (currently unstructured/unused by methods)

metadata:

metadata for node/tip data (currently used to store some community information)

Extends

Class "phylo4d" directly; Class "phylo4", by class "phylo4d".

Author(s)

Jim Regetz

Examples

  showClass("phylo4com")

ecoPD documentation built on May 2, 2019, 5:22 p.m.