Base Package for Phylogenetic Structures and Comparative Data
Adding data to a phylo4 or a phylo4d object
Tree traversal and utility functions
Validity checking for phylo4 objects
edgeLength methods
Edges accessors
Get tree from tree+data object
Format data for use in phylo4d objects
Node and Edge look-up functions
Labels for phylo4/phylo4d objects
MRCA
multiPhylo4 and extended classes
nodeId methods
nTips, nNodes, nEdges
Class "pdata"
Constructor for pdata (phylogenetic data) class
The phylo4 class
Create a phylogenetic tree
Tests for presence of data associated with trees stored as phylo4d obj...
phylo4d class
Combine a phylogenetic tree with data
Utilities and Tools for Phylogenetics
Set or return options of phylobase
Bubble plots for phylo4d objects
matrix classes for phylobase
Calculate node x and y coordinates
Plot a phylo4 object
print a phylogeny
Create a phylo4, phylo4d or data.frame object from a NEXUS or a ...
reordering trees within phylobase objects
Methods to test, access (and modify) the root of a phylo4 object.
Converting between phylo4/phylo4d and other phylogenetic tree formats
shortestPath-methods
Methods for creating subsets of phylogenies
Summary for phylo4/phylo4d objects
Retrieving or updating tip and node data in phylo4d objects
Plotting trees and associated data
Phylogeny plotting
Test trees for polytomies, inline nodes (singletons), or reticulation
Provides a base S4 class for comparative methods, incorporating one or more trees and trait data.
Useful links