Learn R Programming
⚠️There's a newer version (0.8.12) of this package.Take me there.

phylobase (version 0.8.2)

Base Package for Phylogenetic Structures and Comparative Data

Description

Provides a base S4 class for comparative methods, incorporating one or more trees and trait data.

Copy Link

Version

Install

install.packages('phylobase')

Monthly Downloads

3,772

Version

0.8.2

License

GPL (>= 2)

Issues

6

Pull Requests

0

Stars

19

Forks

0

Maintainer

Francois Michonneau

Last Published

January 22nd, 2016

Functions in phylobase (0.8.2)

subset-methods

Methods for creating subsets of phylogenies
checkPhylo4

Validity checking for phylo4 objects
formatData

Format data for use in phylo4d objects
phylobase.options

Set or return options of phylobase
phylobase-package

Utilities and Tools for Phylogenetics
phylo4-methods

Create a phylogenetic tree
hasTipData

Tests for presence of data associated with trees stored as phylo4d objects
phylo4d-class

phylo4d class
reorder-methods

reordering trees within phylobase objects
pdata-class

Class "pdata"
phylo4d-methods

Combine a phylogenetic tree with data
print

print a phylogeny
phylo4-class

The phylo4 class
phylobubbles

Bubble plots for phylo4d objects
phylo4-labels

Labels for phylo4/phylo4d objects
addData

Adding data to a phylo4 or a phylo4d object
ancestor

Tree traversal and utility functions
geospiza

Data from Darwin's finches
nodeId

nodeId methods
owls4

'Owls' data from ape
edges

Edges accessors
shortestPath

shortestPath-methods
phylomat-class

matrix classes for phylobase
hasEdgeLength

edgeLength methods
MRCA

MRCA
multiPhylo-class

multiPhylo4 and extended classes
extractTree

Get tree from tree+data object
isRooted

Methods to test, access (and modify) the root of a phylo4 object.
Import Nexus and Newick files

Create a phylo4, phylo4d or data.frame object from a NEXUS or a Newick file
treePlot-methods

Phylogeny plotting
hasSingle

Test trees for polytomies, inline nodes (singletons), or reticulation
nTips

nTips, nNodes, nEdges
tdata

Retrieving or updating tip and node data in phylo4d objects
phyloXXYY

Calculate node x and y coordinates
pdata

Constructor for pdata (phylogenetic data) class
tip.data.plot

Plotting trees and associated data
plotOneTree

Plot a phylo4 object
getNode

Node and Edge look-up functions
setAs

Converting between phylo4/phylo4d and other phylogenetic tree formats
summary-methods

Summary for phylo4/phylo4d objects