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phylobase (version 0.8.4)

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.

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Version

Install

install.packages('phylobase')

Monthly Downloads

5,990

Version

0.8.4

License

GPL (>= 2)

Issues

6

Pull Requests

0

Stars

19

Forks

0

Maintainer

Francois Michonneau

Last Published

April 21st, 2017

Functions in phylobase (0.8.4)

extractTree

Get tree from tree+data object
formatData

Format data for use in phylo4d objects
geospiza

Data from Darwin's finches
getNode

Node and Edge look-up functions
hasEdgeLength

edgeLength methods
edges

Edges accessors
MRCA

MRCA
addData

Adding data to a phylo4 or a phylo4d object
ancestor

Tree traversal and utility functions
checkPhylo4

Validity checking for phylo4 objects
pdata-class

Class "pdata"
pdata

Constructor for pdata (phylogenetic data) class
phylo4-class

The phylo4 class
treePlot-methods

Phylogeny plotting
phylomat-class

matrix classes for phylobase
plotOneTree

Plot a phylo4 object
owls4

'Owls' data from ape
print

print a phylogeny
Import Nexus and Newick files

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

reordering trees within phylobase objects
isRooted

Methods to test, access (and modify) the root of a phylo4 object.
nTips

nTips, nNodes, nEdges
nodeId

nodeId methods
phylo4d-class

phylo4d class
phylo4d-methods

Combine a phylogenetic tree with data
phylo4-labels

Labels for phylo4/phylo4d objects
multiPhylo-class

multiPhylo4 and extended classes
phyloXXYY

Calculate node x and y coordinates
phylobase-package

Utilities and Tools for Phylogenetics
setAs

Converting between phylo4/phylo4d and other phylogenetic tree formats
shortestPath

shortestPath-methods
phylo4-methods

Create a phylogenetic tree
hasTipData

Tests for presence of data associated with trees stored as phylo4d objects
phylobase.options

Set or return options of phylobase
phylobubbles

Bubble plots for phylo4d objects
tdata

Retrieving or updating tip and node data in phylo4d objects
tip.data.plot

Plotting trees and associated data
subset-methods

Methods for creating subsets of phylogenies
summary-methods

Summary for phylo4/phylo4d objects
hasSingle

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