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phylobase (version 0.6.4)

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

6,162

Version

0.6.4

License

GPL (>= 2)

Maintainer

Ben Bolker

Last Published

November 20th, 2012

Functions in phylobase (0.6.4)

checkPhylo4

Validity checking for phylo4 objects
plotOneTree

Plot a phylo4 object
as

Converting between phylo4/phylo4d and other phylogenetic tree formats
phylo4d

Combine a phylogenetic tree with data
Import Nexus and Newick files

Create a phylo4, phylo4d or data.frame object from a Nexus or a Newick file
phylobubbles

Bubble plots for phylo4d objects
phylo4-methods

Create a phylogenetic tree
tip.data.plot

Plotting trees and associated data
getNode

node and edge look-up functions
tdata

Retrieving or updating tip and node data in phylo4d objects
printphylo4

print a phylogeny
phylobase-package

Utilities and Tools for Phylogenetics
multiPhylo-class

multiPhylo4 and extended classes
reorder-methods

reordering trees within phylobase objects
phylo4d-class

phylo4d class
treewalk

tree traversal and utility functions
pdata-class

Class "pdata"
geospiza

Data from Darwin's finches
phylo4-accessors

Methods for S4 phylogeny classes
phyloXXYY

Calculate node x and y coordinates
phylo4-display

Displaying phylo4 object
hasSingle

Test trees for polytomies, inline nodes, or reticulation
phylo4d-hasData

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

Format data for use in phylo4d objects
phylobase.options

Set or return options of phylobase
phylog-class

Class "phylog"
treePlot-methods

Phylogeny plotting
nData

Retrieves the number of datasets in phylo4d objects
addData

Adding data to a phylo4 or a phylo4d object
pdata

Constructor for pdata (phylogenetic data) class
phylo4-class

The phylo4 class
subset-methods

Methods for creating subsets of phylogenies
phylomat-class

matrix classes for phylobase
extractTree

Get tree from tree+data object
phylo4-labels

Labels for phylo4/phylo4d objects
phylo4d-display

Display methods for phylo4d objects