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phylobase (version 0.8.8)

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

5,741

Version

0.8.8

License

GPL (>= 2)

Issues

6

Pull Requests

0

Stars

19

Forks

0

Maintainer

Francois Michonneau

Last Published

February 11th, 2020

Functions in phylobase (0.8.8)

edges

Edges accessors
phylo4-labels

Labels for phylo4/phylo4d objects
hasEdgeLength

edgeLength methods
setAs

Converting between phylo4/phylo4d and other phylogenetic tree formats
MRCA

MRCA
phylo4-class

The phylo4 class
addData

Adding data to a phylo4 or a phylo4d object
ancestor

Tree traversal and utility functions
extractTree

Get tree from tree+data object
multiPhylo-class

multiPhylo4 and extended classes
phylomat-class

matrix classes for phylobase
pdata

Constructor for pdata (phylogenetic data) class
formatData

Format data for use in phylo4d objects
phylo4d-class

phylo4d class
geospiza

Data from Darwin's finches
owls4

'Owls' data from ape
phylo4d-methods

Combine a phylogenetic tree with data
checkPhylo4

Validity checking for phylo4 objects
pdata-class

Class "pdata"
shortestPath

shortestPath-methods
print

print a phylogeny
summary-methods

Summary for phylo4/phylo4d objects
plotOneTree

Plot a phylo4 object
reorder-methods

reordering trees within phylobase objects
subset-methods

Methods for creating subsets of phylogenies
isRooted

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

Bubble plots for phylo4d objects
hasTipData

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

nodeId methods
phylo4-methods

Create a phylogenetic tree
nTips

nTips, nNodes, nEdges
phylobase.options

Set or return options of phylobase
phyloXXYY

Calculate node x and y coordinates
getNode

Node and Edge look-up functions
Import Nexus and Newick files

Create a phylo4, phylo4d or data.frame object from a NEXUS or a Newick file
phylobase-package

Utilities and Tools for Phylogenetics
tdata

Retrieving or updating tip and node data in phylo4d objects
hasSingle

Test trees for polytomies, inline nodes (singletons), or reticulation
tip.data.plot

Plotting trees and associated data
treePlot-methods

Phylogeny plotting