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phylobase (version 0.8.10)

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

4,810

Version

0.8.10

License

GPL (>= 2)

Issues

6

Pull Requests

0

Stars

19

Forks

0

Maintainer

Francois Michonneau

Last Published

March 1st, 2020

Functions in phylobase (0.8.10)

hasEdgeLength

edgeLength methods
nodeId

nodeId methods
setAs

Converting between phylo4/phylo4d and other phylogenetic tree formats
nTips

nTips, nNodes, nEdges
phylobubbles

Bubble plots for phylo4d objects
geospiza

Data from Darwin's finches
phylobase.options

Set or return options of phylobase
addData

Adding data to a phylo4 or a phylo4d object
edges

Edges accessors
shortestPath

shortestPath-methods
ancestor

Tree traversal and utility functions
multiPhylo-class

multiPhylo4 and extended classes
getNode

Node and Edge look-up functions
phylo4-methods

Create a phylogenetic tree
phylo4-class

The phylo4 class
pdata

Constructor for pdata (phylogenetic data) class
print

print a phylogeny
owls4

'Owls' data from ape
phyloXXYY

Calculate node x and y coordinates
phylo4d-class

phylo4d class
pdata-class

Class "pdata"
Import Nexus and Newick files

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

Combine a phylogenetic tree with data
checkPhylo4

Validity checking for phylo4 objects
hasTipData

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

Retrieving or updating tip and node data in phylo4d objects
subset-methods

Methods for creating subsets of phylogenies
hasSingle

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

Plot a phylo4 object
tip.data.plot

Plotting trees and associated data
isRooted

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

Summary for phylo4/phylo4d objects
treePlot-methods

Phylogeny plotting
phylobase-package

Utilities and Tools for Phylogenetics
phylomat-class

matrix classes for phylobase
reorder-methods

reordering trees within phylobase objects
formatData

Format data for use in phylo4d objects
MRCA

MRCA
phylo4-labels

Labels for phylo4/phylo4d objects
extractTree

Get tree from tree+data object