RDocumentation
Moon
Learn R
Search all packages and functions
⚠️
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
Copy
Link to current version
Version
Version
0.8.12
0.8.10
0.8.8
0.8.6
0.8.4
0.8.2
0.8.0
0.6.8
0.6.5.2
0.6.4
0.6.3
0.6.2
0.6.1
0.6.0
0.5
Down Chevron
Install
install.packages('phylobase')
Monthly Downloads
5,859
Version
0.8.2
License
GPL (>= 2)
Issues
6
Pull Requests
0
Stars
17
Forks
0
Repository
https://github.com/fmichonneau/phylobase
Maintainer
Francois Michonneau
Last Published
January 22nd, 2016
Functions in phylobase (0.8.2)
Search functions
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