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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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Install
install.packages('phylobase')
Monthly Downloads
5,859
Version
0.8.4
License
GPL (>= 2)
Issues
6
Pull Requests
0
Stars
17
Forks
0
Repository
https://github.com/fmichonneau/phylobase
Maintainer
Francois Michonneau
Last Published
April 21st, 2017
Functions in phylobase (0.8.4)
Search functions
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