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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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Install
install.packages('phylobase')
Monthly Downloads
5,859
Version
0.8.8
License
GPL (>= 2)
Issues
6
Pull Requests
0
Stars
17
Forks
0
Repository
https://github.com/fmichonneau/phylobase
Maintainer
Francois Michonneau
Last Published
February 11th, 2020
Functions in phylobase (0.8.8)
Search functions
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