phylobase

v. 
by Francois Michonneau
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Type Package
LinkingTo Rcpp
License GPL (>= 2)
URL https://github.com/fmichonneau/phylobase
BugReports https://github.com/fmichonneau/phylobase/issues
LazyData true
Collate 'oldclasses-class.R' 'internal-constructors.R' 'phylo4-methods.R' 'RcppExports.R' 'checkdata.R' 'phylo4-class.R' 'getNode-methods.R' 'formatData.R' 'phylo4d-class.R' 'phylo4d-methods.R' 'MRCA-methods.R' 'addData-methods.R' 'ancestors.R' 'phylo4-accessors.R' 'root-methods.R' 'nodeId-methods.R' 'edgeLength-methods.R' 'setAs-methods.R' 'extractTree.R' 'labels-methods.R' 'multiphylo4-class.R' 'pdata.R' 'phylo4d-accessors.R' 'phylobase-package.R' 'phylobase.options.R' 'phylomats-class.R' 'print-methods.R' 'readNCL.R' 'reorder-methods.R' 'shortestPath-methods.R' 'subset-methods.R' 'summary-methods.R' 'tbind.R' 'tdata-methods.R' 'treePlot.R' 'treestruc.R' 'zzz.R'
VignetteBuilder knitr
RoxygenNote 5.0.1
NeedsCompilation yes
Packaged 2016-01-22 16:13:13 UTC; francois
Repository CRAN
Date/Publication 2016-01-23 00:32:41

Base Package for Phylogenetic Structures and Comparative Data

Provides a base S4 class for comparative methods, incorporating one or more trees and trait data.

Functions in phylobase

Name Description
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
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