phylobase v0.8.4

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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
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
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
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
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Details

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 6.0.1
NeedsCompilation yes
Packaged 2017-04-21 21:15:46 UTC; francois
Repository CRAN
Date/Publication 2017-04-21 23:40:13 UTC

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