/usr/lib/R/site-library/phylobase/INDEX is in r-cran-phylobase 0.8.4-2.
This file is owned by root:root, with mode 0o644.
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1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 | Import Nexus and Newick files
Create a 'phylo4', 'phylo4d' or 'data.frame'
object from a NEXUS or a Newick file
MRCA MRCA
addData Adding data to a phylo4 or a phylo4d object
ancestor Tree traversal and utility functions
checkPhylo4 Validity checking for phylo4 objects
edges Edges accessors
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
hasSingle Test trees for polytomies, inline nodes
(singletons), or reticulation
hasTipData Tests for presence of data associated with
trees stored as phylo4d objects
isRooted Methods to test, access (and modify) the root
of a phylo4 object.
multiPhylo-class multiPhylo4 and extended classes
nTips nTips, nNodes, nEdges
nodeId nodeId methods
owls4 'Owls' data from ape
pdata Constructor for pdata (phylogenetic data) class
pdata-class Class "pdata"
phylo4-class The phylo4 class
phylo4-labels Labels for phylo4/phylo4d objects
phylo4-methods Create a phylogenetic tree
phylo4d-class phylo4d class
phylo4d-methods Combine a phylogenetic tree with data
phyloXXYY Calculate node x and y coordinates
phylobase-package Utilities and Tools for Phylogenetics
phylobase.options Set or return options of phylobase
phylobubbles Bubble plots for phylo4d objects
phylomat-class matrix classes for phylobase
plotOneTree Plot a phylo4 object
print print a phylogeny
reorder-methods reordering trees within phylobase objects
setAs Converting between phylo4/phylo4d and other
phylogenetic tree formats
shortestPath shortestPath-methods
subset-methods Methods for creating subsets of phylogenies
summary-methods Summary for phylo4/phylo4d objects
tdata Retrieving or updating tip and node data in
phylo4d objects
tip.data.plot Plotting trees and associated data
treePlot-methods Phylogeny plotting
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