phylobase v0.8.6

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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
hasEdgeLength edgeLength methods
edges Edges accessors
extractTree Get tree from tree+data object
formatData Format data for use in phylo4d objects
pdata-class Class "pdata"
owls4 'Owls' data from ape
hasTipData Tests for presence of data associated with trees stored as phylo4d objects
pdata Constructor for pdata (phylogenetic data) class
subset-methods Methods for creating subsets of phylogenies
summary-methods Summary for phylo4/phylo4d objects
MRCA MRCA
phylomat-class matrix classes for phylobase
addData Adding data to a phylo4 or a phylo4d object
plotOneTree Plot a phylo4 object
phylo4-labels Labels for phylo4/phylo4d objects
multiPhylo-class multiPhylo4 and extended classes
phylo4d-class phylo4d class
treePlot-methods Phylogeny plotting
hasSingle Test trees for polytomies, inline nodes (singletons), or reticulation
ancestor Tree traversal and utility functions
phylo4d-methods Combine a phylogenetic tree with data
tdata Retrieving or updating tip and node data in phylo4d objects
nTips nTips, nNodes, nEdges
phylobubbles Bubble plots for phylo4d objects
checkPhylo4 Validity checking for phylo4 objects
phylobase.options Set or return options of phylobase
tip.data.plot Plotting trees and associated data
phylo4-class The phylo4 class
nodeId nodeId methods
phylobase-package Utilities and Tools for Phylogenetics
phyloXXYY Calculate node x and y coordinates
shortestPath shortestPath-methods
setAs Converting between phylo4/phylo4d and other phylogenetic tree formats
isRooted Methods to test, access (and modify) the root of a phylo4 object.
reorder-methods reordering trees within phylobase objects
Import Nexus and Newick files Create a phylo4, phylo4d or data.frame object from a NEXUS or a Newick file
print print a phylogeny
geospiza Data from Darwin's finches
getNode Node and Edge look-up functions
phylo4-methods Create a phylogenetic tree
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Vignettes of phylobase

Name
auto/developer.el
auto/phylobase.el
phylobase.Rnw
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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 6.1.1
Encoding UTF-8
NeedsCompilation yes
Packaged 2019-02-02 15:37:09 UTC; francois
Repository CRAN
Date/Publication 2019-02-02 16:10:03 UTC

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