phylobase v0.8.8

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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
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
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Vignettes of phylobase

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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 7.0.2
Encoding UTF-8
NeedsCompilation yes
Packaged 2020-02-10 03:38:46 UTC; francois
Repository CRAN
Date/Publication 2020-02-11 21:40:02 UTC

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