phylobase v0.8.10


Monthly downloads



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
nodeId nodeId methods
setAs Converting between phylo4/phylo4d and other phylogenetic tree formats
nTips nTips, nNodes, nEdges
phylobubbles Bubble plots for phylo4d objects
geospiza Data from Darwin's finches
phylobase.options Set or return options of phylobase
addData Adding data to a phylo4 or a phylo4d object
edges Edges accessors
shortestPath shortestPath-methods
ancestor Tree traversal and utility functions
multiPhylo-class multiPhylo4 and extended classes
getNode Node and Edge look-up functions
phylo4-methods Create a phylogenetic tree
phylo4-class The phylo4 class
pdata Constructor for pdata (phylogenetic data) class
print print a phylogeny
owls4 'Owls' data from ape
phyloXXYY Calculate node x and y coordinates
phylo4d-class phylo4d class
pdata-class Class "pdata"
Import Nexus and Newick files Create a phylo4, phylo4d or data.frame object from a NEXUS or a Newick file
phylo4d-methods Combine a phylogenetic tree with data
checkPhylo4 Validity checking for phylo4 objects
hasTipData Tests for presence of data associated with trees stored as phylo4d objects
tdata Retrieving or updating tip and node data in phylo4d objects
subset-methods Methods for creating subsets of phylogenies
hasSingle Test trees for polytomies, inline nodes (singletons), or reticulation
plotOneTree Plot a phylo4 object Plotting trees and associated data
isRooted Methods to test, access (and modify) the root of a phylo4 object.
summary-methods Summary for phylo4/phylo4d objects
treePlot-methods Phylogeny plotting
phylobase-package Utilities and Tools for Phylogenetics
phylomat-class matrix classes for phylobase
reorder-methods reordering trees within phylobase objects
formatData Format data for use in phylo4d objects
phylo4-labels Labels for phylo4/phylo4d objects
extractTree Get tree from tree+data object
No Results!

Vignettes of phylobase

No Results!

Last month downloads


Type Package
LinkingTo Rcpp
License GPL (>= 2)
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
Encoding UTF-8
NeedsCompilation yes
Packaged 2020-03-01 07:30:03 UTC; francois
Repository CRAN
Date/Publication 2020-03-01 08:00:06 UTC

Include our badge in your README