phylobase: Base Package for Phylogenetic Structures and Comparative Data

Provides a base S4 class for comparative methods, incorporating one or more trees and trait data.

AuthorR Hackathon et al. (alphabetically: Ben Bolker, Marguerite Butler, Peter Cowan, Damien de Vienne, Dirk Eddelbuettel, Mark Holder, Thibaut Jombart, Steve Kembel, Francois Michonneau, David Orme, Brian O'Meara, Emmanuel Paradis, Jim Regetz, Derrick Zwickl)
Date of publication2016-01-23 00:32:41
MaintainerFrancois Michonneau <francois.michonneau@gmail.com>
LicenseGPL (>= 2)
Version0.8.2
https://github.com/fmichonneau/phylobase

View on CRAN

Man pages

addData-methods: Adding data to a phylo4 or a phylo4d object

ancestors: Tree traversal and utility functions

checkPhylo4: Validity checking for phylo4 objects

edgeLength-methods: edgeLength methods

edges-accessors: Edges accessors

extractTree: Get tree from tree+data object

formatData: Format data for use in phylo4d objects

geospiza: Data from Darwin's finches

getNode-methods: Node and Edge look-up functions

labels-methods: Labels for phylo4/phylo4d objects

MRCA: MRCA

multiPhylo-class: multiPhylo4 and extended classes

nodeId-methods: nodeId methods

nTips-methods: nTips, nNodes, nEdges

owls4: 'Owls' data from ape

pdata: Constructor for pdata (phylogenetic data) class

pdata-class: Class "pdata"

phylo4-class: The phylo4 class

phylo4d-accessors: Tests for presence of data associated with trees stored as...

phylo4d-class: phylo4d class

phylo4d-methods: Combine a phylogenetic tree with data

phylo4-methods: Create a phylogenetic tree

phylobase.options: Set or return options of phylobase

phylobase-package: Utilities and Tools for Phylogenetics

phylobubbles: Bubble plots for phylo4d objects

phylomat-class: matrix classes for phylobase

phyloXXYY: Calculate node x and y coordinates

plotOneTree: Plot a phylo4 object

print-methods: print a phylogeny

readNexus: Create a 'phylo4', 'phylo4d' or 'data.frame' object from a...

reorder-methods: reordering trees within phylobase objects

root-methods: Methods to test, access (and modify) the root of a phylo4...

setAs-methods: Converting between phylo4/phylo4d and other phylogenetic tree...

shortestPath-methods: shortestPath-methods

subset-methods: Methods for creating subsets of phylogenies

summary-methods: Summary for phylo4/phylo4d objects

tdata-methods: Retrieving or updating tip and node data in phylo4d objects

tip.data.plot: Plotting trees and associated data

treePlot-methods: Phylogeny plotting

treeStructure-methods: Test trees for polytomies, inline nodes (singletons), or...

Files in this package

phylobase
phylobase/inst
phylobase/inst/nexmlfiles
phylobase/inst/nexmlfiles/comp_analysis.xml
phylobase/inst/nexusfiles
phylobase/inst/nexusfiles/treeWithPolyExcludedData.nex
phylobase/inst/nexusfiles/MultiLineTrees.nex
phylobase/inst/nexusfiles/NastyLabels2.nex
phylobase/inst/nexusfiles/NastyLabels.nex
phylobase/inst/nexusfiles/minNex.nex
phylobase/inst/nexusfiles/co1.nex
phylobase/inst/nexusfiles/noStateLabels.nex
phylobase/inst/nexusfiles/treeWithDiscreteData.nex
phylobase/inst/nexusfiles/shorebird_underscore.nex
phylobase/inst/nexusfiles/treeWithUnderscoreLabels.nex
phylobase/inst/nexusfiles/testSubsetTaxa.nex
phylobase/inst/nexusfiles/treeWithContinuousData.nex
phylobase/inst/nexusfiles/minSeq.nex
phylobase/inst/nexusfiles/test_min.nex
phylobase/inst/nexusfiles/treeWithSpecialCharacters.nex
phylobase/inst/nexusfiles/newick.tre
phylobase/inst/nexusfiles/treeWithDiscAndContData.nex
phylobase/inst/nexusfiles/treeRoundingError.nex
phylobase/inst/nexusfiles/ExContData.Rdata
phylobase/inst/doc
phylobase/inst/doc/phylobase.Rnw
phylobase/inst/doc/phylobase.pdf
phylobase/tests
phylobase/tests/testprune.R
phylobase/tests/phylo4dtests.R
phylobase/tests/phylosubtest.R
phylobase/tests/phylotorture.R
phylobase/tests/plottest.R
phylobase/tests/roundtrip.R
phylobase/tests/misctests.R
phylobase/tests/testthat
phylobase/tests/testthat/test.badnex.R
phylobase/tests/testthat/test.phylobase.options.R
phylobase/tests/testthat/test.class-phylo4d.R
phylobase/tests/testthat/test.formatData.R
phylobase/tests/testthat/test.readNCL.R
phylobase/tests/testthat/test.tbind.R
phylobase/tests/testthat/test.methods-oldclasses.R
phylobase/tests/testthat/test.treePlot.R
phylobase/tests/testthat/test.treewalk.R
phylobase/tests/testthat/test.checkdata.R
phylobase/tests/testthat/test.treestruc.R
phylobase/tests/testthat/test.phylo4.R
phylobase/tests/testthat/test.subset.R
phylobase/tests/testthat/test.class-phylo4.R
phylobase/tests/testthat/test.pdata.R
phylobase/tests/testthat/test.methods-phylo4.R
phylobase/tests/testthat/test.setAs-Methods.R
phylobase/tests/testthat/test.prune.R
phylobase/tests/test-all.R
phylobase/src
phylobase/src/Makevars
phylobase/src/checkPhylo4.cpp
phylobase/src/reorderRobust.c
phylobase/src/phyloXX.c
phylobase/src/descendants.c
phylobase/src/ancestors.c
phylobase/src/reorderBinary.c
phylobase/src/Makevars.win
phylobase/src/RcppExports.cpp
phylobase/NAMESPACE
phylobase/NEWS.md
phylobase/data
phylobase/data/geospiza_raw.rda
phylobase/data/owls4.rda
phylobase/data/geospiza.rda
phylobase/R
phylobase/R/oldclasses-class.R phylobase/R/readNCL.R phylobase/R/getNode-methods.R phylobase/R/tdata-methods.R phylobase/R/nodeId-methods.R phylobase/R/pdata.R phylobase/R/phylo4-class.R phylobase/R/summary-methods.R phylobase/R/phylo4d-accessors.R phylobase/R/phylomats-class.R phylobase/R/edgeLength-methods.R phylobase/R/labels-methods.R phylobase/R/shortestPath-methods.R phylobase/R/extractTree.R phylobase/R/checkdata.R phylobase/R/print-methods.R phylobase/R/RcppExports.R phylobase/R/phylo4d-class.R phylobase/R/reorder-methods.R phylobase/R/phylo4-methods.R phylobase/R/multiphylo4-class.R phylobase/R/setAs-methods.R phylobase/R/addData-methods.R phylobase/R/MRCA-methods.R phylobase/R/ancestors.R phylobase/R/phylo4-accessors.R phylobase/R/formatData.R phylobase/R/treePlot.R phylobase/R/phylo4d-methods.R phylobase/R/tbind.R phylobase/R/phylobase.options.R phylobase/R/subset-methods.R phylobase/R/root-methods.R phylobase/R/zzz.R phylobase/R/phylobase-package.R phylobase/R/treestruc.R phylobase/R/internal-constructors.R
phylobase/vignettes
phylobase/vignettes/phylobase.Rnw
phylobase/vignettes/auto
phylobase/vignettes/auto/phylobase.el
phylobase/vignettes/auto/developer.el
phylobase/MD5
phylobase/build
phylobase/build/vignette.rds
phylobase/DESCRIPTION
phylobase/man
phylobase/man/treeStructure-methods.Rd phylobase/man/summary-methods.Rd phylobase/man/root-methods.Rd phylobase/man/phylo4-methods.Rd phylobase/man/edges-accessors.Rd phylobase/man/addData-methods.Rd phylobase/man/owls4.Rd phylobase/man/tdata-methods.Rd phylobase/man/shortestPath-methods.Rd phylobase/man/MRCA.Rd phylobase/man/extractTree.Rd phylobase/man/geospiza.Rd phylobase/man/phylomat-class.Rd phylobase/man/tip.data.plot.Rd phylobase/man/phylobubbles.Rd phylobase/man/setAs-methods.Rd phylobase/man/plotOneTree.Rd phylobase/man/subset-methods.Rd phylobase/man/phylo4d-class.Rd phylobase/man/nodeId-methods.Rd phylobase/man/phylo4d-accessors.Rd phylobase/man/multiPhylo-class.Rd phylobase/man/edgeLength-methods.Rd phylobase/man/phylo4d-methods.Rd phylobase/man/pdata.Rd phylobase/man/reorder-methods.Rd phylobase/man/getNode-methods.Rd phylobase/man/phylobase.options.Rd phylobase/man/formatData.Rd phylobase/man/readNexus.Rd phylobase/man/treePlot-methods.Rd phylobase/man/pdata-class.Rd phylobase/man/labels-methods.Rd phylobase/man/phyloXXYY.Rd phylobase/man/print-methods.Rd phylobase/man/ancestors.Rd phylobase/man/nTips-methods.Rd phylobase/man/checkPhylo4.Rd phylobase/man/phylobase-package.Rd phylobase/man/phylo4-class.Rd

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

All documentation is copyright its authors; we didn't write any of that.