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.

Author
R 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 publication
2016-01-23 00:32:41
Maintainer
Francois Michonneau <francois.michonneau@gmail.com>
License
GPL (>= 2)
Version
0.8.2
URLs

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