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 publication2014-05-08 14:46:52
MaintainerFrancois Michonneau <francois.michonneau@gmail.com>
LicenseGPL (>= 2)
Version0.6.9-1
http://phylobase.R-forge.R-project.org

View on R-Forge

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 Nexus or...

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...

Functions

[ Man page
addData Man page
addData-methods Man page
addData,phylo4d-method Man page
addData,phylo4-method Man page
ancestor Man page
ancestors Man page
as Man page
as-method Man page
as,phylo4,phylo-method Man page
as_phylo4vcov Man page
as,phylo,phylo4d-method Man page
as,phylo,phylo4-method Man page
check_pdata Man page
checkPhylo4 Man page
checkPhylo4Data Man page
checkTree Man page
children Man page
depthTips Man page
depthTips,phylo4-method Man page
depthTips,phylo4-methods Man page
descendants Man page
edgeId Man page
edgeId,phylo4-method Man page
edgeLabels Man page
edgeLabels<- Man page
edgeLabels<-,phylo4,character-method Man page
edgeLabels,phylo4-method Man page
edgeLength Man page
edgeLength<- Man page
edgeLength<-,phylo4,ANY-method Man page
edgeLength<-,phylo4-method Man page
edgeLength,phylo4-method Man page
edgeOrder Man page
edgeOrder,phylo4-method Man page
edges Man page
edges,phylo4-method Man page
extractTree Man page
formatData Man page
geospiza Man page
geospiza_raw Man page
getEdge Man page
getEdge-methods Man page
getEdge,phylo4-method Man page
getNode Man page
getNode,phylo4-method Man page
hasDuplicatedLabels Man page
hasDuplicatedLabels,phylo4,ANY-method Man page
hasDuplicatedLabels,phylo4-method Man page
hasEdgeLabels Man page
hasEdgeLabels,phylo4-method Man page
hasEdgeLength Man page
hasEdgeLength,phylo4-method Man page
hasNodeData Man page
hasNodeData-methods Man page
hasNodeData,phylo4d-method Man page
hasNodeLabels Man page
hasNodeLabels,phylo4-method Man page
hasPoly Man page
hasPoly,phylo4-method Man page
hasRetic Man page
hasRetic,phylo4-method Man page
hasSingle Man page
hasSingle,phylo4-method Man page
hasTipData Man page
hasTipData-method,phylo4d-method Man page
hasTipData,phylo4d-method Man page
head Man page
head,phylo4-method Man page
Import Nexus and Newick files Man page
internalEdges Man page
internalEdges,phylo4-method Man page
isRooted Man page
isRooted,phylo4-method Man page
isUltrametric Man page
isUltrametric,phylo4-method Man page
labels Man page
labels<- Man page
labels<-,phylo4,ANY,ANY,character-method Man page
labels,phylo4-method Man page
MRCA Man page
MRCA,phylo4-method Man page
MRCA,phylo-method Man page
multiPhylo4-class Man page
multiPhylo4d-class Man page
multiPhylo-class Man page
names Man page
names,phylo4-method Man page
nData Man page
nData,phylo4d-method Man page
nEdges Man page
nEdges,phylo4-method Man page
nNodes Man page
nNodes,phylo4-method Man page
nodeData Man page
nodeData<- Man page
nodeData-method Man page
nodeData<-,phylo4d,ANY-method Man page
nodeData<-,phylo4d-method Man page
nodeData,phylo4d-method Man page
nodeDepth Man page
nodeDepth,phylo4-method Man page
nodeId Man page
nodeId,phylo4-method Man page
nodeLabels Man page
nodeLabels<- Man page
nodeLabels<-,phylo4,character-method Man page
nodeLabels,phylo4-method Man page
nodeType Man page
nodeType,phylo4-method Man page
nTips Man page
nTips,phylo4-method Man page
nTips,phylo-method Man page
owls4 Man page
pdata Man page
[,pdata,ANY,ANY,ANY-method Man page
[[,pdata,ANY,ANY-method Man page
[[,pdata,ANY,missing-method Man page
pdata-class Man page
[<-,pdata-method Man page
[,pdata-method Man page
[[<-,pdata-method Man page
[[,pdata-method Man page
phylo4 Man page
[,phylo4,ANY,ANY,ANY-method Man page
[,phylo4,character,missing-method Man page
[,phylo4,character,missing,missing-method Man page
phylo4-class Man page
phylo4d Man page
[,phylo4d,ANY,character,missing-method Man page
[,phylo4d,ANY,logical,missing-method Man page
[,phylo4d,ANY,numeric,missing-method Man page
phylo4d-class Man page
phylo4d,matrix,matrix-method Man page
phylo4d,matrix-method Man page
phylo4d,phylo4d-method Man page
phylo4d,phylo4d,phylo4d-method Man page
phylo4d,phylo4-method Man page
phylo4d,phylo4,phylo4-method Man page
phylo4d,phylo-method Man page
phylo4d,phylo,phylo-method Man page
phylo4-labels Man page
[,phylo4,logical,missing-method Man page
[,phylo4,logical,missing,missing-method Man page
phylo4,matrix-method Man page
phylo4-methods Man page
[,phylo4,missing,missing-method Man page
[,phylo4,missing,missing,missing-method Man page
[,phylo4,numeric,missing-method Man page
[,phylo4,numeric,missing,missing-method Man page
phylo4_orderings Man page
phylo4,phylo-method Man page
phylo4vcov-class Man page
phylobase Man page
phylobase.options Man page
phylobase-package Man page
phylobubbles Man page
phylomat-class Man page
phylomat-setAs Man page
phyloXXYY Man page
plot Man page
plot,ANY,ANY-method Man page
plotOneTree Man page
plot,pdata,missing-method Man page
plot,phylo4-method Man page
plot,phylo4,missing-method Man page
print Man page
print,phylo4-method Man page
prune Man page
prune,phylo4d-method Man page
prune,phylo4-method Man page
ptypes Man page
readNCL Man page
readNewick Man page
readNexus Man page
reorder Man page
reorder-methods Man page
reorder,phylo4-method Man page
rootNode Man page
rootNode<- Man page
rootNode<-,phylo4-method Man page
rootNode,phylo4-method Man page
setAs Man page
setAs,phylo4,data.frame-method Man page
setAs,phylo4,phylog-method Man page
setAs,phylo4vcov,phylo4-method Man page
setAs,phylo,phylo4vcov-method Man page
shortestPath Man page
shortestPath-phylo Man page
shortestPath-phylo4 Man page
shortestPath,phylo4-method Man page
shortestPath,phylo-method Man page
show Man page
show,phylo4-method Man page
siblings Man page
subset Man page
subset-methods Man page
subset,phylo4-method Man page
sumEdgeLength Man page
sumEdgeLength,phylo4-method Man page
summary Man page
summary-methods Man page
summary,phylo4d-method Man page
summary,phylo4-method Man page
tail Man page
tail,phylo4-method Man page
tbind Man page
tdata Man page
tdata<- Man page
tdata<-,phylo4d,ANY-method Man page
tdata<-,phylo4d-method Man page
tdata,phylo4d-method Man page
terminalEdges Man page
terminalEdges,phylo4-method Man page
tipData Man page
tipData<- Man page
tipData-method Man page
tipData<-,phylo4d,ANY-method Man page
tipData<-,phylo4d-method Man page
tipData,phylo4d-method Man page
tip.data.plot Man page
tipLabels Man page
tipLabels<- Man page
tipLabels<-,phylo4,character-method Man page
tipLabels,phylo4-method Man page
treePlot Man page
treePlot-method Man page
treePlot-methods Man page
treePlot,phylo4,phylo4d-method Man page

Files

DESCRIPTION
NAMESPACE
NEWS
R
R/MRCA-methods.R R/RcppExports.R R/addData-methods.R R/ancestors.R R/checkdata.R R/edgeLength-methods.R R/extractTree.R R/formatData.R R/getNode-methods.R R/internal-constructors.R R/labels-methods.R R/multiphylo4-class.R R/nodeId-methods.R R/oldclasses-class.R R/pdata.R R/phylo4-accessors.R R/phylo4-class.R R/phylo4-methods.R R/phylo4d-accessors.R R/phylo4d-class.R R/phylo4d-methods.R R/phylobase-package.R R/phylobase.options.R R/phylomats-class.R R/print-methods.R R/readNCL.R R/reorder-methods.R R/root-methods.R R/setAs-methods.R R/shortestPath-methods.R R/subset-methods.R R/summary-methods.R R/tbind.R R/tdata-methods.R R/treePlot.R R/treestruc.R R/zzz.R
build
build/vignette.rds
data
data/geospiza.rda
data/geospiza_raw.rda
data/owls4.rda
inst
inst/doc
inst/doc/developer.Rnw
inst/doc/developer.pdf
inst/doc/phylobase.Rnw
inst/doc/phylobase.pdf
inst/nexusfiles
inst/nexusfiles/ExContData.Rdata
inst/nexusfiles/MultiLineTrees.nex
inst/nexusfiles/NastyLabels.nex
inst/nexusfiles/NastyLabels2.nex
inst/nexusfiles/badnex.nex
inst/nexusfiles/co1.nex
inst/nexusfiles/minNex.nex
inst/nexusfiles/minSeq.nex
inst/nexusfiles/multiLines.Rdata
inst/nexusfiles/newick.tre
inst/nexusfiles/noStateLabels.nex
inst/nexusfiles/shorebird_underscore.nex
inst/nexusfiles/treeRoundingError.nex
inst/nexusfiles/treeWithContinuousData.nex
inst/nexusfiles/treeWithDiscAndContData.nex
inst/nexusfiles/treeWithDiscreteData.nex
inst/nexusfiles/treeWithPolyExcludedData.nex
inst/nexusfiles/treeWithSpecialCharacters.nex
inst/nexusfiles/treeWithUnderscoreLabels.nex
man
man/MRCA.Rd man/addData-methods.Rd man/ancestors.Rd man/checkPhylo4.Rd man/edgeLength-methods.Rd man/edges-accessors.Rd man/extractTree.Rd man/formatData.Rd man/geospiza.Rd man/getNode-methods.Rd man/labels-methods.Rd man/multiPhylo-class.Rd man/nTips-methods.Rd man/nodeId-methods.Rd man/owls4.Rd man/pdata-class.Rd man/pdata.Rd man/phylo4-class.Rd man/phylo4-methods.Rd man/phylo4d-accessors.Rd man/phylo4d-class.Rd man/phylo4d-methods.Rd man/phyloXXYY.Rd man/phylobase-package.Rd man/phylobase.options.Rd man/phylobubbles.Rd man/phylomat-class.Rd man/plotOneTree.Rd man/print-methods.Rd man/readNexus.Rd man/reorder-methods.Rd man/root-methods.Rd man/setAs-methods.Rd man/shortestPath-methods.Rd man/subset-methods.Rd man/summary-methods.Rd man/tdata-methods.Rd man/tip.data.plot.Rd man/treePlot-methods.Rd man/treeStructure-methods.Rd
src
src/GetNCL.cpp
src/Makevars
src/Makevars.win
src/RcppExports.cpp
src/ancestors.c
src/checkPhylo4.cpp
src/descendants.c
src/ncl
src/ncl/ncl.h
src/ncl/nxsallocatematrix.h
src/ncl/nxsassumptionsblock.h
src/ncl/nxsblock.h
src/ncl/nxscdiscretematrix.h
src/ncl/nxscharactersblock.h
src/ncl/nxscxxdiscretematrix.h
src/ncl/nxsdatablock.h
src/ncl/nxsdefs.h
src/ncl/nxsdiscretedatum.h
src/ncl/nxsdistancedatum.h
src/ncl/nxsdistancesblock.h
src/ncl/nxsemptyblock.h
src/ncl/nxsexception.h
src/ncl/nxsmultiformat.h
src/ncl/nxspublicblocks.h
src/ncl/nxsreader.h
src/ncl/nxssetreader.h
src/ncl/nxsstring.h
src/ncl/nxstaxablock.h
src/ncl/nxstoken.h
src/ncl/nxstreesblock.h
src/ncl/nxsunalignedblock.h
src/ncl/nxsutilcopy.h
src/nxsassumptionsblock.cpp
src/nxsblock.cpp
src/nxscharactersblock.cpp
src/nxscxxdiscretematrix.cpp
src/nxsdatablock.cpp
src/nxsdistancedatum.cpp
src/nxsdistancesblock.cpp
src/nxsemptyblock.cpp
src/nxsexception.cpp
src/nxsmultiformat.cpp
src/nxspublicblocks.cpp
src/nxsreader.cpp
src/nxssetreader.cpp
src/nxsstring.cpp
src/nxstaxablock.cpp
src/nxstoken.cpp
src/nxstreesblock.cpp
src/nxsunalignedblock.cpp
src/phyloXX.c
src/reorderBinary.c
src/reorderRobust.c
tests
tests/doRUnit.R tests/misctests.R
tests/misctests.Rout.save
tests/phylo4dtests.R
tests/phylo4dtests.Rout.save
tests/phylosubtest.R
tests/phylosubtest.Rout.save
tests/phylotorture.R
tests/phylotorture.Rout.save
tests/plottest.R
tests/plottest.Rout.save
tests/roundtrip.R
tests/roundtrip.Rout.save
tests/test-all.R tests/testprune.R
tests/testprune.Rout.save
tests/testthat
tests/testthat/test.badnex.R tests/testthat/test.checkdata.R tests/testthat/test.class-phylo4.R tests/testthat/test.class-phylo4d.R tests/testthat/test.formatData.R tests/testthat/test.methods-oldclasses.R tests/testthat/test.methods-phylo4.R tests/testthat/test.pdata.R tests/testthat/test.phylo4.R tests/testthat/test.phylobase.options.R tests/testthat/test.prune.R tests/testthat/test.readNCL.R tests/testthat/test.setAs-Methods.R tests/testthat/test.subset.R tests/testthat/test.tbind.R tests/testthat/test.treePlot.R tests/testthat/test.treestruc.R tests/testthat/test.treewalk.R
vignettes
vignettes/developer.Rnw
vignettes/phylobase.Rnw

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

Please suggest features or report bugs with the GitHub issue tracker.

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