Files in phytools
Phylogenetic Tools for Comparative Biology (and Other Things)
MD5
NAMESPACE
DESCRIPTION
R/fastBM.R
R/readNexus.R
R/pbtree.R
R/writeNexus.R
R/ctt.R
R/fastAnc.R
R/ratebytree.R
R/backbonePhylo.R
R/map.overlap.R
R/sim.history.R
R/read.newick.R
R/collapseTree.R
R/phylo.to.map.R
R/phylo.impute.R
R/compare.chronograms.R
R/cophylo.R
R/plotTree.errorbars.R
R/phylANOVA.R
R/locate.yeti.R
R/add.random.R
R/phyl.RMA.R
R/phylomorphospace.R
R/cospeciation.R
R/map.to.singleton.R
R/evol.rate.mcmc.R
R/read.simmap.R
R/simBMphylo.R
R/utilities.R
R/threshBayes.R
R/estDiversity.R
R/pgls.Ives.R
R/evolvcv.lite.R
R/add.everywhere.R
R/dotTree.R
R/rerootingMethod.R
R/optim.phylo.ls.R
R/fancyTree.R
R/resolveNodes.R
R/skewers.R
R/fitDiversityModel.R
R/phylo.heatmap.R
R/splitplotTree.R
R/project.phylomorphospace.R
R/bd.R
R/ancThresh.R
R/fitmultiMk.R
R/anc.trend.R
R/densityTree.R
R/multirateBM.R
R/mcmcLambda.R
R/densityMap.R
R/sim.rates.R
R/drop.tip.simmap.R
R/phylosig.R
R/cotangleplot.R
R/fitMk.parallel.R
R/roundPhylogram.R
R/locate.fossil.R
R/consensus.edges.R
R/tree.grow.R
R/ratebystate.R
R/plotBranchbyTrait.R
R/brownie.lite.R
R/ls.consensus.R
R/plotTree.datamatrix.R
R/plotTree.wBars.R
R/plotrix_fn.R
R/exhaustiveMP.R
R/fitMk.R
R/anc.ML.R
R/Dtest.R
R/phyl.cca.R
R/rateshift.R
R/brownieREML.R
R/mrp.supertree.R
R/phylomorphospace3d.R
R/starTree.R
R/sim.corrs.R
R/fitHRM.R
R/bmPlot.R
R/add.species.to.genus.R
R/writeAncestors.R
R/mcmcBM.full.R
R/branching.diffusion.R
R/ltt.R
R/multi.mantel.R
R/make.simmap.R
R/phyl.resid.R
R/fitBayes.R
R/treeSlice.R
R/anc.Bayes.R
R/ltt95.R
R/fitpolyMk.R
R/phyl.pca.R
R/mcmcBM.R
R/fitPagel.R
R/export.as.xml.R
R/multiRF.R
R/parsimony.R
R/phyl.pairedttest.R
R/mcmcMk.R
R/make.era.map.R
R/evol.vcv.R
R/ansi_phylo.R
R/asr.R
R/allFurcTrees.R
R/write.simmap.R
R/strahlerNumber.R
R/contMap.R
R/plotSimmap.R
R/phenogram.R
R/paintSubTree.R
inst/CITATION
data/datalist
data/bat_virus.data.rda
data/tropidurid.data.rda
data/eel.tree.rda
data/primate.tree.rda
data/cordylid.tree.rda
data/liolaemid.data.rda
data/flatworm.tree.rda
data/anole.data.rda
data/darter.tree.rda
data/butterfly.tree.rda
data/tortoise.tree.rda
data/bonyfish.tree.rda
data/wasp.data.rda
data/liolaemid.tree.rda
data/tortoise.geog.rda
data/salamanders.rda
data/betaCoV.tree.rda
data/tropidurid.tree.rda
data/butterfly.data.rda
data/anoletree.rda
data/elapidae.tree.rda
data/cordylid.data.rda
data/vertebrate.tree.rda
data/sunfish.data.rda
data/wasp.trees.rda
data/mammal.data.rda
data/bonyfish.data.rda
data/bat.tree.rda
data/eel.data.rda
data/primate.data.rda
data/vertebrate.data.rda
data/mammal.geog.rda
data/sunfish.tree.rda
data/mammal.tree.rda
data/flatworm.data.rda
man/getSisters.Rd
man/drop.clade.Rd
man/setMap.Rd
man/anc.Bayes.Rd
man/roundBranches.Rd
man/anc.ML.Rd
man/reroot.Rd
man/phylo.impute.Rd
man/add.random.Rd
man/vcvPhylo.Rd
man/branching.diffusion.Rd
man/multi.mantel.Rd
man/plotTree.wBars.Rd
man/mapped.states.Rd
man/starTree.Rd
man/fitBayes.Rd
man/di2multi.simmap.Rd
man/reorderSimmap.Rd
man/phyloDesign.Rd
man/brownie.lite.Rd
man/getExtant.Rd
man/pscore.Rd
man/anc.trend.Rd
man/posterior.evolrate.Rd
man/sim.history.Rd
man/reorder.backbonePhylo.Rd
man/posthoc.Rd
man/bmPlot.Rd
man/to.matrix.Rd
man/writeAncestors.Rd
man/splitEdgeColor.Rd
man/sim.rates.Rd
man/fastAnc.Rd
man/cophylo.Rd
man/rstate.Rd
man/splitTree.Rd
man/as.Qmatrix.Rd
man/evol.vcv.Rd
man/densityMap.Rd
man/exhaustiveMP.Rd
man/multiC.Rd
man/ancThresh.Rd
man/rep.phylo.Rd
man/anoletree.Rd
man/phylo.toBackbone.Rd
man/ltt95.Rd
man/locate.fossil.Rd
man/drop.tip.contMap.Rd
man/minRotate.Rd
man/optim.phylo.ls.Rd
man/ave.rates.Rd
man/Dtest.Rd
man/midpoint.root.Rd
man/mergeMappedStates.Rd
man/roundPhylogram.Rd
man/nodelabels.cophylo.Rd
man/collapse.to.star.Rd
man/aic.w.Rd
man/make.simmap.Rd
man/collapseTree.Rd
man/skewers.Rd
man/plot.backbonePhylo.Rd
man/simBMphylo.Rd
man/phylo.to.map.Rd
man/mrp.supertree.Rd
man/phylomorphospace3d.Rd
man/sim.ratebystate.Rd
man/evolvcv.lite.Rd
man/threshDIC.Rd
man/strahlerNumber.Rd
man/add.arrow.Rd
man/plotBranchbyTrait.Rd
man/tree.grow.Rd
man/describe.simmap.Rd
man/phenogram.Rd
man/fastMRCA.Rd
man/fitDiversityModel.Rd
man/brownieREML.Rd
man/phyl.vcv.Rd
man/rescale.Rd
man/getDescendants.Rd
man/phyl.resid.Rd
man/likMlambda.Rd
man/phylosig.Rd
man/densityTree.Rd
man/sampleFrom.Rd
man/expand.clade.Rd
man/rescaleSimmap.Rd
man/linklabels.Rd
man/phylANOVA.Rd
man/map.overlap.Rd
man/read.simmap.Rd
man/getCladesofSize.Rd
man/ansi_phylo.Rd
man/ratebytree.Rd
man/genSeq.Rd
man/pgls.Ives.Rd
man/write.simmap.Rd
man/dotTree.Rd
man/density.multiSimmap.Rd
man/paintSubTree.Rd
man/edgeProbs.Rd
man/geo.legend.Rd
man/fitMk.Rd
man/fancyTree.Rd
man/matchNodes.Rd
man/phyl.cca.Rd
man/force.ultrametric.Rd
man/phyl.RMA.Rd
man/plotTree.errorbars.Rd
man/add.color.bar.Rd
man/read.newick.Rd
man/fitPagel.Rd
man/add.species.to.genus.Rd
man/add.simmap.legend.Rd
man/cospeciation.Rd
man/make.era.map.Rd
man/minSplit.Rd
man/consensus.edges.Rd
man/pbtree.Rd
man/plotSimmap.Rd
man/print.backbonePhylo.Rd
man/phyl.pairedttest.Rd
man/nodeHeights.Rd
man/edge.widthMap.Rd
man/drop.tip.multiSimmap.Rd
man/phyl.pca.Rd
man/as.multiPhylo.Rd
man/orderMappedEdge.Rd
man/evol.rate.mcmc.Rd
man/ancr.Rd
man/rotateNodes.Rd
man/multirateBM.Rd
man/ladderize.simmap.Rd
man/ratebystate.Rd
man/add.everywhere.Rd
man/phytools-package.Rd
man/lambda.transform.Rd
man/countSimmap.Rd
man/ltt.Rd
man/gammatest.Rd
man/drop.leaves.Rd
man/fastBM.Rd
man/threshState.Rd
man/drop.tip.simmap.Rd
man/estDiversity.Rd
man/resolveNode.Rd
man/ctt.Rd
man/getStates.Rd
man/rerootingMethod.Rd
man/averageTree.Rd
man/compare.chronograms.Rd
man/allFurcTrees.Rd
man/locate.yeti.Rd
man/paste.tree.Rd
man/cladelabels.Rd
man/splitplotTree.Rd
man/applyBranchLengths.Rd
man/modified.Grafen.Rd
man/writeNexus.Rd
man/get.treepos.Rd
man/bd.Rd
man/map.to.singleton.Rd
man/contMap.Rd
man/plotTree.datamatrix.Rd
man/phylo.heatmap.Rd
man/labelnodes.Rd
man/export.as.xml.Rd
man/multiRF.Rd
man/bind.tip.Rd
man/rateshift.Rd
man/markChanges.Rd
man/ls.tree.Rd
man/fit.bd.Rd
man/phylomorphospace.Rd
man/untangle.Rd
man/findMRCA.Rd
man/plotThresh.Rd
man/treeSlice.Rd
man/threshBayes.Rd
man/bind.tree.simmap.Rd
man/plotTree.Rd
man/sim.corrs.Rd
