Files in phytools

Phylogenetic Tools for Comparative Biology (and Other Things)

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/fitgammaMk.R R/evol.rate.mcmc.R R/fitmultiBM.R R/read.simmap.R R/simBMphylo.R R/utilities.R R/fitThresh.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/plotTree.lollipop.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/bounded_bm.R R/fitBiogeog.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/fitfnMk.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/plotFanTree.wTraits.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 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/bounded_bm.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/gamma_pruning.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/fitmultiBM.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/fitThresh.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.lollipop.Rd man/plotTree.Rd man/sim.corrs.Rd