API for phytools
Phylogenetic Tools for Comparative Biology (and Other Things)
| Global functions | |
|---|---|
| .Qmatrix.from.gfit | Source code |
| .check.pkg | Source code |
| AIC.ratebytree | Source code |
| AccDelTran | Source code |
| Arctext | Source code |
| Asp | Source code |
| BRANCHING | Source code |
| Combinations | Source code |
| Diag | Source code |
| Draw.arc | Source code |
| Draw.circle | Source code |
| Draw.ellipse | Source code |
| Dtest | Man page Source code |
| EXPM | Source code |
| Fitch | Source code |
| GetYmult | Source code |
| HPD | Source code Source code |
| MAX | Source code |
| MIN | Source code |
| MULTI2DI | Source code |
| Map.Overlap | Man page Source code |
| Nedge.contMap | Source code |
| Nedge.cophylo | Source code |
| Nedge.densityMap | Source code |
| Nnode.contMap | Source code |
| Nnode.cophylo | Source code |
| Nnode.densityMap | Source code |
| Ntip.contMap | Source code |
| Ntip.cophylo | Source code |
| Ntip.densityMap | Source code |
| Palette | Source code |
| RANGE | Source code |
| SIGNIF | Source code |
| SetMap | Source code |
| TEXTBOX | Source code |
| TIPHEIGHTS | Source code |
| TREEDIST | Source code |
| Textbox | Source code |
| VCV | Source code |
| acctran | Source code |
| add.arrow | Man page Source code |
| add.color.bar | Man page Source code |
| add.everywhere | Man page Source code |
| add.random | Man page Source code |
| add.scalebar | Source code |
| add.simmap.legend | Man page Source code |
| add.species.to.genus | Man page Source code |
| add.to.branches.and.nodes | Source code |
| aic.w | Man page Source code |
| allFurcTrees | Man page Source code |
| allMatch | Source code |
| allRotations | Man page Source code |
| anc.BM | Source code |
| anc.Bayes | Man page Source code |
| anc.EB | Source code |
| anc.ML | Man page Source code |
| anc.OU | Source code |
| anc.trend | Man page Source code |
| ancThresh | Man page Source code |
| ancr | Man page Source code |
| ancr.anova.fitMk | Source code |
| ancr.bounded_bm | Source code |
| ancr.default | Source code |
| ancr.fitHRM | Source code |
| ancr.fitMk | Source code |
| ancr.fitThresh | Source code |
| ancr.fitgammaMk | Source code |
| ancr.fitpolyMk | Source code |
| anole.data | Man page |
| anoletree | Man page |
| anova.evolvcv.lite | Source code |
| anova.fit.bd | Source code |
| anova.fitHRM | Source code |
| anova.fitMk | Source code |
| anova.fitPagel | Source code |
| anova.fitgammaMk | Source code |
| anova.fitpolyMk | Source code |
| ansi_phylo | Man page Source code |
| ant.geog | Man page |
| ant.tree | Man page |
| apeAce | Source code |
| applyBranchLengths | Man page Source code |
| arc.cladelabels | Man page Source code |
| arcPhylogram | Source code |
| as.Qmatrix | Man page Source code |
| as.Qmatrix.ace | Source code |
| as.Qmatrix.corhmm | Source code |
| as.Qmatrix.default | Source code |
| as.Qmatrix.fitMk | Man page Source code |
| as.Qmatrix.fitgammaMk | Source code |
| as.Qmatrix.fitpolyMk | Source code |
| as.Qmatrix.matrix | Source code |
| as.multiPhylo | Man page Source code |
| as.multiPhylo.multiSimmap | Man page Source code |
| as.multiPhylo.phylo | Man page Source code |
| as.phylo.simmap | Source code |
| as.prcomp | Man page Source code |
| as.prcomp.default | Source code |
| as.prcomp.phyl.pca | Source code |
| as.princomp | Man page Source code |
| as.princomp.default | Source code |
| as.princomp.phyl.pca | Source code |
| ave.rates | Man page Source code |
| averageTree | Man page Source code |
| backbone.toPhylo | Man page Source code |
| backbone.toTrans | Source code |
| bat.tree | Man page |
| bat_virus.data | Man page |
| bd | Man page Source code |
| betaCoV.tree | Man page |
| bind.tip | Man page Source code |
| bind.tree.simmap | Man page Source code |
| biogeog_pruning | Source code |
| biplot.phyl.pca | Man page Source code |
| bm | Source code |
| bmPlot | Man page Source code |
| bonyfish.data | Man page |
| bonyfish.tree | Man page |
| bounce | Source code |
| bounded_bm | Man page Source code |
| branch.and.bound | Source code |
| branching.diffusion | Man page Source code |
| brownie.lite | Man page Source code |
| brownieREML | Man page Source code |
| butterfly.data | Man page |
| butterfly.tree | Man page |
| bySegments | Source code |
| c.multiSimmap | Source code |
| c.simmap | Source code |
| calcD | Source code |
| circles | Source code |
| cladebox | Man page Source code |
| cladelabels | Man page Source code |
| cladogram | Source code |
| coef.phyl.RMA | Man page Source code |
| collapse.to.star | Man page Source code |
| collapseTree | Man page Source code |
| compare.chronograms | Man page Source code |
| compute.ancestor.nodes | Source code |
| compute.brlen.simmap | Source code |
| compute.mr | Man page Source code |
| consensus.edges | Man page Source code |
| contMap | Man page Source code |
| cophylo | Man page Source code |
| cordylid.data | Man page |
| cordylid.tree | Man page |
| cospeciation | Man page Source code |
| cotangleplot | Man page Source code |
| countSimmap | Man page Source code |
| crop.to.h | Source code |
| ctt | Man page Source code |
| darter.tree | Man page |
| density.anc.Bayes | Man page Source code |
| density.mcmcMk | Man page Source code |
| density.multiSimmap | Man page Source code |
| density.threshBayes | Source code |
| densityMap | Man page Source code |
| densityTree | Man page Source code |
| describe.simmap | Man page Source code |
| di2multi.contMap | Man page Source code |
| di2multi.densityMap | Man page Source code |
| di2multi.multiSimmap | Man page Source code |
| di2multi.simmap | Man page Source code |
| dot.legend | Man page Source code |
| dotTree | Man page Source code |
| dotTree.continuous | Source code |
| dotTree.discrete | Source code |
| drawCurve | Source code |
| drop.clade | Man page Source code |
| drop.leaves | Man page Source code |
| drop.tip.contMap | Man page Source code |
| drop.tip.densityMap | Man page Source code |
| drop.tip.multiSimmap | Man page Source code |
| drop.tip.simmap | Man page Source code |
| drop.tip.singleton | Man page Source code |
| droptipTree | Source code |
| ebTree | Source code |
| edge.widthMap | Man page Source code |
| edgeProbs | Man page Source code |
| edgelabels.cophylo | Man page Source code |
| eel.data | Man page |
| eel.tree | Man page |
| eigen_pruning | Source code |
| elapidae.tree | Man page |
| errorbar.contMap | Man page Source code |
| estDiversity | Man page Source code |
| evol.rate.mcmc | Man page Source code |
| evol.vcv | Man page Source code |
| evolvcv.lite | Man page Source code |
| exhaustive.search | Source code |
| exhaustiveMP | Man page Source code |
| expand | Source code |
| expand.clade | Man page Source code |
| expand.range | Source code |
| expand_range | Source code |
| expected_disparity | Source code |
| export.as.xml | Man page Source code |
| extinctionTree | Source code |
| extract.clade.simmap | Man page Source code Source code |
| extract.strahlerNumber | Man page Source code |
| fan | Source code |
| fancyTree | Man page Source code |
| fastAnc | Man page Source code |
| fastBM | Man page Source code |
| fastDist | Man page Source code |
| fastHeight | Man page Source code |
| fastMRCA | Man page Source code |
| findMRCA | Man page Source code |
| fit.bd | Man page Source code |
| fit.yule | Man page Source code |
| fitBayes | Man page Source code |
| fitBiogeog | Source code |
| fitDiversityModel | Man page Source code |
| fitHRM | Man page Source code |
| fitMk | Man page Source code |
| fitMk.parallel | Man page Source code |
| fitPagel | Man page Source code |
| fitThresh | Man page Source code |
| fitcontMk | Man page Source code |
| fitfnMk | Man page Source code |
| fitgammaMk | Man page Source code |
| fitmultiBM | Man page Source code |
| fitmultiMk | Man page Source code |
| fitmultiTrend | Man page Source code |
| fitpolyMk | Man page Source code |
| fitsemiThresh | Man page Source code |
| fitted.multi.mantel | Source code |
| flatworm.data | Man page |
| flatworm.tree | Man page |
| foldtoLower | Source code |
| force.ultrametric | Man page Source code |
| fossilML | Source code |
| gamma_pruning | Man page Source code |
| gammatest | Man page Source code |
| genSeq | Man page Source code |
| genus.to.species.tree | Man page Source code |
| geo.legend | Man page Source code |
| geo.palette | Man page Source code |
| get.asp | Source code |
| get.treepos | Man page Source code |
| getAncestors | Source code |
| getBS | Source code |
| getBranch | Source code |
| getChanges | Source code |
| getCladesofSize | Man page Source code |
| getDescendants | Man page Source code |
| getEdgeLength | Source code Source code |
| getExtant | Man page Source code |
| getExtinct | Man page Source code |
| getLabel | Source code |
| getParent | Man page Source code |
| getPars | Source code |
| getSisters | Man page Source code |
| getState | Source code |
| getStates | Man page Source code |
| getnode | Man page Source code |
| graph.polyMk | Man page Source code |
| gtt | Man page Source code |
| hide.hidden | Man page Source code |
| hide.hidden.ancr | Source code |
| hide.hidden.default | Source code |
| inv.ncombn | Source code |
| inv.ncombn2 | Source code |
| is.Qmatrix | Source code |
| isOdd | Source code |
| isSingleton | Source code |
| joint_asr | Source code |
| keep.tip.contMap | Man page Source code |
| keep.tip.densityMap | Man page Source code |
| keep.tip.multiSimmap | Man page Source code |
| keep.tip.simmap | Man page Source code |
| labelSubTree | Source code |
| labelnodes | Man page Source code |
| ladderize.simmap | Man page Source code |
| lambda.transform | Man page Source code |
| lambdaTree | Source code Source code |
| lik.bd | Man page Source code |
| lik.multiple | Source code |
| lik.single | Source code |
| likLiab | Source code |
| likMlambda | Man page Source code |
| likSurface.rateshift | Man page |
| lik_thresh | Source code |
| likelihood.lambda | Source code |
| linklabels | Man page Source code |
| liolaemid.data | Man page |
| liolaemid.tree | Man page |
| ln.mean | Source code |
| locate.fossil | Man page Source code |
| locate.yeti | Man page Source code |
| logLik.anc.ML | Source code |
| logLik.anc.trend | Source code |
| logLik.ancr | Source code |
| logLik.bounded_bm | Source code |
| logLik.brownie.lite | Source code |
| logLik.fit.bd | Source code |
| logLik.fitDiversityModel | Man page Source code |
| logLik.fitMk | Source code |
| logLik.fitThresh | Source code |
| logLik.fitgammaMk | Source code |
| logLik.fitmultiMk | Source code |
| logLik.fitpolyMk | Source code |
| logLik.fitsemiThresh | Source code |
| logLik.multiSimmap | Source code |
| logLik.multirateBM | Source code |
| logLik.pgls.Ives | Source code |
| logLik.rateshift | Source code |
| logLik.rerootingMethod | Source code |
| logLik.simmap | Source code |
| logMNORM | Source code |
| logPrior | Source code |
| log_lik | Source code |
| log_relik | Source code |
| ls.consensus | Man page Source code |
| ls.tree | Man page Source code |
| ltt | Man page Source code |
| ltt.default | Source code |
| ltt.multiPhylo | Man page Source code |
| ltt.multiSimmap | Man page Source code |
| ltt.phylo | Man page Source code |
| ltt.simmap | Man page Source code |
| ltt95 | Man page Source code |
| make.era.map | Man page Source code |
| make.simmap | Man page Source code |
| make.sym | Source code |
| make.transparent | Man page Source code |
| makeMappedEdge | Source code |
| makeQ | Source code |
| makelinks | Source code |
| makeq | Source code |
| mammal.data | Man page |
| mammal.geog | Man page |
| mammal.tree | Man page |
| map.overlap | Man page Source code |
| map.to.singleton | Man page Source code |
| mapped.states | Man page Source code |
| marginal_asr | Source code |
| marginal_asr_gamma | Source code |
| marginal_local | Source code |
| markChanges | Man page Source code |
| matchDatatoTree | Source code |
| matchLabels | Man page Source code |
| matchNodes | Man page Source code |
| matchTreetoData | Source code |
| matchType | Source code |
| maxLambda | Source code |
| mccr | Man page Source code |
| mcmcBM | Source code |
| mcmcBM.full | Source code |
| mcmcLambda | Source code |
| mcmcMk | Man page Source code |
| mcmcQ | Source code |
| mergeAdjacent | Source code |
| mergeMappedStates | Man page Source code |
| midpoint.root | Man page Source code |
| midpoint_root | Man page Source code |
| minChanges | Source code |
| minRotate | Man page Source code |
| minSplit | Man page Source code |
| minTreeDist | Man page Source code |
| ml_phyl.pca | Source code |
| modified.Grafen | Man page Source code |
| modified.text_to_tree | Source code |
| mrp.supertree | Man page Source code |
| mtom | Source code |
| multi.mantel | Man page Source code |
| multi2di.contMap | Man page Source code |
| multi2di.densityMap | Man page Source code |
| multi2di.multiSimmap | Man page Source code |
| multi2di.simmap | Man page Source code |
| multiC | Man page Source code |
| multiOU | Man page Source code |
| multiRF | Man page Source code |
| multirateBM | Man page Source code |
| namesplit | Source code |
| ncombn | Source code |
| newick | Source code |
| node.paths | Man page Source code |
| nodeHeights | Man page Source code |
| nodeheight | Man page Source code |
| nodelabels.cophylo | Man page Source code |
| old.gamma_pruning | Source code |
| optim.phylo.ls | Man page Source code |
| orderMappedEdge | Man page Source code |
| p.func | Source code |
| paintBranches | Man page Source code |
| paintSubTree | Man page Source code |
| parallel_pruning | Source code |
| paste.tree | Man page Source code |
| pbtree | Man page Source code |
| pgls.Ives | Man page Source code |
| pgls.SEy | Man page Source code |
| phenogram | Man page Source code |
| phenogram95 | Man page Source code |
| phyl.RMA | Man page Source code |
| phyl.cca | Man page Source code |
| phyl.pairedttest | Man page Source code |
| phyl.pca | Man page Source code |
| phyl.resid | Man page Source code |
| phyl.vcv | Man page Source code |
| phylANOVA | Man page Source code |
| phylo.heatmap | Man page Source code |
| phylo.impute | Man page Source code |
| phylo.to.map | Man page Source code |
| phylo.toBackbone | Man page Source code |
| phyloDesign | Man page Source code |
| phyloScattergram | Man page Source code |
| phylogram | Source code |
| phylomorphospace | Man page Source code |
| phylomorphospace3d | Man page Source code |
| phylosig | Man page Source code |
| phytools | Man page |
| phytools-package | Man page |
| plot.Qmatrix | Man page Source code |
| plot.anc.Bayes | Man page Source code |
| plot.ancThresh | Source code |
| plot.ancr | Man page Source code |
| plot.backbonePhylo | Man page Source code |
| plot.changesMap | Man page Source code |
| plot.contMap | Man page Source code |
| plot.cophylo | Man page Source code |
| plot.cospeciation | Man page Source code |
| plot.ctt | Source code |
| plot.density.mcmcMk | Man page Source code |
| plot.density.threshBayes | Source code |
| plot.densityMap | Man page Source code |
| plot.describe.simmap | Man page Source code |
| plot.edge.widthMap | Man page Source code |
| plot.expand.clade | Man page Source code |
| plot.fitBayes | Source code |
| plot.fitHRM | Man page Source code |
| plot.fitMk | Man page Source code |
| plot.fitPagel | Man page Source code |
| plot.fitcontMk | Source code |
| plot.fitfnMk | Source code |
| plot.fitgammaMk | Source code |
| plot.fitpolyMk | Man page Source code |
| plot.gfit | Man page Source code |
| plot.gtt | Source code |
| plot.ltt | Source code |
| plot.ltt.multiSimmap | Source code |
| plot.ltt.simmap | Source code |
| plot.ltt95 | Man page Source code |
| plot.mccr | Source code |
| plot.mcmcMk | Man page Source code |
| plot.multiCophylo | Source code |
| plot.multiCtt | Source code |
| plot.multiLtt | Source code |
| plot.multiSimmap | Man page Source code |
| plot.multirateBM | Source code |
| plot.multirateBM_plot | Source code |
| plot.phyl.RMA | Man page Source code |
| plot.phyl.pca | Source code |
| plot.phylo.to.map | Man page Source code |
| plot.phyloScattergram | Source code |
| plot.phylosig | Man page Source code |
| plot.rateshift | Man page Source code |
| plot.rerootingMethod | Source code |
| plot.simBMphylo | Man page Source code |
| plot.simmap | Man page Source code |
| plot.summary.evol.rate.mcmc | Man page Source code |
| plot.threshBayes | Source code |
| plotBranchbyTrait | Man page Source code |
| plotCladogram | Source code |
| plotContMap | Source code |
| plotDensityMap | Source code |
| plotFan | Source code |
| plotFanTree.wTraits | Man page Source code |
| plotPhylogram | Source code |
| plotSimmap | Man page Source code |
| plotThresh | Man page Source code |
| plotTree | Man page Source code |
| plotTree.barplot | Man page Source code |
| plotTree.boxplot | Man page Source code |
| plotTree.datamatrix | Man page Source code |
| plotTree.errorbars | Man page Source code |
| plotTree.lollipop | Man page Source code |
| plotTree.singletons | Man page Source code |
| plotTree.splits | Man page Source code |
| plotTree.wBars | Man page Source code |
| posterior.evolrate | Man page Source code |
| posthoc | Man page Source code |
| posthoc.ratebytree | Man page Source code |
| prbt.cont | Source code |
| prbt.disc | Source code |
| prbt.div | Source code |
| primate.data | Man page |
| primate.tree | Man page |
| print.Dtest | Source code |
| print.Qmatrix | Man page Source code |
| print.aic.w | Source code |
| print.anc.Bayes | Source code |
| print.anc.ML | Source code |
| print.anc.trend | Source code |
| print.ancThresh | Source code |
| print.ancr | Source code |
| print.ancr.bounded_bm | Source code |
| print.backbonePhylo | Man page Source code |
| print.bounded_bm | Source code |
| print.brownie.lite | Source code |
| print.brownieREML | Source code |
| print.contMap | Source code |
| print.cophylo | Source code |
| print.cospeciation | Man page Source code |
| print.ctt | Source code |
| print.density.mcmcMk | Source code |
| print.density.threshBayes | Source code |
| print.densityMap | Source code |
| print.describe.simmap | Source code |
| print.edge.widthMap | Source code |
| print.evol.rate.mcmc | Man page Source code |
| print.evol.vcv | Source code |
| print.evolvcv.lite | Source code |
| print.expand.clade | Source code |
| print.fastAnc | Source code |
| print.fit.bd | Man page Source code |
| print.fitBayes | Source code |
| print.fitDiversityModel | Man page Source code |
| print.fitHRM | Source code |
| print.fitMk | Source code |
| print.fitPagel | Source code |
| print.fitThresh | Source code |
| print.fitgammaMk | Source code |
| print.fitmultiMk | Source code |
| print.fitpolyMk | Source code |
| print.fitsemiThresh | Source code |
| print.gammatest | Source code |
| print.geo.legend | Source code |
| print.geo.palette | Source code |
| print.gtt | Source code |
| print.ltt | Source code |
| print.ltt.multiSimmap | Source code |
| print.ltt.simmap | Source code |
| print.ltt95 | Source code |
| print.mccr | Source code |
| print.mcmcMk | Source code |
| print.multi.mantel | Source code |
| print.multiCophylo | Source code |
| print.multiCtt | Source code |
| print.multiLtt | Source code |
| print.multiSimmap | Source code |
| print.multirateBM | Source code |
| print.multirateBM_plot | Source code |
| print.pgls.Ives | Source code |
| print.phyl.RMA | Source code |
| print.phyl.cca | Source code |
| print.phyl.pairedttest | Source code |
| print.phyl.pca | Source code |
| print.phylANOVA | Source code |
| print.phylo.impute | Source code |
| print.phylo.to.map | Source code |
| print.phyloScattergram | Source code |
| print.phylosig | Source code |
| print.posthoc.ratebytree | Source code |
| print.ratebystate | Source code |
| print.ratebytree | Source code |
| print.rateshift | Source code |
| print.rerootingMethod | Source code |
| print.simBMphylo | Source code |
| print.simmap | Source code |
| print.summary.evol.rate.mcmc | Man page Source code |
| print.threshBayes | Source code |
| printDotDot | Source code |
| printmessage | Source code |
| probMatch | Source code |
| project.phylomorphospace | Man page Source code |
| pruning | Source code |
| pscore | Man page Source code |
| qb | Source code |
| qpd | Source code |
| ratebystate | Man page Source code |
| ratebytree | Man page Source code |
| rateshift | Man page Source code |
| rbt.cont | Source code |
| rbt.disc | Source code |
| rbt.div | Source code |
| read.newick | Man page Source code |
| read.simmap | Man page Source code |
| readNexus | Man page Source code |
| readNexusData | Source code |
| remlMlambda | Source code |
| reml_phyl.pca | Source code |
| reorder.backbonePhylo | Man page Source code |
| reorder.simmap | Source code |
| reorderPhylo | Source code |
| reorderSimmap | Man page Source code |
| rep.multiPhylo | Man page Source code |
| rep.phylo | Man page Source code |
| repPhylo | Man page Source code |
| reroot | Man page Source code |
| rerootingMethod | Man page Source code |
| rescale | Man page Source code |
| rescale.default | Source code |
| rescale.multiSimmap | Man page Source code |
| rescale.simmap | Man page Source code |
| rescaleSimmap | Man page Source code |
| rescaleTree | Source code |
| residuals.multi.mantel | Source code |
| residuals.phyl.RMA | Source code |
| resolveAllNodes | Man page Source code |
| resolveNode | Man page Source code |
| rootedge.to.singleton | Man page Source code |
| rotate.multi | Man page Source code |
| rotateNodes | Man page Source code |
| roundBranches | Man page Source code |
| roundPhylogram | Man page Source code |
| rss | Source code |
| rstate | Man page Source code |
| salamanders | Man page |
| sampleFrom | Man page Source code |
| scaleByMap | Source code |
| scaleN | Source code |
| sch | Source code |
| scores | Man page Source code |
| scores.default | Source code |
| scores.phyl.pca | Man page Source code |
| setMap | Man page Source code |
| setMap.contMap | Man page Source code |
| setMap.default | Source code |
| setMap.densityMap | Man page Source code |
| setMap.multirateBM_plot | Man page Source code |
| setMap.phyloScattergram | Man page Source code |
| sigmoidPhylogram | Man page Source code |
| sim.Mk | Man page Source code |
| sim.absorbing | Man page Source code |
| sim.corrs | Man page Source code |
| sim.ctt | Man page Source code |
| sim.history | Man page Source code |
| sim.multiCtt | Man page Source code |
| sim.multiMk | Man page Source code |
| sim.multiTrend | Man page |
| sim.ratebystate | Man page Source code |
| sim.rates | Man page Source code |
| sim.reflective | Man page Source code |
| simBM | Source code |
| simBMphylo | Man page Source code |
| simOU | Source code |
| simmap | Man page Source code |
| simmap.anova.fitMk | Source code |
| simmap.default | Source code |
| simmap.fitMk | Source code |
| simmap.fitpolyMk | Source code |
| simmap.simmap | Source code |
| skewers | Man page Source code |
| smap | Source code |
| splinePhylogram | Man page Source code |
| splitEdgeColor | Man page Source code |
| splitTree | Man page Source code |
| splitplotTree | Man page Source code |
| spreadlabels | Source code |
| starTree | Man page Source code |
| statdist | Source code |
| strahlerNumber | Man page Source code |
| summary.anc.Bayes | Source code |
| summary.cophylo | Source code |
| summary.evol.rate.mcmc | Man page Source code |
| summary.fitMk | Source code |
| summary.fitmultiMk | Source code |
| summary.mcmcMk | Source code |
| summary.multiSimmap | Man page Source code |
| summary.phyl.pca | Source code |
| summary.simmap | Man page Source code |
| sunfish.data | Man page |
| sunfish.tree | Man page |
| t2bin_v1 | Source code |
| t2bin_v2 | Source code |
| tTests | Source code |
| text_to_tree | Source code |
| th | Source code |
| thresh2bin | Source code |
| threshBayes | Man page Source code |
| threshCol | Source code |
| threshDIC | Man page Source code |
| threshState | Man page |
| tipRotate | Man page Source code |
| tiplabels.cophylo | Man page Source code |
| to.matrix | Man page Source code Source code |
| to.symmetric | Source code |
| to.upper | Source code |
| to.vector | Source code |
| to_binned | Source code |
| tortoise.geog | Man page |
| tortoise.tree | Man page |
| tr | Source code |
| traitgram3d | Source code |
| tree.grow | Man page Source code |
| treeSlice | Man page Source code |
| tropidurid.data | Man page |
| tropidurid.tree | Man page |
| unfoldLower | Source code |
| untangle | Man page Source code |
| update_map | Source code |
| updownPhylogram | Source code |
| upper.diag | Source code |
| vcvPhylo | Man page Source code |
| vertebrate.data | Man page |
| vertebrate.tree | Man page |
| wasp.data | Man page |
| wasp.trees | Man page |
| whale.tree | Man page |
| whichorder | Source code |
| write.simmap | Man page Source code |
| write.v1 | Source code |
| write.v2 | Source code |
| writeAnc | Source code |
| writeAncestors | Man page Source code |
| writeNex | Source code |
| writeNexus | Man page Source code |
| x_by_y | Source code |
| yetiML | Source code |
| yetiREML | Source code |
