| phytools: Phylogenetic Tools for comparative biology (and other things) | phytools-package phytools |
| Add an arrow pointing to a tip or node on the tree | add.arrow |
| Add color bar to a plot | add.color.bar |
| Add tip to all edges in a tree | add.everywhere |
| Add tips at random to the tree | add.random |
| Add legend to stochastically mapped tree | add.simmap.legend |
| Add species to genus on a phylogeny or bind simulated species subtrees to a backbone genus tree | add.species.to.genus genus.to.species.tree |
| Computes Akaike weights | aic.w |
| Generate all bi- and multifurcating unrooted trees | allFurcTrees |
| Bayesian ancestral character estimation | anc.Bayes density.anc.Bayes plot.anc.Bayes |
| Ancestral character estimation using likelihood | anc.ML |
| Ancestral character estimation with a trend | anc.trend |
| Compute marginal or joint ancestral state estimates | ancr hide.hidden plot.ancr |
| Ancestral character estimation under the threshold model using Bayesian MCMC | ancThresh |
| Phylogenetic datasets | anole.data anoletree ant.geog ant.tree bat.tree bat_virus.data betaCoV.tree bonyfish.data bonyfish.tree butterfly.data butterfly.tree cordylid.data cordylid.tree darter.tree eel.data eel.tree elapidae.tree flatworm.data flatworm.tree liolaemid.data liolaemid.tree mammal.data mammal.geog mammal.tree primate.data primate.tree salamanders sunfish.data sunfish.tree tortoise.geog tortoise.tree tropidurid.data tropidurid.tree vertebrate.data vertebrate.tree wasp.data wasp.trees whale.tree |
| Graph a phylogeny using only ANSI characters | ansi_phylo |
| Applies the branch lengths of a reference tree to a target | applyBranchLengths |
| Conversion to object of class '"multiPhylo"' | as.multiPhylo as.multiPhylo.multiSimmap as.multiPhylo.phylo |
| Convert a fitted M_k_ model to a Q-matrix | as.Qmatrix as.Qmatrix.fitMk plot.Qmatrix print.Qmatrix |
| Average the posterior rates | ave.rates |
| Compute an average tree from a set of trees and related operations | averageTree ls.consensus minTreeDist |
| Convert object of class '"birthdeath"' to raw birth & death rates | bd |
| Attaches a new tip to a tree | bind.tip |
| Binds two trees of class '"simmap"' | bind.tree.simmap |
| Simulates and visualizes continuous trait evolution on a phylogeny | bmPlot sim.absorbing sim.multiTrend sim.reflective |
| Fits bounded and wrapped Brownian motion models | bounded_bm |
| Animation of branching random diffusion | branching.diffusion |
| Likelihood test for rate variation in a continuous trait | brownie.lite |
| REML version of 'brownie.lite' | brownieREML |
| Add labels to subtrees of a plotted phylogeny | arc.cladelabels cladebox cladelabels |
| Collapse a subtree to a star phylogeny | collapse.to.star |
| Interactive tree visualizer | collapseTree |
| Compares two chronograms with precisely matching nodes in a visual manner | compare.chronograms |
| Compute consensus edges for a tree under some criterion | consensus.edges |
| Map continuous trait evolution on the tree | contMap errorbar.contMap plot.contMap |
| Creates a co-phylogenetic plot | cophylo cotangleplot plot.cophylo |
| Conducts a statistical test of cospeciation between two trees | cospeciation plot.cospeciation print.cospeciation |
| Counts the number of character changes on a object of class '"simmap"' or '"multiSimmap"' | countSimmap |
| Generates (or simulates) a 'changes through time' plot from a set of stochastic map character histories | ctt sim.ctt sim.multiCtt |
| Computes a posterior distribution for the number and types of changes on the tree | density.multiSimmap plot.changesMap |
| Plot posterior density of stochastic mapping on a tree | densityMap plot.densityMap |
| Plots a posterior sample of trees | densityTree make.transparent |
| Summarizes a stochastic mapped tree or set of trees | describe.simmap plot.describe.simmap summary.multiSimmap summary.simmap |
| Collapse or resolve polytomies in a tree with a character painted on the edges | di2multi.contMap di2multi.densityMap di2multi.multiSimmap di2multi.simmap multi2di.contMap multi2di.densityMap multi2di.multiSimmap multi2di.simmap |
| Creates a phylogenetic dot plot | dot.legend dotTree |
| Drop a clade from a tree | drop.clade |
| Drop all the leaves (tips) from a tree | drop.leaves |
| Drop tip or tips from an object of class '"contMap"' or '"densityMap"' | drop.tip.contMap drop.tip.densityMap keep.tip.contMap keep.tip.densityMap |
| Drop or keep tip or tips from an object of class '"multiSimmap"' | drop.tip.multiSimmap keep.tip.multiSimmap |
| Drop tips or extract clade from tree with mapped discrete character | drop.tip.simmap extract.clade.simmap keep.tip.simmap |
| Conducts correlational D-test from stochastic mapping | Dtest |
| Map continuous trait evolution on the tree | edge.widthMap plot.edge.widthMap |
| Compute the relative frequencies of state changes along edges | edgeProbs |
| Estimate diversity at each node of the tree | estDiversity |
| Bayesian MCMC method for identifying exceptional phenotypic diversification in a phylogeny | evol.rate.mcmc plot.summary.evol.rate.mcmc print.evol.rate.mcmc print.summary.evol.rate.mcmc summary.evol.rate.mcmc |
| Likelihood test for variation in the evolutionary variance-covariance matrix | evol.vcv |
| Likelihood test for a shift in the evolutionary correlation between traits | evolvcv.lite |
| Exhaustive and branch & bound MP optimization | exhaustiveMP |
| Expands (or contracts) the tip-spacing of a given clade or clades | expand.clade plot.expand.clade |
| Export trees & data in XML format | export.as.xml |
| Plots special types of phylogenetic trees | fancyTree phenogram95 phyloScattergram |
| (Reasonably) fast estimation of ML ancestral states | fastAnc |
| (Reasonably) fast quantitative trait simulation on phylogenies | fastBM |
| Get the MRCA (or height above the root of the MRCA) of a pair of tip taxa | fastDist fastHeight fastMRCA |
| Get the MRCA of a set of taxa | findMRCA |
| Fits birth-death (speciation/extinction) model to reconstructed phylogeny | fit.bd fit.yule lik.bd print.fit.bd |
| Evolutionary model fitting with intraspecific variability using Bayesian MCMC | fitBayes |
| Fits binary discrete character evolution model where the transition rate varies as a function of a continuous trait | fitcontMk |
| Fit diversity-dependent phenotypic evolution model | fitDiversityModel logLik.fitDiversityModel print.fitDiversityModel |
| Fits extended M_k_ model for discrete character evolution | density.mcmcMk fitfnMk fitgammaMk fitHRM fitMk fitMk.parallel fitmultiMk fitpolyMk graph.polyMk mcmcMk plot.density.mcmcMk plot.fitHRM plot.fitMk plot.fitpolyMk plot.gfit plot.mcmcMk |
| Fits multi-rate (or multi-trend) discrete character dependent continuous trait evolution | fitmultiBM fitmultiTrend |
| Function to test for correlated evolution of binary traits | fitPagel plot.fitPagel |
| Fits binary, multi-state, and semi-threshold models using the discretized diffusion approximation | fitsemiThresh fitThresh |
| Coerces a phylogenetic tree to be ultrametric | force.ultrametric |
| Internally used function | gamma_pruning |
| gamma test of Pybus & Harvey (2000) | gammatest |
| Simulate a DNA alignment on the tree under a model | genSeq |
| Adds a geological (or other temporal) legend to a plotted tree | geo.legend geo.palette |
| Get position or node of a plotted tree interactively | get.treepos getnode |
| Get all subtrees larger than or equal to a specified size | getCladesofSize |
| Get descendant node numbers | getDescendants getParent |
| Returns a list of the extant or extinct lineages in a tree containing non-contemporaneous tips | getExtant getExtinct |
| Get the sister node number, label, or set of nodes for a node or tip | getSisters |
| Get the states at nodes or tips from a mapped tree | getStates |
| Function to interactively label nodes of a plotted tree | labelnodes |
| Ladderize a tree with a mapped discrete character | ladderize.simmap |
| lambda transformation of matrix | lambda.transform |
| Likelihood for joint lambda | likMlambda |
| Function to add tip labels to a plotted tree with linking lines | linklabels |
| Locate a fossil lineage in a tree using continuous characters | locate.fossil |
| Locate a cryptic, recently extinct, or missing taxon on a tree | locate.yeti |
| Least squares branch lengths for a given tree | ls.tree |
| Creates lineage-through-time plot (including extinct lineages) | gtt ltt ltt.multiPhylo ltt.multiSimmap ltt.phylo ltt.simmap mccr |
| Creates a (1-alpha)% CI for a set of LTTs | ltt95 plot.ltt95 |
| Create "era" map on a phylogenetic tree | make.era.map |
| Simulate stochastic character maps on a phylogenetic tree or trees | make.simmap simmap |
| Proportional overlap between two mapped character histories on a tree | Map.Overlap map.overlap |
| Converts a tree without singletons to a tree with singleton nodes | drop.tip.singleton map.to.singleton plotTree.singletons rootedge.to.singleton |
| Returns a vector, matrix, or list of the mapped states on a tree or set of trees | mapped.states |
| Add marked changes to a plotted tree with mapped discrete character | markChanges |
| Matches nodes between two trees | matchLabels matchNodes |
| Merge two or more mapped states into one state | mergeMappedStates |
| Midpoint root a phylogeny | midpoint.root midpoint_root |
| Rotates all nodes of the tree to minimize the difference in order with a vector | minRotate tipRotate |
| Finding the minimum (median) split in the posterior sample | minSplit |
| Computes modified Grafen edge lengths | modified.Grafen node.paths |
| Matrix representation parsimony supertree estimation | compute.mr mrp.supertree |
| Multiple matrix regression (partial Mantel test) | multi.mantel |
| Returns a list with phylogenetic VCV matrix for each mapped state | multiC |
| Function to fit a multi-rate Brownian evolution model | multirateBM |
| Computes Robinson-Foulds distance between a set of trees | multiRF |
| Compute the heights above the root of each node | nodeheight nodeHeights |
| Add labels to a plotted "cophylo" object | edgelabels.cophylo nodelabels.cophylo tiplabels.cophylo |
| Phylogeny inference using the least squares method | optim.phylo.ls |
| Order the columns of 'mapped.edge' to match across trees | orderMappedEdge |
| Paint sub-trees with a discrete character | paintBranches paintSubTree |
| Paste two trees together | paste.tree |
| Simulate pure-birth or birth-death stochastic tree or trees | pbtree |
| Phylogenetic regression with intraspecific sampling error | pgls.Ives pgls.SEy |
| Plot traitgram (phenogram) | phenogram |
| Phylogenetic canonical correlation analysis | phyl.cca |
| Phylogenetic paired _t_-test | phyl.pairedttest |
| Phylogenetic principal components analysis | as.prcomp as.princomp biplot.phyl.pca phyl.pca scores scores.phyl.pca |
| Phylogenetic size-correction via GLS regression | phyl.resid |
| Phylogenetic reduced major axis (RMA) regression | coef.phyl.RMA phyl.RMA plot.phyl.RMA |
| Compute evolutionary VCV matrix for a tree & dataset | phyl.vcv |
| Phylogenetic ANOVA and post-hoc tests | phylANOVA |
| Creates a phylogenetic heat map | phylo.heatmap |
| Phylogenetic imputation for multivariate continuous character data | phylo.impute |
| Plot tree with tips linked to geographic coordinates | phylo.to.map plot.phylo.to.map |
| Converts tree to backbone or vice versa | backbone.toPhylo phylo.toBackbone |
| Compute design matrix for least squares analyses | phyloDesign |
| Creates phylomorphospace plot | phylomorphospace project.phylomorphospace |
| Creates three-dimensional phylomorphospace plot | phylomorphospace3d |
| Compute phylogenetic signal with two methods | phylosig plot.phylosig |
| Plots backbone tree with triangles as clades | plot.backbonePhylo |
| Plot branch colors by a quantitative trait or value | plotBranchbyTrait |
| Plot stochastic character mapped tree | plot.multiSimmap plot.simmap plotSimmap |
| Tree plotting with posterior probabilities of ancestral states from the threshold model | plotThresh |
| Plots rooted phylogenetic tree | plotTree |
| Plot a tree with a discrete (or continuous) character data matrix at the tips | plotFanTree.wTraits plotTree.datamatrix |
| Plot a tree with error bars around divergence dates | plotTree.errorbars |
| Plot a tree with one or more matched lollipop plots | plotTree.lollipop |
| Plot a tree with bars at the tips | plotTree.barplot plotTree.boxplot plotTree.wBars |
| Analysis of the posterior sample from evol.rate.mcmc | posterior.evolrate |
| Generic post-hoc test | posthoc |
| Print method for backbone phylogeny | print.backbonePhylo |
| Compute the parsimony score | pscore |
| Method for investigating the rate of one trait as a function of the state of another | ratebystate |
| Likelihood test for rate variation among trees, clades, or traits | posthoc.ratebytree ratebytree |
| Find the temporal position of one or more rate shifts | likSurface.rateshift plot.rateshift rateshift |
| Newick or Nexus style tree reader | read.newick readNexus |
| Read SIMMAP style trees from file | read.simmap |
| Reorders a backbone phylogeny | reorder.backbonePhylo |
| Reorder edges of a '"simmap"' tree | reorderSimmap |
| Replicate a tree or set of trees | rep.multiPhylo rep.phylo repPhylo |
| Re-root a tree along an edge | reroot |
| Get marginal ancestral state reconstructions by re-rooting | rerootingMethod |
| Rescale phylogenetic objects of different types | rescale |
| Rescale object of class '"simmap"' | rescale.multiSimmap rescale.simmap rescaleSimmap |
| Compute all possible resolutions of a node or all nodes in a multifurcating tree | resolveAllNodes resolveNode |
| Rotates a node or set of nodes in a phylogenetic tree | allRotations rotate.multi rotateNodes |
| Rounds the branch lengths of a tree | roundBranches |
| Plot a round, sigmoidal, or spline phylogram or cladogram | roundPhylogram sigmoidPhylogram splinePhylogram |
| Pick a random state according to a vector of probabilities | rstate |
| Sample from a set of distributions | sampleFrom |
| Set color map for various phylogenetic objects of classes | setMap setMap.contMap setMap.densityMap setMap.multirateBM_plot setMap.phyloScattergram |
| Multivariate Brownian simulation with multiple correlations and rates | sim.corrs |
| Simulate character history or a discrete character at the tips of the tree under some model | sim.history sim.Mk sim.multiMk |
| Conduct simulation of state dependent rate variation | sim.ratebystate |
| Brownian or OU simulation with multiple evolutionary regimes | multiOU sim.rates |
| Creates a graphical illustration of Brownian motion evolution on a phylogeny | plot.simBMphylo simBMphylo |
| Matrix comparison using the method of random skewers | skewers |
| Split edge colors when descendant edges have different mapped states | splitEdgeColor |
| Plots a phylogeny in two columns | plotTree.splits splitplotTree |
| Split tree at a point | splitTree |
| Create star phylogeny | starTree |
| Computes Strahler number for trees and nodes | extract.strahlerNumber strahlerNumber |
| Threshold model using Bayesian MCMC | threshBayes |
| Deviance Information Criterion from the threshold model | threshDIC |
| Computes value for a threshold character from a liability and thresholds | threshState |
| Convert a character vector to a binary matrix | to.matrix |
| Creates an animation of a tree growing from left-to-right or upwards | tree.grow |
| Slices the tree at a particular point and returns all subtrees, or the tree rootward of the point | treeSlice |
| Attempts to untangle crossing branches for plotting | untangle |
| Calculates cophenetic (i.e., phylogenetic VCV) matrix | vcvPhylo |
| Write a stochastic character mapped tree to file | write.simmap |
| Write a tree to file with ancestral states and (optionally) CIs at nodes | writeAncestors |
| Write a tree to file in Nexus format | writeNexus |
