Phylogenetic Tools for Comparative Biology (and Other Things)

add.arrow | Add an arrow pointing to a tip or node on the tree |

add.color.bar | Add color bar to a plot |

add.everywhere | Add tip to all edges in a tree |

add.random | Add tips at random to the tree |

add.simmap.legend | Add legend to stochastically mapped tree |

add.species.to.genus | Add species to genus on a phylogeny or bind simulated species... |

aic.w | Computes AIC weights |

allFurcTrees | Generate all bi- and multifurcating unrooted trees |

anc.Bayes | Bayesian ancestral character estimation |

anc.ML | Ancestral character estimation using likelihood |

ancThresh | Ancestral character estimation under the threshold model... |

anc.trend | Ancestral character estimation with a trend |

anoletree | Phylogeny of Greater Antillean anole ecomorph species with... |

applyBranchLengths | Applies the branch lengths of a reference tree to a target |

as.multiPhylo | Conversion to object of class '"multiPhylo"' |

averageTree | Compute an average tree from a set of trees and related... |

ave.rates | Average the posterior rates |

bd | Convert object of class "birthdeath" to raw birth & death... |

bind.tip | Attaches a new tip to a tree |

bind.tree.simmap | Attaches a new tip to a tree |

bmPlot | Simulates and visualizes discrete-time Brownian evolution on... |

branching.diffusion | Animation of branching random diffusion |

brownie.lite | Likelihood test for rate variation in a continuous trait |

brownieREML | REML version of brownie.lite |

cladelabels | Add labels to subtrees of a plotted phylogeny |

collapse.to.star | Collapse a subtree to a star phylogeny |

collapseTree | Interactive tree visualizer |

compare.chronograms | Compares to chronograms with precisely matching nodes in a... |

consensus.edges | Compute consensus edges for a tree under some criterion |

contMap | Map continuous trait evolution on the tree |

cophylo | Creates a co-phylogenetic plot |

cospeciation | Conducts a statistical test of cospeciation between two trees |

countSimmap | Counts the number of character changes on a SIMMAP style tree... |

ctt | Generates (or simulates) a 'changes through time' plot from a... |

densityMap | Plot posterior density of stochastic mapping on a tree |

density.multiSimmap | Computes a posterior distribution for the number and types of... |

densityTree | Plots a posterior sample of trees |

describe.simmap | Summarizes a stochastic mapped tree or set of trees |

di2multi.simmap | Collapse branches of zero length to polytomy in stochastic... |

dotTree | Creates a phylogenetic dot plot |

drop.clade | Drop a clade from a tree |

drop.leaves | Drop all the leaves (tips) from a tree |

drop.tip.contMap | Drop tip or tips from an object of class "contMap" or... |

drop.tip.simmap | Drop tips or extract clade from tree with mapped discrete... |

Dtest | Conducts correlational D-test from stochastic mapping |

edgeProbs | Compute the relative frequencies of state changes along edges |

estDiversity | Estimate diversity at each node of the tree |

evol.rate.mcmc | Bayesian MCMC method for identifying exceptional phenotypic... |

evol.vcv | Likelihood test for variation in the evolutionary VCV matrix |

evolvcv.lite | Likelihood test for a shift in the evolutionary correlation... |

exhaustiveMP | Exhaustive and branch & bound MP optimization |

expand.clade | Expands (or contracts) the tip-spacing of a given clade or... |

export.as.xml | Export trees & data in XML format |

fancyTree | Plots special types of phylogenetic trees |

fastAnc | (Reasonably) fast estimation of ML ancestral states |

fastBM | (Reasonably) fast quantitative trait simulation on... |

fastMRCA | Get the MRCA (or height above the root of the MRCA) of a pair... |

findMRCA | Get the MRCA of a set of taxa |

fitBayes | Evolutionary model fitting with intraspecific variability... |

fit.bd | Fits birth-death (speciation/extinction) model to... |

fitDiversityModel | Fit diversity-dependent phenotypic evolution model |

fitMk | Fits Mk model |

fitPagel | Function to test for correlated evolution of binary traits |

force.ultrametric | Forces a phylogenetic tree to be ultrametric |

gammatest | Gamma test of Pybus & Harvey (2000) |

genSeq | Simulate a DNA alignment on the tree under a model |

geo.legend | Adds a geological (or other temporal) legend to a plotted... |

getCladesofSize | Get all subtrees larger than or equal to a specified size |

getDescendants | Get descendant node numbers |

getExtant | Returns a list of the extant or extinct lineages in a tree... |

getSisters | Get the sister node number, label, or set of nodes for a node... |

getStates | Get the states at nodes or tips from a mapped tree |

get.treepos | Internal functions |

labelnodes | Function to interactively label nodes of a plotted tree |

ladderize.simmap | Ladderize a tree with a mapped discrete character |

lambda.transform | Lambda transformation of matrix |

likMlambda | Likelihood for joint lambda |

linklabels | Function to add tip labels to a plotted tree with linking... |

locate.fossil | Locate a fossil lineage in a tree using continuous characters |

locate.yeti | Locate a cryptic, recently extinct, or missing taxon on a... |

ls.tree | Least squares branch lengths for a given tree |

ltt | Creates lineage-through-time plot (including extinct... |

ltt95 | Creates a (1-alpha)-percent CI for a set of LTTs |

make.era.map | Create "era" map on a phylogenetic tree |

make.simmap | Simulate stochastic character maps on a phylogenetic tree or... |

map.overlap | Proportional overlap between two mapped character histories... |

mapped.states | Returns a vector, matrix, or list of the mapped states on a... |

map.to.singleton | Converts a mapped tree to a tree with singleton nodes |

markChanges | Add marked changes to a plotted tree with mapped discrete... |

matchNodes | Matches nodes between two trees |

mergeMappedStates | Merge two or more mapped states into one state |

midpoint.root | Midpoint root a phylogeny |

minRotate | Rotates all nodes of the tree to minimize the difference in... |

minSplit | Finding the minimum (median) split in the posterior sample |

modified.Grafen | Computes modified Grafen edge lengths |

mrp.supertree | Matrix representation parsimony supertree estimation |

multiC | Returns a list with phylogenetic VCV matrix for each mapped... |

multi.mantel | Multiple matrix regression (partial Mantel test) |

multiRF | Computes Robinson-Foulds distance between a set of trees |

nodeHeights | Compute the heights above the root of each node |

nodelabels.cophylo | Add labels to a plotted "cophylo" object |

optim.phylo.ls | Phylogeny inference using the least squares method |

orderMappedEdge | Order the columns of mapped.edge to match across trees |

paintSubTree | Paint sub-trees with a discrete character |

paste.tree | Paste two trees together |

pbtree | Simulate pure-birth or birth-death stochastic tree or trees |

pgls.Ives | Phylogenetic regression with intraspecific sampling error |

phenogram | Plot phenogram (traitgram) |

phylANOVA | Phylogenetic ANOVA and post-hoc tests |

phyl.cca | Phylogenetic canonical correlation analysis |

phyloDesign | Compute design matrix for least squares analyses |

phylo.heatmap | Creates a phylogenetic heat map |

phylomorphospace | Creates phylomorphospace plot |

phylomorphospace3d | Creates tree-dimensional phylomorphospace plot |

phylosig | Compute phylogenetic signal with two methods |

phylo.toBackbone | Converts tree to backbone or vice versa |

phylo.to.map | Plot tree with tips linked to geographic coordinates |

phyl.pairedttest | Phylogenetic paired t-test |

phyl.pca | Phylogenetic principal components analysis |

phyl.resid | Phylogenetic size-correction via GLS regression |

phyl.RMA | Phylogenetic reduced major axis (RMA) regression |

phyl.vcv | Compute evolutionary VCV matrix for a tree & dataset |

phytools-package | phytools: Phylogenetic Tools for comparative biology (and... |

plot.backbonePhylo | Plots backbone tree with triangles as clades |

plotBranchbyTrait | Plot branch colors by a quantitative trait or value |

plotSimmap | Plot stochastic character mapped tree |

plotThresh | Tree plotting with posterior probabilities of ancestral... |

plotTree | Plots rooted phylogenetic tree |

plotTree.datamatrix | Plot a tree with a discrete character data matrix at the tips |

plotTree.errorbars | Plot a tree with error bars around divergence dates |

plotTree.wBars | Plot a tree with bars at the tips |

posterior.evolrate | Analysis of the posterior sample from evol.rate.mcmc |

posthoc | Generic post-hoc test |

print.backbonePhylo | Print method for backbone phylogeny |

ratebystate | Method for investigating the rate of one trait as a function... |

ratebytree | Likelihood test for rate variation among trees |

rateshift | Find the temporal position of one or more rate shifts |

read.newick | Robust Newick style tree reader |

read.simmap | Read SIMMAP style trees from file |

reorder.backbonePhylo | Reorders a backbone phylogeny |

reorderSimmap | Reorder edges of a simmap tree |

rep.phylo | Replicate a tree or set of trees |

reroot | Re-root a tree along an edge |

rerootingMethod | Get marginal ancestral state reconstructions by re-rooting |

rescaleSimmap | Rescale SIMMAP style tree |

resolveNode | Compute all possible resolutions of a node or all nodes in a... |

rotateNodes | Rotates a node or set of nodes in a phylogenetic tree |

roundBranches | Rounds the branch lengths of a tree |

roundPhylogram | Plot a round phylogram |

rstate | Pick a random state according to a vector of probabilities |

sampleFrom | Sample from a set of distributions |

setMap | Set color map for objects of class '"contMap"' or... |

sim.corrs | Multivariate Brownian simulation with multiple correlations... |

sim.history | Simulate character history or a discrete character at the... |

sim.ratebystate | Conduct simulation of state dependent rate variation |

sim.rates | Brownian or OU simulation with multiple evolutionary regimes |

skewers | Matrix comparison using the method of random skewers |

splitEdgeColor | Split edge colors when descendant edges have different mapped... |

splitplotTree | Plots a phylogeny in two columns |

splitTree | Split tree at a point |

starTree | Create star phylogeny |

strahlerNumber | Computes Strahler number for trees and nodes |

threshBayes | Threshold model using Bayesian MCMC |

threshDIC | Deviance Information Criterion from the threshold model |

threshState | Computes value for a threshold character from a liability and... |

to.matrix | Convert a character vector to a binary matrix |

treeSlice | Slices the tree at a particular point and returns all... |

untangle | Attempts to untangle crossing branches for plotting |

vcvPhylo | Calculates cophenetic (i.e., phylogenetic VCV) matrix |

writeAncestors | Write a tree to file with ancestral states and (optionally)... |

writeNexus | Write a tree to file in Nexus format |

write.simmap | Write a stochastic character mapped tree to file |

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