![[R logo]](../../../doc/html/logo.jpg){kind=logo}
![[Up]](../../../doc/html/left.jpg){kind=small}
![[Top]](../../../doc/html/up.jpg){kind=small}
| phytools-package | phytools: Phylogenetic Tools for comparative biology (and other things) |
| add.everywhere | Add tip to all edges in a tree |
| add.to.branches.and.nodes | Add tip to branches and nodes of the tree |
| allFurcTrees | Generate all bi- and multifurcating unrooted trees |
| anc.trend | Ancestral character estimation with a trend |
| ave.rates | Compute weighted average evolutionary rates |
| branch.and.bound | Perform branch & bound parsimony search |
| branching.diffusion | Animation of branching random diffusion |
| brownie.lite | Likelihood test for rate variation |
| compute.ancestor.nodes | Compute all ancestral nodes |
| drop.clade | Drop clade from a tree |
| drop.tip.simmap | Drop tip from SIMMAP format tree |
| estDiversity | Estimate diversity at each node of the tree |
| evol.rate.mcmc | Bayesian MCMC method for identifying exceptional phenotypic diversification in a phylogeny |
| evol.vcv | Likelihood test for variation in the evolutionary VCV matrix |
| exhaustive.search | Exhaustive MP search |
| exhaustiveMP | Exhaustive and branch & bound MP optimization |
| expm | Matrix exponential |
| fastBM | Fast Brownian simulation |
| fitDiversityModel | Fit diversity-dependent phenotypic evolution model |
| gammatest | Gamma test of Pybus & Harvey (2000) |
| lambda.transform | Lambda transformation of matrix |
| likelihood | Likelihood of evolutionary vcv matrix, for a particular lambda |
| likelihood.lambda | Likelihood of lambda transformation |
| ls.tree | Least squares branch lengths for a given tree |
| ltt | Creates lineage-through-time plot (including extinct lineages) |
| make.simmap | Simulate stochastic character map on a phylogenetic tree |
| map.overlap | Ancestral character estimation with a trend |
| minSplit | Finding the minimum (median) split in the posterior sample |
| mrp.supertree | Matrix representation parsimony supertree estimation |
| nodeHeights | Estimate diversity at each node of the tree |
| optim.phylo.ls | Phylogeny inference using the least squares method |
| paste.tree | Paste tree |
| phyl.cca | Phylogenetic canonical correlation analysis |
| 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 | Internal function |
| phylANOVA | Generate all bi- and multifurcating unrooted trees |
| phyloDesign | Compute design matrix for least squares analyses |
| phylomorphospace | Creates phylomorphospace plot |
| phylosig | Compute phylogenetic signal with two methods |
| phytools | phytools: Phylogenetic Tools for comparative biology (and other things) |
| plotSimmap | Plot stochastic character mapped tree |
| plotTree | Plots rooted phylogenetic tree |
| posterior.evolrate | Analysis of the posterior sample from evol.rate.mcmc |
| read.newick | Read Newick style tree |
| read.simmap | Read SIMMAP style trees from file |
| reorderSimmap | Reorder edges of a simmap tree |
| reroot | Re-root a tree along an edge |
| rstate | Pick a random state according to a vector of probabilities |
| sim.history | Simulate stochastic character history under some model |
| sim.rates | Brownian simulationn with multiple evolutionary rates |
| splitTree | Split tree at a point |
| starTree | Create star phylogeny |
| treeSlice | Slices the tree at a particular point and returns all subtrees |
| tTests | Generate all bi- and multifurcating unrooted trees |
| whichorder | Which order are the edges of the tree |
| write.simmap | Simulate stochastic character map on a phylogenetic tree |