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| phytools-package | phytools: Phylogenetic Tools for comparative biology (and other things) |
| add.everywhere | Add tip to all edges in a tree |
| allFurcTrees | Generate all bi- and multifurcating unrooted trees |
| anc.Bayes | Bayesian ancestral character estimation |
| anc.ML | Ancestral character estimation using likelihood |
| anc.trend | Ancestral character estimation with a trend |
| ancThresh | Ancestral character estimation under the threshold model using Bayesian MCMC |
| bmPlot | Simulates and visualizes discrete-time Brownian evolution on a phylogeny |
| branching.diffusion | Animation of branching random diffusion |
| brownie.lite | Likelihood test for rate variation |
| brownieREML | REML version of brownie.lite |
| contMap | Map continuous trait evolution on the tree |
| densityMap | Plot posterior density of stochastic mapping on a tree |
| 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 |
| evolvcv.lite | Likelihood test for a shift in the evolutionary correlation between traits |
| exhaustiveMP | Exhaustive and branch & bound MP optimization |
| expm | Matrix exponential |
| export.as.xml | Export trees & data in XML format |
| fancyTree | Plots special types of phylogenetic trees |
| fastAnc | Fast estimation of ML ancestral states |
| fastBM | Fast Brownian simulation |
| fastMRCA | Get the MRCA of a pair of tip taxa |
| findMRCA | Get the MRCA of a set of taxa |
| fitBayes | Evolutionary model fitting with intraspecific variability using Bayesian MCMC |
| fitDiversityModel | Fit diversity-dependent phenotypic evolution model |
| gammatest | Gamma test of Pybus & Harvey (2000) |
| getDescendants | Get descendant node numbers |
| getExtant | Returns a list of the extant or extinct lineages in a tree containing non-contemporaneous tips |
| getExtinct | Returns a list of the extant or extinct lineages in a tree containing non-contemporaneous tips |
| lambda.transform | Lambda transformation of matrix |
| likMlambda | Likelihood for joint lambda |
| ls.tree | Least squares branch lengths for a given tree |
| ltt | Creates lineage-through-time plot (including extinct lineages) |
| make.era.map | Create "era" map on a phylogenetic tree |
| make.simmap | Simulate stochastic character map on a phylogenetic tree |
| map.overlap | Proportional overlap between two mapped character histories on a tree |
| matchNodes | Matches nodes between two trees |
| minSplit | Finding the minimum (median) split in the posterior sample |
| mrp.supertree | Matrix representation parsimony supertree estimation |
| multi.mantel | Multiple matrix regression (partial Mantel test) |
| multiC | Returns a list with phylogenetic VCV matrix for each mapped state |
| nodeHeights | Compute the heights above the root of each node |
| optim.phylo.ls | Phylogeny inference using the least squares method |
| paintSubTree | Paint sub-trees with a discrete character |
| paste.tree | Paste two trees together |
| pbtree | Simulate pure-birth stochastic tree or trees |
| pgls.Ives | Phylogenetic regression with intraspecific sampling error |
| phenogram | Plot phenogram (traitgram) |
| 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 | Compute evolutionary VCV matrix for a tree & dataset |
| phylANOVA | Phylogenetic ANOVA and post-hoc tests |
| phyloDesign | Compute design matrix for least squares analyses |
| phylomorphospace | Creates phylomorphospace plot |
| phylomorphospace3d | 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 |
| rescaleSimmap | Rescale SIMMAP style tree |
| rstate | Pick a random state according to a vector of probabilities |
| sampleFrom | Sample from a set of distributions |
| sim.corrs | Multivariate Brownian simulation with multiple correlations and rates |
| sim.history | Simulate stochastic character history under some model |
| sim.rates | Brownian simulation with multiple evolutionary rates |
| splitTree | Split tree at a point |
| starTree | Create star phylogeny |
| threshBayes | Threshold model using Bayesian MCMC |
| threshDIC | Deviance Information Criterion from the threshold model |
| treeSlice | Slices the tree at a particular point and returns all subtrees |
| vcvPhylo | Calculates cophenetic (i.e., phylogenetic VCV) matrix |
| write.simmap | Write a stochastic character mapped tree to file |
| writeNexus | Write a stochastic character mapped tree to file |
| xkcdTree | Plot xkcd style tree |