Computes AIC weights
Add tips at random to the tree
Add tip to all edges in a tree
Add color bar to a plot
Add legend to stochastically mapped tree
Add species to genus on a phylogeny or bind simulated species subtrees to a backbone genus tree
Conducts correlational D-test from stochastic mapping
Add an arrow pointing to a tip or node on the tree
Generate all bi- and multifurcating unrooted trees
Bayesian ancestral character estimation
Applies the branch lengths of a reference tree to a target
Ancestral character estimation under the threshold model using Bayesian MCMC
Simulates and visualizes discrete-time Brownian evolution on a phylogeny
Interactive tree visualizer
Convert object of class "birthdeath" to raw birth & death rates
Ancestral character estimation with a trend
Ancestral character estimation using likelihood
Likelihood test for rate variation in a continuous trait
Compute an average tree from a set of trees and related operations
Compares two chronograms with precisely matching nodes in a visual manner
Phylogenetic datasets
Conversion to object of class "multiPhylo"
Average the posterior rates
Collapse a subtree to a star phylogeny
Generates (or simulates) a 'changes through time' plot from a set of stochastic map character histories
Add labels to subtrees of a plotted phylogeny
Collapse or resolve polytomies in a tree with a character painted on the edges
Counts the number of character changes on a object of class "simmap" or "multiSimmap"
Computes a posterior distribution for the number and types of changes on the tree
Plot posterior density of stochastic mapping on a tree
Drop tip or tips from an object of class "contMap" or "densityMap"
REML version of brownie.lite
Compute consensus edges for a tree under some criterion
Map continuous trait evolution on the tree
Creates a phylogenetic dot plot
Drop a clade from a tree
Get the MRCA of a set of taxa
Drop all the leaves (tips) from a tree
Bayesian MCMC method for identifying exceptional phenotypic diversification in a phylogeny
Attaches a new tip to a tree
Likelihood test for variation in the evolutionary variance-covariance matrix
Attaches a new tip to a tree
Convert a fitted Mk model to a Q-matrix
Drop tips or extract clade from tree with mapped discrete character
Plots a posterior sample of trees
Plots special types of phylogenetic trees
Animation of branching random diffusion
Gamma test of Pybus & Harvey (2000)
Summarizes a stochastic mapped tree or set of trees
Creates a co-phylogenetic plot
Forces a phylogenetic tree to be ultrametric
Get position or node of a plotted tree interactively
Locate a fossil lineage in a tree using continuous characters
Fits birth-death (speciation/extinction) model to reconstructed phylogeny
Order the columns of mapped.edge to match across trees
Function to add tip labels to a plotted tree with linking lines
(Reasonably) fast estimation of ML ancestral states
Drop tip or tips from an object of class "multiPhylo" or "multiSimmap"
Likelihood test for a shift in the evolutionary correlation between traits
Map continuous trait evolution on the tree
Get the sister node number, label, or set of nodes for a node or tip
Exhaustive and branch & bound MP optimization
Evolutionary model fitting with intraspecific variability using Bayesian MCMC
Fit diversity-dependent phenotypic evolution model
Conducts a statistical test of cospeciation between two trees
Get all subtrees larger than or equal to a specified size
Create "era" map on a phylogenetic tree
Paint sub-trees with a discrete character
Get the states at nodes or tips from a mapped tree
Compute the relative frequencies of state changes along edges
Creates phylomorphospace plot
Simulate stochastic character maps on a phylogenetic tree or trees
Simulate a DNA alignment on the tree under a model
Estimate diversity at each node of the tree
Get the MRCA (or height above the root of the MRCA) of a pair of tip taxa
Export trees & data in XML format
(Reasonably) fast quantitative trait simulation on phylogenies
Expands (or contracts) the tip-spacing of a given clade or clades
Function to interactively label nodes of a plotted tree
Fits Mk model
\(\lambda\) transformation of matrix
Locate a cryptic, recently extinct, or missing taxon on a tree
Least squares branch lengths for a given tree
Ladderize a tree with a mapped discrete character
Adds a geological (or other temporal) legend to a plotted tree
Function to test for correlated evolution of binary traits
Creates lineage-through-time plot (including extinct lineages)
Rotates all nodes of the tree to minimize the difference in order with a vector
Midpoint root a phylogeny
Creates a (1-\(\alpha\))-percent CI for a set of LTTs
Proportional overlap between two mapped character histories on a tree
Returns a list of the extant or extinct lineages in a tree containing non-contemporaneous tips
Converts a tree without singletons to a tree with singleton nodes
Get descendant node numbers
Matches nodes between two trees
Returns a vector, matrix, or list of the mapped states on a tree or set of trees
Merge two or more mapped states into one state
Computes modified Grafen edge lengths
Finding the minimum (median) split in the posterior sample
Phylogenetic size-correction via GLS regression
Likelihood for joint \(\lambda\)
Function to fit a multi-rate Brownian evolution model
Returns a list with phylogenetic VCV matrix for each mapped state
Computes Robinson-Foulds distance between a set of trees
Matrix representation parsimony supertree estimation
Compute the heights above the root of each node
Phylogenetic reduced major axis (RMA) regression
Add marked changes to a plotted tree with mapped discrete character
Multiple matrix regression (partial Mantel test)
Phylogenetic principal components analysis
Phylogenetic paired t-test
Get marginal ancestral state reconstructions by re-rooting
Add labels to a plotted "cophylo" object
Creates tree-dimensional phylomorphospace plot
Phylogeny inference using the least squares method
Rescale SIMMAP style tree
Compute evolutionary VCV matrix for a tree & dataset
Attempts to untangle crossing branches for plotting
Paste two trees together
Calculates cophenetic (i.e., phylogenetic VCV) matrix
Converts tree to backbone or vice versa
Print method for backbone phylogeny
Compute phylogenetic signal with two methods
Phylogenetic canonical correlation analysis
phytools: Phylogenetic Tools for comparative biology (and other things)
Compute design matrix for least squares analyses
Simulate pure-birth or birth-death stochastic tree or trees
Plots rooted phylogenetic tree
Simulate character history or a discrete character at the tips of the tree under some model
Plot a tree with a discrete character data matrix at the tips
Newick or Nexus style tree reader
Method for investigating the rate of one trait as a function of the state of another
Phylogenetic ANOVA and post-hoc tests
Brownian or OU simulation with multiple evolutionary regimes
Conduct simulation of state dependent rate variation
Compute all possible resolutions of a node or all nodes in a multifurcating tree
Read SIMMAP style trees from file
Creates a graphical illustration of Brownian motion evolution on a phylogeny
Phylogenetic regression with intraspecific sampling error
Rotates a node or set of nodes in a phylogenetic tree
Write a tree to file with ancestral states and (optionally) CIs at nodes
Write a stochastic character mapped tree to file
Creates a phylogenetic heat map
Threshold model using Bayesian MCMC
Analysis of the posterior sample from evol.rate.mcmc
Generic post-hoc test
Plots backbone tree with triangles as clades
Plot branch colors by a quantitative trait or value
Deviance Information Criterion from the threshold model
Plot a tree with error bars around divergence dates
Replicate a tree or set of trees
Plot phenogram (traitgram)
Plot stochastic character mapped tree
Phylogenetic imputation for multivariate continuous character data
Set color map for various phylogenetic objects of classes
Re-root a tree along an edge
Plot tree with tips linked to geographic coordinates
Multivariate Brownian simulation with multiple correlations and rates
Create star phylogeny
Reorder edges of a simmap tree
Computes Strahler number for trees and nodes
Plot a tree with bars at the tips
Reorders a backbone phylogeny
Pick a random state according to a vector of probabilities
Split edge colors when descendant edges have different mapped states
Matrix comparison using the method of random skewers
Write a tree to file in Nexus format
Tree plotting with posterior probabilities of ancestral states from the threshold model
Sample from a set of distributions
Computes value for a threshold character from a liability and thresholds
Split tree at a point
Rounds the branch lengths of a tree
Find the temporal position of one or more rate shifts
Plot a round phylogram
Likelihood test for rate variation among trees, clades, or traits
Plots a phylogeny in two columns
Convert a character vector to a binary matrix
Creates an animation of a tree growing from left-to-right or upwards
Slices the tree at a particular point and returns all subtrees, or the tree rootward of the point