Drop tips or extract clade from tree with mapped discrete character
Compute the relative frequencies of state changes along edges
Get the MRCA of a set of taxa
Fits birth-death (speciation/extinction) model to reconstructed phylogeny
Get descendant node numbers
Returns a list of the extant or extinct lineages in a tree containing non-contemporaneous tips
Function to interactively label nodes of a plotted tree
Ladderize a tree with a mapped discrete character
Returns a vector, matrix, or list of the mapped states on a tree or set of trees
Add marked changes to a plotted tree with mapped discrete character
Returns a list with phylogenetic VCV matrix for each mapped state
Computes Robinson-Foulds distance between a set of trees
Paint sub-trees with a discrete character
Paste two trees together
Phylogenetic principal components analysis
Phylogenetic size-correction via GLS regression
Plots backbone tree with triangles as clades
Plot branch colors by a quantitative trait or value
Read SIMMAP style trees from file
Reorders a backbone phylogeny
Sample from a set of distributions
Set color map for objects of class "contMap"
or "densityMap"
Matrix comparison using the method of random skewers
Split edge colors when descendant edges have different mapped states
Calculates cophenetic (i.e., phylogenetic VCV) matrix
Write a stochastic character mapped tree to file
Bayesian ancestral character estimation
Ancestral character estimation using likelihood
Conversion to object of class "multiPhylo"
Average the posterior rates
Compares to chronograms with precisely matching nodes in a visual manner
Creates a co-phylogenetic plot
Conducts a statistical test of cospeciation between two trees
Estimate diversity at each node of the tree
Bayesian MCMC method for identifying exceptional phenotypic diversification in a phylogeny
Export trees & data in XML format
Simulate a DNA alignment on the tree under a model
Adds a geological (or other temporal) legend to a plotted tree
Locate a cryptic, recently extinct, or missing taxon on a tree
Least squares branch lengths for a given tree
Matches nodes between two trees
Merge two or more mapped states into one state
Finding the minimum (median) split in the posterior sample
Computes modified Grafen edge lengths
Simulate pure-birth or birth-death stochastic tree or trees
Phylogenetic regression with intraspecific sampling error
Converts tree to backbone or vice versa
Compute design matrix for least squares analyses
Plots rooted phylogenetic tree
Plot a tree with error bars around divergence dates
Method for investigating the rate of one trait as a function of the state of another
Likelihood test for rate variation among trees
Rescale SIMMAP style tree
Compute all possible resolutions of a node or all nodes in a multifurcating tree
Applies the branch lengths of a reference tree to a target
Add legend to stochastically mapped tree
Add species to genus on a phylogeny or bind simulated species subtrees to a backbone genus tree
Phylogeny of Greater Antillean anole ecomorph species with mapped discrete character
Split tree at a point
Add labels to subtrees of a plotted phylogeny
Plots a phylogeny in two columns
Computes value for a threshold character from a liability and thresholds
Convert a character vector to a binary matrix
Evolutionary model fitting with intraspecific variability using Bayesian MCMC
Collapse a subtree to a star phylogeny
Counts the number of character changes on a SIMMAP style tree or set of trees
Fit diversity-dependent phenotypic evolution model
Computes a posterior distribution for the number and types of changes on the tree
Exhaustive and branch & bound MP optimization
Expands (or contracts) the tip-spacing of a given clade or clades
Fits Mk model
Function to test for correlated evolution of binary traits
Lambda transformation of matrix
Likelihood for joint lambda
Creates lineage-through-time plot (including extinct lineages)
Creates a (1-\(\alpha\))-percent CI for a set of LTTs
Compute the heights above the root of each node
Add labels to a plotted "cophylo" object
Phylogenetic canonical correlation analysis
Phylogenetic paired t-test
Creates a phylogenetic heat map
Plot a tree with bars at the tips
Plot tree with tips linked to geographic coordinates
Analysis of the posterior sample from evol.rate.mcmc
Reorder edges of a simmap tree
Replicate a tree or set of trees
Rotates a node or set of nodes in a phylogenetic tree
Rounds the branch lengths of a tree
Create star phylogeny
Computes Strahler number for trees and nodes
Write a tree to file with ancestral states and (optionally) CIs at nodes
Write a tree to file in Nexus format
Computes AIC weights
Generate all bi- and multifurcating unrooted trees
Compute an average tree from a set of trees and related operations
Convert object of class "birthdeath" to raw birth & death rates
Simulates and visualizes discrete-time Brownian evolution on a phylogeny
Animation of branching random diffusion
Plot posterior density of stochastic mapping on a tree
Plots a posterior sample of trees
Likelihood test for variation in the evolutionary VCV matrix
Get the MRCA (or height above the root of the MRCA) of a pair of tip taxa
Likelihood test for a shift in the evolutionary correlation between traits
Forces a phylogenetic tree to be ultrametric
Gamma test of Pybus & Harvey (2000)
(Reasonably) fast quantitative trait simulation on phylogenies
Function to add tip labels to a plotted tree with linking lines
(Reasonably) fast estimation of ML ancestral states
Internal functions
Get all subtrees larger than or equal to a specified size
Matrix representation parsimony supertree estimation
Plots special types of phylogenetic trees
Multiple matrix regression (partial Mantel test)
Phylogeny inference using the least squares method
Locate a fossil lineage in a tree using continuous characters
Order the columns of mapped.edge to match across trees
Proportional overlap between two mapped character histories on a tree
Converts a mapped tree to a tree with singleton nodes
Creates phylomorphospace plot
Creates tree-dimensional phylomorphospace plot
Compute phylogenetic signal with two methods
phytools: Phylogenetic Tools for comparative biology (and other things)
Find the temporal position of one or more rate shifts
Midpoint root a phylogeny
Robust Newick style tree reader
Re-root a tree along an edge
Get marginal ancestral state reconstructions by re-rooting
Conduct simulation of state dependent rate variation
Brownian or OU simulation with multiple evolutionary regimes
Threshold model using Bayesian MCMC
Deviance Information Criterion from the threshold model
Rotates all nodes of the tree to minimize the difference in order with a vector
Plot phenogram (traitgram)
Phylogenetic reduced major axis (RMA) regression
Add tip to all edges in a tree
Add tips at random to the tree
Ancestral character estimation with a trend
Ancestral character estimation under the threshold model using Bayesian MCMC
Add an arrow pointing to a tip or node on the tree
Add color bar to a plot
Compute consensus edges for a tree under some criterion
Map continuous trait evolution on the tree
Matrix exponential
Likelihood test for rate variation in a continuous trait
REML version of brownie.lite
Creates a phylogenetic dot plot
Drop a clade from a tree
Drop all the leaves (tips) from a tree
Create "era" map on a phylogenetic tree
Simulate stochastic character maps on a phylogenetic tree or trees
Drop tip or tips from an object of class "contMap" or "densityMap"
Get the sister node number, label, or set of nodes for a node or tip
Get the states at nodes or tips from a mapped tree
Phylogenetic ANOVA and post-hoc tests
Compute evolutionary VCV matrix for a tree & dataset
Plot a round phylogram
Plot stochastic character mapped tree
Pick a random state according to a vector of probabilities
Tree plotting with posterior probabilities of ancestral states from the threshold model
Multivariate Brownian simulation with multiple correlations and rates
Simulate stochastic character history under some model
Generic post-hoc test
Print method for backbone phylogeny
Slices the tree at a particular point and returns all subtrees, or the tree rootward of the point
Attempts to untangle crossing branches for plotting
Attaches a new tip to a tree
Summarizes a stochastic mapped tree or set of trees
Collapse branches of zero length to polytomy in stochastic map style tree
Attaches a new tip to a tree
Interactive tree visualizer