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