a_N                     Computes a_n
aldous.test             Visualizing balance via scatter diagrams
all.equal.treeshape     Compare two objects of class treeshape
as.phylo.treeshape      Conversion among tree objects
as.treeshape            Conversion among tree objects
aux_lik                 Probability of the sampled node position
bind.trees              Binds two tree together
build_tree              Internal BetaAlphaEta function
carnivora.treeshape     Phylogeny of carnivores.
change_int              Internal function
change_int_eta          Internal function
cladesize               Compute the number of children of a randomly
                        chosen node
colless                 Compute the Colless' shape statistic on tree
                        data
colless.test            Perform a test on the Yule or PDA hypothesis
                        based on the Colless or the Sackin statistic
cutreeshape             Cut objects of class "treeshape"
cytochromc              Phylogeny of the cytochrome C family.
depth                   Gets the node depths of the tree
enhance                 Internal function
enhance_eta             Internal function
get_PD_sample           Computes the proportion of conserved PD
get_extinction_list     Gives the tips of the phylogeny in their
                        extinction order
get_tree_beta           Beta parameter as a function of the proportion
                        of remaining tips
hivtree.treeshape       Phylogenetic Tree of 193 HIV-1 Sequences
insert                  Insert an element in a vector
lambda.epsilon          Computes lambda_epsilon
lambda_N                Computation of lambda_epsilon
likelihood.test         Test the Yule model vs PDA (uniform) model.
maxlik.betasplit        Maximum likelihood of beta in the
                        Beta-splitting model
mcmc_alpha              Inference of the alpha parameter
mcmc_eta                Inference of the alpha and eta parameters
nodes_depths_ordonnes   Gets the node depths of the tree
plot.treeshape          Plot phylogenetic treeshapes.
primates                Phylogeny of the primates.
rbactrian               Proposal for the mcmc functions
rhodopsin               Phylogeny of rhodopsin proteins.
rtreeshape              Generate a list of random binary trees
                        according to a given model
sackin                  Compute the Sackin's index of a tree
shape.statistic         Computes the log of the likelihood ratio
                        (yule/pda)
shift.test              Testing diversification rate variation in
                        phylogenetic trees
simulate.R              Simulate R knowing K=k
simulate.R.K            Simulate (R,K)
simulate.Tau.X          Simulate (Tau, X_Tau-)
simulate.Yi             Simulates the random variables Y_i
simulate_kingman        Ranked topology with Kingman's coalescent
                        depths
simulate_tree           Simulates ranked topology
simulate_yule           Ranked topology with Birth-death process depths
smaller.clade.spectrum
                        Compute the smaller clade spectrum of a tree.
spectrum.treeshape      Compute the spectrum of a tree
split                   Computes the splits at each node of a tree
subtree.test            Test the Yule or PDA hypothesis
summary.treeshape       Print a summary of an object of class
                        "treeshape"
tipsubtree              Extract a subtree that contains pre-specified
                        tip names or labels
transform               Internal function
transform_eta           Internal function
treeshape               Builds an object of class treeshape
universal.treeshape     Universal phylogenetic tree of life
yule_lengths            Internal BetaAlphaEta function
