Analyses of Phylogenetic Treeshape

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Documentation for package ‘apTreeshape’ version 1.5-0.1

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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
as.treeshape.phylo Conversion among tree objects
aux_lik Probability of the sampled node position
a_N Computes a_n
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_extinction_list Gives the tips of the phylogeny in their extinction order
get_PD_sample Computes the proportion of conserved PD
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
sackin.test Perform a test on the Yule or PDA hypothesis based on the Colless or the Sackin statistic
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