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apTreeshape

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Version

Install

install.packages('apTreeshape')

Monthly Downloads

96

Version

1.5-0.1

License

GPL (>= 2)

Maintainer

Michael Blum

Last Published

October 12th, 2020

Functions in apTreeshape (1.5-0.1)

enhance_eta

Internal function
enhance

Internal function
depth

Gets the node depths of the tree
cytochromc

Phylogeny of the cytochrome C family.
index.test

Perform a test on the Yule or PDA hypothesis based on the Colless or the Sackin statistic
bind.trees

Binds two tree together
hivtree.treeshape

Phylogenetic Tree of 193 HIV-1 Sequences
cutreeshape

Cut objects of class "treeshape"
lambda_N

Computation of lambda_epsilon
likelihood.test

Test the Yule model vs PDA (uniform) model.
get_tree_beta

Beta parameter as a function of the proportion of remaining tips
get_extinction_list

Gives the tips of the phylogeny in their extinction order
rbactrian

Proposal for the mcmc functions
rtreeshape

Generate a list of random binary trees according to a given model
insert

Insert an element in a vector
lambda.epsilon

Computes lambda_epsilon
change_int

Internal function
get_PD_sample

Computes the proportion of conserved PD
shape.statistic

Computes the log of the likelihood ratio (yule/pda)
split

Computes the splits at each node of a tree
spectrum.treeshape

Compute the spectrum of a tree
shift.test

Testing diversification rate variation in phylogenetic trees
rhodopsin

Phylogeny of rhodopsin proteins.
cladesize

Compute the number of children of a randomly chosen node
simulate_tree

Simulates ranked topology
simulate_kingman

Ranked topology with Kingman's coalescent depths
primates

Phylogeny of the primates.
treeshape

Builds an object of class treeshape
simulate.Tau.X

Simulate (Tau, X_Tau-)
transform_eta

Internal function
simulate.Yi

Simulates the random variables Y_i
plot.treeshape

Plot phylogenetic treeshapes.
sackin

Compute the Sackin's index of a tree
colless

Compute the Colless' shape statistic on tree data
maxlik.betasplit

Maximum likelihood of beta in the Beta-splitting model
change_int_eta

Internal function
mcmc_alpha

Inference of the alpha parameter
nodes_depths_ordonnes

Gets the node depths of the tree
yule_lengths

Internal BetaAlphaEta function
mcmc_eta

Inference of the alpha and eta parameters
universal.treeshape

Universal phylogenetic tree of life
simulate.R.K

Simulate (R,K)
simulate.R

Simulate R knowing K=k
subtree.test

Test the Yule or PDA hypothesis
simulate_yule

Ranked topology with Birth-death process depths
summary.treeshape

Print a summary of an object of class "treeshape"
smaller.clade.spectrum

Compute the smaller clade spectrum of a tree.
tipsubtree

Extract a subtree that contains pre-specified tip names or labels
transform

Internal function
apTreeshape-internal

Internal apTreeshape Functions
as.treeshape

Conversion among tree objects
a_N

Computes a_n
aux_lik

Probability of the sampled node position
build_tree

Internal BetaAlphaEta function
aldous.test

Visualizing balance via scatter diagrams
as.phylo.treeshape

Conversion among tree objects
all.equal.treeshape

Compare two objects of class treeshape
carnivora.treeshape

Phylogeny of carnivores.