Man pages for bcm-uga/apTreeshape
Analyses of Phylogenetic Treeshape

aldous.testVisualizing balance via scatter diagrams
all.equal.treeshapeCompare two objects of class treeshape
a_NComputes a_n
apTreeshape-internalInternal apTreeshape Functions
as.phylo.treeshapeConversion among tree objects
as.treeshapeConversion among tree objects
aux_likProbability of the sampled node position
bind.treesBinds two tree together
build_treeInternal BetaAlphaEta function
carnivora.treeshapePhylogeny of carnivores.
change_intInternal function
change_int_etaInternal function
cladesizeCompute the number of children of a randomly chosen node
collessCompute the Colless' shape statistic on tree data
cutreeshapeCut objects of class "treeshape"
cytochromcPhylogeny of the cytochrome C family.
depthGets the node depths of the tree
enhanceInternal function
enhance_etaInternal function
get_extinction_listGives the tips of the phylogeny in their extinction order
get_PD_sampleComputes the proportion of conserved PD
get_tree_betaBeta parameter as a function of the proportion of remaining...
hivtree.treeshapePhylogenetic Tree of 193 HIV-1 Sequences
index.testPerform a test on the Yule or PDA hypothesis based on the...
insertInsert an element in a vector
lambda.epsilonComputes lambda_epsilon
lambda_NComputation of lambda_epsilon
likelihood.testTest the Yule model vs PDA (uniform) model.
maxlik.betasplitMaximum likelihood of beta in the Beta-splitting model
mcmc_alphaInference of the alpha parameter
mcmc_etaInference of the alpha and eta parameters
nodes_depths_ordonnesGets the node depths of the tree
plot.treeshapePlot phylogenetic treeshapes.
primatesPhylogeny of the primates.
rbactrianProposal for the mcmc functions
rhodopsinPhylogeny of rhodopsin proteins.
rtreeshapeGenerate a list of random binary trees according to a given...
sackinCompute the Sackin's index of a tree
shape.statisticComputes the log of the likelihood ratio (yule/pda)
shift.testTesting diversification rate variation in phylogenetic trees
simulate_kingmanRanked topology with Kingman's coalescent depths
simulate.RSimulate R knowing K=k
simulate.R.KSimulate (R,K)
simulate.Tau.XSimulate (Tau, X_Tau-)
simulate_treeSimulates ranked topology
simulate.YiSimulates the random variables Y_i
simulate_yuleRanked topology with Birth-death process depths
smaller.clade.spectrumCompute the smaller clade spectrum of a tree.
spectrum.treeshapeCompute the spectrum of a tree
splitComputes the splits at each node of a tree
subtree.testTest the Yule or PDA hypothesis
summary.treeshapePrint a summary of an object of class "treeshape"
tipsubtreeExtract a subtree that contains pre-specified tip names or...
transformInternal function
transform_etaInternal function
treeshapeBuilds an object of class treeshape
universal.treeshapeUniversal phylogenetic tree of life
yule_lengthsInternal BetaAlphaEta function
bcm-uga/apTreeshape documentation built on April 4, 2018, 9:19 p.m.