Man pages for bcm-uga/apTreeshape
Analyses of Phylogenetic Treeshape
| aldous.test | Visualizing balance via scatter diagrams |
| all.equal.treeshape | Compare two objects of class treeshape |
| a_N | Computes a_n |
| apTreeshape-internal | Internal apTreeshape Functions |
| 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 |
| 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... |
| hivtree.treeshape | Phylogenetic Tree of 193 HIV-1 Sequences |
| index.test | Perform a test on the Yule or PDA hypothesis based on the... |
| 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... |
| 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_kingman | Ranked topology with Kingman's coalescent depths |
| simulate.R | Simulate R knowing K=k |
| simulate.R.K | Simulate (R,K) |
| simulate.Tau.X | Simulate (Tau, X_Tau-) |
| simulate_tree | Simulates ranked topology |
| simulate.Yi | Simulates the random variables Y_i |
| 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... |
| 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 |
