- DESCRIPTION file.
- Code demos. Use demo() to run them.

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 |