Statistical Inference of Annotated Phylogenetic Trees

ape-methods | APE wrappers |

aphylo-class | Annotated Phylogenetic Tree |

aphylo_cv | Leave-one-out Cross Validation |

aphylo_estimates-class | Parameter estimation of Annotated Phylogenetic Trees |

aphylo-index | Indexing aphylo objects |

aphylo-methods | Plot and print methods for 'aphylo' objects |

aphylo-model | Formulas in 'aphylo' |

aphylo-package | Statistical Inference in Annotated Phylogenetic Trees |

approx_geodesic | Approximation of Geodesic distances using Matrix Powers |

as.phylo | Extensions to the 'as.phylo' function |

bprior | Default priors for aphylo_mcmc |

fakeexperiment | Fake Experimental Data |

faketree | Fake Phylogenetic Tree |

list_offspring | List each nodes' offspring |

LogLike | Computes Log-likelihood |

mislabel | Switch labels acoording to mislabeling probabilities |

panther-tree | Reads PANTHER db trees |

plot.aphylo_prediction_score | Visualize predictions |

plot_logLik | Plot Log-Likelihood function of the model |

plot_multivariate | Multiavariate plot (surface) |

posterior-probabilities | Posterior probabilities based on parameter estimates |

rdrop_annotations | Randomly drop leaf annotations |

sim_annotated_tree | Simulation of Annotated Phylogenetic Trees |

sim_fun_on_tree | Simulate functions on a ginven tree |

sim_tree | Random tree generation |

states | Matrix of states |

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