Likelihood Analysis of Speciation/Extinction Rates from Phylogenies

agamids | Ultrametric Phylogeny of Australian Agamid Lizards |

bd | Fit Rate-Constant Birth-Death Model to Branching Times |

birthdeathSim | birthdeathSim |

calcLHbd | Calculate Likelihood of Branching Times Under Birth-Death... |

DensityDependent | Fit Density Dependent Speciation Model to Branching Times |

fitContinuousBirthDeath | Fit model with continuous-time varying speciation/extinction... |

fitdAICrc | Test for Rate Variation Using delta-AICrc Test Statistic |

fitdAICrc.batch | Generate Null Distribution of dAICrc |

gamStat | gamStat |

getBtimes | Get Branching Times From Parenthetic-Format Tree ('Newick') |

getBtimes.batch | Branching Times for Batch of Phylogenies |

laser-internals | internal functions for package laser |

laser-package | LASER |

magsand | Estimate speciation rates for crown and stem groups |

mccrTest | Conduct monte carlo constant rates (gamma statistic) test |

plethodon | plethodon |

plotLtt | plotLtt |

plotNodeNumbers.phylo | Plot phylogenetic tree with node numbers |

plotRate | Plot speciation and extinction rates through time |

pureBirth | pureBirth |

RandomTrees | Random Phylogenetic Trees |

scaleBranchingtimes | Scale Branching Times |

truncateTree | Truncate a Set of Branching Times |

warblers | Branching times from phylogeny of North American Dendroica... |

yule-n-rate | yule-n-rate |

yuleSim | yuleSim |

yuleWindow | Fit Yule Model (Pure Birth) to Temporal Window of Branching... |

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