Tools to work with MCMCTree

A | A matrix |

array2matrix | Convert an array into a matrix |

bayes.factors | Calculate Bayes factors and posterior model probabilities |

C | 29 3D landmarks from the skulls of 19 carnivoran specimens... |

carnivores19x29.raw | 29 3D landmarks from the skulls of 19 carnivoran specimens |

C.arr.unal | 29 3D landmarks from the skulls of 19 carnivoran specimens... |

C.mat.unal | 29 3D landmarks from the skulls of 19 carnivoran specimens... |

C.PS | Object of class procSym output by Morpho after PA |

ctlMCMCtree | Generating the control file to run MCMCtree when using... |

gauss.quad | Estimate marginal likelihood by thermodynamic integration |

lmk_imp | Import various landmark files for different specimens at once |

make.beta | Make beta values for marginal likelihood calculation |

make.bfctlf | Prepare mcmctree or bpp control files for marginal likelihood... |

matrix2array | Convert a matrix into an array |

proc2MCMCtree | Procrustes alignment output in MCMCtree format for Bayesian... |

R.sh | Estimated shrinkage correlation matrix |

sim.morpho | Simulate a continuous morphological alignment |

sim.pop | Simulate a population matrix |

sim.R | Correlation matrix for simulations |

sim.tree | Simulated 8-species tree |

stepping.stones | Estimate marginal likelihood by stepping stones |

treeMCMCtree | Generating a tree file in MCMCtree format when using... |

V | 29 3D landmarks from the skulls of 19 carnivoran specimens... |

var.foxes | Vector with the population variance of Vulpes vulpes |

V.arr.unal | 29 3D landmarks from the skulls of 21 Vulpes vulpes specimens... |

V.mat.unal | 29 3D landmarks from the skulls of 19 carnivoran specimens... |

V.PS.nov1 | Object of class array output by Morpho after PA |

vulpes21x29.raw | 29 3D landmarks from the skulls of 21 Vulpes vulpes specimens |

write.morpho | Generate a file with a morphological alignment for MCMCtree |

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