Range Ancestral State Estimation for Phylogeography and Comparative Analyses

add.dens | Plot the Posterior Density for each Ancestor in 3D Space |

add.polygons | Plot the Distributions for the Phylogenetic Tips in 3D |

bigauss_pdf | Bivariate Gaussian PDF |

bm_ase | Bayesian Ancestral State Estimation with Points |

bm_loglik_ancestors | Likelihood of ancestors using points |

bm_loglik_duo | Likelihood of a 2-dimensional point with one daughter and one... |

bm_loglik_tree | Point Brownian motion tree likelihood |

bm_loglik_tree_constrained | Range Brownian motion tree likelihood |

bm_loglik_trio | Fast likelihood of a 2-dimensional point with two daughters... |

bm_propose_duo | MCMC proposal for a 2-dimensional point with one daughter and... |

bm_propose_trio | MCMC proposal for a 2-dimensional point with two daughters... |

data.for.3d | Transform Output for 3D Plotting |

make_bm_est_sigma2 | Estimate Sigma and Sigma Variance |

make_bm_loglik_ancestors_poly | Fast likelihood of ancestors using polygons |

name.poly | Name & Order Polygons According to the Phylogeny |

phylo.3d | Plots a Phylogenic Tree in 3D |

point.like.bm | n-dimensional Maximum Likelihood of Point Brownian Motion |

poly_center | Calculate the Polygon Center |

ranges.like.bm | n-dimensional Maximumn Likelihood of Range Brownian Motion |

rase | Bayesian Range Ancestral State Estimation of Polygons |

rase_data | Psophia Data Used for rase Package |

rase-package | Range Ancestral State Estimation |

rase.slice | Ancestral State Estimation At Any Given Time Slice |

shape.to.rase | Transform a Shapefile into 'owin.object' Format |

tree.slice | Identify Tree Branches That Intersect With a Given Time... |

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