wrightscape

bm_path_sim | brownian motion path simulator |

bootstrap | bootstrap: a function to compute bootstrap replicates |

bootstrap.multiOU | function to bootstrap a multiOU object |

brownie_path_sim | Release of constraint path simulator |

convert | toggles between ouch and ape format trees |

custom.llik.closure | returns a custom-built likelihood function |

custom_multiType | get the likelihood of a custom model custom_multiType allows... |

evaluate_likelihood | get the likelihood of the specified model using the specified... |

format_data | format data in ape format into ouch format |

get_clade | A function that returns the edge numbers of all branches... |

get_indices | Helper function to work with llik.closure indexing |

getParameters | get parameters of a fitted object |

getParameters.multiOU | get parameters for the multiOU model |

getParameters.wrighttree | An internal S3 method to get the parameters from the... |

labrids | labrids data |

lca_calc | Wrappers for the C functions that actually calculate the... |

llik.closure | returns the likelihood function for the chosen submodel |

loglik.multiOU | get the log likelihood |

loglik.wrighttree | An internal S3 method to get the likelihood of a wrightscape... |

mrcaOUCH | Finds the most recent common ancestor on an OUCH formatted... |

multiOU_lik_lca | compute the likelihood by passing data to the C level... |

multiTypeOU | Fits the generic multitype OU. |

ou_path_sim | OU path simulator |

paintBranches | Paints branches with regimes changing at nodes specified |

paint_phy | returns a phylogenetic tree painted for ouwie and data |

parrotfish | parrotfish data |

release_path_sim | Release of constraint path simulator |

setup_pars | Helper function to work with llik.closure indexing |

simulate.multiOU | simulate the multiOU model |

simulate.wrighttree | An internal S3 method, simulates the data of a wrightscape... |

summary.multiOU | Summarize a multiOU fit's outputs, including bootstraps, if... |

tip_plot | creates a color-coded plot of how well each tip fits it's... |

update.multiOU | update the model fit |

wrightscape | fit the full model entirely in C code, for speed. |

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