Description Usage Arguments Details Value

View source: R/bayou-likelihood.R View source: R/bayou-likelihood.R

Function for calculating likelihood of an OU model in bayou using pruning algorithm or matrix inversion

1 |

`pars` |
A list of parameters to calculate the likelihood |

`tree` |
A phylogenetic tree of class 'phylo' |

`X` |
A named vector giving the tip data |

`SE` |
A named vector or single number giving the standard errors of the data |

`model` |
Parameterization of the OU model. Either "OU", "QG" or "OUrepar". |

`invert` |
A logical indicating whether the likelihood should be solved by matrix inversion, rather than the pruning algorithm. This is primarily present to test that calculation of the likelihood is correct. |

This function can be used for calculating single likelihoods using previously implemented methods. It is
likely to become deprecated and replaced by `bayou.lik`

in the future, which is based on `phylolm`

's threepoint
algorithm, which works on non-ultrametric trees and is substantially faster.

A list returning the log likelihood ("loglik"), the weight matrix ("W"), the optima ("theta"), the residuals ("resid") and the expected values ("Exp").

bayou documentation built on May 29, 2017, 3:32 p.m.

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