Description Usage Arguments Value Author(s) References Examples

LikConstant calculates the likelihood of constant speciation and extinction rates for a given phylogenetic tree, conditioning on the age of the tree.

1 | ```
LikConstant(lambda,mu,sampling,x,root=1,survival=1)
``` |

`lambda,mu` |
Speciation and extinction rate. |

`sampling` |
Sampling is the probability of an extant species being sampled and included into the tree. |

`x` |
Vector of speciation times in the phylogeny. Time is measured increasing going into the past with the present being time 0. x can be obtained from a phylogenetic tree using getx(TREE). |

`root` |
If root = 1 then max(x) is the mrca (crown age), if root = 0 then max(x) is the age of a branch ancestral to the mrca (stem age). |

`survival` |
If survival = 1: The likelihood is conditioned on survival of the process (recommended). Otherwise survival = 0. |

`res` |
-log likelihood of the birth and death rates given the tree. |

Tanja Stadler

T. Stadler. On incomplete sampling under birth-death models and connections to the sampling-based coalescent. Jour. Theo. Biol. 261: 58-66, 2009.

1 | ```
# see manual of LikShifts()
``` |

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