Description Usage Arguments Details Value Author(s) References

Uses estimated speciation and extinction rates to sample the number of speciation events 'hidden' by subsequent extinction on each branch of a tree following Bokma (2008). For use with the psi and multipsi models.

1 | ```
sampleHiddenSp(phy, lambda.sp = NULL, mu.ext = NULL, useMean = FALSE)
``` |

`phy` |
Phylogenetic tree in phylo format |

`lambda.sp` |
Estimate of the rate of speciation "lambda" |

`mu.ext` |
Estimate of the rate of extinction "mu" |

`useMean` |
A logical indicating whether to output the average or expected number of hidden speciation events per branch, which may be non-integer (if |

The expected number of hidden speciation events are calculated for each branch given its start and end times, and estimates of lambda and mu which are assumed to be constant across the tree. To properly account for uncertainty in the effect of extinction on the number of nodes affecting each branch of a tree, it may be appropriate to repeat model-fitting on many realizations of `Sobs`

on the tree of interest (similar to evaluating phylogenetic uncertainty)

Phylogenetic tree in `phylo`

format, with an added element `Sobs`

, a vector of numbers of hidden speciation events per branch, in the same order as the branches in the `phylo`

object

Travis Ingram

Bokma, F. 2008. Detection of "punctuated equilibrium" by Bayesian estimation of speciation and extinction rates, ancestral character states, and rates of anagenetic and cladogenetic evolution on a molecular phylogeny. Evolution 62: 2718-2726.

Ingram, T. 2011. Speciation along a depth gradient in a marine adaptive radiation. Proc. R. Soc. B 278: 613-618.

Embedding an R snippet on your website

Add the following code to your website.

For more information on customizing the embed code, read Embedding Snippets.