PBD-package: Protracted birth-death model of diversification
Description
This package computes the (maximum) likelihood of the protracted speciation model for a given set of branching times
This package is a likelihood-based statistical package to estimate parameters
under the protracted speciation model.
First version: 0.8
New in version 0.9
- Bug fix for stem age
New in version 0.91
- Reports loglik = -Inf on an error in the deSolve package (function ode)
New in version 0.92
- Correcting order of parameters of pbd_sim
New in version 0.93
- pbd_sim produces a tree, a matrix containing all events in the simulation, and a tree with one sample per species.
New in version 1.0
- Conditioning is also possible on a range of values of the number of species.
New in version 1.1
- Simulation of the protracted speciation tree has more features.
Arguments
Details
ll{
Package: PBD
Type: Package
Version: 1.1
Date: 2015-9-16
License: GPL-2
}
pbd_loglik computes the likelihood of the protracted birth-death model of
diversification, given a set of parameters and a data set of phylogenetic branching times.
pbd_ML finds the parameters that maximizes the likelihood computed by pbd_loglik.
References
- Etienne, R.S. & J. Rosindell 2012. Systematic Biology 61: 204-213.
- Lambert, A., H. Morlon & R.S. Etienne 2014. Journal of Mathmematical Biology 70: 367-397. doi:10.1007/s00285-014-0767-x
- Etienne, R.S., H. Morlon & A. Lambert 2014. Evolution 68: 2430-2440 doi:10.1111/evo.12433
.