Package: TreeSimGM
Type: Package
Title: Simulating Phylogenetic Trees under a General Model
Version: 1.1
Date: 2013-01-01
Author: Oskar Hagen, Tanja Stadler
Maintainer: Oskar Hagen <oskar.is.hagen@gmail.com>
Depends: TreeSim
Description: The package is a flexible simulation tool for phylogenetic
trees under a general model. It is possible to assume any
probability distribution for the waiting time until speciation
and extinction independently. Thus, TreeSimGM allows to
simulate stochastic phylogenetic trees using any probability
distribution and parameters for speciation and extinction. The
speciation modes have all binary splits and are: (i) symmetric,
where for every speciation event new waiting times until
speciation and extinction are drawn for both daughter lineages;
and (ii) asymmetric, where a speciation event results in one
species with new waiting times, and another that carries the
extinction time and age of its ancestor. Those two modes were
inspired by allopatric and peripatric speciation
respectively.Both models (symmetric and asymmetric) were
created and implemented so that different processes
(distributions) for speciation and extinction could be
independently and explicitly specified. It is also possible to
have an implicit extinction process by setting the extinction
rate to zero.
License: GPL-2
LazyLoad: yes
Packaged: 2013-02-20 21:12:11 UTC; oskar
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2013-02-21 07:52:51

Description: The package is a flexible simulation tool for phylogenetic trees under a general model. It is possible to assume any probability distribution for the waiting time until speciation and extinction independently. Thus, TreeSimGM allows to simulate stochastic phylogenetic trees using any probability distribution and parameters for speciation and  extinction. The speciation modes have all binary splits and are: (i) symmetric, where for every speciation event new waiting times until speciation and extinction are drawn for both daughter lineages; and (ii) asymmetric, where a speciation event results in one species with new waiting times, and another that carries the extinction time and age of its ancestor. Those two modes were inspired by allopatric and peripatric speciation respectively.Both models (symmetric and asymmetric) were created and implemented so that different processes (distributions) for speciation and extinction could be independently and explicitly specified. It is also possible to have an implicit extinction process by setting the extinction rate to zero.