TreeSimGM: Simulating Phylogenetic Trees under a General Model

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.

Author
Oskar Hagen, Tanja Stadler
Date of publication
2014-07-25 07:39:50
Maintainer
Oskar Hagen <oskar.hagen@outlook.com>
License
GPL-2
Version
1.2

View on CRAN

Man pages

sim.age
Simulating General Model Trees on Age
sim.taxa
Simulating General Model Trees on a fixed number of extant...
TreeSimGM-package
Simulating Phylogenies under a General Model (symmetric &...

Files in this package

TreeSimGM
TreeSimGM/NAMESPACE
TreeSimGM/R
TreeSimGM/R/sim.age.R
TreeSimGM/R/mytree.symmetric.taxa.R
TreeSimGM/R/mytree.asymmetric.taxa.R
TreeSimGM/R/sim.taxa.R
TreeSimGM/R/mytree.asymmetric.age.R
TreeSimGM/R/mytree.symmetric.age.R
TreeSimGM/MD5
TreeSimGM/DESCRIPTION
TreeSimGM/man
TreeSimGM/man/sim.taxa.Rd
TreeSimGM/man/TreeSimGM-package.Rd
TreeSimGM/man/sim.age.Rd