Description: Simulation methods for phylogenetic trees where (i) all tips are sampled at one time point or (ii) tips are sampled sequentially through time. (i) For sampling at one time point, simulations are performed under a constant rate birth-death process, conditioned on having a fixed number of final tips (sim.bd.taxa()), or a fixed age (sim.bd.age()), or a fixed age and number of tips (sim.bd.taxa.age()). When conditioning on the number of final tips, the method allows for shifts in rates and mass extinction events during the birth-death process (sim.rateshift.taxa()). The function sim.bd.age() (and sim.rateshift.taxa() without extinction) allow the speciation rate to change in a density-dependent way. The LTT plots of the simulations can be displayed using LTT.plot(), LTT.plot.gen() and LTT.average.root(). TreeSim further samples trees with n final tips from a set of trees generated by the common sampling algorithm stopping when a fixed number m>>n of tips is first reached (sim.gsa.taxa()). This latter method is appropriate for m-tip trees generated under a big class of models (details in the sim.gsa.taxa() man page). For incomplete phylogeny, the missing speciation events can be added through simulations (corsim()). (ii) sim.rateshifts.taxa() is generalized to sim.bdsky.stt() for serially sampled trees, where the trees are conditioned on either the number of sampled tips or the age. Furthermore, for a multitype-branching process with sequential sampling, trees on a fixed number of tips can be simulated using sim.bdtypes.stt.taxa(). This function further allows to simulate under epidemiological models with an exposed class. The function sim.genespeciestree() simulates coalescent gene trees within birth-death species trees, and sim.genetree() simulates coalescent gene trees.

Package: TreeSimGM
Type: Package
Title: Simulating Phylogenetic Trees under a General Model
Version: 1.0
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: 2013-02-14 09:18:57 UTC; oskar
Repository: CRAN
Date/Publication: 2013-02-14 10:38:58