Package: TreeSim
Type: Package
Title: Simulating trees under the birth-death model
Version: 1.9
Date: 2013-06-09
Author: Tanja Stadler
Maintainer: Tanja Stadler <tanja.stadler@env.ethz.ch>
Depends: ape, geiger
Description: The package simulates 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).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 appropriately trees with n final tips
        from a set of trees generated by the common sampling algorithm
        stopping when a fixed number m>>n of leaves 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.
License: GPL-2
LazyLoad: yes
Packaged: 2013-06-09 17:00:40 UTC; tanja
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2013-06-09 19:08:09
