Package: TreeSim
Type: Package
Title: Simulating trees under the birth-death model
Version: 1.7
Date: 2012-11-19
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: 2012-11-20 09:32:31 UTC; tanja
Repository: CRAN
Date/Publication: 2012-11-20 11:34:08

Package: TreeSim
Type: Package
Title: Simulating trees under the birth-death model
Version: 1.8
Date: 2013-04-10
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: 2013-04-16 13:37:23 UTC; tanja
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2013-04-16 18:14:07