TreeSim: Simulating Phylogenetic Trees

Share:

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.

Author
Tanja Stadler
Date of publication
2015-10-05 17:07:39
Maintainer
Tanja Stadler <tanja.stadler@bsse.ethz.ch>
License
GPL-2
Version
2.2

View on CRAN

Man pages

corsim
corsim: Simulating the missing speciation events in an...
cuttree
cuttree: Cutting off the tree to prune recent branches.
getx
getx: Calculating the vector of speciation / transmission...
LTT.plot
LTT.plot: Plots the lineages through time of a set of...
LTT.plot.gen
LTT.plot.gen: Calculates the number of lineages through time...
sim.bd.age
sim.bd.age: Simulating birth-death trees of a fixed age.
sim.bdsky.stt
sim.bdsky.stt: Simulating sequentially sampled birth-death,...
sim.bd.taxa
sim.bd.taxa: Simulating birth-death trees on a fixed number...
sim.bd.taxa.age
sim.bd.taxa.age: Simulating birth-death trees with a given...
sim.bdtypes.stt.taxa
sim.bdtypes.stt.taxa: Simulating multitype birth-death trees...
sim.genespeciestree
sim.genespeciestree: Simulating birth-death species trees...
sim.genetree
sim.genetree: Simulating coalescent gene trees.
sim.gsa.taxa
sim.gsa.taxa: Sampling trees on n tips from bigger trees.
sim.rateshift.taxa
sim.rateshift.taxa: Simulating trees incorporating mass...
TreeSim-package
TreeSim: Simulating Phylogenetic Trees

Files in this package

TreeSim
TreeSim/NAMESPACE
TreeSim/R
TreeSim/R/sim.bd.taxa.age.help.R
TreeSim/R/sim2.bd.fast.single.mrca.R
TreeSim/R/sim.bd.taxa.loop.R
TreeSim/R/sim.genetree.R
TreeSim/R/sim2.bd.rateshift.single.R
TreeSim/R/cuttree.R
TreeSim/R/sim.bd.age.help.R
TreeSim/R/sim2.bd.reverse.single.R
TreeSim/R/sim2.bd.fast.age.R
TreeSim/R/sim.rateshift.taxa.help.R
TreeSim/R/numbspecies.R
TreeSim/R/corsim.R
TreeSim/R/sim.rateshift.taxa.R
TreeSim/R/LTT.plot.gen.R
TreeSim/R/sim2.bd.age.R
TreeSim/R/age.nodes.R
TreeSim/R/sim.bdsky.stt.R
TreeSim/R/gettimeperiod.R
TreeSim/R/sim2.bd.rateshift.R
TreeSim/R/sim.bd.taxa.age.loop.R
TreeSim/R/gettimelength.R
TreeSim/R/intp1.R
TreeSim/R/sim2.bd.fast.single.R
TreeSim/R/sim.rateshift.taxa.loop.R
TreeSim/R/LTT.general.R
TreeSim/R/sim.bdtypes.stt.taxa.R
TreeSim/R/sim.bd.taxa.R
TreeSim/R/sim2.bd.mrca.reconst.R
TreeSim/R/sim2.bd.reverse.R
TreeSim/R/LTT.plot.R
TreeSim/R/sim2.bd.mrca.R
TreeSim/R/sim.bd.age.loop.R
TreeSim/R/sim.genespeciestree.R
TreeSim/R/age.tips.R
TreeSim/R/reconstructed.age.R
TreeSim/R/sim2.bd.gsa.R
TreeSim/R/sim.bd.age.R
TreeSim/R/reconstructed.taxa.single.R
TreeSim/R/sim.gsa.taxa.R
TreeSim/R/sim.bd.taxa.help.R
TreeSim/R/reconstructed.taxa.R
TreeSim/R/add.rootedge.R
TreeSim/R/sim2.bd.origin.R
TreeSim/R/collapse.singles.R
TreeSim/R/sim2.bd.R
TreeSim/R/branching.times.complete.R
TreeSim/R/stats.R
TreeSim/R/get.times.polytomy.R
TreeSim/R/LTT.average.root.R
TreeSim/R/getnumbs.R
TreeSim/R/extinction.times.R
TreeSim/R/sim2.gsa.R
TreeSim/R/sim2.bd.ssa.R
TreeSim/R/sim.bd.taxa.age.R
TreeSim/R/sim2.bd.fast.single.origin.R
TreeSim/R/sim2.bd.fast.R
TreeSim/R/getx.R
TreeSim/MD5
TreeSim/DESCRIPTION
TreeSim/man
TreeSim/man/sim.bdsky.stt.Rd
TreeSim/man/LTT.plot.Rd
TreeSim/man/sim.bdtypes.stt.taxa.Rd
TreeSim/man/TreeSim-package.Rd
TreeSim/man/sim.bd.age.Rd
TreeSim/man/sim.genetree.Rd
TreeSim/man/sim.rateshift.taxa.Rd
TreeSim/man/cuttree.Rd
TreeSim/man/getx.Rd
TreeSim/man/sim.bd.taxa.age.Rd
TreeSim/man/sim.bd.taxa.Rd
TreeSim/man/sim.gsa.taxa.Rd
TreeSim/man/sim.genespeciestree.Rd
TreeSim/man/corsim.Rd
TreeSim/man/LTT.plot.gen.Rd