TreeSim

Package: TreeSim
Type: Package
Title: Simulating Phylogenetic Trees
Version: 2.2
Date: 2015-10-05
Author: Tanja Stadler
Maintainer: Tanja Stadler <tanja.stadler@bsse.ethz.ch>
Depends: ape, laser, geiger
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.
License: GPL-2
LazyLoad: yes
Packaged: 2015-10-05 12:14:49 UTC; tstadler
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2015-10-05 17:07:39

Install log

* installing to library '/home/ddbj/local/lib64/R/library'
* installing *source* package 'TreeSim' ...
** package 'TreeSim' successfully unpacked and MD5 sums checked
** R
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'TreeSim'
    finding HTML links ... done
    LTT.plot                                html  
    LTT.plot.gen                            html  
    TreeSim-package                         html  
    corsim                                  html  
    cuttree                                 html  
    getx                                    html  
    sim.bd.age                              html  
    sim.bd.taxa                             html  
    sim.bd.taxa.age                         html  
    sim.bdsky.stt                           html  
    sim.bdtypes.stt.taxa                    html  
    sim.genespeciestree                     html  
    sim.genetree                            html  
    sim.gsa.taxa                            html  
    sim.rateshift.taxa                      html  
** building package indices
** testing if installed package can be loaded
* DONE (TreeSim)
Making 'packages.html' ... done