TreeSimGM

Package: TreeSimGM
Type: Package
Title: Simulating Phylogenetic Trees under a General Model
Version: 1.2
Date: 2013-07-23
Author: Oskar Hagen, Tanja Stadler
Maintainer: Oskar Hagen <oskar.hagen@outlook.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: 2014-07-24 23:54:50 UTC; Oskar
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-07-25 07:39:50

Install log

* installing to library '/home/ddbj/local/lib64/R/library'
* installing *source* package 'TreeSimGM' ...
** package 'TreeSimGM' successfully unpacked and MD5 sums checked
** R
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'TreeSimGM'
    finding HTML links ... done
    TreeSimGM-package                       html  
Rd warning: /tmp/RtmpBMV0vb/R.INSTALL20b06234df9b/TreeSimGM/man/TreeSimGM-package.Rd:33: missing file link 'TreeSim'
Rd warning: /tmp/RtmpBMV0vb/R.INSTALL20b06234df9b/TreeSimGM/man/TreeSimGM-package.Rd:34: missing file link 'ape'
    sim.age                                 html  
    sim.taxa                                html  
** building package indices
** testing if installed package can be loaded
* DONE (TreeSimGM)
Making 'packages.html' ... done