| Name : R-TreeSim
| |
| Version : 2.4
| Vendor : obs://build_opensuse_org/devel:languages:R
|
| Release : lp154.18.1
| Date : 2024-06-14 10:49:07
|
| Group : Development/Libraries/Other
| Source RPM : R-TreeSim-2.4-lp154.18.1.src.rpm
|
| Size : 0.17 MB
| |
| Packager : https://www_suse_com/
| |
| Summary : Simulating Phylogenetic Trees
|
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.
|
RPM found in directory: /packages/linux-pbone/ftp5.gwdg.de/pub/opensuse/repositories/devel:/languages:/R:/autoCRAN/15.4/x86_64 |
