Package: laser
Version: 2.4-1
Date: 2013-09-03
Title: Likelihood Analysis of Speciation/Extinction Rates from
Phylogenies
Author: Dan Rabosky, Klaus Schliep
Maintainer: Dan Rabosky <drabosky@umich.edu>
Depends: R (>= 2.6), ape, geiger (>= 1.99-3)
Suggests:
Description: laser implements maximum likelihood methods based on the
birth-death process to test whether diversification rates have
changed over time and whether rates vary among lineages.
License: GPL (>= 2)
Packaged: 2013-09-04 10:43:28 UTC; danrabosky
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2013-09-04 14:58:43
Package: DAMOCLES
Type: Package
Title: Dynamic Assembly Model of Colonization, Local Extinction and
Speciation
Version: 1.1
Date: 2015-03-05
Depends: R (>= 3.0), geiger, caper, ape, deSolve, matrixStats
Imports: expm, picante
Author: Rampal S. Etienne & Alex L. Pigot
Maintainer: Rampal S. Etienne <r.s.etienne@rug.nl>
License: GPL-2
Description: Simulates and computes (maximum) likelihood of a dynamical model of community assembly that takes into account phylogenetic history.
Packaged: 2015-03-05 15:23:08 UTC; p223208
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2015-03-05 17:36:50
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
Package: surface
Type: Package
Title: Fitting Hansen Models to Investigate Convergent Evolution
Version: 0.4-1
Date: 2014-02-14
Author: Travis Ingram
Maintainer: Travis Ingram <travis.ingram@otago.ac.nz>
Depends: R (>= 2.6), ape, ouch, MASS, geiger
Suggests: igraph
Description: SURFACE is a data-driven phylogenetic comparative method for fitting stabilizing selection models to continuous trait data, building on the ouch package. The main functions fit a series of Hansen models using stepwise AIC, then identify cases of convergent evolution where multiple lineages have shifted to the same adaptive peak.
License: GPL (>= 2)
URL: http://www.people.fas.harvard.edu/~ingram/web/surface.html
Packaged: 2014-02-14 09:32:26 UTC; ingram
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-02-14 11:22:36
providing 
.