Package: BioGeoBEARS
Type: Package
Title: BioGeography with Bayesian (and likelihood) Evolutionary
        Analysis in R Scripts
Version: 0.1.1
Date: 2013-06-23
Authors@R: c(person("Nicholas J.", "Matzke", email =
        "matzke@berkeley.edu", role = c("aut", "cre", "cph")))
Maintainer: Nicholas J. Matzke <matzke@berkeley.edu>
Depends: rexpokit, cladoRcpp, optimx, FD, ape, methods, parallel,
        compiler, LaplacesDemon, phylobase
LinkingTo: ape
Suggests: xtable
Description: BioGeoBEARS allows probabilistic inference of both
        historical biogeography (ancestral geographic ranges on a
        phylogeny) as well as comparison of different models of range
        evolution.  It reproduces the model available in LAGRANGE (Ree
        and Smith 2008), as well as making available numerous
        additional models. For example, LAGRANGE as typically run has
        two free parameters, d (dispersal rate, i.e. the rate of range
        addition along a phylogenetic branch) and e (extinction rate,
        really the rate of local range loss along a phylogenetic
        branch). LAGRANGE also has a fixed cladogenic model which gives
        equal probability to a number of allowed range inheritance
        events, e.g.: (1) vicariance, (2) a new species starts in a
        subset of the ancestral range, (3) the ancestral range is
        copied to both species; in all cases, at least one species must
        have a starting range of size 1.  LAGRANGE assigns equal
        probability to each of these events, and zero probability to
        other events.  BioGeoBEARS adds an additional cladogenic event:
        founder-event speciation (the new species jumps to a range
        outside of the ancestral range), and also allows the relative
        weighting of the different sorts of events to be made into free
        parameters, allowing optimization and standard model choice
        procedures to pick the best model. The relative probability of
        different descendent range sizes is also parameterized and thus
        can also be specified or estimated.  The flexibility available
        in BioGeoBEARS also enables the natural incorporation of (1)
        imperfect detection of geographic ranges in the tips, and (2)
        inclusion of fossil geographic range data, when the fossils are
        tips on the phylogeny.
License: GPL (>= 2)
LazyLoad: yes
ByteCompile: true
Packaged: 2013-06-24 02:21:00 UTC; nickm
Author: Nicholas J. Matzke [aut, cre, cph]
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2013-06-24 08:13:17
