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