BioGeoBEARS (version 0.2.1)

bears_2param_standard_fast_symOnly_simp: 2-parameter model, no cladogenesis model (as in BayArea or other purely continuous-time model)

Description

(Forcing no speciation model.) This implements a 2-parameter model, as in LAGRANGE or bears_2param_standard_fast, but omits the speciation/cladogenesis model. This means that the model is purely continuous-time, as when biogeographic range is treated as a discrete character in software designed for inference on morphological () or molecular data (). This model is that implemented in BayArea, if no distance-dependent effect on dispersal probability is assumed. Such distance-dependence could easily be added with a third parameter, however.

Usage

bears_2param_standard_fast_symOnly_simp(trfn = "Psychotria_5.2.newick", geogfn = "Psychotria_geog.data", max_range_size = NULL, num_cores_to_use = NULL)

Arguments

trfn

The filename of the phylogenetic tree, in NEWICK format (http://evolution.genetics.washington.edu/phylip/newicktree.html). Tipnames should match the names in geogfn. See read.tree in APE for reading in phylogenetic trees.

geogfn

A PHYLIP-style file with geographic range data (see getranges_from_LagrangePHYLIP) for each tipname. This is the same format used by C++ LAGRANGE (SmithRee2010_CPPversion).

max_range_size

The maximum rangesize, in number of areas. Having a smaller maximum range size means that you can have more areas (the size of the state space is greatly reduced; see numstates_from_numareas.

num_cores_to_use

If >1, parallel processing will be attempted. Note: parallel processing via library (parallel) will work in Mac command-line R, but not in Mac GUI R.app.

Value

bears_output A list of outputs. bears_output$optim_result

Details

BayArea is a new program by Landis, Matzke, Moore, and Huelsenbeck; see Landis et al. (2013). However, BayArea does not currently implement cladogenesis models; it only has continuous-time model for evolutionary change along branches. In effect, this means that the cladogenesis model is sympatric speciation with complete range copying with probability 1.

References

Felsenstein, Joe. The Newick tree format. http://evolution.genetics.washington.edu/phylip/newicktree.html http://phylo.wikidot.com/matzke-2013-international-biogeography-society-poster https://code.google.com/p/lagrange/

Landis_Matzke_etal_2013_BayArea

Matzke_2012_IBS

ReeSmith2008

Ree2009configurator

SmithRee2010_CPPversion

See Also

numstates_from_numareas, getranges_from_LagrangePHYLIP, read.tree, calc_loglike_sp

Examples

test=1

# Get the example files directory
extdata_dir = np(system.file("extdata", package="BioGeoBEARS"))
# tmp hard code:
# extdata_dir = "/Dropbox/_njm/__packages/BioGeoBEARS_setup/inst/extdata/"

# Set the filenames (Hawaiian Psychotria from Ree & Smith 2008)
trfn = np(paste(extdata_dir, "/Psychotria_5.2.newick", sep=""))
tr = read.tree(file=trfn)

geogfn = np(paste(extdata_dir, "/Psychotria_geog.data", sep=""))

# Look at the tree and ranges, for kicks
getranges_from_LagrangePHYLIP(lgdata_fn=geogfn)
tr

## Not run: 
# # Run the ML search
# bears_output = bears_2param_standard_fast_symOnly(trfn=trfn, geogfn=geogfn)
# bears_output
# ## End(Not run)