BioGeoBEARS (version 0.2.1)

bears_3param_standard_fast_fixnode: 3-parameter model, adding j (founder-event speciation)

Description

This implements a 3-parameter model, basically LAGRANGE or bears_2param_standard_fast, but with a parameter j controlling the relative weight of "founder-event speciation" (Matzke (2012)) versus vicariance+sympatric speciation (which are mandated in LAGRANGE and bears_2param_standard_fast.

Usage

bears_3param_standard_fast_fixnode(trfn = "Psychotria_5.2.newick", geogfn = "Psychotria_geog.data", max_range_size = NULL, num_cores_to_use = NULL, fixnode = fixnode, fixlikes = fixlikes)

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.

fixnode

If the state at a particular node is going to be fixed (e.g. for ML marginal ancestral states), give the node number.

fixlikes

The state likelihoods to be used at the fixed node. I.e. 1 for the fixed state, and 0 for the others.

Value

bears_output A list of outputs. bears_output$optim_result

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/

Matzke_2012_IBS

ReeSmith2008

Ree2009configurator

SmithRee2010_CPPversion

Landis_Matzke_etal_2013_BayArea

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_3param_standard_fast(trfn=trfn, geogfn=geogfn)
# bears_output
# ## End(Not run)