BioGeoBEARS (version 0.2.1)

bears_5param_standard_fast_diffstart: 5-parameter model, with different starting points for optimization

Description

This implements the same model as bears_5param_standard_fast, but uses different starting points and slightly different constraints.

Usage

bears_5param_standard_fast_diffstart(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

As the number of parameters increases, the importance of starting ML optimization runs from different places increases. Several starting points should be tried, especially if the likelihood surface seems flat.

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

bears_2param_standard_fast, 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_5param_standard_fast_diffstart(trfn=trfn, geogfn=geogfn)
# bears_output
# ## End(Not run)