BioGeoBEARS (version 0.2.1)

bears_2param_standard_slowQ_slowSP: 2-parameter model, fixed cladogenesis model -- slow version

Description

This implements the same 2-parameter model found in LAGRANGE or bears_2param_standard_fast, but using the original slower options for matrix exponentiation and cladogenesis events.

Usage

bears_2param_standard_slowQ_slowSP(trfn = "Psychotria_5.2.newick", geogfn = "Psychotria_geog.data", max_range_size = 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.

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_2param_standard_slowQ_slowSP(trfn=trfn, geogfn=geogfn)
# bears_output
# ## End(Not run)