bears_2param_standard_fast_symOnly_simp: 2-parameter model, no cladogenesis model (as in BayArea or...
In BioGeoBEARS: BioGeography with Bayesian (and Likelihood) Evolutionary Analysis in R Scripts

Description Usage Arguments Details Value Note Author(s) References See Also Examples

(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.

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

`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`.

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.

bears_output A list of outputs. bears_output$optim_result

Go BEARS!

Nicholas J. Matzke matzke@berkeley.edu

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

numstates_from_numareas, getranges_from_LagrangePHYLIP, read.tree, calc_loglike_sp

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)