bears_6param_standard_fast_ys_v: 6-parameter model, adding j (founder-event speciation), v...
In BioGeoBEARS: BioGeography with Bayesian (and Likelihood) Evolutionary Analysis in R Scripts

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

This implements a 6-parameter model, basically LAGRANGE or bears_2param_standard_fast, but with a parameter j controlling the relative weight of "founder-event speciation" (Matzke (2012)), and another parameter v controlling the relative weight of vicariance. The remainder of the weight (weights must sum to 1) is taken up by the range-copying and range-subset forms of sympatric speciation utilized in LAGRANGE and bears_2param_standard_fast. A fifth parameter, maxent_constraint_01, controls the relative probability of daughter lineages of different rangesizes. A sixth parameter, maxent_constraint_01v, controls the relative probability of daughter lineages of different rangesizes, but only for the vicariance events, which are rather different from other types of speciation events. If maxent_constraint_01v=0.0001, the smaller-ranged daughter lineage will have size 1 area, with probability 1. If maxent_constraint_01v=0.5, all different rangesizes will have equal probability, and if maxent_constraint_01v=0.9999, the largest possible range will have probability 1 – but note that in a vicariance context, this would mean at maximum rangesize of 50 the areas.

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  bears_6param_standard_fast_ys_v(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`.

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/

Matzke_2012_IBS

ReeSmith2008

Ree2009configurator

SmithRee2010_CPPversion

Landis_Matzke_etal_2013_BayArea

bears_2param_standard_fast, 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_6param_standard_fast_ys_v(trfn=trfn, geogfn=geogfn)
bears_output

## End(Not run)