plot_cladogenesis_size_probabilities: Graphical display of P(daughter rangesize) for your input 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

This function produces a graphical summary of the daughter rangesize aspect of the cladogenesis model stored in a BioGeoBEARS_run_object. This could be either an input model, or the result of the ML parameter search.

1 2	plot_cladogenesis_size_probabilities(BioGeoBEARS_run_object, plotwhat = "est", statenames = NULL)

`BioGeoBEARS_run_object`	The input run object.
`plotwhat`	Default is "input", which means plotting the starting model.
`statenames`	State names to pass to `plot_cladogenesis_size_probabilities`. If `NULL` (default), these are auto-generated assuming all areas up to the maximum number are allowed.

The LAGRANGE DEC model assumes that at cladogenesis events, one daughter species has a range size of 1 area, and the other daughter either inherits the full ancestral range (sympatric-subset speciation), inherits the remainder of the ancestral range (vicariance), or as the same range (sympatric-range copying, which is the only option when the ancestor range is of size 1 area.

BioGeoBEARS enables numerous additional models. To see how these are similar or different from the LAGRANGE DEC cladogenesis model, this function can be used. E.g., comparison of LAGRANGE DEC to a DIVA-like model is instructive: see examples. DIVA disallows sympatric-subset speciation (probability 0 under this model), but allows classic vicariance (a species with 4 areas splitting into 2 daughters, each occupying 2 areas). LAGRANGE DEC gives 0 probability to a 4->(2,2) history, allowing only 4->(3,1) or 4->(1,3) histories.

Several additional plots relating to the cladogenesis model are also produced. Best used via plot_BioGeoBEARS_model.

Nothing

Go BEARS!

Nicholas J. Matzke matzke@berkeley.edu

http://phylo.wikidot.com/matzke-2013-international-biogeography-society-poster

Matzke_2012_IBS

plot_BioGeoBEARS_model, define_BioGeoBEARS_run, define_BioGeoBEARS_model_object