plot_cladogenesis_size_probabilities: Graphical display of P(daughter rangesize) for your input or inferred speciation model

Description

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.

Usage

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

Arguments

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.

Value

Nothing

Details

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.

References

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

Matzke_2012_IBS

Examples

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