plot_BioGeoBEARS_model: Graphical display of your anagenetic and cladogenetic biogeography models

Description

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

Usage

plot_BioGeoBEARS_model(obj, obj_is_run_or_results = NULL, plotwhat = "init", titletxt = "", statenames = NULL)

Arguments

obj

The input object, either a BioGeoBEARS_run_object (if so, set obj_is_run_or_results="run" or an output object from bears_optim_run (if so, specify obj_is_run_or_results="results".

obj_is_run_or_results

Specify "run" or "results", as described above for parameter obj.

plotwhat

Default is "init", which means plotting the starting model parameters. "est" plots the estimated model parameters.

titletxt

Additional text for the title of the plot

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

nada

Details

Understanding of phylogenetic methoods in historical biogeography methods is hampered by the difficulty of displaying the models the computer is using. This function is one attempt to improve the situation, by plotting the relative weights of the various parameters.

References

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

Matzke_2012_IBS

Examples

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