plot_BioGeoBEARS_model: Graphical display of your anagenetic and cladogenetic...
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 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_BioGeoBEARS_model(obj, obj_is_run_or_results = NULL, plotwhat = "init", titletxt = "", statenames = NULL)

`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.

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.

nada

Go BEARS!

Nicholas J. Matzke matzke@berkeley.edu

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

Matzke_2012_IBS

plot_cladogenesis_size_probabilities, define_BioGeoBEARS_run, define_BioGeoBEARS_model_object