simstates_to_probs_of_each_area: Convert simulated states to probabilities of each area
In BioGeoBEARS: BioGeography with Bayesian (and Likelihood) Evolutionary Analysis in R Scripts

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

View source: R/BioGeoBEARS_simulate_v1.R

Basically this function assigns probability 1 to occupied areas according to the simulated state for a node, and probability 0 for the other areas. These data – the simulated truth – can then be compared to the inferred probabilities of presence in each area, from infprobs_to_probs_of_each_area.

1 2	simstates_to_probs_of_each_area(simulated_states_by_node, states_list, relprobs_matrix)

`simulated_states_by_node`	The simulated states by node (0-based indices).
`states_list`	A list of the possible states/geographic ranges, in 0-based index form.
`relprobs_matrix`	A relative probabilities matrix returned by `bears_2param_standard_fast` or a similar function. The user should specify WHICH matrix in the results_object – i.e., scaled conditional likelihoods on downpass or uppass, or actual marginal probabilities of ancestral states. (The latter is the main thing of interest.) This specification is done via e.g. `relprobs_matrix = results_object$relative_probs_of_each_state_at_branch_top_AT_node_DOWNPASS`..

area_probs The probability of presence in each area.

Go BEARS!

Nicholas J. Matzke matzke@berkeley.edu

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

Matzke_2012_IBS

simulate_biogeog_history, infprobs_to_probs_of_each_area

testval=1

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