infprobs_to_probs_of_each_area: Convert probabilities of each state, to the probabilities of...
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

Biogeographic inference in LAGRANGE and DIVA has focused heavily on inference of the exact ancestral state/geographic range. However, when the state space is large, there is often considerable uncertainty in the exact ancestral range. Even the ancestral state that confers the maximum likelihood on the data, and thus is the most probable ancestor, may have less than 50 probability, or even less (25 size of the state space. This function converts the probability of specific states/geographic ranges into the probability of presence/absence in each area. This can typically be inferred with much higher confidence.

1 2	infprobs_to_probs_of_each_area(relprobs_matrix, states_list)

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..

states_list

A list of the possible states/geographic ranges, in 0-based index form.

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

bears_2param_standard_fast, get_ML_states, get_ML_probs, infprobs_to_probs_of_each_area_from_relprobs

testval=1

Loading required package: rexpokit
Loading required package: cladoRcpp
Loading required package: ape
Loading required package: phylobase

Attaching package: 'phylobase'

The following object is masked from 'package:ape':

    edges