get_ML_probs: Get the probability of the ML state for each node, from a...
In BioGeoBEARS: BioGeography with Bayesian (and Likelihood) Evolutionary Analysis in R Scripts

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

View source: R/BioGeoBEARS_simulate_v1.R

This function extracts the probability of the ML states from the results list produced by bears_2param_standard_fast or a similar ML search function.

1	get_ML_probs(relprobs_matrix, unlist_TF = TRUE)

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..

unlist_TF

Unlist the output? Default TRUE.

This is useful for displaying e.g. pie charts of the probability of the ML ancestral state at each node.

Note, though, that it is somewhat peculiar and arbitrary to focus on the ancestral states just at nodes, particularly in the context of fossils with time ranges and geographic ranges.

inf_probsvec The inferred vector of probabilities of ML states.

Go BEARS!

Nicholas J. Matzke matzke@berkeley.edu

http://phylo.wikidot.com/matzke-2013-international-biogeography-society-poster http://blog.phytools.org/2013/03/marginal-ancestral-state-reconstruction.html https://code.google.com/p/lagrange/

Matzke_2012_IBS

get_ML_probs, bears_2param_standard_fast, get_ML_state_indices

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