get_ML_states: Get ML states from a BioGeoBEARS model results list
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 ML states from the results list produced by bears_2param_standard_fast or a similar ML search function.

1	get_ML_states(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.

Currently, the scaled conditional probabilities are used to determine the optimum states. However, this is not strictly correct, as these use only tips-down information (Felsenstein (2004); see also this post by Revell: http://blog.phytools.org/2013/03/marginal-ancestral-state-reconstruction.html). This is what LAGRANGE seems to do when reporting ancestral states, also (personal observation, perhaps imperfect, especially if the scaled conditional likelihoods and the marginal ancestral state probabilities turn out to be very close). What is desired is the marginal ancestral state reconstructions. Most authors discuss ML ancestral state reconstruction as being a matter of re-rooting the tree at each node, yielding the marginal estimate for that node, conditional on the rest of the tree. However, this procedure assumes a time-reversible model on both branches and cladogenesis events, and we have neither in biogeography. Probably, the solution is just an up-pass from the root, calculating the probabilities on the forward model and multiplying by likelihoods from the downpass. However, this has not yet been implemented.

inf_statesvec The inferred vector of 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/

Felsenstein2004

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