This function extracts the ML states from the results
list produced by
or a similar ML search function.
A relative probabilities matrix
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:
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.
Nicholas J. Matzke email@example.com
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
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