Hi Marko.

This is possible to do, of course. We could just traverse the tree, find the state with the highest posterior probability at each node, and paint the edge by that state using phytools::paintBranches. We could even (with a bit more difficult) traverse our "densityMap" object and find the state with the highest PP at the midpoint of each edge.


However, I might counsel against it for the following reasons.

Firstly, doing so (that is, identifying a set of values at nodes with highest posterior probability at each node) ignores the substantial uncertainty that can be associated with ancestral character estimation. For instance, if we imagine that a set of internal nodes all have posterior probability of state "A" more or less equal to but slightly greater than 0.5 (for a binary character), we would 'reconstruct' all of these nodes to be in state "A" - but this would actually be virtually meaningless with respect to our confidence that these nodes are indeed in state "A".

Secondly, to the extent that we *do* want one set of states for all internal nodes in the tree, a reasonable choice for these states would be those that maximized the probability of the data (that is, the Maximum Likelihood states). Unfortunately, these are not guaranteed to be the states that have the highest marginal posterior probability at all the nodes of the tree. (This is explained in various places, including in the book 'Computational Molecular Evolution' by Yang.)

On the other hand, if the rate of character evolution for our character is relatively low then our marginal posterior probabilities and joint likelihood states will likely more-or-less coincide, and these are also probably quite similar to our MP states. In that case it would perhaps be reasonable to summarize our reconstructed character histories in the way you've proposed.

I hope these comments are helpful - and thank you for using phytools!

All the best, Liam

Liam J. Revell, Associate Professor of Biology
University of Massachusetts Boston
web: http://faculty.umb.edu/liam.revell/
email: liam.rev...@umb.edu
blog: http://blog.phytools.org

On 2/24/2017 6:38 PM, marko.djura...@dbe.uns.ac.rs wrote:
Dear r-sig-phylo participants,

I have data set where tips are assigned to 3 discrete states (aquatic,
semi-aquatic and terrestrial). Because the definition of "semi-aquatic"
is quite arbitrary and some species in the tree lack field observations
of their ecology, I decided to use a matrix of state priors for
stochastic mapping in the phytools package. That approach will allow me
to account for uncertainties/lack of information for some tips in the
phylogeny. I fitted 3 models (ER, SYM, and ARD) where Q was empirically
estimated and nsim was set to 1000. According to AIC value, the SYM
model was the best-fitted one. Describe.simmap showed that mean total
time spent in the state "semi-aquatic" was 0. Thus, all mapped trees
were actually binary and I was able to employ the densityMap function to
obtain an object, let's say "obj", which contains a single tree with the
posterior density for the "aquatic" and "terrestrial" states from 1000
stochastic maps.

Here is the question:
Is it straightforward idea to paint back the obj$tree with just two
colors where colors are determined by a threshold value of posterior
probability (indicated as a legend bar in the bottom left part of the
graph)?
For instance, is it appropriate to paint a tree edges with a color A if
PP is lower or equal than 0.5 and color B if PP is greater than 0.5?

Some R packages for model fitting allow simmap tree as input, but if my
question makes sense, it would be better to provide consensus tree from
n stochastic maps instead to use one stochastic map as input.

Thank you for your time.
Kind regards,
Marko

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