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.`

## Advertising

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 _______________________________________________ R-sig-phylo mailing list - R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo Searchable archive at http://www.mail-archive.com/r-sig-phylo@r-project.org/