Re: [R-sig-phylo] make.simmap -- strange posterior probability for root using ARD model?

[Liam Revell]

Dear Jesse.

The most logical explanation is that in the fitted ARD model the rate of 
transition away from the rare state is >> than the fitted transition 
rates to it (or even that the ML value of these rates is zero). 
Conditioning on this fitted model make it highly probably that the root 
is in the rare state (and that the state is rare among extant taxa of 
the tree). Is this consistent with the parameter values of the fitted Mk 
model for your data?

Another option that is available in make.simmap is Q="mcmc". This 
samples values for the transition matrix Q (given a model, such as 
model="ARD") in proportion to their posterior probability using MCMC and 
then stochastic histories according to their probability given the 
sampled value of Q. In theory this should make the result less dependent 
on the specific fitted value of Q.

To dig any deeper I would need to have your data & tree.

All the best, Liam

Liam J. Revell
Associate Professor, University of Massachusetts Boston
Profesor Asistente, Universidad Católica de la Ssma Concepción
web: http://faculty.umb.edu/liam.revell/, http://www.phytools.org

On 12/21/2018 4:41 PM, Jesse Delia wrote:
> Hello all,
> 
> I have, what I think is, a strange result from make.simmap (phytools V 
> 0.6.44). Using an ARD model, I'm getting a high probability for the 
> rarest state in my dataset. Based on trait distribution, this seems like 
> a red flag but I cant figure out whether there is an issue.
> 
> If anyone can have a look, I reproduced my dataset and tree, but its a 
> bit long and will post upon request. In the meantime, just wondering 
> whether this result is cause for concern? I pasted the plotted results 
> below, not sure if it will post to the board.
> 
> Thanks for all your help!
> 
> Jesse
> 
> Rplot.jpg
> 
> ___
> 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/
> 
___
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/

Re: [R-sig-phylo] mixing trait values from distinct models of evolution to reconstruct null morphospace

[David Bapst]

My biggest issue with this setup, as you give it, is that it isn't
clear how you'll make this into a test - is there some summary
statistic of the null morphospace you'll be generating many times, and
then comparing that distribution to the observed value of the
observed, real data? I would suggest thinking more about this aspect.

I hope this helps,
-Dave

On Sun, Dec 16, 2018 at 5:35 PM françois RIGAL  wrote:
>
> Hi all
> I have a conceptual question related to the use of separate models of 
> evolution to reconstruct a morphospace.
> Ok let’s consider that I have 6 endemic species on an island-like habitats 
> for which I have morphological traits. I want to generate a null expectation 
> for the morphospace of this community keeping the phylogenetic structure 
> unchanged. These 6 species belong to 3 different clades (2 species each). 
> Let’s consider that I have the phylogeny and the traits for all the mainland 
> representative of those three clades. My null hypotheses behind would be that 
> endemic species evolve at the same rate/same direction that mainland species.
> My idea is the following: I fit different models of evolution to each clade 
> separately (endemic species included) e.g. BM, OU and use the parameters of 
> the best model to simulate random traits for each clade. I do 1000 runs and, 
> at each run, I pick up from my random clade-set of traits the 2 endemic 
> species, and re-create therefore a null morphospace for my community of 6 
> endemic species.
> So far, I cannot think about any possible “pitfalls”, but, since I did not 
> find any similar approaches in the literature, I am wondering whether it is 
> problematic to mix in the same null morphospace null trait values that have 
> been generated from distinct phylogenies and models of evolution.
> any comments / advices are welcome
> Many thanks
>
> François
>
> [[alternative HTML version deleted]]
>
> ___
> 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/



-- 
David W. Bapst, PhD
Asst Research Professor, Geology & Geophysics, Texas A & M University
Postdoc, Ecology & Evolutionary Biology, Univ of Tenn Knoxville
https://github.com/dwbapst/paleotree

___
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/