Re: [R-sig-phylo] Multivariate ASR with Discrete Characters

[Joe Felsenstein]

William Gearty --

>
> Thank you Don and Julien for your suggestions. I was able to run threshml
> using Rthreshml from the Rphylip package. However, now I'm not really sure
> what to do with the results. Can I use the output to perform ancestral
> state reconstruction/estimation for the continuous (3) and discrete (1)
> characters? I see that phytools has ancThresh, but that only seems to work
> with a single character.

I don't know what are the limitations of Rphylip's interface
with Threshml, but I can address Threshml itself -- as I
wrote it.

In principle the liabilities sampled at the interior
nodes of the tree could be used to do ancestral
reconstructions at those nodes, in a very straight-
forward way.  Just consider them, not the rest of
the tree, and make a histogram of them at the node.

However I never bothered to put in any interface
to do that.  However note that what Threshml does
is to transform the liabilities to independent variables,
using the current best estimate of the covariance
matrix of liabilities.  The Gibbs sampling (and at the
tips, the Metropolis/Hastings sampling) occurs in
the independent characters.  Then you have to
transform back to the liabilities before you have
samples for those at the interior nodes.

So matters are not simple, but in principle it can
be done.  Note that for continuous traits Threshml
can also be used to sample values at the interior
nodes.  Of course this is a lot more computation
than just using likelihood computations -- I've
checked and the sampling does infer the same
covariances in that case.  In this all-continuous
case the same issue of transforming to independent
characters also comes up.

Joe

Joe Felsenstein j...@gs.washington.edu
 Department of Genome Sciences and Department of Biology,
 University of Washington, Box 355065, Seattle, WA 98195-5065 USA

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Re: [R-sig-phylo] Multivariate ASR with Discrete Characters

[William Gearty]

Thank you Don and Julien for your suggestions. I was able to run threshml
using Rthreshml from the Rphylip package. However, now I'm not really sure
what to do with the results. Can I use the output to perform ancestral
state reconstruction/estimation for the continuous (3) and discrete (1)
characters? I see that phytools has ancThresh, but that only seems to work
with a single character.

I also believe I found Goolsby's model/software
 that Julien alluded to, but it doesn't
seem to be ready for primetime yet.

Thanks,
Will

*William Gearty*

Postdoctoral Research Fellow

University of Nebraska–Lincoln

School of Biological Sciences

williamgearty.com


On Tue, Mar 3, 2020 at 11:30 AM Donald Miles  wrote:

> Hello William,
>
> You can use the threshBayes function in the package phytools to implement
> Felsensteins threshold model. One can combine continuous and discrete
> traits in the same analysis.
>
> Cheers,
>
> Don Miles
>
> On Tue, Mar 3, 2020 at 11:50 AM Julien Clavel 
> wrote:
>
>> Hi William,
>>
>> If you want to perform a joint reconstruction of the ancestral states for
>> both continuous and discrete traits (e.g. to look at the evolutionary
>> correlations) I think that you should have a look at the threshold model of
>> Felsenstein (a bivariate version is available in phytools; I also remember
>> an Evolution meeting where E. Goolsby was working on an efficient
>> implementation of the model). The model assumes that discrete traits are
>> governed by a latent process which is continuous which makes possible to
>> fit a multivariate model with other continuous traits (although maybe with
>> a reduced power).
>>
>> All the best,
>>
>> Julien
>>
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