Re: [R-sig-phylo] simulating rate shifts

[Theodore Garland Jr]

Hi Eric,

The thing is that it becomes very cumbersome to write user-friendly software 
with generalized simulation routines to allow various (unlimited?) ad hoc 
changes in rates of trait evolution, selection regimes (e.g., OU), rates of 
speciation, etc.  so, the expedient approach is often called for.

Cheers,
Ted

Theodore Garland, Jr., Professor
Department of Biology
University of California, Riverside
Riverside, CA 92521
Office Phone:  (951) 827-3524
Facsimile:  (951) 827-4286 (not confidential)
Email:  tgarl...@ucr.edu
http://www.biology.ucr.edu/people/faculty/Garland.html
http://scholar.google.com/citations?hl=enuser=iSSbrhwJ

Director, UCR Institute for the Development of Educational Applications

Editor in Chief, Physiological and Biochemical Zoology

Fail Lab: Episode One
http://testtube.com/faillab/zoochosis-episode-one-evolution
http://www.youtube.com/watch?v=c0msBWyTzU0


From: R-sig-phylo [r-sig-phylo-boun...@r-project.org] on behalf of Eric 
[eric...@hotmail.com]
Sent: Saturday, August 01, 2015 1:12 AM
To: Liam J. Revell
Cc: r-sig-phylo@r-project.org
Subject: Re: [R-sig-phylo] simulating rate shifts

Hi Liam,

Yes, this is what I meant. I’m a little surprised that no process-based 
simulation - rather than prune-and-graft - method exists. In any case, thank 
you for the example, it is very helpful.

Regards,
Eric


 On Jul 31, 2015, at 8:07 PM, Liam J. Revell liam.rev...@umb.edu wrote:

 Hi Emmanuel  Eric.

 I think it's possible that Eric is interested in simulating shifts in the 
 lineage diversification (speciation and/or extinction) rate, rather than the 
 rate of phenotypic trait evolution.

 It is possible to simulate various scenarios of trait-based diversification 
 in the package diversitree, I believe; however if you are merely interested 
 in taking (or simulating some tree) and then imagining (and simulating) a 
 different diversification process for part of that tree, then this is exactly 
 the same as simulating first one tree under process 1 - then pruning a 
 subtree, simulating a replacement subtree under process 2, and attaching the 
 new subtree from whence the previous subtree was removed.

 Since this is easier said then done, I posted a more detailed worked example 
 on my blog here: 
 http://blog.phytools.org/2015/07/simulating-arbitrary-shift-in.html.

 All the best, Liam

 Liam J. Revell, Assistant 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 7/31/2015 10:57 AM, Emmanuel Paradis wrote:
 Hi Eric,

 See the function rTraitCont in ape: the parameters of the BM or OU model
 can be branch-specific, so it's easy to specify a change in parameter(s)
 at a given node. There's an example there:

 http://www.mpcm-evolution.org/practice/online-practical-material-chapter-13/chapter-13-2-traits


 Cheers,

 Emmanuel

 Le 30/07/2015 11:31, Eric Lewitus a écrit :
 Hello,

 There are several functions available for simulating rate shifts in
 trees (e.g., SimTree, TESS), but these implement tree-wide shifts,
 which are somewhat unrealistic, rather than shifts descending from a
 particular node. Is it possible to implement a more realistic rate
 shifted tree? Has such a thing already been implemented?

 Thanks.
[[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/


 Pour nous remonter une erreur de filtrage, veuillez vous rendre ici :
 http://f.security-mail.net/301iAWLdbwV



 ___
 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/

___
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] simulating rate shifts

[Liam J. Revell]

Hi Eric.

If you want to do a process-based simulation, what is the process that 
you want to simulate? If you want to simulate a process in which the 
rate of diversification changes randomly in the tree as a 
continuous-time Markov process, or by some other related process, then 
this it may be equivalent to BiSSE or related state-dependent 
diversification model which I believe can all be simulated using the 
package diversitree.


The problem with this is that if you simulate trees in which the rate of 
diversification changes stochastically, then you might have one change, 
or two, or none at all, and there is no way of predicting a priori where 
those changes will occur on the tree. Does this make sense?


If, on the other hand, you want to simulate a tree in which there was 
first one rate of diversification, then a single shift occurred to a 
second rate on one lineage or at some point in the past, then this is 
the way to do that.


All the best, Liam

Liam J. Revell, Assistant 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 8/1/2015 4:12 AM, Eric wrote:

Hi Liam,

Yes, this is what I meant. I’m a little surprised that no process-based 
simulation - rather than prune-and-graft - method exists. In any case, thank 
you for the example, it is very helpful.

Regards,
Eric



On Jul 31, 2015, at 8:07 PM, Liam J. Revell liam.rev...@umb.edu wrote:

Hi Emmanuel  Eric.

I think it's possible that Eric is interested in simulating shifts in the 
lineage diversification (speciation and/or extinction) rate, rather than the 
rate of phenotypic trait evolution.

It is possible to simulate various scenarios of trait-based diversification in 
the package diversitree, I believe; however if you are merely interested in 
taking (or simulating some tree) and then imagining (and simulating) a 
different diversification process for part of that tree, then this is exactly 
the same as simulating first one tree under process 1 - then pruning a subtree, 
simulating a replacement subtree under process 2, and attaching the new subtree 
from whence the previous subtree was removed.

Since this is easier said then done, I posted a more detailed worked example on 
my blog here: 
http://blog.phytools.org/2015/07/simulating-arbitrary-shift-in.html.

All the best, Liam

Liam J. Revell, Assistant 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 7/31/2015 10:57 AM, Emmanuel Paradis wrote:

Hi Eric,

See the function rTraitCont in ape: the parameters of the BM or OU model
can be branch-specific, so it's easy to specify a change in parameter(s)
at a given node. There's an example there:

http://www.mpcm-evolution.org/practice/online-practical-material-chapter-13/chapter-13-2-traits


Cheers,

Emmanuel

Le 30/07/2015 11:31, Eric Lewitus a écrit :

Hello,

There are several functions available for simulating rate shifts in
trees (e.g., SimTree, TESS), but these implement tree-wide shifts,
which are somewhat unrealistic, rather than shifts descending from a
particular node. Is it possible to implement a more realistic rate
shifted tree? Has such a thing already been implemented?

Thanks.
[[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/


Pour nous remonter une erreur de filtrage, veuillez vous rendre ici :
http://f.security-mail.net/301iAWLdbwV




___
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/