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: [email protected]
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.
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