Hi Richard.
Do you want to compute the relative frequencies with which there are
changes of different types along edges of the tree? If so, I just posted
code to help you do this. Let me know if it makes sense:
http://blog.phytools.org/2015/11/computing-frequency-of-changes-along.html
All the best, Liam
Liam J. Revell, Associate Professor of Biology
University of Massachusetts Boston
web: http://faculty.umb.edu/liam.revell/
email: [email protected]
blog: http://blog.phytools.org
On 11/6/2015 10:38 PM, Todd Oakley wrote:
Richard,
Check out time tree Stochastic Character Mapping (ttSCM), perhaps? This
might be what you mean by 'plotted density map' ?. There are some R
scripts available at the link below, based on phytools SCM functions, if
this might be what you are after.
http://oakley-web.eemb.ucsb.edu/ASMO13/
Todd
On Nov 6, 2015, at 7:29 AM, Richard Harris <[email protected]
<mailto:[email protected]>> wrote:
Hi Liam,
Thanks for your reply.
I have already got my ancestral states by stochastic mapping, however
the markChanges only adds changes from an particular individual
stochastic map. I am looking more for a way to mark the most likely
branch/ branches that a change occurs on either a plotted phylo tree
or a plotted density map.
Cheers,
Richard.
----------------------------------------
Subject: Re: [R-sig-phylo] ASR tree with highlighted state-changes
To: [email protected] <mailto:[email protected]>;
[email protected] <mailto:[email protected]>
From: [email protected] <mailto:[email protected]>
Date: Thu, 5 Nov 2015 10:14:46 -0500
Hi Richard.
One probabilistic ASR method that samples character histories is the
method of stochastic mapping (Huelsenbeck et al. 2003). This method is
implemented in the phytools function make.simmap, and stochastic map
trees can be visualized using an S3 plot methods for objects of class
"simmap" generated by the function. Another helper function markChanges
can add hash marks to the tree to demarcated sampled character state
changes. That being noted, any single stochastic map is pretty much
meaningless, and to make inferences we need to integrate over of a
sample of 100 or 1,000 maps.
If you want to do parsimony ancestral state reconstruction this is
implemented in phangorn under (I believe) the 'ACCTRAN' criterion. This
is described in a vignette which can be viewed here:
https://cran.r-project.org/web/packages/phangorn/vignettes/Ancestral.pdf.
All the best, Liam
Liam J. Revell, Associate Professor of Biology
University of Massachusetts Boston
web: http://faculty.umb.edu/liam.revell/
email: [email protected] <mailto:[email protected]>
blog: http://blog.phytools.org
On 11/5/2015 8:22 AM, Richard Harris wrote:
Hi,
I am looking for possible code (if any code exists) for creating a
tree/ graphical representation of ancestral state reconstruction
with discrete traits that clearly highlights state-changes or where
state changes are predicted to occur?
Thanks.
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