[Mesquitelist] average proportional likelihoods across trees

[Wayne Maddison]

It seem to work for me on a quick test.  Could I have a copy of your file to try it with your case, assuming you still care months later?
Wayne


On 26 Apr 2011, at 4:53 PM, Ben Winger wrote:

> Greetings,
> 
> I am trying to reconstruct ancestral states of a binary character using a Mk1 model, across 1000 trees from a posterior set of Bayesian Trees. I would like to obtain an average proportional likelihood for each character state for each node in the tree across the tree set (conditional on the presence of the node in each tree). The Mesquite manual says that this should be possible when using maximum-likelihood by selecting Trace Character Over Trees and then selecting Calculate: Average Frequencies Across Trees. However, when I do this I get the error note:
> 
> "Ancestral state reconstructor does not calculate frequencies, so the Average Frequencies mode is not available"
> 
> Is this a bug? The manual suggests that this method should work for probabilities like proportional likelihoods, in addition to values that are true "frequencies".  
> 
> Thanks for any assistance. I looked through the recent archives of this list, but did not notice this topic covered previously--my apologies if it has.
> 
> Ben
> 
> -- 
> Ben Winger
> PhD Candidate 
> Committee on Evolutionary Biology
> University of Chicago
> 
> Division of Birds
> The Field Museum of Natural History
> 1400 S. Lake Shore Dr.
> Chicago, IL 60605
> bwinger at uchicago.edu
> _______________________________________________
> Mesquitelist mailing list
> Mesquitelist at mesquiteproject.org
> http://mesquiteproject.org/mailman/listinfo/mesquitelist

--------------
Wayne Maddison
    Professor and Canada Research Chair, Depts. of Zoology and Botany
    & Co-Director, Beaty Biodiversity Museum
6270 University Boulevard
University of British Columbia
Vancouver, BC  V6T 1Z4   Canada

Home page: http://salticidae.org/wpm/home.html
Mesquite: http://mesquiteproject.org; MacClade: http://macclade.org
Beaty Biodiversity Museum: http://beatymuseum.ubc.ca