[Mesquitelist] Logging the results of analyses
Wayne Maddison
wmaddisn at interchange.ubc.ca
Sun May 3 18:29:43 PDT 2009
The most powerful way to do this is via scripting. In scripting you
can obtain the results as text then save them to files. Give the
command getLastResultString or getLastResult to the module, and then
put the returned string into a text file. I'll attach an example
script.
If you want the results for a whole series of trees, visible in the
tree window, then you can go to the tree window, set up the
calculation in the tree window as desired, then choose Step Through
Trees in the Tree window.
You can also save results from charts, including parameter values
estimated in some cases.
Do any of these do what you want?
Wayne
At 12:48 PM +0200 24.4.2009, Aidan Budd wrote:
>Hi Alejandro
>
>Thanks for writing back so quickly
>
>In fact, that's not what I'm trying to do - rather, I have a set of
>phylogenies which describe relatioships between different sets of taxa
>(they are trees esimated from several different gene families)
>
>I'm looking, then, for trends in the evolutionary dynamics of features of
>the proteins, and (amongst other things) would be interested to see
>whether there are common trends in different types of characters across
>the different families
>
>While I'll want to look through the results of each family "manually", I'd
>also like to write the results in a way that doesn't involve
>copying-and-pasting the likelihoods and rate parameter values for each
>analysis into a spreadsheet, to make overal trends easier to spot - hence
>looking for a way to get the results of these analyses printed out from
>MESQUTE
>
>Perhaps I should just use Pagel's software directly, or use PAUP*, or
>something else, if I'm looking to generate those kinds of summaries
>(although i'd stick with using MESQUITE for the browsing of the data -
>just seems a shame to repeat the same thing in different software liket
>that...)
>
>Thanks again
>
>Aidan
>
>
>On Fri, 24 Apr 2009, Alejandro Gonzalez Voyer wrote:
>
>> Hello Aidan,
>>
>> I've missed previous posts so I'm not 100% certain if I understood your
>> question correctly. If what you want to do is compare an independent versus
>> a dependent model of evolution for two binary traits across a subsample of
>> likely phylogenies (taking phylogenetic uncertainty into account) then you
>> should instead use Bayestraits. In Bayestraits you can also compare rates of
>> "gains" versus "losses" of the two traits etc.
>> You could have a look at: Pagel and Meade 2006 Bayesian analysis of
>> correlated evolution of discrete characters by Reversible-Jump Markov Chain
>> Monte Carlo. Am Nat 167: 808-825.
>>
>> Cheers,
>>
>> Alejandro
>>
>> -----Original Message-----
>> From: mesquitelist-bounces at mesquiteproject.org
>> [mailto:mesquitelist-bounces at mesquiteproject.org] On Behalf Of Aidan Budd
>> Sent: den 24 april 2009 12:29
>> To: mesquitelist at mesquiteproject.org
>> Subject: [Mesquitelist] Logging the results of analyses
>>
>> hi again, MESQUITEers
>>
>> I'm looking for a way to have MESQUITE write the **results** of its
>> analyses to a text file
>>
>> Thanks to Daniel, I can now do the ML analysis of binary characters I was
>> looking for in MESQUITE (comparing Mk1 and AsymmMk1 with LRTs).
>>
>> I'm doing this for 100 or so different tree/character datasets, and would
>> like to keep a text record of the results of each analysis i.e. the
>> likelihoods under the two different models, the results of correlation
>> analyses etc. - I'll be browsing through each analysis using MESQUITE's
>> GUI, but I'd also like to store information in a file to look at in a
>> spreadsheet etc. (e.g. to compare the forward/backward rates of all ML
>> AsymmMk1 models from all trees and characters - is forward always faster
>> than backward? - questions like that)
>>
>> The MESQUITE log records the commands I issue, but I was hoping to find
>> also a facility that logs also/only the **results** of analyses of this
>> kind.
>>
>> I know I can look at the text representation of the trees, but this only
> > describes the results of the most-recently done analysis (e.g. if I first
>> check for correlation between characters 1 and 2, and then between
>> characters 2 and 3, this window will only describe the log likelihood
>> difference between chars 2 and 3) - I'd like to record the results of
>> **all** these analyses.
>>
>> Any pointers to how to convince MESQUITE to do something like this much
>> appreciated!
>>
>> Or perhaps this is simply something that MESQUITE isn't designed to be
>> able to do and I should be trying out alternative software...?
>>
>> Thanks
>>
>> Aidan
>>
>>
>
>--
>----------------------------------------------------------------------
>Aidan Budd, PhD tel:+49 (0)6221 387 8530
>EMBL - European Molecular Biology Laboratory fax:+49 (0)6221 387 8517
>Meyerhofstr. 1, 69117 Heidelberg, Germany
>
>http://www.embl-heidelberg.de/~budd/
>http://www-db.embl.de/jss/EmblGroupsHD/per_1807.html
>
>_______________________________________________
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>Mesquitelist at mesquiteproject.org
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--
--------------------------------------------------------
Wayne Maddison
Professor and Canada Research Chair
Depts. of Zoology and Botany and
Biodiversity Research Centre
& Director
Beaty Biodiversity Museum
6270 University Boulevard
University of British Columbia
Vancouver, BC V6T 1Z4 Canada
email: wmaddisn at interchange.ubc.ca FAX: +1 604 822-2416
Mesquite: http://mesquiteproject.org
MacClade: http://macclade.org
Salticidae: http://salticidae.org
Tree of Life: http://tolweb.org
Beaty Biodiversity Museum: http://beatymuseum.ubc.ca
Home page: http://salticidae.org/wpm/home.html
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