Printing parameters only to log file; no tree output

[Santiago Sánchez]

Dear Users and Developers,

I was wondering if there is a way to run BEAST and only print estimated parameters to the log file. In other words, to override printing trees to the .trees file.

Would this make the run go faster in any way?

Cheers,

Santiago 

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Santiago Sánchez-Ramírez

Department of Ecology and Evolutionary Biology, University of Toronto

Department of Natural History (Mycology), Royal Ontario Museum

100 Queen's Park

Toronto, ON

M5S 2C6

Canada

Other email: santiago...@mail.utoronto.ca

Tel. 416-586-8025

[Santiago Sánchez]

---------- Forwarded message ----------
From: Santiago Sánchez <santiag...@gmail.com>
Date: 2013/3/20
Subject: Re: Printing parameters only to log file; no tree output
To: Kai He <hk20013...@gmail.com>


Hi Kai,

Thank you. Yes, I comment-out the whole "write tree log to file" block, and it worked fine.

Yes, and it doesn't seem things are going faster..

Cheers,

Santiago

2013/3/20 Kai He <hk20013...@gmail.com>

I'm pretty sure you can delete the following

<!-- write tree log to file                                                  -->

<logTree id="treeFileLog" logEvery="10000" nexusFormat="true" fileName="test.(time).trees.txt" sortTranslationTable="true">

<treeModel idref="treeModel"/>

<trait name="rate" tag="rate">

<discretizedBranchRates idref="branchRates"/>

</trait>

<posterior idref="posterior"/>

</logTree>

<logTree id="substTreeFileLog" logEvery="10000" nexusFormat="true" fileName="test.(subst).trees" branchLengths="substitutions">

<treeModel idref="treeModel"/>

<discretizedBranchRates idref="branchRates"/>

<trait name="rate" tag="rate">

<discretizedBranchRates idref="branchRates"/>

</trait>

</logTree>

But I don't think it will speed up... 

Kai He

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--
Santiago Sánchez-Ramírez

Department of Ecology and Evolutionary Biology, University of Toronto

Department of Natural History (Mycology), Royal Ontario Museum

100 Queen's Park

Toronto, ON

M5S 2C6

Canada

Other email: santiago...@mail.utoronto.ca

Tel. 416-586-8025

[Andrew Rambaut]

It won't make things faster. It still has as much computation to do irrespective of whether you write the trees to disk or not.

Andrew