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beast-dev / beast-mcmc

Bayesian Evolutionary Analysis Sampling Trees
http://beast.community
GNU Lesser General Public License v2.1
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Suggest a standard demographic log file format #340

Open msuchard opened 9 years ago

msuchard commented 9 years ago

Originally reported on Google Code with ID 329

I suggest that BEAUti generates a second log file containing the demographic model output
when using parameter rich models like skyline. In the code snippets below, the nodeHeightsStatistic
is used to generate a vector of change- points (including skyline grouping, if required).
This means the entire skyline/skyride can be reconstructed from one of these removing
the need to specify and load trees files into Tracer. 

<log id="demoLog" logEvery="5000" fileName="gmrf.demo">
    <parameter idref="skyride.logPopSize"/>
    <nodeHeightsStatistic id="changePoint">
        <treeModel idref="treeModel"/>
    </nodeHeightsStatistic>
</log>

<log id="demoLog" logEvery="5000" fileName="bsp.demo">
    <parameter idref="skyline.popSize"/>
    <parameter idref="skyline.groupSize"/>
    <nodeHeightsStatistic id="changePoint">
        <treeModel idref="treeModel"/>
        <parameter idref="skyline.groupSize"/>
    </nodeHeightsStatistic>
</log>

Reported by rambaut on 2010-07-28 09:38:40

msuchard commented 9 years ago

Reported by rambaut on 2010-08-16 08:06:09

msuchard commented 9 years ago 
It would also be good to put a description of what the model is (BSP linear, stepwise,
GMRF etc.) in the comment lines of the logfile.

Reported by rambaut on 2010-08-24 09:09:09

msuchard commented 9 years ago

Reported by rambaut on 2011-07-27 11:44:39

msuchard commented 9 years ago

Reported by rambaut on 2012-02-17 08:48:24

msuchard commented 9 years ago

Reported by rambaut on 2015-03-05 09:38:39