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katylettuce / beast-mcmc

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Suggest a standard demographic log file format #329

Open GoogleCodeExporter opened 9 years ago

GoogleCodeExporter commented 9 years ago 
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>

Original issue reported on code.google.com by ramb...@gmail.com on 28 Jul 2010 at 9:38

GoogleCodeExporter commented 9 years ago

Original comment by ramb...@gmail.com on 16 Aug 2010 at 8:06

GoogleCodeExporter 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.

Original comment by ramb...@gmail.com on 24 Aug 2010 at 9:09

GoogleCodeExporter commented 9 years ago

Original comment by ramb...@gmail.com on 27 Jul 2011 at 11:44

GoogleCodeExporter commented 9 years ago

Original comment by ramb...@gmail.com on 17 Feb 2012 at 8:48

GoogleCodeExporter commented 9 years ago

Original comment by ramb...@gmail.com on 5 Mar 2015 at 9:38