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Hi Cole,
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<div class="">I would be happy to help you with changes to the source code. I agree with Sibert, the attached document could be quickly integrated into the ADMB user manual. This is by far the most comprehensive documentation on all the options. </div>
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<div class="">Steve</div>
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<div class="">On Nov 13, 2014, at 9:05 AM, Cole Monnahan <<a href="mailto:monnahc@uw.edu" class="">monnahc@uw.edu</a>> wrote:</div>
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<div dir="ltr" class=""><span class="" style="font-family:arial,sans-serif; font-size:12.5714282989502px">Hi ADMB developers,</span><br class="" style="font-family:arial,sans-serif; font-size:12.5714282989502px">
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We're grad students at the University of Washington and we've been looking through the source code to better understand how MCMC is implemented in ADMB. I started doing this because I wanted to specify an arbitrary covariance matrix, but Jim Ianelli encouraged
me to explore some of the algorithms for the other available options. I couldn't find documentation for them, so I began writing them up with the idea of putting them into the ADMB manual. As time went on it grew more from a technical description to a starting
place for users who had never used ADMB for Bayesian analyses before (as we were). So we're calling it a "guide" for lack of a better term. Our intent, as recommended by Jim, is to put it on the ADMB website, probably in a similar place to my other short write-up
about the <a href="http://www.admb-project.org/examples/admb-tricks/covariance-calculations" target="_blank" class="">bounding functions</a>.</div>
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In doing this work we developed a list of updates we think would be worthwhile to include in future versions. We're not experienced C++ programmers, but we would be happy to work with someone to help implement those into the source. <br class="">
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Some proposed ideas for changes:<br class="">
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<li class="" style="margin-left:15px">Set mcsave default to 1, current default is to save nothing which would be unexpected for a lot of users.</li><li class="" style="margin-left:15px">Warn users if mcsave is invoked with the hybrid method (it has no effect).<br class="">
</li><li class="" style="margin-left:15px">Create new output file similar to .hst that outputs useful information of the analysis (mcmc options used, time started, ended, acceptance ratios, final scaling factor, etc.). <br class="">
</li><li class="" style="margin-left:15px">Another file similiar to the .psv file (which contains only parameters) that stores the draws of sd_report variables.</li><li class="" style="margin-left:15px">Remove need for a sdreport variable for MCMC (checked with Dave, not needed).<br class="">
</li><li class="" style="margin-left:15px">Use a random seed if none is provided by user, or at least warn user of the default which is to use the same seed value (36519). In practice most users are reusing the same seed across models -- maybe not a good idea except
for reproducibility which could be done by looking at the seed in the .hst file.<br class="">
</li><li class="" style="margin-left:15px">Clean up the console output for both Metropolis and hybrid runs.</li></ul>
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So please have a quick look through and let us know if (1) you find anything incorrect, and (2) whether you think it should be added into the ADMB manual or left as a separate document.<br class="">
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Thanks,<br class="">
Cole, Melissa, and Peter</div>
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<span id="cid:CBF74062-B971-4E59-A9A9-FE0B0C34D480@hsd1.wa.comcast.net."><admb_guide.pdf></span>_______________________________________________<br class="">
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