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<p>Richard,<o:p></o:p></p>
<p>Correlation( S<sub>a</sub>, S<sub>b</sub> ) = Covariance( S<sub>a</sub>, S<sub>b</sub>
) / (ó<sub>a</sub> * ó<sub>a</sub>). <o:p></o:p></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'>So you can check if the </span><span style='font-size:10.0pt;
font-family:"Tahoma","sans-serif"'>.cov file using the data from the .cor file.<o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'>Mark<o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'><o:p> </o:p></span></p>
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<p class=MsoNormal style='margin:0in;margin-bottom:.0001pt'><span
style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'>Hi Mark,<o:p></o:p></span></p>
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<p class=MsoNormal style='margin:0in;margin-bottom:.0001pt'><span
style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'> <o:p></o:p></span></p>
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<p class=MsoNormal style='margin:0in;margin-bottom:.0001pt'><span
style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'>Thank you again for
your help. I have tried using different seeds to get MCMC chains and it worked
for me. <o:p></o:p></span></p>
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<p class=MsoNormal style='margin:0in;margin-bottom:.0001pt'><span
style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'> <o:p></o:p></span></p>
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<p class=MsoNormal style='margin:0in;margin-bottom:.0001pt'><span
style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'>Now I have an
enquiry on the .cov file. After an mpd run, admb generates file
admodel.cov, which I guess contains the covariance matrix in binary. But I
am not sure about it for two reasons: 1. the numbers look a little small
to me; 2. in the examples of ADMB's user manual, there are functions to
calculate covariance matrix. I would be very grateful if you
could explain wether the contents of the .cov file are covariances
and whether they are transformed or not. <o:p></o:p></span></p>
</div>
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<p class=MsoNormal style='margin:0in;margin-bottom:.0001pt'><span
style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'> <o:p></o:p></span></p>
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<p class=MsoNormal style='margin:0in;margin-bottom:.0001pt'><span
style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'>Thanks,<o:p></o:p></span></p>
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<p class=MsoNormal style='margin:0in;margin-bottom:.0001pt'><span
style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'>Richard<br>
<br>
>>> Richard Bian 27/07/2010 11:08 a.m. >>><o:p></o:p></span></p>
</div>
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<p class=MsoNormal style='margin:0in;margin-bottom:.0001pt'><span
style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'>Mark,<o:p></o:p></span></p>
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<p class=MsoNormal style='margin:0in;margin-bottom:.0001pt'><span
style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'> <o:p></o:p></span></p>
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<p class=MsoNormal style='margin:0in;margin-bottom:.0001pt'><span
style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'>Thank you very much
for your suggestion. I will give it a go and see what I get.<o:p></o:p></span></p>
</div>
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<p class=MsoNormal style='margin:0in;margin-bottom:.0001pt'><span
style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'> <o:p></o:p></span></p>
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<p class=MsoNormal style='margin:0in;margin-bottom:.0001pt'><span
style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'>Regards,<o:p></o:p></span></p>
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<p class=MsoNormal style='margin:0in;margin-bottom:.0001pt'><span
style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'>Richard<br>
<br>
>>> "Mark Maunder" <mmaunder@iattc.org> 27/07/2010
10:55 a.m. >>><o:p></o:p></span></p>
</div>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'>Richard,<o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'>You can use the -mcseed N command line option to generate
different mcmc chains. I think it will start at the same place (the mode of the
joint posterior) but will take a different path based on a different set of
random numbers.<o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'>I hope this helps,<o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'>Mark<o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'><o:p> </o:p></span></p>
<div>
<p class=MsoNormal style='margin:0in;margin-bottom:.0001pt'><span
style='font-size:11.0pt;color:#1F497D'><o:p> </o:p></span></p>
<p class=MsoNormal style='margin:0in;margin-bottom:.0001pt'><span
style='color:#1F497D'> <o:p></o:p></span></p>
<p class=MsoNormal style='margin:0in;margin-bottom:.0001pt'><span
style='font-size:11.0pt;color:#1F497D'>Mark Maunder <o:p></o:p></span></p>
<p class=MsoNormal style='margin:0in;margin-bottom:.0001pt'><span
style='color:#1F497D'>Head of the Stock Assessment Program<o:p></o:p></span></p>
<p class=MsoNormal style='margin:0in;margin-bottom:.0001pt'><span
style='color:#1F497D'>Inter-American Tropical Tuna Commission<br>
8604 La Jolla Shores Drive<br>
La Jolla, CA, 92037-1508, USA<br>
<br>
Tel: (858) 546-7027<br>
Fax: (858) 546-7133<br>
<a href="mailto:mmaunder@iattc.org">mmaunder@iattc.org</a><br>
</span><span style='font-size:10.0pt;font-family:"Arial","sans-serif";
color:#1F497D'><a
href="http://www.fisheriesstockassessment.com/TikiWiki/tiki-index.php?page=Mark+Maunder">http://www.fisheriesstockassessment.com/TikiWiki/tiki-index.php?page=Mark+Maunder</a></span><span
style='font-size:11.0pt;color:#1F497D'><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0in;margin-bottom:.0001pt'><span
style='font-size:11.0pt;color:#1F497D'><o:p> </o:p></span></p>
<p class=MsoNormal style='margin:0in;margin-bottom:.0001pt'><span
style='font-size:11.0pt;color:#1F497D'>Visit the AD Model Builder project at<br>
<a href="http://admb-project.org/"><span style='color:#810081'>http://admb-project.org/</span></a></span><span
style='color:#1F497D'><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0in;margin-bottom:.0001pt'><span
style='color:#1F497D'> <o:p></o:p></span></p>
<p class=MsoNormal style='margin:0in;margin-bottom:.0001pt'><span
style='font-size:11.0pt;color:#1F497D'>See the following website for
information on fisheries stock assessment<o:p></o:p></span></p>
<p class=MsoNormal style='margin:0in;margin-bottom:.0001pt'><span
style='font-size:11.0pt;color:#1F497D'><a
href="http://www.fisheriesstockassessment.com/">http://www.fisheriesstockassessment.com/</a><o:p></o:p></span></p>
</div>
<p class=MsoNormal><span style='font-size:10.0pt;font-family:"Arial","sans-serif";
color:#1F497D'> </span><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'><o:p></o:p></span></p>
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<div style='border:none;border-top:solid #B5C4DF 1.0pt;padding:3.0pt 0in 0in 0in'>
<p class=MsoNormal style='margin:0in;margin-bottom:.0001pt'><b><span
style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'>From:</span></b><span
style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'> Richard Bian
[mailto:r.bian@niwa.co.nz] <br>
<b>Sent:</b> Monday, July 26, 2010 3:05 PM<br>
<b>To:</b> Mark Maunder<br>
<b>Subject:</b> inquiry on MCMC runs in ADMB<o:p></o:p></span></p>
</div>
</div>
<p class=MsoNormal><o:p> </o:p></p>
<div>
<div>
<p class=MsoNormal style='margin:0in;margin-bottom:.0001pt'><span
style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'>Dear Mark,<o:p></o:p></span></p>
</div>
<div>
<p class=MsoNormal style='margin:0in;margin-bottom:.0001pt'><span
style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'> <o:p></o:p></span></p>
</div>
<div>
<p class=MsoNormal style='margin:0in;margin-bottom:.0001pt'><span
style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'>To evaluate MCMC
chains for a model I built using ADMB, I need to set start points (eg, add
random displacements to MPD) to an MCMC chain. Could you please suggest
what I should do to set specific start points for an MCMC run. <o:p></o:p></span></p>
</div>
<div>
<p class=MsoNormal style='margin:0in;margin-bottom:.0001pt'><span
style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'> <o:p></o:p></span></p>
</div>
<div>
<p class=MsoNormal style='margin:0in;margin-bottom:.0001pt'><span
style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'>Thank you in
advance!<o:p></o:p></span></p>
</div>
<div>
<p class=MsoNormal style='margin:0in;margin-bottom:.0001pt'><span
style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'> <o:p></o:p></span></p>
</div>
<div>
<p class=MsoNormal style='margin:0in;margin-bottom:.0001pt'><span
style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'>Richard<o:p></o:p></span></p>
</div>
<div>
<p class=MsoNormal style='margin:0in;margin-bottom:.0001pt'><span
style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'> <o:p></o:p></span></p>
</div>
<div>
<p class=MsoNormal style='margin:0in;margin-bottom:.0001pt'><span
style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'> <o:p></o:p></span></p>
</div>
</div>
<div>
<p class=MsoNormal style='margin:0in;margin-bottom:.0001pt'><span
style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'>Dr. Richard Bian<br>
Scientist - Fisheries Modelling<br>
National Institute of Water & Atmospheric Research<br>
41 Market Place<br>
Auckland Central 1010, New Zealand<br>
Tel: +64 9 375 2054 Fax: +64 9 375 2051<o:p></o:p></span></p>
</div>
<div>
<p class=MsoNormal style='margin:0in;margin-bottom:.0001pt'><span
style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'> <o:p></o:p></span></p>
</div>
<p class=MsoNormal style='margin:0in;margin-bottom:.0001pt'><span
style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'><o:p> </o:p></span></p>
<div>
<p class=MsoNormal style='margin:0in;margin-bottom:.0001pt'><span
style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'>NIWA is the trading
name of the National Institute of Water & Atmospheric Research Ltd. <o:p></o:p></span></p>
</div>
<p class=MsoNormal style='margin:0in;margin-bottom:.0001pt'><span
style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'><o:p> </o:p></span></p>
<div>
<p class=MsoNormal style='margin:0in;margin-bottom:.0001pt'><span
style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'>NIWA is the trading
name of the National Institute of Water & Atmospheric Research Ltd. <o:p></o:p></span></p>
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