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</o:shapelayout></xml><![endif]--></head><body lang=EN-US link=blue vlink=purple><div class=WordSection1><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif"'>Hi Alex,<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif"'>To further clarify where the problem lies, you might try to read the binary files .psv files that are produced by the -mcmc command.<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif"'><o:p> </o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif"'>There’s a link to some example R code in <a href="http://admb-project.org/documentation/faq#how-to-run-mcmc">http://admb-project.org/documentation/faq#how-to-run-mcmc</a> (page 16 of the linked document from Anders shows application of the readBin function).<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0p
t;font-f
if"'>-Ian<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif"'><o:p> </o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif"'><o:p> </o:p></span></p><div style='border:none;border-left:solid blue 1.5pt;padding:0in 0in 0in 4.0pt'><div><div style='border:none;border-top:solid #B5C4DF 1.0pt;padding:3.0pt 0in 0in 0in'><p class=MsoNormal><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"'> users-bounces@admb-project.org [mailto:users-bounces@admb-project.org] <b>On Behalf Of </b>Campbell, Alex<br><b>Sent:</b> Thursday, June 09, 2011 1:30 AM<br><b>To:</b> users@admb-project.org<br><b>Subject:</b> [ADMB Users] mceval output inconsistent with mcmc display<o:p></o:p></span></p></div></div><p class=MsoNormal><o:p> </o:p></p><p><span style='font-size:10.0pt;font-family:"Arial","sa
ns-serif
he current value of the (negative log) likelihood (twice for some reason) then "mcmc sim x acceptance rate y1 y2" like this:</span><o:p></o:p></p><p><span style='font-size:10.0pt;font-family:"Arial","sans-serif"'>757.732553269085 757.732553269085</span> <br><span style='font-size:10.0pt;font-family:"Arial","sans-serif"'> mcmc sim 401 acceptance rate 0.0698254364089776 0.14</span> <o:p></o:p></p><p><span style='font-size:10.0pt;font-family:"Arial","sans-serif"'>I've checked the code to make sure it is actually the likelihood being displayed and it seems to be but tell me if I'm wrong. when I use mceval the parameter values are inconsistent with this displayed likelihood (their likelihood is much lower). How could this be happening? by the end of a million iteration run the displayed likelihood was 603 which seems within reason. the corresponding parameter values obtained from mceval were around -700! and needless to say a really terrible fit. </span><o:p><
/o:p></p
e:10.0pt;font-family:"Arial","sans-serif"'>any idea what could be going wrong? Am I interpreting the displayed output correctly? The current likelihood should be the current *accepted* likelihood, so should translate to valid parameters in the saved to psv and read during mceval.? Code and input files are rather big - I won't spam people with it. I can send directly if anyone volunteers. This is what I'm doing for the mceval section if that sheds any light (I doubt it). </span><o:p></o:p></p><p><span style='font-size:10.0pt;font-family:"Arial","sans-serif"'> if (mceval_phase()) {</span> <br><span style='font-size:10.0pt;font-family:"Arial","sans-serif"'> cout << a_sr << " " << b_sr << " " << c_sr << " " << iota << " " << vartheta << " " << vartheta_ce << " " << nexpp << " ";</span><o:p></o:p></p><p><s
pan styl
family:"Arial","sans-serif"'> for (int i=1;i<=nyears;i++) {</span> <br><span style='font-size:10.0pt;font-family:"Arial","sans-serif"'> cout << xi(i) << " ";</span> <br><span style='font-size:10.0pt;font-family:"Arial","sans-serif"'> } </span><br><span style='font-size:10.0pt;font-family:"Arial","sans-serif"'> cout << log_sigma_xi << " ";</span> <br><span style='font-size:10.0pt;font-family:"Arial","sans-serif"'> for (int i=1;i<=(nyears_spatial*ncells);i++) {</span> <br><span style='font-size:10.0pt;font-family:"Arial","sans-serif"'> cout << psi(i) << " ";</span> <br><span style='font-size:10.0pt;font-family:"Arial","sans-serif"'> }</span> <br><span style='font-size:10.0pt;font-family:"Arial","sans-serif"'> cout << l
og_gamma
lt;< rho_psi << " ";</span> <br><span style='font-size:10.0pt;font-family:"Arial","sans-serif"'> cout << log_sigma_psi << " ";</span> <br><span style='font-size:10.0pt;font-family:"Arial","sans-serif"'> cout << sigma_C << " " << sigma_E << " ";</span> <br><span style='font-size:10.0pt;font-family:"Arial","sans-serif"'> cout << early_kappa << " ";</span> <br><span style='font-size:10.0pt;font-family:"Arial","sans-serif"'> //cout << rho_psi_cl << " ";</span> <br><span style='font-size:10.0pt;font-family:"Arial","sans-serif"'> //cout << log_sigma_psi_cl << " ";</span> <br><span style='font-size:10.0pt;font-family:"Arial","sans-serif"'> cout << E1980 << " " << E1985 << " " <<
nexpp2 &
<span style='font-size:10.0pt;font-family:"Arial","sans-serif"'> //cout << mu_psi_cl << " ";</span> <br><span style='font-size:10.0pt;font-family:"Arial","sans-serif"'> }</span> <o:p></o:p></p><p class=MsoNormal><o:p> </o:p></p><p><span style='font-size:10.0pt;font-family:"Arial","sans-serif"'>This has occurred both using admb 10.0 on a windoze box and admb 9.1 (I think) on a bigger, faster, 64-bit windoze box. I've also discovered more linux-windoze inconsistencies but that's another story for another day..</span><o:p></o:p></p><p><span style='font-size:10.0pt;font-family:"Arial","sans-serif"'>-alex</span> <o:p></o:p></p><p class=MsoNormal style='margin-bottom:12.0pt'><br><br><br><o:p></o:p></p><table class=MsoNormalTable border=0 cellpadding=0 style='background:white'><tr><td style='padding:.75pt .75pt .75pt .75pt'><p class=MsoNormal><span style='color:black'><br>********************************DISCLAIMER*******************
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