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</o:shapelayout></xml><![endif]--></head><body lang=EN-CA link=blue vlink=purple><div class=WordSection1><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>Hi Rick,<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><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>I tried BETWEEN_PHASES, with and without estimating F’s as parameters. Initially it would only do a couple iterations without changing anything. Upping the convergence criterion made it do some fitting, and this tack played out at .000000001. Estimating F as parameters actually increased the objective function value, and no changes to the originally sought parameter estimates occurred (reference year abundances at ages 1-14 for which Q’s sought). Without estimating them the objective function value declined slightly but with a single overall constant change to the parameters (constant priors of 13.2 all became 18.96). Finally did a test run with the fitted parameters from the ACON model as priors. With these priors ADMB adjusted the parameters variously up and down and improved the OFV (ACON 3973, ADMB 3337), with very little spinning.<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><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>At this point I can’t think how to implement it for VPA, where I would need it to handle much less informative starts. Might this reflect the problem Larry Jacobson reported for NEFSC (Chris Legault)? Have to check into how the ACON optimizer works, which may be customized just for VPA.<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><p class=MsoNormal><span lang=EN-US style='font-size:10.0pt;font-family:"Arial","sans-serif";color:#1F497D'>Mark Fowler</span><span style='color:#1F497D'> <br></span><span lang=EN-US style='font-size:10.0pt;font-family:"Arial","sans-serif";color:#1F497D'>Population Ecology Division</span><span style='color:#1F497D'> <br></span><span lang=EN-US style='font-size:10.0pt;font-family:"Arial","sans-serif";color:#1F497D'>Bedford Inst of Oceanography</span><span style='color:#1F497D'> <br></span><span lang=EN-US style='font-size:10.0pt;font-family:"Arial","sans-serif";color:#1F497D'>Dept Fisheries & Oceans</span><span style='color:#1F497D'> <br></span><span lang=EN-US style='font-size:10.0pt;font-family:"Arial","sans-serif";color:#1F497D'>Dartmouth NS Canada</span><span style='color:#1F497D'> <br></span><span lang=EN-US style='font-size:10.0pt;font-family:"Arial","sans-serif";color:#1F497D'>B2Y 4A2</span><span style='color:#1F497D'> <br></span><span lang=EN-US style='font-size:10.0pt;font-family:"Arial","sans-serif";color:#1F497D'>Tel. (902) 426-3529</span><span style='color:#1F497D'> <br></span><span lang=EN-US style='font-size:10.0pt;font-family:"Arial","sans-serif";color:#1F497D'>Fax (902) 426-9710</span><span style='color:#1F497D'> <br></span><span lang=EN-US style='font-size:10.0pt;font-family:"Arial","sans-serif";color:#1F497D'>Email Mark.Fowler@dfo-mpo.gc.ca</span><span style='color:#1F497D'> <br></span><span lang=EN-US style='font-size:10.0pt;font-family:"Arial","sans-serif";color:#1F497D'>Home Tel. (902) 461-0708</span><span style='color:#1F497D'> <br></span><span lang=EN-US style='font-size:10.0pt;font-family:"Arial","sans-serif";color:#1F497D'>Home Email mark.fowler@ns.sympatico.ca</span><span lang=EN-US style='color:#1F497D'> </span><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'><o:p></o:p></span></p><p class=MsoNormal><b><span lang=EN-US style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'>From:</span></b><span lang=EN-US style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'> Richard Methot - NOAA Federal [mailto:richard.methot@noaa.gov] <br><b>Sent:</b> March 11, 2013 3:43 PM<br><b>To:</b> Fowler, Mark<br><b>Cc:</b> dave fournier; users@admb-project.org<br><b>Subject:</b> Re: [ADMB Users] very small number math<o:p></o:p></span></p><p class=MsoNormal><o:p> </o:p></p><div><p class=MsoNormal>Mark,<o:p></o:p></p><div><p class=MsoNormal><o:p> </o:p></p></div><div><p class=MsoNormal>The approach I take for stable estimation of F rates is to use a well-defined starting point for the search and to search over a fixed number of iterations. In particular, I get the starting point from Pope's approximation to calculate an exploitation rate (for each fleet relative to the mid-year available biomass for that fleet); then convert these U's into an approximation for each F, then tune these F's over a fixed number of iterations. This converges well enough with just 4 iterations even with multiple fleets. The trick to rapid convergence is to base the updated F values based on the anticipated total Z after adjusting the Fs, not the current total Z. Note that this is in a separable model, so it is looking for the F that matches catch biomass conditioned on a set of selectivity parameters.<o:p></o:p></p><div><p class=MsoNormal><o:p> </o:p></p></div><div><p class=MsoNormal>This approach leads to very steep gradients for other parameters when F is high and the catch data is considered to be precise, so convergence of the overall model is slow because the model is constantly maintaining a good fit to the catch data. For these cases, I find it useful to switch over (during BETWEEN_PHASES) to treating the F's as ADMB model parameters, rather than as a set of scaling factors to match the catch. When treating the F's as parameters, the model tends to wait until the last iterations to get a good fit to the catches.<o:p></o:p></p></div><div><p class=MsoNormal><o:p> </o:p></p></div><div><p class=MsoNormal>Overall, I find that the variance on other model outputs (such as final population biomass) is rather insensitive to F as coefficient vs. F as parameter, but haven't tested this in high F situations.<o:p></o:p></p></div><div><p class=MsoNormal><o:p> </o:p></p></div><div><p class=MsoNormal>Rick<o:p></o:p></p></div></div></div><div><p class=MsoNormal style='margin-bottom:12.0pt'><o:p> </o:p></p><div><p class=MsoNormal>On Mon, Mar 11, 2013 at 10:35 AM, Fowler, Mark <<a href="mailto:Mark.Fowler@dfo-mpo.gc.ca" target="_blank">Mark.Fowler@dfo-mpo.gc.ca</a>> wrote:<o:p></o:p></p><p class=MsoNormal>Yes, and I use epsilon for proper parameters. The situation I'm<br>addressing is 'non-ADMB' iterative mortality (F) estimates. These are<br>just loop functions to estimate F's to create population and mortality<br>matrices. Obviously candidates as parameters, but I needed to keep them<br>as originally written. I was translating a particular type of VPA<br>written in a language called ACON to R and ADMB. Only the reference year<br>abundances are estimated with a serious optimizing function in the<br>original model (to reasonably estimate catchabilities). Initially this<br>served for truthing until I finished the translations. Hence the issue<br>of dealing with extremely small values are the profusion of F loops. And<br>I'm doing these in an equivalent manner to your suggestion, I just don't<br>use epsilon per se because I like to restrict it to parameters.<br><br>I've since been keeping the loops while comparing vulnerabilities to<br>local minima across the three programs, so only the reference year<br>abundances are optimized directly. Both optim and the ACON optimizer<br>(NLLS) clearly work left to right on parameter sets. The optim function<br>gets trapped in local minima with high uninformative constants for<br>priors on a vector that grades high to low. Starting left-most they go<br>up, which is correct relative to numbers to the right but wrong in<br>absolute terms. NLLS starts out similarly (run with few iterations you<br>get the same answer) but doesn't stay there, so maybe breaks the<br>left-to-right rule at some point to explore the range, or has some<br>threshold point at which it gives up on the first parameter. So far I'm<br>stymied with ADMB. I'm thinking maybe the F estimations confound<br>tracking of gradients?<br><br><br>> Mark Fowler<br> Population Ecology Division<br>> Bedford Inst of Oceanography<br>> Dept Fisheries & Oceans<br>> Dartmouth NS Canada<br> B2Y 4A2<br> Tel. <a href="tel:%28902%29%20426-3529">(902) 426-3529</a><br> Fax <a href="tel:%28902%29%20426-9710">(902) 426-9710</a><br> Email <a href="mailto:Mark.Fowler@dfo-mpo.gc.ca">Mark.Fowler@dfo-mpo.gc.ca</a><br> Home Tel. <a href="tel:%28902%29%20461-0708">(902) 461-0708</a><br> Home Email <a href="mailto:mark.fowler@ns.sympatico.ca">mark.fowler@ns.sympatico.ca</a><o:p></o:p></p><div><div><p class=MsoNormal><br><br>-----Original Message-----<br>From: <a href="mailto:users-bounces@admb-project.org">users-bounces@admb-project.org</a><br>[mailto:<a href="mailto:users-bounces@admb-project.org">users-bounces@admb-project.org</a>] On Behalf Of dave fournier<br>Sent: March 8, 2013 11:52 AM<br>To: <a href="mailto:users@admb-project.org">users@admb-project.org</a><br>Subject: Re: [ADMB Users] very small number math<br><br>This is proabably a good use of phases. In the early phase you add<br>something<br><br>like<br><br> x/(eps+y)<br><br>and let eps get smaller or 0 in a later phase.<br>_______________________________________________<br>Users mailing list<br><a href="mailto:Users@admb-project.org">Users@admb-project.org</a><br><a href="http://lists.admb-project.org/mailman/listinfo/users" target="_blank">http://lists.admb-project.org/mailman/listinfo/users</a><br>_______________________________________________<br>Users mailing list<br><a href="mailto:Users@admb-project.org">Users@admb-project.org</a><br><a href="http://lists.admb-project.org/mailman/listinfo/users" target="_blank">http://lists.admb-project.org/mailman/listinfo/users</a><o:p></o:p></p></div></div></div><p class=MsoNormal><br><br clear=all><o:p></o:p></p><div><p class=MsoNormal><o:p> </o:p></p></div><p class=MsoNormal>-- <br><b><span style='font-size:10.0pt;font-family:"Arial","sans-serif";color:#666666'>Richard D. Methot Jr. Ph.D.</span></b><br><i><span style='font-size:10.0pt;font-family:"Arial","sans-serif";color:#666666'>NOAA Fisheries - </span></i><i><span style='font-family:"Arial","sans-serif";color:#666666'>Science Advisor for Stock Assessments</span></i><o:p></o:p></p><div><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Arial","sans-serif";color:#666666'>Office: 206-860-3365</span><br><span style='font-size:10.0pt;font-family:"Arial","sans-serif";color:#666666'>Mobile: 301-787-0241</span><o:p></o:p></p></div></div></div></body></html>