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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'>Thank you, Rick. I’ve never even considered what BETWEEN_PHASES might be used for. The F loops already correspond to your suggestions, typically 2-3 iterations each. I’ll take your advice, don’t really need to maintain equivalence to the other models in this respect at this point. But I’ll try just doing the F estimation BETWEEN_PHASES without parameterizing them first to see if that solves the problem. <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>