[ADMB Users] Restricting magnitude of random effects estimates, achieving convergence of RE models

Mark Maunder mmaunder at iattc.org
Tue Aug 3 14:48:08 PDT 2010



Not sure if this helps, but I was having the same problem with a model I was running for impact analysis. I had two models running simultaneously one with the covariates estimated and one with them fixed at zero to determine the impact of the covariates. Since the second model shared the parameters of the first model but did not fit to any data, it should not influence the results. I got the nan, so turned off the second model and it worked. Then shifted the second model to only get called from the report section and it still worked. 


So you might want to place any calculations that are not required to calculate the objective function in function called from the report section (and/or called only if in the sd_phase()).


Hope this helps,







Mark Maunder 

Head of the Stock Assessment Program

Inter-American  Tropical Tuna Commission
8604 La Jolla Shores Drive
La Jolla, CA, 92037-1508, USA
Tel: (858) 546-7027
Fax: (858) 546-7133
mmaunder at iattc.org


Visit the AD Model Builder project at
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From: users-bounces at admb-project.org [mailto:users-bounces at admb-project.org] On Behalf Of Chris Gast
Sent: Tuesday, August 03, 2010 2:28 PM
To: users at admb-project.org
Subject: [ADMB Users] Restricting magnitude of random effects estimates,achieving convergence of RE models


Hello again,


I'm simulating age-at-harvest data (and accompanying effort data) and trying to fit a series of 12 models, the most complex of which contains 3 random effects vectors (all normally-distributed).  I'm varying the dimensionality of the problem, but my current scenario involves random effects vectors of dimension ~25.  There are also approximately 15 to 40 fixed parameters (6 of which are means and standard deviations corresponding to the random effects vectors).


A frequent problem I've encountered is that during estimation, ADMB often elevates the magnitude of random effects estimates such that the objective function value enters NaN territory, from which it cannot recover.  I've tried using random_effects_bounded_vectors, but this frequently leads to optimization failure ("hessian does not appear to be positive definite"), regardless of the magnitude of the limits I impose.  I've concocted a penalty function that helps alleviate this problem (most of the time): Prior to multiplying the log-likelihood by -1, I subtract 10 times the sum of squared random effects estimates.  In code, this looks like:


....previous log-likelihood computations....






totL -= sumt*10;


totL *= -1;


where t is defined as a random_effects_vector, sumt is a dvariable, and totL is the objective function value.  Sometimes a value of 10 works, and sometimes an unreasonable (but equally arbitrary) value of 100,000 is necessary to obtain convergence.  


Prior to this code, I use the usual


totL += -(nyears)*log(csigma)-.5*norm2(t/csigma);


or alternatively


totL  += -.5*norm2(t);

tt = csigma*t;


with appropriate definitions for the variance parameter csigma, and t and tt.  I'll also note that each of the random effects occurs within either an exponential or logistic transformation of some demographic process.


Of course, the higher the arbitrary scale factor (10 - 100,000), the greater restriction I am placing on the variance parameter, csigma.  This is a parameter of some interest for me, and I don't want to limit its range.


I'm willing to accept that some models will fail to fit, particularly because many models are simplifications of the true simulation model.  The problem is that to obtain a reasonable number of "successful" simulations, I need to limit the failure rate of such models.


Does anyone have some experience with such a problem that they'd be willing to share? How have others dealt with problems of this nature?  Is there some customary penalty function of which I'm unaware?




Thanks very much,


Chris Gast

University of Washington

Quantitative Ecology and Resource Management







Chris Gast
cmgast at gmail.com

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