On Beverton - Holt SR with autocorrelation

[Eros Quesada]

Hi,

We are testing the predictive power of different methods in estimating recruitment. May I ask you how autocorrelation is taken into account in the ss3 model with regard to the formula of the Beverton - Holt SR relationship, when the option for autocorrelation is selected, please?

I went through the manual and found reference to Johnson, 2016 ( https://doi.org/10.1016/j.fishres.2016.06.004), but I still would appreciate your help to understand how ss3 behaves internally to account for autocorrelation in the BH SR function.

Thank you in advance and have a great day,

Best regards,

Eros Quesada

[Richard Methot - NOAA Federal]

Hello Eros.  I'm glad to see this technical question about the details of SS3.

Autocorrelation of recruitment deviations is taken into account in the calculation of the -logL for the recruitment deviations.  The code is:

      if (SR_autocorr == 0)

      {

        recr_like += norm2(recdev(recdev_first, recdev_end)) / two_sigmaRsq;

      }

      else

      {

        rho = SRparm(N_SRparm2);

        recr_like += square(recdev(recdev_first)) / two_sigmaRsq;

        for (y = recdev_first + 1; y <= recdev_end; y++)

        {

          recr_like += square(recdev(y) - rho * recdev(y - 1)) / ((1.0 - rho * rho) * two_sigmaRsq);

        }

      }

Richard  D. Methot Jr.

Stock Assessment Research Scientist (ST)

Northwest Fisheries Science Center

NOAA Fisheries | U.S. Department of Commerce

Office: (425) 666-9893

Mobile: (301) 830-2454

www.fisheries.noaa.gov 

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[Eros Quesada]

Hi,

Thank you for the feedback and the code provided!

Best

Eros