Set up of dyn_bzero in control file extra_std part

[Carolina Minte-Vera]

Dear all, I a trying to get the std of B/X%dynamic_bzero, when I choose the options in the starter file:

5 # Depletion basis:  denom is: 0=skip; 1=X*SPBvirgin; 2=X*SPBmsy; 3=X*SPB_styr; 4=X*SPB_endyr; 5=X*dyn_Bzero;  values>=11 invoke N multiyr with 10s & 100s digit; append .1 to invoke log(ratio); e.g. 122.1 produces log(12 year trailing average of B/Bmsy)
0.3 # Fraction (X) for Depletion denominator (e.g. 0.4)

I get the following error:

reading forecast file
 reading from control file
End of control file successful! 999
Warning 7 Fatal Error! must select dyn_bzero in control file extra_std for it to be used as depletion denominator
Also see warning.sso
Exiting SS3!

trying to set up end of thr the control file as below:

2 # (0/1/2) read specs for more stddev reporting: 0 = skip, 1 = read specs for reporting stdev for selectivity, size, and numbers, 2 = add options for M,Dyn. Bzero, SmryBio
0 1 -1 5 # Selectivity: (1) 0 to skip or fleet, (2) 1=len/2=age/3=combined, (3) year, (4) N selex bins; NOTE: combined reports in age bins
 0 5 # Growth: (1) 0 to skip or growth pattern, (2) growth ages; NOTE: does each sex
 0 -1 1 # Numbers-at-age: (1) 0 to skip or area(-1 for all), (2) year, (3) N ages;  NOTE: sums across morphs
 0 1 # Mortality: (1) 0 to skip or growth pattern, (2) N ages for mortality; NOTE: does each sex
 1 # Dyn_Bzero: 0 to skip, 1 to do, 2 w/ recr
 1  # SmryBio: 0 to skip, 1 to do
 -1  # vector with selex std bins (-1 in first bin to self-generate)
 -1  # vector with growth std ages (-1 in first bin to self-generate)
 -1  # vector with NatAge std bins (-1 in first bin to self-generate)
999

also gives me an error :

Unsuccessful end of control file. Check echoinput for clues.  Last read is: -1

Does anyone have experience on setting this part of the control file correctly?

Thank you!

Carolina

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Carolina Minte-Vera

[Ian Taylor - NOAA Federal]

Hi Carolina,

I don't see anything obviously wrong on the inputs, but the echoinput.sso might help.

Here's an example of a model with expanded extra_std section and uncertainty in Dyn_Bzero turned on: https://github.com/nmfs-ost/ss3-test-models/blob/main/models/Simple_Lorenzen_tv_trend/control.ss#L336-L346. If that doesn't help you figure out the issue, could you email the model input files to NMFS.Stock...@noaa.gov?

-Ian

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[Carolina Minte-Vera]

Thank you so much Ian!

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Carolina Minte-Vera

[Carolina Minte-Vera]

Thank you Ian, based on your example I had to comment the last 3 lines with -1, as those are optional.  It worked!

This is what I used:

2 # (0/1/2) read specs for more stddev reporting: 0 = skip, 1 = read specs for reporting stdev for selectivity, size, and numbers, 2 = add options for M,Dyn. Bzero, SmryBio

 0 1 196 15 # Selectivity: (1) 0 to skip or fleet, (2) 1=len/2=age/3=combined, (3) year, (4) N selex bins; NOTE: combined reports in age bins
 0 0 # Growth: (1) 0 to skip or growth pattern, (2) growth ages; NOTE: does each sex
 0 196 0 # Numbers-at-age: (1) 0 or area(-1 for all), (2) year, (3) N ages;  NOTE: sums across morphs
 0 1 #13 Mortality: (1) 0 to skip or growth pattern, (2) N ages for mortality; NOTE: does each sex
1 # Dyn Bzero: 0 to skip, 1 to include, or 2 to add recr
0 # SmryBio: 0 to skip, 1 to include
 # -1 # list of bin #'s for selex std (-1 in first bin to self-generate)
 # -1 # list of ages for growth std (-1 in first bin to self-generate)
 # -1 # list of ages for NatAge std (-1 in first bin to self-generate)
 999

Em sex., 9 de mai. de 2025 às 15:32, Ian Taylor - NOAA Federal <ian.t...@noaa.gov> escreveu:

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Carolina Minte-Vera