F method 2, Baranov continuous F

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Jintao Wang, modified 2 Years ago.

F method 2, Baranov continuous F

Youngling Posts: 34 Join Date: 8/9/16 Recent Posts

When using F method=2, it would not work. The last line has six spaces,but it need to fill in seven spaces, like the picture showed in attachment from SSI. What does the seventh space represent? And I'm a little confused about method 2, does the last line represent F will use the hybrid method before 1980, the switch to F as parameter after 1980?

#Fishing Mortality info
0.2 # F ballpark
-2001 # F ballpark year (neg value to disable)
2 # F_Method: 1=Pope; 2=instan. F; 3=hybrid (hybrid is recommended)
2.99 # max F or harvest rate, depends on F_Method
# no additional F input needed for Fmethod 1
1# if Fmethod=2; read overall start F value; overall phase; N detailed inputs to read
# if Fmethod=3; read N iterations for tuning for Fmethod 3
0.1 4 1 # overall start F value, overall phase, N detailed inputs
# Fleet Yr Seas F_value se phase (for detailed setup of F_Method=2; -Yr to fill remaining years)
1 1980 1 0.1 0.1 1

Kathryn Doering, modified 2 Years ago.

RE: F method 2, Baranov continuous F

Youngling Posts: 57 Join Date: 2/19/19 Recent Posts

Hi Jintao,

Thanks for reporting this! The SSI asking for a 7th value appears to be a bug and I was able to replicate it. Before it gets fixed, this seventh value will need to be deleted manually from the control file once it is written. I apologize for the inconvenience.

The lines are all representing starting values for the F's as parameters. The first 2 values of this line:

0.1 4 1 # overall start F value, overall phase, N detailed inputs

Tells Stock synthesis to use 0.1 as the starting value for all Fs and that they should be estimated in phase 4. However, if you want to start specific Fs at a different starting value or estimate them in a different phase, then the "detailed inputs" should be used. In the control file shared, there is 1 detailed input:

# Fleet Yr Seas F_value se phase (for detailed setup of F_Method=2; -Yr to fill remaining years)
1 1980 1 0.1 0.1 1

Which means that the starting value of the F parameter in 1980 for fleet 1 and season 1 will start at 0.1 (with a se of 0.1) and be estimated in phase 1. In this case, only the phase in which the F is estimated is different than the overall starting values.

If there is no reason to start F's at a different starting value or phase in the model, than no detailed inputs need to be added.

Also note that there is now an "option 4" of F method that allows some fleets to be hybrid and some to use Fs as a parameter.

Hope this helps,

Kathryn

Jintao Wang, modified 2 Years ago.

RE: F method 2, Baranov continuous F

Youngling Posts: 34 Join Date: 8/9/16 Recent Posts

Thank you for your reply

Kathryn Doering, modified 2 Years ago.

RE: F method 2, Baranov continuous F

Youngling Posts: 57 Join Date: 2/19/19 Recent Posts

Hi Jintao,

You are right that there is a problem with the detailed input lines in the SSI, which assumes 7 values are needed, not 6. However, Stock Synthesis should be able to run the correct configuration (shown in the last forum post I wrote). I double checked this was true with a different model.

Let me know if you ware still having issues.

Thank you,

Kathryn

Kathryn Doering, modified 2 Years ago.

RE: F method 2, Baranov continuous F

Youngling Posts: 57 Join Date: 2/19/19 Recent Posts

Hi Jintao,

The SSI should now be working as expected when using F method 2 (asking for 6 inputs instead of 7). The new version can be downloaded at https://vlab.noaa.gov/web/stock-synthesis/document-library/-/document_library/0LmuycloZeIt/view_file/9416166 .

Thanks,

Kathryn

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