Guidance on how to estimate Fs for years with missing catches

[chantelwetzel-noaa]

User Question
If you have missing catches (for example years of catches followed by a gap and then data again etc.), can synthesis somehow estimate the missing catches?

Potential Solution
Actually a good and logical question and not easy for SS3 because it is not an effort driven model.
a. assign a catch value for those years. It should be reasonable because a logL will be calculated for it.
b. assign a very high se to those catch values so deviations from the input catch amount will only be lightly penalized
c. use F_Method=2 (or better, F method 4) so that parameter approach willl be used for this fleet.
d. above is enough to work, but the F's for those years could fluctuate wildly
e. stabilze those F values by entering an effort time series, e.g. a survey of type=2
f. a dummy effort time series could work. If years 2012-2014 are missing catch, then enter an effort value of 1.0 for those years at at least one adjacent year for which SS3 is already able to estimate the F. This will stabilize the missing year F's to be similar to the F for adjacent years.

Action
Add guidance to the manual for situations where catch years are missing and how one could go about estimating those removals via Fs.

[Rick-Methot-NOAA]

suggest getting input from Max to see if it works as advertised for him. Also, it is similar to the bycatch-only approach that the SEFSC uses for their shrimp trawl fishery that has 100% discard. We have some of their examples.

[e-perl-NOAA]

@Rick-Methot-NOAA I don't remember including information about this when you updated the fishing mortality-related text. Is this still something that we should include with the fishing mortality info or somewhere else?

[Rick-Methot-NOAA]

I agree. There should be a bullet about this in the "some notes" list. Something like:
It is possible to estimate Fpar for a particular fleet x time even if it has an unknown catch observation. This certainly is true if there is a discard observation for that fleet x time, but the effect of the Fpar on the population age composition and trends also allows the survey and composition data to influence the estimates of the Fpars. A catch observation must exist in order to trigger SS3 to estimate a Fpar for that fleet x time, so enter a dummy (but reasonable) value for the catch observation and give it a very large se.