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lkerr / groundfish-MSE

Development of Robust Management Strategies for Northeast Groundfish Fisheries in a Changing Climate
MIT License
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Year references #68

Open samtruesdell opened 5 years ago

samtruesdell commented 5 years ago

In the multistock code we made a bunch of changes in 7/2019 to the year references (e.g., changing y to y-1 etc. We should take some time and go through the advice code and make sure that we are referring to the correct years because it is a little confusing.

mle2718 commented 5 years ago

In particular this part of get_advice.R

  # Absolute Catch advice, inherits units of waa
  # This need to be revisited-- having a hard time with the indexing.  Do we want to feed in N=J1N[y-1,] or N=J1N[y,], or
  # the projection/expectation of J1N[y,] computed at time y-1? 
  quota <- get_catch(F_full = adviceF, M = M, 
                     N = J1N[y,], selC = slxC[y,])
samtruesdell commented 5 years ago

Yes we want the current year there. Further, this was based on the actual N at age rather than the estimated so I changed that. Basically I set it up to calculate the Jan 1 biomass in year y given the Jan 1 biomass in year y-1 and that years mortality. The only odd part is the assumption to make about recruitment -- I set it as the previous year's recruitment which assumes autocorrelation which is one reasonable assumption. I'm leaving this issue open because I still want to go back and check up on the indices.

I did some work on my now defunct branch -- I think the move is to merge it locally into yours and then push it up...hopefully that works!

samtruesdell commented 5 years ago

We made a bunch of changes to indexing, but this issue should still be addressed once we are satisfied with a "final" multistock model