nmfs-ost
[Feature]: Add standard errors for area-specific quantities
Describe the solution you would like.
From Brett Crisafulli in Western Australia
"As recommended by Andre, it would be great in SS3 if it were able to output standard errors for area-specific time series for biomass and fishing mortality. We hope that this would not be a difficult change to make and be something of value to other users."
Describe alternatives you have considered
NA
Statistical validity, if applicable
No response
Describe if this is needed for a management application
No response
Additional context
No response
This is feasible, but will take a moderate amount of work. The sdreport quantities are created here: https://github.com/nmfs-ost/ss3-source-code/blob/9b3fcf98f14769c3893c2696ecc73e4d3ba1c99c/SS_param.tpl#L622-L632
So each that became area-specific would be *nareas longer such that the areas would be end-to-end in each vector and appropriate quantity labels would be created.
Propose to do only SSB and F. SSB by area (and morph) already exists as: SSB_pop_gp(styr-3,YrMax,1,pop,1,N_GP)
F will be harder. Z by area exists for all "g": Z_rate(styr-3*nseas,k,1,pop,1,gmorph,0,nages) and is already output
natM also, but only main morphs, not the platoons: 4darray natM(styr-3nseas,k,0,pop,1,N_GPgender*N_settle_timings,0,nages)
we also have: ivector GP3(1,gmorph) // index for main genderGPatsettlement
So, a new way to show F is F(t,p,g,a) = Z_rate(t,p,g,a) - natM(t,p,GP3(g),a)
That should be added to ther report file, but first verify whether or not predM is already in natM; it certainly is in Z_rate.
Open to ideas as to how to summarize across morph and age to get each area's F statistic. it gets messy quickly!
Err OK. You want me to extend SS to allow users to specify they want area-specific SE? I agree with Rick that area-specific F would be messy
