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recruitment deviation objects should be Nyrs-1? #27
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Changed per above in fe484a6. |
This sounds reasonable. |
Yes, length bin 1 contains the new recruits plus those left from last year. But, as recruitment is the first thing that happens, in the initial year there is no way to distinguish the new recruits from those prior to the model start. As the N in length bin 1 is an estimated parameter then these are already being accounted for. One could use the expected recruitment (e.g. average for option 9) added on to N1, but can't have this first year value be an independent estimated parameter (rec dev). |
Sounds good. The new pin file code makes the recdev vector for Nyrs-1 thefaylab/hydradata@6861e68 |
I am having some similar issues with regard to recruitment and selectivity for some of the GB stocks with the 5 bin model. I haven't actually run the 10bin version of that with the recent files yet. |
It probably also makes sense to have a 'last yr' specification for recruitment devs so that those at the end of the time series aren't estimated if they represent year classes not yet observed fully in fishery/surveys. (e.g. SS) |
I haven't made a 10 bin GB dataset yet, we would have to make some decisions about the input stomach weights and a few other currently fixed input parameters to make that work. The 10 bin NOBA takes many hours to run on my computer so may not be worth your time right now! |
Ah. Clearly my brain is mush. Sorry! |
My brain was too mushy to make those decisions for 10 bin. :-) still is! |
Recruitment in the first year is confounded with the initial N in the first size bin.
@sgaichas I addressed this (for now) by reducing the length of the recdev objects, thus recruitment only happens in years 2:Nyr.
Does this make sense?
To get things to work properly, the relevant
.pin
file vectors trimming by 1 year for each species if we stay with this. (done manually for now)The text was updated successfully, but these errors were encountered: