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MattCallahan-NOAA / gapproductssynopsis

Synopsis of catch, length, and age structure from the gap_products bottom trawl survey data.
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Consider new/alternative species for some regions? #6

Open Lewis-Barnett-NOAA opened 2 hours ago

Lewis-Barnett-NOAA commented 2 hours ago

Ivonne requested that we consider including rougheye and blackspotted rockfish (combined, given our historical ID issues) for the AI.

MattCallahan-NOAA commented 2 hours ago

So two issues here:

Species selection: I think regional specific species choices are a good idea, I actually did take a somewhat different approach for the AI and included the species with the top 10 or so biomass estimates from gap_products in addition to the ones initially requested. It is probably worth discussing further whether there are a core group of species that we should run everywhere to compare across regions regardless of data paucity. I did run blackspotted for the AI.

Species complexes: There are a couple of other rockfish that fall in this boat too. I think that currently GAP_PRODUCTS has estimates for blackspotted/rougheye (before the IDs were good, essentially zero recently), blackspotted, and rougheye. We can sum the total biomass estimates but not the variances, so we would lose our quantification of uncertainty for those groups. Alternatively, combined estimates could be calculated within GAPINDEX and then we could just present the estimates for that.

MargaretSiple-NOAA commented 1 hour ago

Hi Matt and Lewis! I think starting with the FMP species/complexes is a good place to start. Based on requests I have gotten from PT etc, that is the list that gets requested the most. I don't know Matt if you're using gapindex or another pathway, but gapindex has really nice infrastructure for calculating indices for complexes. For REBS, I include the species codes for rougheye, blackspotted, and the "rougheye/blackspotted unid" fish. gapindex calculates total biomass estimates and variances for the complex.

In my data report code, I just calculate the indices for the complexes separately from the single species stocks because it's easier. It's not very elegant, but it works. And it will create a table that is analogous to the ones from GAP_PRODUCTS. I hope that was useful!

MattCallahan-NOAA commented 30 minutes ago

Thanks Megsie, that is helpful and I will lean on your gapindex code if I go that route. Dark and Dusky Rockfish in the GOA would be another.

My current workflow consists of a script that pulls gap_products data off of AKFIN and generates figures for a species and area, and another script that runs a loop over a list of species creating a quarto html output for each. I would have to have a separate workflow for complexes if I needed to calculate the estimates outside of gap_products, which is doable but I am a little leery of customizing reports as that will be more time initially and to maintain.

It's probably worth meeting with Bridget/Lewis/et al to discuss which edits to prioritize.

Lewis-Barnett-NOAA commented 23 minutes ago

Agreed! I think we can decide what the priorities are, and keeping things general across regions might be best until we really see how these are used. For example, it seemed like Ivonne may have had other formats that she prefers for her ESR anyhow...and we aren't going to over-customize these by region in reality to keep it more maintainable.

On Fri, Oct 25, 2024 at 11:58 AM MattCallahan-NOAA @.***> wrote:

Thanks Megsie, that is helpful and I will lean on your gapindex code if I go that route. Dark and Dusky Rockfish in the GOA would be another.

My current workflow consists of a script that pulls gap_products data off of AKFIN and generates figures for a species and area, and another script that runs a loop over a list of species creating a quarto html output for each. I would have to have a separate workflow for complexes if I needed to calculate the estimates outside of gap_products, which is doable but I am a little leery of customizing reports as that will be more time initially and to maintain.

It's probably worth meeting with Bridget/Lewis/et al to discuss which edits to prioritize.

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