ATF, Kam, Shortracker Rockfish plots for SAFE reports

[EmilyMarkowitz-NOAA]

Due: Monday October 31, 2022

[Paraphrased from request in email 10/26 with Kalei and Meaghan] We discussed shooting for Friday, but totally ok if on Monday. Hope that timing is ok for you as well Meaghan but if not, then prioritize KAM first and then can do ATF as my reviewers already said Tuesday ok for them.

Data product requested (stratum CPUE, etc.):

[Paraphrased from request in email 10/26 with Kalei and Meaghan] I want to send a HUGE THANK YOU to Em for helping with all these graphics for arrowtooth (ATF), Kamchatka (KAM), and shortraker rockfish (SR). This is really helpful for us and very thankful for this. Also, I'm just a big fan of all the new awesome graphics from GAP and would love to give them more visibility where possible. Also I do want to reiterate, PLEASE say NO to any of this if the request is too much or you just don't have time for this. Totally OK. But if these are possible, here's what would be AMAZING to have (in order of priority, if that makes a difference):

1.) Eastern Bering Sea: ATF 1992-2022

• [x] CPUE plots 3 row x 2 col plus NBS and BSS (one with coldpool outline in red or yellow, one without)
• [x] M and F side by side length comps EBS only
• [x] M and F side by side age comps EBS only
• [x] M and F side by side length comps BSS only
• [x] M and F side by side age comps BSS only

2.) Eastern Bering Sea: KAM 1991-2022 (although note from Lyle Britt that high confidence in speciation did not start until 1992 for ATF and KAM)

• [ ] CPUE plots 3 row x 2 col plus NBS and BSS (one with coldpool outline in red or yellow, one without)
• [x] M and F side by side length comps EBS only
• [x] M and F side by side age comps EBS only
• [x] M and F side by side length comps BSS only
• [x] M and F side by side age comps BSS only

3.) Aleutian Islands Survey: ATF 1991-2022

• [x] Bubble plots 3 row x 1 col
• [x] CPUE plots 3 row x 1 col
• [x] M and F side by side length comps
• [x] M and F side by side age comps

4.) Aleutian Islands Survey: KAM 1991-2022

• [x] Bubble plots 3 row x 1 col
• [x] CPUE plots 3 row x 1 col
• [x] M and F side by side length comps
• [x] M and F side by side age comps

5.) Aleutian Islands Survey: SR 1991-2022

• [x] Bubble plots 3 row x 1 col
• [x] CPUE plots 3 row x 1 col
• Totally forgot we already have the ridges plot for Shortraker lengths, so all good there!

6.) Eastern Bering Sea Slope (BSS): SR 2002-2016

• [ ] CPUE plots 3 row x 2 col, not sure how this will look, but might need an outline of EBS and NBS survey just for reference? This may be a really odd one to do, so no worries if it doesn't work.

Species: ATF, Kam, Shortracker Rockfish

Region (GOA, AI, Bering Sea): Eastern Bering Sea, northern Bering Sea, Bering Sea Slope, and AI

Research team making the request (PI /requester name, and tag team members with GitHub accounts, or email address if requestor does not have a GitHub account. Division is nice too.): @kshotwell (kalei.shotwell AT noaa.gov) @mdbryan (meaghan.bryan AT noaa.gov)

[EmilyMarkowitz-NOAA]

Can do! Still working on it, but plots and scripts will be available here in our data requests google drive folder. Will update as soon as plots are completed. These figures are already mostly made using the functions I wrote for the gap_bs_data_report repository.

• [x] @Duane-Stevenson-NOAA Can you give me permission to the files in the EBSSLOPE schema? It should be very easy to integrate these data once I have access.

• [x] Future: I am so stoked that the SAFE authors like the new figures!!! @kshotwell and @mdbryan: This winter let's plan and list what all of the authors would like plots of and we can make those even as soon as the data is available! Or maybe I can even make a tool that authors can use at their convenience... ✌️

• [x] @MargaretSiple-NOAA, with this future idea in mind, can you post links to your AI plot scripts here so we can think about combining our scripts and efforts for next year? You sent them and I lost them 😨

[MargaretSiple-NOAA]

Yes, thank you for reminding me! All my figure plots are here: https://github.com/MargaretSiple-NOAA/goa-ai-data-reports/blob/main/R/make_figures.R . To just start pumping out plots, you just run the first 95-ish lines of this, which will source the make_figures.R script after downloading the tables you need, etc.

The draft plots, which I am not entirely satisfied with (they don't have a scale bar OR a legend yet... smh), look like this:

[Duane-Stevenson-NOAA]

Hi Em,

I'm assuming that the info you want is CPUE by haul, correct? If so, I think the table you are looking for is EBSSLOPE.CPUELISTRNK. I have granted select privileges to you for this table. If it looks like there is something unusual or incomplete about these data, you may have to consult with Jerry. He knows the structure of the slope tables much better than I do.

Duane

On Sun, Oct 30, 2022 at 3:06 PM Em Markowitz (NOAA) < @.***> wrote:

Can do! Still working on it, but plots and scripts will be available here https://drive.google.com/drive/folders/1cvPy-_CgjiSsPy9Yxj38GXcTt2uUMmOP?usp=share_link in our data requests google drive folder https://drive.google.com/drive/folders/1hfNhfOmIDC7dSigbsz4P3amZWj4jMv_u?usp=sharing. Will update as soon as plots are completed. These figures are already mostly made using the functions https://github.com/EmilyMarkowitz-NOAA/gap_bs_data_report/blob/main/code/functions.R I wrote for the gap_bs_data_report https://github.com/EmilyMarkowitz-NOAA/gap_bs_data_report repository.

• @Duane-Stevenson-NOAA https://github.com/Duane-Stevenson-NOAA Can you give me permission to the files in the EBSSLOPE schema? It should be very easy to integrate these data once I have access.

Future: I am so stoked that the SAFE authors like the new figures!!! This winter let's plan and list what all of the authors would like plots of and we can make those even as soon as the data is available! Or maybe I can even make a tool that authors can use at their convenience... ✌️

• @MargaretSiple-NOAA https://github.com/MargaretSiple-NOAA, with this future idea in mind, can you post links to your AI plot scripts here so we can think about combining our scripts and efforts for next year? You sent them and I lost them 😨

— Reply to this email directly, view it on GitHub https://github.com/afsc-gap-products/data-requests/issues/41#issuecomment-1296359068, or unsubscribe https://github.com/notifications/unsubscribe-auth/ANKDWARWS3OD4MCYA7BQJQTWF3WPJANCNFSM6AAAAAARSRGAGI . You are receiving this because you were mentioned.Message ID: @.***>

-- Duane Stevenson, Ph.D. Supervisory Fish Biologist Groundfish Assessment Program NMFS, Alaska Fisheries Science Center

[EmilyMarkowitz-NOAA]

Thanks all!

• The figures and code are now available on the aforementioned google drive! Please review and let me know if you need me to make any changes.
• I have also shared all of the code etc. on this repo. Here we can workshop figure+ requests for anyone doing stock assessment reports. We can add it to the (afsc-gap-products GitHub org)[https://github.com/afsc-gap-products] once we have a more final product. I've added @MargaretSiple-NOAA @kshotwell @mdbryan for the moment, but am happy to invite others to collaborate.
• @MargaretSiple-NOAA I didn't really get to incorporate your code (I ran out of time 😞 but we can work on that for the next round!
• I chatted with @Duane-Stevenson-NOAA and Jerry offline about the BSS data and we decided that it requires per-review before we can use the cpue and length comp data, and that we need to find/create the age comp tables before we can address the BSS portions of the above data request! Maybe we can add this data for the December SS meeting?

So, done for now (I think)! Anything I forgot? Closing this issue but will start a new thread for future and BSS needs.