DATA 1 Commercial Data

[brianlangseth-NOAA]

Issues listed in the data spreadsheet for the commercial fleet(s)

• Commercial Landings

  • WA (PacFIN for recent years, Ian to check with Theresa about any changes in historical estimates vs what was used in 2017)
  • OR (reconstruction to be provided by Ali Whitman via Google Drive)
  • CA (CalCOM or PacFIN, tbd, EJ to send out the CalCOM data, also see CA landings caught in other states: https://docs.google.com/spreadsheets/d/1b-4ofPClK8AI9aUHc2HTonyND51Ub9aw/edit#gid=1942013360)

• Commercial Comps

  • Length comps
  • Ages
  • Discard comps (Andi provided these, more discussion is in DATA 4 Discard Data #22)

• CPUE

  • PacFIN logbook CPUE (1981-1997). Email conversation with Ali Whitman and John Wallace (who worked on 2017 analysis) led to conclusion that index can be retained with no changes from previous models. However, changes in boundary between areas will require new stratification at 40-10 instead of 42 degrees
  • nearshore logbook index for OR

• Discard rates

  • Discard rates (Chantel provided these, more discussion is in DATA 4 Discard Data #22)

[kellijohnson-NOAA]

@iantaylor-NOAA you mentioned above that you would check with WDFW about their commercial reconstruction. Did you get a response? If so, do they recommend taking the values from the last assessment for all years < 1981? If no, then where should we be getting these values from? Do you want me to email Theresa?

[iantaylor-NOAA]

Sorry I didn't follow up with more info here. Theresa said we can use the values from the 2017 assessment.

A bit more info is in the responses below from March 23 email under subject "questions about WDFW data for 2021 Lingcod assessment" where the responses were in red in the email and are in bold below.

Commercial

1. Are the commercial data from recent years up to date in PacFIN? Yes
2. Do you know if the tribal catches are also included in PacFIN? I understand that there were covid impacts on the tribal data sources for 2020, which is fine, but want to make sure we are making use of the data up to 2019 appropriately. Tribal landings are complete in PacFIN. (complete as we received the information) Composition data may be lacking in 2020 because Neah Bay was closed to port sampling.
3. Have there been any changes to the WA historical catch reconstructions for Lingcod since 2017? Nope. It would be easy to just re-use the pre-PacFIN total catches from Washington as included in the previous assessment. Go ahead.
4. In 2017, an index was developed from PacFIN logbook CPUE covering the years 1981-1997. Do you know of any changes to these historical data that we should be aware of? Nope, no changes.

Recreational

1. Can we use RecFIN for the recreational catch and biological samples from Washington? Not the complete catch history. RecFIN has for both length and age data.
2. The 2017 assessment says "WDFW provided recreational dockside fisheries data from 1981 to present. In consultation with state representatives, it was determined that the dockside index was more reliable so the MRFSS recreational data were not used." Are data from the more recent years available such that we could extend this time series? Yes. I think RecFIN also has the data now.
   Are there any new data sources from WDFW which were not available in 2017 that we should know about? Maybe our nearshore rod and reel survey.

[kellijohnson-NOAA]

Thank you @iantaylor-NOAA and sorry I didn't check my email, I think I was cc'd on that one.

@melissahaltuch-NOAA can you provide access to the WA reconstruction? I only see recreational information for WA in the analyses from 2017 folder on google drive and I cannot use the SS dat file landings are a combination of OR and WA by gear type.

[melissahaltuch-NOAA]

Hi Kel, I uploaded the commercial landings files/folder to the drive here <https://drive.google.com/drive/u/0/folders/1LJlrxcEXImIn4KDPuSUhuRsmn4CCU-5U>. I put the files that I think you are looking for into the main folder and zipped and loaded the full commercial catch folder from the assessment as well. The 2017 data files are also loaded in the Archive on the network drive, if that helps. I'm happy to talk through anything in here, just give me a shout. m

…

On Thu, Apr 22, 2021 at 9:23 AM Kelli Johnson ***@***.***> wrote: Thank you @iantaylor-NOAA <https://github.com/iantaylor-NOAA> and sorry I didn't check my email, I think I was cc'd on that one. @melissahaltuch-NOAA <https://github.com/melissahaltuch-NOAA> can you provide access to the WA reconstruction? I only see recreational information for WA in the analyses from 2017 folder <https://drive.google.com/file/d/13F_u8BTYieTVSKIiLOHwqUDEUhJQejyN/view?usp=sharing> on google drive and I cannot use the SS dat file landings are a combination of OR and WA by gear type. — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#19 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AFP5YECZUKF7HZW4F2YX3EDTKBEQXANCNFSM4V6HYOJA> .

-- Melissa A. Haltuch, Ph.D Research Fishery Biologist, NOAA Fisheries *University of Washington, School of Aquatic and Fishery Science, Associate Affiliate ***@***.*** ***@***.***> 206.860.3480

[kellijohnson-NOAA]

Thanks @melissahaltuch-NOAA ... one quick question regarding the year we should end the reconstruction. The previous assessment says through 1995 but the notes in the .R file say through 1994. It looks like you used through 1994?

[melissahaltuch-NOAA]

The .R file would be correct, the assessment is a typo.

…

On Thu, Apr 22, 2021 at 12:20 PM Kelli Johnson ***@***.***> wrote: Thanks @melissahaltuch-NOAA <https://github.com/melissahaltuch-NOAA> ... one quick question regarding the year we should end the reconstruction. The previous assessment says through 1995 but the notes in the .R file say through 1994. It looks like you used through 1994? — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#19 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AFP5YEAKRQUOPHIJY5JBT3LTKBZHZANCNFSM4V6HYOJA> .

-- Melissa A. Haltuch, Ph.D Research Fishery Biologist, NOAA Fisheries *University of Washington, School of Aquatic and Fishery Science, Associate Affiliate ***@***.*** ***@***.***> 206.860.3480

[kellijohnson-NOAA]

Getting closer ... here is the latest time series (yellow) compared to what was used in 2019 (gray). Still need to document differences in

• Northern 1980-1997 trawl fleet
• Northern 2010s trawl
• Southern 1950s fixed gear fleet

Thoughts?

[iantaylor-NOAA]

Match seems very good with clear improvements replacing linear ramp in pre-1930 CA or constant values in 1910s WA and OR.
If there's a logical explanation for differences in the two areas you identify (I would call the first "Northern 1980-1997" trawl fleet), that would surely be adequate, with the possible addition of documenting differences in Northern 2010s trawl

[kellijohnson-NOAA]

@aliwhitman do you know if there were changes to the OR reconstruction relative to what was provided to MH in 2017?

@iantaylor-NOAA those years almost exactly align with the use of WA commercial reconstruction overlap with PacFIN data. I will double check that both MH and I used the correct values there.

[aliwhitman]

No changes to the OR historical commercial reconstruction between this assessment and 2017. Let me know if you want me to double check any values.

[aliwhitman]

Oh and looking at your figure, I would also note that OR reconstruction goes up through 1986, and then it's all PacFIN landings. There are occasionally minor changes to PacFIN landings when errors are found and corrected, but to my knowledge, there's nothing on the OR landings that would create that large of a difference in the landings.

[kellijohnson-NOAA]

I found a less than symbol that was the wrong direction for Oregon that was leading to me including up to 1986 from PacFIN rather than since 1987. Anyway, WA and OR now look great.

[aliwhitman]

well that does look better! nice work.

[iantaylor-NOAA]

Looks really good to me. Nice work @kellijohnson-NOAA

[aliwhitman]

Okay so the above CPUE item on the list appears to be a separate trawl logbook CPUE index for the north/south models. This would be separate from the OR nearshore logbook index, which is from our fixed gear fleet.

Unfortunately, I don't have great information on what this was or is. Patrick Mirick has left ODFW, and he didn't leave me any documentation on this. It appears to be from 1981 - 1997 and was analyzed using VAST, which is out of my league currently. There's some information on filtering that was included in the 2017 assessment document:

• erroneous tow information (i.e. tow location on land)
• tows with misreported depth information or with large differences between the logbook and map depths
• tows inside Puget Sound
• tows west of the EEZ

Not sure what else I can help with on this one but happy to try!

[iantaylor-NOAA]

Email conversations with @aliwhitman and John Wallace about the PacFIN trawl logbook CPUE led to the conclusion that the QA/QC that ODFW conducted on the trawl logbooks did not impact the 1981-1997 range of years that was used in the 2017 assessment and we can therefore just roll over the same index inputs and description without new analysis.

[kellijohnson-NOAA]

I will work on getting documentation for the topics in this issue this week. But, I think we have all of the data except the CPUE as data objects.

• document all of the choices
• get PacFIN trawl logbook CPUE into the package as a data object

[iantaylor-NOAA]

PacFIN trawl logbook CPUE was added last week as data_index_CommTrawl in cba95b1.

[iantaylor-NOAA]

@kellijohnson-NOAA, do you still need to document the choices (checkbox added 20 days ago), or can we close this?