2024 NMFS GOA/AI Trawl Survey data

[hutniczak]

Data product requested: CATCH, LENGTH, HAUL, BIOMASS, SIZECOMP (details below) for 2024

Output type: csv or xlsx

Species: Pacific halibut

Region (GOA, AI, Bering Sea): All

Research team making the request:
International Pacific Halibut Commission - Barbara Hutniczak, Fisheries Regulations & Data Services Branch manager ([email protected]) and IPHC data services ([email protected])

The IPHC is making its annual data request for trawl survey data. For reference, previous request is available at: https://github.com/afsc-gap-products/data-requests/issues/72

Details:
• CATCH
o CRUISEJOIN
o HAULJOIN
o CATCHJOIN
o REGION
o VESSEL
o CRUISE
o HAUL
o SPECIES_CODE
o WEIGHT
o NUMBER_FISH
• LENGTH
o CRUISEJOIN
o HAULJOIN
o CATCHJOIN
o REGION
o VESSEL
o CRUISE
o HAUL
o SPECIES_CODE
o LENGTH
o FREQUENCY
o SEX
o SAMPLE_TYPE
o LENGTH_TYPE
• HAUL
o CRUISEJOIN
o HAULJOIN
o REGION
o VESSEL
o CRUISE
o HAUL
o HAUL_TYPE
o PERFORMANCE
o START_TIME
o DURATION
o DISTANCE_FISHED
o NET_WIDTH
o NET_MEASURED
o NET_HEIGHT
o STRATUM
o START_LATITUDE
o END_LATITUDE
o START_LONGITUDE
o END_LONGITUDE
o STATIONID
o GEAR_DEPTH
o BOTTOM_DEPTH
o BOTTOM_TYPE
o SURFACE_TEMPERATURE
o GEAR_TEMPERATURE
o WIRE_LENGTH
o GEAR
o ACCESSORIES
o SUBSAMPLE
• BIOMASS
o SPECIES_CODE
o SPECIES_NAME
o COMMON_NAME
o YEAR
o STRATUM
o MEANWGTCPUE
o VARMNWGTCPUE
o BIOMASS
o VARBIO
o LOWERB
o UPPERB
o DEGREEFWGT
o MEANNUMCPUE
o VARMNNUMCPUE
o POPULATION
o VARPOP
o LOWERP
o UPPERP
o DEGREEFNUM
o HAULCOUNT
o CATCOUNT
o NUMCOUNT
o LENCOUNT
• SIZECOMP (abundance)
o SPECIES_CODE
o SPECIES_NAME
o COMMON_NAME
o YEAR
o STRATUM
o LENGTH
o MALES
o FEMALES
o UNSEXED
o TOTAL
If available, please share by 10 October 2024. Any assistance you can provide would be greatly appreciated.

[Ned-Laman-NOAA]

Added @AlexandraDowlin-NOAA to respond to this data request for the GOA/AI team

[Duane-Stevenson-NOAA]

@AlexandraDowlin-NOAA when you get to this let me know. You may be able to use the code that I have already created for the Bering Sea data.

[Ned-Laman-NOAA]

I was hopeful that I could find the code run last year for the Gulf, but didn't. I think Nancy may've responded to this request for the Gulf last year.

[Ned-Laman-NOAA]

I think this is the plan for 2024 and am inviting comment.
We will co-opt the code that Duane shared here and modify it to run for the Aleutians.
We will save said code in the Aleutians folder at the link above which is on the GAP Shared Google Drive and label it to indicate this request is for 2024.
Somehow, we should also link this response to the data request repo issue #72 which was the same annual request from IPHC but in 2023 for the GOA.

[Ned-Laman-NOAA]

The IPHC posed a question as part of last year's GOA 2023 data request that went unanswered by me until now (see my response below):

" Our main concern is the consistency of methods applied. As mentioned earlier, it’s not clear to us whether there are any additional methods beyond summing the strata and calculating the combined variance from the biomass file we already received."

The details for our standard biomass estimation techniques and the code that currently generates them are documented in the gapindex repository on GitHub.com and follow the methods described by Alverson and Pereyra (1969) and Wakabayashi et al. (1985). These are the techniques we've been using for the last few decades to generate our design-based bottom trawl estimates of abundance in Alaska.

Alverson, D. L. and Pereyra, W. T. 1969. Demersal fish explorations in the Northeastern {Pacific Ocean} -- An evaluation of exploratory fishing methods and analytical approaches to stock size and yield forecasts. J. Fish. Res. Bd. Can. 26(8):1985-2001. doi = {10.1139/f69-188}

Wakabayashi, K., R. G. Bakkala, and M. S. Alton. 1985. Methods of the Japan demersal trawl surveys, p. 7-29. In R. G. Bakkala and K. Wakabayashi (Editors), Results of cooperative Japan groundfish investigations in the Bering Sea during May-August 1979. Int. N. Pac. Fish. Comm. Bull. 44.

[Duane-Stevenson-NOAA]

Hello Barbara (@hutniczak ),

Please find the data files you requested here. In that directory, you will find two folders, one for the Aleutian Islands (AI) and one for the Bering Sea (EBS). Each of those folders has the following series of files:

IPHC_2024_Catch
IPHC_2024_Haul
IPHC_2024_Length
IPHC_2024_Biomass
IPHC_2024_Sizecomp

The biomass and sizecomp files were generated using different tables than we have used in the past, as we have restructured our data product delivery system. To demonstrate how the files are different, I have included in the Bering Sea folder two each of the biomass and sizecomp files, one generated using the historic table format (e.g., ....Biomass_EBS.csv) and one generated using the new table format (e.g., ....newBiomass_EBS.csv). Hopefully the new format will serve your purposes, as that will be the format we produce in the future.

Please let me know if you have any questions.

Duane

[Duane-Stevenson-NOAA]

My apologies, Barbara!

It seems that we can't grant access to that folder to non-NOAA users. Please use this link for the data.

Thank you,

Duane

[hutniczak]

Hi @Duane-Stevenson-NOAA ,

Thank you for sharing the data. I believe there are two additional clarifications:

1. In the past, we would receive biomass and sizecomp table for all years to account for any modifications for previous year. Can we extend our request to cover the whole time series if these were revised since our previous request.
2. In the past, the biomass and sizecomp files would also include aggregated biomass file - we are interested in basically update of the following file: 2023 biomass summary file Can you confirm that aggregate for AI is stratum = 99904 and for new EBS file is stratum = 99900?

[Duane-Stevenson-NOAA]

Hi Barbara,

I can answer your questions for the Bering Sea files.

1. I have updated the newBiomass_EBS and newSizecomp_EBS files to include all years from 1987-present.
2. Yes, the new stratum designation for the entire EBS survey area is 99900 (equivalent to the old 999).

Let me know if these new files look right to you. Ned can clarify the situation with the Aleutian data.

Duane

[Ned-Laman-NOAA]

Hi Barbara,

I've regenerated the data we initially shared with you from the Aleutians this year to include the latest (2024) and the rest of the historic standardized survey time series data (since 1991).

You will find the data at that same link Duane shared above or go directly to the Aleutian folder here. What's in the folder?

The code used to generate the data sets (AI_GOA_IPHC_data_request.R) and the following tables:

IPHC_Catch.csv
IPHC_Haul.csv
IPHC_Length.csv
IPHC_Biomass.csv
IPHC_Sizecomp.csv

and for reference

RACE_Species_Codes.csv
Area_ID_Descriptions.csv

Note the following:

AreaID 99904 is indeed the entire Aleutians combined. I've now included in the BIOMASS and SIZECOMP data tables, the area type, name, and description for all of the areas we reference for the Aleutians. You can find that information in the reference table as well plus the analogs for the Gulf of Alaska and Bering Sea.

What you won't see are the upper and lower confidence bounds around biomass estimates nor the degrees of freedom associated. We no longer produce those and I'm happy to discuss with you why that is the case. You also will not see separate columns for males, females, and unsexed halibut in the SIZECOMP table, but can use the SEX column to separate males (1), females (2), and unsexed (3) using our sex codes.

If you have any questions or would like to discuss this further, please don't hesitate to contact myself or Susanne McDermott who is now the lead for the Aleutian survey now and in the future.

Ned

[hutniczak]

Hi @Ned-Laman-NOAA and @Duane-Stevenson-NOAA

Thank you for accommodating our request so efficiently. That should cover all our needs. We will be in touch in case of any further questions.

Basia

[hutniczak]

Hi @Ned-Laman-NOAA and @Duane-Stevenson-NOAA

We have also received physical otoliths from the survey. Would you be able to provide us with the associated specimen tables as well?

The table would be in the following format, which we use for ageing Pacific halibut:

<style> </style>

CRUISEJOIN	HAULJOIN	REGION	VESSEL	CRUISE	HAUL	SPECIMENID	BIOSTRATUM	SPECIES_CODE	LENGTH	SEX	WEIGHT	AGE	MATURITY	MATURITY_TABLE	GONAD_WT	AUDITJOIN	SPECIMEN_SUBSAMPLE_METHOD	SPECIMEN_SAMPLE_TYPE	AGE_DETERMINATION_METHOD
-749	-20576	BS	94	202102	1	1	0	10120	530	1	1640					-350459	1	1

[Ned-Laman-NOAA]

Here are the 2024 Specimen data from the Aleutians.
IPHC_Specimen.csv

[Duane-Stevenson-NOAA]

And here are the 2024 specimen data <https://drive.google.com/file/d/1C2VeT-piMcK4Ht-qq4yjXmWFWPt3S6D2/view?usp=drive_link> for halibut from the Bering Sea. Duane

…

On Thu, Oct 3, 2024 at 12:21 PM hutniczak ***@***.***> wrote: Hi @Ned-Laman-NOAA <https://github.com/Ned-Laman-NOAA> and @Duane-Stevenson-NOAA <https://github.com/Duane-Stevenson-NOAA> We have also received physical otoliths from the survey. Would you be able to provide us with the associated specimen tables as well? The table would be in the following format, which we use for ageing Pacific halibut: <style> </style> CRUISEJOIN HAULJOIN REGION VESSEL CRUISE HAUL SPECIMENID BIOSTRATUM SPECIES_CODE LENGTH SEX WEIGHT AGE MATURITY MATURITY_TABLE GONAD_WT AUDITJOIN SPECIMEN_SUBSAMPLE_METHOD SPECIMEN_SAMPLE_TYPE AGE_DETERMINATION_METHOD -749 -20576 BS 94 202102 1 1 0 10120 530 1 1640 -350459 1 1 — Reply to this email directly, view it on GitHub <#98 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ANKDWAVIDTK5NN6RQKXPRDTZZWKKVAVCNFSM6AAAAABNSWKRHWVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDGOJSGE2TMOBUGA> . 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