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Calculation of Design-Based Indices of Abundance and Composition for AFSC GAP Bottom Trawl Surveys
https://afsc-gap-products.github.io/gapindex/
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Data input for Agecomp scripts (PERFORMANCE codes) #24

Closed zoyafuso-NOAA closed 1 year ago

zoyafuso-NOAA commented 1 year ago

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

I noticed that across the different scripts that run age composition, there are slight differences regarding which specimen data are used:

EBS: On line 10 of G:/EBSother/SCRIPTS_FOR_STOCK_ASSESSMENT/AGECOMP/agecomp_ebs_plusnw_stratum.sql, there's a note that specimen records can come from hauls with negative performance codes.

NBS: On line 25 of G:/EBSother/SCRIPTS_FOR_STOCK_ASSESSMENT/NBS/agecomp_nbs_stratum.sql, there's the clause "WHERE PERFORMANCE >= 0", meaning specimen records can only come from hauls with performance code >= 0.

AI/GOA: Ned, I looked at the A.agecomp function that is contained in G:/GOA/R/agecomp/.RData. I assume that specimen records can come from any haul regardless of the PERFORMANCE code, is this correct? For example, I don't see a call that subsets specimen records from hauls with PERFORMANCE >= 0 in that function.

Is there historical context for excluding negative performance hauls from the biomass/abundance calculations but including negative performance hauls in the age composition calculations? Ideally we should stick to one rule for consistency but I wonder if there was a discussion about this prior to me coming into the group.

Thanks in advance, Zack

Ned-Laman-NOAA commented 1 year ago

Zack, Otoliths from negative performance hauls can happen in a couple of ways. When there are cm/sex/area collections, sometimes a rare length would be spotted in a bad haul and kept to fill out the length bins. We no longer routinely work up bad catches so that angle is going away. In addition, occasionally there are tows coded "good" at sea that get coded "bad" on the bench. In either case, the data from any haul with a negative performance code or with a haul-type other than 3 will be disallowed from biomass estimation. There are some other criteria but those are the main ones and the rest (along with those two) are rolled up into the ABUNDANCE_HAUL = 'Y' field. In my opinion, given the way we collect data now with respect to bad hauls and our intention of identifying biomass-worthy tows, it doesn't make sense to allow ages from tows that aren't part of the biomass estimate data population. I'm open to hearing other opinions though.

Lewis-Barnett-NOAA commented 1 year ago

I agree with Ned that ages from bad performing hauls should not be used for compositional estimates (via expansion from only satisfactory performing hauls).

However, I do think they can still be used for constructing age-length keys or other length-at-age estimation (barring any kind of crazy spatial bias in collection of otoliths from bad hauls).

On Fri, May 12, 2023 at 10:02 AM Ned Laman @.***> wrote:

Zack, Otoliths from negative performance hauls can happen in a couple of ways. When there are cm/sex/area collections, sometimes a rare length would be spotted in a bad haul and kept to fill out the length bins. We no longer routinely work up bad catches so that angle is going away. In addition, occasionally there are tows coded "good" at sea that get coded "bad" on the bench. In either case, the data from any haul with a negative performance code or with a haul-type other than 3 will be disallowed from biomass estimation. There are some other criteria but those are the main ones and the rest (along with those two) are rolled up into the ABUNDANCE_HAUL = 'Y' field. In my opinion, given the way we collect data now with respect to bad hauls and our intention of identifying biomass-worthy tows, it doesn't make sense to allow ages from tows that aren't part of the biomass estimate data population. I'm open to hearing other opinions though.

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zoyafuso-NOAA commented 1 year ago

I'm also leaning towards consistency of included hauls between the biomass/abundance index and composition production scripts. Thanks Ned and Lewis for the input.

Duane-Stevenson-NOAA commented 1 year ago

Sorry to be late to the party on this, but I concur with the opinions of Ned and Lewis. Going forward, I don't think this will be an issue in the EBS and NBS data as we never collect age specimens from bad tows anymore, and we don't (to my knowledge) change any tows from good to bad after the fact.

Duane

On Fri, May 12, 2023 at 12:13 PM Lewis-Barnett-NOAA < @.***> wrote:

I agree with Ned that ages from bad performing hauls should not be used for compositional estimates (via expansion from only satisfactory performing hauls).

However, I do think they can still be used for constructing age-length keys or other length-at-age estimation (barring any kind of crazy spatial bias in collection of otoliths from bad hauls).

On Fri, May 12, 2023 at 10:02 AM Ned Laman @.***> wrote:

Zack, Otoliths from negative performance hauls can happen in a couple of ways. When there are cm/sex/area collections, sometimes a rare length would be spotted in a bad haul and kept to fill out the length bins. We no longer routinely work up bad catches so that angle is going away. In addition, occasionally there are tows coded "good" at sea that get coded "bad" on the bench. In either case, the data from any haul with a negative performance code or with a haul-type other than 3 will be disallowed from biomass estimation. There are some other criteria but those are the main ones and the rest (along with those two) are rolled up into the ABUNDANCE_HAUL = 'Y' field. In my opinion, given the way we collect data now with respect to bad hauls and our intention of identifying biomass-worthy tows, it doesn't make sense to allow ages from tows that aren't part of the biomass estimate data population. I'm open to hearing other opinions though.

— Reply to this email directly, view it on GitHub < https://github.com/afsc-gap-products/gapindex/issues/24#issuecomment-1546034826 , or unsubscribe < https://github.com/notifications/unsubscribe-auth/AAKMJP3ZCL7GKUJQBZFZUQLXFZUJ7ANCNFSM6AAAAAAX6XRTYY

. You are receiving this because you are subscribed to this thread.Message ID: @.***>

-- Lewis Barnett, PhD (he/him/his) Research Fish Biologist

NOAA Fisheries, Alaska Fisheries Science Center 7600 Sand Point Way NE, Bldg 4 Seattle, Washington 98115 Google Voice: (206) 526-4111

— Reply to this email directly, view it on GitHub https://github.com/afsc-gap-products/gapindex/issues/24#issuecomment-1546169243, or unsubscribe https://github.com/notifications/unsubscribe-auth/ANKDWAXC4WGYYQCLE6UXHADXF2DU3ANCNFSM6AAAAAAX6XRTYY . 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