Compile data - Composition data

[brianlangseth-NOAA]

Set up composition data for

• [x] surveys
• [x] recreational comps (see datasets in #11)
  • [x] start with non-expanded length comps (commit 131cb7a and 02b1fa5)
  • [x] create length comp with only MRFSS data (excluding debWV data commit 02b1fa5) as possible sensitivity
  • [x] as possible sensitivity can create combined comp with MRFSS and debWV data, though would want to remove MRFSS data in 1997-1998. This is a lower priority as this will fall somewhere between the mrfss only sensitivity and base assumption
  • [x] Need to include trips in the sample size calculations (done with commit 7281d92 and finished with 4e3945b)
  • [x] Should confirm trip calcs with states (see discussion #55)
  • [x] Wanting to do expanded rec comps (commit 06c13bb shows no diff for OR, some different in some years with WA - but we are using WA sport data not recfin)
  • [x] Need to do age comps (we do not plan to keep fish with ages out of length comps. See email exchange on 4/4 initiated by Ian, though could explore as possible sensitivity. Effect likely to be small and restricted to effect on data weights) Done in commit 4e3945b
• [x] pacfin
  • [x] length (commit 5000c89)
  • [x] age (commit 1b9cc8c)

[brianlangseth-NOAA]

See https://github.com/pfmc-assessments/california-data/discussions/2#discussioncomment-4596049 in california repo about CPFV and BIO samples in recfin

"The CPFV entries are for individuals observed while sampling onboard and correspond to discarded fish that are measured prior to release on each drift for a subset of anglers..."

[brianlangseth-NOAA]

In conversations with @EJDick-NOAA, he recommends that CRFSS (i.e. recfin) composition be catch-weighted. (he is nearly done with that process) and that MRFSS be unweighted

[EJDick-NOAA]

In conversations with @EJDick-NOAA, he recommends that CRFSS (i.e. recfin) composition be catch-weighted. (he is nearly done with that process) and that MRFSS be unweighted

@brianlangseth-NOAA To follow up regarding MRFSS length comps, Karpov et al. (1995; CDFG Fish Bulletin 176, pp. 18-19) used unweighted comps, and wrote, "...sample size by district was assumed to represent size of the landings. That assumption is valid for MRFSS data since MRFSS sampling effort was generally allocated in proportion to an area's fishing effort." Implicitly, this also assumes that catch rates were equal across strata, but we don't have raw data to reconstruct MRFSS estimates and unweighted comps are the best we can do for this data set.

[brianlangseth-NOAA]

@iantaylor-NOAA We are combining landings in PacFIN with discards from the GEMM to model total removals. When working up the PacFIN comps, I expanded based on PacFIN landings, and assumed partition 2 (retained fish only) because that is what the pacfin data reflect (pacfin is landings and for canary is pretty much just retained fish). However we are using this data to inform total removals in the model. Should I therefore expand based on total removals, and/or use partition 0 (retained and discarded)?

[iantaylor-NOAA]

Hi Brian, The partition input to PacFIN.Utilities::writeComps() doesn't impact the expansion at all, it just gets passed to the column in the resulting table for input to SS3. Since your model will be using partition 0 (all mortality), using partition = 0 in the expansion saves you having to change those values in your data file later.

In case it's useful, here's some code where I've taken the output from writeComps() and gotten it closer to the SS3 format (but taking just the FthenM element of the list, adding fleet numbering, and removing columns (that part will change in the future to using numbers of fish as the input for petrale): https://github.com/pfmc-assessments/petrale/blob/main/R/process_pacfin_bds.R#L498-L591.

[brianlangseth-NOAA]

Noting that a sensitivity for rec comps is to include the released fish in rec comps. Right now we are excluding. SPre-assessment data workshop presentation shows support. Some additional discussion prior to workshop can be found in #41