Code used for model-based indices of abundance and distribution from bottom trawl survey data, produced by the AFSC GAP ModSquad in the Gulf of Alaska and Bering Sea. Model-based indices of abundance and distribution are produced using spatiotemporal delta-GLMMs implemented in sdmTMB. Model-based age composition estimates follow a similar approach, but employ a multivariate extension and are implemented in tinyVAST.
Primary contact: @Lewis-Barnett-NOAA
Provide model-based estimates of abundance and their standard error from GAP survey data for stock assessment authors in conjunction with traditional design-based estimators.
- Species requests & alternate model-based runs/settings in from leads from MESA, SSMA, ESP, ESR by 15 January
- Run "hindcasts" with previous years of survey data to finalize models prior to inclusion of new data (February 15 - April, code frozen by May)
- Merge new frozen code (index & data retrieval code) in git repo
- Upload all output files for hindcast and data used to produce the indices to the appropriate region hindcast folder in the corresponding year of the ModSquad google drive folder
- Notify the assessment lead & ModSquad lead (Lewis) that you’ve completed hindcasts (March - April)
- Run hindcast model structure again after survey with updated and validated data (August - Sept, completed by 30 September) and upload results and data used to produce the indices to the appropriate region production folder within the corresponding year folder on google drive
- Notify the assessment lead & ModSquad lead (Lewis) that you’ve completed the production estimates
Feb 15 - April is the time window for any model exploration/iteration, as requested
- December - ModSquad leadership meets/communicates to prioritize species + research plans
- January 15 - Deadline for SAFE authors to submit product requests
- late January - ModSquad planning meeting with program leads as needed
- February 15 - SAFE author's revised requests given ModSquad capacity and discussion from REFM meeting
- March 1 - TOR memo finalized and posted on the web
- April 1 - Crab hindcasts completed
- May 1 - Groundfish hindcasts completed (stop all research, decide on which to recommend or not recommend for use in base stock assessment model)
- August 25 - Model-based estimates for EBS crabs completion target date
- September 25 - Model-based estimates for NBS crabs target date
- September 30 - Model-based estimates for groundfishes completion target date, pending bottom trawl data QAQC timeline
- October 15 - Final deadline for completing groundfish model-based estimates
- ModSquad folder
- ModSquad training materials
- Common troubleshooting guidance
- Also see vignettes and workshop materials for sdmTMB and tinyVAST
- 2025:
- R v4.0.2: sdmTMB v0.6.0, tinyVAST v0.7.0-alpha, TMB v1.7.22, Matrix v1.4-0, DHARMa v0.4.5; or,
- MRAN v4.0.2: sdmTMB v0.5.0, tinyVAST v0.1.0-alpha, TMB v1.7.16, Matrix v1.2-18, DHARMa v0.3.2
- 2024:
- Rv4.0.2: VAST v3.9.0, FishStatsUtils v2.10.0, cpp VAST_v13_1_0, TMB v1.7.22, Matrix v1.4-0, DHARMa 0.4.5; or,
- MRAN v4.0.2: VAST v3.9.0, FishStatsUtils v2.10.0, cpp VAST_v13_1_0, TMB v1.7.16, Matrix v1.2-18, DHARMa v0.3.2
- 2023:
- Rv4.0.2: VAST v3.9.0, FishStatsUtils v2.10.0, cpp VAST_v13_1_0, TMB v1.7.22, Matrix v1.4-0, DHARMa 0.4.5; or,
- MRAN v4.0.2: VAST v3.9.0, FishStatsUtils v2.10.0, cpp VAST_v13_1_0, TMB v1.7.16, Matrix v1.2-18, DHARMa v0.3.2
- 2022:
- Rv4.0.2: VAST v3.8.2, FishStatsUtils v2.10.0, cpp VAST_v13_1_0, TMB v1.7.22, Matrix v1.4-0, DHARMa 0.4.5; or,
- MRAN v4.0.2: VAST v3.9.0, FishStatsUtils v2.10.0, cpp VAST_v13_1_0, TMB v1.7.16, Matrix v1.2-18, DHARMa v0.3.2
- 2021: Rv4.0.2: VAST v3.6.1, FishStatsUtils v2.8.0, cpp VAST_v12_0_0, TMB v1.7.18, Matrix v1.2.18
- 2020: VAST v3.3.0, FishStatsUtils v2.5.0, cpp VAST_v8_2_0
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