model-based-indices

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.

Authors

Primary contact: @Lewis-Barnett-NOAA

Mission

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. - TOR or Terms Of Reference - Annual product request form - ESP submission tool

GAP Work Plan

• 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

General Production Timeline Estimate

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

Resources

• ModSquad folder
• ModSquad training materials
• Common troubleshooting guidance
• Also see vignettes and workshop materials for sdmTMB and tinyVAST

Minimum standard of versions of software and key dependencies (i.e., using these versions or later)

• 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 VASTv131_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 VASTv131_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 VASTv131_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 VASTv131_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 VASTv131_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 VASTv131_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 VASTv120_0, TMB v1.7.18, Matrix v1.2.18
• 2020: VAST v3.3.0, FishStatsUtils v2.5.0, cpp VASTv82_0

NOAA README

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NOAA License

Software code created by U.S. Government employees is not subject to copyright in the United States (17 U.S.C. §105). The United States/Department of Commerce reserve all rights to seek and obtain copyright protection in countries other than the United States for Software authored in its entirety by the Department of Commerce. To this end, the Department of Commerce hereby grants to Recipient a royalty-free, nonexclusive license to use, copy, and create derivative works of the Software outside of the United States.

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