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ICES Methods WG

(See README for practical matters regarding the upcoming meeting in Woods Hole)

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List of Active Research Topics

1. State-space vs. traditional models (T Miller), 12

   • Retrospective patterns and process variability (A Nielsen), 8
   • Profile diagnostics and likelihood (N Cadigan), 6
   • M in a state-space assessment model (N Cadigan), 5

2. Internal vs. external stock recruitment (N Cadigan), 7

3. Selectivity as part of management advice, 6

4. Time-varying selectivity

5. Length distributions and stock status

See also: Strawman paper organization

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Proposal Format

• Working title
• Participants
  • Coordinator(s)
• Background
  • Area of research
  • Brief literature review
  • Remaining questions
  • Why is this important
• Objectives
• Plan
  • Methods, data
  • Tasks, who's doing what
  • Milestones, timeline
• References
• Appendix
  • Preliminary diagram, table, plots

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Git Commands

Command	Purpose
git clone	download a project from GitHub to computer
git status	review changes I have made
git diff	view what has changed
git commit	commit changes to my local repository
git push	push commits to remote repository
git pull	get newest changes from repote repository
git log	view history

Also: git add, git rm, git merge

Official GitHub help page links can be found at the bottom of the ices-tools-dev/doc page, and a link to the official Git handbook is provided in the bottom section of the ices-tools-prod/doc.

Many people use Git through RStudio. Other useful links related to Git include:

• https://git-scm.com/downloads
• https://git-for-windows.github.io
• https://tortoisegit.org/download/

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Evaluation of Topics

The main objective of this first meeting is to identify the research topics that the working group will pursue. We will be especially interested in topics that bring together and compare a wide range of approaches, methods, and datasets.

We are looking for paper-size topics that are well suited to analyze and write as teams. When choosing which topics to prioritize, we will consider things like:

• Is this topic important for many stock assessment scientists?

• What are the standard papers that people cite for this topic?

• Is there another working group already working on this topic?

• How can this be structured into the format of a medium-size journal paper?

• What kind of work is required, and how much work?

• Do we have a suitable number of participants that would like to analyze and write this together?

• Who would like to lead this group and what will the role of coauthors be?

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Set Aside for Later Consideration

The following topics have been set aside, based on ranking by WG attendees.

1. Collinearity among survey time-series

2. Management strategy evaluation

3. Online stock assessment environments

4. Fitting models to unaggregated data

5. Fitting models to length data

6. Methods to evaluate MPAs

7. Spatial smoothing of catch and survey data

8. Spatially explicit stock assessment

9. Stock recruitment cyclic dynamics for small pelagics

10. Missing data/short term forecast best practices

11. Evaluating uncertainty, 8

    • Incorporating data uncertainty (N Cadigan), 6

12. Appropriate level of model complexity, 6

    • Data-limited stock assessment, 5