10  Pre-Flight Checklist for Publications

10.1 Crosscheck

As discussed in Chapter 8 and Chapter 9, your analysis should be regularly checked for correctness and adherence to Lab agreements, not just at the end of the project. However, it’s useful to have a final check (by you and at least one other person) before submitting for publication. Regular code review will make this final check quicker and easier, so please do both.

Note: For pre-prints, run through this checklist for both uploading to the pre-print server as well as for when you formally submit the project to a journal.

10.2 Pre-Flight Checklist

10.2.1 Repository and Files

• Confirm again that no sensitive data is included in the repository. Check files, Jupyter caches, etc.
• There is a README file (any of: README.md, README.Rmd, README.qmd).
• README contains clear instructions on how to run the code. See Section 9.7.2 for details.
• Create a new public repository for the project and archive the private repository.

10.2.2 Code and Reproducibility

• The code follows the team style guide. See Section 9.2 for details.
• Query code from user interfaces, e.g., Redivis or BigQuery, are up to date in version control.
• The code uses a package environment to lock packages. See Section 9.9 for details.
• Manuscript is generatable via Quarto. See Section 9.5 for details.
• Run the code one last time in a fresh environment, preferably on a different computer. See Section 9.8 for details.

10.2.3 Submission

• Follow Data Use Agreement requirements regarding project review from a third party prior to submission.
• Check if journal has specific code and reproducibility guidelines.
• Check figures and tables for correctness.
• Check https://www.zotero.org/styles for a citation style file for the journal of interest. Include the file in your Quarto metadata and in the repository.
• For sensitive data, confirm small cell definition for the project. Check that no small cells are included in tables or figures. See for Chapter 4 for details.
• Use a GitHub release for the submission version. See Section 9.6.1 for details.
• If there are any research outputs other than a manuscript, such as a (simulated/synthetic) data, register them for a DOI at a service like OSF or Zenodo.

10.2.4 Acceptance

• If the project exists as a pre-print, update the pre-print page to include information about the peer-reviewed publication.

10.2.5 Opt-in Workflows (Section 9.10)

• Opt-in: Pipeline code is documented and with clear instructions for running the pipeline. See Section 9.10.1 for details.
• Opt-in: If code contains tests, tests pass. See Section 9.10.2 for details.
• Opt-in: Dockerfile is included in repository with clear instructions for running the image. See Section 9.10.3 for details.