Chapter 8 Guide for Editors

Software Peer Review at rOpenSci is managed by a team of editors. We are piloting a system of a rotating Editor-in-Chief (EiC).

This chapter presents the responsibilities of the Editor-in-Chief, of any editor in charge of a submission, and how to respond to an out-of-scope submission.

If you’re a guest editor, thanks for helping! Please contact the editor who invited you to handle a submission for any question you might have.

8.1 EiC Responsibilities

The EiC serves for 3 months or a time agreed to by all members of the editorial board. The EiC plays the following roles

  • Watches all issues posted to the software-review repo.
  • Assigns package submissions to other editors, including self, to handle. Mostly this just rotates among editors, unless the EiC thinks an editor is particularly suited to a package, or an editor rejects due to being too busy or because of conflicting interests.
  • Raises scope/overlap issue with all editors if they see an ambiguous case. This may also be done by handling editors (see below). To initiate discussion, this is posted to the rOpenSci Slack software review channel, tagging all editors.
  • Responds to pre-submission inquiries and meta issues posted to the software-review and software-review-meta repos, similarly pinging channel if discussion is needed. Any editor should feel free to step in on these. See this section about how to respond to out-of-scope (pre-) submissions.
  • Responds to referrals from JOSS or other publication partners.
  • Monitors pace of review process and reminds other editors to move packages along as needed.

8.2 Handling Editor’s Checklist

8.2.1 Upon submission:

  • Tag issue with 1/editor-checks tag and assign a main editor. Please strive to finish the checks and start looking for reviewers within 5 working days.
  • Use the editor template to guide initial checks and record your response to the submission. You can also streamline your editor checks by using the pkgreviewr package created by associated editor Anna Krystalli
  • Check that template has been properly filled out.
  • Check against policies for fit and overlap. Initiate discussion via Slack #onboarding channel if needed for edge cases that haven’t been caught by previous checks by the EiC. If reject, see this section about how to respond.
  • Check that mandatory parts of template are complete. If not, direct authors toward appropriate instructions.
  • Run automated tests: spelling::spell_check_package(), goodpractice::gp() (most exceptions will need to be justified by the author in the particular context of their package.), devtools::spell_check(). Run covr::package_coverage() using NOT_CRAN if needed, as well. Check that documentation is generated using roxygen2, not by hand (this isn’t part of automatic tests yet). Report relevant outputs in the issue thread.
  • For packages needing continuous integration on multiple platforms (cf criteria in this section of the CI chapter) make sure the package gets tested on multiple platforms (having the package built on both Travis and AppVeyor for instance).
  • Wherever possible when asking for changes, direct authors to automatic tools such as usethis and styler, and to online resources (sections of this guide, sections of the R packages book) to make your feedback easier to use. Example of editor’s checks.
  • If initial checks show major gaps, request changes before assigning reviewers.
  • If the package raises a new issue for rOpenSci policy, start a conversation in Slack or open a discussion on the rOpenSci forum to discuss it with other editors (example of policy discussion).

8.2.2 Assign reviewers:

  • Switch numbered tag to 2/seeking-reviewers.
  • Ask author to add a rOpenSci review badge to their README. Badge URL is https://badges.ropensci.org/<issue_id>_status.svg. Full link should be:
[![](https://badges.ropensci.org/<issue_id>_status.svg)](https://github.com/ropensci/software-review/issues/<issue_id>)
  • Use the #onboarding Slack channel for discussion about potential reviewers.
  • Use the email template if needed for inviting reviewers
    • When inviting reviewers, include something like “if I don’t hear from you in a week, I’ll assume you are unable to review,” so as to give a clear deadline when you’ll move on to looking for someone else.
  • Assign a due date 3 weeks after all reviewers have been found.
  • Once two or more reviewers are found, assign reviewers by tagging in the issue with the following format:
Reviewer: @githubname1 
Reviewer: @githubname2
Due date: YYYY-MM-DD
  • Switch numbered tag to 3/reviewers-assigned once reviewers are assigned.
  • Invite authors and reviewers to rOpenSci Slack if they aren’t on this Slack already.

8.2.3 During review:

  • Check in with reviewers and authors occasionally. Offer clarification and help as needed.
  • In general aim for 3 weeks for review, 2 weeks for subsequent changes, and 1 week for reviewer approval of changes.
  • Upon all reviews being submitted, change the review status tag to 4/review-in-awaiting-changes to update the reminder bot.
  • If the author stops responding, refer to the policies and/or ping the other editors in the Slack channel for discussion. Importantly, if a reviewer was assigned to a closed issue, contact them when closing the issue to explain the decision, thank them once again for their work, and make a note in our database to assign them to a submission with high chances of smooth software review next time (e.g. a package author who has already submitted packages to us).
  • Upon changes being made, change the review status tag to 5/awaiting-reviewer-response.

8.2.4 After review:

  • Change the status tag to 6/approved.
  • You can use the comment template.
  • Add review/er information to the review database.
  • If authors intend to submit to CRAN, direct them to the section about CRAN gotchas and offer to provide support through this process.
  • Ask authors to migrate to ropensci
    • Create a two-person team in rOpenSci’s “ropensci” GitHub organization, named for the package, with yourself and the package author as members.
    • Have the author transfer the repository to ropensci
    • Go to the repository settings in rOpenSci’s “ropensci” GitHub organization and give the author “Admin” access to the repository.
  • Ask author to:
    • Add rOpenSci footer to README [![ropensci_footer](https://ropensci.org/public_images/ropensci_footer.png)](https://ropensci.org)
    • Add a CodeMeta file by running codemetar::write_codemeta() (codemetar GitHub repo)
    • Change any needed links, such those for CI badges
    • Re-activate CI services
      • For Travis, activating the project in the ropensci account should be sufficient
      • For AppVeyor, tell the author to update the GitHub link in their badge, but do not transfer the project: AppVeyor projects should remain under the authors’ account. The badge is [![AppVeyor Build Status](https://ci.appveyor.com/api/projects/status/github/ropensci/pkgname?branch=master&svg=true)](https://ci.appveyor.com/project/individualaccount/pkgname).
      • For Codecov, the webhook may need to be reset by the author.
  • Add a “peer-reviewed” topic to the repo.
  • Close the software-review issue.

8.2.5 For joint JOSS submissions:

  • After repo is transferred to ropensci and admin rights assigned, have author generate a new release with a DOI.
  • Ask author to submit package via http://joss.theoj.org/papers/new
  • Watch for paper to pop up at http://joss.theoj.org/papers, then add the following comment to the submission thread:

    This submission has been accepted to rOpenSci. The review thread can be found at [LINK TO SOFTWARE REVIEW ISSUE]

8.2.6 Package promotion:

8.3 Responding to out-of-scope submissions

Thank authors for their submission, explain the reasons for the decision, and direct them to other publication venues if relevant, and to the rOpenSci discussion forum. Use wording from Aims and scope in particular regarding the evolution of scope over time, and the overlap and differences between unconf/staff/software-review development.

Examples of out-of-scope submissions and responses.