Joss-reviews: [REVIEW]: gwdegree: A Shiny App to Aid Interpretation of Geometrically-Weighted Degree Estimates in Exponential Random Graph Models

[whedon]

Submitting author: @michaellevy (Michael Levy)
Repository: https://github.com/michaellevy/gwdegree
Version: v0.1.1
Editor: @arfon
Reviewer: @amoeba
Archive: http://dx.doi.org/10.5281/zenodo.57495

Status

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Reviewer questions

Conflict of interest

• [x] As the reviewer I confirm that there are no conflicts of interest for me to review this work (such as being a major contributor to the software).

  General checks

• [x] Repository: Is the source code for this software available at the repository url?

• [x] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?

• [x] Version: Does the release version given match the GitHub release (v0.1.0)?

  Functionality

• [x] Installation: Does installation proceed as outlined in the documentation?

• [x] Functionality: Have the functional claims of the software been confirmed?

• [x] Performance: Have any performance claims of the software been confirmed?

  Documentation

• [x] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?

• [x] Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
• [x] Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
• [x] Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g. API method documentation)?
• [x] Automated tests: Are there automated tests or manual steps described so that the function of the software can be verified?
• [x] Community guidelines: Are there clear guidelines for third parties wishing to 1) Contribute to the software 2) Report issues or problems with the software 3) Seek support
  

  Software paper

Paper PDF: 10.21105.joss.00036.pdf

• [x] Authors: Does the paper.md file include a list of authors with their affiliations?
• [x] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
• [x] References: Do all archival references that should have a DOI list one (e.g. papers, datasets, software)?

[arfon]

/ cc @openjournals/joss-reviewers - would anyone be willing to review this submission?

If you would like to review this submission then please comment on this thread so that others know you're doing a review (so as not to duplicate effort). Something as simple as :hand: I am reviewing this will suffice.

Reviewer instructions

• Please work through the checklist at the start of this issue.
• If you need any further guidance/clarification take a look at the reviewer guidelines here http://joss.theoj.org/about#reviewer_guidelines
• Please make a publication recommendation at the end of your review

Any questions, please ask for help by commenting on this issue! 🚀

[amoeba]

✋ I can review this today.

[amoeba]

Grade: 2 (Minor revisions)

General comments:

The software is easy to use and I was pleased to find a high level of attention to detail on the design of the interactive tool and the accompanying writing. The software works and works well. I can see clear research application.

Specific notes requiring action:

• License: Repository does contain a plain-text LICENSE file but the file does not contain the text of an OSI-approved license. The DESCRIPTION file does, however. @arfon How is JOSS handling this case, which seems to apply to submissions of R packages that must go through submission to CRAN?
• Version: The GitHub repository does not have any releases. Submitted version is 0.1.0, CRAN version is 0.1.1. @arfon do we need to get the JOSS version in line with the CRAN version? I tested the CRAN-submitted 0.1.1 version.
• Installation:: While the software does install as described in the documentation (README.md in the repo), the information was hard to find. Suggest breaking the README into sections, including a section for 'Installation' or at least putting the installation information in an easier to find location.
• Performance: No specific performance claims were made, and I find the application performs adequately and I would expect the software to have acceptable performance on other computers.
• Example usage: The software is an interactive tool and I found the tool contained in-context instruction on usage.
• Functionality documentation: See above.
• Community guidelines:: No on (1), (2), and (3). Suggest adding these sections to README.
• Paper:
  
  
  
  • Paper contains "Use" instructions, which — according to my maybe-wrong interpretation of — the JOSS Reviewer Guidelines forbid. Suggest removing the "Use" paragraph from the paper.
  
  

Comments on the README.me in the repo:

• README references 'tabs' but if the user starts with the readme, they haven't seen the app (and its tabs). Consider explaining or showing the app before referencing the tabs.
• The link "There is a working version online", 404s. Suggest fixing link.
• As noted specifically above, I would suggest breaking the README up into a few major sections, covering installation, usage, a high-level overview of the software, and the community guidelines sections. The writing you have is already very good.

Please let me know if I can explain anything in more detail. Thanks!

[michaellevy]

Thanks for the quick review, @amoeba! I think I've addressed all these things in michaellevy/gwdegree@dbdbc47. A couple points:

• v0.1.0 is what I originally submitted, but v0.1.1 (current on CRAN and GitHub) is much prefered. Recognizing the journal wants to review just one version, I hope this can be accommodated.
• I left the LICENSE file as is, per CRAN's protocol; not sure if it would bother anyone to include the text of the license there. Happy to test this on my next update.

[amoeba]

Grade: 1 (Accept)

I reviewed your changes and they address all of my concerns. Thanks!

I subsequently checked off the remaining items on the Reviewer questions checklist. In #37, it seems like JOSS may be okay with R packages that are on CRAN following the CRAN guidelines, which you have done. I've checked off the corresponding list item. It really does look like CRAN will reject a submission that includes the text of a license in a LICENSE file.

@arfon I reviewed v 0.1.1, and this submission is for 0.1.0. Can we just change this submission to be for 0.1.1 and be done?

[arfon]

• I left the LICENSE file as is, per CRAN's protocol; not sure if it would bother anyone to include the text of the license there. Happy to test this on my next update.

This is OK I think @michaellevy

Thanks for the rapid review @amoeba!

@arfon I reviewed v 0.1.1, and this submission is for 0.1.0. Can we just change this submission to be for 0.1.1 and be done?

Sounds good to me.

@michaellevy - I think the final thing here is to make an archive of the software in Zenodo/figshare/other similar service and update this thread with the archive DOI.

[michaellevy]

Great! Here is the archive:

Thanks @arfon and @amoeba, this whole process has been smooth, fast, and edifying.

[arfon]

@michaellevy - this is now accepted into JOSS! Your DOI will be http://dx.doi.org/10.21105/joss.00036 . The Crossref processing queues are a little backed up right now but the DOI should be live in the next couple of hours ⚡ 🚀 💥