[REVIEW]: polyCub: An R package for Integration over Polygons

[whedon]

Submitting author: @bastistician (Sebastian Meyer)
Repository: https://github.com/bastistician/polyCub
Version: 0.7.0
Editor: @karthik
Reviewer: @wrathematics
Archive: 10.5281/zenodo.2559486

Status

Status badge code:

HTML: <a href="http://joss.theoj.org/papers/5b55a804b26dab315d532b283d10283a"><img src="http://joss.theoj.org/papers/5b55a804b26dab315d532b283d10283a/status.svg"></a>
Markdown: [![status](http://joss.theoj.org/papers/5b55a804b26dab315d532b283d10283a/status.svg)](http://joss.theoj.org/papers/5b55a804b26dab315d532b283d10283a)

Reviewers and authors:

Please avoid lengthy details of difficulties in the review thread. Instead, please create a new issue in the target repository and link to those issues (especially acceptance-blockers) in the review thread below. (For completists: if the target issue tracker is also on GitHub, linking the review thread in the issue or vice versa will create corresponding breadcrumb trails in the link target.)

Reviewer instructions & questions

@wrathematics, please carry out your review in this issue by updating the checklist below. If you cannot edit the checklist please:

1. Make sure you're logged in to your GitHub account
2. Be sure to accept the invite at this URL: https://github.com/openjournals/joss-reviews/invitations

The reviewer guidelines are available here: https://joss.theoj.org/about#reviewer_guidelines. Any questions/concerns please let @karthik know.

✨ Please try and complete your review in the next two weeks ✨

Review checklist for @wrathematics

Conflict of interest

• As the reviewer I confirm that I have read the JOSS conflict of interest policy and that there are no conflicts of interest for me to review this work.

Code of Conduct

• I confirm that I read and will adhere to the JOSS code of conduct.

General checks

• Repository: Is the source code for this software available at the repository url?
• License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
• Version: Does the release version given match the GitHub release (0.7.0)?
• Authorship: Has the submitting author (@bastistician) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?

Functionality

• Installation: Does installation proceed as outlined in the documentation?
• Functionality: Have the functional claims of the software been confirmed?
• Performance: If there are any performance claims of the software, have they been confirmed? (If there are no claims, please check off this item.)

Documentation

• A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
• Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
• Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
• Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
• Automated tests: Are there automated tests or manual steps described so that the function of the software can be verified?
• 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

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

[whedon]

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @wrathematics it looks like you're currently assigned as the reviewer for this paper 🎉.

⭐ Important ⭐

If you haven't already, you should seriously consider unsubscribing from GitHub notifications for this (https://github.com/openjournals/joss-reviews) repository. As a reviewer, you're probably currently watching this repository which means for GitHub's default behaviour you will receive notifications (emails) for all reviews 😿

To fix this do the following two things:

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2. You may also like to change your default settings for this watching repositories in your GitHub profile here: https://github.com/settings/notifications

For a list of things I can do to help you, just type:

@whedon commands

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

👉 Check article proof 📄 👈

[wrathematics]

Sorry this took me so long. I think everything basically looks good. A few very minor comments:

• The README.md file describes how to contribute, report problems, and seek support. But I think it's somewhat popular to have a CONTRIBUTING.md file. Personally I prefer having that information in a README, but you might consider creating one.
• I found one minor compiler warning. I submitted an issue on your repo, but as I say, it's quite minor so you may close the issue if you wish to ignore.
• Your README.md is quite thorough. You might consider turning it into a package vignette.
• I would personally like to see some benchmarks (perhaps in a future vignette). Even if you just compared the performance/accuracy tradeoffs that you outline in the paper, I think it would be very helpful.

As far as the JOSS review is concerned, I don't consider any of these issues blockers.

[karthik]

Thanks very much @wrathematics!
@bastistician Please let me know if you want to address these optional fixes before acceptance.

[bastistician]

Thanks a lot for the review, @wrathematics! (BTW: I wouldn't judge two weeks as a long review period.)
I really like your suggestion of turning the README into a package vignette as well as including some benchmarks therein. Let me do that before acceptance (@karthik).

[labarba]

👋 @bastistician — We haven't heard from you in a while. What's your status? Are you able to work on this revision soon?

[bastistician]

Thanks for asking. I had this on my todo list for a while... and have now started to implement the above suggestions. Sorry for the delay!

[bastistician]

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

👉 Check article proof 📄 👈

[bastistician]

I have

• implemented the suggested improvements and increased the package version to 0.7.1
• not yet tagged that release nor submitted to CRAN
• made minor modifications in the paper (referencing the new vignette), see the updated article proof

@wrathematics : May I include your name as a reviewer in the package DESCRIPTION (with role="rev")?

@karthik : How do we proceed? Is there an intended release schedule at JOSS? I would like the package to be cited using this JOSS publication, so I have included a reference in the package CITATION file. However, the DOI will only be registered later, and the volume and issue number are probably not yet fixed (or can I assume "4(33)" as indicated in the footnote of the current proof?). Should I release the package on CRAN prior to or after JOSS acceptance and archiving on Zenodo?

[karthik]

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

👉 Check article proof 📄 👈

[karthik]

@whedon commands

[karthik]

@whedon check references

[whedon]

Attempting to check references...

[whedon]

OK DOIs

- http://doi.org/10.1214/14-AOAS743 is OK
- http://doi.org/10.1007/s10543-007-0131-2 is OK
- http://doi.org/10.1093/sysbio/syv057 is OK
- http://doi.org/10.18637/jss.v077.i11 is OK
- http://doi.org/10.18637/jss.v012.i06 is OK
- http://doi.org/10.1016/j.cpc.2005.01.010 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[karthik]

@bastistician Can you please deposit the latest version of your package on Zenodo and share the DOI with me here? 🙏

[bastistician]

@karthik Today, I have released the package on CRAN (version 0.7.1) and created a corresponding GitHub release, which has subsequently been pushed to Zenodo. Here is the DOI:

https://doi.org/10.5281/zenodo.2559486

[karthik]

@whedon set zenodo.2559486 as archive

[whedon]

zenodo.2559486 doesn't look like an archive DOI.

[karthik]

@whedon set 10.5281/zenodo.2559486 as archive

[whedon]

OK. 10.5281/zenodo.2559486 is the archive.

[karthik]

@whedon accept

[whedon]

Attempting dry run of processing paper acceptance...

[whedon]

OK DOIs

- http://doi.org/10.1214/14-AOAS743 is OK
- http://doi.org/10.1007/s10543-007-0131-2 is OK
- http://doi.org/10.1093/sysbio/syv057 is OK
- http://doi.org/10.18637/jss.v077.i11 is OK
- http://doi.org/10.18637/jss.v012.i06 is OK
- http://doi.org/10.1016/j.cpc.2005.01.010 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[whedon]

Check final proof 👉 openjournals/joss-papers#478

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#478, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true

[karthik]

LGTM. EICs, this is ready to accept.

[arfon]

LGTM. EICs, this is ready to accept.

Thanks @karthik. In the future can you ping @openjournals/joss-eics?

[arfon]

@whedon accept deposit=true

[whedon]

Doing it live! Attempting automated processing of paper acceptance...

[whedon]

🚨🚨🚨 THIS IS NOT A DRILL, YOU HAVE JUST ACCEPTED A PAPER INTO JOSS! 🚨🚨🚨

Here's what you must now do:

0. Check final PDF and Crossref metadata that was deposited 👉 openjournals/joss-papers#485
1. Wait a couple of minutes to verify that the paper DOI resolves https://doi.org/10.21105/joss.01056
2. If everything looks good, then close this review issue.
3. Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? notify your editorial technical team...

[arfon]

@wrathematics - many thanks for your review here and to @karthik for editing this submission ✨

@bastistician - your paper is now accepted into JOSS ⚡🚀💥

[whedon]

🎉🎉🎉 Congratulations on your paper acceptance! 🎉🎉🎉

If you would like to include a link to your paper from your README use the following code snippets:

Markdown:
[![DOI](http://joss.theoj.org/papers/10.21105/joss.01056/status.svg)](https://doi.org/10.21105/joss.01056)

HTML:
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  <img src="http://joss.theoj.org/papers/10.21105/joss.01056/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: http://joss.theoj.org/papers/10.21105/joss.01056/status.svg
   :target: https://doi.org/10.21105/joss.01056

This is how it will look in your documentation:

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