[REVIEW]: Phonetic Algorithms in R

[whedon]

Submitting author: @howardjp (James P. Howard, II)
Repository: https://github.com/howardjp/phonics
Version: v0.7.6
Editor: @jasonclark
Reviewer: @alexhanna
Archive: 10.5281/zenodo.1041982

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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 (v0.7.6)?
• Authorship: Has the submitting author (@howardjp) 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. I'm here to help you with some common editorial tasks. @alexhanna it looks like you're currently assigned as the reviewer for this paper 🎉.

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[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

https://github.com/openjournals/joss-papers/blob/joss.00480/joss.00480/10.21105.joss.00480.pdf

[howardjp]

@alexhanna Just wanted to give you a heads up, there are a handful of non-substantive changes in the development branch. If/when this paper is approved, I intend to push 1.0.0, so this paper will ultimately describe that version.

[jasonclark]

@alexhanna Let me know if you have questions about this review. I'm around all next week.

[alexhanna]

Thanks, Jason. Will get to this this week.

…

On Sun, Dec 17, 2017 at 12:33 AM, Jason A. Clark ***@***.***> wrote: @alexhanna <https://github.com/alexhanna> Let me know if you have questions about this review. I'm around all next week. — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#480 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AAwvDTvX4ZtDxQGpgojWnjhbGxVoXfvMks5tBFM0gaJpZM4Qz6sG> .

-- Alex Hanna alex-hanna.com @alexhanna

[alexhanna]

Sorry, it's been much longer than a week.

This looks generally good. Things that are missing:

• LICENSE
• Community guidelines (CONTRIBUTING)
• and API for all the functions it implements.

Otherwise code looks good and all the tests check out.

[howardjp]

@alexhanna Hello, it's all good, we have our off days.

With respect to the license, the R package system demands that a file called "LICENSE" exist and in the format shown. If you're agreeable, I could add a COPYRIGHT.md file that included the BSD license information?

I have "Contribution guidelines" in the README. Do I need to break this out into a separate file?

Finally, as for an API, every function is documented (I wouldn't be able to pass the R release checks if not). The manual is completely produced at install time. Here's a link to the automatically generated PDF.

[alexhanna]

- LICENSE: I think that's fine. - Contribution guidelines are good in the README, I think I overlooked that part - It's my first time reviewing an R package and I didn't know these were autogenerated. Looks good.

…

On Sun, Jan 21, 2018 at 8:28 PM, James Howard ***@***.***> wrote: @alexhanna <https://github.com/alexhanna> Hello, it's all good, we have our off days. With respect to the license, the R package system demands that a file called "LICENSE" exist and in the format show. If you're agreeable, I could add a COPYRIGHT.md file that included the BSD license information? I have "Contribution guidelines" in the README. Do I need to break this out into a separate file? Finally, as for an API, every function is documented (I wouldn't be able to pass the R release checks if not). The manual is completely produced at install time. Here's a link to the automatically generated PDF <https://cran.r-project.org/web/packages/phonics/phonics.pdf>. — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#480 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AAwvDUs8y1Di0eRob0-ey45cOlfpSDxyks5tM-Q5gaJpZM4Qz6sG> .

-- Alex Hanna alex-hanna.com @alexhanna

[howardjp]

Awesome. I will add the COPYRIGHT file to develop branch. That shouldn't take more than a few seconds :)

[howardjp]

Well, it took more than a few seconds, but here we go. Done. As I noted, I plan to release a 1.0.0 with this article. So with that, I'll merge the changes into master.

[alexhanna]

Always takes longer than expected!

@jasonclark I think this one's good to go.

[howardjp]

Thank you very much, @alexhanna!

[arfon]

@jasonclark - is this ready to accept?

[jasonclark]

@arfon @alexhanna Yes, I think we are ready. This one got a bit caught up in the holidays cycle. Thanks for everyone's work to get us this far.

[arfon]

@howardjp - At this point could you make an archive of the reviewed software in Zenodo/figshare/other service and update this thread with the DOI of the archive? I can then move forward with accepting the submission.

[howardjp]

Here ya go! https://doi.org/10.5281/zenodo.1041982

[arfon]

@whedon set 10.5281/zenodo.1041982 as archive

[whedon]

OK. 10.5281/zenodo.1041982 is the archive.

[arfon]

@alexhanna - many thanks for your review here and to @jasonclark for editing this submission ✨

@howardjp - your paper is now accepted into JOSS and your DOI is https://doi.org/10.21105/joss.00480 ⚡️ 🚀 💥

[whedon]

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