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[REVIEW]: kdensity: An R package for kernel density estimation with parametric starts and asymmetric kernels #1566

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whedon opened this issue Jul 12, 2019 · 80 comments

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@whedon
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commented Jul 12, 2019

Submitting author: @JonasMoss (Jonas Moss)
Repository: https://github.com/JonasMoss/kdensity
Version: 1.1.0
Editor: @terrytangyuan
Reviewer: @gvegayon, @TrashBirdEcology
Archive: 10.5281/zenodo.3466547

Status

status

Status badge code:

HTML: <a href="http://joss.theoj.org/papers/28cef1f13a184adc6260fc513139c7ef"><img src="http://joss.theoj.org/papers/28cef1f13a184adc6260fc513139c7ef/status.svg"></a>
Markdown: [![status](http://joss.theoj.org/papers/28cef1f13a184adc6260fc513139c7ef/status.svg)](http://joss.theoj.org/papers/28cef1f13a184adc6260fc513139c7ef)

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) by leaving comments 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

@gvegayon, 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.readthedocs.io/en/latest/reviewer_guidelines.html. Any questions/concerns please let @terrytangyuan know.

Please try and complete your review in the next two weeks

Review checklist for @gvegayon

Conflict of interest

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: 1.1.0
  • Authorship: Has the submitting author (@JonasMoss) 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)?

Review checklist for @TrashBirdEcology

Conflict of interest

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: 1.1.0
  • Authorship: Has the submitting author (@JonasMoss) 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

  • Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
  • 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.
  • 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

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commented Jul 12, 2019

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @gvegayon it looks like you're currently assigned to review 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:

  1. Set yourself as 'Not watching' https://github.com/openjournals/joss-reviews:

watching

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

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

@whedon commands

For example, to regenerate the paper pdf after making changes in the paper's md or bib files, type:

@whedon generate pdf
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commented Jul 12, 2019

Attempting PDF compilation. Reticulating splines etc...
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commented Jul 12, 2019

@terrytangyuan

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commented Jul 12, 2019

@TrashBirdEcology I also added you as the reviewer since JOSS now requires at least two reviewers. Feel free to review this paper when you get back. Thanks.

@terrytangyuan

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commented Jul 22, 2019

👋 @gvegayon You mentioned that you would be able to start the review on 22nd. Feel free to start the review while @TrashBirdEcology is still traveling.

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commented Jul 24, 2019

OK @JonasMoss @terrytangyuan, I've finished my first round. Overall, everything looks good (very nice job @JonasMoss!), and there are only a few issues that I would like the authors to address. The most important is regarding related R packages.

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commented Jul 31, 2019

Thanks @gvegayon! @JonasMoss Could you address those issues pointed out?

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commented Aug 1, 2019

@terrytangyuan Sure! Thanks a lot @gvegayon

@JonasMoss

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commented Aug 5, 2019

@gvegayon Okay! I've addressed the issues. Details are on the Github issues pages.

@terrytangyuan

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commented Aug 5, 2019

@gvegayon Please take another look when you get a chance. Also ping @TrashBirdEcology to review when you are back from traveling.

@TrashBirdEcology

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commented Aug 6, 2019

@terrytangyuan I have completed a code and paper review of this package.

I have opened the following issues to the authors repository: issue 56, 56, 57, 58.

Although most are minor, the first recommendation in Issue 59 should be addressed prior to approval:

In the function kdensity.R, you have a stop command if NAs are present in X. The line following the stop command removes NAs. So either replace 'stop' with 'warning' or 'message', or remove ` x = x[!is.na(x)] entirely:

I have checked off all but the Installation instructions and the Installation checklist boxes, per Issue 56.

@JonasMoss

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commented Aug 7, 2019

Thanks a lot @TrashBirdEcology! I've addressed your issues with details on the repository's issues page.

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commented Aug 21, 2019

👋 @gvegayon @TrashBirdEcology I think this is ready for another round of review whenever you get a chance. Thanks!

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commented Sep 3, 2019

OK @JonasMoss, the changes look good. Only one minor issue regarding a broken link. Thanks.

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commented Sep 3, 2019

@gvegayon Great! Fixed it now. =)

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commented Sep 28, 2019

@gvegayon @TrashBirdEcology It looks like some items in the review list are not checked yet. Could you take a look? If everything looks good, we can move forward with this submission soon. Thanks.

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commented Oct 1, 2019

@whedon generate pdf

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commented Oct 1, 2019

Attempting PDF compilation. Reticulating splines etc...
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commented Oct 1, 2019

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commented Oct 1, 2019

@whedon check references

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commented Oct 1, 2019

Attempting to check references...
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commented Oct 1, 2019


OK DOIs

- 10.1214/aos/1176324627 is OK
- 10.1093/biomet/asm068 is OK
- 10.1023/A:1004165218295 is OK
- 10.1016/S0167-9473(99)00010-9 is OK
- 10.1201/9781315140919 is OK
- 10.1111/j.2517-6161.1994.tb02006.x is OK
- 10.18637/jss.v084.i05 is OK
- 10.21105/joss.00870 is OK

MISSING DOIs

- None

INVALID DOIs

- None
@kyleniemeyer

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commented Oct 1, 2019

@JonasMoss looks to be resolved now!

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commented Oct 1, 2019

@JonasMoss nearly there! I just have one final paper edit: could you add a sentence or two at the beginning of the paper to satisfy this requirement:

A summary describing the high-level functionality and purpose of the software for a diverse, non-specialist audience.

(from our list of things that JOSS papers should contain)

@JonasMoss

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commented Oct 3, 2019

@kyleniemeyer OK! We added two sentences to the beginning of the paper now.

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commented Oct 3, 2019

@whedon generate pdf

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commented Oct 3, 2019

Attempting PDF compilation. Reticulating splines etc...
@whedon

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commented Oct 3, 2019

@kyleniemeyer

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commented Oct 3, 2019

@JonasMoss thanks! just one minor correction: I think you are missing "R" at near the beginning of the second sentence: "This (R Core Team, 2019) package..." -> "This R (R Core Team, 2019) package..."

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commented Oct 3, 2019

@kyleniemeyer Thanks. Fixed.

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commented Oct 3, 2019

@whedon generate pdf

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commented Oct 3, 2019

Attempting PDF compilation. Reticulating splines etc...
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commented Oct 3, 2019

@kyleniemeyer

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commented Oct 3, 2019

@whedon accept

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commented Oct 3, 2019

Attempting dry run of processing paper acceptance...
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commented Oct 3, 2019


OK DOIs

- 10.1214/aos/1176324627 is OK
- 10.1093/biomet/asm068 is OK
- 10.1023/A:1004165218295 is OK
- 10.1016/S0167-9473(99)00010-9 is OK
- 10.1201/9781315140919 is OK
- 10.1111/j.2517-6161.1994.tb02006.x is OK
- 10.18637/jss.v084.i05 is OK
- 10.21105/joss.00870 is OK

MISSING DOIs

- None

INVALID DOIs

- None
@whedon

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commented Oct 3, 2019

Check final proof 👉 openjournals/joss-papers#1004

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#1004, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true
@kyleniemeyer

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commented Oct 3, 2019

@whedon accept deposit=true

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commented Oct 3, 2019

Doing it live! Attempting automated processing of paper acceptance...
@whedon whedon added the accepted label Oct 3, 2019
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commented Oct 3, 2019

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

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commented Oct 3, 2019

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

Here's what you must now do:

  1. Check final PDF and Crossref metadata that was deposited 👉 openjournals/joss-papers#1005
  2. Wait a couple of minutes to verify that the paper DOI resolves https://doi.org/10.21105/joss.01566
  3. If everything looks good, then close this review issue.
  4. Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? notify your editorial technical team...

@kyleniemeyer

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commented Oct 3, 2019

Congrats @JonasMoss on your article's publication in JOSS!

Many thanks to @gvegayon & @TrashBirdEcology for reviewing, and @terrytangyuan for editing, this submission.

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commented Oct 3, 2019

🎉🎉🎉 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](https://joss.theoj.org/papers/10.21105/joss.01566/status.svg)](https://doi.org/10.21105/joss.01566)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.01566">
  <img src="https://joss.theoj.org/papers/10.21105/joss.01566/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.01566/status.svg
   :target: https://doi.org/10.21105/joss.01566

This is how it will look in your documentation:

DOI

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Journal of Open Source Software is a community-run journal and relies upon volunteer effort. If you'd like to support us please consider doing either one (or both) of the the following:

@TrashBirdEcology

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commented Oct 9, 2019

Congrats @JonasMoss !

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