Joss-reviews: [REVIEW]: kdensity: An R package for kernel density estimation with parametric starts and asymmetric kernels

[whedon]

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 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

• [x] 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

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

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: 1.1.0
• [x] Authorship: Has the submitting author (@JonasMoss) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?

Functionality

• [x] Installation: Does installation proceed as outlined in the documentation?
• [x] Functionality: Have the functional claims of the software been confirmed?
• [x] 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

• [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

• [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)?

Review checklist for @TrashBirdEcology

Conflict of interest

• [x] 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

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

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: 1.1.0
• [x] Authorship: Has the submitting author (@JonasMoss) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?

Functionality

• [x] Installation: Does installation proceed as outlined in the documentation?
• [x] Functionality: Have the functional claims of the software been confirmed?
• [x] 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

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

• [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)?

[whedon]

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 :tada:.

:star: Important :star:

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:

1. 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

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

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

:point_right: Check article proof :page_facing_up: :point_left:

[terrytangyuan]

@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]

👋 @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.

[gvegayon]

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.

[terrytangyuan]

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

[JonasMoss]

@terrytangyuan Sure! Thanks a lot @gvegayon

[JonasMoss]

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

[terrytangyuan]

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

[trashbirdecology]

@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]

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

[terrytangyuan]

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

[gvegayon]

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

[JonasMoss]

@gvegayon Great! Fixed it now. =)

[terrytangyuan]

@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.

[trashbirdecology]

@terrytangyuan done

[gvegayon]

Same here @terrytangyuan

[terrytangyuan]

Thanks everyone!

@JonasMoss At this point could you make a new release of this software that includes the changes that have resulted from this review. Then, please make an archive of the software in Zenodo/figshare/other service and update this thread with the DOI of the archive? For the Zenodo/figshare archive, please make sure that:

The title of the archive is the same as the JOSS paper title
That the authors of the archive are the same as the JOSS paper authors
I can then move forward with accepting the submission.

[JonasMoss]

Thanks! Here's the doi of the Zenodo archive.
10.5281/zenodo.3466547
https://zenodo.org/record/3466547

[terrytangyuan]

@whedon set 1.1.0 as version

[whedon]

OK. 1.1.0 is the version.

[terrytangyuan]

@whedon set 10.5281/zenodo.3466547 as archive

[whedon]

OK. 10.5281/zenodo.3466547 is the archive.

[terrytangyuan]

@whedon accept

[whedon]

Attempting dry run of processing paper acceptance...

[whedon]

PDF failed to compile for issue #1566 with the following error:

pandoc-citeproc: Cannot decode byte 'x20': Data.Text.Internal.Encoding.decodeUtf8: Invalid UTF-8 stream
Error running filter pandoc-citeproc:
Filter returned error status 1
Looks like we failed to compile the PDF

[terrytangyuan]

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

PDF failed to compile for issue #1566 with the following error:

pandoc-citeproc: Cannot decode byte 'x20': Data.Text.Internal.Encoding.decodeUtf8: Invalid UTF-8 stream
Error running filter pandoc-citeproc:
Filter returned error status 1
Looks like we failed to compile the PDF

[terrytangyuan]

@JonasMoss Could you take a look at your recent changes to see what caused the above compilation failure?

[JonasMoss]

I changed the encoding from ANSI to UTF-8 at the Github repo now.

@whedon generate pdf

[terrytangyuan]

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

:point_right: Check article proof :page_facing_up: :point_left:

[terrytangyuan]

@whedon accept

[whedon]

Attempting dry run of processing paper acceptance...

[whedon]

```Reference check summary:

OK DOIs

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

MISSING DOIs

• None

INVALID DOIs

• doi:10.2307/2346189 is INVALID
  ```

[whedon]

Check final proof :point_right: https://github.com/openjournals/joss-papers/pull/1000

If the paper PDF and Crossref deposit XML look good in https://github.com/openjournals/joss-papers/pull/1000, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.
@whedon accept deposit=true

[terrytangyuan]

@JonasMoss Could you fix the invalid DOI shown above?

[JonasMoss]

@terrytangyuan Fixed.

[terrytangyuan]

@whedon accept

[whedon]

Attempting dry run of processing paper acceptance...

[whedon]

```Reference check summary:

OK DOIs

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

MISSING DOIs

• None

INVALID DOIs

• doi:10.2307/2346189 is INVALID
  ```

[whedon]

Check final proof :point_right: https://github.com/openjournals/joss-papers/pull/1001

If the paper PDF and Crossref deposit XML look good in https://github.com/openjournals/joss-papers/pull/1001, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.
@whedon accept deposit=true

[terrytangyuan]

@whedon check references

[whedon]

Attempting to check references...

[whedon]

```Reference check summary:

OK DOIs

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

MISSING DOIs

• None

INVALID DOIs

• doi:10.2307/2346189 is INVALID
  ```

[whedon]

```Reference check summary:

OK DOIs

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

MISSING DOIs

• None

INVALID DOIs

• doi:10.2307/2346189 is INVALID
  ```

[terrytangyuan]

@openjournals/joss-eics Could you take it from here? The paper looks good to me. I manually verified that the DOI has been fixed.

[kyleniemeyer]

Hi @JonasMoss, not sure if this is causing the whedon error (and if so, why it's only showing up for one of them), but if you look in the list of references, a number of them have repeated "doi:" in the DOIs.

Please remove the extra doi: from these references: Chen 1999, Chen 2000, Hjort 1995, Jones 2007, Marron 1994, Silverman 2018 (and any others, if I missed any)

(in other words, change doi = {doi:10.1214/aos/1176324627} to just doi = {10.1214/aos/1176324627} (e.g.) in the references where applicable.)

[JonasMoss]

@kyleniemeyer OK, done it.

The doi 10.2307/2346189 was in fact invalid acccording to doi.org though. I replaced it with the correct doi.

The string "10.2307/2346189" isn't in the paper.bib on the Github repo (i.e. search finds nothing), so it looks like whedon isn't looking at the right place. Perhaps the document must be compiled again?

[kyleniemeyer]

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

:point_right: Check article proof :page_facing_up: :point_left:

[kyleniemeyer]

@whedon check references

[whedon]

Attempting to check references...

[whedon]

```Reference check summary:

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]

@JonasMoss looks to be resolved now!

[kyleniemeyer]

@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]

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

[kyleniemeyer]

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

:point_right: Check article proof :page_facing_up: :point_left:

[kyleniemeyer]

@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..."

[JonasMoss]

@kyleniemeyer Thanks. Fixed.

[kyleniemeyer]

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

:point_right: Check article proof :page_facing_up: :point_left:

[kyleniemeyer]

@whedon accept

[whedon]

Attempting dry run of processing paper acceptance...

[whedon]

```Reference check summary:

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]

Check final proof :point_right: https://github.com/openjournals/joss-papers/pull/1004

If the paper PDF and Crossref deposit XML look good in https://github.com/openjournals/joss-papers/pull/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]

@whedon accept deposit=true

[whedon]

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

[whedon]

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

[whedon]

🚨🚨🚨 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 :point_right: https://github.com/openjournals/joss-papers/pull/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]

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

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

[whedon]

:tada::tada::tada: Congratulations on your paper acceptance! :tada::tada::tada:

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:

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[trashbirdecology]

Congrats @JonasMoss !