Joss-reviews: [REVIEW]: perccalc: An R package for estimating percentiles from categorical variables

[whedon]

Submitting author: @cimentadaj (Jorge Cimentada)
Repository: https://github.com/cimentadaj/perccalc/
Version: v1.0.5
Editor: @majensen
Reviewer: @briatte, @amoeba
Archive: 10.5281/zenodo.3559855

Status

Status badge code:

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Markdown: [![status](https://joss.theoj.org/papers/6aa957144bec59d3c1b02aa945ed9468/status.svg)](https://joss.theoj.org/papers/6aa957144bec59d3c1b02aa945ed9468)

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

@briatte & @amoeba, 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 @majensen know.

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

Review checklist for @briatte

Conflict of interest

• [x] I confirm that I have read the JOSS conflict of interest (COI) policy and that: I have no COIs with reviewing this work or that any perceived COIs have been waived by JOSS for the purpose of this review.

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] Contribution and authorship: Has the submitting author (@cimentadaj) 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 functionality 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] Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
• [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] State of the field: Do the authors describe how this software compares to other commonly-used packages?
• [x] Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
• [x] References: Is the list of references complete, and is everything cited appropriately that should be cited (e.g., papers, datasets, software)? Do references in the text use the proper citation syntax?

Review checklist for @amoeba

Conflict of interest

• [x] I confirm that I have read the JOSS conflict of interest (COI) policy and that: I have no COIs with reviewing this work or that any perceived COIs have been waived by JOSS for the purpose of this review.

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] Contribution and authorship: Has the submitting author (@cimentadaj) 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 functionality 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] Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
• [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] State of the field: Do the authors describe how this software compares to other commonly-used packages?
• [x] Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
• [x] References: Is the list of references complete, and is everything cited appropriately that should be cited (e.g., papers, datasets, software)? Do references in the text use the proper citation syntax?

[whedon]

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @briatte, @amoeba 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:

[majensen]

BTW, @briatte, thanks for volunteering to review! (I took you at your word...)

[briatte]

@majensen No problem. I'm planning to review the package next week, probably Thursday or Friday.

[amoeba]

Hey @majensen, @cimentadaj, I've conducted my first pass at the review checklist and things look very good overall. I have some items I'd like @cimentadaj to address so at this point my review is a conditional accept. See: https://github.com/cimentadaj/perccalc/issues/2.

[briatte]

Hi @majensen, @cimentadaj and @amoeba

I'm also done with my review: conditional accept with very minor revisions, some of which are nitpicky to the point that @cimentadaj might reasonably decide to ignore them entirely.

@amoeba -- There's a small risk that I might have accidentally checked one item on your review list. I'm very sorry for that -- please accept my apologies: I'm still learning to do JOSS reviews, plus it was early morning and I had had only one coffee (this has been fixed since).

[cimentadaj]

Hi everyone

Thanks for the reviews. I'm probably gonna check them out first week of November and finish them at that time. Is that good?

[majensen]

@cimentadaj sounds good to me. That accords with my schedule too :D
Thanks all very much!

[cimentadaj]

I've answered to all comments from both reviewers here. As I outlined there, I'm happy to review some points if they feel like their points weren't addressed.

Thank you both for reviewing the paper/package, the comments have been very helpful to ship the next version to CRAN flawlessly!

[majensen]

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

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

[majensen]

@briatte, @amoeba -- based on @cimentadaj comments at issue 2, are you guys prepared to check off the remaining boxes?
Assuming so, @cimentadaj, would you like to merge your review branch into master?

[cimentadaj]

@majensen, we're almost there. Still elucidating whether we keep/remove the example section. I think we'll have this figured out by the end of the week.

[arfon]

@whedon check references

[whedon]

Attempting to check references...

[whedon]

```Reference check summary:

OK DOIs

• None

MISSING DOIs

• https://doi.org/10.1177/2332858416657343 may be missing for title: Recent trends in income, racial, and ethnic school readiness gaps at kindergarten entry
• https://doi.org/10.1177/2332858416649593 may be missing for title: Patterns of cross-national variation in the association between income and academic achievement
• https://doi.org/10.1007/springerreference_205246 may be missing for title: Categorical data analysis
• https://doi.org/10.2307/589632 may be missing for title: Intergenerational class mobility in three Western European societies: England, France and Sweden

INVALID DOIs

• None
  ```

[amoeba]

@majensen my review is now an _Accept_ after @cimentadaj 's recent change to the paper, removing the examples, as per https://github.com/cimentadaj/perccalc/issues/2#issuecomment-558031545.

[briatte]

Same here, I'm also Accept at that stage.

[majensen]

@amoeba and @briatte thanks very much; and thanks @cimentadaj for your hard work and responsiveness.
@briatte, can you review your checklist and make sure everything is checked off; there are a couple of ticks necessary and I don't want to assume.

I will perform my final proofreading tasks - might lead to a PR - and then will make the formal recommendation.

[majensen]

(right after @cimentadaj merges the review branch...)

[majensen]

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

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

[majensen]

@cimentadaj : created https://github.com/cimentadaj/perccalc/pull/7 with some minor edits

[majensen]

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

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

[majensen]

@cimentadaj - Here are the final steps. Can I get you to create a tag for the latest master, and then archive that tag with Zenodo or similar? Then please provide the DOI from the archive in this thread. I will push the recommendation from there to the editors-in-chief.
Thanks!!

[majensen]

(BTW, here's an overview for Zenodo, if you haven't used it before: https://github.com/openjournals/joss-reviews/issues/1839#issuecomment-560048729)

[cimentadaj]

Thanks, the DOI is 10.5281/zenodo.3559855 and can be found here.

[majensen]

@openjournals/joss-eics, I recommend this paper for publication and ask that you begin the final steps. Thanks!

[danielskatz]

Thanks - will do shortly

[danielskatz]

@majensen - if you can tell whedon the archive and version, that helps the AEiC... (See https://joss.readthedocs.io/en/latest/editing.html#after-reviewers-recommend-acceptance)

[majensen]

Thanks @danielskatz will do

[majensen]

@whedon set 10.5281/zenodo.3559855 as archive

[whedon]

OK. 10.5281/zenodo.3559855 is the archive.

[majensen]

@whedon set v1.0.5 as version

[whedon]

OK. v1.0.5 is the version.

[danielskatz]

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

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

[danielskatz]

@whedon check references

[whedon]

Attempting to check references...

[whedon]

```Reference check summary:

OK DOIs

• https://doi.org/10.1177/2332858416657343 is OK
• https://doi.org/10.1177/2332858416653924 is OK
• https://doi.org/10.1177/2332858416649593 is OK
• https://doi.org/10.2307/589632 is OK

MISSING DOIs

• https://doi.org/10.1007/springerreference_205246 may be missing for title: Categorical data analysis
• https://doi.org/10.18637/jss.v045.i03 may be missing for title: mice: Multivariate Imputation by Chained Equations in R

INVALID DOIs

• None
  ```

[danielskatz]

👋 @cimentadaj - please add the DOI (https://doi.org/10.18637/jss.v045.i03) for the van Buuren paper to you bib file. Also, should there be some link for the reference to Ordinal?

[cimentadaj]

Thanks @danielskatz, should be fixed now for the van Buuren paper and the Agresti book.

[danielskatz]

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

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

[danielskatz]

@whedon check references

[whedon]

Attempting to check references...

[whedon]

```Reference check summary:

OK DOIs

• https://doi.org/10.1177/2332858416657343 is OK
• https://doi.org/10.1177/2332858416653924 is OK
• https://doi.org/10.1177/2332858416649593 is OK
• 10.1002/0470114754 is OK
• https://doi.org/10.2307/589632 is OK
• https://doi.org/10.18637/jss.v045.i03 is OK

MISSING DOIs

• None

INVALID DOIs

• None
  ```

[danielskatz]

There are a number of other small changes, which I've suggested fixes for in https://github.com/cimentadaj/perccalc/pull/8 - please merge, or let me know which you disagree with.

[danielskatz]

👋 @briatte - There are a number of checkboxes that you didn't check. Can you check them please, or explain why they can't yet be checked?

[danielskatz]

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

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

[majensen]

Hey @briatte, sorry, we need you to check off the rest of the boxes on your review - thanks

[majensen]

@danielskatz : My guess is @briatte is OOO, since he is usu. very responsive. In view of comment from @briatte 's comment at https://github.com/openjournals/joss-reviews/issues/1796#issuecomment-558501728 and previous, I would recommend moving forward with the publication.

[danielskatz]

If you are sure this is ok, please check the missing box for @briatte, then let me know, and I will do the further processing in the next 24 hours.

[majensen]

@danielskatz boxes checked thanks

[danielskatz]

@whedon accept

[whedon]

Attempting dry run of processing paper acceptance...

[whedon]

```Reference check summary:

OK DOIs

• https://doi.org/10.1177/2332858416657343 is OK
• https://doi.org/10.1177/2332858416653924 is OK
• https://doi.org/10.1177/2332858416649593 is OK
• 10.1002/0470114754 is OK
• https://doi.org/10.2307/589632 is OK
• https://doi.org/10.18637/jss.v045.i03 is OK

MISSING DOIs

• None

INVALID DOIs

• None
  ```

[whedon]

Check final proof :point_right: https://github.com/openjournals/joss-papers/pull/1164

If the paper PDF and Crossref deposit XML look good in https://github.com/openjournals/joss-papers/pull/1164, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.
@whedon accept deposit=true

[danielskatz]

@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/1165
2. Wait a couple of minutes to verify that the paper DOI resolves https://doi.org/10.21105/joss.01796
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...

[danielskatz]

Thanks to @briatte and @amoeba for reviewing and @majensen for editing!
And congratulations to @cimentadaj!

[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.01796/status.svg)](https://doi.org/10.21105/joss.01796)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.01796">
  <img src="https://joss.theoj.org/papers/10.21105/joss.01796/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.01796/status.svg
   :target: https://doi.org/10.21105/joss.01796

This is how it will look in your documentation:

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[cimentadaj]

Thanks to everyone for the great review!