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[REVIEW]: perccalc: An R package for estimating percentiles from categorical variables #1796

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whedon opened this issue Oct 10, 2019 · 47 comments
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@whedon whedon commented Oct 10, 2019

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

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/6aa957144bec59d3c1b02aa945ed9468"><img src="https://joss.theoj.org/papers/6aa957144bec59d3c1b02aa945ed9468/status.svg"></a>
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

  • 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

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?
  • 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

  • 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 functionality 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

  • Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
  • A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
  • State of the field: Do the authors describe how this software compares to other commonly-used packages?
  • Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
  • 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

  • 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

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?
  • 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

  • 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 functionality 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

  • Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
  • A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
  • State of the field: Do the authors describe how this software compares to other commonly-used packages?
  • Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
  • 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?
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@whedon whedon commented Oct 10, 2019

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 🎉.

⭐️ 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

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
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@whedon whedon commented Oct 10, 2019

Attempting PDF compilation. Reticulating splines etc...
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@whedon whedon commented Oct 10, 2019

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@majensen majensen commented Oct 10, 2019

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

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@briatte briatte commented Oct 10, 2019

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

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@amoeba amoeba commented Oct 19, 2019

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: cimentadaj/perccalc#2.

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@briatte briatte commented Oct 21, 2019

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).

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@cimentadaj cimentadaj commented Oct 22, 2019

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?

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@majensen majensen commented Oct 22, 2019

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

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@cimentadaj cimentadaj commented Nov 8, 2019

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!

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@majensen majensen commented Nov 9, 2019

@whedon generate pdf

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@whedon whedon commented Nov 9, 2019

Attempting PDF compilation. Reticulating splines etc...
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@whedon whedon commented Nov 9, 2019

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@majensen majensen commented Nov 13, 2019

@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?

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@cimentadaj cimentadaj commented Nov 13, 2019

@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.

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@arfon arfon commented Nov 13, 2019

@whedon check references

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@whedon whedon commented Nov 13, 2019

Attempting to check references...
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@whedon whedon commented Nov 13, 2019


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
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@amoeba amoeba commented Nov 25, 2019

@majensen my review is now an Accept after @cimentadaj 's recent change to the paper, removing the examples, as per cimentadaj/perccalc#2 (comment).

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@briatte briatte commented Nov 26, 2019

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

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@majensen majensen commented Nov 28, 2019

@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.

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@majensen majensen commented Nov 28, 2019

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

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@majensen majensen commented Nov 28, 2019

@whedon generate pdf

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@whedon whedon commented Nov 28, 2019

Attempting PDF compilation. Reticulating splines etc...
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@whedon whedon commented Nov 28, 2019

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@majensen majensen commented Nov 28, 2019

@cimentadaj : created cimentadaj/perccalc#7 with some minor edits

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@majensen majensen commented Nov 29, 2019

@whedon generate pdf

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@whedon whedon commented Nov 29, 2019

Attempting PDF compilation. Reticulating splines etc...
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@whedon whedon commented Nov 29, 2019

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@majensen majensen commented Nov 29, 2019

@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!!

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@majensen majensen commented Dec 1, 2019

(BTW, here's an overview for Zenodo, if you haven't used it before: #1839 (comment))

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@cimentadaj cimentadaj commented Dec 2, 2019

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

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@majensen majensen commented Dec 2, 2019

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

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@danielskatz danielskatz commented Dec 2, 2019

Thanks - will do shortly

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@danielskatz danielskatz commented Dec 2, 2019

@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)

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@majensen majensen commented Dec 2, 2019

Thanks @danielskatz will do

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@majensen majensen commented Dec 2, 2019

@whedon set 10.5281/zenodo.3559855 as archive

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@whedon whedon commented Dec 2, 2019

OK. 10.5281/zenodo.3559855 is the archive.

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@majensen majensen commented Dec 2, 2019

@whedon set v1.0.5 as version

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@whedon whedon commented Dec 2, 2019

OK. v1.0.5 is the version.

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@danielskatz danielskatz commented Dec 2, 2019

@whedon generate pdf

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@whedon whedon commented Dec 2, 2019

Attempting PDF compilation. Reticulating splines etc...
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@whedon whedon commented Dec 2, 2019

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@danielskatz danielskatz commented Dec 2, 2019

@whedon check references

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@whedon whedon commented Dec 2, 2019

Attempting to check references...
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@whedon whedon commented Dec 2, 2019


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
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@danielskatz danielskatz commented Dec 2, 2019

👋 @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?

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