Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

[REVIEW]: dropout: an R Package for Addressing Dropouts, Missing Values, and Sectional Challenges in Survey Data Analysis #6181

Closed
editorialbot opened this issue Jan 6, 2024 · 73 comments
Closed

[REVIEW]: dropout: an R Package for Addressing Dropouts, Missing Values, and Sectional Challenges in Survey Data Analysis #6181

editorialbot opened this issue Jan 6, 2024 · 73 comments
Assignees
@samhforbes
Labels
accepted C++ HTML published Papers published in JOSS R recommend-accept Papers recommended for acceptance in JOSS. review TeX Track: 4 (SBCS) Social, Behavioral, and Cognitive Sciences

Comments

@editorialbot
Copy link
Collaborator

editorialbot commented Jan 6, 2024 •
edited

Submitting author: @hendr1km (Hendrik Mann)
Repository: https://github.com/hendr1km/dropout
Branch with paper.md (empty if default branch):
Version: v2.1.1
Editor: @samhforbes
Reviewers: @medewitt, @max-alletsee, @Darthpathos
Archive: 10.6084/m9.figshare.25355746.v1

Status

status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/721cbec4ff9ab3a56a6ad9782d296ac6"><img src="https://joss.theoj.org/papers/721cbec4ff9ab3a56a6ad9782d296ac6/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/721cbec4ff9ab3a56a6ad9782d296ac6/status.svg)](https://joss.theoj.org/papers/721cbec4ff9ab3a56a6ad9782d296ac6)

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

@medewitt & @max-alletsee & @Darthpathos, your review will be checklist based. Each of you will have a separate checklist that you should update when carrying out your review.
First of all you need to run this command in a separate comment to create the checklist:

@editorialbot generate my checklist

The reviewer guidelines are available here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html. Any questions/concerns please let @samhforbes know.

✨ Please start on your review when you are able, and be sure to complete your review in the next six weeks, at the very latest ✨

Checklists

📝 Checklist for @max-alletsee

📝 Checklist for @Darthpathos
@editorialbot editorialbot added C++ HTML R review Track: 4 (SBCS) Social, Behavioral, and Cognitive Sciences labels Jan 6, 2024
@editorialbot editorialbot mentioned this issue Jan 6, 2024
Closed
@editorialbot
Copy link
Collaborator Author

Hello humans, I'm @editorialbot, a robot that can help you with some common editorial tasks.

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

@editorialbot commands

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

@editorialbot generate pdf

@editorialbot
Copy link
Collaborator Author 

Software report:

github.com/AlDanial/cloc v 1.88  T=0.10 s (551.2 files/s, 150720.4 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
JavaScript                       7           2148           1964           7247
HTML                            13            377             43           1351
CSS                             11            127             59            584
Markdown                         5             74              0            167
R                                7             71            123            158
C++                              3             36             15            132
TeX                              1             16              0            108
YAML                             4             21              4             90
Rmd                              2             99            174             69
XML                              1              0              0             42
SVG                              1              0              1             11
JSON                             1              0              0              1
-------------------------------------------------------------------------------
SUM:                            56           2969           2383           9960
-------------------------------------------------------------------------------


gitinspector failed to run statistical information for the repository

@editorialbot
Copy link
Collaborator Author

Wordcount for paper.md is 1724

@editorialbot
Copy link
Collaborator Author 

Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1051/0004-6361/201629272 is OK
- 10.1051/0004-6361/201322068 is OK
- 10.4097/kjae.2013.64.5.402 is OK
- 10.21105/joss.01686 is OK

MISSING DOIs

- None

INVALID DOIs

- None

@editorialbot
Copy link
Collaborator Author

👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

@samhforbes
Copy link

@medewitt, @max-alletsee, @Darthpathos this is our review thread. Please check the instructions in the first post, and follow your reviewer checklist to review. You can open issues in the software repo for anything you would like addressed, and anything you'd like to discuss feel free to bring it up here, or ping me if you'd like input from me.
Thank you all for agreeing to review.

@max-alletsee
Copy link

max-alletsee commented Jan 7, 2024 •
edited

Review checklist for @max-alletsee

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 https://github.com/hendr1km/dropout?
  • License: Does the repository contain a plain-text LICENSE or COPYING file with the contents of an OSI approved software license?
  • Contribution and authorship: Has the submitting author (@hendr1km) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
  • Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines
  • Data sharing: If the paper contains original data, data are accessible to the reviewers. If the paper contains no original data, please check this item.
  • Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
  • Human and animal research: If the paper contains original data research on humans subjects or animals, does it comply with JOSS's human participants research policy and/or animal research policy? If the paper contains no such data, please check this item.

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: Does the paper have a section titled 'Statement of need' that clearly states what problems the software is designed to solve, who the target audience is, and its relation to other work?
  • 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?

@Darthpathos
Copy link

Darthpathos commented Jan 8, 2024 via email •
edited by samhforbes

@Darthpathos
Copy link

Darthpathos commented Jan 9, 2024 via email

@danielskatz
Copy link

@Darthpathos - Your checklist is in the issue: see #6181 (comment)

@Darthpathos
Copy link

Darthpathos commented Jan 9, 2024 via email

@samhforbes
Copy link

Hi @Darthpathos, @medewitt & @max-alletsee how are reviews going? Do please let me know if there's anything I can assist with.

@medewitt
Copy link

medewitt commented Feb 21, 2024 •
edited

Review checklist for @medewitt

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 https://github.com/hendr1km/dropout?
  • License: Does the repository contain a plain-text LICENSE or COPYING file with the contents of an OSI approved software license?
  • Contribution and authorship: Has the submitting author (@hendr1km) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
  • Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines
    • Most development over 3 weeks, 3 months overall development timeline
    • Single author
    • 78 commits
    • < 300 lines of R/C++ code (i.e., non-documentation, non-autogenerated)
  • Data sharing: If the paper contains original data, data are accessible to the reviewers. If the paper contains no original data, please check this item.
  • Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
  • Human and animal research: If the paper contains original data research on humans subjects or animals, does it comply with JOSS's human participants research policy and/or animal research policy? If the paper contains no such data, please check this item.

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: Does the paper have a section titled 'Statement of need' that clearly states what problems the software is designed to solve, who the target audience is, and its relation to other work?
  • 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?

This was referenced Feb 21, 2024
Closed
Closed
Closed
Closed
Closed
@max-alletsee
Copy link

Dear @hendr1km, dear @samhforbes,

apologies that it took longer to review this submission, life got in the way (even more than I expected).

I have finished my review based on the last version of the software paper that can be found in commit 3085dae, which is slightly different from the proof above and addresses several comments made by @medewitt.

I have myself added three minor comments: #8, #9 and #11, plus a small comment that is technically outside the scope of this review but would be helpful for end users (#10).

From my perspective, all comments are minor and will be easy to fix. I applaud the author for his effort of creating this package and the accompanying paper.

This was referenced Feb 24, 2024
Closed
Closed
Closed
@editorialbot
Copy link
Collaborator Author 

Attempting dry run of processing paper acceptance...

@editorialbot
Copy link
Collaborator Author 

Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.18637/jss.v105.i07 is OK
- 10.1051/0004-6361/201629272 is OK
- 10.1051/0004-6361/201322068 is OK
- 10.4097/kjae.2013.64.5.402 is OK
- 10.21105/joss.01686 is OK

MISSING DOIs

- No DOI given, and none found for title: 41 Percent Of Fliers Think You’re Rude If You Recl...
- No DOI given, and none found for title: daqapo: Data Quality Assessment for Process-Orient...
- No DOI given, and none found for title: mde: Missing Data Explorer
- No DOI given, and none found for title: Gaps in Globular Cluster Streams: Pal 5 and the Ga...
- No DOI given, and none found for title: Galactic Dynamics: Second Edition
- No DOI given, and none found for title: Fidgit: An ungodly union of GitHub and Figshare
- No DOI given, and none found for title: Rcpp: Seamless R and C++ Integration
- No DOI given, and none found for title: R: A Language and Environment for Statistical Comp...
- No DOI given, and none found for title: dplyr: A Grammar of Data Manipulation

INVALID DOIs

- None

@editorialbot
Copy link
Collaborator Author

👋 @openjournals/sbcs-eics, this paper is ready to be accepted and published.

Check final proof 👉📄 Download article

If the paper PDF and the deposit XML files look good in openjournals/joss-papers#5146, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

@editorialbot editorialbot added the recommend-accept Papers recommended for acceptance in JOSS. label Mar 18, 2024
@oliviaguest
Copy link
Member

are those DOIs all OK? 😊

@samhforbes
Copy link

As far as I could see none of the missing ones actually had DOIs

@oliviaguest
Copy link
Member

Excellent, sorry for holding this up then. ☺️

@oliviaguest
Copy link
Member

@editorialbot recommend-accept

@editorialbot
Copy link
Collaborator Author 

Attempting dry run of processing paper acceptance...

@editorialbot
Copy link
Collaborator Author

👋 @openjournals/sbcs-eics, this paper is ready to be accepted and published.

Check final proof 👉📄 Download article

If the paper PDF and the deposit XML files look good in openjournals/joss-papers#5170, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

@editorialbot
Copy link
Collaborator Author 

Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.18637/jss.v105.i07 is OK
- 10.1051/0004-6361/201629272 is OK
- 10.1051/0004-6361/201322068 is OK
- 10.4097/kjae.2013.64.5.402 is OK
- 10.21105/joss.01686 is OK

MISSING DOIs

- No DOI given, and none found for title: 41 Percent Of Fliers Think You’re Rude If You Recl...
- No DOI given, and none found for title: daqapo: Data Quality Assessment for Process-Orient...
- No DOI given, and none found for title: mde: Missing Data Explorer
- No DOI given, and none found for title: Gaps in Globular Cluster Streams: Pal 5 and the Ga...
- No DOI given, and none found for title: Galactic Dynamics: Second Edition
- No DOI given, and none found for title: Fidgit: An ungodly union of GitHub and Figshare
- No DOI given, and none found for title: Rcpp: Seamless R and C++ Integration
- No DOI given, and none found for title: R: A Language and Environment for Statistical Comp...
- No DOI given, and none found for title: dplyr: A Grammar of Data Manipulation

INVALID DOIs

- None

@oliviaguest
Copy link
Member

@hendr1km please see: hendr1km/dropout#12 (in for a penny in for a pound, as they say) ☺️

@Darthpathos
Copy link

Darthpathos commented Mar 25, 2024 via email

@hendr1km
Copy link

@oliviaguest I have merged the commit. Thanks a lot!

@oliviaguest
Copy link
Member

@editorialbot recommend-accept

@editorialbot
Copy link
Collaborator Author 

Attempting dry run of processing paper acceptance...

@oliviaguest
Copy link
Member

@Darthpathos I assume your job is done as a reviewer since the editor recommended acceptance. ☺️

@editorialbot
Copy link
Collaborator Author

👋 @openjournals/sbcs-eics, this paper is ready to be accepted and published.

Check final proof 👉📄 Download article

If the paper PDF and the deposit XML files look good in openjournals/joss-papers#5193, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

@editorialbot
Copy link
Collaborator Author 

Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.18637/jss.v105.i07 is OK
- 10.1051/0004-6361/201629272 is OK
- 10.1051/0004-6361/201322068 is OK
- 10.4097/kjae.2013.64.5.402 is OK
- 10.21105/joss.01686 is OK

MISSING DOIs

- No DOI given, and none found for title: 41 Percent Of Fliers Think You’re Rude If You Recl...
- No DOI given, and none found for title: daqapo: Data Quality Assessment for Process-Orient...
- No DOI given, and none found for title: mde: Missing Data Explorer
- No DOI given, and none found for title: Gaps in Globular Cluster Streams: Pal 5 and the Ga...
- No DOI given, and none found for title: Galactic Dynamics: Second Edition
- No DOI given, and none found for title: Fidgit: An ungodly union of GitHub and Figshare
- No DOI given, and none found for title: Rcpp: Seamless R and C++ Integration
- No DOI given, and none found for title: R: A Language and Environment for Statistical Comp...
- No DOI given, and none found for title: dplyr: A Grammar of Data Manipulation

INVALID DOIs

- None

@oliviaguest
Copy link
Member

@editorialbot accept

@editorialbot
Copy link
Collaborator Author 

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

@editorialbot
Copy link
Collaborator Author

Ensure proper citation by uploading a plain text CITATION.cff file to the default branch of your repository.

If using GitHub, a Cite this repository menu will appear in the About section, containing both APA and BibTeX formats. When exported to Zotero using a browser plugin, Zotero will automatically create an entry using the information contained in the .cff file.

You can copy the contents for your CITATION.cff file here:

CITATION.cff 

cff-version: "1.2.0"
authors:
- family-names: Mann
  given-names: Hendrik
  orcid: "https://orcid.org/0009-0007-3222-899X"
doi: 10.6084/m9.figshare.25355746.v1
message: If you use this software, please cite our article in the
  Journal of Open Source Software.
preferred-citation:
  authors:
  - family-names: Mann
    given-names: Hendrik
    orcid: "https://orcid.org/0009-0007-3222-899X"
  date-published: 2024-03-30
  doi: 10.21105/joss.06181
  issn: 2475-9066
  issue: 95
  journal: Journal of Open Source Software
  publisher:
    name: Open Journals
  start: 6181
  title: "dropout: an R Package for Addressing Dropouts, Missing Values,
    and Sectional Challenges in Survey Data Analysis"
  type: article
  url: "https://joss.theoj.org/papers/10.21105/joss.06181"
  volume: 9
title: "dropout: an R Package for Addressing Dropouts, Missing Values,
  and Sectional Challenges in Survey Data Analysis"

If the repository is not hosted on GitHub, a .cff file can still be uploaded to set your preferred citation. Users will be able to manually copy and paste the citation.

Find more information on .cff files here and here.

@editorialbot
Copy link
Collaborator Author

🐘🐘🐘 👉 Toot for this paper 👈 🐘🐘🐘

@editorialbot
Copy link
Collaborator Author

🚨🚨🚨 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 👉 Creating pull request for 10.21105.joss.06181 joss-papers#5194
  2. Wait five minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.06181
  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...

@editorialbot editorialbot added accepted published Papers published in JOSS labels Mar 30, 2024
@oliviaguest
Copy link
Member

Huge thanks to the reviewers @medewitt, @max-alletsee, @Darthpathos and editor @samhforbes! ✨ JOSS appreciates your work and effort. ✨ Also, big congratulations to the authors, @hendr1km! 🥳 🍾

@editorialbot
Copy link
Collaborator Author

🎉🎉🎉 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.06181/status.svg)](https://doi.org/10.21105/joss.06181)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.06181">
  <img src="https://joss.theoj.org/papers/10.21105/joss.06181/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.06181/status.svg
   :target: https://doi.org/10.21105/joss.06181

This is how it will look in your documentation:

DOI

We need your help!

The 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:

@Darthpathos
Copy link

Darthpathos commented Mar 31, 2024 via email

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Assignees

@samhforbes samhforbes

Labels
accepted C++ HTML published Papers published in JOSS R recommend-accept Papers recommended for acceptance in JOSS. review TeX Track: 4 (SBCS) Social, Behavioral, and Cognitive Sciences
Projects
None yet
Milestone
No milestone
Development

No branches or pull requests
9 participants
@danielskatz @oliviaguest @max-alletsee @Darthpathos @samhforbes @medewitt @darthpathos76 @editorialbot @hendr1km