[REVIEW]: dataquieR: assessment of data quality in epidemiological research

[whedon]

Submitting author: @struckma
Repository: https://gitlab.com/libreumg/dataquier.git
Version: 1.0.6
Editor: @csoneson
Reviewers: @borishejblum, @cmirzayi
Archive: 10.5281/zenodo.4767836

⚠️ JOSS reduced service mode ⚠️

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Status

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Markdown: [![status](https://joss.theoj.org/papers/74d30b187f5756fc4f58a745014bdcda/status.svg)](https://joss.theoj.org/papers/74d30b187f5756fc4f58a745014bdcda)

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

@tgerke & @borishejblum, 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

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✨ 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 ✨

Review checklist for @borishejblum

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

• I confirm that I read and will adhere to the JOSS 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 (@) 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

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: Does the paper have a section titled 'Statement of Need' that clearly states 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 @cmirzayi

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

• I confirm that I read and will adhere to the JOSS 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 (@) 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

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: Does the paper have a section titled 'Statement of Need' that clearly states 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?

[whedon]

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

⚠️ JOSS reduced service mode ⚠️

Due to the challenges of the COVID-19 pandemic, JOSS is currently operating in a "reduced service mode". You can read more about what that means in our blog post.

⭐ 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:

2. 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]

Software report (experimental):

github.com/AlDanial/cloc v 1.88  T=1.18 s (187.1 files/s, 64271.6 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
SVG                             24              0              0          55206
R                              184           1432           3685          14463
Rmd                              7            129            245            439
Markdown                         3             49              0            186
CSS                              1              1              0             37
YAML                             2              5              1             30
-------------------------------------------------------------------------------
SUM:                           221           1616           3931          70361
-------------------------------------------------------------------------------


Statistical information for the repository 'df1cf7977be68e8e6c4388d8' was
gathered on 2021/03/08.
No commited files with the specified extensions were found.

[whedon]

PDF failed to compile for issue #3093 with the following error:

Can't find any papers to compile :-(

[csoneson]

👋🏼 @struckma, @tgerke, @borishejblum - this is the review thread for the submission. All of our communications will happen here from now on.

Both reviewers have checklists at the top of this thread. As you go over the submission, please check any items that you feel have been satisfied. There are also links to the JOSS reviewer guidelines.

The JOSS review is different from most other journals. Our goal is to work with the authors to help them meet our criteria instead of merely passing judgment on the submission. As such, the reviewers are encouraged to submit issues directly in the software repository. If you do so, please mention this thread so that a link is created (and I can keep an eye on what is happening). Please also feel free to comment and ask questions in this thread. It is often easier to post comments/questions/suggestions as you come across them instead of waiting until you've reviewed the entire package.

Please feel free to ping me (@csoneson) if you have any questions or concerns. Thanks!

[csoneson]

@whedon generate pdf from branch JOSS

[whedon]

Attempting PDF compilation from custom branch JOSS. Reticulating splines etc...

[whedon]

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

[csoneson]

👋 @tgerke, @borishejblum - just wanted to quickly check in that you have all you need for your reviews. Don't hesitate to ping me if you have any questions. Thanks!

[whedon]

👋 @tgerke, please update us on how your review is going (this is an automated reminder).

[whedon]

👋 @borishejblum, please update us on how your review is going (this is an automated reminder).

[borishejblum]

Following my review, I have 2 comments @struckma:

• the LICENSE file does not contain the necessary disclaimer (see https://opensource.org/licenses/BSD-2-Clause) BUT this is due to CRAN requirements => no action required
• "State of Need" section should be renamed "Statement of Need"

[csoneson]

@tgerke - could you update us on how your review is going?

[csoneson]

Ping @tgerke

@tgerke - could you update us on how your review is going?

[struckma]

Dear @borishejblum,

thank you for your hints so far (in #3093 (comment)). We have addressed your point about the section heading (Statement of Need), thank you for the hint. Regarding the license-disclaimer, indeed, this is because of CRAN.

I'll trigger a rebuild now.

All, have a nice weekend, thank you so far.

[struckma]

@whedon generate pdf from branch JOSS

[whedon]

Attempting PDF compilation from custom branch JOSS. Reticulating splines etc...

[danielskatz]

as you've discovered, commands to @whedon need to be the first line of a comment

[whedon]

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

[struckma]

Dear @csoneson,

thank you for being our editor. Since the review process seems to have stalled, is there something we can do about it? I don't want to be impatient, but my colleagues are asking me about progress, and I do not know how to answer? Thank you for your advice

Stephan

[csoneson]

Hi @struckma - I have reached out to @tgerke offline and sent a follow-up email today - if we don't hear back there soon I'll look for an additional reviewer to bring this forward.

@borishejblum - did you have a chance to look over the authors' modifications in response to the issues you raised?

[struckma]

Thank you very much.

[borishejblum]

@csoneson - yes, I did have a look at the authors' repsonse, and they adequatly address the issues I raised. I have no further comments.

[csoneson]

Great, thank you @borishejblum - could you please also tick off the last boxes in your checklist above?

[borishejblum]

done :-)

[csoneson]

Just to say that I have started looking for an additional reviewer here.

[whedon]

OK. 10.5281/zenodo.4767836 is the archive.

[csoneson]

@whedon set 1.0.6 as version

[whedon]

OK. 1.0.6 is the version.

[struckma]

Thank you,
I will address #3093 (comment) in the afternoon.

[struckma]

Dear @csoneson,

regarding Maechler et al., we use the official citation of that package from CRAN:

https://cran.r-project.org/web/packages/robustbase/citation.html

I have no clue, why they grouped Anna di Palma together, but maybe, this altogether is Maria's surname? Since we don't know, we would prefer to leave the original citation as it is to avoid skipping Ms Di Palma's wishes. Would that be okay for you?

The other change we have done.

Thank you.

[struckma]

@whedon generate pdf from branch JOSS

[whedon]

Attempting PDF compilation from custom branch JOSS. Reticulating splines etc...

[whedon]

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

[csoneson]

Yes, I agree (I missed the M and jumped to conclusions too quickly) - using the official citation is the right way to go! I'm going to hand this off now to the associate editor in chief on rotation who will take you through the last steps.

[csoneson]

@whedon accept

[whedon]

Attempting dry run of processing paper acceptance...

[whedon]

PDF failed to compile for issue #3093 with the following error:

 Can't find any papers to compile :-(

[csoneson]

@whedon accept from branch JOSS

[whedon]

Attempting dry run of processing paper acceptance...

[whedon]

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

Check final proof 👉 openjournals/joss-papers#2321

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#2321, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true from branch JOSS 

[whedon]

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

OK DOIs

- 10.18637/jss.v067.i01 is OK
- 10.5334/dsj-2015-002 is OK
- 10.18637/jss.v040.i03 is OK
- 10.13063/2327-9214.1244 is OK
- 10.1146/annurev-statistics-060116-054114 is OK
- 10.18637/jss.v090.i06 is OK
- 10.21105/joss.01509 is OK
- doi: 10.3205/mibe000202 is OK
- 10.21203/rs.3.rs-119457/v1 is OK
- 10.18637/jss.v032.i03 is OK
- 10.18637/jss.v021.i12 is OK
- 10.1038/sdata.2018.118 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[kyleniemeyer]

@whedon accept deposit=true from branch JOSS

Looks good to me!

[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:

0. Check final PDF and Crossref metadata that was deposited 👉 Creating pull request for 10.21105.joss.03093 joss-papers#2323
1. Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.03093
2. If everything looks good, then close this review issue.
3. Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

[kyleniemeyer]

Congratulations @struckma on your article's publication in JOSS!

Many thanks to @borishejblum and @cmirzayi for reviewing this, and @csoneson for editing.

[whedon]

🎉🎉🎉 Congratulations on your paper acceptance! 🎉🎉🎉

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[![DOI](https://joss.theoj.org/papers/10.21105/joss.03093/status.svg)](https://doi.org/10.21105/joss.03093)

HTML:
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  <img src="https://joss.theoj.org/papers/10.21105/joss.03093/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.03093/status.svg
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[struckma]

Thank all the contributors again, really a great publication experience.