[REVIEW]: Deident: An R package for data anonymization 1 #7157

editorialbot · 2024-08-29T09:55:45Z

Submitting author: @Stat-Cook (Robert Cook)
Repository: https://github.com/Stat-Cook/deident
Branch with paper.md (empty if default branch):
Version: 1.1.1
Editor: @spholmes
Reviewers: @PatrickRWright, @nrennie
Archive: 10.6084/m9.figshare.28033418

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The text was updated successfully, but these errors were encountered:

editorialbot · 2024-08-29T09:55:48Z

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editorialbot · 2024-08-29T09:56:05Z

Software report:

github.com/AlDanial/cloc v 1.90  T=0.05 s (2378.7 files/s, 253299.2 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
HTML                            46           1362            158           6457
R                               55            624            921           1734
CSS                              3             98             52            442
XML                              2              0              0            295
JavaScript                       3             64             32            256
CSV                              2              0              0            202
Markdown                         4             54              0            187
TeX                              3             14              0            118
YAML                             5              2              4             70
Rmd                              4            141            287             44
SVG                              1              0              1             11
-------------------------------------------------------------------------------
SUM:                           128           2359           1455           9816
-------------------------------------------------------------------------------

Commit count by author:

    92	Rob
    17	Robert Cook

editorialbot · 2024-08-29T09:56:09Z

Paper file info:

📄 Wordcount for paper.md is 1060

✅ The paper includes a Statement of need section

editorialbot · 2024-08-29T09:56:11Z

License info:

🟡 License found: Other (Check here for OSI approval)

editorialbot · 2024-08-29T09:57:30Z

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

spholmes · 2024-08-29T10:00:47Z

Hi @Stat-Cook:
The paper format is a bit off, could you put the references in their own section, as it stands they appear in the acknowledgements.
Thanks
Susan

Stat-Cook · 2024-08-29T10:07:41Z

@spholmes Sure - is there a github command to produce the article proof? Might take a couple of generations.
Nevermind - it turns out if I read I find out.

Stat-Cook · 2024-08-29T10:09:35Z

@editorialbot generate pdf

editorialbot · 2024-08-29T10:10:57Z

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

Stat-Cook · 2024-08-29T10:20:31Z

@spholmes references are fixed.

PatrickRWright · 2024-08-29T10:50:00Z

Review checklist for @PatrickRWright

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 https://github.com/Stat-Cook/deident?
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 (@Stat-Cook) 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?

PatrickRWright · 2024-08-29T10:53:42Z

"Contribution and authorship": I can't judge the contribution of the authors aside from @Stat-Cook since they do not appear in the commit history of the software. I suggest stating individual contributions in a dedicated section of the paper.

PatrickRWright · 2024-08-29T11:41:24Z

"Worked Example" link here is broken: https://raw.githubusercontent.com/Stat-Cook/deident/master/README.md

PatrickRWright · 2024-08-29T11:53:11Z

For the sake of reprocuding the examples such as e.g. https://stat-cook.github.io/deident/articles/worked_example.html I suggest using a seed and explaining when it is useful an when not in the context of the package.

PatrickRWright · 2024-08-29T12:01:07Z

"Research in the discipline of health data is of increasing interest due to the perception that artificial intelligence (AI) and machine learning (ML) techniques have the promise to bridge gaps in the large, resource-limited sector."
--> I find this sentence too restrictive. "Research in the discipline of health data" has likely always been somewhat equally interesting. I don't see that people care more about health data today (where we have new AI tools) than they may have ten years ago. The current advancements in AI and ML are just adding additional facets to the analytical portfolio.

PatrickRWright · 2024-08-29T12:03:04Z

"This implementation of the “deident” methods is in R, chosen due to the increase" --> increased

Stat-Cook · 2024-08-29T12:16:01Z

"Worked Example" link here is broken: https://raw.githubusercontent.com/Stat-Cook/deident/master/README.md

Should now be fixed.

Stat-Cook · 2024-08-29T12:21:16Z

@PatrickRWright I've added a few issues to the repository - to help with response would you mind either adding to them or opening new issues with amendments/ suggestions?

PatrickRWright · 2024-08-29T12:25:59Z

I'm not sure if that's in line with the rules here since the journal will lose control.

PatrickRWright · 2024-08-29T12:27:27Z

It would be nice to have vignette-stlye examples for all mentioned de-identification methods.

Stat-Cook · 2024-08-29T12:28:20Z

@PatrickRWright I believe it was what I was asked to do for my last review but it has been a while. @spholmes is there any problem with raising issues as part of the review?

PatrickRWright · 2024-08-29T12:29:16Z

"Current applications" -> Is there any citable output from "NuRS and AmreS research projects" that could be mentioned here?

PatrickRWright · 2024-08-29T12:32:03Z

Are there really no other R packages attempting this? I do not know but find it hard to believe.

spholmes · 2024-08-29T12:32:20Z

@PatrickRWright I believe it was what I was asked to do for my last review but it has been a while. @spholmes is there any problem with raising issues as part of the review?

Yes absolutely, we encourage this way of going about things:
openjournals/joss#163
Thanks

editorialbot · 2025-01-17T19:54:10Z

Attempting dry run of processing paper acceptance...

editorialbot · 2025-01-17T19:54:29Z

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

✅ OK DOIs

- 10.1016/S0262-4079(19)31555-6 is OK
- 10.1038/s41746-019-0103-3 is OK
- 10.1038/s41551-018-0305-z is OK
- 10.1145/3406601.3406627 is OK
- 10.32614/cran.package.digest is OK
- 10.1007/11426639_2 is OK
- 10.1007/978-94-024-2174-3_5 is OK
- 10.6028/NIST.IR.8053 is OK
- 10.21105/joss.01686 is OK
- 10.32614/cran.package.babynames is OK

🟡 SKIP DOIs

- 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: Thinking on its own: AI in the NHS
- No DOI given, and none found for title: Ethics in research with human participants.
- No DOI given, and none found for title: Framework for Research Ethics
- No DOI given, and none found for title: What is Personal Information: a guide
- No DOI given, and none found for title: Anonymizer: Anonymize data containing personally i...
- No DOI given, and none found for title: Deidentifyr
- No DOI given, and none found for title: Anonymisation: managing data protection risk code ...
- No DOI given, and none found for title: 6 Steps for Data Pseudonymization

❌ MISSING DOIs

- None

❌ INVALID DOIs

- None

editorialbot · 2025-01-17T19:55:41Z

👋 @openjournals/dsais-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#6343, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

spholmes · 2025-01-17T21:05:17Z

👋 @crvernon, I think this could go to the next level, I checked the references and DOIs, I think they are now sorted

crvernon · 2025-01-21T14:28:40Z

editorialbot · 2025-01-21T14:30:35Z

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

crvernon · 2025-01-21T14:48:07Z

👋 @Stat-Cook - I just need you to address the following before I move to accept this for publication:

In the archive:

The name of your archive should match the name of the paper exactly. Please edit the archive title to match.
Currently, the declared version that you want published is 1.1.0, but your software release and the archive is 1.1.1. I am assuming that you want 1.1.1 to be the version that is published?

In the paper:

LINES 43-45: I find the use of forward slashes in these sentences awkward. Please replace with "or" or something similar. For example, "...the option to serialize or define the pipeline..."
LINE 96: "r" as in the R programming language should be capitalized. To maintain formatting in your bib file, place characters you wish to maintain formatting of in curly brackets.

No need to make a new release after these changes. Let me know when they have been addressed and I'll accept this for publication. Thanks.

Stat-Cook · 2025-01-21T15:38:20Z

@editorialbot generate pdf

editorialbot · 2025-01-21T15:39:46Z

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

Stat-Cook · 2025-01-21T15:42:18Z

@crvernon I've made the changes but they aren't displaying on the proof (above). Do we need to change the version first?

crvernon · 2025-01-21T16:01:06Z

@editorialbot generate pdf

editorialbot · 2025-01-21T16:02:41Z

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

crvernon · 2025-01-21T16:06:48Z

@Stat-Cook - I see the changes in your paper in the above. Now I just need a confirmation of the version number and the changes requested to the archive.

Stat-Cook · 2025-01-21T16:16:39Z

@crvernon Oh brilliant.

Version - Yes, can we please move to 1.1.1?

The figshare archive should now be updated with a new doi: 10.6084/m9.figshare.28033418

crvernon · 2025-01-21T16:17:49Z

@editorialbot set 1.1.1 as version

editorialbot · 2025-01-21T16:17:51Z

Done! version is now 1.1.1

crvernon · 2025-01-21T16:19:33Z

@editorialbot set 10.6084/m9.figshare.28033418 as archive

editorialbot · 2025-01-21T16:19:36Z

Done! archive is now 10.6084/m9.figshare.28033418

crvernon · 2025-01-21T16:19:43Z

@editorialbot accept

editorialbot · 2025-01-21T16:19:45Z

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

editorialbot · 2025-01-21T16:26:39Z

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: Cook
  given-names: Robert M.
  orcid: "https://orcid.org/0000-0003-3343-8271"
- family-names: Asaduzzaman
  given-names: Md
  orcid: "https://orcid.org/0000-0002-8885-6721"
- family-names: Jones
  given-names: Sarahjane
  orcid: "https://orcid.org/0000-0003-4729-4029"
doi: 10.6084/m9.figshare.28033418
message: If you use this software, please cite our article in the
  Journal of Open Source Software.
preferred-citation:
  authors:
  - family-names: Cook
    given-names: Robert M.
    orcid: "https://orcid.org/0000-0003-3343-8271"
  - family-names: Asaduzzaman
    given-names: Md
    orcid: "https://orcid.org/0000-0002-8885-6721"
  - family-names: Jones
    given-names: Sarahjane
    orcid: "https://orcid.org/0000-0003-4729-4029"
  date-published: 2025-01-21
  doi: 10.21105/joss.07157
  issn: 2475-9066
  issue: 105
  journal: Journal of Open Source Software
  publisher:
    name: Open Journals
  start: 7157
  title: "Deident: An R package for data anonymization"
  type: article
  url: "https://joss.theoj.org/papers/10.21105/joss.07157"
  volume: 10
title: "Deident: An R package for data anonymization"

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.

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editorialbot · 2025-01-21T16:26:44Z

🐘🐘🐘 👉 Toot for this paper 👈 🐘🐘🐘

editorialbot · 2025-01-21T16:26:44Z

🦋🦋🦋 👉 Bluesky post for this paper 👈 🦋🦋🦋

editorialbot · 2025-01-21T16:26:45Z

🚨🚨🚨 THIS IS NOT A DRILL, YOU HAVE JUST ACCEPTED A PAPER INTO JOSS! 🚨🚨🚨

Here's what you must now do:

Check final PDF and Crossref metadata that was deposited 👉 Creating pull request for 10.21105.joss.07157 joss-papers#6354
Wait five minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.07157
If everything looks good, then close this review issue.
Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

crvernon · 2025-01-21T16:46:20Z

🥳 Congratulations on your new publication @Stat-Cook! Many thanks to @spholmes for editing and @PatrickRWright and @nrennie for your time, hard work, and expertise!! JOSS wouldn't be able to function nor succeed without your efforts.

Please consider becoming a reviewer for JOSS if you are not already: https://reviewers.joss.theoj.org/join

editorialbot · 2025-01-21T16:46:22Z

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editorialbot added R review TeX Track: 5 (DSAIS) Data Science, Artificial Intelligence, and Machine Learning labels Aug 29, 2024

editorialbot assigned spholmes Aug 29, 2024

editorialbot mentioned this issue Aug 29, 2024

[PRE REVIEW]: Deident: An R package for data anonymization 1 #7078

Closed

editorialbot added the recommend-accept Papers recommended for acceptance in JOSS. label Jan 17, 2025

editorialbot added accepted published Papers published in JOSS labels Jan 21, 2025

crvernon closed this as completed Jan 21, 2025

[REVIEW]: Deident: An R package for data anonymization 1 #7157

[REVIEW]: Deident: An R package for data anonymization 1 #7157

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Review checklist for @PatrickRWright

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Documentation

Software paper

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