[REVIEW]: verdata: An R package for analyzing data from the Truth Commission in Colombia

[editorialbot]

Submitting author: @thegargiulian (Maria Gargiulo)
Repository: https://github.com/HRDAG/verdata
Branch with paper.md (empty if default branch): joss-submission
Version: v.0.9.1
Editor: @Nikoleta-v3
Reviewers: @jamesmbaazam, @JosiahParry
Archive: 10.5281/zenodo.10359636

Status

Status badge code:

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Markdown: [![status](https://joss.theoj.org/papers/f4e966f5983888e45db2f27a1c9971d8/status.svg)](https://joss.theoj.org/papers/f4e966f5983888e45db2f27a1c9971d8)

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

@EugeneHao & @jamesmbaazam, 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 @Nikoleta-v3 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 @jamesmbaazam

📝 Checklist for @JosiahParry

[editorialbot]

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:

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

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[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.88  T=0.02 s (1464.2 files/s, 181447.8 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
R                               20            688            661           1548
Markdown                         3             79              0            129
TeX                              2              8              0             86
YAML                             1              1              4             18
-------------------------------------------------------------------------------
SUM:                            26            776            665           1781
-------------------------------------------------------------------------------


gitinspector failed to run statistical information for the repository

[editorialbot]

Wordcount for paper.md is 1168

[editorialbot]

Failed to discover a valid open source license

[editorialbot]

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

OK DOIs

- 10.1214/18-STS644 is OK
- 10.18637/jss.v045.i03 is OK
- 10.1111/biom.12502 is OK
- 10.1198/108571101750524670 is OK
- 10.1146/annurev-statistics-031017-100641 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[editorialbot]

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

[thegargiulian]

Hi @Nikoleta-v3 , thanks so much for getting this review started!

I just wanted to double check that you've assigned the right reviewers, as I remember that EugeneHao indicated that they wouldn't be available in the next few weeks in #5764. Maybe you meant to assign JosiahParry?

Thank you!

[Nikoleta-v3]

@thegargiulian, thank you very much for catching this 🤦🏻‍♀️. Indeed, I made a mistake.

My sincere apologies, @EugeneHao, for the spam! I will remove you as a reviewer now.

[Nikoleta-v3]

@editorialbot remove @EugeneHao from reviewers

[editorialbot]

@EugeneHao removed from the reviewers list!

[Nikoleta-v3]

@editorialbot add @JosiahParry as reviewer

[editorialbot]

@JosiahParry added to the reviewers list!

[Nikoleta-v3]

Hey @JosiahParry @jamesmbaazam this is the review thread for the paper. All of our communications will happen here from now on.

As a reviewer, the first step is to create a checklist for your review by entering

@editorialbot generate my checklist

as the top of a new comment in this thread.

These checklists contain the JOSS requirements ✅ As you go over the submission, please check any items that you feel have been satisfied. The first comment in this thread also contains 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 and pull requests on the software repository. When doing so, please mention #5844 so that a link is created to this thread (and I can keep an eye on what is happening). Please also feel free to comment and ask questions on this thread. In my experience, it is better to post comments/questions/suggestions as you come across them instead of waiting until you've reviewed the entire package.

We aim for reviews to be completed within about 2-4 weeks. Please let me know if any of you require some more time. We can also use EditorialBot (our bot) to set automatic reminders if you know you'll be away for a known period of time.

Please feel free to ping me (@Nikoleta-v3) if you have any questions/concerns. 😄 🙋🏻

[jamesmbaazam]

Thanks @Nikoleta-v3

[jamesmbaazam]

Review checklist for @jamesmbaazam

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/HRDAG/verdata?
• 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 (@thegargiulian) 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?

[jamesmbaazam]

@editorialbot commands

[editorialbot]

Hello @jamesmbaazam, here are the things you can ask me to do:

# List all available commands
@editorialbot commands

# Get a list of all editors's GitHub handles
@editorialbot list editors

# Check the references of the paper for missing DOIs
@editorialbot check references

# Perform checks on the repository
@editorialbot check repository

# Adds a checklist for the reviewer using this command
@editorialbot generate my checklist

# Set a value for branch
@editorialbot set joss-paper as branch

# Generates the pdf paper
@editorialbot generate pdf

# Generates a LaTeX preprint file
@editorialbot generate preprint

# Get a link to the complete list of reviewers
@editorialbot list reviewers

[JosiahParry]

Review checklist for @JosiahParry

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/HRDAG/verdata?
• 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 (@thegargiulian) 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?

[Nikoleta-v3]

@JosiahParry @jamesmbaazam 👋🏻 😄 any updates on your reviews?

[jamesmbaazam]

Hi @Nikoleta-v3, it's on my to-do list for this week/weekend. Thanks for the nudge.

[Nikoleta-v3]

Thank you for the update 😄🙏🏻

[JosiahParry]

Apologies. Will do this week.

[JosiahParry]

@thegargiulian please add a plain text license to the repository.

[JosiahParry]

I've provided a number of issues that I think need to be addressed to meet the quality of documentation required for a publication.

[editorialbot]

Attempting dry run of processing paper acceptance...

[editorialbot]

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

OK DOIs

- 10.1214/18-STS644 is OK
- 10.18637/jss.v045.i03 is OK
- 10.1111/biom.12502 is OK
- 10.1198/108571101750524670 is OK
- 10.1146/annurev-statistics-031017-100641 is OK
- 10.1017/cls.2015.24 is OK
- 10.1353/sais.2014.0010 is OK
- 10.1080/10402659.2022.2049002 is OK
- 10.31235/osf.io/vqnwu is OK

MISSING DOIs

- None

INVALID DOIs

- None

[editorialbot]

👋 @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#4830, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

[thegargiulian]

@Nikoleta-v3, so sorry! I just found a typo in footnote 2. Is it possible to fix it?

[Nikoleta-v3]

Hey @thegargiulian sure! Go ahead and change it and please let me know once you've done it.

[thegargiulian]

All done @Nikoleta-v3, thank you!

[Nikoleta-v3]

@editorialbot recommend-accept

[editorialbot]

Attempting dry run of processing paper acceptance...

[editorialbot]

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

OK DOIs

- 10.1214/18-STS644 is OK
- 10.18637/jss.v045.i03 is OK
- 10.1111/biom.12502 is OK
- 10.1198/108571101750524670 is OK
- 10.1146/annurev-statistics-031017-100641 is OK
- 10.1017/cls.2015.24 is OK
- 10.1353/sais.2014.0010 is OK
- 10.1080/10402659.2022.2049002 is OK
- 10.31235/osf.io/vqnwu is OK

MISSING DOIs

- None

INVALID DOIs

- None

[editorialbot]

👋 @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#4836, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

[JosiahParry]

Congrats! 👏🏼

[jamesmbaazam]

Congrats @thegargiulian.

[thegargiulian]

Hey @Nikoleta-v3, happy new year!

Just wondering if you had status update on this—I think we're just waiting on the EICs, but let me know if you need anything from our end. Thank you!

[oliviaguest]

@editorialbot recommend-accept

[editorialbot]

Attempting dry run of processing paper acceptance...

[editorialbot]

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

OK DOIs

- 10.1214/18-STS644 is OK
- 10.18637/jss.v045.i03 is OK
- 10.1111/biom.12502 is OK
- 10.1198/108571101750524670 is OK
- 10.1146/annurev-statistics-031017-100641 is OK
- 10.1017/cls.2015.24 is OK
- 10.1353/sais.2014.0010 is OK
- 10.1080/10402659.2022.2049002 is OK
- 10.31235/osf.io/vqnwu is OK

MISSING DOIs

- None

INVALID DOIs

- None

[editorialbot]

👋 @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#4875, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

[oliviaguest]

@editorialbot accept

[editorialbot]

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

[editorialbot]

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: Gargiulo
  given-names: Maria
  orcid: "https://orcid.org/0000-0003-1870-8990"
- family-names: Durán
  given-names: María Juliana
  orcid: "https://orcid.org/0009-0005-3720-8125"
- family-names: Amado
  given-names: Paula Andrea
  orcid: "https://orcid.org/0009-0004-0806-0857"
- family-names: Ball
  given-names: Patrick
contact:
- family-names: Gargiulo
  given-names: Maria
  orcid: "https://orcid.org/0000-0003-1870-8990"
doi: 10.5281/zenodo.10359636
message: If you use this software, please cite our article in the
  Journal of Open Source Software.
preferred-citation:
  authors:
  - family-names: Gargiulo
    given-names: Maria
    orcid: "https://orcid.org/0000-0003-1870-8990"
  - family-names: Durán
    given-names: María Juliana
    orcid: "https://orcid.org/0009-0005-3720-8125"
  - family-names: Amado
    given-names: Paula Andrea
    orcid: "https://orcid.org/0009-0004-0806-0857"
  - family-names: Ball
    given-names: Patrick
  date-published: 2024-01-06
  doi: 10.21105/joss.05844
  issn: 2475-9066
  issue: 93
  journal: Journal of Open Source Software
  publisher:
    name: Open Journals
  start: 5844
  title: "verdata: An R package for analyzing data from the Truth
    Commission in Colombia"
  type: article
  url: "https://joss.theoj.org/papers/10.21105/joss.05844"
  volume: 9
title: "verdata: An R package for analyzing data from the Truth
  Commission in Colombia"

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]

🐘🐘🐘 👉 Toot for this paper 👈 🐘🐘🐘

[editorialbot]

🚨🚨🚨 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.05844 joss-papers#4879
1. Wait five minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.05844
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...

[oliviaguest]

Huge thanks to the reviewers @jamesmbaazam, @JosiahParry and editor @Nikoleta-v3! ✨ JOSS appreciates your work and effort. ✨ Also, big congratulations to the authors @thegargiulian! 🥳 🍾

[editorialbot]

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

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HTML:
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   :target: https://doi.org/10.21105/joss.05844

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