[REVIEW]: TDLM: An R package for a systematic comparison of trip distribution laws and models

[editorialbot]

Submitting author: @maximelenormand (Maxime Lenormand)
Repository: https://github.com/EpiVec/TDLM
Branch with paper.md (empty if default branch): joss
Version: v0.1.1
Editor: @crvernon
Reviewers: @kanishkan91, @MAnalytics
Archive: 10.5281/zenodo.8183755

Status

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Markdown: [![status](https://joss.theoj.org/papers/a117e7eaed38f373fda366bf900f4f02/status.svg)](https://joss.theoj.org/papers/a117e7eaed38f373fda366bf900f4f02)

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

@kanishkan91 & @MAnalytics, 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 @crvernon 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 @kanishkan91

📝 Checklist for @MAnalytics

[editorialbot]

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[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.88  T=0.01 s (511.0 files/s, 24186.4 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
TeX                              1              6              0             56
Markdown                         1              7              0             50
YAML                             1              1              4             18
-------------------------------------------------------------------------------
SUM:                             3             14              4            124
-------------------------------------------------------------------------------


gitinspector failed to run statistical information for the repository

[editorialbot]

Wordcount for paper.md is 357

[editorialbot]

Failed to discover a valid open source license

[editorialbot]

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

OK DOIs

- None

MISSING DOIs

- 10.1038/nature10856 may be a valid DOI for title: A universal model for mobility and migration patterns
- 10.1038/srep05662 may be a valid DOI for title: Limits of Predictability in Commuting Flows in the Absence of Data for Calibration
- 10.1371/journal.pone.0045985 may be a valid DOI for title: A Universal Model of Commuting Networks
- 10.1103/physreve.88.022812 may be a valid DOI for title: Gravity versus radiation models: On the importance of scale and heterogeneity in commuting flows

INVALID DOIs

- None

[crvernon]

👋 @maximelenormand , @kanishkan91 , and @MAnalytics - This is the review thread for the paper. All of our communications will happen here from now on.

Please read the "Reviewer instructions & questions" in the first comment above.

Both reviewers have checklists at the top of this thread (in that first comment) with the JOSS requirements. 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 and pull requests on the software repository. When doing so, please mention #5434 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 the review process to be completed within about 4-6 weeks but please make a start well ahead of this as JOSS reviews are by their nature iterative and any early feedback you may be able to provide to the author will be very helpful in meeting this schedule.

[editorialbot]

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

[crvernon]

👋 - Hello @kanishkan91 and @MAnalytics !

I've noticed that neither of you have a checklist generated for the review yet. Please let me know if you need help with this! Also, please provide an update on your timeline for completion of this review.

Have a great day!

[kanishkan91]

@crvernon Just started my review on this. Should be done in two weeks time. Thanks. I'l just generate my checklist now.

[kanishkan91]

Review checklist for @kanishkan91

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/EpiVec/TDLM?
• 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 (@maximelenormand) 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?

[MAnalytics]

Review checklist for @MAnalytics

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/EpiVec/TDLM?
• 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 (@maximelenormand) 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?

[MAnalytics]

@crvernon checklist generated! My reviews should also be ready in two weeks! Cheers.

[crvernon]

👋 - Hello @kanishkan91 and @MAnalytics !

Just checking in to see how things are going. Please provide an update on your review here. Thanks!

Have a great day!

[kanishkan91]

@crvernon Still working on my review. Should be done this week.

[kanishkan91]

@crvernon @maximelenormand. I'm going through my review and have been opening issues that the author can start addressing. However, I would like to raise a couple of points here sonner rather than later.

1. Lack of test cases- I could not find any test cases for this package. I think this is one of the requirements prior to publication in JOSS. I would recommend the author adds test cases and ensures atleast 60% of the lines of code are covered by a test . This is referenced in this issue- EpiVec/TDLM#3
2. Problems installing- I had a few problems installing this package. This is referenced here- EpiVec/TDLM#9. I traced this issue to a simple fix, which is that the DESCRIPTION file does not impose any version constrains on the dependencies. So, even though I am working with the correct version of R (greater than 4.0.0), the installation seems to fail since the package seems to want the latest for all packages (some of which require a higher version of R). This is referenced in another issue- EpiVec/TDLM#8.
3. Related issue with readr version- I guess this is an example of the issue listed above. A wrong version of the readr package can lead to errors such as the one pasted below (Atleast I think this is related to package versions). I am using readr version 1.4.0. The version should be clarified in the DESCRIPTION file. Note that the error below occurs because the progress parameter is deprecated in the latest version of readr.

4. No windows/Ubuntu build on workflows- Maybe I am missing something but I could not see a workflow for a windows build or Ubuntu build here. Is that correct? If so, those should be added. This is described in another issue here- EpiVec/TDLM#5

I have opened other issues as well, but these are some of the bigger ones that may take some time addressing. Hence wanted to highlight right away. Please let me know if I missed anything in the above.

[maximelenormand]

@crvernon @kanishkan91. Thank you for accepting to review my package. I started to address @kanishkan91's concerns.

1. The package contains several controls to check the arguments and inputs format. All the functions are documented and automated tested in the examples and in the vignette during the R-CMD-check performed with GitHub Actions on windows, mac and ubuntu. Based on that, the "test process" seems to be between OK and Good according to JOSS Review criteria (https://joss.readthedocs.io/en/latest/review_criteria.html). I am OK to add more automated tests and a badge to rigorously quantify the amount of codes covered by the tests but this may take time.

2. It seems that you are using old versions of the R packages needed to run and install TDLM. I followed the CRAN recommendation by not specifying exact versions and not specifying unnecessarily conservative and inconvenient minimal versions. I will try to go through the imports one by one to identify a minimal version.

3. The "process" argument was added in version 2.0.0 of readr (published in July 2021). I added a minimal version for readr (>= 2.0.0) in the description file. It is not easy to identify the relevant (and not too conservative) minimal version for the six TDLM's dependencies but as mentioned in 2. I will do my best to identify a minimal version for each of them.

4. I am using GitHub actions to perform R-CMD-check on windows, mac and ubuntu. I followed your suggestion and added a badge to the repo.

[crvernon]

@editorialbot set 10.5281/zenodo.8183755 as archive

[editorialbot]

Done! archive is now 10.5281/zenodo.8183755

[crvernon]

@editorialbot set v0.1.1 as version

[editorialbot]

Done! version is now v0.1.1

[crvernon]

@maximelenormand - - thanks for putting together a really nice software product! Thanks to @kanishkan91 and @MAnalytics for a constructive and timely review!

I am recommending that your submission be accepted. An EIC will review this shortly and confirm final publication if all goes well.

[crvernon]

@editorialbot recommend-accept

[editorialbot]

I'm sorry human, I don't understand that. You can see what commands I support by typing:

@editorialbot commands

[crvernon]

@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

- 10.1016/j.physrep.2018.01.001 is OK
- 10.1016/j.jtrangeo.2015.12.008 is OK
- 10.1038/nature10856 is OK
- 10.1038/srep05662 is OK
- 10.1371/journal.pone.0045985 is OK
- 10.1103/physreve.88.022812 is OK
- 10.21105/joss.01038 is OK
- 10.5281/zenodo.5171373 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[editorialbot]

👋 @openjournals/csism-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#4471, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

[danielskatz]

Hi @maximelenormand - I'm the track editor who will handle the final processing of your submission. I've proofread the draft paper, and have suggested some changes in EpiVec/TDLM#13 Please merge this, or let me know what you disagree with, then we can continue to acceptance and publication.

[danielskatz]

@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

- 10.1016/j.physrep.2018.01.001 is OK
- 10.1016/j.jtrangeo.2015.12.008 is OK
- 10.1038/nature10856 is OK
- 10.1038/srep05662 is OK
- 10.1371/journal.pone.0045985 is OK
- 10.1103/physreve.88.022812 is OK
- 10.21105/joss.01038 is OK
- 10.5281/zenodo.5171373 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[editorialbot]

👋 @openjournals/csism-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#4472, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

[danielskatz]

@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: Lenormand
  given-names: Maxime
  orcid: "https://orcid.org/0000-0001-6362-3473"
doi: 10.5281/zenodo.8183755
message: If you use this software, please cite our article in the
  Journal of Open Source Software.
preferred-citation:
  authors:
  - family-names: Lenormand
    given-names: Maxime
    orcid: "https://orcid.org/0000-0001-6362-3473"
  date-published: 2023-08-11
  doi: 10.21105/joss.05434
  issn: 2475-9066
  issue: 88
  journal: Journal of Open Source Software
  publisher:
    name: Open Journals
  start: 5434
  title: "TDLM: An R package for a systematic comparison of trip
    distribution laws and models"
  type: article
  url: "https://joss.theoj.org/papers/10.21105/joss.05434"
  volume: 8
title: "TDLM: An R package for a systematic comparison of trip
  distribution laws and models"

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.05434 joss-papers#4473
1. Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.05434
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...

[danielskatz]

Congratulations to @maximelenormand (Maxime Lenormand) on your publication!!

And thanks to @kanishkan91 and @MAnalytics for reviewing, and to @crvernon for editing!
JOSS is volunteer-run, and is completely dependent on your efforts

[editorialbot]

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

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[maximelenormand]

Thanks a lot for your time!