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

editorialbot commented 1 year ago

Submitting author: !--author-handle-->@maximelenormand@crvernon<!--end-editor-- Reviewers: @kanishkan91, @MAnalytics Archive: 10.5281/zenodo.8183755

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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 commented 1 year ago

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

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editorialbot commented 1 year ago

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
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TeX                              1              6              0             56
Markdown                         1              7              0             50
YAML                             1              1              4             18
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SUM:                             3             14              4            124
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gitinspector failed to run statistical information for the repository

editorialbot commented 1 year ago

Wordcount for paper.md is 357

editorialbot commented 1 year ago

Failed to discover a valid open source license

editorialbot commented 1 year ago

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 commented 1 year ago

👋 @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 https://github.com/openjournals/joss-reviews/issues/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 commented 1 year ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

crvernon commented 1 year ago

:wave: - 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 commented 1 year ago

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

kanishkan91 commented 1 year ago

Review checklist for @kanishkan91

Conflict of interest

[x] 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

[x] I confirm that I read and will adhere to the JOSS code of conduct.

General checks

[x] Repository: Is the source code for this software available at the https://github.com/EpiVec/TDLM?
[x] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
[x] 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?
[x] Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines
[x] 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.
[x] Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
[x] 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

[x] Installation: Does installation proceed as outlined in the documentation?
[x] Functionality: Have the functional claims of the software been confirmed?
[x] 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

[x] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
[x] Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
[x] Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
[x] Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
[x] Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
[x] 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

[x] Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
[x] 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?
[x] State of the field: Do the authors describe how this software compares to other commonly-used packages?
[x] Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
[x] 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 commented 1 year ago

Review checklist for @MAnalytics

Conflict of interest

[x] 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

[x] I confirm that I read and will adhere to the JOSS code of conduct.

General checks

[x] Repository: Is the source code for this software available at the https://github.com/EpiVec/TDLM?
[x] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
[x] 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?
[x] Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines
[x] 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.
[x] Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
[x] 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

[x] Installation: Does installation proceed as outlined in the documentation?
[x] Functionality: Have the functional claims of the software been confirmed?
[x] 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

[x] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
[x] Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
[x] Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
[x] Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
[x] Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
[x] 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

[x] Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
[x] 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?
[x] State of the field: Do the authors describe how this software compares to other commonly-used packages?
[x] Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
[x] 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 commented 1 year ago

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

crvernon commented 1 year ago

👋 - 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 commented 1 year ago

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

kanishkan91 commented 1 year ago

@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- https://github.com/EpiVec/TDLM/issues/3 2. Problems installing- I had a few problems installing this package. This is referenced here- https://github.com/EpiVec/TDLM/issues/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- https://github.com/EpiVec/TDLM/issues/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- https://github.com/EpiVec/TDLM/issues/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 commented 1 year ago

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

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.
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.
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.
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.

kanishkan91 commented 1 year ago

@cvernon I have completed my review (As can be seen from the issues opened). @maximelenormand has already started addressing several of these issues (Thanks a ton!). Once all issues are addressed, I'm happy to clear for publication. This is clearly a very useful software.

MAnalytics commented 1 year ago

@editorialbot commands

editorialbot commented 1 year ago

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


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@editorialbot check references

# Perform checks on the repository
@editorialbot check repository

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

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MAnalytics commented 1 year ago

@editorialbot check references

editorialbot commented 1 year ago

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

MAnalytics commented 1 year ago

@editorialbot generate pdf

editorialbot commented 1 year ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

MAnalytics commented 1 year ago

@maximelenormand @kanishkan91 @crvernon

Please, try and run googpractice::gp() and fix some minor styling issues. e.g.,

using '=' instead of '<-'
try and truncate long code lines, etc.

Then I can resume my review from there.

maximelenormand commented 1 year ago

@MAnalytics @crvernon Thank you for accepting to review my package. I run goodpractice::gp() and fixed some styling issues.

MAnalytics commented 1 year ago

@maximelenormand @crvernon Sorry for the delay. It's been very difficult installing the package on Windows OS. Even after following @kanishkan91 suggestions, it's still proving difficult.

maximelenormand commented 1 year ago

@MAnalytics @crvernon Could you please elaborate on the difficulties that you encountered while installing the package? I installed it on several virtual windows machine and also asked different colleagues to do it (both the CRAN and the GitHub versions) and I've never encountered any problem.

MAnalytics commented 1 year ago

@editorialbot generate pdf

editorialbot commented 1 year ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

MAnalytics commented 1 year ago

As for the installation, apologies it was my PC acting out! This is a very nice package and I think would be useful in transportation research! No major issues (separate from the ones already highlighted by @kanishkan91) are identified! But would like to emphasise two minor revisions:

Provide a section in the paper describing the software structure, or the main functions of the software.
Describe how the software compare with the existing software, and if none exist, this should be emphasized as a major contribution of the paper. @crvernon I will be happy to recommend the paper for publication as soon as these two issues are addressed.

MA.

maximelenormand commented 1 year ago

@MAnalytics @kanishkan91 @crvernon Thanks a lot for your reviews. I've just updated the paper by adding a package "Functionality" section describing the main functions of the package. I also added a description and limitations of existing R packages in the "Statement of need" section. Thanks again for the suggestions.

kanishkan91 commented 1 year ago

@whedon generate pdf

editorialbot commented 1 year ago

My name is now @editorialbot

kanishkan91 commented 1 year ago

@editorialbot generate pdf

editorialbot commented 1 year ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

kanishkan91 commented 1 year ago

@maximelenormand Looks great! I checked off the last item.

@crvernon All looks good from my side. I approve for publication.

MAnalytics commented 1 year ago

@crvernon I will also like to approve the paper for publication! Congrats to @maximelenormand

danielskatz commented 1 year ago

@crvernon - it looks like this is ready to proceed?

crvernon commented 1 year ago

@danielskatz yes, I will run through my part this weekend. Thanks!

crvernon commented 1 year ago

@editorialbot check references

editorialbot commented 1 year ago

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

OK DOIs

- 10.5281/zenodo.5171373 is OK

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
- 10.21105/joss.01038 may be a valid DOI for title: Gravity: Estimation Methods for Gravity Models in R

INVALID DOIs

- None

crvernon commented 1 year ago

@editorialbot generate pdf

editorialbot commented 1 year ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

crvernon commented 1 year ago

:wave: @maximelenormand - you are almost there! Here are a few comments from me that I need you to take a look at before we can move forward:

LINES 8-10: Your sentence "Interactions between locations can take several forms, population movements, widely studied in geography, transportation research and urban planning is one of them." is a bit confusing. Perhaps rework this to be something like the following: "Several forms of interaction can occur between locations, one of which is population movements. This particular interaction is widely examined in the fields of geography, transportation research, and urban planning."
LINE 11: "better known as Origin-Destination (OD) matrix" is missing a an so it should read "better known as an Origin-Destination (OD) matrix"
LINE 17: "TDML an R package proposing a set of" should be "TDML an R package providing a set of"
LINE 22: Missing an "s" so "...probability that an individual move from one..." should be "probability that an individual moves from one..."
LINE 24: You may want to find a better word for "dissociated" which usually is used in the context of human cognitive behavior
LINE 41-43: Additional commas not necessary. Instead state: "To overcome these limitations, the TDML R package is based on a two-step approach to generate mobility flows by separating the trip distribution law and gravity or intervening opportunities from the modeling approach used to generate the flows from this law."
LINE 46-47: "...from US Kansas in 2000." should instead be "...from Kansas in the United States for the year 2000."

Additionally, you are missing DOI for the following references and several others, please check these to make sure they use a DOI where available:

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
10.21105/joss.01038 may be a valid DOI for title: Gravity: Estimation Methods for Gravity Models in R

Thanks!

maximelenormand commented 1 year ago

@crvernon Thank you for these suggestions. I have just updated the paper.

crvernon commented 1 year ago

@editorialbot check references

editorialbot commented 1 year ago

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

crvernon commented 1 year ago

@editorialbot generate pdf

editorialbot commented 1 year ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

crvernon commented 1 year ago

Thank you @maximelenormand !

I am going to move forward with getting this paper ready for acceptance.

We want to make sure the archival has the correct metadata that JOSS requires. This includes a title that matches the paper title and a correct author list.

So here is what we have left to do:

[ ] Conduct a GitHub release of the current reviewed version of the software you now have on the main and archive the reviewed software in Zenodo or a similar service (e.g., figshare, an institutional repository)
[ ] Check the archival deposit (e.g., in Zenodo) to ensure it has the correct metadata. This includes the title (should match the paper title) and author list (make sure the list is correct and people who only made a small fix are not on it). You may also add the authors' ORCID.
[ ] Please list the DOI of the archived version here

I can then move forward with accepting the submission.

openjournals / joss-reviews