Joss-reviews: [REVIEW]: Predihood: an open-source tool for describing and predicting neighbourhoods' environment

[whedon]

Submitting author: @fduchatea (Fabien Duchateau)
Repository: https://gitlab.liris.cnrs.fr/fduchate/predihood
Version: 1.0
Editor: @galessiorob
Reviewer: @jdalzatec, @omshinde, @nuest, @martinfleis
Archive: Pending

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Status

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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

@jdalzatec & @omshinde & @nuest & @martinfleis, 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

The reviewer guidelines are available here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html. Any questions/concerns please let @galessiorob 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 ✨

Review checklist for @jdalzatec

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

• [ ] 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 (@fduchatea) 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: 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: 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 @omshinde

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

• [ ] 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 (@fduchatea) 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: 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: 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 @nuest

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 (@fduchatea) 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: 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: 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 @martinfleis

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

• [ ] Repository: Is the source code for this software available at the repository url?
• [x] 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 (@fduchatea) 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: 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: 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. @jdalzatec, @omshinde, @nuest, @martinfleis it looks like you're currently assigned to review this paper :tada:.

:warning: JOSS reduced service mode :warning:

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.

:star: Important :star:

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:

1. 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]

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

OK DOIs

- 10.1109/socialcom.2013.17 is OK
- 10.5220/0009885702940301 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[galessiorob]

@whedon generate pdf

[whedon]

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

[whedon]

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

[galessiorob]

👋 @martinfleis, @omshinde, @nuest and @jdalzatec

Thank you all for volunteering as reviewers for this paper! At the top, you'll find individual checklists to work trough, please let me know if something is not clear or if you need any help.

[nuest]

Thanks! Just as a quick heads up, I'll likely do the review beginning of next week.

[fduchatea]

Thank you reviewing our submission, and sorry for the delay.

About mentioned missing items:

• _Permit individuals to create issues/file tickets against your repository_: it seems that the gitlab instance of our lab requires authentification (of lab members) for creating issues, and this policy will not change. Should we switch to another platform such as gitlab.com?
• _Expand the description of the software_: Should we expand the description here, in README or in the paper?
• _Expand and focus the software's research scope_: Neighbourhoods are a very common concept in studies from diverse domains such as health, social sciences, or biology. For instance,
  Japanese researchers investigated the relationships between social factors and health by taking into account not only behavioural risks, but also housing and neighbourhood environments [1]. In a British study, authors describe how living areas have an impact on physical activities, from which they determine a walkability index at the neighbourhood level for improving future urban planning [2]. Smarts cities also consider neighbourhoods as an ideal unit division for measuring urban quality [3]. Lastly, a survey describes the luxury effect, i.e., the impact of wealthy neighbourhoods on the surrounding biodiversity [4]. However there is no clear definition of the neighbourhood environment.
  Our tool fills this gap by defining neighbourhoods and their environment, characteristics of these neighbourhoods and an interface for using popular machine-learning algorithms. These elements can be extended/enriched.
  Our tool has been currently used to measure the impact of the neighbourhood's environment when people moves in another city [5]. But it could be extended to other application domains: measuring the pollution degree in neighbourhoods, determining whether a neighbourhood is suitable as stopover for migratory birds, etc.
  We can reformulate and add this research scope in the paper if needed (we are already above the 1,000 words limit though).

[1] Takada,M.,Kondo,N.,Hashimoto,H.:Japanesestudyonstratification,health,income,and neighborhood: study protocol and profiles of participants. Journal of epidemiology 24(4), 334–344 (2014)
[2] Frank, L.D., Sallis, J.F., Saelens, B.E., Leary, L., Cain, K., Conway, T.L., Hess, P.M.: The development of a walkability index: application to the neighborhood quality of life study. British journal of sports medicine 44(13), 924–933 (2010)
[3] Garau, C., Pavan, V.M.: Evaluating urban quality: Indicators and assessment tools for smart
sustainable cities. Sustainability 10(3), 575 (2018)
[4] Leong, M., Dunn, R.R., Trautwein, M.D.: Biodiversity and socioeconomics in the city: a review of the luxury effect. Biology Letters 14(5), 20180082 (2018)
[5] Barret,N.,Duchateau,F.,Favetta,F.,Bonneval,L.:Predictingtheenvironmentofaneighbor- hood: a use case for france. In: International Conference on Data Management Technologies and Applications (DATA). pp. 294–301. SciTePress (2020)

[whedon]

:wave: @jdalzatec, please update us on how your review is going.

[whedon]

:wave: @omshinde, please update us on how your review is going.

[whedon]

:wave: @nuest, please update us on how your review is going.

[whedon]

:wave: @martinfleis, please update us on how your review is going.

[martinfleis]

It will likely take some time before I'll manage to do my review. Hard to estimate now, I haven't properly looked into the complexity of the package yet.

[omshinde]

@omshinde, please update us on how your review is going.

It's coming along nicely. I have started reviewing it locally based on the checklist, will keep posted via updating the checklist. Thanks!

[jdalzatec]

@whedon I am playing a bit with the package while going through the checklist. I'll take some more time while reviewing it locally. Thanks!

[whedon]

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

@whedon commands

[galessiorob]

@jdalzatec @martinfleis @omshinde thank you all for the updates, please let me know if you need my help in any way.

@fduchatea thanks for the update on your part, please see my answers below:

Permit individuals to create issues/file tickets against your repository: it seems that the gitlab instance of our lab requires authentification (of lab members) for creating issues, and this policy will not change. Should we switch to another platform such as gitlab.com?

To avoid having you migrate everything to another repo I propose two options:

1. That you open a "review repo" in GitLab that allows us to reference the repo we are reviewing so that the reviewers can link to the specific files they on issues.
   
   
   
   1. That you open a "review repo" in GitHub to do the same as above, however, I think that having the review repo and the actual repo on the same platform would be easier.
   
   

Expand the description of the software: Should we expand the description here, in README or in the paper?

In the paper.

Expand and focus the software's research scope: Neighbourhoods are a very common concept in studies from diverse domains such as health, social sciences, or biology. For instance, Japanese researchers investigated the relationships between social factors and health by taking into account not only behavioural risks, but also housing and neighbourhood environments [1]. In a British study, authors describe how living areas have an impact on physical activities, from which they determine a walkability index at the neighbourhood level for improving future urban planning [2]. Smarts cities also consider neighbourhoods as an ideal unit division for measuring urban quality [3]. Lastly, a survey describes the luxury effect, i.e., the impact of wealthy neighbourhoods on the surrounding biodiversity [4]. However there is no clear definition of the neighbourhood environment.
Our tool fills this gap by defining neighbourhoods and their environment, characteristics of these neighbourhoods and an interface for using popular machine-learning algorithms. These elements can be extended/enriched.
Our tool has been currently used to measure the impact of the neighbourhood's environment when people moves in another city [5]. But it could be extended to other application domains: measuring the pollution degree in neighbourhoods, determining whether a neighbourhood is suitable as stopover for migratory birds, etc.
We can reformulate and add this research scope in the paper if needed (we are already above the 1,000 words limit though).

I think we can just refactor the introduction and the statement of need to reflect the research need and scope by including some of the applications that you listed above. Could you take a first pass at it and I can help refine after that?

[fduchatea]

@galessiorob

Thanks for the hints. We have created a repository with a public tracker:
https://gitlab.com/fduchate/review-repo-predihood

The first sections of the paper have been reformulated to broaden the description.

[fduchatea]

@whedon generate pdf

[whedon]

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