[REVIEW]: ForestAtRisk: A Python package for modelling and forecasting deforestation in the tropics

[whedon]

Submitting author: @ghislainv (Ghislain Vieilledent)
Repository: https://github.com/ghislainv/forestatrisk
Version: v1.0
Editor: @kbarnhart
Reviewer: @molgor, @ethanwhite
Archive: 10.5281/zenodo.4570632

⚠️ JOSS reduced service mode ⚠️

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.

Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/b8fe1d3815c7385a1c3e454270bee041"><img src="https://joss.theoj.org/papers/b8fe1d3815c7385a1c3e454270bee041/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/b8fe1d3815c7385a1c3e454270bee041/status.svg)](https://joss.theoj.org/papers/b8fe1d3815c7385a1c3e454270bee041)

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

@molgor & @ethanwhite, 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 @kbarnhart 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 @molgor

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 (@ghislainv) 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 @ethanwhite

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 (@ghislainv) 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. @molgor, @ethanwhite it looks like you're currently assigned to review this paper 🎉.

⚠️ JOSS reduced service mode ⚠️

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.

⭐ Important ⭐

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:

2. 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

- 10.1038/s41586-020-2649-2 is OK
- 10.1007/bf00116466 is OK
- 10.1007/978-3-319-60801-3_36 is OK
- 10.1016/S0304-3800(02)00059-5 is OK
- 10.1111/j.1461-0248.2004.00702.x is OK
- 10.1038/nature10425 is OK
- 10.1126/science.aam5962 is OK
- 10.1126/science.293.5530.657 is OK
- 10.1016/j.foreco.2015.06.014 is OK
- 10.1101/2020.09.17.295774 is OK
- 10.1111/j.1755-263X.2008.00027.x is OK
- 10.1016/j.envsoft.2013.09.010 is OK
- 10.1038/nature04389 is OK
- 10.5281/zenodo.3553579 is OK
- 10.1201/b10905-5 is OK
- 10.1007/s10980-009-9355-7 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[whedon]

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

[whedon]

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

[whedon]

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

[kbarnhart]

@molgor @ethanwhite, we have an automatic reminder two weeks into the review. Feel free to provide an update if you have one.

[molgor]

Hi Katy, I was trying to start the review now. However, it seems that the invitation sent from @weldon has expired. Do I need a new one? Cheers, Juan

…

El 03/02/2021, a las 21:51, Katy Barnhart ***@***.***> escribió: @molgor <https://github.com/molgor> @ethanwhite <https://github.com/ethanwhite>, we have an automatic reminder two weeks into the review. Feel free to provide an update if you have one. — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#2975 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAKQ4VRAQ2QFBPVER5XZRKTS5IKURANCNFSM4WLK335A>.

[molgor]

I'll try using the command...

Re-invite a reviewer (if they can't update checklists)

@whedon re-invite @molgor as reviewer

[kbarnhart]

@whedon re-invite @molgor as reviewer

[whedon]

OK, the reviewer has been re-invited.

@molgor please accept the invite by clicking this link: https://github.com/openjournals/joss-reviews/invitations

[kbarnhart]

@molgor here is the re-invite link.

[molgor]

Thank you very much Katy. Sorry for answering so late. Best, Juan

…

El 06/02/2021, a las 09:53, Katy Barnhart ***@***.***> escribió: @molgor <https://github.com/molgor> here is the re-invite link. — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#2975 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAKQ4VXMNELJVN5QQP4HPA3S5VQWLANCNFSM4WLK335A>.

[molgor]

Checklist for ForestAtRisk repository

Review checklist for @molgor

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?

  Yes, the repository can be downloaded without any problem using:
  git clone https://github.com/ghislainv/forestatrisk

• License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?

  Yes, the repository includes a file with the GNU - GPLv3 in plain text.

• Contribution and authorship: Has the submitting author (@ghislainv) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?

  Yes, according to the Github /insights/ section, the user @ghislainv (i.e. Ghislain Vieilledent ORCID: 0000-0002-1685-4997) is the only contributor and developer of the software,.

• Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines

  Yes, the software satisfies the suggested requirements list:

  • Age of software (the software began in 2017)
  • Total lines of code (LOC) (more than 1000 LOC)
  • Whether the software has already been cited in academic papers.

  It is my understanding that they have a pre-print paper citing it.

• Whether the software is sufficiently useful that it is likely to be cited by your peer group.

  Certainly, the targeted problem and the statistical methods used are in need by the environmental science community. There are not many Python library capable of implementing CAR processes. The software would allow further developments, analysis and software ensembles.

Functionality

• Installation: Does installation proceed as outlined in the documentation?

  Yes, the instruction given for the conda package manager worked 100% for installing all dependencies and the library itself, However, I did not check the installation with virtualenv The installation test performed without any problem using the
  $forestatrisk command (as stated in the README.md file).

• Functionality: Have the functional claims of the software been confirmed?

Yes, I was able to perform all the processes showed in the Getting Started tutorial. All of them explained in the documentation and manuscript.

• Performance: If there are any performance claims of the software, have they been confirmed? (If there are no claims, please check off this item.)

  I do not fully undestand this. The software was able to run successfully and without a high impact on my laptop computer. Bayesian approaches (CAR models in particular) are computationally intensive, the software seems to perform well using retail hardware.

Documentation

• A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
  minor Issue

  Yes, this statement is clear, as well as their target audience and applicability. However, this information is only present in the paper section and not in the general documentation. It would be valuable to include this section, either in the main repository (i.e. README.md) or in the full documentation website.

• Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.

  yes, instructions brief and clear. The installation is automated and do not require to install dependencies manually.

• Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).

  Yes, however the documentation is not easily accessible within the main repository. I recommend to add links to the Jupyter notebook and the documentation in the README.md. A section or subsection would be enough.

• Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?

  Yes, complete documentation for all visible functions. The author used best practices for documenting the software. Specifically, the use of Sphinx for extracting and building the web documentation.

• Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?

  Agree with @ethanwhite, Github Actions. So I'm happy to accept this.

• 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

Yes, @ghislainv had accepted a PR by @ethanwhite fixing this problem.

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?

  Yes

• A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?

  Yes

• State of the field: Do the authors describe how this software compares to other commonly-used packages?

  Yes, the author provides a comprehensive list of environmental software for modelling vegetation covers. The author clearly states the limitations of that software and how the proposed project contributes to the field with an innovative, flexible and open source tool.

• Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?

  The writing style is within expected academic quality. There were some typos that I suggest in a PR, however, it is not my intention to force the author to acknowledge my suggestions as contributions to the software and they may be dismissed if the author considers so.

• 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?

  Yes, all references are appropriately cited and in natbib format (I believe). Also, most of them include their corresponding DOI links.

[kbarnhart]

@molgor thanks for contributing your review. Are you still not able to edit the check boxes above?

@ethanwhite a friendly reminder that we are about four weeks into the requested six week review time period.

As always, let me know if you have any questions.

[ethanwhite]

Thanks for the reminder @kbarnhart! I've now completed my review and checked everything excepted Statement of need in the Documentation section. As @molgor noted this is well covered in the paper but generally absent from the README and website. I think a few sentences on both should take care of this.

I checked two boxes that @molgor didn't so I'll briefly note my thinking:

• I considered Automated tests satisfied because they are running successfully on GitHub Actions: https://github.com/ghislainv/forestatrisk/actions
• I considered Community guidelines satisfied because they are present in the standard named files in the standard location so I knew where to find them even though the links in the README were broken. I submitted a PR to fix the links: Fix links to contribution and CoC docs ghislainv/forestatrisk#37

@ghislainv - Really nice work! An important package that's been really well developed and documented. It's a pleasure to review good software.

[molgor]

Hi @kbarnhart,
I agree. I'm happy to mark the missing items if @ghislainv accepts @ethanwhite 's PR.

Congratulations @ghislainv, it is a really neat work!

[ghislainv]

Thanks a lot @molgor and @ethanwhite for reviewing the software and for your positive feedbacks. Thanks @kbarnhart for handling the paper review. I really appreciate. I will make the necessary changes to the software documentation and paper and will keep you informed soon.

[ghislainv]

@kbarnhart, @molgor, @ethanwhite: I have answered to your remarks and taken into account your suggestions. In particular, I have added a "Statement of Need" section in the README file of the software and in the Home page of the website.

[ghislainv]

@whedon generate pdf

[whedon]

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

[kbarnhart]

@whedon set 10.5281/zenodo.4570632 as archive

[whedon]

OK. 10.5281/zenodo.4570632 is the archive.

[kbarnhart]

@whedon accept

[whedon]

Attempting dry run of processing paper acceptance...

[kbarnhart]

@ghislainv I've now recommended that this submission be accepted and published the @openjournals/joss-eics will handle final acceptance. Congratulations.

@molgor and @ethanwhite thank you for contributing reviews to this submission.

[whedon]

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

OK DOIs

- 10.1038/s41586-020-2649-2 is OK
- 10.1007/bf00116466 is OK
- 10.1007/978-3-319-60801-3_36 is OK
- 10.1016/S0304-3800(02)00059-5 is OK
- 10.1111/j.1461-0248.2004.00702.x is OK
- 10.1038/nature10425 is OK
- 10.1126/science.aam5962 is OK
- 10.1126/science.293.5530.657 is OK
- 10.1016/j.foreco.2015.06.014 is OK
- 10.1101/2020.09.17.295774 is OK
- 10.1111/j.1755-263X.2008.00027.x is OK
- 10.1016/j.envsoft.2013.09.010 is OK
- 10.1038/nature04389 is OK
- 10.5281/zenodo.3553579 is OK
- 10.1201/b10905-5 is OK
- 10.1007/s10980-009-9355-7 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[whedon]

👋 @openjournals/joss-eics, this paper is ready to be accepted and published.

Check final proof 👉 openjournals/joss-papers#2119

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#2119, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true

[danielskatz]

@ghislainv - this mostly looks good, but I've suggested some changes in ghislainv/forestatrisk#47 - please merge this or let me know what you disagree with. (Note that the paper had both UK and US spelling - I've chosen US to be consistent, though UK consistently would also be ok.)

[kbarnhart]

Thanks @danielskatz!

[ghislainv]

@danielskatz - thanks for your edits, I have merged them.
@kbarnhart , @molgor , @ethanwhite - thanks again for the review of the software and paper.

[danielskatz]

@whedon accept

[whedon]

Attempting dry run of processing paper acceptance...

[whedon]

👋 @openjournals/joss-eics, this paper is ready to be accepted and published.

Check final proof 👉 openjournals/joss-papers#2120

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#2120, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true

[whedon]

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

OK DOIs

- 10.1038/s41586-020-2649-2 is OK
- 10.1007/bf00116466 is OK
- 10.1007/978-3-319-60801-3_36 is OK
- 10.1016/S0304-3800(02)00059-5 is OK
- 10.1111/j.1461-0248.2004.00702.x is OK
- 10.1038/nature10425 is OK
- 10.1126/science.aam5962 is OK
- 10.1126/science.293.5530.657 is OK
- 10.1016/j.foreco.2015.06.014 is OK
- 10.1101/2020.09.17.295774 is OK
- 10.1111/j.1755-263X.2008.00027.x is OK
- 10.1016/j.envsoft.2013.09.010 is OK
- 10.1038/nature04389 is OK
- 10.5281/zenodo.3553579 is OK
- 10.1201/b10905-5 is OK
- 10.1007/s10980-009-9355-7 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[danielskatz]

@whedon accept deposit=true

[whedon]

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

[whedon]

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

[whedon]

🚨🚨🚨 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.02975 joss-papers#2121
1. Wait a couple of minutes to verify that the paper DOI resolves https://doi.org/10.21105/joss.02975
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 @ghislainv (Ghislain Vieilledent)!!

And thanks to @molgor and @ethanwhite for reviewing, and @kbarnhart for editing!

[whedon]

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

If you would like to include a link to your paper from your README use the following code snippets:

Markdown:
[![DOI](https://joss.theoj.org/papers/10.21105/joss.02975/status.svg)](https://doi.org/10.21105/joss.02975)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.02975">
  <img src="https://joss.theoj.org/papers/10.21105/joss.02975/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.02975/status.svg
   :target: https://doi.org/10.21105/joss.02975

This is how it will look in your documentation:

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