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[REVIEW]: gcamfaostat: An R package to prepare, process, and synthesize FAOSTAT data for global agroeconomic and multisector dynamic modeling #6388

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editorialbot opened this issue Feb 21, 2024 · 83 comments
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accepted published Papers published in JOSS R recommend-accept Papers recommended for acceptance in JOSS. review TeX Track: 6 (ESE) Earth Sciences and Ecology

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editorialbot commented Feb 21, 2024

Submitting author: @realxinzhao (Xin Zhao)
Repository: https://github.com/JGCRI/gcamfaostat
Branch with paper.md (empty if default branch):
Version: v1.0.0
Editor: @hugoledoux
Reviewers: @klau506, @HenriKajasilta
Archive: 10.5281/zenodo.10967067

Status

status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/bf4762e8bef702f36b800e0cb4d478a8"><img src="https://joss.theoj.org/papers/bf4762e8bef702f36b800e0cb4d478a8/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/bf4762e8bef702f36b800e0cb4d478a8/status.svg)](https://joss.theoj.org/papers/bf4762e8bef702f36b800e0cb4d478a8)

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

@klau506 & @HenriKajasilta, 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 @hugoledoux 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 @klau506

📝 Checklist for @HenriKajasilta

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

For a list of things I can do to help you, just type:

@editorialbot commands

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

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Software report:

github.com/AlDanial/cloc v 1.88  T=0.16 s (1199.3 files/s, 237585.8 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
HTML                           119           4165            389          16372
R                               45           2210           3124           7472
CSS                              4            152             57            655
Rmd                              6            284            537            414
XML                              1              0              0            360
TeX                              1              5              0            342
YAML                             6             45             11            293
JavaScript                       4             64             32            264
Markdown                         3            138              0            243
SVG                              1              0              1             11
-------------------------------------------------------------------------------
SUM:                           190           7063           4151          26426
-------------------------------------------------------------------------------


gitinspector failed to run statistical information for the repository

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Wordcount for paper.md is 3161

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

OK DOIs

- 10.1088/1748-9326/ac5766 is OK
- 10.1038/s43016-022-00464-4 is OK
- 10.1017/9781009157926.022 is OK
- 10.1038/s41558-023-01661-0 is OK
- 10.1016/j.oneear.2023.08.003 is OK
- 10.1029/2022EF003063 is OK
- 10.1371/journal.pone.0291577 is OK
- 10.1088/1748-9326/ac2965 is OK
- 10.1016/j.scitotenv.2021.146238 is OK
- 10.1142/s2010007820500049 is OK
- 10.1021/acs.est.9b03554 is OK
- 10.5194/gmd-15-429-2022 is OK
- 10.21642/JGEA.070101AF is OK
- 10.1016/j.eap.2021.07.007 is OK
- 10.1111/agec.12086 is OK
- 10.21105/joss.00550 is OK
- 10.5281/zenodo.8010145 is OK
- 10.5194/gmd-12-677-2019 is OK
- 10.5334/jors.266 is OK
- 10.5334/jors.208 is OK
- 10.1038/sdata.2016.18 is OK

MISSING DOIs

- None

INVALID DOIs

- None

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

@klau506
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klau506 commented Feb 22, 2024

Review checklist for @klau506

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

General checks

  • Repository: Is the source code for this software available at the https://github.com/JGCRI/gcamfaostat?
  • License: Does the repository contain a plain-text LICENSE or COPYING file with the contents of an OSI approved software license?
  • Contribution and authorship: Has the submitting author (@realxinzhao) 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?

@HenriKajasilta
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HenriKajasilta commented Feb 23, 2024

Review checklist for @HenriKajasilta

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

General checks

  • Repository: Is the source code for this software available at the https://github.com/JGCRI/gcamfaostat?
  • License: Does the repository contain a plain-text LICENSE or COPYING file with the contents of an OSI approved software license?
  • Contribution and authorship: Has the submitting author (@realxinzhao) 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?

@klau506
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klau506 commented Feb 28, 2024

Dear @hugoledoux and @realxinzhao,

This is an interesting contribution with the potential to be a broadly useful resource and source of documentation. I have read the manuscript and the documentation, installed the software and examined its code; see specific suggestions about both referenced above. Broadly:

  • The manuscript is generally well written but it could benefit from minor modifications. Further details here
  • The documentation is extensive but there are some aspects that may need further precision or clarification. Futher details here
  • The code is well structured and organized. Running devtools::check() on the Rproj currently generates some notes and warnings, some of which could be easily removed. Further details here

I hope this is useful! I appreciate that the authors have done a lot of work, and am happy to clarify/answer questions if useful.

Best,
Clàudia

@HenriKajasilta
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Hi @hugoledoux and @realxinzhao,

I have installed the gcamfaostat package and familiarised myself with the documentation and manuscript. The package clearly has a purpose in its respective field.

I have proposed fixes and suggestions that would improve the usability of the package and help it to meet the JOSS criteria. The resulting issues are here: #10 and #11

Please, let me know if you want me to clarify some of the comments or if I have misunderstood something in the package. I will be happy to take another look at the functionality once the fixes have been made!

Br,
Henri

@realxinzhao
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Thank you so much, @klau506 and @HenriKajasilta for the careful reading of the paper and reviewing of the package, and the very helpful comments and suggestions! We will carefully address them and keep you posted.
Best,
Xin

@hugoledoux hugoledoux removed the waitlisted Submissions in the JOSS backlog due to reduced service mode. label Mar 7, 2024
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👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

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


# List all available commands
@editorialbot commands

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

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

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

# Run checks and provide information on the repository and the paper file
@editorialbot check repository

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

# Generates the pdf paper
@editorialbot generate pdf

# Generates a LaTeX preprint file
@editorialbot generate preprint

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

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Software report:

github.com/AlDanial/cloc v 1.90  T=0.19 s (1136.1 files/s, 454518.0 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
CSV                             23              0              0          47569
HTML                           119           4165            389          16372
R                               45           2210           3124           7474
CSS                              4            152             57            655
Rmd                              6            289            561            416
TeX                              1              6              0            382
XML                              1              0              0            360
YAML                             6             45             11            293
JavaScript                       4             64             32            264
Markdown                         3            107              0            209
SVG                              1              0              1             11
-------------------------------------------------------------------------------
SUM:                           213           7038           4175          74005
-------------------------------------------------------------------------------

Commit count by author:

    73	Zhao, Xin
     8	Xin Zhao
     6	realxinzhao
     1	Xin

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Paper file info:

📄 Wordcount for paper.md is 2229

✅ The paper includes a Statement of need section

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License info:

🟡 License found: Other (Check here for OSI approval)

@realxinzhao
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realxinzhao commented Mar 16, 2024

Dear @hugoledoux, @klau506 and @hugoledoux,

We have now completed the revision of the paper and the package. Thank you for the careful reading of our paper and package. All the comments are very clear, spot-on, and useful! We believe the paper & package have been significantly improved as a result of the very useful comments and suggestions.

The detailed point-by-point point responses are provided below in the issues suggested below:

Manuscript Suggestions #7
Documentation Suggestions #8
Code Suggestions #9
Usability Fixes #10
Comments on the paper #11

Please let us know if you have more comments and suggestions or if we can provide additional information.

Sincerely,
Xin Zhao (for the authors)

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@realxinzhao
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Thank you so much, @kthyng!!

  • The formatting in that paragraph is now fixed.
  • Two places in .bib file is also fixed (with better capitalizations).

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kthyng commented Apr 22, 2024

@realxinzhao I didn't look through all references but at least looks like "R" isn't capitalized yet.

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@realxinzhao
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@kthyng Thank you so much!

These are fixed now in the references. Sorry about the inconvenience (also good to learn the tricks).

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kthyng commented Apr 22, 2024

Ok good @realxinzhao! That R is capitalized, though I see a number of other proper nouns in references that should still be capitalized.

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

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Oops... yes! @kthyng
I think they are fixed now (the titles all match the ones that appear in their journal articles now). Thank you!

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kthyng commented Apr 22, 2024

Ok then we are ready to go!

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kthyng commented Apr 22, 2024

@editorialbot accept

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

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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: Zhao
  given-names: Xin
  orcid: "https://orcid.org/0000-0002-1801-4393"
- family-names: Chepeliev
  given-names: Maksym
  orcid: "https://orcid.org/0000-0001-8585-2314"
- family-names: Patel
  given-names: Pralit
  orcid: "https://orcid.org/0000-0003-3992-1061"
- family-names: Wise
  given-names: Marshall
  orcid: "https://orcid.org/0000-0002-2718-0051"
- family-names: Calvin
  given-names: Katherine
  orcid: "https://orcid.org/0000-0003-2191-4189"
- family-names: Narayan
  given-names: Kanishka
  orcid: "https://orcid.org/0000-0001-8483-6216"
- family-names: Vernon
  given-names: Chris
  orcid: "https://orcid.org/0000-0002-3406-6214"
doi: 10.5281/zenodo.10967067
message: If you use this software, please cite our article in the
  Journal of Open Source Software.
preferred-citation:
  authors:
  - family-names: Zhao
    given-names: Xin
    orcid: "https://orcid.org/0000-0002-1801-4393"
  - family-names: Chepeliev
    given-names: Maksym
    orcid: "https://orcid.org/0000-0001-8585-2314"
  - family-names: Patel
    given-names: Pralit
    orcid: "https://orcid.org/0000-0003-3992-1061"
  - family-names: Wise
    given-names: Marshall
    orcid: "https://orcid.org/0000-0002-2718-0051"
  - family-names: Calvin
    given-names: Katherine
    orcid: "https://orcid.org/0000-0003-2191-4189"
  - family-names: Narayan
    given-names: Kanishka
    orcid: "https://orcid.org/0000-0001-8483-6216"
  - family-names: Vernon
    given-names: Chris
    orcid: "https://orcid.org/0000-0002-3406-6214"
  date-published: 2024-04-22
  doi: 10.21105/joss.06388
  issn: 2475-9066
  issue: 96
  journal: Journal of Open Source Software
  publisher:
    name: Open Journals
  start: 6388
  title: "gcamfaostat: An R package to prepare, process, and synthesize
    FAOSTAT data for global agroeconomic and multisector dynamic
    modeling"
  type: article
  url: "https://joss.theoj.org/papers/10.21105/joss.06388"
  volume: 9
title: "gcamfaostat: An R package to prepare, process, and synthesize
  FAOSTAT data for global agroeconomic and multisector dynamic modeling"

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.

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🐘🐘🐘 👉 Toot for this paper 👈 🐘🐘🐘

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🚨🚨🚨 THIS IS NOT A DRILL, YOU HAVE JUST ACCEPTED A PAPER INTO JOSS! 🚨🚨🚨

Here's what you must now do:

  1. Check final PDF and Crossref metadata that was deposited 👉 Creating pull request for 10.21105.joss.06388 joss-papers#5263
  2. Wait five minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.06388
  3. If everything looks good, then close this review issue.
  4. Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

@editorialbot editorialbot added accepted published Papers published in JOSS labels Apr 22, 2024
@kthyng
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kthyng commented Apr 22, 2024

Congrats on your new publication @realxinzhao! Many thanks to editor @hugoledoux and reviewers @klau506 and @HenriKajasilta for your time, hard work, and expertise!!

@kthyng kthyng closed this as completed Apr 22, 2024
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🎉🎉🎉 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.06388/status.svg)](https://doi.org/10.21105/joss.06388)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.06388">
  <img src="https://joss.theoj.org/papers/10.21105/joss.06388/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.06388/status.svg
   :target: https://doi.org/10.21105/joss.06388

This is how it will look in your documentation:

DOI

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The Journal of Open Source Software is a community-run journal and relies upon volunteer effort. If you'd like to support us please consider doing either one (or both) of the the following:

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kthyng commented Apr 22, 2024

@realxinzhao If you'd like to sign up as a reviewer, you can do so here: https://reviewers.joss.theoj.org/.

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Congrats on your new publication @realxinzhao! Many thanks to editor @hugoledoux and reviewers @klau506 and @HenriKajasilta for your time, hard work, and expertise!!

Thank you all so much, All! This experience of leading a software publication as an economist/human-earth system modeler has been incredibly rewarding. I've learned a tremendous amount from the process, and I deeply appreciate the time and effort you've dedicated to enhancing both the software and the paper.

Best regards,
Xin

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